diff --git a/karma-cleaning/pom.xml b/karma-cleaning/pom.xml
deleted file mode 100644
index 8ef7ad11c..000000000
--- a/karma-cleaning/pom.xml
+++ /dev/null
@@ -1,140 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-
-	<parent>
-		<groupId>edu.isi</groupId>
-		<artifactId>webkarma</artifactId>
-		<version>0.0.1-SNAPSHOT</version>
-	</parent>
-
-	<artifactId>karma-cleaning</artifactId>
-
-	<properties>
-		<hadoop.dist.mahout.version>0.9</hadoop.dist.mahout.version>
-	</properties>
-
-	<dependencies>
-		<dependency>
-			<groupId>edu.isi</groupId>
-			<artifactId>karma-util</artifactId>
-			<version>${project.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<version>4.11</version>
-		</dependency>
-		<dependency>
-			<groupId>javax.mail</groupId>
-			<artifactId>mail</artifactId>
-			<version>1.4</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-math3</artifactId>
-			<version>3.0</version>
-		</dependency>
-		<dependency>
-			<groupId>org.python</groupId>
-			<artifactId>jython-standalone</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-			<version>1.2.16</version>
-		</dependency>
-		<dependency>
-			<groupId>org.slf4j</groupId>
-			<artifactId>slf4j-api</artifactId>
-			<version>1.6.4</version>
-		</dependency>
-		<dependency>
-			<groupId>org.slf4j</groupId>
-			<artifactId>slf4j-log4j12</artifactId>
-			<version>1.6.4</version>
-		</dependency>
-		<dependency>
-			<groupId>xml-apis</groupId>
-			<artifactId>xml-apis</artifactId>
-			<version>1.0.b2</version>
-		</dependency>
-		<!-- The Java API for KML -->
-		<dependency>
-			<groupId>de.micromata.jak</groupId>
-			<artifactId>JavaAPIforKml</artifactId>
-			<version>2.2.0</version>
-		</dependency>
-		<dependency>
-			<groupId>com.hp.hpl.jena</groupId>
-			<artifactId>arq</artifactId>
-			<version>2.8.8</version>
-		</dependency>
-		<dependency>
-			<groupId>com.hp.hpl.jena</groupId>
-			<artifactId>jena</artifactId>
-			<version>2.6.4</version>
-		</dependency>
-		<dependency>
-			<groupId>com.hp.hpl.jena</groupId>
-			<artifactId>iri</artifactId>
-			<version>0.8</version>
-		</dependency>
-		<dependency>
-			<groupId>com.hp.hpl.jena</groupId>
-			<artifactId>tdb</artifactId>
-			<version>0.8.10</version>
-		</dependency>
-		<dependency>
-			<groupId>net.sf.opencsv</groupId>
-			<artifactId>opencsv</artifactId>
-			<version>2.3</version>
-		</dependency>
-		<dependency>
-			<groupId>org.antlr</groupId>
-			<artifactId>antlr</artifactId>
-			<version>3.2</version>
-		</dependency>
-		<dependency>
-			<groupId>org.jdom</groupId>
-			<artifactId>jdom</artifactId>
-			<version>1.1.2</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.poi</groupId>
-			<artifactId>poi</artifactId>
-			<version>3.8-beta5</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.poi</groupId>
-			<artifactId>poi-ooxml</artifactId>
-			<version>3.8-beta5</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-lang3</artifactId>
-			<version>3.1</version>
-		</dependency>
-		<dependency>
-			<groupId>tw.edu.ntu.csie</groupId>
-			<artifactId>libsvm</artifactId>
-			<version>3.17</version>
-		</dependency>
-		<dependency>
-			<groupId>org.perf4j</groupId>
-			<artifactId>perf4j</artifactId>
-			<version>0.9.16</version>
-		</dependency>
-		<dependency>
-			<groupId>commons-lang</groupId>
-			<artifactId>commons-lang</artifactId>
-			<version>2.3</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-math</artifactId>
-			<version>2.2</version>
-		</dependency>
-
-	</dependencies>
-</project>
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/Checker.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/Checker.java
deleted file mode 100644
index d65583c81..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/Checker.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package edu.isi.karma.cleaning.Correctness;
-
-import java.util.ArrayList;
-
-import edu.isi.karma.cleaning.features.RecordClassifier;
-import edu.isi.karma.cleaning.features.RecordFeatureSet;
-
-/*
- * check whether the transformed results are correct
- */
-public class Checker {
-	RecordClassifier clf;
-	public Checker()
-	{
-		RecordFeatureSet rfs1 = new RecordFeatureSet();
-		clf = new RecordClassifier(rfs1);
-
-	}
-	public String binds(String[] exp)
-	{
-		String res = "";
-		if(exp.length == 2)
-		{
-			res = String.format("bef:%s aft:%s", exp[0],exp[1]);
-		}
-		else
-		{
-			res = "NOEXP";
-		}
-		return res;
-	}
-	public void train(ArrayList<String[]> postive, ArrayList<String[]> negative)
-	{
-		clf.init();
-		for(String[] pos:postive)
-		{
-			String tmp = binds(pos);
-			clf.addTrainingData(tmp, "1");
-		}
-		for(String[] neg:negative)
-		{
-			String tmp = binds(neg);
-			clf.addTrainingData(tmp, "-1");
-		}
-		clf.learnClassifer();
-	}
-	
-	public String test(String[] record)
-	{
-		String line = binds(record);
-		String label = clf.getLabel(line);
-		return label;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/FormatFunc.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/FormatFunc.java
deleted file mode 100644
index ec620ff21..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/FormatFunc.java
+++ /dev/null
@@ -1,95 +0,0 @@
-package edu.isi.karma.cleaning.Correctness;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-
-import edu.isi.karma.cleaning.UtilTools;
-
-/*
- * unseen formats detections: 
- * distance to the class center and find the largest distance as the threshold
- * 
- * boundary formats:
- * difference of distances to two classes are below 5% 
- *
- * record = [id, org, tar, label]
- * 
- */
-
-public class FormatFunc implements VerificationFunc {
-	private int funid = 1;
-	private HashMap<String, double[]> cmeans = new HashMap<String, double[]>();
-	private HashMap<String, double[]> mean_var = new HashMap<String, double[]>();
-	private double[] dmetric= null;
-	public FormatFunc(ArrayList<TransRecord> records, double[] dmetric)
-	{
-		dmetric = UtilTools.initArray(dmetric, 1.0);
-		this.dmetric = dmetric;
-		getMeanandDists(records, dmetric);
-		
-	}
-	//identify the mean vector of each cluster
-	private void getMeanandDists(ArrayList<TransRecord> records, double[] dmetric)
-	{
-		HashMap<String, ArrayList<TransRecord>> tmp = new HashMap<String,ArrayList<TransRecord>>();
-		for(TransRecord rec:records)
-		{
-			if(tmp.containsKey(rec.label))
-			{
-				tmp.get(rec.label).add(rec);
-			}
-			else
-			{
-				ArrayList<TransRecord> x = new ArrayList<TransRecord>();
-				x.add(rec);
-				tmp.put(rec.label, x);
-			}
-		}
-		// find the means 
-		for(Map.Entry<String, ArrayList<TransRecord>> stringArrayListEntry : tmp.entrySet())
-		{
-			ArrayList<TransRecord> tdata = stringArrayListEntry.getValue();
-			if(!tdata.isEmpty() || tdata.get(0).features.length > 0)
-			{
-				ArrayList<double[]> tcl = new ArrayList<double[]>();
-				for(int i =0; i< tdata.size(); i++)
-				{
-					 tcl.add(tdata.get(i).features); 
-				}
-				double[] tmean = UtilTools.sum(tcl);
-				tmean = UtilTools.produce(1.0/tdata.size(), tmean);
-				cmeans.put(stringArrayListEntry.getKey(), tmean);
-				// find the max distances
-				// strictly bigger or smaller than [mean-3*delta, mean+3*delta]
-				double d_mean = 0;
-				double d_mu = 0;
-				for(int i =0; i< tdata.size(); i++)
-				{
-					d_mean += UtilTools.distance(tdata.get(i).features, tmean, dmetric);
-				}
-				d_mean = d_mean*1.0/tdata.size();
-				for(int i =0; i< tdata.size(); i++)
-				{
-					d_mu += Math.pow(UtilTools.distance(tdata.get(i).features, tmean, dmetric)-d_mean, 2);
-				}
-				d_mu = Math.sqrt(d_mu/tdata.size());
-				double[] x = {d_mean,d_mu};
-				mean_var.put(stringArrayListEntry.getKey(), x);
-			}
-		}
-		
-		//Prober.printFeatureandWeight(tmp, cmeans, dmetric);
-	}
-			
-	public String verify(TransRecord record) {
-		double dist = UtilTools.distance(record.features, cmeans.get(record.label), dmetric);
-		//difference STRICTLY bigger than 2 standard deviations [68, 95, 99.7] rule
-		if(Math.abs(dist - mean_var.get(record.label)[0]) > 2.0*mean_var.get(record.label)[1])
-		{
-			return String.valueOf(this.funid);
-		}
-		return "0";
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/HypoTester.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/HypoTester.java
deleted file mode 100644
index 89597bcf9..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/HypoTester.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package edu.isi.karma.cleaning.Correctness;
-/*
- * Test whether different correctnesses can pass the hypotest  
- */
-public class HypoTester {
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/OutlierDetector.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/OutlierDetector.java
deleted file mode 100644
index 43af4e9b9..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/OutlierDetector.java
+++ /dev/null
@@ -1,45 +0,0 @@
-package edu.isi.karma.cleaning.Correctness;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-
-import libsvm.svm_parameter;
-import edu.isi.karma.cleaning.features.RecordClassifier;
-import edu.isi.karma.cleaning.features.RecordFeatureSet;
-
-public class OutlierDetector {
-	RecordClassifier clf;
-	public OutlierDetector()
-	{
-		RecordFeatureSet rfs1 = new RecordFeatureSet();
-		clf = new RecordClassifier(rfs1, svm_parameter.ONE_CLASS);
-	}
-	
-	public void train(ArrayList<String> tdata)
-	{
-		for(String line:tdata)
-		{
-			clf.addTrainingData(line, "1");
-		}
-		clf.learnClassifer();
-	}
-	public String getLabel(String input)
-	{
-		String label = clf.getLabel(input);
-		return label;
-	}
-	public static void main(String[] args)
-	{
-		OutlierDetector outDet = new OutlierDetector();
-		String[] dat = {"A", "AA","B", "BB"};
-		String[] tst = {"B", "b", "AAAAAAAAAAAA","."};
-		ArrayList<String> data = new ArrayList<String>(Arrays.asList(dat));
-		outDet.train(data);
-		for(String l:tst)
-		{
-			String out = outDet.getLabel(l);
-			System.out.println(l+": "+out);
-		}
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/Recommander.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/Recommander.java
deleted file mode 100644
index 3c213597b..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/Recommander.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package edu.isi.karma.cleaning.Correctness;
-
-import java.util.ArrayList;
-
-/* recommend 
- * 1 the outlier
-   2 the points on the boundary
-   in the test dataset.
-*/
-public class Recommander {
-	public Recommander()
-	{
-		
-	}
-	//
-	public ArrayList<String> getOutliers()
-	{
-		ArrayList<String> res = new ArrayList<String>();
-		return res;
-	}
-	public ArrayList<String> getBoundaryPoints()
-	{
-		ArrayList<String> res = new ArrayList<String>();
-		return res;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/TransRecord.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/TransRecord.java
deleted file mode 100644
index 0ac2ebfaf..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/TransRecord.java
+++ /dev/null
@@ -1,18 +0,0 @@
-package edu.isi.karma.cleaning.Correctness;
-
-public class TransRecord {
-	public String Id = "";
-	public String org = "";
-	public String tar = "";
-	public String label = "";
-	public String correct = "f";
-	public double[] features = null;
-	public TransRecord(String Id, String org, String tar, String lab, double[] feats)
-	{
-		this.Id = Id;
-		this.org = org;
-		this.tar = tar;
-		this.label = lab;
-		this.features = feats;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/VerificationFunc.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/VerificationFunc.java
deleted file mode 100644
index f4857c94b..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/VerificationFunc.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package edu.isi.karma.cleaning.Correctness;
-
-
-public interface VerificationFunc {
-	//label a record
-	//label 0 correct, >=1 doubious
-	public String verify(TransRecord record);
-	
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/ViewFunc.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/ViewFunc.java
deleted file mode 100644
index 45d058d3c..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Correctness/ViewFunc.java
+++ /dev/null
@@ -1,120 +0,0 @@
-package edu.isi.karma.cleaning.Correctness;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.GrammarTreeNode;
-import edu.isi.karma.cleaning.Partition;
-import edu.isi.karma.cleaning.ProgSynthesis;
-import edu.isi.karma.cleaning.ProgramRule;
-import edu.isi.karma.cleaning.Template;
-import edu.isi.karma.cleaning.Traces;
-
-public class ViewFunc implements VerificationFunc {
-	private HashMap<String, String> data = new HashMap<String, String>();
-	private String contextId; 
-	public ViewFunc(ArrayList<TransRecord> records, ProgSynthesis ps, ProgramRule pr, String contextId)
-	{
-		this.contextId = contextId;
-		Vector<Partition> pars = ps.myprog.partitions;
-		HashMap<String, ArrayList<TransRecord>> resHashMap = cluster(records);
-		for(Partition p: pars)
-		{
-			handlePartition(resHashMap.get(p.label), p.trace, pr.getStringRule(p.label));
-		}
-	}
-	public HashMap<String, ArrayList<TransRecord>> cluster(ArrayList<TransRecord> reds)
-	{
-		HashMap<String, ArrayList<TransRecord>> res = new HashMap<String, ArrayList<TransRecord>>();
-		for(TransRecord r: reds)
-		{
-			if(res.containsKey(r.label))
-			{
-				res.get(r.label).add(r);
-			}
-			else {
-				ArrayList<TransRecord> line = new ArrayList<TransRecord>();
-				line.add(r);
-				res.put(r.label, line);
-			}
-		}
-		return res;
-	}
-	public void handlePartition(ArrayList<TransRecord> records, Traces trace, String prog) {
-		
-		if (identifyIncorrRecord(records, prog)) {
-			return;
-		} else {
-			identifyRecord(records, trace);
-		}
-	}
-
-	// detect the records which prog failed on
-	public boolean identifyIncorrRecord(ArrayList<TransRecord> records,
-			String prog) {
-		ProgramRule pr = new ProgramRule(prog, contextId);
-		boolean res = true;
-		for (TransRecord r : records) {
-			String orgString = r.org;
-			String tar = pr.transform(orgString);
-			if (tar.compareTo(r.tar) != 0) {
-				res = false;
-				data.put(r.org, "1");
-			}
-		}
-		return res;
-	}
-
-	public void identifyRecord(ArrayList<TransRecord> records, Traces trace) {
-		ArrayList<Template> all = new ArrayList<Template>();
-		Collection<Template> tlines = trace.traceline.values();
-		all.addAll(tlines);
-		ArrayList<Template> llines = new ArrayList<Template>();
-		for (Integer k : trace.loopline.keySet()) {
-			llines.addAll(trace.loopline.get(k).values());
-		}
-		all.addAll(llines);
-		ArrayList<String> rdata = new ArrayList<String>();
-		for (TransRecord tr : records) {
-			rdata.add(tr.org);
-		}
-		int cnt = 0;
-		HashMap<String, ArrayList<ArrayList<String>>> views = new HashMap<String, ArrayList<ArrayList<String>>>();
-		for (Template t : all) {
-			Vector<GrammarTreeNode> bd = t.body;
-			ArrayList<ArrayList<String>> equviViews = new ArrayList<ArrayList<String>>();
-			for (GrammarTreeNode gt : bd) {
-				String rule = "";
-				HashSet<String> vs = new HashSet<String>();
-				ArrayList<String> lviews = new ArrayList<String>();
-				do {
-					rule = gt.toProgram();
-					ProgramRule pr = new ProgramRule(rule,contextId);
-					String ares = "";
-					for (String s : rdata) {
-						ares += pr.transform(s);
-					}
-					if (!vs.contains(ares)) {
-						lviews.add(rule);
-					}
-				} while (rule.compareTo("null") != 0);
-				equviViews.add(lviews);
-			}
-			cnt++;
-			views.put(String.valueOf(cnt), equviViews);
-		}
-		
-		
-	}
-
-	public String verify(TransRecord record) {
-		if (data.containsKey(record.org)) {
-			return data.get(record.org);
-		}
-		return "0";
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/DataPreProcessor.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/DataPreProcessor.java
deleted file mode 100644
index 5c3db7a2c..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/DataPreProcessor.java
+++ /dev/null
@@ -1,169 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.features.Feature;
-import edu.isi.karma.cleaning.features.RecordFeatureSet;
-//identify candidate tokens
-//vectorize string to feature vectors
-//decorrelate features
-//rescale features
-
-public class DataPreProcessor {
-	public Collection<String> data;
-	HashMap<String, double[]> data2Vector = new HashMap<String, double[]>();
-	RecordFeatureSet rfs = new RecordFeatureSet();
-
-	public DataPreProcessor(Collection<String> data) {
-		this.data = data;
-	}
-	public HashMap<String, double[]> getStandardData()
-	{
-		return data2Vector;
-	}
-	public void run() {
-		Vector<String> toks = buildDict(data);
-		// vectorize String
-		String[] vocb = toks.toArray(new String[toks.size()]);
-		rfs.addVocabulary(vocb);
-		HashMap<String, double[]> xHashMap = vectorize(data);
-		resacle(xHashMap);
-		// deCorrelat features
-		ArrayList<Integer> toremove = deCorrelate(xHashMap);
-		// update the featureSet and Vectorize the data again
-		rfs.removeFeatures(toremove);
-		// resvectorize the data
-		xHashMap = vectorize(data);
-		// rescale the data
-		// rescale each feature
-		resacle(xHashMap);
-		this.data2Vector = xHashMap;
-	}
-	public void resacle(HashMap<String, double[]> xHashMap)
-	{
-		double[] maxvals = new double[rfs.getFeatureNames().size()];
-		maxvals = UtilTools.initArray(maxvals, -1);
-		double[] minvals = new double[rfs.getFeatureNames().size()];
-		minvals = UtilTools.initArray(minvals, Double.MAX_VALUE);
-		for (double[] tmp : xHashMap.values()) {
-			for (int i = 0; i < tmp.length; i++) {
-				if (tmp[i] > maxvals[i]) {
-					maxvals[i] = tmp[i];
-				}
-				if (tmp[i] < minvals[i]) {
-					minvals[i] = tmp[i];
-				}
-			}
-		}
-		for (Entry<String, double[]> stringEntry : xHashMap.entrySet()) {
-			double[] value = stringEntry.getValue();
-			for (int i = 0; i < value.length; i++) {
-				if (maxvals[i] > minvals[i]) {
-					double tmpval = (value[i] - minvals[i])/(maxvals[i] - minvals[i]);
-					value[i] = Math.pow(tmpval, 0.5);
-				} else {
-					value[i] = 0;
-				}
-			}
-			xHashMap.put(stringEntry.getKey(), value);
-		}
-	}
-	public HashMap<String, double[]> vectorize(Collection<String> data) {
-		HashMap<String, double[]> res = new HashMap<String, double[]>();
-		for (String line : data) {
-			if (!res.containsKey(line)) {
-				double[] row = getFeatureArray(line);
-				res.put(line, row);
-			}
-		}
-		return res;
-	}
-
-	public ArrayList<Integer> deCorrelate(HashMap<String, double[]> data) {
-		ArrayList<Integer> toRemove = new ArrayList<Integer>();
-		HashSet<String> signs = new HashSet<String>();
-		// build singature for each feature
-		for (int i = 0; i < rfs.getFeatureNames().size(); i++) {
-			String sg = "";
-			for (Entry<String, double[]> stringEntry : data.entrySet()) {
-				sg += stringEntry.getValue()[i]+"\n";
-			}
-			if (signs.contains(sg)) {
-				toRemove.add(i);
-			} else {
-				signs.add(sg);
-			}
-		}
-		return toRemove;
-
-	}
-
-	public double[] getFeatureArray(String s) {
-		Collection<Feature> cfeat = rfs.computeFeatures(s, "");
-		Feature[] x = cfeat.toArray(new Feature[cfeat.size()]);
-		double[] res = new double[x.length];
-		for (int i = 0; i < x.length; i++) {
-			res[i] = x[i].getScore();
-		}
-		return res;
-	}
-
-	public static Vector<String> buildDict(Collection<String> data) {
-		HashMap<String, Integer> mapHashSet = new HashMap<String, Integer>();
-		for (String pair : data) {
-			String s1 = pair;
-			if (s1.contains("<_START>")) {
-				s1 = s1.replace("<_START>", "");
-			}
-			if (s1.contains("<_END>")) {
-				s1 = s1.replace("<_END>", "");
-			}
-			Ruler r = new Ruler();
-			r.setNewInput(s1);
-			Vector<TNode> v = r.vec;
-			HashSet<String> curRow = new HashSet<String>();
-			for (TNode t : v) {
-				String k = t.text;
-				k = k.replaceAll("[0-9]+", "DIGITs");
-				// filter punctuation
-				if (k.trim().length() == 1 && !Character.isLetterOrDigit(k.charAt(0))) {
-					continue;
-				}
-				if (k.trim().length() == 0)
-					continue;
-				// only consider K once in one row
-				if (curRow.contains(k)) {
-					continue;
-				} else {
-					curRow.add(k);
-				}
-				if (mapHashSet.containsKey(k)) {
-					mapHashSet.put(k, mapHashSet.get(k) + 1);
-				} else {
-					mapHashSet.put(k, 1);
-				}
-			}
-		}
-		// prune infrequent terms
-		int thresdhold = (int) (data.size() * 0.005);
-		Iterator<Entry<String, Integer>> iter = mapHashSet.entrySet()
-				.iterator();
-		while (iter.hasNext()) {
-			Entry<String, Integer> e = iter.next();
-			if (e.getValue() < thresdhold) {
-				iter.remove();
-			}
-		}
-		Vector<String> res = new Vector<String>();
-		res.addAll(mapHashSet.keySet());
-		return res;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/EmailNotification.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/EmailNotification.java
deleted file mode 100644
index 8289f1dd0..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/EmailNotification.java
+++ /dev/null
@@ -1,75 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.Properties;
-
-import javax.activation.DataHandler;
-import javax.activation.DataSource;
-import javax.activation.FileDataSource;
-import javax.mail.BodyPart;
-import javax.mail.Message;
-import javax.mail.MessagingException;
-import javax.mail.Multipart;
-import javax.mail.PasswordAuthentication;
-import javax.mail.Session;
-import javax.mail.Transport;
-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeBodyPart;
-import javax.mail.internet.MimeMessage;
-import javax.mail.internet.MimeMultipart;
-
-public class EmailNotification {
-
-	public void notify(boolean real, String title)
-	{
-		if(real)
-		{
-			final String username = "wb_4365@163.com";
-			final String password = "225015";
-
-			Properties props = new Properties();
-			props.put("mail.smtp.auth", "true");
-			// props.put("mail.smtp.starttls.enable", "true");
-			props.put("mail.smtp.host", "smtp.163.com");
-			props.put("mail.smtp.port", "25");
-
-			Session session = Session.getInstance(props,
-					new javax.mail.Authenticator() {
-						protected PasswordAuthentication getPasswordAuthentication() {
-							return new PasswordAuthentication(username, password);
-						}
-					});
-
-			try {
-
-				Message message = new MimeMessage(session);
-				message.setFrom(new InternetAddress("wb_4365@163.com"));
-				message.setRecipients(Message.RecipientType.TO,
-						InternetAddress.parse("bowu365@gmail.com"));
-				message.setSubject("Experiment Done: "+title);
-				// Create the message part
-				BodyPart messageBodyPart = new MimeBodyPart();
-				// Fill the message
-				messageBodyPart.setText("This is message body");
-				Multipart multipart = new MimeMultipart();
-				// Set text message part
-				multipart.addBodyPart(messageBodyPart);
-				// Part two is attachment
-				messageBodyPart = new MimeBodyPart();
-				String filename = "./log/mylog.txt";
-				DataSource source = new FileDataSource(filename);
-				messageBodyPart.setDataHandler(new DataHandler(source));
-				messageBodyPart.setFileName(filename);
-				multipart.addBodyPart(messageBodyPart);
-				message.setContent(multipart);
-				Transport.send(message);
-				System.out.println("Done");
-
-			} catch (MessagingException e) {
-				throw new RuntimeException(e);
-			}
-		}
-	}
-	public static void main(String[] args) {
-		
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ExampleCluster.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ExampleCluster.java
deleted file mode 100644
index 849386455..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ExampleCluster.java
+++ /dev/null
@@ -1,684 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Vector;
-
-
-import edu.isi.karma.cleaning.features.Feature;
-
-public class ExampleCluster {
-	public HashMap<String, Boolean> legalParitions = new HashMap<String, Boolean>();
-	Vector<Partition> examples = new Vector<Partition>();
-	HashSet<String> exampleInputs = new HashSet<String>();
-	Vector<Vector<String[]>> constraints = new Vector<Vector<String[]>>();
-	public ProgSynthesis pSynthesis; // data
-	HashMap<String, Vector<String>> uorgclusters = new HashMap<String, Vector<String>>();
-	HashMap<String, double[]> string2Vector = new HashMap<String, double[]>();
-	int unlabelDataAmount = 10;
-	double assignThreshold = 0.1;
-	public int featuresize = 0;
-	public int failedCnt = 0;
-	public double[] weights = {};
-	String contextId;
-	public static enum method {
-		CP, CPIC, SP, SPIC, DP, DPIC
-	};
-
-	public static method option = method.DPIC;
-
-	/*
-	 * example are (id, (input, output)) constrain: true->must link constraints,
-	 * false->cannot link constraints
-	 */
-	public ExampleCluster(String contextId) {
-		this.contextId = contextId;
-	}
-
-	public ExampleCluster(ProgSynthesis pSynthesis, Vector<Partition> examples,
-			HashMap<String, double[]> sData) {
-		this.pSynthesis = pSynthesis;
-		this.examples = examples;
-		this.string2Vector = sData;
-		this.featuresize = pSynthesis.featureSet.getFeatureNames().size();
-		weights = new double[featuresize];
-		for (int i = 0; i < weights.length; i++) {
-			weights[i] = 1;
-		}
-		for (Partition p : examples) {
-			for (Vector<TNode> nodes : p.orgNodes) {
-				exampleInputs.add(UtilTools.print(nodes));
-			}
-		}
-		init();
-	}
-
-	public void updateWeights(double[] weight) {
-		if (weight != null)
-			this.weights = weight;
-	}
-
-	// accepting constraints from previous iterations
-	public void updateConstraints(Vector<Vector<String[]>> cnts) {
-		if (option == method.CPIC || option == method.DPIC
-				|| option == method.SPIC) {
-			HashMap<String, Vector<String[]>> xHashMap1 = new HashMap<String, Vector<String[]>>();
-			for (Vector<String[]> group : cnts) {
-				xHashMap1.put(constraintKey(group), group);
-			}
-			HashSet<String> xHashSet2 = new HashSet<String>();
-			for (Vector<String[]> group : constraints) {
-				xHashSet2.add(constraintKey(group));
-			}
-			for (Map.Entry<String, Vector<String[]>> stringVectorEntry : xHashMap1.entrySet()) {
-				if (!xHashSet2.contains(stringVectorEntry.getKey())) {
-					constraints.add(stringVectorEntry.getValue());
-				}
-			}
-			// update islegal ds
-			for (Vector<String[]> group : constraints) {
-				ArrayList<String> g = new ArrayList<String>();
-				for (String[] p : group) {
-					String line = String.format("%s, %s\n", p[0], p[1]);
-					g.add(line);
-				}
-				String res = "";
-				res = UtilTools.createkey(new ArrayList<String[]>(group));
-				legalParitions.put(res, false);
-			}
-		}
-	}
-
-	public Vector<Vector<String[]>> getConstraints() {
-		return constraints;
-	}
-
-	public String constraintKey(Vector<String[]> group) {
-		ArrayList<String> xArrayList = new ArrayList<String>();
-		for (String[] e : group) {
-			xArrayList.add(Arrays.toString(e));
-		}
-		Collections.sort(xArrayList);
-		return xArrayList.toString();
-	}
-
-	public void init() {
-		if (option == method.DP || option == method.DPIC) {
-			this.unlabelDataAmount = 10;
-		} else {
-			this.unlabelDataAmount = 0;
-		}
-	}
-
-	public void diagnose() {
-		System.out.println("" + this.pSynthesis.featureSet.getFeatureNames());
-		System.out.println("" + Arrays.toString(weights));
-	}
-
-	// adaptive partition program learning
-	public Vector<Partition> adaptive_cluster_weightEuclidean(
-			Vector<Partition> pars) {
-		// single example
-		if (pars.size() == 1) {
-			ProgramAdaptator pAdapter = new ProgramAdaptator(contextId);
-			ArrayList<String[]> exps = UtilTools
-					.extractExamplesinPartition(pars);
-			pAdapter.adapt(pSynthesis.msGer.exp2Space,
-					pSynthesis.msGer.exp2program, exps);
-			return pars;
-		}
-		while (true) {
-			// find partitions with the smallest distance
-			double mindist = Double.MAX_VALUE;
-			int x_ind = -1;
-			int y_ind = -1;
-			/* print the partitioning information* */
-			// ProgTracker.printPartition(pars);
-			// ProgTracker.printConstraints(constraints);
-			/***/
-			for (int i = 0; i < pars.size(); i++) {
-				for (int j = i + 1; j < pars.size(); j++) {
-					String key = getStringKey(pars.get(i), pars.get(j));
-					boolean good = true;
-					for (Map.Entry<String, Boolean> stringBooleanEntry : legalParitions.entrySet()) {
-						if (!stringBooleanEntry.getValue() && key.indexOf(stringBooleanEntry.getKey()) != -1) {
-							good = false;
-							break;
-						}
-					}
-					if (!good) {
-						legalParitions.put(key, false);
-						continue;
-					}
-					double par_dist = getDistance(pars.get(i), pars.get(j),
-							pars);
-					if (par_dist < mindist) {
-						mindist = par_dist;
-						x_ind = i;
-						y_ind = j;
-					}
-				}
-			}
-			if (x_ind == -1 || y_ind == -1) {
-				break;
-			}
-			/* print the partitioning information* */
-			// ProgTracker.printPartitions(pars.get(x_ind), pars.get(y_ind));
-			/***/
-			Partition z = pars.get(x_ind).mergewith(pars.get(y_ind));
-
-			if (adaptive_isLegalPartition(z)) {
-				legalParitions.put(z.getHashKey(), true);
-				// update the partition vector
-				pars = UpdatePartitions(x_ind, y_ind, pars);
-				continue;
-			} else {
-				legalParitions.put(
-						getStringKey(pars.get(x_ind), pars.get(y_ind)), false);
-				// update the constraints
-				Vector<String[]> clique = new Vector<String[]>();
-				for (int k = 0; k < pars.get(x_ind).orgNodes.size(); k++) {
-					String org = UtilTools.print(pars.get(x_ind).orgNodes
-							.get(k));
-					String tar = UtilTools.print(pars.get(x_ind).tarNodes
-							.get(k));
-					String[] pair = { org, tar };
-					clique.add(pair);
-				}
-				for (int k = 0; k < pars.get(y_ind).orgNodes.size(); k++) {
-					String org = UtilTools.print(pars.get(y_ind).orgNodes
-							.get(k));
-					String tar = UtilTools.print(pars.get(y_ind).tarNodes
-							.get(k));
-					String[] pair = { org, tar };
-					clique.add(pair);
-				}
-				constraints.add(clique);
-				// update the distance metrics
-				updateDistanceMetric(pars);
-			}
-		}
-		if (pars.size() > 1)
-			updateDistanceMetric(pars); // tune the final weight given the
-										// current
-		// clusters
-		// assign ulabled data to each partition
-		for (Partition p : pars) {
-			p.orgUnlabeledData.clear();
-		}
-		if (pars.size() >= 2) {
-			assignUnlabeledData(pars);
-		}
-		//this.diagnose();
-		return pars;
-	}
-
-	// use distorted distance function to cluster partitions
-	public Vector<Partition> cluster_weigthEuclidean(Vector<Partition> pars) {
-		// if (this.constraints.size() > 0)
-		// updateDistanceMetric(pars);
-
-		while (true) {
-			// find partitions with the smallest distance
-			double mindist = Double.MAX_VALUE;
-			int x_ind = -1;
-			int y_ind = -1;
-			/* print the partitioning information* */
-			// ProgTracker.printPartition(pars);
-			// ProgTracker.printConstraints(constraints);
-			/***/
-			for (int i = 0; i < pars.size(); i++) {
-				for (int j = i + 1; j < pars.size(); j++) {
-					String key = getStringKey(pars.get(i), pars.get(j));
-					boolean good = true;
-					for (Map.Entry<String, Boolean> stringBooleanEntry : legalParitions.entrySet()) {
-						if (!stringBooleanEntry.getValue() && key.indexOf(stringBooleanEntry.getKey()) != -1) {
-							good = false;
-							break;
-						}
-					}
-					if (!good) {
-						legalParitions.put(key, false);
-						continue;
-					}
-					// double par_dist = getDistance(pars.get(i), pars.get(j));
-					// double par_dist = getCompScore(pars.get(i), pars.get(j),
-					// pars);// sumit heuristic
-					double par_dist = getDistance(pars.get(i), pars.get(j),
-							pars);
-					if (par_dist < mindist) {
-						mindist = par_dist;
-						x_ind = i;
-						y_ind = j;
-					}
-				}
-			}
-			if (x_ind == -1 || y_ind == -1) {
-				break;
-			}
-			/* print the partitioning information* */
-			// ProgTracker.printPartitions(pars.get(x_ind), pars.get(y_ind));
-			/***/
-			Partition z = pars.get(x_ind).mergewith(pars.get(y_ind));
-			if (isLegalPartition(z)) {
-				legalParitions.put(z.getHashKey(), true);
-				// update the partition vector
-				pars = UpdatePartitions(x_ind, y_ind, pars);
-				continue;
-			} else {
-				legalParitions.put(
-						getStringKey(pars.get(x_ind), pars.get(y_ind)), false);
-				// update the constraints
-				Vector<String[]> clique = new Vector<String[]>();
-				for (int k = 0; k < pars.get(x_ind).orgNodes.size(); k++) {
-					String org = UtilTools.print(pars.get(x_ind).orgNodes
-							.get(k));
-					String tar = UtilTools.print(pars.get(x_ind).tarNodes
-							.get(k));
-					String[] pair = { org, tar };
-					clique.add(pair);
-				}
-				for (int k = 0; k < pars.get(y_ind).orgNodes.size(); k++) {
-					String org = UtilTools.print(pars.get(y_ind).orgNodes
-							.get(k));
-					String tar = UtilTools.print(pars.get(y_ind).tarNodes
-							.get(k));
-					String[] pair = { org, tar };
-					clique.add(pair);
-				}
-				constraints.add(clique);
-				// update the distance metrics
-				updateDistanceMetric(pars);
-			}
-		}
-		if (pars.size() > 1)
-			updateDistanceMetric(pars); // tune the final weight given the
-										// current
-		// clusters
-		// assign ulabled data to each partition
-		for (Partition p : pars) {
-			p.orgUnlabeledData.clear();
-		}
-		if (pars.size() >= 2) {
-			assignUnlabeledData(pars);
-		}
-		this.diagnose();
-		return pars;
-	}
-
-	public void assignUnlabeledData(Vector<Partition> pars) {
-		HashMap<String, Double> dists = new HashMap<String, Double>();
-		// find the distance between partitions
-		for (int i = 0; i < pars.size(); i++) {
-			for (int j = i + 1; j < pars.size(); j++) {
-				String d = getStringKey(pars.get(i), pars.get(j));
-				if (!dists.containsKey(d)) {
-					dists.put(d, getDistance(pars.get(i), pars.get(j)));
-				}
-			}
-		}
-		HashMap<Partition, HashMap<String, Double>> testResult = new HashMap<Partition, HashMap<String, Double>>();
-
-		for (String val : string2Vector.keySet()) {
-			Partition p_index = null;
-			Partition p_index_2nd = null;
-			double min_val = Double.MAX_VALUE;
-			double min_val_2nd = Double.MAX_VALUE;
-			// find the two shortest distances.
-			for (Partition p : pars) {
-				double dist = getDistance(val, p);
-				// /
-				// /System.out.println(String.format("%s, %s: %f", val, p.label,
-				// dist));
-				// /
-				if (dist < min_val) {
-					min_val_2nd = min_val;
-					p_index_2nd = p_index;
-					min_val = dist;
-					p_index = p;
-
-				} else if (dist >= min_val && dist < min_val_2nd) {
-					min_val_2nd = dist;
-					p_index_2nd = p;
-				}
-
-			}
-			double var_dist = min_val_2nd - min_val;
-			String tKey = getStringKey(p_index_2nd, p_index);
-			double pDist = dists.get(tKey);
-			if (var_dist > pDist * assignThreshold) {
-				if (!testResult.containsKey(p_index)) {
-					HashMap<String, Double> cluster = new HashMap<String, Double>();
-					cluster.put(val, min_val);
-					testResult.put(p_index, cluster);
-				} else {
-					testResult.get(p_index).put(val, min_val);
-				}
-			}
-			/*
-			 * if (p_index.orgUnlabeledData.size() < 10) {
-			 * p_index.orgUnlabeledData.add(val); }
-			 */
-		}
-		for (Map.Entry<Partition, HashMap<String, Double>> partitionHashMapEntry : testResult.entrySet()) {
-			Map<?, ?> dicttmp = UtilTools.sortByComparator(partitionHashMapEntry.getValue());
-			/** print unlabeled data **/
-			// System.out.println("Partition: " + key.label);
-			// ProgTracker.printUnlabeledData(dicttmp);
-			/****/
-			int cnt = 0;
-			for (Object xkey : dicttmp.keySet()) {
-				if (cnt < unlabelDataAmount * partitionHashMapEntry.getKey().orgNodes.size()) {
-					if (exampleInputs.contains((String) xkey))// exclude
-																// examples from
-																// unlabeled
-																// data
-						continue;
-					partitionHashMapEntry.getKey().orgUnlabeledData.add((String) xkey);
-					cnt++;
-				} else {
-					break;
-				}
-			}
-		}
-	}
-
-	// current return all the examples.
-	// monitor whether all constraints are positive.
-	public ArrayList<String> findMaximalSeperated() {
-		ArrayList<String> dists = new ArrayList<String>();
-		for (Partition e : examples) {
-			for (Vector<TNode> elem : e.orgNodes) {
-				String line = UtilTools.print(elem);
-				dists.add(line);
-			}
-		}
-		return dists;
-	}
-
-	public ArrayList<ArrayList<Double>> convertStringSetToContrainMatrix(
-			ArrayList<String> strings) {
-		ArrayList<ArrayList<Double>> res = new ArrayList<ArrayList<Double>>();
-		for (int i = 0; i < strings.size(); i++) {
-			for (int j = i + 1; j < strings.size(); j++) {
-				String s1 = strings.get(i);
-				String s2 = strings.get(j);
-				double[] s1_vec = getFeatureArray(s1);
-				double[] s2_vec = getFeatureArray(s2);
-				ArrayList<Double> xArrayList = new ArrayList<Double>();
-				for (int k = 0; k < s1_vec.length; k++) {
-					xArrayList.add(s2_vec[k] - s1_vec[k]); // does sign matter?
-				}
-				res.add(xArrayList);
-			}
-		}
-		return res;
-	}
-
-	// input with current contraints
-	public void updateDistanceMetric(Vector<Partition> pars) {
-		if (option == method.DP || option == method.DPIC) {
-			GradientDecendOptimizer gdo = new GradientDecendOptimizer();
-			// calculate example array and individual groups
-			ArrayList<double[]> centers = new ArrayList<double[]>();
-			ArrayList<ArrayList<double[]>> individuals = new ArrayList<ArrayList<double[]>>();
-			for (Partition p : pars) {
-				ArrayList<double[]> list = new ArrayList<double[]>();
-				double[] center = new double[featuresize];
-				center = UtilTools.initArray(center, 0);
-				for (Vector<TNode> org : p.orgNodes) {
-					String res = UtilTools.print(org);
-					double[] vec = string2Vector.get(res);
-					list.add(vec);
-					center = addArray(center, vec);
-				}
-				individuals.add(list);
-				center = UtilTools.produce(1.0 / p.orgNodes.size(), center);
-				centers.add(center);
-			}
-			// calculate instance array
-			ArrayList<double[]> instances = new ArrayList<double[]>();
-			for (Map.Entry<String, double[]> stringEntry : string2Vector.entrySet()) {
-				double[] elem = stringEntry.getValue();
-				instances.add(elem);
-			}
-			// calculate constraint array
-			ArrayList<ArrayList<double[]>> constraintgroup = new ArrayList<ArrayList<double[]>>();
-			for (Vector<String[]> consts : constraints) {
-				ArrayList<double[]> group = new ArrayList<double[]>();
-				for (String[] exp : consts) {
-					double[] e = string2Vector.get(exp[0]);
-					group.add(e);
-				}
-				constraintgroup.add(group);
-			}
-			double[] w = gdo.doOptimize(centers, instances, constraintgroup,
-					individuals, this.weights);
-			this.weights = w;
-		} else {
-			this.weights = new double[featuresize];
-			weights = UtilTools.initArray(this.weights, 1);
-		}
-	}
-
-	public double[] getFeatureArray(String s) {
-		Collection<Feature> cfeat = pSynthesis.featureSet
-				.computeFeatures(s, "");
-		Feature[] x = cfeat.toArray(new Feature[cfeat.size()]);
-		double[] res = new double[x.length];
-		for (int i = 0; i < x.length; i++) {
-			res[i] = x[i].getScore();
-		}
-		return res;
-	}
-
-	public double getDistance(String a, Partition b) {
-		// find a string
-		double[] x = string2Vector.get(a);
-		double mindist = Double.MAX_VALUE;
-		for (Vector<TNode> orgs : b.orgNodes) {
-			double[] e = string2Vector.get(UtilTools.print(orgs));
-			double d = getDistance(x, e);
-			if (d < mindist)
-				mindist = d;
-		}
-		return mindist;
-	}
-
-	public double getDistance(Partition a, Partition b, Vector<Partition> pars) {
-		double res = 0.0;
-		if (option == method.DPIC || option == method.DP) {
-			res = getDistance(a, b); // use the closest points' distance as the
-										// cluster distance
-		} else if (option == method.SP || option == method.SPIC) {
-			res = getCompScore(a, b, pars);
-		} else {
-			double[] x = getPartitionVector(a);
-			double[] y = getPartitionVector(b);
-			res = UtilTools.distance(x, y);
-		}
-		return res;
-	}
-
-	/*
-	 * public double getDistance(Partition a, Partition b) { double[] x =
-	 * getPartitionVector(a); double[] y = getPartitionVector(b); return
-	 * getDistance(x, y); }
-	 */
-
-	public double getDistance(Partition a, Partition b) {
-		double mindist = Double.MAX_VALUE;
-		for (Vector<TNode> orgs : a.orgNodes) {
-			String e = UtilTools.print(orgs);
-			double d = getDistance(e, b);
-			if (d < mindist)
-				mindist = d;
-		}
-		return mindist;
-	}
-
-	public double getCompScore(Partition a, Partition b, Vector<Partition> pars) {
-		String key = getStringKey(a, b);
-		for (Map.Entry<String, Boolean> stringBooleanEntry : legalParitions.entrySet()) {
-			if (key.indexOf(stringBooleanEntry.getKey()) != -1 && !stringBooleanEntry.getValue()) {
-				return Double.MAX_VALUE;
-			}
-		}
-		Partition p = a.mergewith(b);
-		if (!isLegalPartition(p)) {
-			legalParitions.put(key, false);
-			// update the constraints
-			Vector<String[]> clique = new Vector<String[]>();
-			for (int k = 0; k < a.orgNodes.size(); k++) {
-				String org = UtilTools.print(a.orgNodes.get(k));
-				String tar = UtilTools.print(a.tarNodes.get(k));
-				String[] pair = { org, tar };
-				clique.add(pair);
-			}
-			for (int k = 0; k < b.orgNodes.size(); k++) {
-				String org = UtilTools.print(b.orgNodes.get(k));
-				String tar = UtilTools.print(b.tarNodes.get(k));
-				String[] pair = { org, tar };
-				clique.add(pair);
-			}
-			constraints.add(clique);
-			return Double.MAX_VALUE;
-		}
-		double validCnt = 1e-3; // avoid overflowing
-		for (int x = 0; x < pars.size(); x++) {
-			if (pars.get(x) == a || pars.get(x) == b) {
-				continue;
-			}
-			Partition q = p.mergewith(pars.get(x));
-			if (isLegalPartition(q)) {
-				validCnt++;
-			}
-		}
-		return 1.0 / validCnt;
-	}
-
-	public double getDistance(double[] a, double[] b) {
-		double sum = 0.0;
-		for (int i = 0; i < a.length; i++) {
-			sum += Math.pow(a[i] - b[i], 2) * weights[i];
-		}
-
-		return Math.sqrt(sum);
-	}
-	//check b can be copied from a
-	public boolean iscovered(String a, String b)
-	{
-		String[] elems = b.split("\\*");
-		boolean covered = true;
-		for(String e: elems)
-		{
-			if(a.indexOf(e)== -1)
-			{
-				covered = false;
-				break;
-			}
-		}
-		return covered;
-	}
-	public boolean adaptive_isLegalPartition(Partition p) {
-		if (p == null) {
-			failedCnt++;
-			return false;
-		}
-		
-		String key = p.getHashKey();
-		if (legalParitions.containsKey(key)) {
-			return legalParitions.get(key);
-		}
-		// test whether its subset fails
-		for (Map.Entry<String, Boolean> stringBooleanEntry : legalParitions.entrySet()) {
-			if (!stringBooleanEntry.getValue() && iscovered(key, stringBooleanEntry.getKey())) {
-				return false;
-			}
-		}
-		ProgramAdaptator pAdapter = new ProgramAdaptator(contextId);
-		ArrayList<Partition> nPs = new ArrayList<Partition>();
-		nPs.add(p);
-		ArrayList<String[]> examps = UtilTools.extractExamplesinPartition(nPs);
-		String fprogram = pAdapter.adapt(pSynthesis.msGer.exp2Space,pSynthesis.msGer.exp2program, examps);
-		if (fprogram.indexOf("null")!= -1) {
-			failedCnt++;
-			legalParitions.put(key, false);
-			return false;
-		} else {
-			legalParitions.put(key, true);
-			return true;
-		}
-	}
-
-	public boolean isLegalPartition(Partition p) {
-		if (p == null) {
-			failedCnt++;
-			return false;
-		}
-		String key = p.getHashKey();
-		if (legalParitions.containsKey(key)) {
-			return legalParitions.get(key);
-		}
-		// test whether its subset fails
-		for (Map.Entry<String, Boolean> stringBooleanEntry : legalParitions.entrySet()) {
-			if (!stringBooleanEntry.getValue() && key.indexOf(stringBooleanEntry.getKey()) != -1) {
-				return false;
-			}
-		}
-		Vector<Partition> xPar = new Vector<Partition>();
-		xPar.add(p);
-		Collection<ProgramRule> cpr = pSynthesis.producePrograms(xPar);
-		if (cpr == null || cpr.isEmpty()) {
-			failedCnt++;
-			legalParitions.put(key, false);
-			return false;
-		} else {
-			legalParitions.put(key, true);
-			return true;
-		}
-	}
-
-	public Vector<Partition> UpdatePartitions(int i, int j,
-			Vector<Partition> pars) {
-		Partition p = pars.get(i).mergewith(pars.get(j));
-		Vector<Partition> res = new Vector<Partition>();
-		res.addAll(pars);
-		res.set(i, p);
-		res.remove(j);
-		return res;
-	}
-
-	public String getStringKey(Partition a, Partition b) {
-		ArrayList<Partition> pars = new ArrayList<Partition>();
-		pars.add(a);
-		pars.add(b);
-		String res = Partition.getStringKey(pars);
-		return res;
-	}
-
-	// get a vector that can represent a partition
-	public double[] getPartitionVector(Partition p) {
-
-		ArrayList<double[]> vecs = new ArrayList<double[]>();
-		for (Vector<TNode> orgs : p.orgNodes) {
-			vecs.add(string2Vector.get(UtilTools.print(orgs)));
-		}
-		double[] vec = UtilTools.sum(vecs);
-		vec = UtilTools.produce(1.0 / p.orgNodes.size(), vec);
-		return vec;
-	}
-
-	public double[] addArray(double[] a, double[] b) {
-		double[] x = new double[a.length];
-		for (int i = 0; i < a.length; i++) {
-			x[i] = a[i] + b[i];
-		}
-		return x;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ExampleSelection.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ExampleSelection.java
deleted file mode 100644
index f6c31638d..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ExampleSelection.java
+++ /dev/null
@@ -1,382 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning;
-
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.QuestionableRecord.OutlierDetector;
-
-public class ExampleSelection {
-	public HashMap<String, Vector<TNode>> org = new HashMap<String, Vector<TNode>>();
-	public HashMap<String, Vector<TNode>> tran = new HashMap<String, Vector<TNode>>();
-	public HashMap<String, String[]> raw = new HashMap<String, String[]>();
-	public boolean isDetectingQuestionableRecord = false;
-	public OutlierDetector out;
-	// testdata rowid:{tar, tarcolor}
-	public HashMap<String, HashMap<String, String[]>> testdata = new HashMap<String, HashMap<String, String[]>>();
-	public int way = 7;
-	public HashSet<String> dictionary = new HashSet<String>();
-
-	public ExampleSelection() {
-		this.out = new OutlierDetector();
-	}
-
-	public String Choose() {
-		String ID = "";
-		switch (way) {
-		case 1:
-			ID = this.way1();
-			break;
-		case 2:
-			ID = this.way2();
-			break;
-		case 3:
-			ID = this.way3();
-			break;
-		case 4:
-			ID = this.way4();
-			break;
-		case 6:
-			ID = this.way6();
-			break;
-		case 7:
-			ID = this.way7();
-			break;
-		case 8:
-			ID = this.way8();
-			break;
-		case 9:
-			ID = this.way9();
-			break;
-		default:
-			ID = "";
-		}
-		return ID;
-	}
-
-	public Vector<String[]> getOrgTarPair(HashMap<String, String[]> exps) {
-		Vector<String[]> result = new Vector<String[]>();
-		for (Map.Entry<String, String[]> stringEntry : exps.entrySet()) {
-			String[] record = stringEntry.getValue();
-			String[] tmp = { record[0], record[1] };
-			result.add(tmp);
-		}
-		return result;
-	}
-
-	// exps: rowId: {org, tar, tarcode,classlabel}
-	// example: partition id: [{raw,tarcode}]
-	public void inite(HashMap<String, String[]> exps,
-			HashMap<String, Vector<String[]>> examples) {
-		// inite the class center vector
-
-		if (way >= 6) {
-			if (firsttime) {
-				out = new OutlierDetector();
-				out.buildDict(this.getOrgTarPair(exps));
-				dictionary = out.dict;
-			}
-			out.buildMeanVector(examples, dictionary);
-		}
-		Ruler ruler = new Ruler();
-		for (Map.Entry<String, String[]> stringEntry : exps.entrySet()) {
-			String e = stringEntry.getValue()[0];
-			ruler.setNewInput(e);
-			org.put(stringEntry.getKey(), ruler.vec);
-			if (way >= 6) {
-				String raw = stringEntry.getValue()[0];
-				String[] pair = { raw, stringEntry.getValue()[2] };
-				if (testdata.containsKey(stringEntry.getValue()[3])) {
-					HashMap<String, String[]> xelem = testdata.get(stringEntry.getValue()[3]);
-					if (!xelem.containsKey(stringEntry.getKey())) {
-						xelem.put(stringEntry.getKey(), pair);
-					}
-				} else {
-					HashMap<String, String[]> vstr = new HashMap<String, String[]>();
-					vstr.put(stringEntry.getKey(), pair);
-					testdata.put(stringEntry.getValue()[3], vstr);
-				}
-			}
-		}
-
-		this.raw = exps;
-	}
-
-	// choose the most ambiguous
-	public String way1() {
-		String ID = "";
-		int maximum = -1;
-		for (String key : org.keySet()) {
-			int s = this.ambiguityScore(org.get(key));
-			if (s > maximum) {
-				ID = key;
-				maximum = s;
-			}
-		}
-		return ID;
-	}
-
-	// return the least ambiguous
-	public String way2() {
-		String ID = "";
-		int minimum = Integer.MAX_VALUE;
-		for (String key : org.keySet()) {
-			int s = this.ambiguityScore(org.get(key));
-			if (s < minimum) {
-				ID = key;
-				minimum = s;
-			}
-		}
-		return ID;
-	}
-
-	// return the first incorrect one, simulated ideal user
-	public String way3() {
-		String ID = "";
-		int minimum = Integer.MAX_VALUE;
-		for (String key : raw.keySet()) {
-			int s = Integer.valueOf(key);
-			if (s < minimum) {
-				ID = key;
-				minimum = s;
-			}
-		}
-		return ID;
-	}
-
-	public int ambiguityScore(Vector<TNode> vec) {
-		HashMap<String, Integer> d = new HashMap<String, Integer>();
-		int score = 0;
-		for (int i = 0; i < vec.size(); i++) {
-			if (d.containsKey(vec.get(i).text))
-				continue;
-			for (int j = 0; j < vec.size(); j++) {
-				if (vec.get(j).text.compareTo(vec.get(i).text) == 0 && i != j
-						&& vec.get(j).text.compareTo(" ") != 0) {
-					score++;
-				}
-			}
-			if (!d.containsKey(vec.get(i).text)) {
-				d.put(vec.get(i).text, score);
-			}
-		}
-		return score;
-	}
-
-	// only try to find the wrong ones
-	public static boolean firsttime = true;
-
-	public String way4() {
-		if (firsttime) {
-			firsttime = false;
-			return raw.keySet().iterator().next();
-		}
-		for (Map.Entry<String, String[]> stringEntry : raw.entrySet()) {
-
-			if (stringEntry.getValue()[2].indexOf("_FATAL_ERROR_") != -1) {
-				return stringEntry.getKey();
-			}
-		}
-		return this.way2();
-	}
-
-	public String way6() {
-		int max = 2; // only the one with _FATAL_ERROR_ inside
-		if (firsttime) {
-			firsttime = false;
-			return this.way2();
-		}
-		Vector<String> examples = new Vector<String>();
-		for (Map.Entry<String, String[]> stringEntry : raw.entrySet()) {
-			int cnt = 0;
-			String[] tmp = stringEntry.getValue()[2]
-					.split("((?<=_\\d_FATAL_ERROR_)|(?=_\\d_FATAL_ERROR_))");
-
-			for (String tmpstring : tmp) {
-				int errnum = 0;
-				if (tmpstring.indexOf("_FATAL_ERROR_") == -1) {
-					continue;
-				}
-				errnum = Integer.valueOf(tmpstring.substring(1, 2));
-				cnt += errnum;
-			}
-			if (cnt > max) {
-				max = cnt;
-				examples.clear();
-				examples.add(stringEntry.getKey());
-			}
-			if (cnt == max && max > 1) {
-				examples.add(stringEntry.getKey());
-			}
-		}
-		// if now _FATAL_ERROR_ detected use outlier detection
-		if (examples.size() == 0) {
-			String row = "";
-			row = way8();
-			return row;
-		} else { // select the most ambigious among all the record with same
-					// number of FATALERROR
-			String idString = "";
-			int min = 10000;
-			for (String key : examples) {
-				int s = this.ambiguityScore(org.get(key));
-				if (s < min) {
-					min = s;
-					idString = key;
-				}
-			}
-			return idString;
-		}
-	}
-
-	public String way7() {
-		// this.printdata();
-		int max = 2; // only the one with _FATAL_ERROR_ inside
-		if (firsttime) {
-			firsttime = false;
-			return this.way2();
-		}
-		Vector<String> examples = new Vector<String>();
-		for (Map.Entry<String, String[]> stringEntry : raw.entrySet()) {
-			int cnt = 0;
-			String[] tmp = stringEntry.getValue()[2]
-					.split("((?<=_\\d_FATAL_ERROR_)|(?=_\\d_FATAL_ERROR_))");
-			for (String tmpstring : tmp) {
-				int errnum = 0;
-				if (tmpstring.indexOf("_FATAL_ERROR_") == -1) {
-					continue;
-				}
-				errnum = Integer.valueOf(tmpstring.substring(1, 2));
-				cnt += errnum;
-			}
-			if (cnt > max) {
-				max = cnt;
-				examples.clear();
-				examples.add(stringEntry.getKey());
-			}
-			if (cnt == max && max > 1) {
-				examples.add(stringEntry.getKey());
-			}
-		}
-		// if no _FATAL_ERROR_ detected use outlier detection
-		if (examples.size() == 0) {
-			isDetectingQuestionableRecord = true;
-			String row = "";
-			double tmax = -1;
-			for (Map.Entry<String, HashMap<String, String[]>> stringHashMapEntry : this.testdata.entrySet()) {
-				String trowid = out.getOutliers(stringHashMapEntry.getValue(),
-						out.rVectors.get(stringHashMapEntry.getKey()), tmax, dictionary);
-				tmax = out.currentMax;
-				if (trowid.length() > 0) {
-					row = trowid;
-				}
-			}
-			return row;
-		} else { // select the most ambigious among all the record with same
-					// number of FATALERROR
-			isDetectingQuestionableRecord = false;
-			String idString = "";
-			int min = 10000;
-			for (String key : examples) {
-				int s = this.ambiguityScore(org.get(key));
-				if (s < min) {
-					min = s;
-					idString = key;
-				}
-			}
-			return idString;
-		}
-	}
-
-	// shortest result
-	// exps: rowId: {org, tar, tarcode,classlabel}
-	public String way8() {
-		if (firsttime) {
-			firsttime = false;
-			return this.way3();
-		}
-		String idString = "";
-		int shortest = 10000;
-		for (String rowid : raw.keySet()) {
-			String xrow = raw.get(rowid)[1];
-			if (xrow.indexOf("_FATAL_ERROR_") != -1) {
-				xrow = raw.get(rowid)[0];
-			}
-			if (xrow.length() < shortest) {
-				shortest = xrow.length();
-				idString = rowid;
-			}
-		}
-		return idString;
-	}
-
-	// longest result
-	public String way9() {
-		if (firsttime) {
-			firsttime = false;
-			return this.way3();
-		}
-		String idString = "";
-		int longest = -1;
-		for (String rowid : raw.keySet()) {
-			String xrow = raw.get(rowid)[1];
-			if (xrow.indexOf("_FATAL_ERROR_") != -1) {
-				xrow = raw.get(rowid)[0];
-			}
-			if (xrow.length() > longest) {
-				longest = xrow.length();
-				idString = rowid;
-			}
-		}
-		return idString;
-	}
-
-	public void clear() {
-		this.raw.clear();
-		org.clear();
-		tran.clear();
-		this.testdata.clear();
-	}
-
-	public void printdata() {
-		String s1 = "";
-		String s2 = "";
-		for (Map.Entry<String, HashMap<String, String[]>> stringHashMapEntry : this.testdata.entrySet()) {
-			HashMap<String, String[]> r = stringHashMapEntry.getValue();
-			s1 += "partition " + stringHashMapEntry.getKey() + "\n";
-			for (String[] elem : r.values()) {
-				s1 += Arrays.toString(elem) + "\n";
-			}
-		}
-		System.out.println("" + s1);
-		for (String[] v : this.raw.values()) {
-			s2 += Arrays.toString(v) + "\n";
-		}
-		System.out.println(s2);
-
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ExampleTraces.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ExampleTraces.java
deleted file mode 100644
index 6e8936d16..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ExampleTraces.java
+++ /dev/null
@@ -1,86 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Vector;
-/*
- *store the traces for all the examples
- * */
-/*
- *store the traces for all the examples
- * */
-public class ExampleTraces {
-	public HashMap<String, Traces> expTraces = new HashMap<String, Traces>();
-	String contextId;
-	public ExampleTraces(String contextId)
-	{
-		this.contextId = contextId;
-	}
-	public Traces createTrace(String[] example)
-	{
-		Vector<TNode> orgNodes = new Vector<TNode>();
-		Vector<TNode> tarNodes = new Vector<TNode>();
-		Ruler ruler = new Ruler();
-		ruler.setNewInput("<_START>"+example[0]+"<_END>");
-		orgNodes = ruler.vec;
-		ruler.setNewInput(example[1]);
-		tarNodes = ruler.vec;
-		Traces t = new Traces(orgNodes, tarNodes, contextId);
-		this.addTrace(example, t);
-		return t;
-	}
-	public void addTrace(String[] example, Traces t)
-	{
-		String key = String.format("%s|%s", example[0],example[1]);
-		expTraces.put(key, t);
-	}
-	public Traces getTrace(String[] example)
-	{
-		String key = String.format("%s|%s", example[0],example[1]);
-		return expTraces.get(key);
-	}
-	public Vector<Vector<Segment>> getCurrentSegments(String[] example)
-	{
-		Vector<Vector<Segment>> res = new Vector<Vector<Segment>>();
-		Traces t = this.getTrace(example);
-		Collection<Template> x = t.traceline.values();
-		for(Template tmp:x)
-		{
-			Vector<Segment> line = new Vector<Segment>();
-			for(GrammarTreeNode node:tmp.body)
-			{
-				line.add((Segment)node);
-			}
-			res.add(line);
-		}
-		return res;
-	}
-	public String getSegmentValue(Segment s)
-	{
-		if(s.isConstSegment())
-		{
-			return UtilTools.print(s.constNodes);
-		}
-		else
-		{
-			return s.tarString;
-		}
-	}
-	public Vector<int[]> getSegmentPos(Segment s)
-	{
-		if(s.isConstSegment())
-		{
-			return null;
-		}
-		else
-		{
-			Vector<int[]> poses = new Vector<int[]>();
-			for(Section sec:s.section)
-			{
-				int[] x = {sec.pair[0].absPosition.get(0),sec.pair[1].absPosition.get(0)};
-				poses.add(x);
-			}
-			return poses;
-		}
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/GradientDecendOptimizer.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/GradientDecendOptimizer.java
deleted file mode 100644
index 135ef8e3c..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/GradientDecendOptimizer.java
+++ /dev/null
@@ -1,377 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.Collections;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class GradientDecendOptimizer {
-	public double c_coef = 1;
-	public double relativeCoef = 1;
-	public static double ratio =0.4;
-	public double stepsize = 0.1;
-	public double maximalIternumber = 50;
-	public double wIternumber = 100;
-	public boolean coef_initialized = false;
-	public double manualCoef = 1;
-
-	Logger ulogger = LoggerFactory.getLogger(GradientDecendOptimizer.class);
-
-	public GradientDecendOptimizer() {
-	}
-
-	// used to calculate the value of objective function.
-	public double objectiveFunction(ArrayList<double[]> r,
-			ArrayList<double[]> s, ArrayList<double[]> t_star,
-			double[] w) {
-		double res = 0.0;
-		for (double[] x : r) {
-			res += UtilTools.product(x, w);
-		}
-		double ml = 0.0;
-		
-		for (double[] e : s) {
-			ml += Math.pow(UtilTools.product(e, w), 0.5);
-		}
-		double tmp = 0.0;
-		for (double[] x : t_star) {
-			tmp += Math.pow(UtilTools.product(x, w), 0.5);
-		}
-		return res +  c_coef * Math.log(ml) - c_coef
-				* Math.log(tmp);
-	}
-
-	// compute the gradient according to the formula in slides
-	public double[] getGradient(ArrayList<double[]> r, ArrayList<double[]> s,
-			ArrayList<double[]> t_star, double[] w_old) {
-
-		int featuresize = w_old.length;
-		double[] r_sum = UtilTools.sum(r);
-		double[] res = new double[featuresize];
-		// calculate the first component
-		double t_scalar_sqrt_sum = 0;
-		for (double[] e : t_star) {
-			t_scalar_sqrt_sum += Math.sqrt(UtilTools.product(e, w_old));
-		}
-		// System.out.println("scalar_sqrt_sum: "+scalar_sqrt_sum);
-		t_scalar_sqrt_sum = 1.0 / t_scalar_sqrt_sum;
-		// calculate the coefficent for each t_i
-		double[] vects = new double[featuresize];
-		for (int i = 0; i < vects.length; i++) {
-			vects[i] = 0;
-		}
-		for (double[] e : t_star) {
-			double cof = Math.pow(UtilTools.product(e, w_old) + (1e-4), -0.5);
-			double[] x = UtilTools.produce(cof, e);
-			for (int j = 0; j < x.length; j++) {
-				vects[j] += x[j];
-			}
-		}
-		// calculate the coefficent for each t_i
-		double s_scalar_sqrt_sum = 0;
-		for (double[] e : s) {
-			s_scalar_sqrt_sum += Math.sqrt(UtilTools.product(e, w_old));
-		}
-		// System.out.println("scalar_sqrt_sum: "+scalar_sqrt_sum);
-		s_scalar_sqrt_sum = 1.0 / (s_scalar_sqrt_sum+1e-6);
-		double[] svects = new double[featuresize];
-		for (int i = 0; i < svects.length; i++) {
-			svects[i] = 0;
-		}
-		for (double[] e : s) {
-			double cof = Math.pow(UtilTools.product(e, w_old) + (1e-4), -0.5);
-			//System.out.println("coef: "+cof);
-			//System.out.println("e: "+Arrays.toString(e));
-			double[] x = UtilTools.produce(cof, e);
-			//System.out.println("x: "+Arrays.toString(x));
-			for (int j = 0; j < x.length; j++) {
-				svects[j] += x[j];
-			}
-		}
-		//
-		// System.out.println("scalar_sum: "+scalar_sqrt_sum);
-		// System.out.println("vects: "+Arrays.toString(vects));
-
-		if (!coef_initialized) {
-			this.manualCoef = selectcoef(r_sum, vects);
-			coef_initialized = true;
-			this.c_coef = 2.0 * manualCoef / t_scalar_sqrt_sum;
-		}
-		// computer the gradient using subcomponents
-		for (int i = 0; i < res.length; i++) {
-			res[i] = r_sum[i] + this.relativeCoef * manualCoef * svects[i]- manualCoef * vects[i];
-			//res[i] = this.relativeCoef * manualCoef *s_scalar_sqrt_sum*svects[i]- manualCoef *t_scalar_sqrt_sum*vects[i];;
-			//res[i] = this.relativeCoef * manualCoef *svects[i]- manualCoef *vects[i];
-		}
-
-		return res;
-	}
-
-	public double selectcoef(double[] r_rum, double[] tvec) {
-		ArrayList<Double> ratios = new ArrayList<Double>();
-		for (int i = 0; i < r_rum.length; i++) {
-			if (tvec[i] != 0 && r_rum[i] != 0) {
-				double x = r_rum[i] * 1.0 / tvec[i];
-				ratios.add(x);
-			}
-		}
-		if (ratios.isEmpty())
-			return 1;
-		Collections.sort(ratios, Collections.reverseOrder());
-		// System.out.println("ratios: "+ratios);
-		Double result = 0.0;
-		/*
-		 * double smallest = ratios.get(ratios.size() - 1); for (Double right :
-		 * ratios) { if (right / smallest <= 10) { result = right; } }
-		 */
-		result = ratios.get(0);
-		return result;
-	}
-	//approximate the largrange multiplier
-	public double[] normalizeW(double[] w)
-	{
-		double sum = 0.0;
-		double goal = w.length;
-		double[] nw = new double[w.length];
-		for(int i = 0; i < w.length; i++)
-		{
-			sum += w[i];
-		}
-		for(int i = 0; i < w.length; i++)
-		{
-			nw[i] =w[i]*goal*1.0/sum;
-		}
-		return nw;
-	}
-	// as the objective function is convex. Could check the trend each step
-	public double[] doOptimize(ArrayList<double[]> examples,
-			ArrayList<double[]> instances,
-			ArrayList<ArrayList<double[]>> constraints,
-			ArrayList<ArrayList<double[]>> individualExps, double[] w) {
-
-		double[] w_0 = new double[examples.get(0).length];
-		double[] oldGradient = new double[examples.get(0).length];
-		if (w == null)
-		// init it to 1
-		{
-			for (int i = 0; i < w_0.length; i++) {
-				w_0[i] = 1;
-				oldGradient[i] = Double.MAX_VALUE;
-			}
-		} else {
-			w_0 = w;
-		}
-		int cntor = 0;
-		while (cntor < maximalIternumber) {
-			ArrayList<double[]> r = compute_r(examples, instances, w_0);
-			//ArrayList<double[]> r = new ArrayList<double[]>();
-			ArrayList<double[]> t = compute_t(constraints, w_0);
-			ArrayList<double[]> s = compute_s(individualExps, w_0);
-			// System.out.println("t>>>");
-			// TestTools.print(t);
-			// System.out.println("s>>>");
-			// TestTools.print(s);
-			if (!s.isEmpty())
-			{
-				this.relativeCoef = t.size()*ratio/s.size();
-				//relativeCoef = 2;
-			}
-			double[] gradient = getGradient(r, s, t, w_0);
-			if(UtilTools.distance(gradient, oldGradient) < 10e-5)
-			{
-				break;
-			}
-			oldGradient = gradient;
-			if(!s.isEmpty())
-			{
-				int negtiveCnt = 0;
-				for(int i = 0; i < gradient.length; i++)
-				{
-					if(gradient[i] < 0)
-					{
-						negtiveCnt ++;
-					}
-				}
-				double offset = 1.0;
-				for(int x = 0; x < individualExps.size(); x++)
-				{
-					offset += individualExps.get(x).size();
-				}
-				offset = offset/ individualExps.size();
-				//String sx = String.format("s: %d, t: %d,nG: %f, relative: %f, offset:%f", s.size(), t.size(),(negtiveCnt*1.0/gradient.length), this.relativeCoef,offset );
-			}
-			int wcnt = 0;
-			double rstepsize = this.stepsize;
-			while (wcnt < wIternumber) {
-
-				double[] w_1 = new double[w_0.length];
-				for (int i = 0; i < w_0.length; i++) {
-					w_1[i] = w_0[i] - rstepsize * gradient[i];
-				}
-				for (int i = 0; i < w_1.length; i++) {
-					if (w_1[i] < 0) {
-						w_1[i] = 0;
-					}
-				}
-				w_1 = normalizeW(w_1);
-				// the function should always decline
-				double v_old = objectiveFunction(r, s, t, w_0);
-				double v_new = objectiveFunction(r, s, t, w_1);
-				// System.out.println(String.format("values: %f, %f", v_old,
-				// v_new));
-				if (v_new > v_old) {
-					rstepsize = 0.1 * rstepsize; // jump over optimal point.
-													// reduce step size an then
-					wcnt++; // redo
-					continue;
-				}
-				// check stop condition
-				if (UtilTools.distance(w_0, w_1) < 10e-4) {
-					w_0 = w_1;
-					break;
-				}
-				w_0 = w_1;
-				wcnt++;
-			}
-			cntor++;
-		}
-		return w_0;
-	}
-
-	// compute the r vectors
-	public ArrayList<double[]> compute_r(ArrayList<double[]> centers,
-			ArrayList<double[]> instances, double[] w) {
-		ArrayList<double[]> res = new ArrayList<double[]>();
-		// assign instance to different centers
-		for (double[] e : instances) {
-			double[] cent_vec = null;
-			double min_dist = Double.MAX_VALUE;
-			for (double[] o : centers) {
-				double tmpdist = UtilTools.distance(e, o, w);
-				if (tmpdist <= min_dist) {
-					min_dist = tmpdist;
-					cent_vec = o;
-				}
-			}
-			// calculate a r vector
-			double[] r1 = new double[e.length];
-			for (int i = 0; i < r1.length; i++) {
-				r1[i] = Math.pow(e[i] - cent_vec[i], 2);
-			}
-			res.add(r1);
-		}
-		return res;
-	}
-
-	// compute the t vectors
-	public ArrayList<double[]> compute_t(
-			ArrayList<ArrayList<double[]>> constraints, double[] w) {
-		ArrayList<double[]> res = new ArrayList<double[]>();
-		// for each constraint group, find most apart two points
-		for (ArrayList<double[]> group : constraints) {
-			double max_dist = 0;
-			double[] x = null;
-			double[] y = null;
-			for (int i = 0; i < group.size(); i++) {
-				for (int j = i + 1; j < group.size(); j++) {
-					double tmp = UtilTools.distance(group.get(i), group.get(j),
-							w);
-					if (tmp >= max_dist) {
-						max_dist = tmp;
-						x = group.get(i);
-						y = group.get(j);
-					}
-				}
-			}
-			double[] t = new double[w.length];
-			for (int i = 0; i < t.length; i++) {
-				t[i] = Math.pow(x[i] - y[i], 2);
-			}
-			res.add(t);
-		}
-		return res;
-	}
-
-	// computer the s vectors
-	public ArrayList<double[]> compute_s(ArrayList<ArrayList<double[]>> groups,
-			double[] w) {
-		ArrayList<double[]> res = new ArrayList<double[]>();
-		for (ArrayList<double[]> group : groups) {
-			if (group.size() <= 1)
-				continue;
-			ArrayList<double[]> tmp = new ArrayList<double[]>();
-			for (int i = 0; i < group.size(); i++) {
-				double[] t = new double[w.length];
-				if (i == group.size() - 1) {
-					for (int k = 0; k < t.length; k++) {
-						t[k] = Math.pow(group.get(i)[k] - group.get(0)[k], 2);
-					}
-					tmp.add(t);
-					break;
-				} else {
-					for (int k = 0; k < t.length; k++) {
-						t[k] = Math.pow(group.get(i)[k] - group.get(i + 1)[k],
-								2);
-					}
-					tmp.add(t);
-				}
-			}
-			double[] groupsum = UtilTools.sum(tmp);
-			res.add(groupsum);
-		}
-		return res;
-	}
-
-	//@Test
-	public void test1() {
-		double[] p1 = { 1, 2 };
-		double[] p2 = { 50, 1 };
-		double[] p3 = { 50, 2 };
-		double[] p4 = { 50, 3 };
-		double[] p5 = { 55, 1.5 };
-		double[] p6 = { 60, 2 };
-		double[] p7 = { 60, 3 };
-		ArrayList<double[]> examples = new ArrayList<double[]>();
-		double[] center1 = { 37.75, 1.75 };
-		double[] center2 = { 60, 2.5 };
-		examples.add(center1);
-		examples.add(center2);
-		ArrayList<double[]> instances = new ArrayList<double[]>();
-		instances.add(p1);
-		instances.add(p2);
-		instances.add(p3);
-		instances.add(p4);
-		instances.add(p5);
-		instances.add(p6);
-		instances.add(p7);
-		ArrayList<ArrayList<double[]>> mconstraints = new ArrayList<ArrayList<double[]>>();
-		ArrayList<ArrayList<double[]>> cconstraints = new ArrayList<ArrayList<double[]>>();
-		// group 1
-		ArrayList<double[]> group1 = new ArrayList<double[]>();
-		group1.add(p1);
-		group1.add(p2);
-		group1.add(p3);
-		group1.add(p4);
-		// group1.add(p3);
-		// group1.add(p4);
-		mconstraints.add(group1);
-		ArrayList<double[]> group2 = new ArrayList<double[]>();
-		group2.add(p6);
-		group2.add(p7);
-		mconstraints.add(group2);
-		ArrayList<double[]> group3 = new ArrayList<double[]>();
-		group3.add(p1);
-		group3.add(p2);
-		group3.add(p3);
-		group3.add(p4);
-		group3.add(p6);
-		group3.add(p7);
-		cconstraints.add(group3);
-		double[] res = doOptimize(examples, instances, cconstraints,
-				mconstraints, null);
-		assert (res[0] < res[1]);
-		assert (res[0] < 1e-5);
-		// System.out.println("Final Weights: " + Arrays.toString(res));
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/GrammarTreeNode.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/GrammarTreeNode.java
deleted file mode 100644
index e5bf5bd00..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/GrammarTreeNode.java
+++ /dev/null
@@ -1,13 +0,0 @@
-package edu.isi.karma.cleaning;
-
-public interface GrammarTreeNode {
-	public String toProgram();
-	public GrammarTreeNode mergewith(GrammarTreeNode a);
-	public String getNodeType();
-	public double getScore();
-	public String getrepString(); // return a string represent the type info of		// the grammar tree node
-	public void createTotalOrderVector(); // use the predefined partial order to
-	public void emptyState();
-	public long size();
-	public String getProgram(); // return the program generated from this node;
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/InterpreterType.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/InterpreterType.java
deleted file mode 100644
index 1895ee7a0..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/InterpreterType.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package edu.isi.karma.cleaning;
-
-public interface InterpreterType {
-	public void func(String name, Object x);
-
-	public String execute(String value);
-
-	public String execute_debug(String value);
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Interpretor.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Interpretor.java
deleted file mode 100644
index bedbf2301..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Interpretor.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import org.python.core.PyObject;
-import org.python.core.PyString;
-import org.python.util.PythonInterpreter;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import edu.isi.karma.webserver.ContextParametersRegistry;
-import edu.isi.karma.webserver.ServletContextParameterMap;
-import edu.isi.karma.webserver.ServletContextParameterMap.ContextParameter;
-
-public class Interpretor {
-	private PyObject interpreterClass;
-	private static Logger logger = LoggerFactory.getLogger(Interpretor.class);
-	public Interpretor(String contextId) {
-		PythonInterpreter interpreter = new PythonInterpreter();
-		ServletContextParameterMap contextParameters = ContextParametersRegistry.getInstance().getContextParameters(contextId);
-		String dirpathString = contextParameters.getParameterValue(ContextParameter.WEBAPP_PATH) + 
-									"/" + contextParameters
-									.getParameterValue(ContextParameter.PYTHON_SCRIPTS_DIRECTORY);
-		
-									;
-		if(dirpathString == null || dirpathString.length() <= 1) {
-			dirpathString = "../karma-web/src/main/webapp/resources/pythonCleaningscripts";
-		}
-		logger.info("Setting Python Scripts Directory for karma-cleaning: "
-				+ dirpathString);
-		interpreter.exec("import sys");
-		interpreter.exec("sys.path.append('" + dirpathString + "')");
-		// /Users/bowu/projects/IDCT/src/edu/isi/karma/cleaning
-		interpreter.exec("sys.path.append('" + dirpathString + "')");
-		interpreter.exec("from FunctionList import *");
-		interpreter.exec("from Interpreter import *");
-		// interpreter.exec("print sys.path");
-		interpreterClass = interpreter.get("Interpreter");
-	}
-
-	/**
-	 * The create method is responsible for performing the actual coercion of
-	 * the referenced python module into Java bytecode
-	 */
-
-	public InterpreterType create(String scripts) {
-
-		PyObject buildingObject = interpreterClass.__call__(new PyString(
-				scripts));
-		InterpreterType ele = (InterpreterType) buildingObject
-				.__tojava__(InterpreterType.class);
-		return ele;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/LinearSolver.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/LinearSolver.java
deleted file mode 100644
index 43d2c6d01..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/LinearSolver.java
+++ /dev/null
@@ -1,89 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.apache.commons.math.optimization.GoalType;
-import org.apache.commons.math.optimization.OptimizationException;
-import org.apache.commons.math.optimization.RealPointValuePair;
-import org.apache.commons.math.optimization.linear.LinearConstraint;
-import org.apache.commons.math.optimization.linear.LinearObjectiveFunction;
-import org.apache.commons.math.optimization.linear.Relationship;
-import org.apache.commons.math.optimization.linear.SimplexSolver;
-
-public class LinearSolver {
-	private LinearSolver() {
-	}
-
-	public static void main(String[] args) {
-		//add residue to objective function
-		LinearObjectiveFunction f = new LinearObjectiveFunction(new double[] {-3,-3,4,0,0,0
-				}, 0);
-		Collection<LinearConstraint> constraints = new ArrayList<LinearConstraint>();
-		//data contraint
-		constraints.add(new LinearConstraint(new double[] { 1, 1,-1,0,0,0},
-				Relationship.LEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { 0, 1,0,1,0,0},
-				Relationship.GEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { -1, -1,0,0,1,0},
-				Relationship.GEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { -1, 0,0,0,0,1},
-				Relationship.GEQ, 0));
-		/*
-		constraints.add(new LinearConstraint(new double[] { 0, 1,0,-1,0},
-				Relationship.GEQ, -1));
-		constraints.add(new LinearConstraint(new double[] { 0, 1,0,0,-1},
-				Relationship.GEQ, -1));
-		*/
-		
-		//auxiliary variable should be the biggest
-		constraints.add(new LinearConstraint(new double[] { -1, -1,1,0,0,0},
-				Relationship.GEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { 0, -1,0,1,0,0},
-				Relationship.GEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { -1, -1,0,0,1,0},
-				Relationship.GEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { -1, 0,0,0,0,1},
-				Relationship.GEQ, 0));
-		//all parameters are positive
-		constraints.add(new LinearConstraint(new double[] { 1, 0,0,0,0,0},
-				Relationship.GEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { 0, 1,0,0,0,0},
-				Relationship.GEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { 0, 0,1,0,0,0},
-				Relationship.GEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { 0, 0,0,1,0,0},
-				Relationship.GEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { 0, 0,0,0,1,0},
-				Relationship.GEQ, 0));
-		constraints.add(new LinearConstraint(new double[] { 0, 0,0,0,0,1},
-				Relationship.GEQ, 0));
-		//max - max constraint >0
-		constraints.add(new LinearConstraint(new double[] { 0, 0,2,-1,-1,-1},
-				Relationship.GEQ, 0));
-		//sum of weight equal 1
-		constraints.add(new LinearConstraint(new double[] { 1, 1,0,0,0},
-				Relationship.EQ, 1));
-
-		// create and run the solver
-		RealPointValuePair solution;
-		try {
-			solution = new SimplexSolver().optimize(f,
-					constraints, GoalType.MINIMIZE, false);
-			// get the solution
-			double x = solution.getPoint()[0];
-			double y = solution.getPoint()[1];
-			double p = solution.getPoint()[2];
-			double q1 = solution.getPoint()[3];
-			double q2 = solution.getPoint()[4];
-
-			double min = solution.getValue();
-			System.out.println(String.format("%f,%f,%f,%f,%f,%f",x,y,p,q1,q2,min));
-		} catch (OptimizationException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-
-		
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Loop.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Loop.java
deleted file mode 100644
index 662d55f8d..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Loop.java
+++ /dev/null
@@ -1,114 +0,0 @@
-package edu.isi.karma.cleaning;
-
-public class Loop implements GrammarTreeNode {
-	public Segment loopbody;
-	public String program = "null";
-	public int looptype;
-	public static final int LOOP_START = 0;
-	public static final int LOOP_END = 1;
-	public static final int LOOP_BOTH = 2;
-	public static final int LOOP_MID = 3;
-	String contextId; 
-	public Loop(Segment loopbody, int looptype, String contextId) {
-		this.contextId = contextId;
-		if (loopbody.section.isEmpty()) {
-			this.loopbody = new Segment(loopbody.constNodes, contextId);
-		} else {
-			this.loopbody = new Segment(loopbody.section, true, contextId);
-		}
-		this.looptype = looptype;
-		this.loopbody.isinloop = true;
-	}
-
-	public String verifySpace() {
-		String res = "";
-		res= this.loopbody.verifySpace();
-		this.program = res;
-		return res;
-	}
-
-	public Loop mergewith(Loop a) {
-		if (this.looptype == a.looptype) {
-			Segment segment = this.loopbody.mergewith(a.loopbody);
-			if (segment == null)
-				return null;
-			Loop l = new Loop(segment, looptype,contextId);
-			return l;
-		} else {
-			return null;
-		}
-	}
-
-	public Loop mergewith(Segment a) {
-		Segment segment = this.loopbody.mergewith(a);
-		if (segment == null)
-			return null;
-		Loop l = new Loop(segment, looptype,contextId);
-		return l;
-	}
-
-	public String toString() {
-		return "[loop]" + this.loopbody.toString();
-	}
-
-	private double score = 0.0;
-
-	public double getScore() {
-		double r = score;
-		this.score = 0.0;
-		return r;
-	}
-
-	public String toProgram() {
-		String res = this.loopbody.toProgram();
-		if (res.length() == 0) {
-			this.loopbody.emptyState();
-		}
-		return res;
-	}
-
-	public GrammarTreeNode mergewith(GrammarTreeNode a) {
-		if (a.getNodeType().compareTo("loop") == 0) {
-			return this.mergewith((Loop) a);
-		} else if (a.getNodeType().compareTo("Segment") == 0) {
-			return this.mergewith((Segment) a);
-		} else
-			return null;
-	}
-
-	public String getNodeType() {
-		return "loop";
-	}
-
-	public String getrepString() {
-		return this.loopbody.getrepString();
-	}
-
-	public void createTotalOrderVector() {
-		// TODO Auto-generated method stub
-
-	}
-
-	public String getRule(int index) {
-		if (index >= loopbody.size() || index < 0) {
-			return "null";
-		} else {
-			return loopbody.getRule(index);
-		}
-	}
-
-	public long size() {
-		return this.loopbody.size();
-	}
-
-	public void emptyState() {
-		this.loopbody.emptyState();
-
-	}
-
-	@Override
-	public String getProgram() {
-		return this.program;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Messager.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Messager.java
deleted file mode 100644
index 064edaf6c..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Messager.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.HashMap;
-import java.util.Vector;
-//used to carry information accross iterations
-
-public class Messager {
-	double[] weights = null;
-	Vector<Vector<String[]>> cm_constr = new Vector<Vector<String[]>>();
-	HashMap<String, Traces> exp2Space = new HashMap<String, Traces>();
-	HashMap<String, String> exp2program = new HashMap<String,String>();
-	//ExampleTraces expTraces = new ExampleTraces();
-	public Messager()
-	{
-		
-	}
-	public void updateCM_Constr(Vector<Vector<String[]>> conVector)
-	{
-		this.cm_constr.addAll(conVector);
-	}
-	public void updateWeights(double[] weights)
-	{
-		this.weights = weights;
-	}
-	public double[] getWeights()
-	{
-		return this.weights;
-	}
-	public Vector<Vector<String[]>> getConstraints()
-	{
-		return cm_constr;
-	}
-}
-
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/MyLogger.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/MyLogger.java
deleted file mode 100644
index 85fa4872b..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/MyLogger.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.util.HashMap;
-
-public class MyLogger {
-	public static BufferedWriter out;
-	public static String user_id = "";
-	public static HashMap<String, Long> timespan = new HashMap<String, Long>();
-
-	public MyLogger() {
-		if (out == null) {
-			try {
-				out = new BufferedWriter(new FileWriter(new File(
-						"./log/mylog.txt"), false));
-			} catch (Exception e) {
-				// LoggerFactory.getLogger(MyLogger.class).info(e.toString());
-				out = null;
-			}
-		}
-	}
-
-	public static void logsth(String context) {
-		try {
-			out.write(context);
-			out.flush();
-		} catch (Exception e) {
-			// mvn LoggerFactory.getLogger(MyLogger.class).info(e.toString());
-		}
-	}
-
-	public static void setTime(String id, Long time) {
-		timespan.put(id, time);
-	}
-
-	public static long getDuration(String id) {
-		if (timespan.containsKey(id)) {
-			return (System.currentTimeMillis() - timespan.get(id)) / 1000;
-		} else {
-			return -1;
-		}
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/OptimizePartition.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/OptimizePartition.java
deleted file mode 100644
index 090d2aa5f..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/OptimizePartition.java
+++ /dev/null
@@ -1,246 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Vector;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import edu.isi.karma.cleaning.features.RecordClassifier;
-
-public class OptimizePartition {
-	public HashMap<String, Partition> existedPartition = new HashMap<String, Partition>();
-	public HashSet<String> existedFringe = new HashSet<String>();
-	public HashMap<String, Double> key2Partition = new HashMap<String, Double>();
-	public HashMap<String, Boolean> legalParitions = new HashMap<String, Boolean>();
-	public ProgSynthesis pSynthesis;
-	public PartitionClassifierType classifier;
-	public HashMap<Vector<Partition>, Double> fringe = new HashMap<Vector<Partition>, Double>();
-	public int failedCnt = 0;
-	public Logger ulogger = LoggerFactory.getLogger(RecordClassifier.class);
-	public OptimizePartition(ProgSynthesis ps,PartitionClassifierType classifier) {
-		pSynthesis = ps;
-		this.classifier = classifier;
-	}
-	public String getPartitionKey(int a, int b, Vector<Partition> pars) {
-		String s = a + "," + b;
-		
-		for (Partition p : pars) {
-			s += p.getHashKey() + "\n===\n";
-		}
-		return s.trim();
-	}
-
-	public Entry<Vector<Partition>, Double> findSkey(
-			HashMap<Vector<Partition>, Double> fringe) {
-		Entry<Vector<Partition>, Double> minEntry = null;
-
-		for (Map.Entry<Vector<Partition>, Double> entry : fringe.entrySet()) {
-			if (minEntry == null || entry.getValue() < minEntry.getValue()) {
-				minEntry = entry;
-			}
-		}
-		return minEntry;
-	}
-
-	public boolean existClassifer(Vector<Partition> pars) {
-		RecordClassifier rClassifier = (RecordClassifier)this.classifier;
-		rClassifier.init();
-		int cnt = 0;
-		for (Partition p : pars) {
-			String label = "attr_" + cnt;
-			cnt++;
-			for (int i = 0; i < p.orgNodes.size(); i++) {
-				String data = UtilTools.print(p.orgNodes.get(i));
-				rClassifier.addTrainingData(data, label);
-			}
-		}
-		rClassifier.learnClassifer();
-		return rClassifier.selfVerify();
-	}
-
-	public Vector<Partition> astarSearch(Vector<Partition> pars) {
-		if (pars.size() == 1) {
-			return pars;
-		}
-		fringe = new HashMap<Vector<Partition>, Double>();
-		fringe.put(pars, Double.MAX_VALUE);
-		Vector<Partition> res = new Vector<Partition>();
-		while (!fringe.isEmpty()) {
-			//ulogger.info("Fringe size: "+fringe.size());
-			// choose one with minimal value from fringe to expand
-			Entry<Vector<Partition>, Double> elem = this.findSkey(fringe);
-			// extend from current elem
-			HashMap<Vector<Partition>, Double> candidates = this
-					.generateCandidates(elem.getKey());
-			// check if partitoning ends
-			if (candidates == null) {
-				// check whether exist consistent classifier
-				if(elem.getKey().size() == 1)
-				{
-					res = elem.getKey();
-					break;
-				}
-				if (existClassifer(elem.getKey())) {
-					res = elem.getKey();
-					break;
-				}
-			}
-			// update the fringe
-			fringe = candidates;
-			
-		}
-		return res;
-	}
-
-	public HashMap<Vector<Partition>, Double> generateCandidates(
-			Vector<Partition> pars) {
-		HashMap<Vector<Partition>, Double> res = null;
-		for (int i = 0; i < pars.size(); i++) {
-			for (int j = i + 1; j < pars.size(); j++) {
-				double s = 0;
-				String lkey = this.getPartitionKey(i, j, pars);
-				if (this.key2Partition.containsKey(lkey)) {
-					s = key2Partition.get(lkey);
-				} else {
-					s = getCompScore(i, j, pars);
-					key2Partition.put(lkey, s);
-				}
-				if (s == Double.MAX_VALUE) {
-					continue;
-				}
-				if (i != -1 && j != -1) {
-					Vector<Partition> next = UpdatePartitions(i, j, pars);
-					if(res == null)
-						res = new HashMap<Vector<Partition>, Double>();
-					if(!fringe.containsKey(next))
-						res.put(next, s);
-				}
-			}
-		}
-		return res;
-	}
-
-	public Vector<Partition> UpdatePartitions(int i, int j,
-			Vector<Partition> pars) {
-		String key = getMergedKey(pars.get(i), pars.get(j));
-		Partition p;
-		if(!existedPartition.containsKey(key))
-		{
-			p = pars.get(i).mergewith(pars.get(j));
-			existedPartition.put(key, p);
-		}
-		else
-		{
-			p = existedPartition.get(key);
-		}
-		Vector<Partition> res = new Vector<Partition>();
-		res.addAll(pars);
-		res.set(i, p);
-		res.remove(j);
-		return res;
-	}
-	
-	// return number of partitions as the distance. 
-	// if two partitions are not compatitable, return the largest double
-	public double getCompScore2(int i, int j, Vector<Partition> pars)
-	{
-		String key = this.getMergedKey(pars.get(i), pars.get(j));
-		Partition p;
-		if(!existedPartition.containsKey(key))
-		{
-			p = pars.get(i).mergewith(pars.get(j));
-			existedPartition.put(key, p);
-		}
-		else
-		{
-			p = existedPartition.get(key);
-		}
-		if (p == null || !isLegalPartition(p)) {
-			failedCnt ++;
-			return Double.MAX_VALUE;
-		}
-		else
-		{
-			return pars.size()-1;
-		}
-	}
-	// return Num_of_partition/mergable_paritions as distance function 
-	// if two partitions are not compatitable, return the largest double
-	public double getCompScore(int i, int j, Vector<Partition> pars) {
-		String key = this.getMergedKey(pars.get(i), pars.get(j));
-		Partition p;
-		if(!existedPartition.containsKey(key))
-		{
-			p = pars.get(i).mergewith(pars.get(j));
-			existedPartition.put(key, p);
-		}
-		else
-		{
-			p = existedPartition.get(key);
-		}
-		if (p == null || !isLegalPartition(p)) {
-			return Double.MAX_VALUE;
-		}
-		int validCnt = 0;
-		for (int x = 0; x < pars.size(); x++) {
-			if (x == i || x == j) {
-				continue;
-			}
-			Partition q = p.mergewith(pars.get(x));
-			if (q != null && isLegalPartition(p)) {
-				validCnt++;
-			}
-		}
-		return (pars.size()-1)*1.0/validCnt;
-	}
-
-	public boolean isLegalPartition(Partition p) {
-		String key = p.getHashKey();
-		if (legalParitions.containsKey(key)) {
-			return legalParitions.get(key);
-		}
-		// test whether its subset fails
-		for (Entry<String, Boolean> stringBooleanEntry : legalParitions.entrySet()) {
-			if (!stringBooleanEntry.getValue() && key.indexOf(stringBooleanEntry.getKey()) != -1) {
-				return false;
-			}
-		}
-		Vector<Partition> xPar = new Vector<Partition>();
-		xPar.add(p);
-		Collection<ProgramRule> cpr = pSynthesis.producePrograms(xPar);
-		if (cpr == null || cpr.isEmpty()) {
-			legalParitions.put(key, false);
-			return false;
-		} else {
-			legalParitions.put(key, true);
-			return true;
-		}
-	}
-	//speed optimization
-	public String getMergedKey(Partition a, Partition b)
-	{
-		ArrayList<String> xArrayList = new ArrayList<String>();
-		for(int i = 0; i< a.orgNodes.size(); i++)
-		{
-			String line = UtilTools.print(a.orgNodes.get(i));
-			xArrayList.add(line);
-		}
-		for(int i = 0; i< b.orgNodes.size(); i++)
-		{
-			String line = UtilTools.print(b.orgNodes.get(i));
-			xArrayList.add(line);
-		}
-		Collections.sort(xArrayList);
-		return xArrayList.toString();
-	}
-	public static void main(String[] args) {
-
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ParseTreeNode.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ParseTreeNode.java
deleted file mode 100644
index 21d3eaf2b..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ParseTreeNode.java
+++ /dev/null
@@ -1,91 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-
-public class ParseTreeNode {
-	nodetype type = nodetype.root;
-	String value = "";
-	String tmpEval = "";
-	public static enum nodetype {
-	    loop,segment, position,root
-	}
-	ParseTreeNode parent;
-	ArrayList<ParseTreeNode> children = new ArrayList<ParseTreeNode>();
-	String contextId;
-	public ParseTreeNode(nodetype type, String value, String contextId)
-	{
-		this.type = type;
-		this.value = value;
-		this.contextId = contextId;
-	}
-	public void addChildren(ParseTreeNode node)
-	{
-		this.children.add(node);
-		//this.value = ""; //need to update based on 
-		node.parent = this;
-	}
-	public ArrayList<ParseTreeNode> getChildren()
-	{
-		return this.children;
-	}
-	//convert the tree back to program, only need to be used on the root node
-	//not work if only the position expression is updated
-	public String toProgram()
-	{
-		String prog = "";
-		if(this.type == nodetype.root)
-		{
-			for(ParseTreeNode node:this.children)
-			{
-				prog+= node.toProgram()+"+";
-			}
-			if(prog.length() > 0)
-			{
-				prog =  prog.substring(0,prog.length()-1);
-			}
-		}
-		else if(this.type == nodetype.segment)
-		{
-			if(this.children.isEmpty())
-			{
-				prog = this.value;
-			}
-			else
-			{
-				prog = String.format("substr(value,%s,%s)", this.children.get(0).value,this.children.get(1).value);
-			}
-		}
-		return prog;
-	}
-	public String toString()
-	{
-		String root = value+"(";
-		String res = "";
-		for(ParseTreeNode node: children)
-		{
-			res += node.toString();
-		}
-		return root+res+")";
-	}
-	//evaluate the current subexpression on input
-	public String eval(String input)
-	{
-		try
-		{
-		ProgramRule ptmp = new ProgramRule(this.value, contextId);
-		String res = "";
-		res = ptmp.transform(input);
-		//recursively evaluate the children nodes.
-		for(ParseTreeNode ptn: this.children)
-		{
-			ptn.eval(input);
-		}
-		this.tmpEval = res;
-		return res;
-		}
-		catch(Exception e)
-		{
-			return "";
-		}
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Partition.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Partition.java
deleted file mode 100644
index c8d53473a..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Partition.java
+++ /dev/null
@@ -1,170 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Vector;
-
-import org.apache.commons.lang.builder.HashCodeBuilder;
-
-public class Partition implements GrammarTreeNode {
-	public Traces trace;
-	public Vector<Vector<TNode>> orgNodes;
-	public Vector<Vector<TNode>> tarNodes;
-	public Vector<String> orgUnlabeledData = new Vector<String>();
-	public Vector<String> mapping = new Vector<String>();
-	public String label; // the class label of current partition
-	public String cls;
-	public String program = "";
-	public String contextId;
-	public Partition(String contextId)
-	{	
-		this.contextId = contextId;
-	}
-	public Partition(Traces t,Vector<Vector<TNode>> orgNodes, Vector<Vector<TNode>> tarNodes)
-	{
-		this.trace = t;
-		this.orgNodes = orgNodes;
-		this.tarNodes = tarNodes;
-		
-	}
-	public long size() {
-		return trace.size();
-	}
-
-	public Partition(Vector<Vector<TNode>> org, Vector<Vector<TNode>> tar) {
-		this.orgNodes = org;
-		this.tarNodes = tar;
-		Vector<Traces> ts = new Vector<Traces>();
-		for (int i = 0; i < orgNodes.size(); i++) {
-			Traces t = new Traces(orgNodes.get(i), tarNodes.get(i),contextId);
-			ts.add(t);
-		}
-		Traces iterTraces = ts.get(0);
-		for (int i = 1; i < ts.size(); i++) {
-			iterTraces = iterTraces.mergewith(ts.get(i));
-		}
-		this.trace = iterTraces;
-	}
-	public void setunLabeledData(Vector<String> orgUdata)
-	{
-		this.orgUnlabeledData = orgUdata;
-	}
-	public void setTraces(Traces t)
-	{
-		this.trace = t;
-	}
-
-	public void setExamples(Vector<Vector<TNode>> orgNodes,
-			Vector<Vector<TNode>> tarNodes) {
-		this.orgNodes = orgNodes;
-		this.tarNodes = tarNodes;
-	}
-
-	public void setLabel(String option) {
-		this.label = option;
-	}
-
-	public Partition mergewith(Partition b) {
-		Traces mt = this.trace.mergewith(b.trace);
-		// add the examples
-		Vector<Vector<TNode>> norg = new Vector<Vector<TNode>>();
-		Vector<Vector<TNode>> ntar = new Vector<Vector<TNode>>();
-		norg.addAll(this.orgNodes);
-		norg.addAll(b.orgNodes);
-		ntar.addAll(this.tarNodes);
-		ntar.addAll(b.tarNodes);
-		if (mt != null) {
-			Partition p = new Partition(contextId);
-			p.setExamples(norg, ntar);
-			p.setTraces(mt);
-			return p;
-		} else {
-			return null;
-		}
-	}
-	@Override
-	public int hashCode()
-	{
-		String s = this.getHashKey();
-		return new HashCodeBuilder(17, 31).append(s).toHashCode();
-	}
-	public String getHashKey()
-	{
-		ArrayList<Partition> pars = new ArrayList<Partition>();
-		pars.add(this);
-		return Partition.getStringKey(pars);
- 	}
-	public static String getStringKey(ArrayList<Partition> pars)
-	{
-		String s = "";
-		ArrayList<String[]> lines = new ArrayList<String[]>();
-		for(Partition p: pars)
-		{
-			for (int i = 0; i < p.orgNodes.size(); i++) {
-				String s1 = UtilTools.print(p.orgNodes.get(i));
-				String s2 = UtilTools.print(p.tarNodes.get(i));
-				String[] line = {s1,s2};
-				lines.add(line);
-			}
-		}
-		s = UtilTools.createkey(lines);
-		return s.trim();
-	}
-
-	public String toString() {
-		String s = "partition:" + this.label + "\n";
-		s += "Examples:\n";
-		ArrayList<String> lines = new ArrayList<String>();
-		for(int i = 0; i<this.orgNodes.size(); i++)
-		{
-			String line= UtilTools.print(this.orgNodes.get(i))+"   "+UtilTools.print(this.tarNodes.get(i))+"\n";
-			lines.add(line);
-		}
-		Collections.sort(lines);
-		s += Arrays.toString(lines.toArray());
-		return s;
-	}
-
-	private double score = 0.0;
-
-	public double getScore() {
-		double r = score;
-		this.score = 0.0;
-		return r;
-	}
-
-	public String toProgram() {
-		String res =  this.trace.toProgram();
-		this.program = res;
-		return res;
-
-	}
-
-	public GrammarTreeNode mergewith(GrammarTreeNode a) {
-		Partition p = (Partition) a;
-		p = this.mergewith(p);
-		return p;
-	}
-
-	public String getNodeType() {
-		return "partition";
-	}
-
-	public String getrepString() {
-		return "Partition";
-	}
-
-	public void createTotalOrderVector() {
-		
-	}
-
-	public void emptyState() {
-		this.trace.emptyState();
-	}
-
-	@Override
-	public String getProgram() {
-		return this.program;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/PartitionClassifier.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/PartitionClassifier.java
deleted file mode 100644
index 2ad04d538..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/PartitionClassifier.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.Vector;
-
-import org.python.core.PyObject;
-
-
-public class PartitionClassifier {
-	public String clssettingString = "";
-	public String[] vocabs;
-
-	public PartitionClassifier() {
-	}
-
-	public PartitionClassifierType create2(Vector<Partition> pars,PartitionClassifierType ele,DataPreProcessor dpp)
-	{
-		ele.init();
-		for(int i = 0; i<pars.size(); i++)
-		{
-			Partition partition = pars.get(i);
-			for (int j = 0; j < partition.orgNodes.size(); j++) {
-				String s = UtilTools.print(partition.orgNodes.get(j));
-				String label = partition.label;
-				ele.addTrainingData(s, label);
-			}
-			for(int j = 0; j < partition.orgUnlabeledData.size(); j++)
-			{
-				String label = partition.label;
-				String s = partition.orgUnlabeledData.get(j);
-				ele.addTrainingData(s, label);
-			}
-		}
-		this.clssettingString = ele.learnClassifer();
-		return ele;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/PartitionClassifierType.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/PartitionClassifierType.java
deleted file mode 100644
index 24f5c3a67..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/PartitionClassifierType.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package edu.isi.karma.cleaning;
-
-public interface PartitionClassifierType {
-	//public void addTrainingData(String value, double[] val ,String label);
-	public void addTrainingData(String value,String label);
-	public String learnClassifer();
-
-	public String getLabel(String value);
-	public void init();
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Patcher.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Patcher.java
deleted file mode 100644
index 2c0c8addf..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Patcher.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package edu.isi.karma.cleaning;
-import java.util.Vector;
-
-
-public class Patcher {
-	public Vector<GrammarTreeNode> patchSpace = new Vector<GrammarTreeNode>();
-	public Vector<GrammarTreeNode> groundTruth = new Vector<GrammarTreeNode>();
-	public Vector<ParseTreeNode> programNodes = new Vector<ParseTreeNode>();
-	public Vector<ParseTreeNode> replaceNodes = new Vector<ParseTreeNode>();
-}
\ No newline at end of file
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Position.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Position.java
deleted file mode 100644
index 4f5c81352..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Position.java
+++ /dev/null
@@ -1,453 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.SortedSet;
-import java.util.TreeMap;
-import java.util.TreeSet;
-import java.util.Vector;
-
-public class Position implements GrammarTreeNode {
-	public Vector<TNode> leftContextNodes = new Vector<TNode>();
-	public Vector<TNode> rightContextNodes = new Vector<TNode>();
-	public Vector<Integer> absPosition = new Vector<Integer>();
-	public Vector<Integer> counters = new Vector<Integer>();
-	public Vector<String> orgStrings = new Vector<String>();
-	public Vector<String> tarStrings = new Vector<String>();
-	public boolean isinloop = false;
-	public int curState = 0;
-	public static Interpretor itInterpretor = null;
-	public int fixedlength = 0;
-	public String program = "null";
-	public String contextId;
-	public Position(Vector<Integer> absPos, Vector<TNode> lcxt,
-			Vector<TNode> rcxt, Vector<String> orgStrings,
-			Vector<String> tarStrings, boolean loop, String contextId) {
-		this.contextId = contextId;
-		this.absPosition = absPos;
-		this.orgStrings.addAll(orgStrings);
-		this.tarStrings.addAll(tarStrings);
-		if (itInterpretor == null)
-			itInterpretor = new Interpretor(contextId);
-		// occurance of a reg pattern
-		this.counters.add(-1);
-		this.counters.add(1);
-		this.leftContextNodes = lcxt;
-		this.rightContextNodes = rcxt;
-		this.isinloop = loop;
-		createTotalOrderVector();
-	}
-
-	public Position(Position p, boolean loop) {
-		this.absPosition = p.absPosition;
-		// occurance of a reg pattern
-		this.counters.add(-1);
-		this.counters.add(1);
-		this.leftContextNodes = p.leftContextNodes;
-		this.rightContextNodes = p.rightContextNodes;
-		this.isinloop = loop;
-		createTotalOrderVector();
-	}
-
-	public void getString(Vector<TNode> x, int cur, String path, Double value,
-			HashMap<String, Double> smap, boolean isleft) {
-		if (fixedlength == 0 && !smap.keySet().contains(path)) {
-			String res = UtilTools.escape(path);
-			if (!smap.containsKey(res) && res.length() != 0)
-				smap.put(res, value); // store the string of all sizes
-		}
-		if (x == null || x.isEmpty()) {
-			return;
-		}
-		if (cur >= x.size() || cur < 0) {
-			if (fixedlength == 1 && !smap.keySet().contains(path)) {
-				String res = UtilTools.escape(path);
-				if (!smap.containsKey(res) && res.length() != 0)
-					smap.put(res, value); // store the string of all sizes
-			}
-			return;
-		}
-		TNode t = x.get(cur);
-		if (t.text.compareTo("ANYTOK") != 0 && t.text.length() > 0) {
-			if (!isleft)
-				getString(x, cur + 1, path + t.text, value + 2, smap, false);
-			else {
-				getString(x, cur - 1, t.text + path, value + 2, smap, true);
-			}
-		}
-		String s = "";
-		if (t.type == TNode.NUMTYP) {
-			s += "NUM";
-		} else if (t.type == TNode.WORD) {
-			s += "WORD";
-		} else if (t.type == TNode.SYBSTYP) {
-			s += "SYB";
-		} else if (t.type == TNode.BNKTYP) {
-			s += "BNK";
-		} else if (t.type == TNode.UWRDTYP) {
-			s += "UWRD";
-		} else if (t.type == TNode.LWRDTYP) {
-			s += "LWRD";
-		} else if (t.type == TNode.STARTTYP) {
-			s += "START";
-		} else if (t.type == TNode.ENDTYP) {
-			s += "END";
-		} else if (t.type == TNode.ANYTYP) {
-			s += "ANYTYP";
-		} else {
-			s += "" + t.getType();
-		}
-		if (!isleft)
-			getString(x, cur + 1, path + s, value + 1, smap, false);
-		else {
-			getString(x, cur - 1, s + path, value + 1, smap, true);
-		}
-	}
-
-	// option: left or right context
-	public Vector<TNode> mergeCNXT(Vector<TNode> a, Vector<TNode> b,
-			String option) {
-		Vector<TNode> xNodes = new Vector<TNode>();
-		if (a == null || b == null)
-			return null;
-		else {
-			int leng = Math.min(a.size(), b.size());
-			if (option.compareTo(Segment.LEFTPOS) == 0) {
-				for (int i = 1; i <= leng; i++) {
-
-					TNode t = a.get(a.size() - i);
-					TNode t1 = b.get(b.size() - i);
-					if (t == null || t1 == null) {
-						break;
-					}
-					if (t.mergableType(t1) == -1) {
-						break;
-					} else {
-						int type = t.mergableType(t1);
-						if (t.text.compareTo(t1.text) == 0) {
-							TNode tx = new TNode(type, t.text);
-							xNodes.add(0, tx);
-						} else {
-							TNode tx = new TNode(type, "ANYTOK");
-							xNodes.add(0, tx);
-						}
-					}
-				}
-			} else if (option.compareTo(Segment.RIGHTPOS) == 0) {
-				for (int i = 0; i < leng; i++) {
-
-					TNode t = a.get(i);
-					TNode t1 = b.get(i);
-					if (t == null || t1 == null) {
-						break;
-					}
-					if (t.mergableType(t1) == -1) {
-						break;
-					} else {
-						int type = t.mergableType(t1);
-						if (t.text.compareTo(t1.text) == 0) {
-							TNode tx = new TNode(type, t.text);
-							xNodes.add(tx);
-						} else {
-							TNode tx = new TNode(type, "ANYTOK");
-							xNodes.add(tx);
-						}
-					}
-				}
-			}
-		}
-		if (xNodes.isEmpty())
-			return null;
-		return xNodes;
-	}
-
-	public Position mergewith(Position b) {
-		if (this == null || b == null)
-			return null;
-		Vector<Integer> tmpIntegers = new Vector<Integer>();
-		tmpIntegers.addAll(this.absPosition);
-		tmpIntegers.retainAll(b.absPosition);
-		Vector<Integer> tmpIntegers2 = new Vector<Integer>();
-		tmpIntegers2.addAll(this.counters);
-		tmpIntegers2.retainAll(b.counters);
-		Vector<TNode> tl = b.leftContextNodes;
-		Vector<TNode> tr = b.rightContextNodes;
-		Vector<TNode> g_lcxtNodes = mergeCNXT(this.leftContextNodes, tl,
-				Segment.LEFTPOS);
-		Vector<TNode> g_rcxtNodes = mergeCNXT(this.rightContextNodes, tr,
-				Segment.RIGHTPOS);
-		// this.leftContextNodes = g_lcxtNodes;
-		// this.rightContextNodes = g_rcxtNodes;
-		if (tmpIntegers.isEmpty() && g_lcxtNodes == null
-				&& g_rcxtNodes == null)
-			return null;
-		boolean loop = this.isinloop || b.isinloop;
-
-		Vector<String> aStrings = new Vector<String>();
-		Vector<String> bStrings = new Vector<String>();
-
-		if (this.orgStrings.size() == 1
-				&& this.orgStrings.size() == b.tarStrings.size()
-				&& this.orgStrings.get(0).compareTo(b.orgStrings.get(0)) == 0) {
-			aStrings.addAll(this.orgStrings);
-			String[] s1 = this.tarStrings.get(0).split(",");
-			String[] s2 = b.tarStrings.get(0).split(",");
-			HashSet<Integer> hset = new HashSet<Integer>();
-			for (int x = 0; x < s1.length; x++) {
-				int v = Integer.valueOf(s1[x]);
-				if (!hset.contains(v)) {
-					hset.add(v);
-				}
-			}
-			for (int x = 0; x < s2.length; x++) {
-				int v = Integer.valueOf(s2[x]);
-				if (!hset.contains(v)) {
-					hset.add(v);
-				}
-			}
-			SortedSet<Integer> poses = new TreeSet<Integer>(hset);
-			Iterator<Integer> iter = poses.iterator();
-			String rep = "";
-			while (iter.hasNext()) {
-				rep += iter.next() + ",";
-			}
-			rep = rep.substring(0, rep.length() - 1);
-			bStrings.add(rep);
-		} else {
-			aStrings.addAll(this.orgStrings);
-			aStrings.addAll(b.orgStrings);
-			bStrings.addAll(this.tarStrings);
-			bStrings.addAll(b.tarStrings);
-		}
-		return new Position(tmpIntegers, g_lcxtNodes, g_rcxtNodes, aStrings,
-				bStrings, loop, contextId);
-	}
-
-	public void setinLoop(boolean res) {
-		this.isinloop = res;
-	}
-
-	// score sum(gToken)/size
-	public double getScore() {
-		double sum = 0.0;
-		int lsize = 0;
-		if (this.leftContextNodes != null) {
-			lsize = leftContextNodes.size();
-		}
-		int rsize = 0;
-		if (this.rightContextNodes != null) {
-			rsize = rightContextNodes.size();
-		}
-		if (lsize == 0 && rsize == 0)
-			return 1;
-		else {
-			for (int i = 0; i < lsize; i++) {
-				if (leftContextNodes.get(i).text.compareTo("ANYTOK") != 0
-						&& leftContextNodes.get(i).type != TNode.ANYTYP) {
-					sum++;
-				}
-			}
-			for (int i = 0; i < rsize; i++) {
-				if (rightContextNodes.get(i).text.compareTo("ANYTOK") != 0
-						&& rightContextNodes.get(i).type != TNode.ANYTYP) {
-					sum++;
-				}
-			}
-			return sum * 1.0 / (lsize + rsize);
-		}
-	}
-
-	public void emptyState() {
-		this.curState = 0;
-	}
-
-	public Vector<String> rules = new Vector<String>();
-
-	public String toProgram() {
-/*		if (curState >= rules.size())
-			return "null";
-		String rule = rules.get(curState);
-		if (!isinloop)
-			rule = rule.replace("counter", counters.get(1) + "");
-		curState++;
-		*/
-		
-		String res = this.VerifySpace(curState);
-		return res;
-	}
-
-	public String getRule(int index) {
-		if (index >= rules.size())
-			return "null";
-		String rule = rules.get(index);
-		if (!isinloop)
-			rule = rule.replace("counter", counters.get(1) + "");
-		return rule;
-	}
-
-	public long size() {
-		return this.rules.size();
-	}
-
-	public String VerifySpace(int itercnt) {
-		String rule = "null";
-		int ruleNo = 0;
-		while (ruleNo < this.rules.size()) {
-			rule = getRule(ruleNo);
-			ruleNo++;
-			// System.out.println("verifying..."+rule);
-			if (isinloop) {
-				// replace the counter with number and verify it
-				if (rule.indexOf("counter") == -1) {
-					this.program = "null";
-					return "null";
-				}
-				boolean isvalid = true;
-				for (int j = 0; j < this.orgStrings.size(); j++) {
-					int cnt = 1;
-					String r = "";
-					while (r.indexOf("None") == -1) {
-						String tmpRule = rule.replace("counter",
-								String.valueOf(cnt));
-						ProgramRule programRule = new ProgramRule(tmpRule, contextId);
-						String val = programRule.transform(this.orgStrings
-								.get(j));
-						if (val.indexOf("None") != -1)
-							break;
-						r += val + ",";
-						cnt++;
-					}
-					if (r.length() <= 1)
-					{
-						this.program = "null";
-						return "null";
-					}
-					if (this.tarStrings.get(j).compareTo(
-							r.substring(0, r.length() - 1)) != 0) {
-						isvalid = false;
-						break;
-					}
-				}
-				if (isvalid) {
-					if (itercnt == 0)
-					{
-						this.program = rule;
-						return rule;
-					}
-					else
-						itercnt--; // valid number - 1
-				}
-
-			} else {
-				ProgramRule pr = new ProgramRule(rule, contextId);
-				boolean isValid = true;
-				for (int k = 0; k < this.orgStrings.size(); k++) {
-					String val = String.valueOf(pr.transform(this.orgStrings
-							.get(k)));
-					if (this.tarStrings.get(k).compareTo(val) != 0) {
-						isValid = false;
-					}
-				}
-				if (isValid) {
-					if (itercnt == 0)
-					{
-						this.program = rule;
-						return rule;
-					}
-					else
-						itercnt--;
-				}
-			}
-		}
-		this.program = "null";
-		return "null";
-	}
-
-	public void createTotalOrderVector() {
-		HashMap<String, Double> lMap = new HashMap<String, Double>();
-		HashMap<String, Double> rMap = new HashMap<String, Double>();
-		if (this.leftContextNodes != null) {
-			String path = "";
-			getString(this.leftContextNodes, this.leftContextNodes.size() - 1,
-					path, 1.0, lMap, true);
-		} else {
-			lMap.put("ANY", 1.0);
-		}
-		if (this.rightContextNodes != null) {
-			String path = "";
-			getString(this.rightContextNodes, 0, path, 1.0, rMap, false);
-		} else {
-
-			rMap.put("ANY", 1.0);
-		}
-		String reString = "";
-		String reString2 = "";
-		String reString3 = "";
-		SortedMap<Double, Vector<String>> sortedMap = new TreeMap<Double, Vector<String>>();
-		String negString = "";
-		for (Map.Entry<String, Double> stringDoubleEntry : lMap.entrySet()) {
-			for (Map.Entry<String, Double> stringDoubleEntry1 : rMap.entrySet()) {
-				if (stringDoubleEntry.getKey().compareTo(stringDoubleEntry1.getKey()) == 0 && stringDoubleEntry.getKey().compareTo("ANY") == 0)
-					continue;
-				Double key = stringDoubleEntry.getValue() + stringDoubleEntry1.getValue();
-				reString = String.format(
-						"indexOf(value,\'%s\',\'%s\',1*counter)", stringDoubleEntry.getKey(), stringDoubleEntry1.getKey());
-				reString2 = String.format(
-						"indexOf(value,\'%s\',\'%s\',2*counter)", stringDoubleEntry.getKey(), stringDoubleEntry1.getKey());
-				reString3 = String.format(
-						"indexOf(value,\'%s\',\'%s\',3*counter)", stringDoubleEntry.getKey(), stringDoubleEntry1.getKey());
-				negString = String.format(
-						"indexOf(value,\'%s\',\'%s\',-1*counter)", stringDoubleEntry.getKey(), stringDoubleEntry1.getKey());
-				if (sortedMap.containsKey(key)) {
-					sortedMap.get(key).add(reString);
-					sortedMap.get(key).add(reString2);
-					sortedMap.get(key).add(reString3);
-					sortedMap.get(key).add(negString);
-				} else {
-					Vector<String> svec = new Vector<String>();
-					svec.add(reString);
-					svec.add(reString2);
-					svec.add(reString3);
-					svec.add(negString);
-					sortedMap.put(key, svec);
-				}
-			}
-		}
-		while (!sortedMap.isEmpty()) {
-			Double key = sortedMap.firstKey();
-			rules.addAll(sortedMap.get(key));
-			sortedMap.remove(key);
-		}
-		// append the absolute position to the end
-		for (int k = 0; k < this.absPosition.size(); k++) {
-			String line = String.format("%d", this.absPosition.get(k));
-			rules.add(line);
-		}
-	}
-	public String toString() {
-		return "(" + UtilTools.print(this.leftContextNodes) + ","
-				+ UtilTools.print(this.rightContextNodes) + ")";
-	}
-
-	public GrammarTreeNode mergewith(GrammarTreeNode a) {
-		Position p = (Position) a;
-		p = this.mergewith(p);
-		return p;
-	}
-
-	public String getNodeType() {
-		return "position";
-	}
-
-	public String getrepString() {
-		return this.toString();
-	}
-
-	@Override
-	public String getProgram() {
-		return this.program;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/PositionSet.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/PositionSet.java
deleted file mode 100644
index f93baaaeb..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/PositionSet.java
+++ /dev/null
@@ -1,89 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.Collection;
-
-public class PositionSet implements GrammarTreeNode {
-
-	ArrayList<Position> spaces = new ArrayList<Position>();
-	int size = 1;
-
-	public PositionSet(Collection<Position> poss) {
-		this.spaces.addAll(poss);
-		if (spaces != null && !spaces.isEmpty())
-			for (Position p : spaces) {
-				if (p != null) {
-					size = p.rules.size();
-					break;
-				}
-			}
-	}
-
-	@Override
-	public String toProgram() {
-		for (Position p : spaces) {
-			if (p != null) {
-				String rule1 = p.VerifySpace(0);
-				if (rule1.indexOf("null") == -1) {
-					return rule1;
-				}
-			}
-		}
-		return "null";
-	}
-
-	@Override
-	public GrammarTreeNode mergewith(GrammarTreeNode a) {
-		Position position = (Position) a;
-		ArrayList<Position> x = new ArrayList<Position>();
-		for (int i = 0; i < this.spaces.size(); i++) {
-			Position xp = spaces.get(i).mergewith(position);
-			x.add(xp);
-		}
-		PositionSet ps = new PositionSet(x);
-		return ps;
-	}
-
-	@Override
-	public String getNodeType() {
-		// TODO Auto-generated method stub
-		return this.getClass().getName();
-	}
-
-	@Override
-	public double getScore() {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	@Override
-	public String getrepString() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void createTotalOrderVector() {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void emptyState() {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public long size() {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	@Override
-	public String getProgram() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgSynthesis.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgSynthesis.java
deleted file mode 100644
index 26fc49dac..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgSynthesis.java
+++ /dev/null
@@ -1,435 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Vector;
-
-import org.perf4j.StopWatch;
-import org.perf4j.log4j.Log4JStopWatch;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import edu.isi.karma.cleaning.Research.ConfigParameters;
-import edu.isi.karma.cleaning.features.Feature;
-import edu.isi.karma.cleaning.features.RecordClassifier;
-import edu.isi.karma.cleaning.features.RecordFeatureSet;
-
-public class ProgSynthesis {
-	public static int time_limit = 20;
-	Vector<Vector<TNode>> orgVector = new Vector<Vector<TNode>>();
-	Vector<Vector<TNode>> tarVector = new Vector<Vector<TNode>>();
-	String bestRuleString = "";
-	// for tracking the stats
-	public long learnspan = 0;
-	public long genspan = 0;
-	public long ruleNo = 0;
-	public HashMap<String, double[]> string2Vector = new HashMap<String, double[]>();
-	public PartitionClassifierType classifier;
-	public RecordFeatureSet featureSet = null;
-	public Vector<Vector<String[]>> constraints = new Vector<Vector<String[]>>();
-	public HashMap<String, Boolean> legalParitions = new HashMap<String, Boolean>();
-	public MyLogger logger = new MyLogger();
-	private static Logger ulogger = LoggerFactory
-			.getLogger(ProgSynthesis.class);
-	public Program myprog;
-	public OptimizePartition partitioner; // A* search for a consistent program
-	public ExampleCluster partiCluster;
-	public DataPreProcessor dataPreProcessor;
-	public Messager msGer;
-	public String contextId;
-	public ProgSynthesis(String contextId) {
-		this.contextId = contextId;
-	}
-
-	public void inite(Vector<String[]> examples, String[] vocb) {
-		for (int i = 0; i < examples.size(); i++) {
-			Ruler r = new Ruler();
-			r.setNewInput(examples.get(i)[0]);
-			orgVector.add(r.vec);
-			Ruler r1 = new Ruler();
-			r1.setNewInput(examples.get(i)[1]);
-			tarVector.add(r1.vec);
-		}
-		RecordFeatureSet rSet = new RecordFeatureSet();
-		rSet.addVocabulary(vocb);
-		this.featureSet = rSet;
-		RecordClassifier r2 = new RecordClassifier(rSet);
-		this.classifier = r2;
-		partitioner = new OptimizePartition(this, r2);
-	}
-	
-	public void inite(Vector<String[]> examples, DataPreProcessor dp, Vector<Vector<String[]>> constraints) {
-		for (int i = 0; i < examples.size(); i++) {
-			Ruler r = new Ruler();
-			r.setNewInput(examples.get(i)[0]);
-			orgVector.add(r.vec);
-			Ruler r1 = new Ruler();
-			r1.setNewInput(examples.get(i)[1]);
-			tarVector.add(r1.vec);
-		}
-		featureSet = dp.rfs;
-		RecordClassifier r2 = new RecordClassifier(featureSet);
-		this.classifier = r2;
-		this.constraints = constraints;
-		string2Vector = dp.getStandardData();
-	}
-	public void inite(Vector<String[]> examples, DataPreProcessor dp, Messager msger) {
-		for (int i = 0; i < examples.size(); i++) {
-			Ruler r = new Ruler();
-			r.setNewInput(examples.get(i)[0]);
-			orgVector.add(r.vec);
-			Ruler r1 = new Ruler();
-			r1.setNewInput(examples.get(i)[1]);
-			tarVector.add(r1.vec);
-		}
-		featureSet = dp.rfs;
-		RecordClassifier r2 = new RecordClassifier(featureSet);
-		this.classifier = r2;
-		string2Vector = dp.getStandardData();
-		this.dataPreProcessor = dp;
-		this.msGer = msger;
-	}
-	public Vector<Vector<Integer>> generateCrossIndex(Vector<Integer> poss,
-			Vector<Vector<Integer>> p, int index) {
-		Vector<Vector<Integer>> qVector = new Vector<Vector<Integer>>();
-		if (index >= poss.size()) {
-			return p;
-		}
-		int curleng = poss.get(index);
-		if (p.isEmpty()) {
-			for (int i = 0; i < curleng; i++) {
-				Vector<Integer> x = new Vector<Integer>();
-				x.add(i);
-				qVector.add(x);
-			}
-		} else {
-			for (int j = 0; j < p.size(); j++) {
-				for (int i = 0; i < curleng; i++) {
-					@SuppressWarnings("unchecked")
-					Vector<Integer> x = (Vector<Integer>) p.get(j).clone();
-					x.add(i);
-					qVector.add(x);
-				}
-			}
-		}
-		qVector = generateCrossIndex(poss, qVector, index + 1);
-		return qVector;
-	}
-
-	public double getCompScore(int i, int j, Vector<Partition> pars) {
-		Partition p = pars.get(i).mergewith(pars.get(j));
-		if (p == null || !isLegalPartition(p)) {
-			return -Double.MAX_VALUE;
-		}
-		int validCnt = 0;
-		for (int x = 0; x < pars.size(); x++) {
-			if (x == i || x == j) {
-				continue;
-			}
-			Partition q = p.mergewith(pars.get(x));
-			if (q != null && isLegalPartition(p)) {
-				validCnt++;
-			}
-		}
-		return validCnt;
-	}
-
-	public Vector<Partition> initePartitions() {
-		Vector<Partition> pars = new Vector<Partition>();
-		// inite partition for each example
-		for (int i = 0; i < orgVector.size(); i++) {
-			Vector<Vector<TNode>> ovt = new Vector<Vector<TNode>>();
-			Vector<Vector<TNode>> tvt = new Vector<Vector<TNode>>();
-			ovt.add(this.orgVector.get(i));
-			tvt.add(this.tarVector.get(i));
-			Partition pt = new Partition(ovt, tvt);
-			pars.add(pt);
-		}
-		return pars;
-	}
-
-	public boolean isLegalPartition(Partition p) {
-		String key = p.getHashKey();
-		if (legalParitions.containsKey(key)) {
-			return legalParitions.get(key);
-		}
-		// test whether its subset fails
-
-		for (Map.Entry<String, Boolean> stringBooleanEntry : legalParitions.entrySet()) {
-			if (!stringBooleanEntry.getValue() && key.indexOf(stringBooleanEntry.getKey()) != -1) {
-				return false;
-			}
-		}
-		Vector<Partition> xPar = new Vector<Partition>();
-		xPar.add(p);
-		Collection<ProgramRule> cpr = this.producePrograms(xPar);
-		if (cpr == null || cpr.isEmpty()) {
-			legalParitions.put(key, false);
-			return false;
-		} else {
-			legalParitions.put(key, true);
-			return true;
-		}
-	}
-
-	public void mergePartitions(Vector<Partition> pars) {
-		double maxScore = 0;
-		int[] pos = { -1, -1 };
-		for (int i = 0; i < pars.size(); i++) {
-			for (int j = i + 1; j < pars.size(); j++) {
-				double s = getCompScore(i, j, pars);
-				if (s < 0) {
-					continue;
-				}
-				if (s >= maxScore) {
-					pos[0] = i;
-					pos[1] = j;
-					maxScore = s;
-				}
-			}
-		}
-		if (pos[0] != -1 && pos[1] != -1)
-			UpdatePartitions(pos[0], pos[1], pars);
-	}
-
-	public void UpdatePartitions(int i, int j, Vector<Partition> pars) {
-		Partition p = pars.get(i).mergewith(pars.get(j));
-		pars.set(i, p);
-		pars.remove(j);
-	}
-
-	public String getBestRule() {
-		return this.bestRuleString;
-	}
-
-	public double[] getFeatureArray(String s) {
-		Collection<Feature> cfeat = featureSet.computeFeatures(s, "");
-		Feature[] x = cfeat.toArray(new Feature[cfeat.size()]);
-		double[] res = new double[x.length];
-		for (int i = 0; i < x.length; i++) {
-			res[i] = x[i].getScore();
-		}
-		return res;
-	}
-
-	public Vector<Partition> ProducePartitions(boolean condense) {
-		Vector<Partition> pars = this.initePartitions();
-		partiCluster = new ExampleCluster(this, pars, string2Vector);
-		partiCluster.updateConstraints(msGer.getConstraints());
-		partiCluster.updateWeights(msGer.weights);
-		if (condense) {
-			pars = partiCluster.cluster_weigthEuclidean(pars);
-		}
-		this.ruleNo = pars.size();
-		/*
-		 * int size = pars.size(); while (condense) {
-		 * this.mergePartitions(pars); if (size == pars.size()) { break; } else
-		 * { size = pars.size(); } }
-		 */
-		return pars;
-	}
-	
-	public Collection<ProgramRule> producePrograms(Vector<Partition> pars) {
-		Program prog = new Program(pars, this.classifier,this.dataPreProcessor, contextId);
-		this.myprog = prog;
-		HashSet<ProgramRule> rules = new HashSet<ProgramRule>();
-		int prog_cnt = 1;
-		int i = 0;
-		while (i < prog_cnt) {
-			ProgramRule r = prog.toProgram1();
-			if (r == null)
-				return null;
-			String xString = "";
-			int termCnt = 0;
-			boolean findRule = true;
-			while ((xString = this.validRule(r, pars)) != "GOOD" && findRule) {
-				if (xString.compareTo("NO_CLASIF") == 0) {
-					return null; // indistinguishable classes.
-				}
-				for (Partition p : prog.partitions) {
-					if (p.label.compareTo(xString) == 0) {
-						String newRule = p.toProgram();
-						if (ConfigParameters.debug == 1)
-							System.out.println("updated Rule: " + p.label
-									+ ": " + newRule);
-						if (newRule.contains("null")) {
-							findRule = false;
-							break;
-						}
-						r.updateClassworker(xString, newRule);
-					}
-				}
-				termCnt++;
-			}
-			if (findRule)
-			{
-				rules.add(r);
-			}
-			i++;
-		}
-		return rules;
-	} 
-	public Collection<ProgramRule> run_main_all()
-	{
-		long t1 = System.currentTimeMillis();
-		Vector<Partition> par = this.ProducePartitions(true);
-		Program prog = new Program(par, this.classifier,this.dataPreProcessor,contextId);
-		Collection<ProgramRule> cpr = this.produceProgram_all(par,prog);
-		Traces.AllSegs.clear();
-		//record the learning time
-		this.learnspan = (long) ((System.currentTimeMillis()-t1)*1.0/1000);
-		return cpr;
-	}
-	public Collection<ProgramRule> adaptive_main()
-	{
-		StopWatch stopWatch0 = new Log4JStopWatch("adaptive_main");
-		long t1 = System.currentTimeMillis();
-		StopWatch stopWatch = new Log4JStopWatch("adaptive_producePartition");
-		Vector<Partition> par = this.adaptive_producePartition();
-		stopWatch.stop();
-		StopWatch stopWatch1 = new Log4JStopWatch("adaptive_produceProgram");
-		Collection<ProgramRule> cpr = this.adaptive_produceProgram(par);
-		stopWatch1.stop();
-		Traces.AllSegs.clear();
-		//record the learning time
-		this.learnspan = (long) ((System.currentTimeMillis()-t1)*1.0/1000);
-		stopWatch0.stop();
-		return cpr;
-	}
-	public Collection<ProgramRule> produceProgram_all(Vector<Partition> pars, Program prog)
-	{
-		this.myprog = prog;
-		HashSet<ProgramRule> rules = new HashSet<ProgramRule>();
-		int prog_cnt = Integer.MAX_VALUE;
-		int i = 0;
-		while(i < prog_cnt) {
-			ProgramRule r = prog.toProgram1();
-			//System.out.println(""+r.toString());
-			if (r == null)
-				break;
-			String xString = "";
-			int termCnt = 0;
-			boolean findRule = true;
-			while ((xString = this.validRule(r, pars)) != "GOOD" && findRule) {
-				if (xString.compareTo("NO_CLASIF") == 0) {
-					break; // indistinguishable classes.
-				}
-				for (Partition p : prog.partitions) {
-					if (p.label.compareTo(xString) == 0) {
-						String newRule = p.toProgram();
-						if (ConfigParameters.debug == 1)
-							System.out.println("updated Rule: " + p.label
-									+ ": " + newRule);
-						if (newRule.contains("null")) {
-							findRule = false;
-							break;
-						}
-						r.updateClassworker(xString, newRule);
-					}
-				}
-				termCnt++;
-			}
-			if (findRule)
-			{
-				rules.add(r);
-			}
-			i++;
-		}
-		return rules;
-	}
-	public Collection<ProgramRule> adaptive_produceProgram(Vector<Partition> pars)
-	{		
-		Program prog = new Program(pars, this.classifier,this.dataPreProcessor,contextId);
-		this.myprog = prog;
-		HashSet<ProgramRule> rules = new HashSet<ProgramRule>();
-		int prog_cnt = 1;
-		int i = 0;
-		while (i < prog_cnt) {
-			ProgramRule r = prog.toProgram2(msGer);
-			if (r == null)
-				return null;
-			String xString = "";
-			int termCnt = 0;
-			boolean findRule = true;
-			while ((xString = this.validRule(r, pars)) != "GOOD" && findRule) {
-				if (xString.compareTo("NO_CLASIF") == 0) {
-					return null; // indistinguishable classes.
-				}
-				for (Partition p : prog.partitions) {
-					if (p.label.compareTo(xString) == 0) {
-						String newRule = p.toProgram();
-						if (ConfigParameters.debug == 1)
-							System.out.println("updated Rule: " + p.label
-									+ ": " + newRule);
-						if (newRule.contains("null")) {
-							findRule = false;
-							break;
-						}
-						r.updateClassworker(xString, newRule);
-					}
-				}
-				termCnt++;
-			}
-			if (findRule)
-			{
-				rules.add(r);
-			}
-			i++;
-		}
-		return rules;
-	}
-	public Vector<Partition> adaptive_producePartition()
-	{	
-		Vector<Partition> pars = this.initePartitions();
-		partiCluster = new ExampleCluster(this, pars, string2Vector);
-		partiCluster.updateConstraints(msGer.getConstraints());
-		partiCluster.updateWeights(msGer.weights);
-		//update the program space and hypothesis space
-		pars = partiCluster.adaptive_cluster_weightEuclidean(pars);
-		this.ruleNo = pars.size();
-		return pars;
-	}
-	public Collection<ProgramRule> run_main() {
-		long t1 = System.currentTimeMillis();
-		StopWatch stopWatch0 = new Log4JStopWatch("main");
-		StopWatch stopWatch = new Log4JStopWatch("producePartition");
-		Vector<Partition> vp = this.ProducePartitions(true);
-		stopWatch.stop();
-		StopWatch stopWatch1 = new Log4JStopWatch("producePrograms");
-		Collection<ProgramRule> cpr = this.producePrograms(vp);
-		stopWatch1.stop();
-		Traces.AllSegs.clear();
-		stopWatch0.stop();
-		this.learnspan = (long) ((System.currentTimeMillis()-t1)*1.0/1000);
-		return cpr;
-	}
-
-	public String validRule(ProgramRule p, Vector<Partition> vp) {
-		for (Partition px : vp) {
-			for (int i = 0; i < px.orgNodes.size(); i++) {
-				String s1 = UtilTools.print(px.orgNodes.get(i));
-				String labelString = p.getClassForValue(s1);
-				if (labelString.compareTo(px.label) != 0) {
-					//logger.error(vp.toString());
-					ulogger.error("classification error on examples " + s1
-							+ "as: " + labelString);
-					// return "NO_CLASIF";
-				}
-				InterpreterType worker = p.getWorkerForClass(px.label);
-				String s2 = "";
-				try {
-					s2 = new String(worker.execute(s1).getBytes(), "UTF-8");
-				} catch (Exception e) {
-					return "DECODE_ERROR";
-				}
-				String s3 = UtilTools.print(px.tarNodes.get(i));
-				if (s3.compareTo(s2) != 0) {
-					return labelString;
-				}
-			}
-		}
-		return "GOOD";
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgTracker.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgTracker.java
deleted file mode 100644
index 66410739d..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgTracker.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.Map;
-import java.util.Vector;
-
-public class ProgTracker {
-	private ProgTracker() {
-	}
-
-	public static void printPartition(Vector<Partition> pars) {
-		System.out.println("-----------");
-		System.out.println("CURRENT_PARS" + pars.toString());
-		System.out.println("-----------");
-	}
-
-	public static void printConstraints(Vector<Vector<String[]>> constr) {
-		String res = "";
-		for (Vector<String[]> line : constr) {
-			String s = "CONST: ";
-			for (String[] p : line) {
-				s += p[0] + ", " + p[1] + " |";
-			}
-			s += "\n";
-			res += s;
-		}
-		System.out.println("" + res);
-	}
-
-	public static void printPartitions(Partition a, Partition b) {
-		System.out.println("TOMERGE:" + a + "\n" + b);
-	}
-
-	@SuppressWarnings("rawtypes")
-	public static void printUnlabeledData(Map dicttmp) {
-		for (Object o : dicttmp.entrySet()) {
-			System.out.println(String.format("Entry: %s,%f", ((Map.Entry) o).getKey(), ((Map.Entry) o).getValue()));
-		}
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Program.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Program.java
deleted file mode 100644
index 9f504a011..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Program.java
+++ /dev/null
@@ -1,240 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.Vector;
-
-import org.perf4j.StopWatch;
-import org.perf4j.log4j.Log4JStopWatch;
-
-public class Program implements GrammarTreeNode {
-	public Vector<Partition> partitions = new Vector<Partition>();
-	public String cls = "";
-	public double score = 0.0;
-	public PartitionClassifierType classifier;
-	public DataPreProcessor dpPreProcessor;
-	public String program = "null";
-	public String contextId;
-	public Program(Vector<Partition> pars, PartitionClassifierType classifier, DataPreProcessor dpp, String contextId) {
-		this.contextId = contextId;
-		this.partitions = pars;
-		this.dpPreProcessor = dpp;
-		for (int i = 0; i < this.partitions.size(); i++) {
-			this.partitions.get(i).setLabel("attr_" + i);
-			// if(ConfigParameters.debug == 1)
-			// System.out.println(this.partitions.get(i).toString());
-		}
-		if(pars.size()>1)
-		{
-			this.classifier = classifier;
-		}
-		this.emptyState();
-	}
-
-	public void learnClassifier() {
-		PartitionClassifier pcf = new PartitionClassifier();
-		PartitionClassifierType classifier = pcf.create2(this.partitions,
-				this.classifier,this.dpPreProcessor);
-		this.classifier = classifier;
-		// this.cls = pcf.clssettingString;
-		// this.cls = "x";
-		// for(Partition p:this.partitions)
-		// {
-		// p.cls = this.cls;
-		// }
-	}
-
-	public double getScore() {
-		double r = score;
-		this.score = 0.0;
-		return r;
-	}
-
-	public String toProgram() {
-		if (this.partitions.size() > 1) {
-			String res = "switch([";
-			for (Partition p : this.partitions) {
-				String r = String.format(
-						"(getClass(\"%s\",value)[1:7]==%s,%s)", p.cls, p.label,
-						p.toProgram());
-				res += r + ",";
-				score += p.getScore();
-			}
-			score = score / this.partitions.size();
-			res = res.substring(0, res.length() - 1);
-			res += "])";
-			this.program = res;
-			return res;
-		} else {
-			String s = partitions.get(0).toProgram();
-			score = this.partitions.get(0).getScore();
-			this.program = s;
-			return s;
-		}
-	}
-	public void filterUnlabeledData(ProgramRule pr)
-	{
-		for(Partition p:this.partitions)
-		{
-			Iterator<String> iter = p.orgUnlabeledData.iterator();
-			while(iter.hasNext())
-			{
-				String val = iter.next();
-				String res = pr.getWorkerForClass(p.label).execute(val);
-				if(res == null || res.length() == 0)
-				{
-					iter.remove();
-				}
-			}
-		}
-	}
-	public ProgramRule toProgram2(Messager msger){
-		ProgramRule pr = new ProgramRule(this, contextId);
-		ProgramAdaptator programAdaptator = new ProgramAdaptator(contextId);
-		if (this.partitions.size() > 1) {
-			//StopWatch spw1 = new Log4JStopWatch("Codeblock-genprogram");
-			for (Partition p : this.partitions) {
-				if (p.tarNodes.get(0).isEmpty()) {
-					pr.addRule(p.label, "substr(value,0,0)");
-					continue;
-				}
-				//String rule = p.toProgram();
-				String key = p.getHashKey(); 
-				String rule = "null";
-				if(msger.exp2program.containsKey(key))
-				{
-					rule = msger.exp2program.get(key);
-				}
-				else
-				{
-					ArrayList<Partition> xpars = new ArrayList<Partition>();
-					xpars.add(p);
-					ArrayList<String[]> examples = UtilTools.extractExamplesinPartition(xpars);
-					rule = programAdaptator.adapt(msger.exp2Space, msger.exp2program, examples);
-				}
-				if (rule.contains("null"))
-					return null;
-				pr.addRule(p.label, rule);
-				score += p.getScore();
-			}
-			score = score / this.partitions.size();
-			filterUnlabeledData(pr);
-			this.learnClassifier();
-			return pr;
-		} else {
-			if (partitions.size() <= 0) {
-				return null;
-			}
-			if (partitions.get(0).tarNodes.get(0).isEmpty()) {
-				pr.addRule(partitions.get(0).label, "substr(value,0,0)");
-				return pr;
-			}
-			String key = partitions.get(0).getHashKey();
-			String s = "null";
-			if(msger.exp2program.containsKey(key))
-			{
-				s = msger.exp2program.get(key);
-			}
-			else
-			{
-				ArrayList<Partition> xpars = new ArrayList<Partition>();
-				xpars.add(partitions.get(0));
-				ArrayList<String[]> examples = UtilTools.extractExamplesinPartition(xpars);
-				s = programAdaptator.adapt(msger.exp2Space, msger.exp2program, examples);
-			}
-			if (s.contains("null"))
-				return null;
-			score = this.partitions.get(0).getScore();
-			pr.addRule(partitions.get(0).label, s);
-			return pr;
-		}
-	}
-	public ProgramRule toProgram1() {
-		ProgramRule pr = new ProgramRule(this, contextId);
-		if (this.partitions.size() > 1) {
-			for (Partition p : this.partitions) {
-				if (p.tarNodes.get(0).isEmpty()) {
-					pr.addRule(p.label, "substr(value,0,0)");
-					continue;
-				}
-				StopWatch stopWatch = new Log4JStopWatch("toProgram1");
-				String rule = p.toProgram();
-				stopWatch.stop();
-
-				if (rule.contains("null"))
-					return null;
-				pr.addRule(p.label, rule);
-				score += p.getScore();
-			}
-			score = score / this.partitions.size();
-			filterUnlabeledData(pr);
-			this.learnClassifier();
-			return pr;
-		} else {
-			if (partitions.size() <= 0) {
-				return null;
-			}
-			if (partitions.get(0).tarNodes.get(0).isEmpty()) {
-				pr.addRule(partitions.get(0).label, "substr(value,0,0)");
-				return pr;
-			}
-			String s = partitions.get(0).toProgram();
-			if (s.contains("null"))
-				return null;
-			score = this.partitions.get(0).getScore();
-			pr.addRule(partitions.get(0).label, s);
-			return pr;
-		}
-	}
-
-	public String toString() {
-		String resString = "";
-		for (Partition p : this.partitions) {
-			resString += p.toString() + "\n";
-			/*for(String s:p.orgUnlabeledData)
-			{
-				resString += s+"\n";
-			}*/
-		}
-		return resString;
-	}
-
-	public GrammarTreeNode mergewith(GrammarTreeNode a) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	public String getNodeType() {
-		return "program";
-	}
-
-	public String getrepString() {
-		return "Program";
-	}
-
-	public void createTotalOrderVector() {
-		// TODO Auto-generated method stub
-
-	}
-
-	public void emptyState() {
-		// TODO Auto-generated method stub
-		for(Partition p:partitions)
-		{
-			p.emptyState();
-		}
-	}
-
-	public long size() {
-		long size = 0;
-		for (Partition p : partitions) {
-			size += p.size();
-		}
-		return size;
-	}
-
-	@Override
-	public String getProgram() {
-		return this.program;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgramAdaptator.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgramAdaptator.java
deleted file mode 100644
index c9730b563..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgramAdaptator.java
+++ /dev/null
@@ -1,864 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Vector;
-
-import org.perf4j.StopWatch;
-import org.perf4j.log4j.Log4JStopWatch;
-
-import edu.isi.karma.cleaning.Research.Prober;
-
-public class ProgramAdaptator {
-	public ParseTreeNode program;
-	public String contextId;
-	public ProgramAdaptator(String contextId)
-	{
-		this.contextId = contextId;
-	}
-	public String adapt(HashMap<String, Traces> exp2Space,
-			HashMap<String, String> exp2program, ArrayList<String[]> examples) {
-		ArrayList<Integer> keys = chooseLargestSubset(exp2program, examples);
-		String key2 = UtilTools.createkey(examples);
-		if(exp2program.containsKey(key2))
-		{
-			return exp2program.get(key2);
-		}
-		if(!keys.isEmpty())
-		{
-			ExampleTraces tool = new ExampleTraces(contextId);
-			Traces t1 = tool.createTrace(examples.get(0));
-			String prog = t1.toProgram();
-			ArrayList<String[]> tmpKey = new ArrayList<String[]>();
-			tmpKey.add(examples.get(0));
-			String tK = UtilTools.createkey(tmpKey);
-			exp2Space.put(tK, t1);
-			exp2program.put(tK, prog);
-			keys.add(0);
-			//return prog;
-		}
-		ArrayList<String[]> inExps = new ArrayList<String[]>();
-		for (Integer i : keys) {
-			inExps.add(examples.get(i));
-		}
-		String subkey = this.formKey(examples, keys, true);
-		Traces wholespace = getProgramSpace(subkey, exp2Space);
-		ArrayList<String[]> outExps = getRestExamples(examples, keys);
-		String prog =  getProgram(subkey, exp2program);
-		
-		for(String[] exp:outExps)
-		{
-			if(prog.compareTo("null")==0)
-			{
-				System.out.println("cannot adapt the program");
-				break;
-			}
-			prog = adapteOneExample(wholespace, exp, prog, inExps, exp2Space, exp2program);
-			inExps.add(exp);
-			String nkey = formKey(inExps, new ArrayList<Integer>(), false);
-			wholespace = exp2Space.get(nkey);			
-		}
-		return prog;
-	}
-
-	public String adapteOneExample(Traces wholespace, String[] exp,
-			String program,ArrayList<String[]> inExps,HashMap<String, Traces> exp2Space, HashMap<String, String> exp2program) {
-		ProgramParser programParser = new ProgramParser(contextId);
-		ParseTreeNode ptree = programParser.parse(program);
-		// add unknown examples incrementally
-		String evres = "";
-		evres = ptree.eval(exp[0]);
-		ArrayList<String[]> exps = new ArrayList<String[]>();
-		String skey = UtilTools.createkey(exps);
-		Traces tIn = null;
-		if(exp2Space.containsKey(skey))
-		{
-			tIn = exp2Space.get(skey); 
-		}
-		else
-		{
-			tIn = createSingleTrace(exp); 
-		}
-		HashMap<String, ArrayList<String>> prog2Evals = new HashMap<String,ArrayList<String>>();
-		HashMap<String, String> prog2Nevals = new HashMap<String,String>();
-		if(evres.compareTo(exp[1]) == 0)
-		{
-			Traces nTraces = wholespace.mergewith(tIn);
-			ArrayList<String[]> expr = new ArrayList<String[]>();
-			expr.add(exp);
-			expr.addAll(inExps);
-			String nKey = formKey(expr,new ArrayList<Integer>(), false);				
-			exp2program.put(nKey, program);
-			exp2Space.put(nKey, nTraces);
-			return program;
-		}
-		ArrayList<ArrayList<Patcher>> tree_refers = createCandidates(ptree, tIn);
-		//prepare the necessary information 
-		Vector<String> orgs = new Vector<String>();
-		//get all original values
-		for(GrammarTreeNode node: wholespace.traceline.values().iterator().next().body)
-		{
-			Segment xn = (Segment)node;
-			if(!xn.isConstSegment())
-			{
-				orgs = xn.section.get(0).orgStrings;
-				break;
-			}
-		}
-		ArrayList<ParseTreeNode> progs = ptree.children;
-		for (ParseTreeNode node : progs) {
-			ArrayList<String> tmpTars = new ArrayList<String>();
-			for (String org : orgs) {
-				ProgramRule tpp = new ProgramRule(node.value, contextId);
-				String tmpSeg= tpp.transform(org);
-				tmpTars.add(tmpSeg);
-			}
-			prog2Evals.put(node.value, tmpTars);
-		}
-		for (ParseTreeNode node : progs) {
-			ProgramRule tpp = new ProgramRule(node.value, contextId);
-			String tmpSeg= tpp.transform(exp[0]);			
-			prog2Nevals.put(node.value, tmpSeg);
-		}
-		//nothing to change	
-		for (ArrayList<Patcher> tTree : tree_refers) {
-			Traces cwspace = wholespace;// clone the original space
-			ArrayList<Patcher> errNodes = align(tTree, cwspace, inExps,prog2Evals,prog2Nevals);
-			if(errNodes == null)
-			{
-				return "null";
-			}
-			// get the correct parts
-			boolean valid = true;
-			if(errNodes.isEmpty()) // no solution exists
-				valid = false;
-			for (Patcher pat : errNodes) {
-				GrammarTreeNode newSpace = updateNewSpace(pat);
-				boolean succeed = updateProgram(pat, newSpace);
-				if (!succeed) {
-					valid = false;
-					break;
-				}
-			}
-			Prober.tracePatchers(program, errNodes, inExps,exp,valid,exp2program);
-			if (valid) {
-				// NEED TO UPDATE THE SUBSPACE RATHER THAN THE WHOLE ONE!!!
-				Traces nTraces = cwspace.mergewith(tIn);
-				ArrayList<String[]> expr = new ArrayList<String[]>();
-				expr.add(exp);
-				expr.addAll(inExps);
-				String nKey = formKey(expr,new ArrayList<Integer>(), false);				
-				// return the successfully adapted program
-				String fprog = this.applyPatch(ptree, errNodes);
-				//update session repo 
-				exp2program.put(nKey, fprog);
-				exp2Space.put(nKey, nTraces);
-				return fprog;
-			}
-		}
-		return "null";
-	}
-	public ArrayList<Patcher> refinePositionLevel(Vector<GrammarTreeNode> gtruth, Vector<ParseTreeNode> pNodes, Vector<GrammarTreeNode> gNodes)
-	{
-		ArrayList<Patcher> res = new ArrayList<Patcher>();
-		if(pNodes.size()!= gtruth.size())
-		{
-			Patcher nPatcher = new Patcher();
-			nPatcher.groundTruth = new Vector<GrammarTreeNode>(gtruth);
-			nPatcher.patchSpace = gNodes;
-			nPatcher.programNodes = pNodes;
-			res.add(nPatcher);
-			return res;
-		}
-		else
-		{
-			for(int i = 0; i < gtruth.size(); i++)
-			{
-				Patcher nPatcher = new Patcher();
-				Segment seg = ((Segment)gtruth.get(i));
-				//check if it constant segment
-				if(seg.section.isEmpty())
-				{
-					Vector<GrammarTreeNode> gs = new Vector<GrammarTreeNode>();
-					gs.add(gNodes.get(i));
-					Vector<ParseTreeNode> ps = new Vector<ParseTreeNode>();
-					ps.add(pNodes.get(i));
-					Vector<GrammarTreeNode> ts = new Vector<GrammarTreeNode>();
-					ts.add(seg);
-					nPatcher.groundTruth = ts;
-					nPatcher.patchSpace = gs;
-					nPatcher.programNodes = ps;
-					res.add(nPatcher);
-					return res;
-				}				
-				String sVal = pNodes.get(i).children.get(0).tmpEval;
-				String eVal = pNodes.get(i).children.get(1).tmpEval;
-				String tsVal =""+seg.section.get(0).pair[0].absPosition.get(0);
-				String teVal =""+seg.section.get(0).pair[1].absPosition.get(0);
-				Segment segSpace = (Segment)gNodes.get(i);
-				Vector<Section> secs = segSpace.section;//
-				//fix end position expression
-				if(tsVal.compareTo(sVal)==0)
-				{
-					ArrayList<Position> ap = new ArrayList<Position>();
-					for(int k = 0; k < secs.size(); k++)
-					{
-						if(secs.get(k).pair[1]!=null)
-							ap.add(secs.get(k).pair[1]);
-					}
-					PositionSet pos = new PositionSet(ap);
-					Vector<GrammarTreeNode> gs = new Vector<GrammarTreeNode>();
-					gs.add(pos);
-					Vector<ParseTreeNode> ps = new Vector<ParseTreeNode>();
-					ps.add(pNodes.get(i).children.get(1));
-					Vector<GrammarTreeNode> ts = new Vector<GrammarTreeNode>();
-					ts.add(seg.section.get(0).pair[1]);
-					nPatcher.groundTruth = ts;
-					nPatcher.patchSpace = gs;
-					nPatcher.programNodes = ps;
-					res.add(nPatcher);
-				}
-				else if(teVal.compareTo(eVal)==0)
-				{
-					ArrayList<Position> ap = new ArrayList<Position>();
-					for(int k = 0; k < secs.size(); k++)
-					{
-						if(secs.get(k).pair[0]!=null)
-							ap.add(secs.get(k).pair[0]);
-					}
-					PositionSet pos = new PositionSet(ap);
-					Vector<GrammarTreeNode> gs = new Vector<GrammarTreeNode>();
-					gs.add(pos);
-					Vector<ParseTreeNode> ps = new Vector<ParseTreeNode>();
-					ps.add(pNodes.get(i).children.get(0));
-					Vector<GrammarTreeNode> ts = new Vector<GrammarTreeNode>();
-					ts.add(seg.section.get(0).pair[0]);
-					nPatcher.groundTruth = ts;
-					nPatcher.patchSpace = gs;
-					nPatcher.programNodes = ps;
-					res.add(nPatcher);
-				}
-				else
-				{
-					//directly update the segment
-					Vector<GrammarTreeNode> gs = new Vector<GrammarTreeNode>();
-					gs.add(gNodes.get(i));
-					Vector<ParseTreeNode> ps = new Vector<ParseTreeNode>();
-					ps.add(pNodes.get(i));
-					Vector<GrammarTreeNode> ts = new Vector<GrammarTreeNode>();
-					ts.add(seg);
-					nPatcher.groundTruth = ts;
-					nPatcher.patchSpace = gs;
-					nPatcher.programNodes = ps;
-					res.add(nPatcher);
-				}	
-			}
-		}
-		return res;
-	}
-	public ArrayList<Patcher> refinePather(Patcher pat, Vector<GrammarTreeNode> gtruth, ArrayList<Path> pathes)
-	{
-		ArrayList<Patcher> res = new ArrayList<Patcher>();
-		if(pathes.isEmpty())
-		{
-			return res;
-		}
-		HashMap<Integer, int[]> prog2Sections = new HashMap<Integer,int[]>();
-		//consolidate the paths into one arraylist
-		//only one segmentation exists
-		Vector<GrammarTreeNode> xtemp = convertPathtoSpace(pathes);
-		//detect the parts that are correct
-		for(Path p:pathes)
-		{
-			int[] pog2Sects = p.indicator;
-			for(int i = 0; i < pog2Sects.length-1; i ++)
-			{
-				//match the (i-1)-th end and i-th start position
-				if(pog2Sects[i] >= 0 && pog2Sects[i+1] >=0)
-				{
-					//check whehther the evaluated result is correct.
-					int[] secR = {pog2Sects[i],pog2Sects[i+1]};					
-					String expected = "";
-					for(int j = secR[0]; j <secR[1]; j++ )
-					{
-						expected += ((Segment)gtruth.get(j)).tarString;
-					}
-					String evaled = p.evalNewExp.get(i);
-					//if yes, detect a reusable subprogram
-					if(evaled.compareTo(expected) == 0)
-					{
-						prog2Sections.put(i, secR);		
-					}											
-				}
-			}		
-		}
-		//split the arraylist into several smaller lists
-		int start = 0;
-		int progStart = 0;
-		for(int i = 0; i < pat.programNodes.size(); i++)
-		{
-			if(prog2Sections.containsKey(i))
-			{
-				int end = prog2Sections.get(i)[0];
-				Vector<GrammarTreeNode> gtru = new Vector<GrammarTreeNode>(pat.groundTruth.subList(start, end+1));
-				Vector<GrammarTreeNode> x = new Vector<GrammarTreeNode>(xtemp.subList(start, end+1));
-				Vector<ParseTreeNode> pNodes = new Vector<ParseTreeNode>(pat.programNodes.subList(progStart, i+1));
-				ArrayList<Patcher> tres = refinePositionLevel(gtru, pNodes, x);
-				start = prog2Sections.get(i)[1]+1;
-				progStart = i+1;
-				res.addAll(tres);
-			}
-		}
-		//add the last section if there is any
-		if(progStart < pat.programNodes.size())
-		{
-			int end = pat.groundTruth.size();
-			Vector<GrammarTreeNode> gtru = new Vector<GrammarTreeNode>(pat.groundTruth.subList(start, end));
-			Vector<GrammarTreeNode> x = new Vector<GrammarTreeNode>(xtemp.subList(start, end));
-			Vector<ParseTreeNode> pNodes = new Vector<ParseTreeNode>(pat.programNodes.subList(progStart, pat.programNodes.size()));
-			ArrayList<Patcher> tres = refinePositionLevel(gtru, pNodes, x);
-			res.addAll(tres);
-		}
-		return res;
-	}
-	public String applyPatch(ParseTreeNode tree, ArrayList<Patcher> pats) {
-		Iterator<Patcher> xiter = pats.iterator();
-		while(xiter.hasNext())
-		{
-			Patcher xPatcher = xiter.next();
-			if(xPatcher.replaceNodes.size() == 1 && xPatcher.programNodes.size()==1)
-			{
-				ParseTreeNode pNode = xPatcher.programNodes.get(0);
-				ParseTreeNode rpNode = xPatcher.replaceNodes.get(0);
-				int x = pNode.parent.children.indexOf(pNode);
-				pNode.parent.children.remove(pNode);
-				pNode.parent.children.add(x, rpNode);
-				xiter.remove();
-			}
-		}
-		HashMap<String, ArrayList<ParseTreeNode>> map = new HashMap<String, ArrayList<ParseTreeNode>>();
-		String[] bitmap = new String[tree.children.size()];
-		for (int i = 0; i < bitmap.length; i++) {
-			bitmap[i] = "null";
-		}
-		for (Patcher pat : pats) {
-			Vector<ParseTreeNode> xNodes = pat.programNodes;
-			int start = tree.children.indexOf(xNodes.get(0));
-			int end = tree.children.indexOf(xNodes.get(xNodes.size() - 1));
-			String key = start + "||" + end;
-			for (int i = start; i <= end; i++) {
-				bitmap[i] = key;
-			}
-			map.put(key, new ArrayList<ParseTreeNode>(pat.replaceNodes));
-		}
-		//
-		ArrayList<ParseTreeNode> nChildren = new ArrayList<ParseTreeNode>();
-		HashSet<String> visited = new HashSet<String>();
-		for (int i = 0; i < bitmap.length; i++) {
-			if (bitmap[i].compareTo("null") != 0 && !visited.contains(bitmap[i])) {
-				String key = bitmap[i];
-				nChildren.addAll(map.get(key));
-				visited.add(key);
-			} else {
-				nChildren.add(tree.children.get(i));
-			}
-		}
-		tree.children = nChildren;
-		return tree.toProgram();
-	}
-
-	public boolean updateProgram(Patcher pat, GrammarTreeNode space) {
-		if (space == null)
-			return false;
-		// replace the previous programNode with new nodes
-		StopWatch stopWatch = new Log4JStopWatch("Adpative_toProgram2");
-		String subProg = space.toProgram();
-
-		stopWatch.stop();
-		if (subProg == null || subProg.indexOf("null") != -1) {
-			return false;
-		}
-
-		ProgramParser xParser = new ProgramParser(contextId);
-		ParseTreeNode nroot = xParser.parse(subProg);
-		ArrayList<ParseTreeNode> children = nroot.getChildren();
-		pat.replaceNodes.clear();
-		pat.replaceNodes.addAll(children);
-		return true;
-	}
-
-	// use the new patch to update the space and return modified program spaces
-	public GrammarTreeNode updateNewSpace(Patcher pat) {
-		GrammarTreeNode res = null;
-		Vector<GrammarTreeNode> space = pat.patchSpace;
-		Vector<GrammarTreeNode> groundTruth = pat.groundTruth;
-		if(space.size() == groundTruth.size())
-		{
-			if(space.size() == 1)
-			{
-				GrammarTreeNode node = space.get(0).mergewith(groundTruth.get(0));
-				res = node;
-			}
-			else
-			{
-				Template x = new Template(space);
-				Template y = new Template(groundTruth);
-				Template r = (Template)x.mergewith(y);
-				res = r;
-			}
-		}
-		return res;
-	}
-	public ArrayList<ArrayList<String>> transpose(ArrayList<ArrayList<String>> vals,ArrayList<String> tarStrings)
-	{
-		ArrayList<ArrayList<String>> res = new ArrayList<ArrayList<String>>();
-		for(int i = 0; i < vals.get(0).size(); i++)
-		{
-			ArrayList<String> line = new ArrayList<String>();
-			String total = "";
-			for( int j = 0; j < vals.size(); j++)
-			{
-				total += vals.get(j).get(i);
-				line.add(vals.get(j).get(i));
-			}
-			res.add(line);
-			tarStrings.add(total);
-		}
-		return res;
-	}
-	public ArrayList<Patcher> align(ArrayList<Patcher> tTree, Traces wSpace,
-			ArrayList<String[]> preExps,HashMap<String, ArrayList<String>> prog2Eval, HashMap<String, String> prog2New) {
-		ArrayList<Patcher> res = new ArrayList<Patcher>();
-		/*Vector<String> orgs = new Vector<String>();
-		//get all original values
-		for(GrammarTreeNode node: wSpace.traceline.values().iterator().next().body)
-		{
-			Segment xn = (Segment)node;
-			if(!xn.isConstSegment())
-			{
-				System.out.println(""+xn.section.toString());
-				orgs = xn.section.get(0).orgStrings;
-			}
-		}*/
-		for (Patcher pat : tTree) {
-			//prepare the raw data
-			ArrayList<String> tarStrings = new ArrayList<String>();
-			ArrayList<ArrayList<String>> tarSegs = new ArrayList<ArrayList<String>>();
-			ArrayList<String> evalNewExp = new ArrayList<String>();
-			ArrayList<ArrayList<String>> tmp = new ArrayList<ArrayList<String>>();
-			for(ParseTreeNode node: pat.programNodes)
-			{
-				ArrayList<String> lvals = prog2Eval.get(node.value);
-				evalNewExp.add(prog2New.get(node.value));
-				tmp.add(lvals);
-			}
-			tarSegs = transpose(tmp, tarStrings);
-			// extract the corresponding program spaces
-			HashMap<Integer, Template> tmpts = wSpace.traceline;
-			Vector<GrammarTreeNode> groundTruth = pat.groundTruth;
-			ArrayList<Path> allPaths = new ArrayList<Path>();
-			for (Map.Entry<Integer, Template> integerTemplateEntry : tmpts.entrySet()) {
-				Vector<GrammarTreeNode> tBody = integerTemplateEntry.getValue().body;
-				ArrayList<Path> paths = extractPath(tBody, tarStrings, tarSegs, evalNewExp);
-				for(Path p: paths)
-				{
-					if(p.sections.size() == groundTruth.size())
-					{
-						allPaths.add(p);
-					}
-				}
-			}
-			ArrayList<Patcher> temPats = refinePather(pat, groundTruth, allPaths);
-			if(temPats.isEmpty())
-				return null;
-			res.addAll(temPats);
-		}
-		return res;
-	}
-
-	public Vector<GrammarTreeNode> convertPathtoSpace(ArrayList<Path> paths) {
-		Vector<Vector<GrammarTreeNode>> res = new Vector<Vector<GrammarTreeNode>>();
-		for (Path p : paths) {
-			Vector<GrammarTreeNode> line = new Vector<GrammarTreeNode>();
-			ArrayList<Section> secs = p.sections;
-			for (Section sec : secs) {
-				Vector<Section> st = new Vector<Section>();
-				st.add(sec);
-				Segment seg = new Segment(st, false, contextId);
-				line.add(seg);
-			}
-			res.add(line);
-		}
-		Traces uTraces = new Traces(contextId);
-		Vector<GrammarTreeNode> tempres = new Vector<GrammarTreeNode>(); 
-		if(!res.isEmpty())
-		{
-			tempres = uTraces.consolidate_tool(res);
-		}
-		return tempres;
-	}
-
-	public ArrayList<Path> extractPath(Vector<GrammarTreeNode> tBody,
-			ArrayList<String> tarStrings,ArrayList<ArrayList<String>> tarSegs, ArrayList<String> evalNewExp) {
-		ArrayList<Path> res = new ArrayList<Path>();
-		ArrayList<Path> seeds = new ArrayList<Path>();
-		// initialize the seeds
-		for (int i = 0; i < tBody.size(); i++) {
-			Segment seg = (Segment) tBody.get(i);
-			for (Section sec : seg.section) {
-				ArrayList<Integer> markers = new ArrayList<Integer>();
-				for (int j = 0; j < sec.tarStrings.size(); j++) {
-					markers.add(0);
-				}
-				Vector<String> subs = sec.tarStrings;
-				ArrayList<Integer> x = updateMarker(subs, tarStrings, markers);
-				if (x != null) {
-					ArrayList<Section> sections = new ArrayList<Section>();
-					sections.add(sec);
-					Path nP = new Path(sections, x, tarStrings, i + 1, tarSegs, evalNewExp);
-					seeds.add(nP);
-				}
-			}
-		}
-		// seeking a sequence of sections that can form the target strings
-		while (!seeds.isEmpty()) {
-			Path path = seeds.remove(0);
-			// check if it succeeds already
-			boolean finished = true;
-			boolean nofit = false;
-			for (int i = 0; i < path.markers.size(); i++) {
-				int strlen = path.tarStrings.get(i).length();
-				int mk = path.markers.get(i);
-				if (mk > strlen) {
-					nofit = true;
-				}
-				if (mk < strlen) {
-					finished = false;
-					break;
-				}
-				
-			}
-			if (finished)
-			{
-				res.add(path);
-				continue;
-			}
-			if (nofit)
-				continue;
-			ArrayList<Path> cands = updatePath(path, tBody);
-			seeds.addAll(cands);
-		}
-		return res;
-	}
-
-	// -1 failed, 0 succeed, 1 finished
-	public ArrayList<Path> updatePath(Path np, Vector<GrammarTreeNode> tBody) {
-		ArrayList<Path> res = new ArrayList<Path>();
-		if(np.tmplateMarker >= tBody.size())
-		{
-			return res;
-		}
-		Segment seg = (Segment) tBody.get(np.tmplateMarker);
-		for (Section as : seg.section) {
-			Vector<String> subs = as.tarStrings;
-			ArrayList<Integer> x = updateMarker(subs, np.tarStrings, np.markers);
-			if (x != null) {
-				Path xp = np.updatePath(as, x);
-				res.add(xp);
-			}
-		}
-		return res;
-	}
-
-	// if anyone is not a prefix of the other return null
-	public ArrayList<Integer> updateMarker(Vector<String> subs,
-			ArrayList<String> target, ArrayList<Integer> markers) {
-		ArrayList<Integer> res = new ArrayList<Integer>();
-		for (int i = 0; i < subs.size(); i++) {
-			String sub = subs.get(i);
-			String tar = target.get(i).substring(markers.get(i));
-			if (tar.indexOf(sub) != 0) {
-				return null;
-			} else {
-				res.add(markers.get(i) + sub.length());
-			}
-		}
-		return res;
-	}
-
-	// identify the correspondence between the subprograms and the concrete
-	// instance tree
-	public ArrayList<ArrayList<Patcher>> createCandidates(ParseTreeNode tree,
-			Traces concrete) {
-		ArrayList<ArrayList<Patcher>> res = new ArrayList<ArrayList<Patcher>>();
-		// get all the parseTree segments
-		ArrayList<ParseTreeNode> segments = tree.getChildren();
-		// get all the different segmentations of the example
-		Vector<Vector<GrammarTreeNode>> segs = concrete.rawlines;
-		for (Vector<GrammarTreeNode> tBody : segs) {
-			if (tBody.size() < segments.size()) {
-				continue;
-			}
-			int len = tBody.size();
-			ArrayList<Patcher> list = new ArrayList<Patcher>();
-			if (len == segments.size()) {
-				// one on one match
-				for (int i = 0; i < len; i++) {
-					String truVal = ((Segment) tBody.get(i)).tarString;
-					if (segments.get(i).tmpEval.compareTo(truVal) == 0) {
-						continue;
-					} else {
-						Patcher pa = new Patcher();
-						Vector<GrammarTreeNode> grt = new Vector<GrammarTreeNode>();
-						grt.add(tBody.get(i));
-						Vector<ParseTreeNode> progs = new Vector<ParseTreeNode>();
-						progs.add(segments.get(i));
-						pa.groundTruth = grt;
-						pa.programNodes = progs;
-						list.add(pa);
-					}
-				}
-			} else {
-				// one prog to multiple trace Nodes
-				multipleAlign(list, tBody, segments);
-			}
-			if (!list.isEmpty()) {
-				res.add(list);
-			}
-		}
-		return res;
-	}
-
-	public void multipleAlign(ArrayList<Patcher> list,
-			Vector<GrammarTreeNode> tbody, ArrayList<ParseTreeNode> segments) {
-		// find anchor point, from the start point and the end
-		int progS = 0;
-		int tS = 0;
-		int endSpan = 0;
-		for (int i = 0; i < tbody.size() && i < segments.size(); i++) {
-			String gTruth = ((Segment) tbody.get(i)).tarString;
-			if (segments.get(progS).tmpEval.compareTo(gTruth) == 0) {
-				progS++;
-				tS++;
-			} else {
-				break;
-			}
-		}
-		for (int i = 0; i < tbody.size() && i < segments.size()&& i>progS && i> tS; i++) {
-			String gTruth = ((Segment) tbody.get(tbody.size()-1-i)).tarString;
-			if (segments.get(segments.size()-1-i).tmpEval.compareTo(gTruth) == 0) {
-				endSpan = i+1;
-			} else {
-				break;
-			}
-		}
-		Vector<GrammarTreeNode> grt = new Vector<GrammarTreeNode>();
-		for (int i = tS; i <= tbody.size()-1-endSpan; i++) {
-			grt.add(tbody.get(i));
-		}
-		Vector<ParseTreeNode> progs = new Vector<ParseTreeNode>();
-		for (int i = progS; i <= segments.size()-1-endSpan; i++) {
-			progs.add(segments.get(i));
-		}
-		if (!grt.isEmpty() && !progs.isEmpty()) {
-			Patcher pa = new Patcher();
-			pa.groundTruth = grt;
-			pa.programNodes = progs;
-			list.add(pa);
-		}
-	}
-
-	public Traces createSingleTrace(String[] exp) {
-		ExampleTraces eTraces = new ExampleTraces(contextId);
-		return eTraces.createTrace(exp);
-	}
-
-	public ArrayList<Integer> chooseLargestSubset(
-			HashMap<String, String> exp2program, ArrayList<String[]> examples) {
-		ArrayList<Integer> res = new ArrayList<Integer>();
-		int maxsize = -1;
-		for (String key : exp2program.keySet()) {
-			ArrayList<Integer> tmp = new ArrayList<Integer>();
-			for (int i = 0; i < examples.size(); i++) {
-				String line = UtilTools.formatExp(examples.get(i));
-				if (key.indexOf(line) != -1)
-					tmp.add(i);
-			}
-			if (tmp.size() > maxsize && formKey(examples, tmp, true).compareTo(key)==0) {
-				res = tmp;
-				maxsize = tmp.size();
-			}
-		}
-		return res;
-	}
-	public String getProgram(String subkey, HashMap<String, String> exp2Prog)
-	{
-		String prog = "";
-		//most compatible program
-		int msize = -1;
-		for(Map.Entry<String, String> stringStringEntry : exp2Prog.entrySet())
-		{
-			int sz = stringStringEntry.getKey().split("\\*").length;
-			if(sz > msize &&UtilTools.iscovered(stringStringEntry.getKey(), subkey))
-			{
-				msize = sz;
-				prog = stringStringEntry.getValue();
-			}
-		}
-		return prog;
-	}
-	public Traces getProgramSpace(String subkey,
-			HashMap<String, Traces> exp2space) {
-		return exp2space.get(subkey);
-	}
-
-	public ArrayList<String[]> getRestExamples(ArrayList<String[]> examples,
-			ArrayList<Integer> keys) {
-		ArrayList<String[]> restExp = new ArrayList<String[]>();
-		for (int i = 0; i < examples.size(); i++) {
-			if (!keys.contains(i)) {
-				restExp.add(examples.get(i));
-			}
-		}
-		return restExp;
-	}
-
-	public String formKey(ArrayList<String[]> examples,
-			ArrayList<Integer> keys, boolean include) {
-		ArrayList<String[]> resList = new ArrayList<String[]>();
-		if (include) {
-			for (int i = 0; i < examples.size(); i++) {
-				if (keys.contains(i)) {
-					resList.add(examples.get(i));
-				}
-			}
-		} else {
-			for (int i = 0; i < examples.size(); i++) {
-				if (!keys.contains(i)) {
-					resList.add(examples.get(i));
-				}
-			}
-		}
-		String key = UtilTools.createkey(resList);
-		return key;
-	}
-}
-
-
-class Path {
-	ArrayList<Section> sections = new ArrayList<Section>();
-	ArrayList<int[]> progCrepLandMarkers = new ArrayList<int[]>();
-	//the individual evaluation results for the new example
-	ArrayList<String> evalNewExp = new ArrayList<String>();
-	// record the progress for this path on all examples
-	ArrayList<Integer> markers = new ArrayList<Integer>();
-	// record the target substring that should be covered
-	ArrayList<String> tarStrings = new ArrayList<String>();
-	// tmplate position marker
-	int tmplateMarker = -1;
-	//each evaled segments
-	ArrayList<ArrayList<String>> tarSegs = new ArrayList<ArrayList<String>>();
-	ArrayList<ArrayList<Integer>> landMarkers = new ArrayList<ArrayList<Integer>>();
-	//point to the start position of the segments
-	//0 unexplored , positive number matched, -2 passed without match
-	int[] indicator = null;
-
-	public Path(ArrayList<Section> sec, ArrayList<Integer> markers,
-			ArrayList<String> tarStrings, int tMarker,ArrayList<ArrayList<String>> tarSegs,ArrayList<String> evalNewExp) 
-	{
-		this.sections = sec;
-		this.markers = markers;
-		this.tarStrings = tarStrings;
-		this.tmplateMarker = tMarker;
-		this.tarSegs = tarSegs;
-		this.evalNewExp = evalNewExp;
-		indicator = new int[evalNewExp.size()+1];
-		for(int i = 0; i < indicator.length; i++)
-		{
-			indicator[i] = 0;
-		}
-		processData();
-	}
-	
-	public void processData()
-	{
-		ArrayList<Integer> xArrayList = new ArrayList<Integer>();
-		for(int i = 0; i < tarSegs.size(); i++)
-		{
-			xArrayList.add(0);
-		}
-		landMarkers.add(xArrayList);
-		for(int i = 0; i < tarSegs.get(0).size(); i++)
-		{
-			ArrayList<Integer> tmp = new ArrayList<Integer>();
-			for(int j = 0; j < tarSegs.size(); j ++)
-			{
-				int curLen = landMarkers.get(i).get(j)+tarSegs.get(j).get(i).length();
-				tmp.add(curLen);
-			}
-			landMarkers.add(tmp);
-		}
-	}
-
-	// 0 equal 1 x partially pass y, -1 x less than y
-	public int compareMarker(ArrayList<Integer> x, ArrayList<Integer> y)
-	{
-		if(x.size() != y.size())
-		{
-			System.out.println("The Landmarker size should match");
-		}
-		boolean equal = true;
-		for(int i = 0; i < x.size(); i++)
-		{
-			if(x.get(i) > y.get(i))
-			{
-				return 1;
-			}
-			if(x.get(i)< y.get(i))
-			{
-				equal = false;
-			}
-		}
-		if(equal)
-			return 0;
-		else
-			return -1;
-	}
-	public void setIndicator(int[] indic)
-	{
-		this.indicator = indic;
-	}
-	public Path updatePath(Section sec, ArrayList<Integer> markers) {
-		//this.sections.add(sec);
-		ArrayList<Section> xsections = new ArrayList<Section>();
-		xsections.addAll(this.sections);
-		xsections.add(sec);
-		ArrayList<Integer> nmarkers = new ArrayList<Integer>();
-		nmarkers = markers;
-		int mark = this.tmplateMarker+1;
-		//update the mapping info
-		int ptr = 0;
-		while(ptr < indicator.length-1 && indicator[ptr]!= -1)
-		{
-			ptr++;
-		}
-		ArrayList<Integer> nextMarker = landMarkers.get(ptr);
-		int cres = this.compareMarker(markers, nextMarker);
-		//check whether it reaches a landmark
-		if(cres == 0)
-		{
-			indicator[ptr] = xsections.size(); 
-		}
-		else if(cres == 1)
-		{
-			indicator[ptr] = -2;
-		}
-		//update the progCrepLandmarker with the new portion
-		Path np = new Path(xsections, nmarkers, tarStrings, mark,this.tarSegs,evalNewExp);
-		np.setIndicator(this.indicator);
-		return np;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgramParser.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgramParser.java
deleted file mode 100644
index 28213b1b7..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgramParser.java
+++ /dev/null
@@ -1,86 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-
-import edu.isi.karma.cleaning.ParseTreeNode.nodetype;
-
-public class ProgramParser {
-	public ParseTreeNode root = null;
-	String contextId;
-	public ProgramParser(String contextId) {
-		this.contextId = contextId;
-	}
-
-	// parse the sub program with a sequence of segment
-	public ArrayList<ParseTreeNode> parseNodeSeq(String nodeseq) {
-		ArrayList<ParseTreeNode> res = new ArrayList<ParseTreeNode>();
-		// find segments
-		String[] tokens = nodeseq.split("\\+(?=([^\"]*\"[^\"]*\")*[^\"]*$)");
-		for (String tok : tokens) {
-			// segment expression
-			ParseTreeNode node = new ParseTreeNode(nodetype.segment, tok, contextId);
-			res.add(node);
-		}
-		return res;
-	}
-	//parse the position program for each segment
-	public void parseSegment(ParseTreeNode seg)
-	{
-		String tok = seg.value;
-		// find the startposition
-		int sposS = tok.indexOf("substr(value,", 0)+13;
-		if (sposS <= 12) {
-			return;
-		}
-		int sposE = 0;
-		if(tok.charAt(sposS)<'9' && tok.charAt(sposS) > '0')
-		{
-			sposE = tok.indexOf(",",sposS)-1;
-		}
-		else
-		{
-			sposE = tok.indexOf("),",sposS+11);
-		}
-		
-		String sposExpre = tok.substring(sposS, sposE + 1);
-		// find the endPosition
-		int eposS = sposE+2;
-		int eposE = tok.length()-1;
-		String eposExpre = tok.substring(eposS, eposE);
-		ParseTreeNode sPosNode = new ParseTreeNode(nodetype.position,
-				sposExpre,contextId);
-		ParseTreeNode ePosNode = new ParseTreeNode(nodetype.position,
-				eposExpre,contextId);
-		seg.addChildren(sPosNode);
-		seg.addChildren(ePosNode);
-	}
-	public ParseTreeNode parse(String prog) {
-		ParseTreeNode root = new ParseTreeNode(nodetype.root, prog,contextId);
-		// find segments
-		String[] tokens = prog.split("\\+(?=([^\"]*\"[^\"]*\")*[^\"]*$)");
-		for (String tok : tokens) {
-			// loop expression, possibily a sequence of loop segments
-			if (tok.indexOf("loop(value,r") != -1) {
-				String exp = tok.substring(13, tok.length() - 2);
-				//create loop node
-				ParseTreeNode pTreeNode = new ParseTreeNode(nodetype.loop, tok,contextId);
-				root.addChildren(pTreeNode);
-				ArrayList<ParseTreeNode> children = this.parseNodeSeq(exp);
-				for(ParseTreeNode n:children)
-				{
-					pTreeNode.addChildren(n);
-					this.parseSegment(n);
-				}
-
-			} else {
-				// segment expression
-				ParseTreeNode node = new ParseTreeNode(nodetype.segment, tok,contextId);
-				root.addChildren(node);
-				// find the startposition
-				this.parseSegment(node);
-			}
-		}
-		return root;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgramRule.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgramRule.java
deleted file mode 100644
index ef0561a5b..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/ProgramRule.java
+++ /dev/null
@@ -1,93 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.HashMap;
-import java.util.Map;
-
-public class ProgramRule {
-	public HashMap<String, InterpreterType> rules = new HashMap<String, InterpreterType>();
-	public HashMap<String, String> strRules = new HashMap<String, String>();
-	public PartitionClassifierType pClassifier;
-	public static Interpretor itInterpretor;
-	public String signString = "";
-	public static final String IDENTITY = "substr(value,'START','END')";
-	public boolean nullRule = false;
-	public String contextId;
-	public ProgramRule(Program prog, String contextId) {
-		this.pClassifier = prog.classifier;
-		initInterpretor();
-	}
-
-	public ProgramRule(String rule, String contextId) {
-		initInterpretor();
-		InterpreterType worker = itInterpretor.create(rule);
-		rules.put("attr_0", worker);
-
-	}
-
-	public String transform(String value) {
-		InterpreterType worker= this.getRuleForValue(value);
-		String s2 = worker.execute(value);
-		return s2;
-	}
-
-	public void initInterpretor() {
-		if (itInterpretor == null)
-			itInterpretor = new Interpretor(contextId);
-	}
-
-	public InterpreterType getRuleForValue(String value) {
-		String c = getClassForValue(value);
-
-		return getWorkerForClass(c);
-	}
-
-	public String getClassForValue(String value) {
-		String labelString = "attr_0";
-		if (value.length() == 0)
-			return labelString;
-		if (pClassifier != null) {
-			labelString = pClassifier.getLabel(value);
-		}
-		return labelString;
-
-	}
-
-	public InterpreterType getWorkerForClass(String category) {
-		if (category != "") {
-			InterpreterType rule = this.rules.get(category);
-			return rule;
-		} else {
-			return rules.values().iterator().next();
-		}
-	}
-
-	public void updateClassworker(String category, String newRule) {
-		this.rules.remove(category);
-		this.strRules.remove(category);
-		addRule(category, newRule);
-
-	}
-
-	public void addRule(String partition, String rule) {
-		InterpreterType worker = itInterpretor.create(rule);
-		this.signString += rule;
-		rules.put(partition, worker);
-		strRules.put(partition, rule);
-	}
-
-	public String getStringRule(String par) {
-		return this.strRules.get(par);
-	}
-
-	public String toString() {
-		String res = "";
-		for (Map.Entry<String, String> stringStringEntry : strRules.entrySet()) {
-			res += String.format("%s:%s\n", stringStringEntry.getKey(), stringStringEntry.getValue());
-		}
-		return res;
-	}
-
-	public static void main(String[] args) {
-
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature1.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature1.java
deleted file mode 100644
index c2c7c5e79..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature1.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.QuestionableRecord;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.TNode;
-
-//counting text feature
-public class Feature1 implements RecFeature {
-	public String target;
-	public Vector<TNode> xNodes = new Vector<TNode>();
-	public double weight = 1.0;
-
-	public Feature1(String tar, Vector<TNode> xNodes, double weight) {
-		target = tar;
-		this.xNodes = xNodes;
-		this.weight = weight;
-	}
-
-	public String getName() {
-		return target;
-	}
-
-	public double computerScore() {
-		double res = 0.0;
-		if (xNodes == null)
-			return 0.0;
-		for (TNode x : xNodes) {
-			if (x.text.compareTo(target) == 0)
-				res += 1;
-		}
-		return res * this.weight;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature2.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature2.java
deleted file mode 100644
index bd6dc07bb..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature2.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.QuestionableRecord;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.TNode;
-
-//type count feature
-public class Feature2 implements RecFeature {
-
-	public int type;
-	public Vector<TNode> xNodes = new Vector<TNode>();
-	public double weight = 1.0;
-
-	public Feature2(int type, Vector<TNode> xNodes, double weight) {
-		this.type = type;
-		this.xNodes = xNodes;
-		this.weight = weight;
-	}
-
-	public String getName() {
-		return String.valueOf(type);
-	}
-
-	public double computerScore() {
-		double res = 0.0;
-		if (xNodes == null)
-			return 0.0;
-		for (TNode x : xNodes) {
-			if (x.type == type)
-				res += 1;
-		}
-		return res * weight;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature3.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature3.java
deleted file mode 100644
index 4466e0a9e..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature3.java
+++ /dev/null
@@ -1,58 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.QuestionableRecord;
-
-// reverse count feature
-public class Feature3 implements RecFeature {
-	int rcnt = 0;
-	String resString;
-	double weight = 1.0;
-
-	// calculate the number of reverse order
-	public Feature3(String res, double weight) {
-		this.resString = res;
-	}
-
-	public String getName() {
-		return resString;
-	}
-
-	@Override
-	public double computerScore() {
-		int pre = -1;
-		double cnt = 0;
-		for (int c = 0; c < resString.length(); c++) {
-			if (Character.isDigit(resString.charAt(c))) {
-				if (pre != -1) {
-					pre = c;
-					continue;
-				}
-				if (c < pre) {
-					pre = c;
-					cnt++;
-				}
-			}
-		}
-		return cnt * this.weight;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature4.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature4.java
deleted file mode 100644
index 95f884654..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/Feature4.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.QuestionableRecord;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.TNode;
-
-public class Feature4 implements RecFeature {
-	public String target;
-	public Vector<TNode> xNodes = new Vector<TNode>();
-	public Vector<TNode> yNodes = new Vector<TNode>();
-	public double weight = 1.0;
-
-	public Feature4(String tar, Vector<TNode> xNodes, Vector<TNode> yNodes,
-			double weight) {
-		target = tar;
-		this.xNodes = xNodes;
-		this.yNodes = yNodes;
-		this.weight = weight;
-	}
-
-	public String getName() {
-		return target;
-	}
-
-	public double computerScore() {
-		int tarCnt = 0;
-		int orgCnt = 0;
-		for (TNode t : xNodes) {
-			String kString = t.text;
-			kString = kString.replaceAll("[0-9]+", "DIGITs");
-			if (kString.compareTo(target) == 0) {
-				orgCnt += 1;
-			}
-		}
-		for (TNode t : yNodes) {
-			String kString = t.text;
-			kString = kString.replaceAll("[0-9]+", "DIGITs");
-			if (kString.compareTo(target) == 0) {
-				tarCnt += 1;
-			}
-		}
-		return (tarCnt - orgCnt) * this.weight;
-	}
-}
\ No newline at end of file
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/FeatureVector.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/FeatureVector.java
deleted file mode 100644
index 555b50ef2..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/FeatureVector.java
+++ /dev/null
@@ -1,115 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.QuestionableRecord;
-
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.Ruler;
-import edu.isi.karma.cleaning.TNode;
-import edu.isi.karma.cleaning.UtilTools;
-
-public class FeatureVector {
-	String[] symbol = { "#", ";", ",", "!", "~", "@", "$", "%", "^", "&", "*",
-			"(", ")", "_", "-", "{", "}", "[", "]", "\"", "'", ":", "?", "<",
-			">", "." };
-	int[] types = { TNode.NUMTYP, TNode.SYBSTYP, TNode.LWRDTYP, TNode.UWRDTYP };
-	Vector<RecFeature> x = new Vector<RecFeature>();
-	HashSet<String> dictionary = new HashSet<String>();
-	public int size;
-
-	public FeatureVector(HashSet<String> dic) {
-		this.dictionary = dic;
-	}
-
-	public int size() {
-		return this.symbol.length + this.types.length + 1
-				+ this.dictionary.size();
-	}
-
-	public Vector<String> getNames() {
-		Vector<String> names = new Vector<String>();
-		for (RecFeature f : this.x) {
-			String name = f.getName();
-			if (name.compareTo(",") == 0) {
-				name = "Comma";
-			}
-			names.add(name);
-		}
-		return names;
-	}
-
-	public Vector<RecFeature> createVector(String raw, String color) {
-		if (raw.contains("<_START>")) {
-			raw = raw.replace("<_START>", "");
-		}
-		if (raw.contains("<_END>")) {
-			raw = raw.replace("<_END>", "");
-		}
-		Vector<RecFeature> v = new Vector<RecFeature>();
-		Ruler r = new Ruler();
-		r.setNewInput(raw);
-		Vector<TNode> vt = new Vector<TNode>();
-		vt = r.vec;
-		HashMap<String, String> tmp = new HashMap<String, String>();
-		try {
-			UtilTools.StringColorCode(raw, color, tmp);
-		} catch (Exception e) {
-			tmp.put("Org", raw);
-			tmp.put("Tar", "ERROR");
-			tmp.put("Orgdis", raw);
-			tmp.put("Tardis", "ERROR");
-		}
-		String tar = tmp.get("Tar");
-		r.setNewInput(tar);
-		Vector<TNode> tarNodes = r.vec;
-		constructVector(vt, tarNodes, color, v, this.dictionary);
-		this.size = v.size();
-		this.x = v;
-		return v;
-	}
-
-	// should normalize the feature values
-	public void constructVector(Vector<TNode> t, Vector<TNode> tarNodes,
-			String color, Vector<RecFeature> v, HashSet<String> dic) {
-		double w = 0.25;
-		double w1 = w / (symbol.length);
-		for (String s : symbol) {
-			Feature1 feature1 = new Feature1(s, tarNodes, w1);
-			v.add(feature1);
-		}
-		double w2 = w / types.length;
-		for (int type : types) {
-			Feature2 feature2 = new Feature2(type, tarNodes, w2);
-			v.add(feature2);
-		}
-		double w3 = w;
-		Feature3 feature3 = new Feature3(color, w3);
-		v.add(feature3);
-		double w4 = w / dic.size();
-		for (String s : dic) {
-			Feature4 f4 = new Feature4(s, t, tarNodes, w4);
-			v.add(f4);
-		}
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/OutlierDetector.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/OutlierDetector.java
deleted file mode 100644
index 46789a094..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/OutlierDetector.java
+++ /dev/null
@@ -1,171 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.QuestionableRecord;
-
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.Ruler;
-import edu.isi.karma.cleaning.TNode;
-
-public class OutlierDetector {
-	public HashMap<String, double[]> rVectors = new HashMap<String, double[]>();
-	public double currentMax = -1;
-	public HashSet<String> dict = new HashSet<String>();
-
-	public OutlierDetector() {
-
-	}
-
-	public double getDistance(double[] x, double[] y) {
-		if (x == null || y==null ||x.length != y.length )
-			return Double.MAX_VALUE;
-		double value = 0.0;
-		for (int i = 0; i < x.length; i++) {
-			value += Math.pow(x[i] - y[i], 2);
-		}
-		return Math.sqrt(value);
-	}
-
-	// find all the word appearing in org and tar records
-	public void buildDict(Collection<String[]> data) {
-		HashMap<String, Integer> mapHashSet = new HashMap<String, Integer>();
-		for (String[] pair : data) {
-			String s1 = pair[0];
-			String s2 = pair[1];
-			if (s1.contains("<_START>")) {
-				s1 = s1.replace("<_START>", "");
-			}
-			if (s1.contains("<_END>")) {
-				s1 = s1.replace("<_END>", "");
-			}
-			if (s2.contains("<_START>")) {
-				s2 = s2.replace("<_START>", "");
-			}
-			if (s2.contains("<_END>")) {
-				s2 = s2.replace("<_END>", "");
-			}
-			Ruler r = new Ruler();
-			r.setNewInput(s1);
-			Vector<TNode> v = r.vec;
-			r.setNewInput(s2);
-			v.addAll(r.vec);
-			HashSet<String> curRow = new HashSet<String>();
-			for (TNode t : v) {
-				String k = t.text;
-				k = k.replaceAll("[0-9]+", "DIGITs");
-				if (k.trim().length() == 0)
-					continue;
-				// only consider K once in one row
-				if (curRow.contains(k)) {
-					continue;
-				} else {
-					curRow.add(k);
-				}
-				if (mapHashSet.containsKey(k)) {
-					mapHashSet.put(k, mapHashSet.get(k) + 1);
-				} else {
-					mapHashSet.put(k, 1);
-				}
-			}
-		}
-		// prune infrequent terms
-		int thresdhold = (int) (data.size() * 0.5);
-		Iterator<Entry<String, Integer>> iter = mapHashSet.entrySet()
-				.iterator();
-		while (iter.hasNext()) {
-			Entry<String, Integer> e = iter.next();
-			if (e.getValue() < thresdhold) {
-				iter.remove();
-			}
-		}
-		this.dict = new HashSet<String>(mapHashSet.keySet());
-	}
-
-	// find outliers for one partition
-	// simple 2d distance
-	// testdata rowid:{tar, tarcolor}
-	public String getOutliers(HashMap<String, String[]> testdata,
-			double[] meanVector, double Max, HashSet<String> dic) {
-		String Id = "";
-		for (String key : testdata.keySet()) {
-			String[] vpair = testdata.get(key);
-			FeatureVector fvFeatureVector = new FeatureVector(dic);
-			Vector<RecFeature> vRecFeatures = fvFeatureVector.createVector(
-					vpair[0], vpair[1]);
-			double[] x = new double[fvFeatureVector.size()];
-			for (int i = 0; i < vRecFeatures.size(); i++) {
-				x[i] = vRecFeatures.get(i).computerScore();
-			}
-			double value = this.getDistance(x, meanVector);
-			if (value > Max) {
-				Max = value;
-				this.currentMax = Max;
-				Id = key;
-			}
-		}
-		return Id;
-	}
-
-	// pid: [{rawstring, code}]
-	public void buildMeanVector(HashMap<String, Vector<String[]>> data,
-			HashSet<String> dict) {
-		rVectors.clear();
-		this.currentMax = -1;
-		if (data == null)
-			return;
-		for (Entry<String, Vector<String[]>> stringVectorEntry : data.entrySet()) {
-			Vector<String[]> vs = stringVectorEntry.getValue();
-			FeatureVector fVector = new FeatureVector(dict);
-			double[] dvec = new double[fVector.size()];
-			for (int i = 0; i < dvec.length; i++) {
-				dvec[i] = 0;
-			}
-			for (String[] elem : vs) {
-				Vector<RecFeature> sFeatures = fVector.createVector(elem[0],
-						elem[1]);
-				for (int j = 0; j < sFeatures.size(); j++) {
-					dvec[j] += sFeatures.get(j).computerScore();
-				}
-			}
-			// get average size
-			for (int i = 0; i < dvec.length; i++) {
-				dvec[i] = dvec[i] * 1.0 / vs.size();
-			}
-			rVectors.put(stringVectorEntry.getKey(), dvec);
-		}
-	}
-
-	public String test(double[] row) {
-		String string = "";
-		for (double d : row) {
-			string += d + ",";
-		}
-		return string.substring(1, string.length() - 1);
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/RecFeature.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/RecFeature.java
deleted file mode 100644
index 88ab5172c..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/QuestionableRecord/RecFeature.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.QuestionableRecord;
-
-public interface RecFeature {
-	public double computerScore();
-
-	public String getName();
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ANode.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ANode.java
deleted file mode 100644
index bc143489b..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ANode.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.Research;
-
-import java.util.Vector;
-
-//used in alignment
-public class ANode {
-	public Vector<Integer> orgPos = new Vector<Integer>();
-	public Vector<Integer> tarPos = new Vector<Integer>();
-	public Vector<Integer> length = new Vector<Integer>();
-	public Vector<String[]> exps = new Vector<String[]>();
-	public Vector<ANode> children = new Vector<ANode>();
-
-	public ANode(Vector<Integer> orgPos, Vector<Integer> tarPos,
-			Vector<Integer> length, Vector<String[]> exps) {
-		this.orgPos = orgPos;
-		this.tarPos = tarPos;
-		this.length = length;
-		this.exps = exps;
-	}
-
-	public void addChild(ANode a) {
-		this.children.add(a);
-	}
-
-	// check whether current node valid based on
-	// all copy node
-	// all constant node and same content
-	public boolean isvalid() {
-		if (orgPos.size() <= 1)
-			return true;
-		for (int i = 1; i < orgPos.size(); i++) {
-			int value = orgPos.get(i) * orgPos.get(i - 1);
-			if (value < 0)
-				return false;
-			if (orgPos.get(i) < 0) {
-				String sub = this.exps.get(i)[1].substring(tarPos.get(i),
-						tarPos.get(i) + length.get(i));
-				String presub = this.exps.get(i - 1)[1].substring(
-						tarPos.get(i - 1),
-						tarPos.get(i - 1) + length.get(i - 1));
-				if (sub.compareTo(presub) != 0) {
-					return false;
-				}
-			}
-		}
-		return true;
-	}
-
-	public void reorderChildren() {
-		// reorder the children to accelerate the search.
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/AdaptationTest.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/AdaptationTest.java
deleted file mode 100644
index 6018742c8..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/AdaptationTest.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package edu.isi.karma.cleaning.Research;
-
-
-import org.apache.log4j.xml.DOMConfigurator;
-
-import edu.isi.karma.cleaning.EmailNotification;
-
-//this class is used to evaluate adaptation function
-public class AdaptationTest {
-	public static void main(String[] args) {
-		DOMConfigurator.configure("/Users/bowu/projects/DataCleaning/log4j2.xml");
-		EmailNotification notification = new EmailNotification();
-		ConfigParameters cfg = new ConfigParameters();
-		cfg.initeParameters();
-		DataCollection.config = cfg.getString();
-		//preload all libraries 
-		//Test.test4("/Users/bowu/Research/testdata/TestSingleFile");
-		//start experiment
-		Test.test4("/Users/bowu/Research/testdata/TestSingleFile");
-		Test.test3("/Users/bowu/Research/testdata/TestSingleFile");
-		notification.notify(true,"NewExpr");
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ClassifierRefiner.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ClassifierRefiner.java
deleted file mode 100644
index a6da16cbc..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ClassifierRefiner.java
+++ /dev/null
@@ -1,56 +0,0 @@
-package edu.isi.karma.cleaning.Research;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-
-import edu.isi.karma.cleaning.Program;
-// input: classifier, results for each record
-//output: a refined classifier
-
-public class ClassifierRefiner {
-	Program prog;
-	HashMap<String, HashMap<String,String>> uData;
-	HashMap<String, ArrayList<String>> clusters = new HashMap<String, ArrayList<String>>();
-	public ClassifierRefiner(Program prog, HashMap<String, HashMap<String,String>> uData)
-	{
-		this.prog = prog;
-		this.uData = uData;
-	}
-	public HashSet<String> selectUdata()
-	{
-		HashSet<String> idSet = new HashSet<String>();
-		
-		return idSet;
-	}
-	//auxiliary functions
-	public void clusterUdata()
-	{
-		for(Map.Entry<String, HashMap<String, String>> stringHashMapEntry : uData.entrySet())
-		{
-			HashMap<String, String> dict = stringHashMapEntry.getValue();
-			String ckey = dict.get("class");
-			String org = dict.get("Org");
-			if(clusters.containsKey(ckey))
-			{
-				clusters.get(ckey).add(org);
-			}
-			else
-			{
-				ArrayList<String> xArrayList = new ArrayList<String>();
-				xArrayList.add(org);
-				clusters.put(ckey, xArrayList);
-			}
-		}
-		//tostring
-		for(Map.Entry<String, ArrayList<String>> stringArrayListEntry : clusters.entrySet())
-		{
-			System.out.println("====="+ stringArrayListEntry.getKey() +"=======");
-			for(String val: stringArrayListEntry.getValue())
-			{
-				System.out.println(String.format("\"%s\", \"%s\"", val, stringArrayListEntry.getKey()));
-			}
-		}
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ConfigParameters.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ConfigParameters.java
deleted file mode 100644
index 740b89ffa..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ConfigParameters.java
+++ /dev/null
@@ -1,76 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.Research;
-
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.util.Properties;
-
-public class ConfigParameters {
-	public static int debug = 0;
-	Properties properties = new Properties();
-	String res = "";
-
-	public ConfigParameters() {
-	}
-
-	public void initeParameters() {
-		// load property file and initialize the parameters;
-		try {
-			// load a properties file
-			properties.load(new FileInputStream(
-					"./src/main/config/transformation.properties"));
-			// get the property value and print it out
-			// Segment.cxtsize_limit =
-			// Integer.parseInt(properties.getProperty("cxt_size").trim());
-			// Template.temp_limit =
-			// Integer.parseInt(properties.getProperty("temp_cap").trim());
-			// Traces.time_limit =
-			// Integer.parseInt(properties.getProperty("time_limit").trim());
-			// ProgSynthesis.time_limit =
-			// Integer.parseInt(properties.getProperty("time_limit").trim());
-			// Segment.time_limit =
-			// Integer.parseInt(properties.getProperty("time_limit").trim());
-			// Section.time_limit =
-			// Integer.parseInt(properties.getProperty("time_limit").trim());
-			// properties.getProperty("iter_end");
-			// ExampleSelection.way =
-			// Integer.parseInt(properties.getProperty("exmp_sel").trim());
-			debug = Integer.parseInt(properties.getProperty("debug").trim());
-			// Template.supermode =
-			// Integer.parseInt(properties.getProperty("supermode").trim());
-			// Section.supermode =
-			// Integer.parseInt(properties.getProperty("supermode").trim());
-			// Position.fixedlength =
-			// Integer.parseInt(properties.getProperty("fixedlength").trim());
-			// res =
-			// String.format("cxt_limit:%d temp_limit: %d, time_limit:%d, exp_sel:%d, supermode:%d,fixedlength:%d\n",Segment.cxtsize_limit,Template.temp_limit,Traces.time_limit,ExampleSelection.way,Template.supermode,Position.fixedlength);
-
-		} catch (IOException ex) {
-			return;
-		}
-	}
-
-	public String getString() {
-		return res;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ConstrainedAlignment.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ConstrainedAlignment.java
deleted file mode 100644
index 18a1d2877..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/ConstrainedAlignment.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package edu.isi.karma.cleaning.Research;
-
-import java.util.Vector;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import edu.isi.karma.cleaning.TNode;
-
-public class ConstrainedAlignment {
-	public Vector<Vector<TNode>> olist;
-	public Vector<Vector<TNode>> tlist;
-	public int expnum;
-
-	public ConstrainedAlignment() {
-
-	}
-
-	public Vector<Integer> findAll(TNode t, Vector<TNode> x) {
-		return null;
-	}
-
-	// inserted same token
-	public void traverse() {
-		// inite
-		Vector<Integer> spos = new Vector<Integer>();
-		for (int i = 0; i < expnum; i++) {
-			spos.add(0);
-		}
-		int[] iters = new int[expnum];
-		for (int i = 0; i < iters.length; i++) {
-			iters[i] = 0;
-		}
-		for (int i = 0; i < expnum; i++) {
-
-		}
-
-	}
-}
-
-class LatentState {
-
-	private static Logger logger = LoggerFactory.getLogger(LatentState.class);
-	static final int SEG = 1;// a segement state
-	static final int UND = 2;
-	static final int ANC = 3;// a anchor state
-	public int StateType;
-	public LatentState nextState;
-	public Vector<int[]> segments;
-
-	public LatentState(Vector<Integer> spos) {
-		this.StateType = LatentState.UND;
-		segments = new Vector<int[]>();
-		if (segments.size() != spos.size()) {
-			logger.error("Length different");
-			return;
-		}
-		for (int i = 0; i < spos.size(); i++) {
-			int p = spos.get(i);
-			int[] a = { p, -1 };
-			segments.add(a);
-		}
-	}
-
-	public void setStart(int s, int lindex) {
-		segments.get(lindex)[0] = s;
-	}
-
-	public void setEnd(int e, int lindex) {
-		segments.get(lindex)[1] = e;
-	}
-
-	public void createNewState(Vector<Integer> spos) {
-		LatentState nState = new LatentState(spos);
-		this.nextState = nState;
-	}
-
-	public void settype(int type) {
-
-	}
-}
\ No newline at end of file
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/DataCollection.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/DataCollection.java
deleted file mode 100644
index 45635be4e..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/DataCollection.java
+++ /dev/null
@@ -1,162 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.Research;
-
-import java.text.DateFormat;
-import java.text.SimpleDateFormat;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.MyLogger;
-
-public class DataCollection {
-	public static String config = "";
-	Vector<FileStat> fstates = new Vector<FileStat>();
-	public HashSet<String> succeededFiles = new HashSet<String>();
-	@SuppressWarnings("unused")
-	public DataCollection() {
-		MyLogger myLogger = new MyLogger();
-	}
-	public void addSucceededFile(String fname)
-	{
-		if( ! succeededFiles.contains(fname));
-			succeededFiles.add(fname);
-	}
-	public void addEntry(FileStat a)
-	{
-		fstates.add(a);
-	}
-
-	public String getDate() {
-		DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
-		Date date = new Date();
-		return dateFormat.format(date);
-	}
-
-	public void print() {
-		MyLogger.logsth("============Detail Information==========="
-				+ this.getDate() + "\n");
-		MyLogger.logsth(DataCollection.config + "\n");
-		for (FileStat f : fstates) {
-			MyLogger.logsth("" + f.toString());
-		}
-	}
-
-	public void print1() {
-		// int[] 0 avg total learn time, 1 avg learn time, 2 t gen time, 3 avg
-		// gen time
-		// 4 tot exec time 5 ave exec time
-		// 6 exp num 7 tot ruleNo 8 checkedrows
-		HashMap<String, Double[]> stats = new HashMap<String, Double[]>();
-		for (FileStat f : fstates) {
-			String fname = f.fileNameString;
-			if (stats.containsKey(fname)) {
-				stats.get(fname)[0] += f.learnTime;
-				stats.get(fname)[2] += f.genTime;
-				stats.get(fname)[4] += f.execTime;
-				if (stats.get(fname)[6] < f.exp_cnt)
-					stats.get(fname)[6] = (double) f.exp_cnt;
-				
-				stats.get(fname)[7] += f.constraintNo;
-				stats.get(fname)[8] += f.checkedrow;
-				stats.get(fname)[9] += f.qRecordNum;
-				stats.get(fname)[10] += f.clfacc ;
-				stats.get(fname)[11] = (double) f.parNum;
-			} else {
-				Double[] x = { (double) f.learnTime, 0.0, (double) f.genTime,
-						0.0, (double) f.execTime, 0.0, (double) f.exp_cnt,
-						(double) f.constraintNo, (double) f.checkedrow,
-						(double) f.qRecordNum, (double) f.clfacc,(double)f.parNum };
-				stats.put(fname, x);
-			}
-		}
-		// get average value
-		MyLogger.logsth("============Summary Information===========\n"
-				+ this.getDate() + "\n");
-		MyLogger.logsth(DataCollection.config + "\n");
-		for (Map.Entry<String, Double[]> stringEntry : stats.entrySet()) {
-			Double[] value = stringEntry.getValue();
-			Double cnt = value[6];
-			value[1] = value[0] * 1.0 / cnt;
-			value[3] = value[2] * 1.0 / cnt;
-			value[5] = value[4] * 1.0 / cnt;
-			value[10] = value[10]*1.0 / cnt;
-			// long the final stats
-			String lineString = "";
-			if(this.succeededFiles.contains(stringEntry.getKey()))
-				lineString = String.format("%s,T_learn,%f,avg_learn,%f,T_gen,%f,avg_gen,%f,T_exec,%f,avg_exec,%f,exp,%f,constraint,%f,clfacc,%f, parNum, %f\n", stringEntry.getKey(),value[0],value[1],value[2],value[3],value[4],value[5],value[6],value[7],value[10],value[11]);
-			else {
-				lineString = String.format("%s_failed,T_learn,%f,avg_learn,%f,T_gen,%f,avg_gen,%f,T_exec,%f,avg_exec,%f,exp,%f,constraint,%f,clfacc,%f,parNum,%f\n", stringEntry.getKey(),value[0],value[1],value[2],value[3],value[4],value[5],value[6],value[7],value[10],value[11]);
-			}
-			MyLogger.logsth(lineString);
-		}
-	}
-}
-
-class FileStat {
-	public String fileNameString = "";
-	public long learnTime = 0; // time used in constructing the version space
-	public long genTime = 0; // time used to generate the first consistent rule
-	public long execTime = 0; // time used in applying the rule
-	public int exp_cnt = 0; // number of examples
-	public String examples = ""; // all the examples
-	public String program = "";// the correct program
-	public long constraintNo = 0; // order of the first consistent rule
-	public long checkedrow = 0;// number of checked rows
-	public long qRecordNum = 0;
-	public long parNum = 0;
-	public double resacc = 0.0;
-	public double clfacc = 0.0;
-
-	public FileStat(String fname, long l, long g, long e, int exp,
-			Vector<String[]> exps, long constraintNo, long checkedrow,
-			long qRecordNum, long parNum, String program,double resacc,double clfacc) {
-		this.fileNameString = fname;
-		this.learnTime = l;
-		this.genTime = g;
-		this.execTime = e;
-		this.exp_cnt = exp;
-		this.constraintNo = constraintNo;
-		//this.checkedrow = checkedrow;
-		//this.qRecordNum = qRecordNum;
-		this.parNum = parNum;
-		examples += "\n";
-		for (String[] p : exps) {
-			String s = p[0] + "\t" + p[1] + "\n";
-			examples += s;
-		}
-		this.program = program;
-		this.resacc = resacc;
-		this.clfacc = clfacc;
-	}
-	public String toString()
-	{
-		String resString = String.format("%s,LearnTime,%d,GenTime,%d,ExecTime,%d,Exp_cnt,%d,Constr_cnt,%d,ParitionNum,%d,Res_acc,%f,Clf_acc,%f", this.fileNameString,this.learnTime,this.genTime,this.execTime,this.exp_cnt,this.constraintNo,this.parNum,this.resacc, this.clfacc);
-		resString += this.examples;
-		resString += this.program + "\n";
-		return resString;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/MultiIndex.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/MultiIndex.java
deleted file mode 100644
index 7f91bbad4..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/MultiIndex.java
+++ /dev/null
@@ -1,143 +0,0 @@
-package edu.isi.karma.cleaning.Research;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-
-public class MultiIndex {
-	public String value = "";
-	public ArrayList<MultiIndex> children = new ArrayList<MultiIndex>();
-	public MultiIndex()
-	{
-		
-	}
-	public void add(List<String> keys, String v)
-	{
-		if(keys.size() <= 0)
-		{
-			MultiIndex m = new MultiIndex();
-			m.value = v;
-			this.children.add(m);
-			return;
-		}
-		else
-		{
-			String key = keys.get(0);
-			List<String> rkeys = keys.subList(1, keys.size());
-			//check if any key is the same
-			boolean isfind = false;
-			for(MultiIndex m: children)
-			{
-				if(m.value.compareTo(key)==0)
-				{
-					m.add(rkeys, v);
-					isfind = true;
-				}
-			}
-			if(!isfind)
-			{
-				MultiIndex multiIndex = new MultiIndex();
-				multiIndex.value = key;
-				multiIndex.add(rkeys, v);
-				this.children.add(multiIndex);
-			}
-		}
-	}
-	public void delete(ArrayList<String> keys)
-	{
-		
-	}
-	public List<String> get(List<String> keys)
-	{
-		//get to the root node
-		MultiIndex rootNode = null;
-		MultiIndex tmpNode = this;
-		for(String k:keys)
-		{
-			boolean isfind = false;
-			for(MultiIndex m:tmpNode.children)
-			{
-				if(m.value == k)
-				{
-					tmpNode = m;
-					isfind = true;
-					break;
-				}
-			}
-			if(isfind)
-			{
-				rootNode = tmpNode;
-			}
-		}
-		ArrayList<String> res = new ArrayList<String>();
-		if(rootNode == null)
-			return res;
-		//retrive all the leaf ndoe of the root node
-		getAllLeaf(rootNode, res);
-		return res;
-	}
-	public void getAllLeaf(MultiIndex m, ArrayList<String> res)
-	{
-		if(m.children.isEmpty())
-		{
-			res.add(m.value);
-		}
-		else
-		{
-			for(MultiIndex iter: m.children)
-			{
-				getAllLeaf(iter, res);
-			}
-		}
-	}
-	public String toString()
-	{
-		String res = "";
-		res += value;
-		res+= "(";
-		for(MultiIndex i:children)
-		{
-			res+= " "+i.value;
-		}
-		res += ")";
-		return res;
-	}
-	public List<String> getPathes()
-	{
-		String s = "";
-		ArrayList<String> ps = new ArrayList<String>();
-		this.travers(s, this, ps);
-		return ps;
-	}
-	public void travers(String s, MultiIndex node, ArrayList<String> paths)
-	{
-		if(node.children.isEmpty())
-		{
-			String x = s+","+node.value;
-			paths.add(x);
-		}
-		else
-		{
-			for(MultiIndex m: node.children)
-			{
-				String xString = s+","+node.value;
-				node.travers(xString, m, paths);
-			}
-		}
-	}
-	public void testMultiIndex()
-	{
-		String[] keys1 = {"e1", "segmentloopsegment", "1"};
-		String[] keys2 = {"e1", "segmentloopsegment", "2"};
-		String[] keys3 = {"e2", "segmentloopsegment", "2"};
-		String[] keys4 = {"e3", "segmentloopsegment", "1"};
-		MultiIndex multiIndex = new MultiIndex();
-		multiIndex.add(Arrays.asList(keys1), "p1");
-		multiIndex.add(Arrays.asList(keys2), "p2");
-		multiIndex.add(Arrays.asList(keys3), "p1");
-		multiIndex.add(Arrays.asList(keys4), "p1");
-		System.out.println(""+multiIndex.get(Arrays.asList(keys1)));		
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/MultipleStringAlign.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/MultipleStringAlign.java
deleted file mode 100644
index d49fd539a..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/MultipleStringAlign.java
+++ /dev/null
@@ -1,179 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.Research;
-
-import java.util.Vector;
-
-public class MultipleStringAlign {
-	public MultipleStringAlign(Vector<String[]> strs) {
-
-	}
-
-	// generate all the possible next state in DFA
-	public void generateChildren(ANode a) {
-		Vector<Vector<int[]>> multiSeqMapping = new Vector<Vector<int[]>>();
-		Vector<Long> indexes = new Vector<Long>();
-		for (int i = 0; i < a.exps.size(); i++) {
-			String[] example = a.exps.get(i);
-			int pos = a.orgPos.get(i);
-			Vector<int[]> mappings = findNext(example[0], example[1], pos);
-			// tarpos, orgstartpos, orgendpos
-			Vector<int[]> nmapping = new Vector<int[]>();
-			for (int[] elem : mappings) {
-				int[] el = { pos, elem[0], elem[1] };
-				nmapping.add(el);
-			}
-			indexes.add((long) nmapping.size());
-			multiSeqMapping.add(nmapping);
-		}
-		// generate combinations
-		Vector<Vector<Integer>> configs = new Vector<Vector<Integer>>();
-		getCrossIndex(indexes, configs);
-		// using a combination to generate the ANode
-		for (int i = 0; i < configs.size(); i++) {
-			Vector<Integer> poses = configs.get(i);
-			Vector<Integer> orgPos = new Vector<Integer>();
-			Vector<Integer> tarPos = new Vector<Integer>();
-			Vector<Integer> length = new Vector<Integer>();
-			for (int j = 0; j < poses.size(); j++) {
-				int[] e = multiSeqMapping.get(j).get(poses.get(j));
-				orgPos.add(e[1]);
-				tarPos.add(e[0]);
-				length.add(e[2] - e[1]);
-			}
-			ANode aNode = new ANode(orgPos, tarPos, length, a.exps);
-			if (aNode.isvalid())
-				a.addChild(aNode);
-		}
-	}
-
-	// iteratively generate the combinations
-	public void getCrossIndex(Vector<Long> indexs,
-			Vector<Vector<Integer>> configs) {
-		int k = indexs.size();
-		int[] com = new int[k];
-		for (int i = 0; i < k; i++)
-			com[i] = 0;
-		while (com[k - 1] < indexs.get(k - 1)) {
-			Vector<Integer> res = new Vector<Integer>();
-			for (int i = 0; i < k; i++) {
-				res.add(com[i]);
-			}
-			configs.add(res);
-			int t = k - 1;
-			while (t != 0 && com[t] == indexs.get(t) - 1)
-				t--;
-			com[t]++;
-			if (t == 0 && com[t] >= indexs.get(0)) {
-				break;
-			}
-			for (int i = t + 1; i < k; i++)
-				com[i] = 0;
-		}
-	}
-
-	// {[orgstartPos, orgendPos ], ...}
-	@SuppressWarnings("unused")
-	public Vector<int[]> findNext(String org, String tar, int pos) {
-		Vector<int[]> segs = new Vector<int[]>();
-		if (tar.length() == 0) {
-			int[] elem = { -1, 0 };
-			segs.add(elem);
-			return segs;
-		}
-		if (pos >= tar.length())
-			return segs;
-		String tmp = "";
-		tmp += String.valueOf(tar.charAt(pos));
-		int q = org.indexOf(tmp);
-		if (q == -1) {
-			int cnt = pos;
-			String tvec = "";
-			while (q == -1) {
-				tvec += String.valueOf(tar.charAt(cnt));
-				cnt++;
-				tmp = "";
-				if (cnt >= tar.length())
-					break;
-				tmp += String.valueOf(tar.charAt(cnt));
-				q = org.indexOf(tmp);
-			}
-			int[] elem = { -1, cnt - pos };
-			segs.add(elem);
-			return segs;
-		}
-		for (int i = pos; i < tar.length(); i++) {
-			String tvec = "";
-			for (int j = pos; j <= i; j++) {
-				tvec += String.valueOf(tar.charAt(j));
-			}
-			Vector<Integer> mappings = new Vector<Integer>();
-			int r = org.indexOf(tvec);
-			while (r != -1) {
-				mappings.add(r);
-				r = org.indexOf(tvec, r + 1);
-			}
-			if (mappings.size() > 1) {
-				Vector<int[]> corrm = new Vector<int[]>();
-				for (int t : mappings) {
-					int[] m = { t, t + tvec.length() };
-					corrm.add(m);
-				}
-				// create a segment now
-				segs.addAll(corrm);
-				continue;
-			} else if (mappings.size() == 1) {
-				Vector<int[]> corrm = new Vector<int[]>();
-				// creating based on whether can find segment with one more
-				// token
-				if (i >= (tar.length() - 1)) {
-					int[] m = { mappings.get(0),
-							mappings.get(0) + tvec.length() };
-					corrm.add(m);
-					segs.addAll(corrm);
-				} else {
-					tvec += String.valueOf(tar.charAt(i + 1));
-					int p = org.indexOf(tvec, 0);
-					String repToken = "";
-					repToken += String.valueOf(tar.charAt(i + 1));
-					int rind = 0;
-					int tokenCnt = 0;
-					while ((rind = org.indexOf(repToken, rind)) != -1) {
-						rind++;
-						tokenCnt++;
-					}
-					if (p == -1 || tokenCnt > 1) {
-						int[] m = { mappings.get(0),
-								mappings.get(0) + tvec.length() - 1 };
-						corrm.add(m);
-						segs.addAll(corrm);
-					} else {
-						continue;
-					}
-				}
-			} else {
-				break;
-			}
-		}
-		return segs;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/Prober.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/Prober.java
deleted file mode 100644
index a9efde914..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/Prober.java
+++ /dev/null
@@ -1,82 +0,0 @@
-package edu.isi.karma.cleaning.Research;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.Partition;
-import edu.isi.karma.cleaning.Patcher;
-import edu.isi.karma.cleaning.ProgramRule;
-import edu.isi.karma.cleaning.TNode;
-import edu.isi.karma.cleaning.UtilTools;
-
-public class Prober {
-	public static ArrayList<String> track1 = new ArrayList<String>();
-	public static String target;
-	public static long adaptedProg = 0;
-	public static MultiIndex records = new MultiIndex();
-	public static String PartitionDisplay1(Vector<Partition> vp) {
-		String res = "";
-		for (Partition p : vp) {
-			res += "Partition: " + p.label + "\n";
-			for (int i = 0; i < p.tarNodes.size(); i++) {
-				String line = UtilTools.print(p.orgNodes.get(i)) + "|"
-						+ UtilTools.print(p.tarNodes.get(i));
-				res += line + "\n";
-			}
-		}
-		return res;
-	}
-	public static void trackProgram(Vector<Partition> pars, ProgramRule r)
-	{
-		for(Partition p: pars)
-		{
-			String rule = r.getStringRule(p.label);
-			for(Vector<TNode> nodes: p.orgNodes)
-			{
-				String exp = UtilTools.print(nodes);
-				String[] keys = {exp};
-				records.add(Arrays.asList(keys), rule);
-			}
-		}
-	}
-	public static void displayProgram()
-	{
-		List<String> pList = records.getPathes();
-		for(String line: pList)
-		{
-			System.out.println(""+line);
-		}
-	}
-	public static void tracePatchers(String ptree,ArrayList<Patcher> errNodes, ArrayList<String[]> iexps, String[] exp, boolean valid,HashMap<String, String> dics)
-	{
-		System.out.println("========Programs to fix==========");
-		System.out.println("Program: "+ptree);
-		String res = "";
-		for(String[] x: iexps)
-		{
-			res += String.format("%s   %s\n", x[0], x[1]);
-		}
-		
-		for(Map.Entry<String, String> stringStringEntry : dics.entrySet())
-		{
-			System.out.println("dict: "+String.format("%s, %s", stringStringEntry.getKey(), stringStringEntry.getValue()));
-		}
-		for(Patcher p:errNodes)
-		{
-			System.out.println("old Exp: \n"+res);
-			System.out.println("new Exp: "+ String.format("%s  %s", exp[0],exp[1]));
-			System.out.println("old subs: "+p.programNodes);
-			System.out.println("new subs: "+p.replaceNodes);
-			if(!valid)
-				System.out.println("Unsuccessful adaptation");
-			else{
-				adaptedProg ++;
-			}
-		}
-		System.out.println("=================================");
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/RecordDistiller.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/RecordDistiller.java
deleted file mode 100644
index 61f224c7f..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/RecordDistiller.java
+++ /dev/null
@@ -1,237 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.Research;
-
-import java.io.File;
-import java.io.FileReader;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Vector;
-
-import au.com.bytecode.opencsv.CSVReader;
-import edu.isi.karma.cleaning.Ruler;
-import edu.isi.karma.cleaning.TNode;
-
-public class RecordDistiller {
-	// {anchor:{"Id": , "Count": , "LefContext":[], "RigContext":[]}
-	public static int cxt_limit = 3;
-	public int totalnumber = 0;
-	public HashMap<String, Anchor> anchors = new HashMap<String, Anchor>();
-
-	public void readRecord(String ID, Vector<TNode> record) {
-		HashMap<String, Integer> curIndices = new HashMap<String, Integer>();
-		for (int i = 1; i < record.size() - 1; i++) // skip the start and end
-													// token
-		{
-			TNode t = record.get(i);
-			String type = t.getType();
-			String anchor = type;
-			if (curIndices.containsKey(type)) {
-				int cnt = curIndices.get(type);
-				curIndices.put(type, cnt + 1);
-				anchor += String.valueOf(cnt);
-			} else {
-				curIndices.put(type, 0);
-				anchor += "0";
-			}
-			// get left and right context
-			String lcxt = "";
-			String rcxt = "";
-			for (int j = i; j < i + RecordDistiller.cxt_limit
-					&& j < record.size(); j++) {
-				rcxt += record.get(j).getType();
-			}
-			for (int j = i; j >= 0 && j > i - cxt_limit; j--) {
-				lcxt += record.get(j).getType();
-			}
-			// update the anchor repository
-			if (this.anchors.containsKey(anchor)) {
-				Anchor an = this.anchors.get(anchor);
-				an.IDs.add(ID);
-				an.count += 1;
-				an.lefCxt.put(ID, lcxt);
-				an.rigCxt.put(ID, rcxt);
-			} else {
-				Vector<String> Ids = new Vector<String>();
-				Ids.add(ID);
-				HashMap<String, String> vlcxt = new HashMap<String, String>();
-				vlcxt.put(ID, lcxt);
-				HashMap<String, String> vrcxt = new HashMap<String, String>();
-				vrcxt.put(ID, rcxt);
-				Anchor nan = new Anchor(anchor, Ids, 1, vlcxt, vrcxt);
-				anchors.put(anchor, nan);
-			}
-		}
-	}
-
-	// identify the anchor tokens
-	public void idenAnchor(int total) {
-		Vector<String> dels = new Vector<String>();
-		for (Map.Entry<String, Anchor> stringAnchorEntry : anchors.entrySet()) {
-			int count = stringAnchorEntry.getValue().count;
-			// if an anchor appears in more 10% records, it's a valid anchor
-			if (count * 1.0 / total < 0.1) {
-				dels.add(stringAnchorEntry.getKey());
-			}
-		}
-		for (String s : dels) {
-			anchors.remove(s);
-		}
-	}
-
-	// identify the representative records of one anchor.
-	// minimal set
-	public HashSet<String> idenAnchorRecords(String anchor) {
-		HashMap<String, Vector<String>> lcxt2ids = new HashMap<String, Vector<String>>();
-		HashMap<String, Vector<String>> rcxt2ids = new HashMap<String, Vector<String>>();
-		for (String Id : this.anchors.get(anchor).lefCxt.keySet()) {
-			String s = this.anchors.get(anchor).lefCxt.get(Id);
-			boolean isnew = true;
-			for (String elem : lcxt2ids.keySet()) {
-				if (elem.indexOf(s) == 0) {
-					s = elem;
-					isnew = false;
-				}
-			}
-			if (isnew) {
-				Vector<String> vs = new Vector<String>();
-				vs.add(Id);
-				lcxt2ids.put(s, vs);
-			} else {
-				lcxt2ids.get(s).add(Id);
-			}
-		}
-		for (String Id : this.anchors.get(anchor).rigCxt.keySet()) {
-			String s = this.anchors.get(anchor).rigCxt.get(Id);
-			boolean isnew = true;
-			for (String elem : rcxt2ids.keySet()) {
-				if (elem.indexOf(s) == 0) {
-					s = elem;
-					isnew = false;
-				}
-			}
-			if (isnew) {
-				Vector<String> vs = new Vector<String>();
-				vs.add(Id);
-				rcxt2ids.put(s, vs);
-			} else {
-				rcxt2ids.get(s).add(Id);
-			}
-		}
-		// generate candiate set
-		HashSet<String> result = new HashSet<String>();
-		for (Map.Entry<String, Vector<String>> stringVectorEntry : lcxt2ids.entrySet()) {
-			if (!stringVectorEntry.getValue().isEmpty()) {
-				String idString = stringVectorEntry.getValue().get(0);
-				if (!result.contains(idString)) {
-					result.add(idString);
-				}
-			}
-		}
-		for (Map.Entry<String, Vector<String>> stringVectorEntry : rcxt2ids.entrySet()) {
-			if (!stringVectorEntry.getValue().isEmpty()) {
-				String idString = stringVectorEntry.getValue().get(0);
-				if (!result.contains(idString)) {
-					result.add(idString);
-				}
-			}
-		}
-		return result;
-	}
-
-	// merge the record sets generated by each anchor
-	// return the final Record ID list
-	public HashSet<String> refineRecords() {
-		HashSet<String> ids = new HashSet<String>();
-		// find the union of the ids of all anchors
-		for (String anchor : this.anchors.keySet()) {
-			HashSet<String> set = this.idenAnchorRecords(anchor);
-			ids.addAll(set);
-		}
-		return ids;
-	}
-
-	public static void main(String[] args) {
-		String dirpath = "/Users/bowu/Research/testdata/TestSingleFile";
-		RecordDistiller distiller = new RecordDistiller();
-		File nf = new File(dirpath);
-		File[] allfiles = nf.listFiles();
-		for (File f : allfiles) {
-			try {
-				if (f.getName().indexOf(".csv") == (f.getName().length() - 4)) {
-					@SuppressWarnings("resource")
-					CSVReader cr = new CSVReader(new FileReader(f), ',', '"',
-							'\0');
-					String[] pair;
-					int id = 0;
-					HashMap<String, String> id2String = new HashMap<String, String>();
-					while ((pair = cr.readNext()) != null) {
-						if (pair == null || pair.length <= 1)
-							break;
-						Ruler ruler = new Ruler();
-						ruler.setNewInput(pair[0]);
-						distiller.readRecord(String.valueOf(id), ruler.vec);
-						id2String.put(String.valueOf(id), pair[0]);
-						id++;
-					}
-					distiller.idenAnchor(id2String.keySet().size());
-					HashSet<String> allids = distiller.refineRecords();
-					for (String xid : allids) {
-						System.out.println(id2String.get(xid));
-					}
-					double compressRate = (allids.size() * 1.0)
-							/ id2String.keySet().size();
-					for (String name : distiller.anchors.keySet()) {
-						System.out.println("Anchor: " + name);
-						for (String dString : distiller.anchors.get(name).IDs) {
-							System.out.print(" " + dString);
-						}
-						System.out.println("\n");
-					}
-					System.out.println(String.valueOf(compressRate));
-				}
-			} catch (Exception e) {
-				System.out.println("" + e.toString());
-			}
-		}
-	}
-}
-
-class Anchor {
-	public String name;
-	public Vector<String> IDs;
-	public int count;
-	// id 2 the left context
-	public HashMap<String, String> lefCxt = new HashMap<String, String>();
-	// id 2 the right context
-	public HashMap<String, String> rigCxt = new HashMap<String, String>();
-
-	public Anchor(String anchor, Vector<String> Ids, int count,
-			HashMap<String, String> lcxt, HashMap<String, String> rcxt) {
-		this.name = anchor;
-		this.IDs = Ids;
-		this.count = count;
-		this.lefCxt = lcxt;
-		this.rigCxt = rcxt;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/Test.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/Test.java
deleted file mode 100644
index e22363510..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/Test.java
+++ /dev/null
@@ -1,1084 +0,0 @@
-package edu.isi.karma.cleaning.Research;
-
-import java.io.File;
-import java.io.FileReader;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Vector;
-
-import au.com.bytecode.opencsv.CSVReader;
-import edu.isi.karma.cleaning.DataPreProcessor;
-import edu.isi.karma.cleaning.EmailNotification;
-import edu.isi.karma.cleaning.ExampleCluster;
-import edu.isi.karma.cleaning.ExampleCluster.method;
-import edu.isi.karma.cleaning.ExampleSelection;
-import edu.isi.karma.cleaning.GradientDecendOptimizer;
-import edu.isi.karma.cleaning.InterpreterType;
-import edu.isi.karma.cleaning.Messager;
-import edu.isi.karma.cleaning.ProgSynthesis;
-import edu.isi.karma.cleaning.ProgramRule;
-import edu.isi.karma.cleaning.UtilTools;
-import edu.isi.karma.webserver.ContextParametersRegistry;
-import edu.isi.karma.cleaning.features.RecordClassifier;
-
-public class Test {
-
-	public static String contextId = ContextParametersRegistry.getInstance().getDefault().getId();
-	// check whether it longest or shortest
-	public static boolean visible(HashMap<String, String[]> xHashMap, String Id) {
-		String[] pair = xHashMap.get(Id);
-		HashMap<String, String> tmp = new HashMap<String, String>();
-		try {
-			UtilTools.StringColorCode(pair[0], pair[1], tmp);
-		} catch (Exception e) {
-			tmp.put("Org", pair[0]);
-			tmp.put("Tar", "ERROR");
-			tmp.put("Orgdis", pair[0]);
-			tmp.put("Tardis", "ERROR");
-		}
-		String tar = tmp.get("Tar");
-		int length = tar.length();
-		boolean sequalBefore = false;
-		boolean lequalBefore = false;
-		boolean shortest = true;
-		boolean longest = true;
-		for (String[] elem : xHashMap.values()) {
-			HashMap<String, String> t = new HashMap<String, String>();
-			try {
-				UtilTools.StringColorCode(elem[0], elem[1], t);
-			} catch (Exception ex) {
-				tmp.put("Org", elem[0]);
-				tmp.put("Tar", "ERROR");
-				tmp.put("Orgdis", elem[0]);
-				tmp.put("Tardis", "ERROR");
-			}
-			String tres = tmp.get("Tar");
-			int newl = tres.length();
-			if (newl >= length) {
-				if (lequalBefore)
-					longest = false;
-				lequalBefore = true;
-			}
-			if (newl <= length) {
-				if (sequalBefore)
-					shortest = false;
-				sequalBefore = true;
-			}
-		}
-		return (shortest || longest);
-	}
-
-	public void parameterSelection(String dirpath) {
-		ArrayList<String> selectParams = new ArrayList<String>();
-		ArrayList<String> runningInfo = new ArrayList<String>();
-		File nf = new File(dirpath);
-		File[] allfiles = nf.listFiles();
-		double[] r = { 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 1.8 };
-		// statistics
-		// list all the csv file under the dir
-		for (File f : allfiles) {
-			if (f.getName().indexOf(".csv") != -1
-					&& f.getName().indexOf(".csv") == (f.getName().length() - 4)) {
-				double minS = Double.MAX_VALUE;
-				double bestRatio = 0.0;
-				for (int i = 0; i < r.length; i++) {
-					GradientDecendOptimizer.ratio = r[i];
-					double s = transform(f);
-					if (s <= minS) {
-						minS = s;
-						bestRatio = r[i];
-
-					}
-					String runinfo = String.format("%s: ratio: %f, value:%f\n",
-							f.getName(), r[i], s);
-					runningInfo.add(runinfo);
-				}
-				String parms = String.format("%s: ratio: %f, BestVal:%f",
-						f.getName(), bestRatio, minS);
-				selectParams.add(parms);
-			}
-		}
-		System.out.println("" + runningInfo.toString());
-		System.out.println(selectParams.toString());
-	}
-
-	public double transform(File f) {
-		double measure = Double.MAX_VALUE;
-		try {
-			Vector<String[]> examples = new Vector<String[]>();
-			Vector<String[]> addExamples = new Vector<String[]>();
-			Vector<String[]> entries = new Vector<String[]>();
-			if (f.getName().indexOf(".csv") != -1
-					&& f.getName().indexOf(".csv") == (f.getName().length() - 4)) {
-				// MyLogger.logsth("========"+f.getName()+"============\n");
-				HashMap<String, String[]> xHashMap = new HashMap<String, String[]>();
-				@SuppressWarnings("resource")
-				CSVReader cr = new CSVReader(new FileReader(f), ',', '"', '\0');
-				String[] pair;
-				int index = 0;
-				Vector<String> vtmp = new Vector<String>();
-				while ((pair = cr.readNext()) != null) {
-					if (pair == null || pair.length <= 1)
-						break;
-					entries.add(pair);
-					vtmp.add(pair[0]);
-					String[] line = { pair[0], pair[1], "", "", "wrong" }; // org,
-																			// tar,
-																			// tarcode,
-																			// label
-					xHashMap.put(index + "", line);
-					index++;
-				}
-				DataPreProcessor dpp = new DataPreProcessor(vtmp);
-				dpp.run();
-				Messager msger = new Messager();
-				Vector<Vector<String[]>> constraints = new Vector<Vector<String[]>>();
-				if (entries.size() <= 1)
-					return Double.MAX_VALUE;
-				ExampleSelection expsel = new ExampleSelection();
-				ExampleSelection.firsttime = true;
-				expsel.inite(xHashMap, null);
-				int target = Integer.parseInt(expsel.Choose());
-				String[] mt = { "<_START>" + entries.get(target)[0] + "<_END>",
-						entries.get(target)[1] };
-				examples.add(mt);
-				ExampleSelection.firsttime = false;
-				// accuracy record code
-				ArrayList<double[]> accArrayList = new ArrayList<double[]>();
-				while (true) // repeat as no incorrect answer appears.
-				{
-					if (examples.size() == 4) {
-						System.out.println("Hello World");
-					}
-					long checknumber = 1;
-					long iterAfterNoFatalError = 0;
-					long isvisible = 0;
-					HashMap<String, Vector<String[]>> expFeData = new HashMap<String, Vector<String[]>>();
-					Vector<String> resultString = new Vector<String>();
-					xHashMap = new HashMap<String, String[]>();
-					ProgSynthesis psProgSynthesis = new ProgSynthesis(contextId);
-					HashMap<String, String> unlabeledData = new HashMap<String, String>();
-					for (int i = 0; i < vtmp.size(); i++) {
-						unlabeledData.put("" + i, vtmp.get(i));
-					}
-					psProgSynthesis.inite(examples, dpp, msger);
-					Vector<ProgramRule> pls = new Vector<ProgramRule>();
-					Collection<ProgramRule> ps = psProgSynthesis.run_main();
-					// collect history contraints
-					msger.updateCM_Constr(psProgSynthesis.partiCluster
-							.getConstraints());
-					msger.updateWeights(psProgSynthesis.partiCluster.weights);
-					// constraints.addAll();
-					if (ps != null) {
-						pls.addAll(ps);
-					} else {
-						System.out.println("Cannot find any rule");
-					}
-					String[] wexam = null;
-					if (pls.size() == 0)
-						break;
-					long t1 = System.currentTimeMillis();
-					int ErrorCnt = 0;
-					int clf_acc_error_cnt = 0;
-					int clf_acc_total_cnt = 0;
-					HashMap<String, HashMap<String, String>> uData = new HashMap<String, HashMap<String, String>>();
-					for (int i = 0; i < pls.size(); i++) {
-						ProgramRule script = pls.get(i);
-						// System.out.println(script);
-						String res = "";
-						for (int j = 0; j < entries.size(); j++) {
-							InterpreterType worker = script
-									.getRuleForValue(entries.get(j)[0]);
-							String classlabel = script.getClassForValue(entries
-									.get(j)[0]);
-							String tmps = worker
-									.execute_debug(entries.get(j)[0]);
-							HashMap<String, String> dict = new HashMap<String, String>();
-							dict.put("class", classlabel);
-							UtilTools.StringColorCode(entries.get(j)[0], tmps,
-									dict);
-							String s = dict.get("Tar");
-							if (Test.isExample(entries.get(j)[0], examples)) {
-								s = entries.get(j)[1];
-							}
-							res += s + "\n";
-							if (ConfigParameters.debug == 1) {
-								String indicator = "wrong";
-								if (s.compareTo(entries.get(j)[1]) == 0)
-									indicator = "correct";
-								if (!uData.containsKey(j + ""))
-									uData.put(j + "", dict);
-							}
-							// classifier accuracy
-
-							boolean existres = false;
-							for (InterpreterType w : script.rules.values()) {
-								String xtmp = w.execute(entries.get(j)[0]);
-								if (xtmp != null
-										&& xtmp.length() > 0
-										&& xtmp.compareTo(entries.get(j)[1]) == 0) {
-									existres = true;
-									break;
-								}
-							}
-							if (existres) {
-								clf_acc_total_cnt++;
-								if (s == null || s.length() == 0
-										|| s.compareTo(entries.get(j)[1]) != 0) {
-									clf_acc_error_cnt++;
-								}
-							}
-							//
-							if (s == null || s.length() == 0) {
-								String[] ts = {
-										"<_START>" + entries.get(j)[0]
-												+ "<_END>", "", tmps,
-										classlabel, "wrong" };
-								xHashMap.put(j + "", ts);
-								wexam = ts;
-								checknumber++;
-							}
-							boolean isfind = false;
-							for (String[] exppair : examples) {
-								if (exppair[0].compareTo("<_START>"
-										+ dict.get("Org") + "<_END>") == 0) {
-									String[] exp = { dict.get("Org"), tmps };
-									if (!expFeData.containsKey(classlabel)) {
-										Vector<String[]> vstr = new Vector<String[]>();
-										vstr.add(exp);
-										expFeData.put(classlabel, vstr);
-									} else {
-										expFeData.get(classlabel).add(exp);
-									}
-									isfind = true;
-								}
-							}
-							// update positive traing data with user
-							// specification
-							for (String[] tmpx : addExamples) {
-								if (tmpx[0].compareTo(dict.get("Org")) == 0
-										&& tmpx[1].compareTo(dict.get("Tar")) == 0) {
-									String[] exp = { dict.get("Org"), tmps };
-									if (!expFeData.containsKey(classlabel)) {
-										Vector<String[]> vstr = new Vector<String[]>();
-										vstr.add(exp);
-										expFeData.put(classlabel, vstr);
-									} else {
-										expFeData.get(classlabel).add(exp);
-									}
-									isfind = true;
-								}
-							}
-							if (!isfind) {
-								String[] ts = {
-										"<_START>" + entries.get(j)[0]
-												+ "<_END>", s, tmps,
-										classlabel, "right" };
-								if (s.compareTo(entries.get(j)[1]) != 0) {
-									ErrorCnt++;
-									wexam = ts;
-									ts[4] = "wrong";
-								}
-								xHashMap.put(j + "", ts);
-							}
-						}
-
-						if (wexam == null
-								|| (entries.size() - ErrorCnt) * 1.0
-										/ entries.size() == 1.0) {
-							wexam = null;
-							break;
-						}
-						resultString.add(res);
-					}
-					double resultacc = (entries.size() - ErrorCnt) * 1.0
-							/ entries.size();
-					double clf_acc = 1 - clf_acc_error_cnt * 1.0
-							/ clf_acc_total_cnt;
-					double[] accarray = { resultacc, clf_acc };
-					// use uData to refiner the result
-					System.out.println("" + psProgSynthesis.myprog.toString());
-					System.out.println(pls.get(0).toString());
-					// cRefiner.clusterUdata();
-					long t2 = System.currentTimeMillis();
-
-					if (wexam != null) {
-						String[] wexp = new String[2];
-						while (true) {
-							expsel = new ExampleSelection();
-							expsel.inite(xHashMap, expFeData);
-							int e = Integer.parseInt(expsel.Choose());
-							// /
-							System.out.println("Recommand Example: "
-									+ Arrays.toString(xHashMap.get("" + e)));
-							// /
-							if (xHashMap.get("" + e)[4].compareTo("right") != 0) {
-								wexp[0] = "<_START>" + entries.get(e)[0]
-										+ "<_END>";
-								wexp[1] = entries.get(e)[1];
-								if (expsel.isDetectingQuestionableRecord) {
-									iterAfterNoFatalError++;
-									// check whether this record is has the
-									// longest or shortest result
-									Boolean v = visible(xHashMap, "" + e);
-									if (v) {
-										isvisible += 1;
-									}
-								}
-								break;
-							} else {
-								// update positive training data
-								addExamples.add(entries.get(e));
-								// update the rest dataset
-								xHashMap.remove("" + e);
-							}
-							checknumber++;
-						}
-
-						examples.add(wexp);
-
-					} else {
-						measure = examples.size();
-						break;
-					}
-				}
-
-			}
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-		return measure;
-	}
-	public static String test_seq(ArrayList<String[]> exps) {
-		String timeres = "";
-		HashMap<String, String[]> xHashMap = new HashMap<String, String[]>();
-		int index = 0;
-		Vector<String> vtmp = new Vector<String>();
-		Vector<String[]> examples = new Vector<String[]>();
-		for (String[] pair : exps) {
-			if (pair == null || pair.length <= 1)
-				break;
-			String[] line = { pair[0], pair[1], "", "", "wrong" };
-			vtmp.add(pair[0]);
-			xHashMap.put(index + "", line);
-			index++;
-		}
-		DataPreProcessor dpp = new DataPreProcessor(vtmp);
-		dpp.run();
-		Messager msger = new Messager();
-		Vector<Vector<String[]>> constraints = new Vector<Vector<String[]>>();
-		ArrayList<double[]> accArrayList = new ArrayList<double[]>();
-		int i = 0;
-		while (i<exps.size()) // repeat as no incorrect answer appears.
-		{
-			String[] tmt = { "<_START>" + exps.get(i)[0] + "<_END>", exps.get(i)[1] };
-			examples.add(tmt);
-			xHashMap = new HashMap<String, String[]>();
-			ProgSynthesis psProgSynthesis = new ProgSynthesis(contextId);
-			psProgSynthesis.inite(examples, dpp, msger);
-			Vector<ProgramRule> pls = new Vector<ProgramRule>();
-			long t1 = System.currentTimeMillis();
-			Collection<ProgramRule> ps = psProgSynthesis.run_main();
-			long span = System.currentTimeMillis()-t1;
-			timeres += span+",";
-			// collect history contraints
-			msger.updateCM_Constr(psProgSynthesis.partiCluster.getConstraints());
-			msger.updateWeights(psProgSynthesis.partiCluster.weights);
-			i++;
-			// constraints.addAll();
-			if (ps != null) {
-				pls.addAll(ps);
-				System.out.println("program: "+ps);
-			} else {
-				System.out.println("Cannot find any rule");
-			}
-			if (pls.size() == 0)
-				break;
-		}
-		return timeres;
-	}
-	public static String test_adaptive_seq(ArrayList<String[]> exps) {
-		String timeres = "";
-		HashMap<String, String[]> xHashMap = new HashMap<String, String[]>();
-		int index = 0;
-		Vector<String> vtmp = new Vector<String>();
-		Vector<String[]> examples = new Vector<String[]>();
-		for (String[] pair : exps) {
-			if (pair == null || pair.length <= 1)
-				break;
-			String[] line = { pair[0], pair[1], "", "", "wrong" };
-			vtmp.add(pair[0]);
-			xHashMap.put(index + "", line);
-			index++;
-		}
-		DataPreProcessor dpp = new DataPreProcessor(vtmp);
-		dpp.run();
-		Messager msger = new Messager();
-		Vector<Vector<String[]>> constraints = new Vector<Vector<String[]>>();
-		ArrayList<double[]> accArrayList = new ArrayList<double[]>();
-		int i = 0;
-		while (i<exps.size()) // repeat as no incorrect answer appears.
-		{
-			String[] tmt = { "<_START>" + exps.get(i)[0] + "<_END>", exps.get(i)[1] };
-			examples.add(tmt);
-			xHashMap = new HashMap<String, String[]>();
-			ProgSynthesis psProgSynthesis = new ProgSynthesis(contextId);
-			psProgSynthesis.inite(examples, dpp, msger);
-			Vector<ProgramRule> pls = new Vector<ProgramRule>();
-			long t1 = System.currentTimeMillis();
-			Collection<ProgramRule> ps = psProgSynthesis.adaptive_main();
-			long span = System.currentTimeMillis()-t1;
-			timeres += span+",";
-			// collect history contraints
-			msger.updateCM_Constr(psProgSynthesis.partiCluster.getConstraints());
-			msger.updateWeights(psProgSynthesis.partiCluster.weights);
-			i++;
-			// constraints.addAll();
-			if (ps != null) {
-				pls.addAll(ps);
-				System.out.println("program: "+ps);
-			} else {
-				System.out.println("Cannot find any rule");
-			}
-			if (pls.size() == 0)
-				break;
-		}
-		return timeres;
-	}
-
-	public static void test3(String dirpath) {
-		HashMap<String, Vector<String>> records = new HashMap<String, Vector<String>>();
-		File nf = new File(dirpath);
-		File[] allfiles = nf.listFiles();
-		// statistics
-		DataCollection dCollection = new DataCollection();
-		// list all the csv file under the dir
-		for (File f : allfiles) {
-			Vector<String[]> examples = new Vector<String[]>();
-			Vector<String[]> addExamples = new Vector<String[]>();
-			Vector<String[]> entries = new Vector<String[]>();
-			try {
-				if (f.getName().indexOf(".csv") != -1
-						&& f.getName().indexOf(".csv") == (f.getName().length() - 4)) {
-					// MyLogger.logsth("========"+f.getName()+"============\n");
-					HashMap<String, String[]> xHashMap = new HashMap<String, String[]>();
-					@SuppressWarnings("resource")
-					CSVReader cr = new CSVReader(new FileReader(f), ',', '"',
-							'\0');
-					String[] pair;
-					int index = 0;
-					Vector<String> vtmp = new Vector<String>();
-					while ((pair = cr.readNext()) != null) {
-						if (pair == null || pair.length <= 1)
-							break;
-						entries.add(pair);
-						vtmp.add(pair[0]);
-						String[] line = { pair[0], pair[1], "", "", "wrong" }; // org,
-																				// tar,
-																				// tarcode,
-																				// label
-						xHashMap.put(index + "", line);
-						index++;
-					}
-					DataPreProcessor dpp = new DataPreProcessor(vtmp);
-					dpp.run();
-					Messager msger = new Messager();
-					Vector<Vector<String[]>> constraints = new Vector<Vector<String[]>>();
-					if (entries.size() <= 1)
-						continue;
-					ExampleSelection expsel = new ExampleSelection();
-					ExampleSelection.firsttime = true;
-					expsel.inite(xHashMap, null);
-					int target = Integer.parseInt(expsel.Choose());
-					String[] mt = {
-							"<_START>" + entries.get(target)[0] + "<_END>",
-							entries.get(target)[1] };
-					examples.add(mt);
-					ExampleSelection.firsttime = false;
-					// accuracy record code
-					ArrayList<double[]> accArrayList = new ArrayList<double[]>();
-
-					while (true) // repeat as no incorrect answer appears.
-					{
-						long checknumber = 1;
-						long iterAfterNoFatalError = 0;
-						HashMap<String, Vector<String[]>> expFeData = new HashMap<String, Vector<String[]>>();
-						Vector<String> resultString = new Vector<String>();
-						xHashMap = new HashMap<String, String[]>();
-						ProgSynthesis psProgSynthesis = new ProgSynthesis(contextId);
-						HashMap<String, String> unlabeledData = new HashMap<String, String>();
-						for (int i = 0; i < vtmp.size(); i++) {
-							unlabeledData.put("" + i, vtmp.get(i));
-						}
-						psProgSynthesis.inite(examples, dpp, msger);
-						Vector<ProgramRule> pls = new Vector<ProgramRule>();
-						Collection<ProgramRule> ps = psProgSynthesis
-								.adaptive_main();
-						// collect history contraints
-						msger.updateCM_Constr(psProgSynthesis.partiCluster
-								.getConstraints());
-						msger.updateWeights(psProgSynthesis.partiCluster.weights);
-						// constraints.addAll();
-						if (ps != null) {
-							pls.addAll(ps);
-						} else {
-							System.out.println("Cannot find any rule");
-						}
-						String[] wexam = null;
-						if (pls.size() == 0)
-							break;
-						long t1 = System.currentTimeMillis();
-						int ErrorCnt = 0;
-						int clf_acc_error_cnt = 0;
-						int clf_acc_total_cnt = 0;
-						HashMap<String, HashMap<String, String>> uData = new HashMap<String, HashMap<String, String>>();
-						for (int i = 0; i < pls.size(); i++) {
-							ProgramRule script = pls.get(i);
-							// System.out.println(script);
-							String res = "";
-							for (int j = 0; j < entries.size(); j++) {
-								InterpreterType worker = script
-										.getRuleForValue(entries.get(j)[0]);
-								String classlabel = script
-										.getClassForValue(entries.get(j)[0]);
-								String tmps = worker.execute_debug(entries
-										.get(j)[0]);
-								HashMap<String, String> dict = new HashMap<String, String>();
-								dict.put("class", classlabel);
-								UtilTools.StringColorCode(entries.get(j)[0],
-										tmps, dict);
-								String s = dict.get("Tar");
-								if (Test.isExample(entries.get(j)[0], examples)) {
-									s = entries.get(j)[1];
-								}
-								res += s + "\n";
-								if (ConfigParameters.debug == 1) {
-									String indicator = "wrong";
-									if (s.compareTo(entries.get(j)[1]) == 0)
-										indicator = "correct";
-									if (!uData.containsKey(j + ""))
-										uData.put(j + "", dict);
-								}
-								// classifier accuracy
-
-								boolean existres = false;
-								for (InterpreterType w : script.rules.values()) {
-									String xtmp = w.execute(entries.get(j)[0]);
-									if (xtmp != null
-											&& xtmp.length() > 0
-											&& xtmp.compareTo(entries.get(j)[1]) == 0) {
-										existres = true;
-										break;
-									}
-								}
-								if (existres) {
-									clf_acc_total_cnt++;
-									if (s == null
-											|| s.length() == 0
-											|| s.compareTo(entries.get(j)[1]) != 0) {
-										clf_acc_error_cnt++;
-									}
-								}
-								//
-								if (s == null || s.length() == 0) {
-									String[] ts = {
-											"<_START>" + entries.get(j)[0]
-													+ "<_END>", "", tmps,
-											classlabel, "wrong" };
-									xHashMap.put(j + "", ts);
-									wexam = ts;
-									checknumber++;
-								}
-								boolean isfind = false;
-								for (String[] exppair : examples) {
-									if (exppair[0].compareTo("<_START>"
-											+ dict.get("Org") + "<_END>") == 0) {
-										String[] exp = { dict.get("Org"), tmps };
-										if (!expFeData.containsKey(classlabel)) {
-											Vector<String[]> vstr = new Vector<String[]>();
-											vstr.add(exp);
-											expFeData.put(classlabel, vstr);
-										} else {
-											expFeData.get(classlabel).add(exp);
-										}
-										isfind = true;
-									}
-								}
-								// update positive traing data with user
-								// specification
-								for (String[] tmpx : addExamples) {
-									if (tmpx[0].compareTo(dict.get("Org")) == 0
-											&& tmpx[1].compareTo(dict
-													.get("Tar")) == 0) {
-										String[] exp = { dict.get("Org"), tmps };
-										if (!expFeData.containsKey(classlabel)) {
-											Vector<String[]> vstr = new Vector<String[]>();
-											vstr.add(exp);
-											expFeData.put(classlabel, vstr);
-										} else {
-											expFeData.get(classlabel).add(exp);
-										}
-										isfind = true;
-									}
-								}
-								if (!isfind) {
-									String[] ts = {
-											"<_START>" + entries.get(j)[0]
-													+ "<_END>", s, tmps,
-											classlabel, "right" };
-									if (s.compareTo(entries.get(j)[1]) != 0) {
-										ErrorCnt++;
-										wexam = ts;
-										ts[4] = "wrong";
-									}
-									xHashMap.put(j + "", ts);
-								}
-							}
-							if (wexam == null
-									|| (entries.size() - ErrorCnt) * 1.0
-											/ entries.size() == 1.0) {
-								wexam = null;
-								break;
-							}
-							resultString.add(res);
-						}
-						double resultacc = (entries.size() - ErrorCnt) * 1.0
-								/ entries.size();
-						double clf_acc = 1 - clf_acc_error_cnt * 1.0
-								/ clf_acc_total_cnt;
-						double[] accarray = { resultacc, clf_acc };
-						// use uData to refiner the result
-						System.out.println(""
-								+ psProgSynthesis.myprog.toString());
-						System.out.println(pls.get(0).toString());
-						// cRefiner.clusterUdata();
-						records.put(f.getName() + examples.size(), resultString);
-						long t2 = System.currentTimeMillis();
-
-						if (wexam != null) {
-							String[] wexp = new String[2];
-							while (true) {
-								expsel = new ExampleSelection();
-								expsel.inite(xHashMap, expFeData);
-								int e = Integer.parseInt(expsel.Choose());
-								if (xHashMap.get("" + e)[4].compareTo("right") != 0) {
-									System.out
-									.println("Recommand Example: "
-											+ Arrays.toString(xHashMap
-													.get("" + e)));
-									wexp[0] = "<_START>" + entries.get(e)[0]
-											+ "<_END>";
-									wexp[1] = entries.get(e)[1];
-									if (expsel.isDetectingQuestionableRecord) {
-										iterAfterNoFatalError++;
-										// check whether this record is has the
-										// longest or shortest result
-										Boolean v = visible(xHashMap, "" + e);
-									}
-									break;
-								} else {
-									// update positive training data
-									addExamples.add(entries.get(e));
-									// update the rest dataset
-									xHashMap.remove("" + e);
-								}
-								checknumber++;
-							}
-
-							examples.add(wexp);
-							FileStat fileStat = new FileStat(f.getName() + "",
-									psProgSynthesis.learnspan,
-									psProgSynthesis.genspan, (t2 - t1),
-									examples.size(), examples,
-									psProgSynthesis.partiCluster.failedCnt,
-									checknumber, iterAfterNoFatalError,
-									psProgSynthesis.myprog.partitions.size(),
-									pls.get(0).toString(), resultacc, clf_acc);
-							dCollection.addEntry(fileStat);
-						} else {
-							FileStat fileStat = new FileStat(f.getName() + "",
-									psProgSynthesis.learnspan,
-									psProgSynthesis.genspan, (t2 - t1),
-									examples.size(), examples,
-									psProgSynthesis.partiCluster.failedCnt,
-									checknumber, iterAfterNoFatalError,
-									psProgSynthesis.myprog.partitions.size(),
-									pls.get(0).toString(), resultacc, clf_acc);
-							dCollection.addEntry(fileStat);
-							dCollection.addSucceededFile(f.getName());
-							break;
-						}
-					}
-				}
-				
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		}
-		dCollection.print();
-		dCollection.print1();
-		Prober.displayProgram();
-		//
-	}
-
-	public static void test4(String dirpath) {
-		HashMap<String, Vector<String>> records = new HashMap<String, Vector<String>>();
-		File nf = new File(dirpath);
-		File[] allfiles = nf.listFiles();
-		// statistics
-		DataCollection dCollection = new DataCollection();
-		RecordClassifier rcf;
-		// list all the csv file under the dir
-		for (File f : allfiles) {
-			Vector<String[]> examples = new Vector<String[]>();
-			Vector<String[]> addExamples = new Vector<String[]>();
-			Vector<String[]> entries = new Vector<String[]>();
-			try {
-				if (f.getName().indexOf(".csv") != -1
-						&& f.getName().indexOf(".csv") == (f.getName().length() - 4)) {
-					// MyLogger.logsth("========"+f.getName()+"============\n");
-					HashMap<String, String[]> xHashMap = new HashMap<String, String[]>();
-					@SuppressWarnings("resource")
-					CSVReader cr = new CSVReader(new FileReader(f), ',', '"',
-							'\0');
-					String[] pair;
-					int index = 0;
-					Vector<String> vtmp = new Vector<String>();
-					while ((pair = cr.readNext()) != null) {
-						if (pair == null || pair.length <= 1)
-							break;
-						entries.add(pair);
-						vtmp.add(pair[0]);
-						String[] line = { pair[0], pair[1], "", "", "wrong" }; // org,
-																				// tar,
-																				// tarcode,
-																				// label
-						xHashMap.put(index + "", line);
-						index++;
-					}
-					DataPreProcessor dpp = new DataPreProcessor(vtmp);
-					dpp.run();
-					Messager msger = new Messager();
-					Vector<Vector<String[]>> constraints = new Vector<Vector<String[]>>();
-					if (entries.size() <= 1)
-						continue;
-					ExampleSelection expsel = new ExampleSelection();
-					ExampleSelection.firsttime = true;
-					expsel.inite(xHashMap, null);
-					int target = Integer.parseInt(expsel.Choose());
-					String[] mt = {
-							"<_START>" + entries.get(target)[0] + "<_END>",
-							entries.get(target)[1] };
-					examples.add(mt);
-					ExampleSelection.firsttime = false;
-					// accuracy record code
-					ArrayList<double[]> accArrayList = new ArrayList<double[]>();
-					long stime = System.currentTimeMillis();
-					boolean overtime = true;
-					while (true) // repeat as no incorrect answer appears.
-					{
-						long checknumber = 1;
-						long iterAfterNoFatalError = 0;
-						long isvisible = 0;
-						HashMap<String, Vector<String[]>> expFeData = new HashMap<String, Vector<String[]>>();
-						Vector<String> resultString = new Vector<String>();
-						xHashMap = new HashMap<String, String[]>();
-						ProgSynthesis psProgSynthesis = new ProgSynthesis(contextId);
-						HashMap<String, String> unlabeledData = new HashMap<String, String>();
-						for (int i = 0; i < vtmp.size(); i++) {
-							unlabeledData.put("" + i, vtmp.get(i));
-						}
-						psProgSynthesis.inite(examples, dpp, msger);
-						Vector<ProgramRule> pls = new Vector<ProgramRule>();
-						Collection<ProgramRule> ps = psProgSynthesis.run_main();
-						// collect history contraints
-						msger.updateCM_Constr(psProgSynthesis.partiCluster
-								.getConstraints());
-						msger.updateWeights(psProgSynthesis.partiCluster.weights);
-						
-						rcf = (RecordClassifier) psProgSynthesis.classifier;
-						// constraints.addAll();
-						if (ps != null) {
-							pls.addAll(ps);
-						} else {
-							System.out.println("Cannot find any rule");
-						}
-						String[] wexam = null;
-						if (pls.size() == 0)
-							break;
-						long t1 = System.currentTimeMillis();
-						int ErrorCnt = 0;
-						int clf_acc_error_cnt = 0;
-						int clf_acc_total_cnt = 0;
-						HashMap<String, HashMap<String, String>> uData = new HashMap<String, HashMap<String, String>>();
-						for (int i = 0; i < pls.size(); i++) {
-							ProgramRule script = pls.get(i);
-							// System.out.println(script);
-							String res = "";
-							for (int j = 0; j < entries.size(); j++) {
-								InterpreterType worker = script
-										.getRuleForValue(entries.get(j)[0]);
-								String classlabel = script
-										.getClassForValue(entries.get(j)[0]);
-								String tmps = worker.execute_debug(entries
-										.get(j)[0]);
-								
-								HashMap<String, String> dict = new HashMap<String, String>();
-								dict.put("class", classlabel);
-								UtilTools.StringColorCode(entries.get(j)[0],
-										tmps, dict);
-								String s = worker.execute(entries.get(j)[0]);
-								dict.put("Tar", s);
-								if (Test.isExample(entries.get(j)[0], examples)) {
-									s = entries.get(j)[1];
-								}
-								res += s + "\n";
-								if (ConfigParameters.debug == 1) {
-									String indicator = "wrong";
-									if (s.compareTo(entries.get(j)[1]) == 0)
-										indicator = "correct";
-									if (!uData.containsKey(j + ""))
-										uData.put(j + "", dict);
-								}
-								// classifier accuracy
-
-								boolean existres = false;
-								for (InterpreterType w : script.rules.values()) {
-									String xtmp = w.execute(entries.get(j)[0]);
-									if (xtmp != null
-											&& xtmp.length() > 0
-											&& xtmp.compareTo(entries.get(j)[1]) == 0) {
-										existres = true;
-										break;
-									}
-								}
-								if (existres) {
-									clf_acc_total_cnt++;
-									if (s == null
-											|| s.length() == 0
-											|| s.compareTo(entries.get(j)[1]) != 0) {
-										clf_acc_error_cnt++;
-									}
-								}
-								//
-								if (s == null || s.length() == 0) {
-									String[] ts = {
-											"<_START>" + entries.get(j)[0]
-													+ "<_END>", "", tmps,
-											classlabel, "wrong" };
-									xHashMap.put(j + "", ts);
-									wexam = ts;
-									checknumber++;
-								}
-								boolean isfind = false;
-								for (String[] exppair : examples) {
-									if (exppair[0].compareTo("<_START>"
-											+ dict.get("Org") + "<_END>") == 0) {
-										String[] exp = { dict.get("Org"), tmps };
-										if (!expFeData.containsKey(classlabel)) {
-											Vector<String[]> vstr = new Vector<String[]>();
-											vstr.add(exp);
-											expFeData.put(classlabel, vstr);
-										} else {
-											expFeData.get(classlabel).add(exp);
-										}
-										isfind = true;
-									}
-								}
-								// update positive traing data with user
-								// specification
-								for (String[] tmpx : addExamples) {
-									if (tmpx[0].compareTo(dict.get("Org")) == 0
-											&& tmpx[1].compareTo(dict
-													.get("Tar")) == 0) {
-										String[] exp = { dict.get("Org"), tmps };
-										if (!expFeData.containsKey(classlabel)) {
-											Vector<String[]> vstr = new Vector<String[]>();
-											vstr.add(exp);
-											expFeData.put(classlabel, vstr);
-										} else {
-											expFeData.get(classlabel).add(exp);
-										}
-										isfind = true;
-									}
-								}
-								if (!isfind) {
-									String[] ts = {
-											"<_START>" + entries.get(j)[0]
-													+ "<_END>", s, tmps,
-											classlabel, "right" };
-									if (s.compareTo(entries.get(j)[1]) != 0) {
-										ErrorCnt++;
-										wexam = ts;
-										ts[4] = "wrong";
-									}
-									xHashMap.put(j + "", ts);
-								}
-							}
-
-							if (wexam == null
-									|| (entries.size() - ErrorCnt) * 1.0
-											/ entries.size() == 1.0) {
-								wexam = null;
-								break;
-							}
-							resultString.add(res);
-						}
-						double resultacc = (entries.size() - ErrorCnt) * 1.0
-								/ entries.size();
-						double clf_acc = 1 - clf_acc_error_cnt * 1.0
-								/ clf_acc_total_cnt;
-						double[] accarray = { resultacc, clf_acc };
-						// use uData to refiner the result
-						System.out.println(""
-								+ psProgSynthesis.myprog.toString());
-						System.out.println(pls.get(0).toString());
-						// cRefiner.clusterUdata();
-						records.put(f.getName() + examples.size(), resultString);
-						long t2 = System.currentTimeMillis();
-
-						if (wexam != null) {
-							String[] wexp = new String[2];
-							while (true) {
-								expsel = new ExampleSelection();
-								expsel.inite(xHashMap, expFeData);
-								int e = Integer.parseInt(expsel.Choose());
-								// /
-								System.out
-										.println("Recommand Example: "
-												+ Arrays.toString(xHashMap
-														.get("" + e)));
-								// /
-								if (xHashMap.get("" + e)[4].compareTo("right") != 0) {
-									wexp[0] = "<_START>" + entries.get(e)[0]
-											+ "<_END>";
-									wexp[1] = entries.get(e)[1];
-									if (expsel.isDetectingQuestionableRecord) {
-										iterAfterNoFatalError++;
-										// check whether this record is has the
-										// longest or shortest result
-										Boolean v = visible(xHashMap, "" + e);
-										if (v) {
-											isvisible += 1;
-										}
-									}
-									break;
-								} else {
-									// update positive training data
-									addExamples.add(entries.get(e));
-									// update the rest dataset
-									xHashMap.remove("" + e);
-								}
-								checknumber++;
-							}
-
-							examples.add(wexp);
-							FileStat fileStat = new FileStat(f.getName() + "",
-									psProgSynthesis.learnspan,
-									psProgSynthesis.genspan, (t2 - t1),
-									examples.size(), examples,
-									psProgSynthesis.partiCluster.failedCnt,
-									checknumber, iterAfterNoFatalError,
-									psProgSynthesis.myprog.partitions.size(),
-									pls.get(0).toString(), resultacc, clf_acc);
-							dCollection.addEntry(fileStat);
-						} else {
-							FileStat fileStat = new FileStat(f.getName() + "",
-									psProgSynthesis.learnspan,
-									psProgSynthesis.genspan, (t2 - t1),
-									examples.size(), examples,
-									psProgSynthesis.partiCluster.failedCnt,
-									checknumber, iterAfterNoFatalError,
-									psProgSynthesis.myprog.partitions.size(),
-									pls.get(0).toString(), resultacc, clf_acc);
-							dCollection.addEntry(fileStat);
-							dCollection.addSucceededFile(f.getName());
-							break;
-						}
-					}
-				}
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		
-		}
-		dCollection.print();
-		dCollection.print1();
-		Prober.displayProgram();
-	}
-
-	public static boolean isExample(String var, Vector<String[]> examples) {
-		boolean is = false;
-		String s = "<_START>" + var + "<_END>";
-		for (String[] x : examples) {
-			if (s.compareTo(x[0]) == 0) {
-				is = true;
-				break;
-			}
-		}
-		return is;
-	}
-
-	public static void hashResultPrint(HashMap<String, Vector<String>> res) {
-		String s = "";
-		for (Map.Entry<String, Vector<String>> stringVectorEntry : res.entrySet()) {
-			s += "==============" + stringVectorEntry.getKey() + "=============\n";
-			for (String value : stringVectorEntry.getValue()) {
-				s += value + "\n";
-			}
-		}
-		System.out.println("" + s);
-	}
-
-	public static void runSeriseExper() {
-		EmailNotification notification = new EmailNotification();
-		ExampleCluster.option = method.CP;
-		Test.test4("/Users/bowu/Research/testdata/TestSingleFile");
-		notification.notify(true,"CP");
-		
-		ExampleCluster.option = method.DPIC;
-		Test.test4("/Users/bowu/Research/testdata/TestSingleFile");
-		notification.notify(true,"DPIC");
-
-
-		ExampleCluster.option = method.DP;
-		Test.test4("/Users/bowu/Research/testdata/TestSingleFile");
-		notification.notify(true,"DP");
-
-		ExampleCluster.option = method.SPIC;
-		Test.test4("/Users/bowu/Research/testdata/TestSingleFile");
-		notification.notify(true,"SPIC");
-
-		ExampleCluster.option = method.SP;
-		Test.test4("/Users/bowu/Research/testdata/TestSingleFile");
-		notification.notify(true,"SP");
-
-		ExampleCluster.option = method.CPIC;
-		Test.test4("/Users/bowu/Research/testdata/TestSingleFile");
-		notification.notify(true,"CPIC");
-
-		
-
-		
-	}
-
-	public static int MaximalNumber = -1;
-	public static int MinimalNumber = 100;
-	public static Vector<String[]> larexamples = new Vector<String[]>();
-	public static Vector<String[]> smalexamples = new Vector<String[]>();
-
-	public static void main(String[] args) {
-		// load parameters
-		ConfigParameters cfg = new ConfigParameters();
-		cfg.initeParameters();
-		DataCollection.config = cfg.getString();
-		Test.test4("/Users/bowu/Research/testdata/TestSingleFile");
-		//Test.test3("/Users/bowu/Research/testdata/TestSingleFile");
-		 //Test.runSeriseExper();
-		// Test test = new Test();
-		// test.parameterSelection("/Users/bowu/Research/testdata/TestSingleFile");
-	}
-}
\ No newline at end of file
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/TestTools.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/TestTools.java
deleted file mode 100644
index 690680d00..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/TestTools.java
+++ /dev/null
@@ -1,71 +0,0 @@
-package edu.isi.karma.cleaning.Research;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Vector;
-
-import au.com.bytecode.opencsv.CSVReader;
-import au.com.bytecode.opencsv.CSVWriter;
-
-public class TestTools {
-	public static void print(ArrayList<double[]> res) {
-		String p = "";
-		for (double[] line : res) {
-			p += Arrays.toString(line);
-			p += "\n";
-		}
-		System.out.println("" + p);
-	}
-
-	public void handledata() throws IOException {
-		File nf = new File("./log/data");
-		File[] allfiles = nf.listFiles();
-		ArrayList<Vector<String[]>> res = new ArrayList<Vector<String[]>>();
-		for (File f : allfiles) {
-			Vector<String[]> entries = new Vector<String[]>();
-			try {
-				if (f.getName().indexOf(".csv") != -1
-						&& f.getName().indexOf(".csv") == (f.getName().length() - 4)) {
-					CSVReader cr = new CSVReader(new FileReader(f), ',', '"',
-							'\0');
-					String[] pair;
-					while ((pair = cr.readNext()) != null) {
-						if (pair == null || pair.length <= 1)
-							break;
-						entries.add(pair);
-					}
-					res.add(entries);
-				}
-			} catch (Exception ex) {
-				ex.printStackTrace();
-			}
-		}
-		String x = "./log/data/00_";
-		for (int i = 0; i < res.size(); i++) {
-			Vector<String[]> temp = new Vector<String[]>();
-			for (int j = 0; j <= i; j++) {
-				temp.addAll(res.get(j));
-			}
-			CSVWriter cWriter;
-			cWriter = new CSVWriter(new FileWriter(x+i+".csv"));
-
-			for (String[] line : temp) {
-				cWriter.writeNext(line);
-			}
-			cWriter.close();
-		}
-	}
-	public static void main(String[] args)
-	{
-		TestTools ttls = new TestTools();
-		try {
-			ttls.handledata();
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/TimerRunner.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/TimerRunner.java
deleted file mode 100644
index e082ddcfc..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/TimerRunner.java
+++ /dev/null
@@ -1,283 +0,0 @@
-package edu.isi.karma.cleaning.Research;
-
-import java.io.File;
-import java.io.FileReader;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Vector;
-
-import au.com.bytecode.opencsv.CSVReader;
-import edu.isi.karma.cleaning.DataPreProcessor;
-import edu.isi.karma.cleaning.ExampleSelection;
-import edu.isi.karma.cleaning.InterpreterType;
-import edu.isi.karma.cleaning.Messager;
-import edu.isi.karma.cleaning.ProgSynthesis;
-import edu.isi.karma.cleaning.ProgramRule;
-import edu.isi.karma.cleaning.UtilTools;
-
-public class TimerRunner implements Runnable {
-	File f;
-	DataCollection dCollection;
-	String contextId;
-	public TimerRunner(File f, DataCollection dCollection, String contextId) {
-		this.f = f;
-		this.dCollection = dCollection;
-		this.contextId = contextId;
-	}
-
-	public void run() {
-		try {
-			HashMap<String, Vector<String>> records = new HashMap<String, Vector<String>>();
-			Vector<String[]> examples = new Vector<String[]>();
-			Vector<String[]> addExamples = new Vector<String[]>();
-			Vector<String[]> entries = new Vector<String[]>();
-			// TODO Auto-generated method stub
-			if (f.getName().indexOf(".csv") != -1
-					&& f.getName().indexOf(".csv") == (f.getName().length() - 4)) {
-				// MyLogger.logsth("========"+f.getName()+"============\n");
-				HashMap<String, String[]> xHashMap = new HashMap<String, String[]>();
-				@SuppressWarnings("resource")
-				CSVReader cr = new CSVReader(new FileReader(f), ',', '"', '\0');
-				String[] pair;
-				int index = 0;
-				Vector<String> vtmp = new Vector<String>();
-				while ((pair = cr.readNext()) != null) {
-					if (pair == null || pair.length <= 1)
-						break;
-					entries.add(pair);
-					vtmp.add(pair[0]);
-					String[] line = { pair[0], pair[1], "", "", "wrong" }; // org,
-																			// tar,
-																			// tarcode,
-																			// label
-					xHashMap.put(String.valueOf(index), line);
-					index++;
-				}
-				DataPreProcessor dpp = new DataPreProcessor(vtmp);
-				dpp.run();
-				Messager msger = new Messager();
-				Vector<Vector<String[]>> constraints = new Vector<Vector<String[]>>();
-				if (entries.size() <= 1)
-					return;
-				ExampleSelection expsel = new ExampleSelection();
-				ExampleSelection.firsttime = true;
-				expsel.inite(xHashMap, null);
-				int target = Integer.parseInt(expsel.Choose());
-				String[] mt = { "<_START>" + entries.get(target)[0] + "<_END>",
-						entries.get(target)[1] };
-				examples.add(mt);
-				ExampleSelection.firsttime = false;
-				// accuracy record code
-				ArrayList<double[]> accArrayList = new ArrayList<double[]>();
-				while (true) // repeat as no incorrect answer appears.
-				{
-					if (examples.size() == 8) {
-						System.out.println("Hello World");
-					}
-					long checknumber = 1;
-					long iterAfterNoFatalError = 0;
-					long isvisible = 0;
-					HashMap<String, Vector<String[]>> expFeData = new HashMap<String, Vector<String[]>>();
-					Vector<String> resultString = new Vector<String>();
-					xHashMap = new HashMap<String, String[]>();
-					ProgSynthesis psProgSynthesis = new ProgSynthesis(contextId);
-					HashMap<String, String> unlabeledData = new HashMap<String, String>();
-					for (int i = 0; i < vtmp.size(); i++) {
-						unlabeledData.put(String.valueOf(i), vtmp.get(i));
-					}
-					psProgSynthesis.inite(examples, dpp, msger);
-					Vector<ProgramRule> pls = new Vector<ProgramRule>();
-					Collection<ProgramRule> ps = psProgSynthesis.run_main();
-					// collect history contraints
-					msger.updateCM_Constr(psProgSynthesis.partiCluster
-							.getConstraints());
-					msger.updateWeights(psProgSynthesis.partiCluster.weights);
-					// constraints.addAll();
-					if (ps != null) {
-						pls.addAll(ps);
-					} else {
-						System.out.println("Cannot find any rule");
-					}
-					String[] wexam = null;
-					if (pls.isEmpty())
-						break;
-					long t1 = System.currentTimeMillis();
-					int ErrorCnt = 0;
-					int clf_acc_error_cnt = 0;
-					int clf_acc_total_cnt = 0;
-					HashMap<String, HashMap<String, String>> uData = new HashMap<String, HashMap<String, String>>();
-					for (int i = 0; i < pls.size(); i++) {
-						ProgramRule script = pls.get(i);
-						// System.out.println(script);
-						String res = "";
-						for (int j = 0; j < entries.size(); j++) {
-							InterpreterType worker = script
-									.getRuleForValue(entries.get(j)[0]);
-							String classlabel = script.getClassForValue(entries
-									.get(j)[0]);
-							String tmps = worker
-									.execute_debug(entries.get(j)[0]);
-							HashMap<String, String> dict = new HashMap<String, String>();
-							dict.put("class", classlabel);
-							UtilTools.StringColorCode(entries.get(j)[0], tmps,
-									dict);
-							String s = dict.get("Tar");
-							res += s + "\n";
-							if (ConfigParameters.debug == 1) {
-								String indicator = "wrong";
-								if (s.compareTo(entries.get(j)[1]) == 0)
-									indicator = "correct";
-								if (!uData.containsKey(String.valueOf(j)))
-									uData.put(String.valueOf(j), dict);
-							}
-							// classifier accuracy
-
-							boolean existres = false;
-							for (InterpreterType w : script.rules.values()) {
-								String xtmp = w.execute(entries.get(j)[0]);
-								if (xtmp != null
-										&& xtmp.length() > 0
-										&& xtmp.compareTo(entries.get(j)[1]) == 0) {
-									existres = true;
-									break;
-								}
-							}
-							if (existres) {
-								clf_acc_total_cnt++;
-								if (s == null || s.length() == 0
-										|| s.compareTo(entries.get(j)[1]) != 0) {
-									clf_acc_error_cnt++;
-								}
-							}
-							//
-							if (s == null || s.length() == 0) {
-								String[] ts = {
-										"<_START>" + entries.get(j)[0]
-												+ "<_END>", "", tmps,
-										classlabel, "wrong" };
-								xHashMap.put(String.valueOf(j), ts);
-								wexam = ts;
-								checknumber++;
-							}
-							boolean isfind = false;
-							for (String[] exppair : examples) {
-								if (exppair[0].compareTo("<_START>"
-										+ dict.get("Org") + "<_END>") == 0) {
-									String[] exp = { dict.get("Org"), tmps };
-									if (!expFeData.containsKey(classlabel)) {
-										Vector<String[]> vstr = new Vector<String[]>();
-										vstr.add(exp);
-										expFeData.put(classlabel, vstr);
-									} else {
-										expFeData.get(classlabel).add(exp);
-									}
-									isfind = true;
-								}
-							}
-							// update positive traing data with user
-							// specification
-							for (String[] tmpx : addExamples) {
-								if (tmpx[0].compareTo(dict.get("Org")) == 0
-										&& tmpx[1].compareTo(dict.get("Tar")) == 0) {
-									String[] exp = { dict.get("Org"), tmps };
-									if (!expFeData.containsKey(classlabel)) {
-										Vector<String[]> vstr = new Vector<String[]>();
-										vstr.add(exp);
-										expFeData.put(classlabel, vstr);
-									} else {
-										expFeData.get(classlabel).add(exp);
-									}
-									isfind = true;
-								}
-							}
-							if (!isfind) {
-								String[] ts = {
-										"<_START>" + entries.get(j)[0]
-												+ "<_END>", s, tmps,
-										classlabel, "right" };
-								if (s.compareTo(entries.get(j)[1]) != 0) {
-									ErrorCnt++;
-									wexam = ts;
-									ts[4] = "wrong";
-								}
-								xHashMap.put(String.valueOf(j), ts);
-							}
-						}
-
-						if (wexam == null
-								|| (entries.size() - ErrorCnt) * 1.0
-										/ entries.size() == 1.0) {
-							wexam = null;
-							break;
-						}
-						resultString.add(res);
-					}
-					double resultacc = (entries.size() - ErrorCnt) * 1.0
-							/ entries.size();
-					double clf_acc = 1 - clf_acc_error_cnt * 1.0
-							/ clf_acc_total_cnt;
-					double[] accarray = { resultacc, clf_acc };
-					// use uData to refiner the result
-					System.out.println("" + psProgSynthesis.myprog.toString());
-					System.out.println(pls.get(0).toString());
-					// cRefiner.clusterUdata();
-					records.put(f.getName() + examples.size(), resultString);
-					long t2 = System.currentTimeMillis();
-
-					if (wexam != null) {
-						String[] wexp = new String[2];
-						while (true) {
-							expsel = new ExampleSelection();
-							expsel.inite(xHashMap, expFeData);
-							int e = Integer.parseInt(expsel.Choose());
-							// /
-							System.out.println("Recommand Example: "
-									+ Arrays.toString(xHashMap.get(String.valueOf(e))));
-							// /
-							if (xHashMap.get(String.valueOf(e))[4].compareTo("right") != 0) {
-								wexp[0] = "<_START>" + entries.get(e)[0]
-										+ "<_END>";
-								wexp[1] = entries.get(e)[1];
-								break;
-							} else {
-								// update positive training data
-								addExamples.add(entries.get(e));
-								// update the rest dataset
-								xHashMap.remove(String.valueOf(e));
-							}
-							checknumber++;
-						}
-
-						examples.add(wexp);
-						FileStat fileStat = new FileStat(f.getName() + "",
-								psProgSynthesis.learnspan,
-								psProgSynthesis.genspan, (t2 - t1),
-								examples.size(), examples,
-								psProgSynthesis.partiCluster.failedCnt,
-								checknumber, iterAfterNoFatalError, isvisible,
-								pls.get(0).toString(), resultacc, clf_acc);
-						dCollection.addEntry(fileStat);
-					} else {
-						FileStat fileStat = new FileStat(f.getName() + "",
-								psProgSynthesis.learnspan,
-								psProgSynthesis.genspan, (t2 - t1),
-								examples.size(), examples,
-								psProgSynthesis.partiCluster.failedCnt,
-								checknumber, iterAfterNoFatalError, isvisible,
-								pls.get(0).toString(), resultacc, clf_acc);
-						dCollection.addEntry(fileStat);
-						dCollection.addSucceededFile(f.getName());
-						break;
-					}
-				}
-			}
-			return;
-		} catch (Exception ex) {
-			System.out.println("" + ex.toString());
-			return;
-		}
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/Tools.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/Tools.java
deleted file mode 100644
index 0e0869fc7..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Research/Tools.java
+++ /dev/null
@@ -1,150 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.cleaning.Research;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Vector;
-
-import au.com.bytecode.opencsv.CSVWriter;
-import edu.isi.karma.cleaning.DataPreProcessor;
-import edu.isi.karma.cleaning.InterpreterType;
-import edu.isi.karma.cleaning.Messager;
-import edu.isi.karma.cleaning.ProgSynthesis;
-import edu.isi.karma.cleaning.ProgramRule;
-import edu.isi.karma.webserver.ContextParametersRegistry;
-
-public class Tools {
-	public static String contextId = ContextParametersRegistry.getInstance().getDefault().getId();
-	public void transformFile(String fpath) {
-		try {
-			Vector<String[]> examples = new Vector<String[]>();
-			// read and write the data
-			File nf = new File(fpath);
-			BufferedReader cr = new BufferedReader(new FileReader(fpath));
-			String pair = "";
-			Vector<String> vtmp = new Vector<String>();
-			while ((pair = cr.readLine()) != null) {
-				pair = pair.trim();
-				if (pair.length() == 0)
-					continue;
-				if (pair.charAt(0) == '\"') {
-					pair = pair.substring(1);
-				}
-				if (pair.charAt(pair.length() - 1) == '\"') {
-					pair = pair.substring(0, pair.length() - 1);
-				}
-				vtmp.add(pair);
-			}
-			DataPreProcessor dpp = new DataPreProcessor(vtmp);
-			dpp.run();
-			Messager msger = new Messager();
-			while (true) {
-
-				Vector<String[]> result = new Vector<String[]>();
-				System.out.print("Enter raw value\n");
-				// open up standard input
-				BufferedReader br = new BufferedReader(new InputStreamReader(
-						System.in));
-				String raw = null;
-				raw = br.readLine();
-				if (raw.compareTo("end") == 0) {
-					break;
-				}
-				System.out.print("Enter tar value\n");
-				// open up standard input
-				String tar = null;
-				tar = br.readLine();
-
-				// learn the program
-				String[] xStrings = { "<_START>" + raw + "<_END>", tar };
-				examples.add(xStrings);
-				for (String[] elem : examples) {
-					System.out.println("Examples inputed: "
-							+ Arrays.toString(elem));
-				}
-				String ofpath = "/Users/bowu/Research/50newdata/tmp/"
-						+ nf.getName();
-				CSVWriter cw = new CSVWriter(new FileWriter(new File(ofpath)));
-				ProgSynthesis psProgSynthesis = new ProgSynthesis(contextId);				
-				psProgSynthesis.inite(examples,dpp,msger); //
-				Collection<ProgramRule> ps = psProgSynthesis.run_main();
-				msger.updateCM_Constr(psProgSynthesis.partiCluster
-						.getConstraints());
-				msger.updateWeights(psProgSynthesis.partiCluster.weights);
-				ProgramRule pr = ps.iterator().next();
-				System.out.println(""+psProgSynthesis.myprog.toString());
-				System.out.println("" + pr.toString());
-				for(String org: vtmp)
-				{
-					String ttar = pr.transform(org);
-					String[] pValue = {org,ttar};
-					cw.writeNext(pValue);
-					System.out.println(String.format("%s,%s", org,ttar ));
-					result.add(pValue);
-				}
-				cw.close();
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-	}
-
-	public void test1() {
-		Vector<String[]> examples = new Vector<String[]>();
-		String[] xStrings = { "<_START>Ruth Asawa<_END>", "Asawa, Ruth" };
-		String[] yStrings = { "<_START>Robert Boardman Howard<_END>",
-				"Howard, Robert Boardman" };
-		// String[] zStrings =
-		// {"<_START>Artist unknown Salem, Massachusetts area<_END>","Artist unknown"};
-		examples.add(xStrings);
-		examples.add(yStrings);
-		ArrayList<String> data = new ArrayList<String>();
-		// examples.add(zStrings);
-		ProgSynthesis psProgSynthesis = new ProgSynthesis(contextId);
-		DataPreProcessor dbDataPreProcessor = new DataPreProcessor(data);
-		Vector<Vector<String[]>> cstrns = new Vector<Vector<String[]>>();
-
-		psProgSynthesis.inite(examples,dbDataPreProcessor,cstrns);
-		Collection<ProgramRule> ps = psProgSynthesis.run_main();
-		ProgramRule pr = ps.iterator().next();
-		System.out.println("" + pr.toString());
-		String val = "J. B. Blunk";
-		InterpreterType rule = pr.getRuleForValue(val);
-		System.out.println(rule.execute(val));
-	}
-
-	public static void main(String[] args) {
-		ConfigParameters cfg = new ConfigParameters();
-		cfg.initeParameters();
-		DataCollection.config = cfg.getString();
-		Tools tools = new Tools();
-		tools.transformFile("/Users/bowu/Research/testdata/workable_singleColumn/n0.csv");
-		//tools.transformFile("/Users/bowu/Research/50newdata/tmp/example.csv");
-		//tools.test1();
-
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Ruler.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Ruler.java
deleted file mode 100644
index 944ed2c0d..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Ruler.java
+++ /dev/null
@@ -1,401 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.cleaning;
-
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.ListIterator;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import org.antlr.runtime.ANTLRStringStream;
-import org.antlr.runtime.CharStream;
-import org.antlr.runtime.Token;
-
-public class Ruler {
-	String Org = "";
-	String Trgt = "";
-	StringTokenizer st = null;
-	String[] seperator = { " ", "," };
-	public Vector<TNode> vec;
-	int curPos = 0;
-	Vector<Object[]> operators = new Vector<Object[]>();
-	Vector<Integer> positions;
-	Vector<TNode> whats;
-	Vector<Integer> consPos;
-
-	public Ruler() {
-		positions = new Vector<Integer>();
-		consPos = new Vector<Integer>();
-		whats = new Vector<TNode>();
-	}
-
-	public Ruler(String x) {
-		positions = new Vector<Integer>();
-		consPos = new Vector<Integer>();
-		whats = new Vector<TNode>();
-		this.initConstantPosition();
-		vec = new Vector<TNode>();
-		Org = x;
-		tokenize();
-	}
-
-	public void initConstantPosition() {
-		String target = ",";
-		for (int i = 0; i < vec.size(); i++) {
-			if (vec.get(i).text.compareTo(target) == 0) {
-				this.consPos.add(i);
-			}
-		}
-
-	}
-
-	public void setNewInput(String x) {
-		this.Org = x;
-		this.Trgt = "";
-		this.vec = new Vector<TNode>();
-		this.curPos = 0;
-		this.tokenize();
-		this.initConstantPosition();
-	}
-
-	public void setNewInput(Vector<TNode> x) {
-		this.Org = x.toString();
-		this.Trgt = "";
-		this.vec = new Vector<TNode>();
-		this.curPos = 0;
-		this.vec = x;
-		this.initConstantPosition();
-	}
-
-	// in current data,search the position of the tvec
-	public static int Search(Vector<TNode> xvec, Vector<TNode> tvec, int bpos) {
-		boolean isFind = false;
-		int p1 = -1;
-		for (int t = bpos; t < xvec.size() - tvec.size() + 1; t++) {
-			p1 = t;
-			for (int x = 0; x < tvec.size(); x++) {
-				int p2 = x;
-				if (xvec.get(p1).sameNode(tvec.get(p2))) {
-					p1++;
-				} else {
-					isFind = false;
-					break;
-				}
-				isFind = true;
-			}
-			if (isFind) {
-				return t;
-			}
-		}
-		return -1;
-	}
-
-	// evalPos()
-	public int evalPos(String input, Vector<TNode> t, String option) {
-		boolean incld = false;
-		if (input.contains("first")) {
-			if (!input.contains("incld")) {
-				incld = false;
-			} else {
-				incld = true;
-			}
-			// int pos1 = this.Search(this.vec,t,0);
-			if (option.compareTo("from_beginning") == 0) {
-				int pos = Ruler.Search(vec, t, 0);
-				if (pos == -1)
-					return -1;
-				if (incld) {
-					return pos;
-				} else {
-					if (pos < vec.size())
-						if (pos > 0) {
-							return pos - 1;
-						} else {
-							return 0;
-						}
-
-					else
-						return vec.size() - 1;
-				}
-
-			} else {
-				@SuppressWarnings("unchecked")
-				Vector<TNode> tmpvec = (Vector<TNode>) this.vec.clone();
-				Collections.reverse(tmpvec);
-				int pos = Ruler.Search(tmpvec, t, 0);
-				if (pos == -1)
-					return -1;
-				if (incld) {
-					if (this.vec.size() - pos - 1 >= 0
-							&& this.vec.size() - pos - 1 <= vec.size())
-						return this.vec.size() - pos - 1;
-					else
-						return 0;
-				} else {
-					if (this.vec.size() - pos >= 0
-							&& this.vec.size() - pos <= vec.size())
-						return this.vec.size() - pos;
-					else
-						return 0;
-				}
-			}
-		}
-		/* LSA to do */
-		else {
-			if (option.compareTo("from_beginning") == 0) {
-				return Integer.parseInt(input) - 1;
-			} else {
-				return this.vec.size() - Integer.parseInt(input);
-			}
-		}
-	}
-
-	public void addOperators(Object[][] opers) {
-		for (int j = 0; j < opers.length; j++) {
-			operators.add(opers[j]);
-		}
-	}
-
-	// seperate by , and " "
-	//
-	public void tokenize() {
-		CharStream cs = new ANTLRStringStream(Org);
-		Tokenizer tk = new Tokenizer(cs);
-		Token t;
-		t = tk.nextToken();
-		while (t.getType() != -1) {
-			int mytype = -1;
-			String txt = "";
-			if (t.getType() == Tokenizer.LWRD) {
-				mytype = TNode.LWRDTYP;
-				txt = t.getText();
-			} else if (t.getType() == Tokenizer.UWRD) {
-				mytype = TNode.UWRDTYP;
-				txt = t.getText();
-			} else if (t.getType() == Tokenizer.BLANK) {
-				mytype = TNode.BNKTYP;
-				txt = t.getText();
-			} else if (t.getType() == Tokenizer.NUMBER) {
-				mytype = TNode.NUMTYP;
-				txt = t.getText();
-			} else if (t.getType() == Tokenizer.SYBS) {
-				// mytype = TNode.SYBSTYP;
-				mytype = (int) t.getText().charAt(0);
-				txt = t.getText();
-			} else if (t.getType() == Tokenizer.START) {
-				mytype = TNode.STARTTYP;
-				txt = "";
-			} else if (t.getType() == Tokenizer.END) {
-				mytype = TNode.ENDTYP;
-				txt = "";
-			}
-			else if(t.getType() == Tokenizer.WRD){
-				mytype = TNode.WORD;
-				txt = t.getText();
-			}
-			TNode tx = new TNode(mytype, txt);
-			vec.add(tx);
-			t = tk.nextToken();
-		}
-	}
-
-	public static void main(String[] args) {
-	}
-
-	// move a position complied with condition
-	// move to n -1
-	// move up to tok -2
-	public void move(int n, TNode tok, int opt) {
-		if (opt == -1) {
-			this.curPos = n;
-		} else if (opt == -2) {
-			Iterator<TNode> iter = vec.iterator();
-			while (iter.hasNext()) {
-				if (iter.next().sameText(tok)) {
-					this.curPos++;
-				}
-			}
-		}
-	}
-
-	public String print() {
-		String res = "";
-		for (int i = 0; i < vec.size(); i++) {
-			String type = "";
-			if (vec.get(i).type == TNode.LWRDTYP)
-				type = "LWRD";
-			else if (vec.get(i).type == TNode.UWRDTYP)
-				type = "UWRD";
-			else if (vec.get(i).type == TNode.SYBSTYP)
-				type = "SYB";
-			else if (vec.get(i).type == TNode.NUMTYP)
-				type = "NUM";
-			else if (vec.get(i).type == TNode.BNKTYP)
-				type = "BNK";
-			res += vec.get(i).text + "<" + type + ">";
-		}
-		return res;
-	}
-
-	public String toString() {
-		String res = "";
-		for (int i = 0; i < vec.size(); i++) {
-			res += vec.get(i).text;
-		}
-		return res;
-	}
-
-	public void doOperation(String oper, String num, Vector<TNode> x, int spos,
-			int epos) {
-		int quan = 0;
-		if (num == null || num.compareTo("anynumber") == 0) {
-			quan = Integer.MAX_VALUE;
-		} else {
-			quan = Integer.parseInt(num);
-		}
-		if (oper.compareTo("del") == 0) {
-			if (spos < 0) {
-				return;// not applicable
-			}
-			if (epos < 0) {
-				return; // not applicable
-			}
-			this.det(quan, x, spos, epos);
-		}
-		if (oper.compareTo("mov") == 0) {
-			if (spos > epos) {
-				this.vec = null;
-				return;
-			}
-			this.mov(x, Integer.parseInt(num), spos, epos);
-		}
-		if (oper.compareTo("ins") == 0) {
-			this.ins(x, spos);
-		}
-	}
-
-	public void collectPoss(int x) {
-		// the consPos show be sorted from small to high
-		for (int i = 0; i < this.consPos.size(); i++) {
-			if (x < consPos.get(i)) {
-				this.positions.add(i);
-			}
-		}
-		this.positions.add(consPos.size());
-	}
-
-	// toks is the token sequence that needed to be inserted into original token
-	// sequence
-	// dpos is the position start of the insertion
-	public void ins(Vector<TNode> toks, int dpos) {
-		if (dpos < vec.size()) {
-			vec.addAll(dpos, toks);
-		} else {
-			vec.addAll(toks);
-		}
-	}
-
-	// dpos is the destination position
-	// toks specify the tokens need to be moved
-	// spos is the start position of the segment
-	// epos is the end position of the segment
-	public void mov(Vector<TNode> toks, int dpos, int spos, int epos) {
-		int pos = 0;
-		int size = 0;
-		if (toks != null) {
-			pos = Ruler.Search(this.vec, toks, spos);
-			if (pos + toks.size() > epos + 1 || pos == -1) {
-				return;
-			}
-			size = toks.size();
-		} else {
-			pos = spos;
-			if (epos == vec.size()) {
-				size = vec.size() - spos;
-			} else {
-				size = epos - spos + 1;
-			}
-		}
-		// update the end position and do the del
-		ListIterator<TNode> l = this.vec.listIterator(pos);
-		// ListIterator<TNode> dl = this.vec.listIterator(dpos);
-		int c = 0;
-		Vector<TNode> x = new Vector<TNode>();
-		for (c = 0; c < size; c++) {
-			// this.collectPoss(pos);
-			TNode tn = l.next();
-			tn.setColor(TNode.MOVCOLOR); // set color for moving.
-			x.add(tn);
-			// this.whats.add(tn);
-			l.remove();
-		}
-		if (dpos <= spos) {
-			if (dpos == vec.size()) {
-				this.vec.addAll(x);
-				return;
-			}
-			this.vec.addAll(dpos, x);
-
-		}
-		if (dpos >= epos) {
-			dpos = dpos - size;
-			if (dpos == vec.size()) {
-				this.vec.addAll(x);
-				return;
-			}
-			this.vec.addAll(dpos, x);
-		}
-	}
-
-	public void det(int n, Vector<TNode> toks, int start, int end) {
-		int cnt = 0;
-		int pos = 0;
-		int deleng = 0;
-		while (cnt < n) {
-			if (toks == null) // don't specify all particular token sequence
-			{
-				pos = start;
-				n = 0;
-				deleng = end - start + 1;
-			} else {
-				pos = Ruler.Search(this.vec, toks, start);
-				deleng = toks.size();
-			}
-			if (pos + deleng > end + 1 || pos == -1) {
-				break;
-			}
-			// update the end position and do the del
-			ListIterator<TNode> l = this.vec.listIterator(pos);
-			int c = 0;
-			for (c = 0; c < deleng; c++) {
-				// this.collectPoss(pos);
-				TNode tn = l.next();
-				this.whats.add(tn);
-				l.remove();
-				pos++;
-
-			}
-			end = end - deleng;
-			cnt++;
-		}
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Section.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Section.java
deleted file mode 100644
index 26ea270fa..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Section.java
+++ /dev/null
@@ -1,238 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.internalfunlibrary.InternalTransformationLibrary;
-
-public class Section implements GrammarTreeNode {
-	public Position[] pair;
-	public int convert = InternalTransformationLibrary.Functions.NonExist.getValue();
-	public static int time_limit = 10;
-	public Vector<int[]> rules = new Vector<int[]>();
-	public int rule_cxt_size = Segment.cxtsize_limit;
-	public int curState = 0;
-	public boolean isinloop = false;
-	public Vector<String> orgStrings = new Vector<String>();
-	public Vector<String> tarStrings = new Vector<String>();
-	public static Interpretor itInterpretor = null;
-	public static final int supermode = 1;
-	public String program = "null";
-	public String contextId;
-
-	public Section(Position[] p, Vector<String> orgStrings,
-			Vector<String> tarStrings, boolean isinloop, String contextId) {
-		this.contextId = contextId;
-		pair = p;
-		this.orgStrings = orgStrings;
-		this.tarStrings = tarStrings;
-		if (itInterpretor == null)
-			itInterpretor = new Interpretor(contextId);
-		/*
-		 * if(supermode == 0) this.createTotalOrderVector();
-		 */
-		this.reiniteRules();
-		this.isinloop = isinloop;
-	}
-	public boolean isValid(String rule)
-	{
-		boolean res = true;
-		ProgramRule convRule = new ProgramRule(rule, contextId);
-		for(int i = 0; i < orgStrings.size(); i++)
-		{
-			if(!(convRule.transform(orgStrings.get(i)).compareTo(tarStrings.get(i))==0))
-			{
-				res = false;
-				return res;
-			}
-		}
-		return res;
-	}
-	public String verifySpace() {
-		String rule = "";
-		this.pair[0].isinloop = this.isinloop;
-		this.pair[1].isinloop = this.isinloop;
-		while (curState < this.rules.size()) {
-			String rule1 = this.pair[0].VerifySpace(rules.get(curState)[0]);
-			String rule2 = this.pair[1].VerifySpace(rules.get(curState)[1]);
-			curState++;
-			if (rule1.indexOf("null") == -1 && rule2.indexOf("null") == -1) {
-				//rule = String.format("substr(value,%s,%s)", rule1, rule2);
-				rule = this.generateRule(rule1, rule2);
-				if(isValid(rule))
-				{
-					this.program = rule;
-					return rule;
-				}
-			}
-			if (rule1.indexOf("null") != -1 && rule2.indexOf("null") != -1) {
-				break;
-			}
-		}
-		this.program = "null";
-		return "null";
-	}
-	public String generateRule(String lpos, String rpos){
-		String def = String.format("substr(value,%s,%s)", lpos, rpos);
-		if(convert == InternalTransformationLibrary.Functions.Cap.getValue()){
-			String func = InternalTransformationLibrary.getName(convert);
-			def = String.format("%s(%s)", func, def);
-		}
-		else if(convert == InternalTransformationLibrary.Functions.Firstletter.getValue()){
-			String func = InternalTransformationLibrary.getName(convert);
-			def = String.format("%s(%s)", func, def);
-		}
-		else if(convert == InternalTransformationLibrary.Functions.Lowercase.getValue()){
-			String func = InternalTransformationLibrary.getName(convert);
-			def = String.format("%s(%s)", func, def);
-		}
-		else if(convert == InternalTransformationLibrary.Functions.Uppercase.getValue()){
-			String func = InternalTransformationLibrary.getName(convert);
-			def = String.format("%s(%s)", func, def);
-		}
-		return def;
-	}
-	public String toProgram() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	public GrammarTreeNode mergewith(GrammarTreeNode a) {
-		Section sec = (Section) a;
-		if(this.convert!= sec.convert){
-			return null;
-		}
-		Position x = this.pair[0].mergewith(sec.pair[0]);
-		Position y = this.pair[1].mergewith(sec.pair[1]);
-		if (x == null || y == null)
-			return null;
-		else {
-			Position[] pa = { x, y };
-			boolean loop = this.isinloop || sec.isinloop;
-			Vector<String> strs = new Vector<String>();
-			Vector<String> tars = new Vector<String>();
-			if (this.orgStrings.size() == sec.orgStrings.size()
-					&& this.orgStrings.size() == 1
-					&& this.orgStrings.get(0).compareTo(sec.orgStrings.get(0)) == 0) {
-				// merge within one example. test the loop expression
-				strs.addAll(this.orgStrings);
-				tars.add(this.tarStrings.get(0) + sec.tarStrings.get(0));
-				loop = true;
-			} else {
-				strs.addAll(this.orgStrings);
-				strs.addAll(sec.orgStrings);
-				tars.addAll(this.tarStrings);
-				tars.addAll(sec.tarStrings);
-			}
-			
-			Section st = new Section(pa, strs, tars, loop,contextId);
-			st.convert = this.convert;
-			return st;
-
-		}
-	}
-
-	public String getNodeType() {
-		return "section";
-	}
-
-	public double getScore() {
-		// TODO Auto-generated method stub
-		return this.pair[0].getScore() + this.pair[1].getScore();
-	}
-
-	@Override
-	public String getrepString() {
-		// TODO Auto-generated method stub
-		return pair[0].getrepString() + pair[1].getrepString();
-	}
-
-	@Override
-	public void createTotalOrderVector() {
-		for (int i = 0; i < pair[0].rules.size(); i++) {
-			for (int j = 0; j < pair[1].rules.size(); j++) {
-				int[] elem = { i, j };
-				rules.add(elem);
-			}
-		}
-	}
-
-	public void reiniteRules() {
-		Vector<Long> indexs = new Vector<Long>();
-		indexs.add((long) 16);
-		indexs.add((long) 16);
-		Vector<Vector<Integer>> configs = new Vector<Vector<Integer>>();
-		rules.clear();
-		getCrossIndex(indexs, 0, "", configs);
-		for (int i = 0; i < configs.size(); i++) {
-			int[] elem = { configs.get(i).get(0), configs.get(i).get(1) };
-			rules.add(elem);
-		}
-	}
-
-	public void getCrossIndex(Vector<Long> indexs, int cur, String path,
-			Vector<Vector<Integer>> configs) {
-		String tpath = path;
-		if (cur >= indexs.size()) {
-			String[] elems = tpath.split(",");
-			Vector<Integer> line = new Vector<Integer>();
-			for (String s : elems) {
-				String x = s.trim();
-				if (x.length() > 0) {
-					line.add(Integer.parseInt(x));
-				}
-			}
-			if (!line.isEmpty()) {
-				configs.add(line);
-			}
-			return;
-		}
-		for (int i = 0; i < indexs.get(cur); i++) {
-			String xtpath = path + i + ",";
-			getCrossIndex(indexs, cur + 1, xtpath, configs);
-		}
-	}
-
-	@Override
-	public void emptyState() {
-		this.curState = 0;
-	}
-
-	public String getRule(long index) {
-		if (index > this.rules.size())
-			return "null";
-		String rule = "";
-		int[] loc = this.rules.get(((int) index));
-		pair[0].isinloop = this.isinloop;
-		pair[1].isinloop = this.isinloop;
-		rule = String.format("substr(value,%s,%s)", pair[0].getRule(loc[0]),
-				pair[1].getRule(loc[1]));
-		return rule;
-	}
-
-	@Override
-	public long size() {
-		return pair[0].rules.size() * pair[1].rules.size();
-	}
-
-	public String toString() {
-		String lp = "";
-		String rp = "";
-		if (pair[0] != null) {
-			lp = pair[0].toString();
-		}
-		if (pair[1] != null) {
-			rp = pair[1].toString();
-		}
-		if(convert != -1)
-		{
-			return lp+", "+rp+(this.convert);
-		}
-		return lp + rp;
-	}
-
-	@Override
-	public String getProgram() {
-		return this.program;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Segment.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Segment.java
deleted file mode 100644
index 59cc8ba5f..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Segment.java
+++ /dev/null
@@ -1,384 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.HashSet;
-import java.util.SortedMap;
-import java.util.TreeMap;
-import java.util.Vector;
-
-public class Segment implements GrammarTreeNode {
-	public Vector<Section> section = new Vector<Section>();
-	public static final int cxtsize_limit = 4;
-	public static final int time_limit = 5;
-	public String tarString = "";
-	public static final String LEFTPOS = "leftpos";
-	public static final String RIGHTPOS = "rightpos";
-	public static final int CONST = -1;
-	public static final int UNDFN = -2;
-	public int start = 0; // start position in tarNodes, Token index
-	public int end = 0; // end position in tarNodes, Token index
-	public Vector<int[]> mappings; // corresponding multiple sources areas in org, Token indexes 
-	public boolean isinloop = false;
-	public Vector<TNode> constNodes = new Vector<TNode>();
-	public String repString = "";
-	public int curState = 0;
-	public Vector<String> segStrings = new Vector<String>();
-	public int VersionSP_size = 0;
-	public String program = "null";
-	public String contextId; 
-	
-	public Segment(Vector<TNode> cont, String contextId) {
-		this.contextId = contextId;
-		constNodes = cont;
-		for(TNode n:cont)
-		{
-			this.tarString += n.text;
-		}
-		createTotalOrderVector();
-	}
-
-	public Segment(int start, int end, Vector<TNode> cont, String contextId) {
-		this.contextId = contextId;
-		this.start = start;
-		this.end = end;
-		this.constNodes = cont;
-		for(TNode n:cont)
-		{
-			this.tarString += n.text;
-		}
-		this.createTotalOrderVector();
-	}
-
-	public Segment(Vector<Section> sections, boolean loop, String contextId) {
-		this.contextId = contextId;
-		this.section = sections;
-		this.isinloop = loop;
-		this.createTotalOrderVector();
-	}
-
-	public Segment(int start, int end, Vector<int[]> mapping,
-			Vector<TNode> orgNodes, Vector<TNode> tarNodes) {
-		this.start = start;
-		this.end = end;
-		this.mappings = mapping;
-		for (int i = start; i < end; i++) {
-			tarString += tarNodes.get(i).text;
-		}
-		initSections(orgNodes);
-		repString = "";
-		if (tarNodes.isEmpty()) {
-			repString += "EMPTY";
-		} else {
-			repString += tarNodes.get(this.start).getType();
-			if (end > start + 1)
-				repString += tarNodes.get(this.end - 1).getType();
-		}
-		this.createTotalOrderVector();
-	}
-
-	/*
-	 * public void setSections(Vector<Position[]> sections) { Vector<Section> s
-	 * = new Vector<Section>(); for(Position[] p:sections) { Section sx = new
-	 * Section(p,this.isinloop); s.add(sx); } this.section = s;
-	 * this.createTotalOrderVector(); }
-	 */
-	public Vector<TNode> getLeftCxt(int c, Vector<TNode> x) {
-		int i = cxtsize_limit;
-		Vector<TNode> res = new Vector<TNode>();
-		while (i > 0) {
-			if ((c - i) < 0) {
-				i--;
-				continue;
-			}
-			res.add(x.get(c - i));
-			i--;
-		}
-		return res;
-	}
-
-	public Vector<TNode> getRightCxt(int c, Vector<TNode> x) {
-		int i = 0;
-		Vector<TNode> res = new Vector<TNode>();
-		while (i < cxtsize_limit) {
-			if ((c + i) >= x.size())
-				break;
-			res.add(x.get(c + i));
-			i++;
-		}
-		return res;
-	}
-
-	// if valid segment reture the first program
-	// else reture "null"
-	public String verifySpace() {
-		String ruleString = "null";
-		if (this.isConstSegment()) {
-			String mdString = "";
-			for (TNode t : this.constNodes) {
-				mdString += t.text;
-			}
-			mdString = "\'" + mdString + "\'";
-			this.program = mdString;
-			return mdString;
-		}
-		for(int i = curState; i< this.section.size(); i++){
-			Section s = this.section.get(i);
-			curState = i; //update current state;
-			s.isinloop = this.isinloop;
-			ruleString = s.verifySpace();			
-			if (ruleString.indexOf("null") == -1) {
-				this.program = ruleString;
-				return ruleString;
-			}
-		}
-		this.program = ruleString;
-		return ruleString;
-	}
-	//only called for the first example
-	public void initSections(Vector<TNode> orgNodes) {
-		for (int[] elem : mappings) {
-			int s = elem[0];
-			int e = elem[1];
-			// record the data
-			Vector<String> orgStrings = new Vector<String>();
-			Vector<String> tarStrings = new Vector<String>();
-			String org = "";
-			for (int i = 0; i < orgNodes.size(); i++) {
-				org += orgNodes.get(i).text;
-			}
-			orgStrings.add(org);
-			tarStrings.add(tarString);
-			// create the startPosition
-			Vector<Integer> sset = new Vector<Integer>();
-			sset = UtilTools.getStringPos(s, orgNodes);
-			Vector<String> tars = new Vector<String>();
-			tars.add(sset.get(0).toString());
-			Position sPosition = new Position(sset, getLeftCxt(s, orgNodes),
-					getRightCxt(s, orgNodes), orgStrings, tars, this.isinloop, contextId);
-			sPosition.isinloop = this.isinloop;
-			// create the endPosition
-			Vector<Integer> eset = new Vector<Integer>();
-			eset = UtilTools.getStringPos(e, orgNodes);
-			Vector<String> tars1 = new Vector<String>();
-			tars1.add(eset.get(0).toString());
-			Position ePosition = new Position(eset, getLeftCxt(e, orgNodes),
-					getRightCxt(e, orgNodes), orgStrings, tars1, this.isinloop, contextId);
-			ePosition.isinloop = this.isinloop;
-
-			if (sPosition != null && ePosition != null) {
-				Position[] pair = { sPosition, ePosition };
-
-				Section xsec = new Section(pair, orgStrings, tarStrings,
-						isinloop, contextId);
-				if(elem.length> 2)
-					xsec.convert = elem[2];
-				section.add(xsec);
-			}
-		}
-	}
-
-	public void setinLoop(boolean res) {
-		this.isinloop = res;
-		for (Section pair : section) {
-			pair.isinloop = res;
-		}
-	}
-
-	public void setCnt(Vector<TNode> cnst) {
-		for (TNode t : cnst) {
-			constNodes.add(t);
-		}
-	}
-
-	public boolean isConstSegment() {
-		if (!this.constNodes.isEmpty()) {
-			return true;
-		} else {
-			return false;
-		}
-	}
-
-	public Segment mergewith(Segment s) {
-		if (this.isConstSegment()) {
-			if (s.isConstSegment()) {
-				if (this.constNodes.size() != s.constNodes.size()) {
-					return null;
-				} else {
-					for (int i = 0; i < this.constNodes.size(); i++) {
-						if (!this.constNodes.get(i).sameNode(
-								s.constNodes.get(i))) {
-							return null;
-						}
-					}
-				}
-			} else {
-				return null;
-			}
-			Segment res = new Segment(0, 0, this.constNodes, contextId);
-			return res;
-		}
-		// merge the position
-		HashSet<String> uniqueKeys = new HashSet<String>();
-		Vector<Section> newSections = new Vector<Section>();
-		for (Section x : this.section) {
-			for (Section y : s.section) {
-				GrammarTreeNode zSection = x.mergewith(y);
-				if (zSection != null) {
-					String ukey = zSection.toString();
-					if (!uniqueKeys.contains(ukey)) {
-						newSections.add((Section) zSection);
-						uniqueKeys.add(ukey);
-					}
-				}
-			}
-		}
-		if (newSections.isEmpty())
-			return null;
-		boolean loop = this.isinloop || s.isinloop;
-		Segment res = new Segment(newSections, loop, contextId);
-		return res;
-	}
-
-	public String getrepString() {
-		if (!this.constNodes.isEmpty() && this.repString.isEmpty()) {
-			repString = UtilTools.print(this.constNodes);
-			return repString;
-
-		} else {
-			return this.repString;
-		}
-
-	}
-
-	public String toString() {
-		if (this.isConstSegment()) {
-			return "<" + this.constNodes + ">";
-		} else {
-			String s = "<";
-			if (this.isinloop) {
-				s += "loop";
-			}
-			for (Section x : this.section) {
-				s += x.toString();
-			}
-			s += ">";
-			return s;
-		}
-	}
-
-	private double score = 0.0;
-
-	public double getScore() {
-		double r = score;
-		this.score = 0.0;
-		return r;
-	}
-
-	public Vector<Integer> rules = new Vector<Integer>();
-
-	public void createTotalOrderVector() {
-		SortedMap<Double, Vector<Integer>> xmap = new TreeMap<Double, Vector<Integer>>();
-		for (int i = 0; i < section.size(); i++) {
-			Double double1 = 0.0;
-			// reverse the order to get higher values sorted in front
-			double1 += section.get(i).getScore();
-			double key = double1;
-			if (xmap.containsKey(key)) {
-				xmap.get(key).add(i);
-			} else {
-				Vector<Integer> vi = new Vector<Integer>();
-				vi.add(i);
-				xmap.put(key, vi);
-			}
-		}
-		while (!xmap.isEmpty()) {
-			Double x = xmap.firstKey();
-			Vector<Integer> v = xmap.get(x);
-			// add the vth pair's rules
-			for (Integer e : v) {
-				rules.add(e);
-			}
-			xmap.remove(x);
-		}
-		// String mdString = "";
-		// if(this.isConstSegment())
-		// {
-		// for(TNode t:this.constNodes)
-		// {
-		// mdString += t.text;
-		// }
-		// //mdString= UtilTools.escape(mdString);
-		// mdString = "\'"+mdString+"\'";
-		// rules.add(mdString);
-		// }
-		rules.add(0);
-		for (Section s : section) {
-			this.VersionSP_size += s.size();
-		}
-		this.VersionSP_size++; // constant segment
-	}
-
-	public long size() {
-		return this.VersionSP_size;
-	}
-
-	public void emptyState() {
-		this.curState = 0;
-		for (Section s : section) {
-			s.emptyState();
-		}
-	}
-
-	public String toProgram() {
-		String s =  verifySpace();
-		return s;
-	}
-
-	public GrammarTreeNode mergewith(GrammarTreeNode a) {
-		GrammarTreeNode s;
-		if (a.getNodeType().compareTo("loop") == 0) {
-			Loop p = (Loop) a;
-			s = p.mergewith(this);
-			return s;
-		} else {
-			s = this.mergewith((Segment) a);
-			return s;
-		}
-	}
-
-	public String getRule(long index) {
-		if (index >= this.size() || index < 0) {
-			return "null";
-		} else {
-			for (int i = 0; i < rules.size(); i++) {
-				if (rules.get(i) == -1) {
-					String mdString = "";
-					if (this.isConstSegment()) {
-						for (TNode t : this.constNodes) {
-							mdString += t.text;
-						}
-						mdString = "\'" + mdString + "\'";
-						return mdString;
-					} else {
-						return "null";
-					}
-				}
-				if (index < section.get(rules.get(i)).size()) {
-					section.get(rules.get(i)).isinloop = this.isinloop;
-					return section.get(rules.get(i)).getRule(index);
-				} else {
-					index = (index - section.get(rules.get(i)).size());
-				}
-			}
-			return "null";
-		}
-	}
-
-	public String getNodeType() {
-		return "segment";
-	}
-
-	@Override
-	public String getProgram() {
-		return this.program;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/SegmentMapper.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/SegmentMapper.java
deleted file mode 100644
index cae227392..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/SegmentMapper.java
+++ /dev/null
@@ -1,242 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.internalfunlibrary.InternalTransformationLibrary;
-import edu.isi.karma.cleaning.internalfunlibrary.TransformFunction;
-import edu.isi.karma.webserver.ContextParametersRegistry;
-
-class Dataitem {
-	public int[] range = { -1, -1 };
-	public int funcid = -1;
-	public int tarpos = -1;
-	public int tarend = -1;
-}
-
-public class SegmentMapper {
-	public static InternalTransformationLibrary itfl = new InternalTransformationLibrary();
-
-	private SegmentMapper() {
-	}
-
-	// only try to find one segment whose starting pos in target is pos
-	public static Vector<Segment> findMapping(Vector<TNode> org,
-			Vector<TNode> tar, int pos) {
-		Vector<Segment> res = new Vector<Segment>();
-		Dataitem root = new Dataitem();
-		root.tarpos = pos;
-		ArrayList<Dataitem> path = new ArrayList<Dataitem>();
-		ArrayList<ArrayList<Dataitem>> ret = new ArrayList<ArrayList<Dataitem>>();
-		
-		recursiveSearch(org, tar, root, path,ret);
-		
-		res = convert2Segments(ret, org, tar);
-		return res;
-	}
-	public static Vector<Segment> convert2Segments(ArrayList<ArrayList<Dataitem>> repo , Vector<TNode> org, Vector<TNode> tar){
-		HashMap<String, ArrayList<Dataitem>> groups = new HashMap<String,ArrayList<Dataitem>>();
-		Vector<Segment> ret = new Vector<Segment>();
-		for(ArrayList<Dataitem> line: repo){
-			if(line.isEmpty()){
-				continue;
-			}
-			Dataitem item =convert(line, org, tar);
-			if(item.range[0] < 0){
-				//create constant segment and return
-				Vector<TNode> cont = new Vector<TNode>();
-				for(int ptr = item.tarpos; ptr<= item.tarend; ptr++){
-					cont.add(tar.get(ptr));
-				}
-				Segment seg = new Segment(item.tarpos, item.tarend+1, cont, contextId);
-				ret.add(seg);
-				return ret;
-			}
-			String key = item.tarpos + ", "+ item.tarend; //key for same segment. a segment can contain multiple sections.
-			if(groups.containsKey(key))
-			{
-				groups.get(key).add(item);
-			}
-			else{
-				ArrayList<Dataitem> tmp = new ArrayList<Dataitem>();
-				tmp.add(item);
-				groups.put(key, tmp);
-			}			
-		}
-		for(Map.Entry<String, ArrayList<Dataitem>> stringArrayListEntry : groups.entrySet()){
-			if(stringArrayListEntry.getValue().size() <= 0 )
-			{
-				continue;
-			}
-			Vector<int[]> kmappings = new Vector<int[]>();
-			for(Dataitem elem: stringArrayListEntry.getValue()){
-				int[] xtmp = {elem.range[0], elem.range[1], elem.funcid};
-				kmappings.add(xtmp);
-			}
-			int start = stringArrayListEntry.getValue().get(0).tarpos;
-			int end = stringArrayListEntry.getValue().get(0).tarend;
-			Segment seg = new Segment(start, end+1, kmappings, org, tar);
-			ret.add(seg);			
-		}
-		return ret;
-	}
-	public static Dataitem convert(ArrayList<Dataitem> path, Vector<TNode> org, Vector<TNode> tar) {
-		int start = 0;
-		int end = 0;
-		int[] mapping = {Integer.MAX_VALUE, Integer.MIN_VALUE, InternalTransformationLibrary.Functions.NonExist.getValue()};
-		for(int i = 0; i < path.size(); i++){
-			if(i == 0)
-				start = path.get(i).tarpos;
-			if(i == path.size() -1)
-				end = path.get(i).tarpos;
-			if(path.get(i).range[0] < mapping[0])
-			{
-				mapping[0] = path.get(i).range[0];
-			}
-			if(path.get(i).range[1] > mapping[1]){
-				mapping[1] = path.get(i).range[1];
-			}
-		}
-		mapping[1] += 1;		
-		if(path.size() <= 0)
-			return null;
-		mapping[2] = path.get(0).funcid;
-		Dataitem ret = new Dataitem();
-		ret.funcid = mapping[2];
-		ret.tarend = end;
-		ret.tarpos = start;
-		ret.range[0] = mapping[0];
-		ret.range[1] = mapping[1];
-		return ret;
-	}
-
-	public static void recursiveSearch(Vector<TNode> org, Vector<TNode> tar,
-			Dataitem root, ArrayList<Dataitem> path, ArrayList<ArrayList<Dataitem>> repo) {
-		if (root.tarpos >= tar.size()) {
-			repo.add(path);
-		}
-		Vector<Dataitem> updated = makeOneMove(org, tar, root);
-		if(updated.isEmpty()){
-			repo.add(path);
-		}
-		
-		for (Dataitem elem : updated) {
-			ArrayList<Dataitem> newlist = new ArrayList<Dataitem>();
-			newlist.addAll(path);
-			newlist.add(elem);
-			Dataitem child = new Dataitem();
-			child.range[0] = elem.range[0];
-			child.range[1] = elem.range[1];
-			child.funcid = elem.funcid;
-			child.tarpos = elem.tarpos + 1;
-			recursiveSearch(org, tar, child, newlist, repo);
-		}
-		return;
-	}
-	//match one token in the target token seq
-	public static Vector<Dataitem> makeOneMove(Vector<TNode> org,
-			Vector<TNode> tar, Dataitem root) {
-		Vector<Dataitem> ret = new Vector<Dataitem>();
-		int tpos = root.tarpos;
-		if(tpos >= tar.size())
-		{
-			return ret;
-		}
-		TNode t = tar.get(tpos);
-		String tstr = t.text;
-		boolean nomapping = true;
-		boolean followChecking = false;
-		int start = 0;
-		int end = org.size();
-		//if not the first time, only resume searching not perform full range search
-		if(root.range[1] != -1){
-			start = root.range[1]+1;
-			end = start+1;
-		}
-		for (int i = start; i < end; i++) {
-			String prefix = "";
-			if (root.funcid == InternalTransformationLibrary.Functions.NonExist.getValue()) {
-				for (TransformFunction tf : itfl.getAllFuncs()) {
-					int pos = checkOneFunction(tf, prefix, org, i, tstr);
-					if (pos != -1) {
-						Dataitem nd = new Dataitem();
-						nd.range[0] = i;
-						nd.range[1] = pos - 1;
-						nd.funcid = tf.getId();
-						nd.tarpos = root.tarpos;
-						nomapping = false;
-						ret.add(nd);
-					}
-				}				
-			} else {
-				followChecking = true;
-				int pos = checkOneFunction(itfl.getFunc(root.funcid), prefix,
-						org, i, tstr);
-				if (pos != -1) {
-					Dataitem nd = new Dataitem();
-					nd.range[0] = i;
-					nd.range[1] = pos - 1;
-					nd.funcid = root.funcid;
-					nd.tarpos = root.tarpos;
-					nomapping = false;
-					ret.add(nd);
-				}
-			}
-		}
-		if(nomapping && !followChecking)
-		{
-			//insert constant
-			Dataitem nd = new Dataitem();
-			nd.range[0] = -1;
-			nd.range[1] = -1;
-			nd.funcid = -2;
-			nd.tarpos = root.tarpos;
-			ret.add(nd);
-		}
-		return ret;
-	}
-
-	// return the ending pos if successful else return -1
-	public static int checkOneFunction(TransformFunction tf, String prefix,
-			Vector<TNode> org, int i, String tar) {
-		if(tf == null)
-			return -1;
-		if (i >= org.size()) {
-			if (prefix.compareTo(tar) == 0) {
-				return i;
-			} else {
-				return -1;
-			}
-		}
-		if (prefix.compareTo(tar) == 0)
-			return i;
-		Vector<TNode> tNodes = new Vector<TNode>();
-		tNodes.add(org.get(i));
-		String con = tf.convert(tNodes);
-		if(con == null || con.isEmpty())
-			return -1;
-		String tmp = prefix + tf.convert(tNodes);
-		if (tar.indexOf(tmp) != 0) {
-			return -1;
-		} else {
-			int t = checkOneFunction(tf, tmp, org, i + 1, tar);
-			return t;
-		}
-	}
-
-	static String contextId = ContextParametersRegistry.getInstance().getDefault().getId();
-			
-	public static void main(String[] args) {
-		String[] s1 = {"<_START>PA2050 <_END>"};
-		String[] s2 = {"2050 PA"};
-		for (int i = 0; i < s1.length; i++) {
-			Vector<TNode> ts1 = UtilTools.convertStringtoTNodes(s1[i]);
-			Vector<TNode> ts2 = UtilTools.convertStringtoTNodes(s2[i]);
-			Vector<Segment> ret = SegmentMapper.findMapping(ts1, ts2, 0);
-			System.out.println("" + ret);
-		}
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/TNode.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/TNode.java
deleted file mode 100644
index 18b589eb7..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/TNode.java
+++ /dev/null
@@ -1,122 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.cleaning;
-
-//type
-public class TNode {
-	public int color = -1;
-	public static final int MOVCOLOR = 0;
-	public static final int DELCOLOR = 1;
-	public static final int INSCOLOR = 2;
-	public static final int ANYTYP = 0;
-	public static final int NUMTYP = 1;
-	public static final int SYBSTYP = 2;
-	public static final int BNKTYP = 3;
-	public static final int UWRDTYP = 4;
-	public static final int STARTTYP = 5;
-	public static final int ENDTYP = 6;
-	public static final int LWRDTYP = 7;
-	public static final int WORD = 8;
-	public static final String ANYTOK = "ANYTOK";
-	public static final int ANYNUM = Integer.MAX_VALUE;
-	public int type;
-	public String text;
-
-	public TNode(int type, String text) {
-		this.type = type;
-		this.text = text;
-	}
-
-	public void setColor(int c) {
-		this.color = c;
-	}
-
-	public int getColor() {
-		return color;
-	}
-
-	public String toString() {
-		return "\"" + text + "\"";
-	}
-
-	public String getType() {
-		if (type == TNode.ANYTYP) {
-			return "ANYTYP";
-		} else if (type == TNode.WORD) {
-			return "Word";
-		} else if (type == TNode.NUMTYP) {
-			return "Number";
-		} else if (type == TNode.SYBSTYP) {
-			return "Symbol";
-		} else if (type == TNode.BNKTYP) {
-			return "Blank";
-		} else if (type == TNode.STARTTYP) {
-			return "START";
-		} else if (type == TNode.ENDTYP) {
-			return "END";
-		} else if (type == TNode.LWRDTYP) {
-			return "LWD";
-		} else if (type == TNode.UWRDTYP) {
-			return "UWD";
-		} else {
-			return "" + (char) this.type;
-		}
-	}
-
-	public boolean sameNode(TNode t) {
-		if (sameText(t) && sameType(t)) {
-			return true;
-		}
-		return false;
-	}
-
-	public boolean sameText(TNode t) {
-		if (this.text.compareTo(TNode.ANYTOK) == 0
-				|| t.text.compareTo(TNode.ANYTOK) == 0) {
-			return true;
-		}
-		if (this.text.compareTo(t.text) == 0) {
-			return true;
-		}
-		return false;
-	}
-
-	public boolean sameType(TNode t) {
-		if (this.type == TNode.ANYTYP || t.type == TNode.ANYTYP) {
-			return true;
-		}
-		if (this.type == t.type)
-			return true;
-		return false;
-	}
-
-	public int mergableType(TNode t) {
-
-		boolean res = this.sameType(t);
-		if (res)
-			return this.type;
-		if ((this.type == TNode.UWRDTYP || this.type == TNode.LWRDTYP || this.type == TNode.WORD)
-				&& (t.type == TNode.LWRDTYP || t.type == TNode.UWRDTYP || t.type == TNode.WORD)) {
-			return TNode.WORD;
-		}
-		return -1;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Template.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Template.java
deleted file mode 100644
index 117fc2495..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Template.java
+++ /dev/null
@@ -1,225 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.Vector;
-
-public class Template implements GrammarTreeNode {
-	public static final int temp_limit = 2048;
-	public int supermode = 1;
-	public Vector<GrammarTreeNode> body = new Vector<GrammarTreeNode>();
-	public Vector<Vector<Integer>> indexes = new Vector<Vector<Integer>>();
-	public int curState = 0;
-	public long size = 1;
-	public String program = "null";
-
-	public Template(Vector<GrammarTreeNode> body) {
-		this.body = body;
-		Vector<Long> x = new Vector<Long>();
-		for (GrammarTreeNode g : body) {
-			x.add(g.size());
-		}
-		for (Long k : x) {
-			size *= k;
-		}
-		getCrossIndex(x, indexes);
-	}
-
-	public String toString() {
-		String str = "";
-		for (GrammarTreeNode gt : body) {
-			str += gt.toString();
-		}
-		return str;
-	}
-
-	/*
-	 * public void getCrossIndex(Vector<Long> indexs, int cur, String path,
-	 * Vector<Vector<Integer>> configs) { String tpath = path; if
-	 * (configs.size() > temp_limit) { return; } if (cur >= indexs.size()) {
-	 * String[] elems = tpath.split(","); Vector<Integer> line = new
-	 * Vector<Integer>(); for (String s : elems) { String x = s.trim(); if
-	 * (x.length() > 0) { line.add(Integer.parseInt(x)); } } if (line.size() >
-	 * 0) { configs.add(line); } return; } for (int i = 0; i < indexs.get(cur);
-	 * i++) { String xtpath = path + i + ","; getCrossIndex(indexs, cur + 1,
-	 * xtpath, configs); } }
-	 */
-	// iteratively generate combinations
-	public void getCrossIndex(Vector<Long> indexs,
-			Vector<Vector<Integer>> configs) {
-		int k = indexs.size();
-		int[] com = new int[k];
-		for (int i = 0; i < k; i++)
-			com[i] = 0;
-		while (com[k - 1] < indexs.get(k - 1)) {
-			Vector<Integer> res = new Vector<Integer>();
-			for (int i = 0; i < k; i++) {
-				// System.out.print(""+com[i]);
-				res.add(com[i]);
-			}
-			configs.add(res);
-			if (configs.size() > temp_limit) {
-				return;
-			}
-			int t = k - 1;
-			while (t != 0 && com[t] == indexs.get(t) - 1)
-				t--;
-			com[t]++;
-			if (t == 0 && com[t] >= indexs.get(0)) {
-				break;
-			}
-			for (int i = t + 1; i < k; i++)
-				com[i] = 0;
-		}
-	}
-
-	public String prog1() {
-		String res = "";
-		for (int i = 0; i < this.body.size(); i++) {
-			GrammarTreeNode gt = body.get(i);
-			if (gt.getNodeType().compareTo("segment") == 0) {
-				Segment seg = (Segment) gt;
-				String s = seg.verifySpace();
-				if (s.indexOf("null") != -1)
-					return "null";
-				res += s + "+";
-			} else if (gt.getNodeType().compareTo("loop") == 0) {
-				Loop p = (Loop) gt;
-				String x = p.verifySpace();
-				if (x.indexOf("null") != -1)
-					return "null";
-				if (p.looptype == Loop.LOOP_START) {
-					res += "loop(value,r\"" + x + "+";
-				} else if (p.looptype == Loop.LOOP_END) {
-					res += x;
-					res += "\")+";
-				} else if (p.looptype == Loop.LOOP_MID) {
-					res += x + "+";
-				} else if (p.looptype == Loop.LOOP_BOTH) {
-					res += "loop(value,r\"" + x + "\")+";
-				}
-			}
-		}
-		if (res.charAt(res.length() - 1) == '+') {
-			res = res.substring(0, res.length() - 1);
-		}
-		if (res.length() > 0 && !res.contains("null")) {
-			return res;
-		} else {
-			return null;
-		}
-	}
-
-	public String toProgram() {
-		if (supermode == 0) {
-			String res =  prog0();
-			this.program = res;
-			return res;
-		} else {
-			String res =  prog1();
-			this.program = res;
-			return res;
-		}
-	}
-
-	public String prog0() {
-		while (true) {
-			if (curState >= indexes.size())
-				return "null";
-			Vector<Integer> xIntegers = indexes.get(curState);
-			String res = "";
-			for (int i = 0; i < xIntegers.size(); i++) {
-				GrammarTreeNode gt = body.get(i);
-				int ind = xIntegers.get(i);
-				if (gt.getNodeType().compareTo("segment") == 0) {
-					res += ((Segment) gt).getRule(ind) + "+";
-				} else if (gt.getNodeType().compareTo("loop") == 0) {
-					Loop p = (Loop) gt;
-					String x = p.getRule(ind);
-					if (p.looptype == Loop.LOOP_START) {
-						res += "loop(value,r\"" + x + "+";
-					} else if (p.looptype == Loop.LOOP_END) {
-						res += x;
-						res += "\")+";
-					} else if (p.looptype == Loop.LOOP_MID) {
-						res += x + "+";
-					} else if (p.looptype == Loop.LOOP_BOTH) {
-						res += "loop(value,r\"" + x + "\")+";
-					}
-				}
-			}
-			if (res.charAt(res.length() - 1) == '+') {
-				res = res.substring(0, res.length() - 1);
-			}
-			if (res.length() > 0 && !res.contains("null")) {
-				curState++; // as Template is conbinatioin of different
-							// strings
-				return res;
-			} else {
-				this.curState += 1;
-			}
-		}
-	}
-
-	@Override
-	public GrammarTreeNode mergewith(GrammarTreeNode a) {
-		Vector<GrammarTreeNode> line2 = ((Template) a).body;
-		Vector<GrammarTreeNode> line1 = this.body;
-		Vector<GrammarTreeNode> nLine = new Vector<GrammarTreeNode>();
-		if (line1.size() != line2.size()) {
-			return null;
-		}
-		for (int i = 0; i < line2.size(); i++) {
-			GrammarTreeNode gt = line1.get(i).mergewith(line2.get(i));
-			if (gt == null) {
-				return null;
-			}
-			nLine.add(gt);
-		}
-		Template x = new Template(nLine);
-		return (GrammarTreeNode) x;
-	}
-
-	@Override
-	public String getNodeType() {
-		// TODO Auto-generated method stub
-		return "template";
-	}
-
-	@Override
-	public double getScore() {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	@Override
-	public String getrepString() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void createTotalOrderVector() {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void emptyState() {
-		curState = 0;
-		for (GrammarTreeNode treeNode : body) {
-			treeNode.emptyState();
-		}
-
-	}
-
-	@Override
-	public long size() {
-		// TODO Auto-generated method stub
-		return this.size;
-	}
-
-	@Override
-	public String getProgram() {
-		return this.program;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Tokenizer.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Tokenizer.java
deleted file mode 100644
index 30d4aa635..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Tokenizer.java
+++ /dev/null
@@ -1,1186 +0,0 @@
-// $ANTLR 3.4 Tokenizer.g 2015-01-23 11:20:47
-
-package edu.isi.karma.cleaning;
-
-import org.antlr.runtime.CharStream;
-import org.antlr.runtime.CommonToken;
-import org.antlr.runtime.EarlyExitException;
-import org.antlr.runtime.IntStream;
-import org.antlr.runtime.Lexer;
-import org.antlr.runtime.MismatchedSetException;
-import org.antlr.runtime.NoViableAltException;
-import org.antlr.runtime.RecognitionException;
-import org.antlr.runtime.RecognizerSharedState;
-import org.antlr.runtime.Token;
-
-@SuppressWarnings({"all", "warnings", "unchecked"})
-public class Tokenizer extends Lexer {
-    public static final int EOF=-1;
-    public static final int BLANK=4;
-    public static final int COL=5;
-    public static final int DIGIT=6;
-    public static final int END=7;
-    public static final int LETTER=8;
-    public static final int LOWER=9;
-    public static final int LWRD=10;
-    public static final int NUMBER=11;
-    public static final int ROW=12;
-    public static final int START=13;
-    public static final int SYBS=14;
-    public static final int SYMBOL=15;
-    public static final int UPPER=16;
-    public static final int UWRD=17;
-    public static final int WRD=18;
-
-    // delegates
-    // delegators
-    public Lexer[] getDelegates() {
-        return new Lexer[] {};
-    }
-
-    public Tokenizer() {} 
-    public Tokenizer(CharStream input) {
-        this(input, new RecognizerSharedState());
-    }
-    public Tokenizer(CharStream input, RecognizerSharedState state) {
-        super(input,state);
-    }
-    public String getGrammarFileName() { return "Tokenizer.g"; }
-
-    public Token nextToken() {
-        while (true) {
-            if ( input.LA(1)==CharStream.EOF ) {
-                Token eof = new CommonToken((CharStream)input,Token.EOF,
-                                            Token.DEFAULT_CHANNEL,
-                                            input.index(),input.index());
-                eof.setLine(getLine());
-                eof.setCharPositionInLine(getCharPositionInLine());
-                return eof;
-            }
-            state.token = null;
-    	state.channel = Token.DEFAULT_CHANNEL;
-            state.tokenStartCharIndex = input.index();
-            state.tokenStartCharPositionInLine = input.getCharPositionInLine();
-            state.tokenStartLine = input.getLine();
-    	state.text = null;
-            try {
-                int m = input.mark();
-                state.backtracking=1; 
-                state.failed=false;
-                mTokens();
-                state.backtracking=0;
-                if ( state.failed ) {
-                    input.rewind(m);
-                    input.consume(); 
-                }
-                else {
-                    emit();
-                    return state.token;
-                }
-            }
-            catch (RecognitionException re) {
-                // shouldn't happen in backtracking mode, but...
-                reportError(re);
-                recover(re);
-            }
-        }
-    }
-
-    public void memoize(IntStream input,
-    		int ruleIndex,
-    		int ruleStartIndex)
-    {
-    if ( state.backtracking>1 ) super.memoize(input, ruleIndex, ruleStartIndex);
-    }
-
-    public boolean alreadyParsedRule(IntStream input, int ruleIndex) {
-    if ( state.backtracking>1 ) return super.alreadyParsedRule(input, ruleIndex);
-    return false;
-    }
-    // $ANTLR start "BLANK"
-    public final void mBLANK() throws RecognitionException {
-        try {
-            int _type = BLANK;
-            int _channel = DEFAULT_TOKEN_CHANNEL;
-            // Tokenizer.g:4:6: ( ( '\\t' | ' ' | '\\r' | '\\n' | '\\u000C' )+ )
-            // Tokenizer.g:4:8: ( '\\t' | ' ' | '\\r' | '\\n' | '\\u000C' )+
-            {
-            // Tokenizer.g:4:8: ( '\\t' | ' ' | '\\r' | '\\n' | '\\u000C' )+
-            int cnt1=0;
-            loop1:
-            do {
-                int alt1=2;
-                int LA1_0 = input.LA(1);
-
-                if ( ((LA1_0 >= '\t' && LA1_0 <= '\n')||(LA1_0 >= '\f' && LA1_0 <= '\r')||LA1_0==' ') ) {
-                    alt1=1;
-                }
-
-
-                switch (alt1) {
-            	case 1 :
-            	    // Tokenizer.g:
-            	    {
-            	    if ( (input.LA(1) >= '\t' && input.LA(1) <= '\n')||(input.LA(1) >= '\f' && input.LA(1) <= '\r')||input.LA(1)==' ' ) {
-            	        input.consume();
-            	        state.failed=false;
-            	    }
-            	    else {
-            	        if (state.backtracking>0) {state.failed=true; return ;}
-            	        MismatchedSetException mse = new MismatchedSetException(null,input);
-            	        recover(mse);
-            	        throw mse;
-            	    }
-
-
-            	    }
-            	    break;
-
-            	default :
-            	    if ( cnt1 >= 1 ) break loop1;
-            	    if (state.backtracking>0) {state.failed=true; return ;}
-                        EarlyExitException eee =
-                            new EarlyExitException(1, input);
-                        throw eee;
-                }
-                cnt1++;
-            } while (true);
-
-
-            }
-
-            state.type = _type;
-            state.channel = _channel;
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "BLANK"
-
-    // $ANTLR start "WRD"
-    public final void mWRD() throws RecognitionException {
-        try {
-            int _type = WRD;
-            int _channel = DEFAULT_TOKEN_CHANNEL;
-            // Tokenizer.g:5:5: ( ( UPPER | LOWER )+ )
-            // Tokenizer.g:5:7: ( UPPER | LOWER )+
-            {
-            // Tokenizer.g:5:7: ( UPPER | LOWER )+
-            int cnt2=0;
-            loop2:
-            do {
-                int alt2=2;
-                int LA2_0 = input.LA(1);
-
-                if ( ((LA2_0 >= 'A' && LA2_0 <= 'Z')||(LA2_0 >= 'a' && LA2_0 <= 'z')||(LA2_0 >= '\u00C0' && LA2_0 <= '\u00D6')||(LA2_0 >= '\u00D8' && LA2_0 <= '\u00F6')||(LA2_0 >= '\u00F8' && LA2_0 <= '\u00FF')) ) {
-                    alt2=1;
-                }
-
-
-                switch (alt2) {
-            	case 1 :
-            	    // Tokenizer.g:
-            	    {
-            	    if ( (input.LA(1) >= 'A' && input.LA(1) <= 'Z')||(input.LA(1) >= 'a' && input.LA(1) <= 'z')||(input.LA(1) >= '\u00C0' && input.LA(1) <= '\u00D6')||(input.LA(1) >= '\u00D8' && input.LA(1) <= '\u00F6')||(input.LA(1) >= '\u00F8' && input.LA(1) <= '\u00FF') ) {
-            	        input.consume();
-            	        state.failed=false;
-            	    }
-            	    else {
-            	        if (state.backtracking>0) {state.failed=true; return ;}
-            	        MismatchedSetException mse = new MismatchedSetException(null,input);
-            	        recover(mse);
-            	        throw mse;
-            	    }
-
-
-            	    }
-            	    break;
-
-            	default :
-            	    if ( cnt2 >= 1 ) break loop2;
-            	    if (state.backtracking>0) {state.failed=true; return ;}
-                        EarlyExitException eee =
-                            new EarlyExitException(2, input);
-                        throw eee;
-                }
-                cnt2++;
-            } while (true);
-
-
-            }
-
-            state.type = _type;
-            state.channel = _channel;
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "WRD"
-
-    // $ANTLR start "UWRD"
-    public final void mUWRD() throws RecognitionException {
-        try {
-            int _type = UWRD;
-            int _channel = DEFAULT_TOKEN_CHANNEL;
-            // Tokenizer.g:6:6: ( UPPER )
-            // Tokenizer.g:
-            {
-            if ( (input.LA(1) >= 'A' && input.LA(1) <= 'Z')||(input.LA(1) >= '\u00C0' && input.LA(1) <= '\u00D6')||(input.LA(1) >= '\u00D8' && input.LA(1) <= '\u00DE') ) {
-                input.consume();
-                state.failed=false;
-            }
-            else {
-                if (state.backtracking>0) {state.failed=true; return ;}
-                MismatchedSetException mse = new MismatchedSetException(null,input);
-                recover(mse);
-                throw mse;
-            }
-
-
-            }
-
-            state.type = _type;
-            state.channel = _channel;
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "UWRD"
-
-    // $ANTLR start "LWRD"
-    public final void mLWRD() throws RecognitionException {
-        try {
-            int _type = LWRD;
-            int _channel = DEFAULT_TOKEN_CHANNEL;
-            // Tokenizer.g:7:6: ( ( LOWER )+ )
-            // Tokenizer.g:7:8: ( LOWER )+
-            {
-            // Tokenizer.g:7:8: ( LOWER )+
-            int cnt3=0;
-            loop3:
-            do {
-                int alt3=2;
-                int LA3_0 = input.LA(1);
-
-                if ( ((LA3_0 >= 'a' && LA3_0 <= 'z')||(LA3_0 >= '\u00DF' && LA3_0 <= '\u00F6')||(LA3_0 >= '\u00F8' && LA3_0 <= '\u00FF')) ) {
-                    alt3=1;
-                }
-
-
-                switch (alt3) {
-            	case 1 :
-            	    // Tokenizer.g:
-            	    {
-            	    if ( (input.LA(1) >= 'a' && input.LA(1) <= 'z')||(input.LA(1) >= '\u00DF' && input.LA(1) <= '\u00F6')||(input.LA(1) >= '\u00F8' && input.LA(1) <= '\u00FF') ) {
-            	        input.consume();
-            	        state.failed=false;
-            	    }
-            	    else {
-            	        if (state.backtracking>0) {state.failed=true; return ;}
-            	        MismatchedSetException mse = new MismatchedSetException(null,input);
-            	        recover(mse);
-            	        throw mse;
-            	    }
-
-
-            	    }
-            	    break;
-
-            	default :
-            	    if ( cnt3 >= 1 ) break loop3;
-            	    if (state.backtracking>0) {state.failed=true; return ;}
-                        EarlyExitException eee =
-                            new EarlyExitException(3, input);
-                        throw eee;
-                }
-                cnt3++;
-            } while (true);
-
-
-            }
-
-            state.type = _type;
-            state.channel = _channel;
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "LWRD"
-
-    // $ANTLR start "NUMBER"
-    public final void mNUMBER() throws RecognitionException {
-        try {
-            int _type = NUMBER;
-            int _channel = DEFAULT_TOKEN_CHANNEL;
-            // Tokenizer.g:8:7: ( ( DIGIT )+ )
-            // Tokenizer.g:8:9: ( DIGIT )+
-            {
-            // Tokenizer.g:8:9: ( DIGIT )+
-            int cnt4=0;
-            loop4:
-            do {
-                int alt4=2;
-                int LA4_0 = input.LA(1);
-
-                if ( ((LA4_0 >= '0' && LA4_0 <= '9')) ) {
-                    alt4=1;
-                }
-
-
-                switch (alt4) {
-            	case 1 :
-            	    // Tokenizer.g:
-            	    {
-            	    if ( (input.LA(1) >= '0' && input.LA(1) <= '9') ) {
-            	        input.consume();
-            	        state.failed=false;
-            	    }
-            	    else {
-            	        if (state.backtracking>0) {state.failed=true; return ;}
-            	        MismatchedSetException mse = new MismatchedSetException(null,input);
-            	        recover(mse);
-            	        throw mse;
-            	    }
-
-
-            	    }
-            	    break;
-
-            	default :
-            	    if ( cnt4 >= 1 ) break loop4;
-            	    if (state.backtracking>0) {state.failed=true; return ;}
-                        EarlyExitException eee =
-                            new EarlyExitException(4, input);
-                        throw eee;
-                }
-                cnt4++;
-            } while (true);
-
-
-            }
-
-            state.type = _type;
-            state.channel = _channel;
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "NUMBER"
-
-    // $ANTLR start "SYBS"
-    public final void mSYBS() throws RecognitionException {
-        try {
-            int _type = SYBS;
-            int _channel = DEFAULT_TOKEN_CHANNEL;
-            // Tokenizer.g:9:5: ( ( SYMBOL ) )
-            // Tokenizer.g:
-            {
-            if ( (input.LA(1) >= '!' && input.LA(1) <= '/')||(input.LA(1) >= ':' && input.LA(1) <= '@')||(input.LA(1) >= '[' && input.LA(1) <= '`')||(input.LA(1) >= '{' && input.LA(1) <= '~')||input.LA(1)=='€' ) {
-                input.consume();
-                state.failed=false;
-            }
-            else {
-                if (state.backtracking>0) {state.failed=true; return ;}
-                MismatchedSetException mse = new MismatchedSetException(null,input);
-                recover(mse);
-                throw mse;
-            }
-
-
-            }
-
-            state.type = _type;
-            state.channel = _channel;
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "SYBS"
-
-    // $ANTLR start "START"
-    public final void mSTART() throws RecognitionException {
-        try {
-            int _type = START;
-            int _channel = DEFAULT_TOKEN_CHANNEL;
-            // Tokenizer.g:10:7: ( '<_START>' )
-            // Tokenizer.g:10:9: '<_START>'
-            {
-            match("<_START>"); if (state.failed) return ;
-
-
-
-            }
-
-            state.type = _type;
-            state.channel = _channel;
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "START"
-
-    // $ANTLR start "END"
-    public final void mEND() throws RecognitionException {
-        try {
-            int _type = END;
-            int _channel = DEFAULT_TOKEN_CHANNEL;
-            // Tokenizer.g:11:5: ( '<_END>' )
-            // Tokenizer.g:11:7: '<_END>'
-            {
-            match("<_END>"); if (state.failed) return ;
-
-
-
-            }
-
-            state.type = _type;
-            state.channel = _channel;
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "END"
-
-    // $ANTLR start "COL"
-    public final void mCOL() throws RecognitionException {
-        try {
-            int _type = COL;
-            int _channel = DEFAULT_TOKEN_CHANNEL;
-            // Tokenizer.g:12:5: ( '<_COL>' )
-            // Tokenizer.g:12:7: '<_COL>'
-            {
-            match("<_COL>"); if (state.failed) return ;
-
-
-
-            }
-
-            state.type = _type;
-            state.channel = _channel;
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "COL"
-
-    // $ANTLR start "ROW"
-    public final void mROW() throws RecognitionException {
-        try {
-            int _type = ROW;
-            int _channel = DEFAULT_TOKEN_CHANNEL;
-            // Tokenizer.g:13:5: ( '<_ROW>' )
-            // Tokenizer.g:13:7: '<_ROW>'
-            {
-            match("<_ROW>"); if (state.failed) return ;
-
-
-
-            }
-
-            state.type = _type;
-            state.channel = _channel;
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "ROW"
-
-    // $ANTLR start "SYMBOL"
-    public final void mSYMBOL() throws RecognitionException {
-        try {
-            // Tokenizer.g:16:2: ( '!' .. '/' | ':' .. '@' | '[' .. '`' | '{' .. '~' | '�' )
-            // Tokenizer.g:
-            {
-            if ( (input.LA(1) >= '!' && input.LA(1) <= '/')||(input.LA(1) >= ':' && input.LA(1) <= '@')||(input.LA(1) >= '[' && input.LA(1) <= '`')||(input.LA(1) >= '{' && input.LA(1) <= '~')||input.LA(1)=='\uFFFD' ) {
-                input.consume();
-                state.failed=false;
-            }
-            else {
-                if (state.backtracking>0) {state.failed=true; return ;}
-                MismatchedSetException mse = new MismatchedSetException(null,input);
-                recover(mse);
-                throw mse;
-            }
-
-
-            }
-
-
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "SYMBOL"
-
-    // $ANTLR start "LETTER"
-    public final void mLETTER() throws RecognitionException {
-        try {
-            // Tokenizer.g:18:2: ( LOWER | UPPER )
-            // Tokenizer.g:
-            {
-            if ( (input.LA(1) >= 'A' && input.LA(1) <= 'Z')||(input.LA(1) >= 'a' && input.LA(1) <= 'z')||(input.LA(1) >= '\u00C0' && input.LA(1) <= '\u00D6')||(input.LA(1) >= '\u00D8' && input.LA(1) <= '\u00F6')||(input.LA(1) >= '\u00F8' && input.LA(1) <= '\u00FF') ) {
-                input.consume();
-                state.failed=false;
-            }
-            else {
-                if (state.backtracking>0) {state.failed=true; return ;}
-                MismatchedSetException mse = new MismatchedSetException(null,input);
-                recover(mse);
-                throw mse;
-            }
-
-
-            }
-
-
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "LETTER"
-
-    // $ANTLR start "LOWER"
-    public final void mLOWER() throws RecognitionException {
-        try {
-            // Tokenizer.g:20:2: ( '\\u0061' .. '\\u007a' | '\\u00df' .. '\\u00f6' | '\\u00f8' .. '\\u00ff' )
-            // Tokenizer.g:
-            {
-            if ( (input.LA(1) >= 'a' && input.LA(1) <= 'z')||(input.LA(1) >= '\u00DF' && input.LA(1) <= '\u00F6')||(input.LA(1) >= '\u00F8' && input.LA(1) <= '\u00FF') ) {
-                input.consume();
-                state.failed=false;
-            }
-            else {
-                if (state.backtracking>0) {state.failed=true; return ;}
-                MismatchedSetException mse = new MismatchedSetException(null,input);
-                recover(mse);
-                throw mse;
-            }
-
-
-            }
-
-
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "LOWER"
-
-    // $ANTLR start "UPPER"
-    public final void mUPPER() throws RecognitionException {
-        try {
-            // Tokenizer.g:22:2: ( '\\u0041' .. '\\u005a' | '\\u00c0' .. '\\u00d6' | '\\u00d8' .. '\\u00de' )
-            // Tokenizer.g:
-            {
-            if ( (input.LA(1) >= 'A' && input.LA(1) <= 'Z')||(input.LA(1) >= '\u00C0' && input.LA(1) <= '\u00D6')||(input.LA(1) >= '\u00D8' && input.LA(1) <= '\u00DE') ) {
-                input.consume();
-                state.failed=false;
-            }
-            else {
-                if (state.backtracking>0) {state.failed=true; return ;}
-                MismatchedSetException mse = new MismatchedSetException(null,input);
-                recover(mse);
-                throw mse;
-            }
-
-
-            }
-
-
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "UPPER"
-
-    // $ANTLR start "DIGIT"
-    public final void mDIGIT() throws RecognitionException {
-        try {
-            // Tokenizer.g:23:16: ( '0' .. '9' )
-            // Tokenizer.g:
-            {
-            if ( (input.LA(1) >= '0' && input.LA(1) <= '9') ) {
-                input.consume();
-                state.failed=false;
-            }
-            else {
-                if (state.backtracking>0) {state.failed=true; return ;}
-                MismatchedSetException mse = new MismatchedSetException(null,input);
-                recover(mse);
-                throw mse;
-            }
-
-
-            }
-
-
-        }
-        finally {
-        	// do for sure before leaving
-        }
-    }
-    // $ANTLR end "DIGIT"
-
-    public void mTokens() throws RecognitionException {
-        // Tokenizer.g:1:39: ( BLANK | WRD | UWRD | LWRD | NUMBER | SYBS | START | END | COL | ROW )
-        int alt5=10;
-        switch ( input.LA(1) ) {
-        case '\t':
-        case '\n':
-        case '\f':
-        case '\r':
-        case ' ':
-            {
-            alt5=1;
-            }
-            break;
-        case 'A':
-        case 'B':
-        case 'C':
-        case 'D':
-        case 'E':
-        case 'F':
-        case 'G':
-        case 'H':
-        case 'I':
-        case 'J':
-        case 'K':
-        case 'L':
-        case 'M':
-        case 'N':
-        case 'O':
-        case 'P':
-        case 'Q':
-        case 'R':
-        case 'S':
-        case 'T':
-        case 'U':
-        case 'V':
-        case 'W':
-        case 'X':
-        case 'Y':
-        case 'Z':
-        case '\u00C0':
-        case '\u00C1':
-        case '\u00C2':
-        case '\u00C3':
-        case '\u00C4':
-        case '\u00C5':
-        case '\u00C6':
-        case '\u00C7':
-        case '\u00C8':
-        case '\u00C9':
-        case '\u00CA':
-        case '\u00CB':
-        case '\u00CC':
-        case '\u00CD':
-        case '\u00CE':
-        case '\u00CF':
-        case '\u00D0':
-        case '\u00D1':
-        case '\u00D2':
-        case '\u00D3':
-        case '\u00D4':
-        case '\u00D5':
-        case '\u00D6':
-        case '\u00D8':
-        case '\u00D9':
-        case '\u00DA':
-        case '\u00DB':
-        case '\u00DC':
-        case '\u00DD':
-        case '\u00DE':
-            {
-            int LA5_2 = input.LA(2);
-
-            if ( (synpred2_Tokenizer()) ) {
-                alt5=2;
-            }
-            else if ( (synpred3_Tokenizer()) ) {
-                alt5=3;
-            }
-            else {
-                if (state.backtracking>0) {state.failed=true; return ;}
-                NoViableAltException nvae =
-                    new NoViableAltException("", 5, 2, input);
-
-                throw nvae;
-
-            }
-            }
-            break;
-        case 'a':
-        case 'b':
-        case 'c':
-        case 'd':
-        case 'e':
-        case 'f':
-        case 'g':
-        case 'h':
-        case 'i':
-        case 'j':
-        case 'k':
-        case 'l':
-        case 'm':
-        case 'n':
-        case 'o':
-        case 'p':
-        case 'q':
-        case 'r':
-        case 's':
-        case 't':
-        case 'u':
-        case 'v':
-        case 'w':
-        case 'x':
-        case 'y':
-        case 'z':
-        case '\u00DF':
-        case '\u00E0':
-        case '\u00E1':
-        case '\u00E2':
-        case '\u00E3':
-        case '\u00E4':
-        case '\u00E5':
-        case '\u00E6':
-        case '\u00E7':
-        case '\u00E8':
-        case '\u00E9':
-        case '\u00EA':
-        case '\u00EB':
-        case '\u00EC':
-        case '\u00ED':
-        case '\u00EE':
-        case '\u00EF':
-        case '\u00F0':
-        case '\u00F1':
-        case '\u00F2':
-        case '\u00F3':
-        case '\u00F4':
-        case '\u00F5':
-        case '\u00F6':
-        case '\u00F8':
-        case '\u00F9':
-        case '\u00FA':
-        case '\u00FB':
-        case '\u00FC':
-        case '\u00FD':
-        case '\u00FE':
-        case '\u00FF':
-            {
-            int LA5_5 = input.LA(2);
-
-            if ( (synpred2_Tokenizer()) ) {
-                alt5=2;
-            }
-            else if ( (synpred4_Tokenizer()) ) {
-                alt5=4;
-            }
-            else {
-                if (state.backtracking>0) {state.failed=true; return ;}
-                NoViableAltException nvae =
-                    new NoViableAltException("", 5, 5, input);
-
-                throw nvae;
-
-            }
-            }
-            break;
-        case '0':
-        case '1':
-        case '2':
-        case '3':
-        case '4':
-        case '5':
-        case '6':
-        case '7':
-        case '8':
-        case '9':
-            {
-            alt5=5;
-            }
-            break;
-        case '<':
-            {
-            int LA5_8 = input.LA(2);
-
-            
-            if ( (synpred7_Tokenizer()) ) {
-                alt5=7;
-            }
-            else if ( (synpred8_Tokenizer()) ) {
-                alt5=8;
-            }
-            else if ( (synpred6_Tokenizer()) ) {
-                alt5=6;
-            }
-            else if ( (synpred9_Tokenizer()) ) {
-                alt5=9;
-            }
-            else if ( (true) ) {
-                alt5=10;
-            }
-            else {
-                if (state.backtracking>0) {state.failed=true; return ;}
-                NoViableAltException nvae =
-                    new NoViableAltException("", 5, 8, input);
-
-                throw nvae;
-
-            }
-            }
-            break;
-        case '!':
-        case '\"':
-        case '#':
-        case '$':
-        case '%':
-        case '&':
-        case '\'':
-        case '(':
-        case ')':
-        case '*':
-        case '+':
-        case ',':
-        case '-':
-        case '.':
-        case '/':
-        case ':':
-        case ';':
-        case '=':
-        case '>':
-        case '?':
-        case '@':
-        case '[':
-        case '\\':
-        case ']':
-        case '^':
-        case '_':
-        case '`':
-        case '{':
-        case '|':
-        case '}':
-        case '~':
-        case '€':
-            {
-            alt5=6;
-            }
-            break;
-        default:
-            if (state.backtracking>0) {state.failed=true; return ;}
-            NoViableAltException nvae =
-                new NoViableAltException("", 5, 0, input);
-
-            throw nvae;
-
-        }
-
-        switch (alt5) {
-            case 1 :
-                // Tokenizer.g:1:41: BLANK
-                {
-                mBLANK(); if (state.failed) return ;
-
-
-                }
-                break;
-            case 2 :
-                // Tokenizer.g:1:47: WRD
-                {
-                mWRD(); if (state.failed) return ;
-
-
-                }
-                break;
-            case 3 :
-                // Tokenizer.g:1:51: UWRD
-                {
-                mUWRD(); if (state.failed) return ;
-
-
-                }
-                break;
-            case 4 :
-                // Tokenizer.g:1:56: LWRD
-                {
-                mLWRD(); if (state.failed) return ;
-
-
-                }
-                break;
-            case 5 :
-                // Tokenizer.g:1:61: NUMBER
-                {
-                mNUMBER(); if (state.failed) return ;
-
-
-                }
-                break;
-            case 6 :
-                // Tokenizer.g:1:68: SYBS
-                {
-                mSYBS(); if (state.failed) return ;
-
-
-                }
-                break;
-            case 7 :
-                // Tokenizer.g:1:73: START
-                {
-                mSTART(); if (state.failed) return ;
-
-
-                }
-                break;
-            case 8 :
-                // Tokenizer.g:1:79: END
-                {
-                mEND(); if (state.failed) return ;
-
-
-                }
-                break;
-            case 9 :
-                // Tokenizer.g:1:83: COL
-                {
-                mCOL(); if (state.failed) return ;
-
-
-                }
-                break;
-            case 10 :
-                // Tokenizer.g:1:87: ROW
-                {
-                mROW(); if (state.failed) return ;
-
-
-                }
-                break;
-
-        }
-
-    }
-
-    // $ANTLR start synpred2_Tokenizer
-    public final void synpred2_Tokenizer_fragment() throws RecognitionException {
-        // Tokenizer.g:1:47: ( WRD )
-        // Tokenizer.g:1:47: WRD
-        {
-        mWRD(); if (state.failed) return ;
-
-
-        }
-
-    }
-    // $ANTLR end synpred2_Tokenizer
-
-    // $ANTLR start synpred3_Tokenizer
-    public final void synpred3_Tokenizer_fragment() throws RecognitionException {
-        // Tokenizer.g:1:51: ( UWRD )
-        // Tokenizer.g:
-        {
-        if ( (input.LA(1) >= 'A' && input.LA(1) <= 'Z')||(input.LA(1) >= '\u00C0' && input.LA(1) <= '\u00D6')||(input.LA(1) >= '\u00D8' && input.LA(1) <= '\u00DE') ) {
-            input.consume();
-            state.failed=false;
-        }
-        else {
-            if (state.backtracking>0) {state.failed=true; return ;}
-            MismatchedSetException mse = new MismatchedSetException(null,input);
-            recover(mse);
-            throw mse;
-        }
-
-
-        }
-
-    }
-    // $ANTLR end synpred3_Tokenizer
-
-    // $ANTLR start synpred4_Tokenizer
-    public final void synpred4_Tokenizer_fragment() throws RecognitionException {
-        // Tokenizer.g:1:56: ( LWRD )
-        // Tokenizer.g:1:56: LWRD
-        {
-        mLWRD(); if (state.failed) return ;
-
-
-        }
-
-    }
-    // $ANTLR end synpred4_Tokenizer
-
-    // $ANTLR start synpred6_Tokenizer
-    public final void synpred6_Tokenizer_fragment() throws RecognitionException {
-        // Tokenizer.g:1:68: ( SYBS )
-        // Tokenizer.g:
-        {
-        if ( (input.LA(1) >= '!' && input.LA(1) <= '/')||(input.LA(1) >= ':' && input.LA(1) <= '@')||(input.LA(1) >= '[' && input.LA(1) <= '`')||(input.LA(1) >= '{' && input.LA(1) <= '~')||input.LA(1)=='\uFFFD' ) {
-            input.consume();
-            state.failed=false;
-        }
-        else {
-            if (state.backtracking>0) {state.failed=true; return ;}
-            MismatchedSetException mse = new MismatchedSetException(null,input);
-            recover(mse);
-            throw mse;
-        }
-
-
-        }
-
-    }
-    // $ANTLR end synpred6_Tokenizer
-
-    // $ANTLR start synpred7_Tokenizer
-    public final void synpred7_Tokenizer_fragment() throws RecognitionException {
-        // Tokenizer.g:1:73: ( START )
-        // Tokenizer.g:1:73: START
-        {
-        mSTART(); if (state.failed) return ;
-
-
-        }
-
-    }
-    // $ANTLR end synpred7_Tokenizer
-
-    // $ANTLR start synpred8_Tokenizer
-    public final void synpred8_Tokenizer_fragment() throws RecognitionException {
-        // Tokenizer.g:1:79: ( END )
-        // Tokenizer.g:1:79: END
-        {
-        mEND(); if (state.failed) return ;
-
-
-        }
-
-    }
-    // $ANTLR end synpred8_Tokenizer
-
-    // $ANTLR start synpred9_Tokenizer
-    public final void synpred9_Tokenizer_fragment() throws RecognitionException {
-        // Tokenizer.g:1:83: ( COL )
-        // Tokenizer.g:1:83: COL
-        {
-        mCOL(); if (state.failed) return ;
-
-
-        }
-
-    }
-    // $ANTLR end synpred9_Tokenizer
-
-    public final boolean synpred8_Tokenizer() {
-        state.backtracking++;
-        int start = input.mark();
-        try {
-            synpred8_Tokenizer_fragment(); // can never throw exception
-        } catch (RecognitionException re) {
-            System.err.println("impossible: "+re);
-        }
-        boolean success = !state.failed;
-        input.rewind(start);
-        state.backtracking--;
-        state.failed=false;
-        return success;
-    }
-    public final boolean synpred4_Tokenizer() {
-        state.backtracking++;
-        int start = input.mark();
-        try {
-            synpred4_Tokenizer_fragment(); // can never throw exception
-        } catch (RecognitionException re) {
-            System.err.println("impossible: "+re);
-        }
-        boolean success = !state.failed;
-        input.rewind(start);
-        state.backtracking--;
-        state.failed=false;
-        return success;
-    }
-    public final boolean synpred9_Tokenizer() {
-        state.backtracking++;
-        int start = input.mark();
-        try {
-            synpred9_Tokenizer_fragment(); // can never throw exception
-        } catch (RecognitionException re) {
-            System.err.println("impossible: "+re);
-        }
-        boolean success = !state.failed;
-        input.rewind(start);
-        state.backtracking--;
-        state.failed=false;
-        return success;
-    }
-    public final boolean synpred3_Tokenizer() {
-        state.backtracking++;
-        int start = input.mark();
-        try {
-            synpred3_Tokenizer_fragment(); // can never throw exception
-        } catch (RecognitionException re) {
-            System.err.println("impossible: "+re);
-        }
-        boolean success = !state.failed;
-        input.rewind(start);
-        state.backtracking--;
-        state.failed=false;
-        return success;
-    }
-    public final boolean synpred2_Tokenizer() {
-        state.backtracking++;
-        int start = input.mark();
-        try {
-            synpred2_Tokenizer_fragment(); // can never throw exception
-        } catch (RecognitionException re) {
-            System.err.println("impossible: "+re);
-        }
-        boolean success = !state.failed;
-        input.rewind(start);
-        state.backtracking--;
-        state.failed=false;
-        return success;
-    }
-    public final boolean synpred7_Tokenizer() {
-        state.backtracking++;
-        int start = input.mark();
-        try {
-            synpred7_Tokenizer_fragment(); // can never throw exception
-        } catch (RecognitionException re) {
-            System.err.println("impossible: "+re);
-        }
-        boolean success = !state.failed;
-        input.rewind(start);
-        state.backtracking--;
-        state.failed=false;
-        return success;
-    }
-    public final boolean synpred6_Tokenizer() {
-        state.backtracking++;
-        int start = input.mark();
-        try {
-            synpred6_Tokenizer_fragment(); // can never throw exception
-        } catch (RecognitionException re) {
-            System.err.println("impossible: "+re);
-        }
-        boolean success = !state.failed;
-        input.rewind(start);
-        state.backtracking--;
-        state.failed=false;
-        return success;
-    }
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Traces.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Traces.java
deleted file mode 100644
index 70884f284..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/Traces.java
+++ /dev/null
@@ -1,950 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-import java.util.Vector;
-
-import edu.isi.karma.webserver.ContextParametersRegistry;
-
-public class Traces implements GrammarTreeNode {
-	public static final int time_limit = 20;
-	public Vector<TNode> orgNodes;
-	public Vector<TNode> tarNodes;
-	public Vector<Vector<GrammarTreeNode>> rawlines; // used for program adaptation
-	public HashMap<Integer, Template> traceline = new HashMap<Integer, Template>();
-	public HashMap<Integer, HashMap<String, Template>> loopline = new HashMap<Integer, HashMap<String, Template>>();
-	public int curState = 0;
-	public Vector<Template> totalOrderVector = new Vector<Template>();
-	// keep all the segment expression to prevent repeated construction
-	public static HashMap<String, Segment> AllSegs = new HashMap<String, Segment>();
-	public String program = "null";
-	public String contextId;
-	public Traces(String contextId)
-	{
-		this.contextId = contextId;
-	}
-	public Traces(Vector<TNode> org, Vector<TNode> tar, String contextId) {
-		this.contextId = contextId;
-		this.orgNodes = org;
-		this.tarNodes = tar;
-		this.createTraces();
-		createTotalOrderVector();
-	}
-
-	public void createTotalOrderVector() {
-		ArrayList<Integer> xArrayList = new ArrayList<Integer>();
-		xArrayList.addAll(traceline.keySet());
-		xArrayList.addAll(loopline.keySet());
-		Integer[] a = new Integer[xArrayList.size()];
-		Arrays.sort(xArrayList.toArray(a));
-		for (Integer elem : a) {
-			if (loopline.get(elem) != null) {
-				totalOrderVector.addAll(loopline.get(elem).values());
-			}
-			if (traceline.get(elem) != null) {
-				totalOrderVector.add(traceline.get(elem));
-			}
-		}
-	}
-
-	public Traces(HashMap<Integer, Template> t,
-			HashMap<Integer, HashMap<String, Template>> l) {
-		this.traceline = t;
-		this.loopline = l;
-		createTotalOrderVector();
-	}
-
-	// initialize the tree to represent the grammar tree
-	public void createTraces() {
-		Vector<Vector<Segment>> lines = new Vector<Vector<Segment>>();
-		HashMap<Integer, Vector<Segment>> pos2Segs = new HashMap<Integer, Vector<Segment>>();
-		Vector<Segment> children = findSegs(0);
-		Vector<Vector<Segment>> tlines = new Vector<Vector<Segment>>();
-		for (Segment c : children) {
-			Vector<Segment> vs = new Vector<Segment>();
-			vs.add(c);
-			tlines.add(vs);
-		}
-		// find all possible segments starting from a position
-		while (!tlines.isEmpty()) {
-			Vector<Vector<Segment>> nlines = new Vector<Vector<Segment>>();
-			Vector<Segment> segs = tlines.remove(0);
-			int curPos = segs.get(segs.size() - 1).end;
-			if (curPos == 0) // target string is empty
-			{
-				lines.add(segs);
-				break;
-			}
-			//use previous created next segments 
-			if (pos2Segs.containsKey(curPos))
-				children = pos2Segs.get(curPos);
-			else {
-				children = findSegs(curPos);
-			}
-			//reach the end and find one trace.[is this a valid sequence?]
-			if (children == null || children.isEmpty()) {
-				lines.add(segs);
-			} 
-			//create a new sequence for each new children node. add them into nlines
-			for (Segment s : children) {
-				Vector<Segment> tmp = new Vector<Segment>();
-				tmp.addAll(segs);
-				tmp.add(s);
-				nlines.add(tmp);
-			}
-			//update the sequence that requiring expanding.
-			tlines.addAll(nlines);
-		}
-		
-		Vector<Vector<GrammarTreeNode>> vSeg = new Vector<Vector<GrammarTreeNode>>();
-		//Vector<Vector<GrammarTreeNode>> lSeg = new Vector<Vector<GrammarTreeNode>>();
-		for (Vector<Segment> vs : lines) {
-			Vector<GrammarTreeNode> vsGrammarTreeNodes = UtilTools
-					.convertSegVector(vs);
-			vSeg.add(vsGrammarTreeNodes);
-		}
-		// detect loops
-		// verify loops
-		/*for (Vector<Segment> vgt : lines) {
-			Vector<Vector<GrammarTreeNode>> lLine = this.genLoop(vgt);
-			if (lLine != null)
-				lSeg.addAll(lLine);
-		}*/
-		// consolidate
-		this.rawlines = vSeg;
-		this.traceline = consolidateDiffSize(vSeg);
-		//this.loopline = consolidateDiffLoop(lSeg);
-	}
-
-	Vector<Segment> findSegs(int pos){
-		Vector<Segment> ret = new Vector<Segment>();
-		ret = SegmentMapper.findMapping(orgNodes, tarNodes, pos);
-		return ret;
-	}
-	// find all segments starting from pos
-	/*Vector<Segment> findSegs(int pos) {
-		Vector<Segment> segs = new Vector<Segment>();
-		if (tarNodes.size() == 0) {
-			int[] mapping = { 0, 0 };
-			Vector<int[]> corrm = new Vector<int[]>();
-			corrm.add(mapping);
-			Segment s = new Segment(0, 0, corrm, orgNodes, tarNodes);
-			segs.add(s);
-			return segs;
-		}
-		if (pos >= tarNodes.size())
-			return segs;
-		Vector<TNode> tmp = new Vector<TNode>();
-		tmp.add(tarNodes.get(pos));
-		// identify the const string
-		int q = Ruler.Search(orgNodes, tmp, 0);
-		if (q == -1) {
-			int cnt = pos;
-			Vector<TNode> tvec = new Vector<TNode>();
-			while (q == -1) {
-				tvec.add(tarNodes.get(cnt));
-				cnt++;
-				tmp.clear();
-				if (cnt >= tarNodes.size())
-					break;
-				tmp.add(tarNodes.get(cnt));
-				q = Ruler.Search(orgNodes, tmp, 0);
-			}
-			String key = UtilTools.print(this.orgNodes)+UtilTools.print(this.tarNodes) + pos + cnt;
-			Segment seg;
-			if (AllSegs.containsKey(key)) {
-				seg = AllSegs.get(key);
-			} else {
-				seg = new Segment(pos, cnt, tvec, contextId);
-				AllSegs.put(key, seg);
-			}
-			segs.add(seg);
-			return segs;
-		}
-		for (int i = pos; i < tarNodes.size(); i++) {
-			Vector<TNode> tvec = new Vector<TNode>();
-			for (int j = pos; j <= i; j++) {
-				tvec.add(tarNodes.get(j));
-			}
-			Vector<Integer> mappings = new Vector<Integer>();
-			int r = Ruler.Search(orgNodes, tvec, 0);
-			while (r != -1) {
-				mappings.add(r);
-				r = Ruler.Search(orgNodes, tvec, r + 1);
-			}
-			if (mappings.size() > 1) {
-				Vector<int[]> corrm = new Vector<int[]>();
-				for (int t : mappings) {
-					int[] m = { t, t + tvec.size() };
-					corrm.add(m);
-				}
-				// create a segment now
-				String key = UtilTools.print(this.orgNodes)+UtilTools.print(this.tarNodes) + pos + (i + 1);
-				Segment s;
-				if (AllSegs.containsKey(key)) {
-					s = AllSegs.get(key);
-				} else {
-					s = new Segment(pos, i + 1, corrm, orgNodes, tarNodes);
-					AllSegs.put(key, s);
-				}
-				if (s.section.size() > 0)
-					segs.add(s);
-				continue;
-			} else if (mappings.size() == 1) {
-				Vector<int[]> corrm = new Vector<int[]>();
-				// creating based on whether can find segment with one more
-				// token
-				if (i >= (tarNodes.size() - 1)) {
-					int[] m = { mappings.get(0), mappings.get(0) + tvec.size() };
-					corrm.add(m);
-					String key = UtilTools.print(this.tarNodes) + UtilTools.print(this.orgNodes)+pos+(i+1);
-					Segment s;
-					if (AllSegs.containsKey(key)) {
-						s = AllSegs.get(key);
-					} else {
-						s = new Segment(pos, i + 1, corrm, orgNodes, tarNodes);
-						AllSegs.put(key, s);
-					}
-					if (s.section.size() > 0)
-						segs.add(s);
-				} else {
-					tvec.add(tarNodes.get(i + 1));
-					int p = Ruler.Search(orgNodes, tvec, 0);
-					Vector<TNode> repToken = new Vector<TNode>();
-					repToken.add(tarNodes.get(i + 1));
-					int rind = 0;
-					int tokenCnt = 0;
-					while ((rind = Ruler.Search(orgNodes, repToken, rind)) != -1) {
-						rind++;
-						tokenCnt++;
-					}
-					if (p == -1
-							|| (tokenCnt > 1 && tarNodes.get(i + 1).text
-									.compareTo(" ") != 0)) {
-						int[] m = { mappings.get(0),
-								mappings.get(0) + tvec.size() - 1 };
-						corrm.add(m);
-						String key = UtilTools.print(this.orgNodes)+UtilTools.print(this.tarNodes) + pos
-								+ (i + 1);
-						Segment s;
-						if (AllSegs.containsKey(key)) {
-							s = AllSegs.get(key);
-						} else {
-							s = new Segment(pos, i + 1, corrm, orgNodes,
-									tarNodes);
-							AllSegs.put(key, s);
-						}
-						if (s.section.size() > 0)
-							segs.add(s);
-					} else {
-						continue;
-					}
-				}
-			} else {
-				break;
-			}
-		}
-		return segs;
-	}*/
-
-	public Traces mergewith(Traces t) {
-		// merge segment lines
-		Set<Integer> keyset = new HashSet<Integer>(this.traceline.keySet());
-		keyset.retainAll(t.traceline.keySet());
-		HashMap<Integer, Template> nLines = new HashMap<Integer, Template>();
-		HashMap<Integer, HashMap<String, Template>> lLines = new HashMap<Integer, HashMap<String, Template>>();
-		for (Integer index : keyset) {
-			Template line1 = this.traceline.get(index);
-			Template line2 = t.traceline.get(index);
-			// System.out.println(""+line1+"\n");
-			// System.out.println(""+line2+"\n");
-			Template nLine = (Template) line1.mergewith(line2);
-			if (nLine == null)
-				continue;
-			nLines.put(index, nLine);
-		}
-		// merge loop and segment lines
-		HashMap<Integer, HashMap<String, Vector<Template>>> allLoops = new HashMap<Integer, HashMap<String, Vector<Template>>>();
-		Set<Integer> keyset1 = new HashSet<Integer>(this.traceline.keySet());
-		keyset1.retainAll(t.loopline.keySet());
-		for (Integer index : keyset1) {
-			Template line1 = this.traceline.get(index);
-			Collection<String> line2s = t.loopline.get(index).keySet();
-			for (String line2 : line2s) {
-				// System.out.println(""+line1+"\n");
-				// System.out.println(""+t.loopline.get(index).get(line2)+"\n");
-				Template nLine = (Template) line1.mergewith(t.loopline.get(
-						index).get(line2));
-				if (nLine == null)
-					continue;
-				if (allLoops.containsKey(index)) {
-					if (allLoops.get(index).containsKey(line2)) {
-						allLoops.get(index).get(line2).add(nLine);
-					} else {
-						Vector<Template> vTemplates = new Vector<Template>();
-						vTemplates.add(nLine);
-						allLoops.get(index).put(line2, vTemplates);
-					}
-				} else {
-					Vector<Template> tgt = new Vector<Template>();
-					tgt.add(nLine);
-					HashMap<String, Vector<Template>> tHashMap = new HashMap<String, Vector<Template>>();
-					tHashMap.put(line2, tgt);
-					allLoops.put(index, tHashMap);
-				}
-			}
-		}
-		// merge loop and segment
-		keyset1 = new HashSet<Integer>(this.loopline.keySet());
-		keyset1.retainAll(t.traceline.keySet());
-		for (Integer index : keyset1) {
-			Collection<String> line2s = this.loopline.get(index).keySet();
-			Template line1 = t.traceline.get(index);
-			for (String line2 : line2s) {
-				// System.out.println(""+line1+"\n");
-				// System.out.println(""+this.loopline.get(index).get(line2)+"\n");
-				Template nLine = (Template) line1.mergewith(this.loopline.get(
-						index).get(line2));
-				if (nLine == null)
-					continue;
-				if (allLoops.containsKey(index)) {
-					if (allLoops.get(index).containsKey(line2)) {
-						allLoops.get(index).get(line2).add(nLine);
-					} else {
-						Vector<Template> vTemplates = new Vector<Template>();
-						vTemplates.add(nLine);
-						allLoops.get(index).put(line2, vTemplates);
-					}
-				} else {
-					Vector<Template> tgt = new Vector<Template>();
-					tgt.add(nLine);
-					HashMap<String, Vector<Template>> tHashMap = new HashMap<String, Vector<Template>>();
-					tHashMap.put(line2, tgt);
-					allLoops.put(index, tHashMap);
-				}
-			}
-		}
-		// merge loop and loop
-		keyset1 = new HashSet<Integer>(this.loopline.keySet());
-		keyset1.retainAll(t.loopline.keySet());
-		for (Integer index : keyset1) {
-			Collection<String> line1s = this.loopline.get(index).keySet();
-			Collection<String> line2s = t.loopline.get(index).keySet();
-			for (String line1 : line1s) {
-				for (String line2 : line2s) {
-					if (line1.compareTo(line2) != 0) {
-						continue;
-					}
-					// System.out.println(""+this.loopline.get(index).get(line1)+"\n");
-					// System.out.println(""+t.loopline.get(index).get(line2)+"\n");
-					Template nLine = (Template) this.loopline.get(index)
-							.get(line1)
-							.mergewith(t.loopline.get(index).get(line2));
-					if (nLine == null)
-						continue;
-					if (allLoops.containsKey(index)) {
-						if (allLoops.get(index).containsKey(line2)) {
-							allLoops.get(index).get(line2).add(nLine);
-						} else {
-							Vector<Template> vTemplates = new Vector<Template>();
-							vTemplates.add(nLine);
-							allLoops.get(index).put(line2, vTemplates);
-						}
-					} else {
-						Vector<Template> tgt = new Vector<Template>();
-						tgt.add(nLine);
-						HashMap<String, Vector<Template>> tHashMap = new HashMap<String, Vector<Template>>();
-						tHashMap.put(line2, tgt);
-						allLoops.put(index, tHashMap);
-					}
-				}
-			}
-		}
-		for (Map.Entry<Integer, HashMap<String, Vector<Template>>> integerHashMapEntry : allLoops.entrySet()) {
-			for (String subkey : integerHashMapEntry.getValue().keySet()) {
-				Template xline = this
-						.consolidate(integerHashMapEntry.getValue().get(subkey));
-				if (lLines.containsKey(integerHashMapEntry.getKey())) {
-					lLines.get(integerHashMapEntry.getKey()).put(subkey, xline);
-				} else {
-					HashMap<String, Template> xHashMap = new HashMap<String, Template>();
-					xHashMap.put(subkey, xline);
-					lLines.put(integerHashMapEntry.getKey(), xHashMap);
-				}
-
-			}
-		}
-		if (lLines.keySet().isEmpty() && nLines.keySet().isEmpty())
-			return null;
-		Traces rTraces = new Traces(nLines, lLines);
-		return rTraces;
-	}
-
-	public GrammarTreeNode union(GrammarTreeNode x, GrammarTreeNode y) {
-		if (x.getNodeType().compareTo("segment") == 0
-				&& y.getNodeType().compareTo("segment") == 0) {
-			Segment s = (Segment) x;
-			Segment t = (Segment) y;
-			Vector<Section> sec = new Vector<Section>();
-			HashSet<String> hset = new HashSet<String>();
-			for (Section nSection : s.section) {
-				String key = nSection.toString();
-				if (hset.contains(key)) {
-					continue;
-				} else {
-					hset.add(key);
-					sec.add(nSection);
-				}
-			}
-			for (Section nSection : t.section) {
-				String key = nSection.toString();
-				if (hset.contains(key)) {
-					continue;
-				} else {
-					hset.add(key);
-					sec.add(nSection);
-				}
-			}
-			boolean loop = s.isinloop || t.isinloop;
-			Segment r;
-			if (s.isConstSegment() && t.isConstSegment())
-				r = new Segment(sec, loop, contextId);
-			else
-				r = new Segment(sec, loop, contextId);
-			return r;
-		}
-		if (x.getNodeType().compareTo("loop") == 0
-				&& y.getNodeType().compareTo("loop") == 0) {
-			Loop s = (Loop) x;
-			Loop t = (Loop) y;
-			Vector<Section> sec = new Vector<Section>();
-			HashSet<String> hset = new HashSet<String>();
-			for (Section nSection : s.loopbody.section) {
-				String key = nSection.toString();
-				if (hset.contains(key)) {
-					continue;
-				} else {
-					hset.add(key);
-					sec.add(nSection);
-				}
-			}
-			for (Section nSection : t.loopbody.section) {
-				String key = nSection.toString();
-				if (hset.contains(key)) {
-					continue;
-				} else {
-					hset.add(key);
-					sec.add(nSection);
-				}
-			}
-			Loop r;
-			if (s.looptype == t.looptype) {
-				Segment loopbody;
-				if (s.loopbody.isConstSegment() && t.loopbody.isConstSegment())
-					loopbody = s.loopbody;
-				else {
-					loopbody = new Segment(sec, true, contextId);
-				}
-				r = new Loop(loopbody, t.looptype, contextId);
-			} else {
-				return null;
-			}
-			return r;
-		}
-		return null;
-	}
-
-	public HashMap<Integer, HashMap<String, Template>> consolidateDiffLoop(
-			Vector<Vector<GrammarTreeNode>> paths) {
-		HashMap<Integer, HashMap<String, Template>> resHashMap = new HashMap<Integer, HashMap<String, Template>>();
-		HashMap<Integer, HashMap<String, Vector<Template>>> tmpStore = new HashMap<Integer, HashMap<String, Vector<Template>>>();
-		for (Vector<GrammarTreeNode> vg : paths) {
-			int key = vg.size();
-			String subkey = "";
-			for (GrammarTreeNode nodetype : vg) {
-				subkey += nodetype.getNodeType();
-			}
-			if (tmpStore.containsKey(key)) {
-				if (tmpStore.get(key).containsKey(subkey)) {
-					tmpStore.get(key).get(subkey).add(new Template(vg));
-				} else {
-					Vector<Template> vte = new Vector<Template>();
-					vte.add(new Template(vg));
-					tmpStore.get(key).put(subkey, vte);
-				}
-			} else {
-				Vector<Template> xVector = new Vector<Template>();
-				if (!isLegalVS(vg))
-					continue;
-				xVector.add(new Template(vg));
-				HashMap<String, Vector<Template>> xHashMap = new HashMap<String, Vector<Template>>();
-				xHashMap.put(subkey, xVector);
-				tmpStore.put(key, xHashMap);
-			}
-		}
-		for (Map.Entry<Integer, HashMap<String, Vector<Template>>> integerHashMapEntry : tmpStore.entrySet()) {
-			for (String kInteger : integerHashMapEntry.getValue().keySet()) {
-				Template x = this.consolidate(integerHashMapEntry.getValue().get(kInteger));
-				if (resHashMap.containsKey(integerHashMapEntry.getKey())) {
-					resHashMap.get(integerHashMapEntry.getKey()).put(kInteger, x);
-				} else {
-					HashMap<String, Template> hashMap = new HashMap<String, Template>();
-					hashMap.put(kInteger, x);
-					resHashMap.put(integerHashMapEntry.getKey(), hashMap);
-				}
-			}
-		}
-		return resHashMap;
-	}
-
-	public HashMap<Integer, Template> consolidateDiffSize(
-			Vector<Vector<GrammarTreeNode>> paths) {
-		HashMap<Integer, Template> resHashMap = new HashMap<Integer, Template>();
-		HashMap<Integer, Vector<Template>> tmpStore = new HashMap<Integer, Vector<Template>>();
-		for (Vector<GrammarTreeNode> vg : paths) {
-			int key = vg.size();
-			if (tmpStore.containsKey(key)) {
-				tmpStore.get(key).add(new Template(vg));
-			} else {
-				Vector<Template> xVector = new Vector<Template>();
-				if (!isLegalVS(vg))
-					continue;
-				xVector.add(new Template(vg));
-				tmpStore.put(key, xVector);
-			}
-		}
-		for (Map.Entry<Integer, Vector<Template>> integerVectorEntry : tmpStore.entrySet()) {
-			// System.out.println(""+tmpStore.get(key).toString());
-			Template x = this.consolidate(integerVectorEntry.getValue());
-			resHashMap.put(integerVectorEntry.getKey(), x);
-		}
-		// System.out.println("end consolidating");
-		return resHashMap;
-	}
-
-	public boolean isLegalVS(Vector<GrammarTreeNode> x) {
-		for (GrammarTreeNode t : x) {
-			if (t.size() <= 0)
-				return false;
-		}
-		return true;
-	}
-	public Vector<GrammarTreeNode> consolidate_tool(Vector<Vector<GrammarTreeNode>> lists)
-	{
-		Vector<GrammarTreeNode> res = lists.get(0);
-		Vector<GrammarTreeNode> result = new Vector<GrammarTreeNode>();
-		for (int i = 1; i < lists.size(); i++) {
-			result = new Vector<GrammarTreeNode>();
-			for (int j = 0; j < res.size(); j++) {
-				GrammarTreeNode t = this.union(res.get(j), lists.get(i).get(j));
-				result.add(t);
-			}
-			res = result;
-		}
-		return res;
-	}
-	public Template consolidate(Vector<Template> paths) {
-		Vector<GrammarTreeNode> res = paths.get(0).body;
-		Vector<GrammarTreeNode> result = new Vector<GrammarTreeNode>();
-		for (int i = 1; i < paths.size(); i++) {
-
-			result = new Vector<GrammarTreeNode>();
-			for (int j = 0; j < res.size(); j++) {
-				GrammarTreeNode t = this.union(res.get(j),
-						paths.get(i).body.get(j));
-				result.add(t);
-			}
-			res = result;
-		}
-		return new Template(res);
-	}
-
-	public Vector<Vector<GrammarTreeNode>> loopPathes = new Vector<Vector<GrammarTreeNode>>();
-
-	public Vector<Vector<GrammarTreeNode>> genLoop(Vector<Segment> curPath) {
-		// cluster chunk with the same head and tail token
-		Vector<Vector<GrammarTreeNode>> res = new Vector<Vector<GrammarTreeNode>>();
-		HashMap<String, Vector<Integer>> map = new HashMap<String, Vector<Integer>>();
-		for (int i = 0; i < curPath.size(); i++) {
-			String rep = curPath.get(i).repString;
-			if (map.containsKey(rep)) {
-				map.get(rep).add(i);
-			} else {
-				Vector<Integer> vIntegers = new Vector<Integer>();
-				vIntegers.add(i);
-				map.put(rep, vIntegers);
-			}
-		}
-		for (Map.Entry<String, Vector<Integer>> stringVectorEntry : map.entrySet()) {
-			Vector<Integer> v = stringVectorEntry.getValue();
-			if (v.size() <= 1 || !this.verfiyLoop(v, curPath))
-				continue;
-			Vector<Vector<GrammarTreeNode>> vtn = this.detectLoop(v, curPath);
-			if (vtn != null && !vtn.isEmpty()) {
-				res.addAll(vtn);
-			}
-		}
-		if (res.isEmpty())
-			return null;
-		else
-			return res;
-	}
-
-	// if there is a cross of the mapping. the loop doesn't exist
-	public boolean verfiyLoop(Vector<Integer> vx, Vector<Segment> segs) {
-		boolean res = true;
-		int pre = -1;
-		for (int i : vx) {
-			Segment s = segs.get(i);
-			if (s.isConstSegment()) {
-				return true;
-			}
-			int pivot = pre;
-			if (s.mappings.size() >= 0) {
-				boolean isFind = false;
-				for (int[] n : s.mappings) {
-					if (n[0] > pivot && !isFind) {
-						pre = n[0];
-						isFind = true;
-					} else if (n[0] < pre && n[0] > pivot && isFind) {
-						pre = n[0];
-					}
-				}
-				if (!isFind) {
-					return false;
-				}
-			}
-		}
-		return res;
-	}
-
-	public Vector<GrammarTreeNode> subVector(Vector<Segment> nodes, int start,
-			int end) {
-		if (start >= end || start < 0 || end > nodes.size())
-			return null;
-		Vector<GrammarTreeNode> vgt = new Vector<GrammarTreeNode>();
-		for (int i = start; i < end; i++) {
-			vgt.add(nodes.get(i));
-		}
-		return vgt;
-	}
-
-	// merge the longest mergable chunk.
-	// if None chunk could be merged together return null
-	public Vector<GrammarTreeNode> createLoop(Vector<GrammarTreeNode> nodes,
-			int span) {
-		Vector<GrammarTreeNode> res = new Vector<GrammarTreeNode>();
-		Vector<Vector<GrammarTreeNode>> gt = new Vector<Vector<GrammarTreeNode>>();
-		int pos = 0;
-		while (pos < nodes.size()) {
-			Vector<GrammarTreeNode> x = new Vector<GrammarTreeNode>();
-			for (int k = pos; k < pos + span && k < nodes.size(); k++) {
-				x.add(nodes.get(k));
-			}
-			gt.add(x);
-			pos += span;
-		}
-		// no loop if only one chunk
-		if (gt.size() == 1) {
-			return null;
-		}
-		int itercnt = 1; // count of the span
-		int curStartPos = 0;// the lowest position the first element
-		int presize = gt.size();
-		while (gt.size() > 1) {
-			Vector<Vector<GrammarTreeNode>> tmp_gt = new Vector<Vector<GrammarTreeNode>>();
-			boolean isLegal = true;
-			for (int j = 0; j < gt.size() - 1; j++) {
-				isLegal = true;
-				Vector<GrammarTreeNode> elem = new Vector<GrammarTreeNode>();
-				Vector<GrammarTreeNode> mx = gt.get(j);
-				Vector<GrammarTreeNode> nx = gt.get(j + 1);
-				if (mx.size() != nx.size())
-					return null;
-
-				for (int r = 0; r < mx.size(); r++) {
-					GrammarTreeNode treeNode = mx.get(r).mergewith(nx.get(r));
-					if (treeNode == null) {
-						isLegal = false;
-						break;
-					}
-					elem.add(treeNode);
-				}
-				if (isLegal) {
-					tmp_gt.add(elem);
-				}
-				if (!isLegal && tmp_gt.isEmpty()) {
-					curStartPos += span;
-				}
-			}
-			if (!isLegal)
-				return null; // nothing merged in this iteration;
-			gt = tmp_gt;
-			itercnt++;
-			if (gt.size() == presize) {
-				break;
-			} else {
-				presize = gt.size();
-			}
-		}
-		// only detect one loop
-		if (gt.size() > 1)
-			return null;
-		//
-		for (int i = 0; i < nodes.size(); i++) {
-			if (i < curStartPos) {
-				res.add(nodes.get(i));
-			} else if (i == curStartPos + itercnt * span - 1) {
-				Vector<GrammarTreeNode> body = gt.get(0);
-				if (span == 1) {
-					Loop loop = new Loop((Segment) body.get(0), Loop.LOOP_BOTH, contextId);
-					res.add(loop);
-					continue;
-				}
-				for (int j = 0; j < body.size(); j++) {
-					if (j == 0) {
-						Loop loop = new Loop((Segment) body.get(j),
-								Loop.LOOP_START, contextId);
-						res.add(loop);
-					} else if (j == body.size() - 1) {
-						Loop loop = new Loop((Segment) body.get(j),
-								Loop.LOOP_END, contextId);
-						res.add(loop);
-					} else {
-						Loop loop = new Loop((Segment) body.get(j),
-								Loop.LOOP_MID, contextId);
-						res.add(loop);
-					}
-				}
-			} else if (i >= curStartPos + itercnt * span) {
-				res.add(nodes.get(i));
-			}
-		}
-		return res;
-	}
-
-	public Vector<Vector<GrammarTreeNode>> detectLoop(Vector<Integer> rep,
-			Vector<Segment> curPath) {
-		int span = rep.get(1) - rep.get(0);
-		Vector<Vector<GrammarTreeNode>> resVector = new Vector<Vector<GrammarTreeNode>>();
-		Vector<GrammarTreeNode> nodelist = new Vector<GrammarTreeNode>();
-		if (span == 1) {
-			int startpos = rep.get(0);
-			int endpos = rep.get(rep.size() - 1);
-			for (int i = 0; i < curPath.size(); i++) {
-				if (i < startpos) {
-					nodelist.add(curPath.get(i));
-				} else if (i == endpos) {
-					Vector<GrammarTreeNode> sublist = this.createLoop(
-							subVector(curPath, startpos, endpos + 1), 1);
-					if (sublist == null)
-						return null;
-					nodelist.addAll(sublist);
-				} else if (i > endpos) {
-					nodelist.add(curPath.get(i));
-				}
-			}
-		} else {
-			int startpos = rep.get(0);
-			int endpos = rep.get(rep.size() - 1);
-			// left overflow
-			if ((startpos - span + 1) < 0 && endpos + span <= curPath.size()) {
-				for (int i = 0; i < curPath.size(); i++) {
-					if (i < startpos) {
-						nodelist.add(curPath.get(i));
-					}
-					if (i == endpos + span - 1) {
-						Vector<GrammarTreeNode> sublist = this.createLoop(
-								subVector(curPath, startpos, endpos + span),
-								span);
-						if (sublist == null)
-							return null;
-						nodelist.addAll(sublist);
-					} else if (i >= endpos + span) {
-						nodelist.add(curPath.get(i));
-					}
-				}
-			}
-			// right overflow
-			else if ((startpos - span + 1) >= 0
-					&& endpos + span > curPath.size()) {
-				for (int i = 0; i < curPath.size(); i++) {
-					if (i < startpos - span + 1) {
-						nodelist.add(curPath.get(i));
-					}
-					if (i == endpos) {
-						Vector<GrammarTreeNode> sublist = this.createLoop(
-								subVector(curPath, startpos - span + 1,
-										endpos + 1), span);
-						if (sublist == null)
-							return null;
-						nodelist.addAll(sublist);
-					} else if (i > endpos) {
-						nodelist.add(curPath.get(i));
-					}
-				}
-			}
-			// two direction overflow
-			else if ((startpos - span + 1) < 0
-					&& endpos + span >= curPath.size()) {
-				// skip the startpos
-				for (int i = 0; i < curPath.size(); i++) {
-					if (i <= startpos) {
-						nodelist.add(curPath.get(i));
-					}
-					if (i == endpos) {
-						Vector<GrammarTreeNode> sublist = this.createLoop(
-								subVector(curPath, startpos + 1, endpos + 1),
-								span);
-						if (sublist == null) {
-							nodelist.clear();
-							break;
-						}
-						nodelist.addAll(sublist);
-					} else if (i > endpos) {
-						nodelist.add(curPath.get(i));
-					}
-				}
-				Vector<GrammarTreeNode> nodelist1 = new Vector<GrammarTreeNode>();
-				// skip the endpos
-				for (int i = 0; i < curPath.size(); i++) {
-					if (i < startpos) {
-						nodelist1.add(curPath.get(i));
-					}
-					if (i == endpos - 1) {
-						Vector<GrammarTreeNode> sublist = this.createLoop(
-								subVector(curPath, startpos, endpos), span);
-						if (sublist == null) {
-							nodelist1.clear();
-							break;
-						}
-						nodelist1.addAll(sublist);
-					} else if (i >= endpos) {
-						nodelist1.add(curPath.get(i));
-					}
-				}
-				if (!nodelist1.isEmpty()) {
-					resVector.add(nodelist1);
-				}
-			} else {
-				for (int i = 0; i < curPath.size(); i++) {
-					// shift left
-					if (i < startpos - span + 1) {
-						nodelist.add(curPath.get(i));
-					}
-					if (i == endpos) {
-						Vector<GrammarTreeNode> sublist = this.createLoop(
-								subVector(curPath, startpos - span + 1,
-										endpos + 1), span);
-						if (sublist == null) {
-							nodelist.clear();
-							break;
-						}
-						nodelist.addAll(sublist);
-					} else if (i > endpos) {
-						nodelist.add(curPath.get(i));
-					}
-				}
-				Vector<GrammarTreeNode> nodelist1 = new Vector<GrammarTreeNode>();
-				for (int i = 0; i < curPath.size(); i++) {
-					// shift right
-					if (i < startpos) {
-						nodelist1.add(curPath.get(i));
-					}
-					if (i == endpos + span - 1) {
-						Vector<GrammarTreeNode> sublist = this.createLoop(
-								subVector(curPath, startpos, endpos + span),
-								span);
-						if (sublist == null) {
-							nodelist1.clear();
-							break;
-						}
-						nodelist1.addAll(sublist);
-					} else if (i >= endpos + span) {
-						nodelist1.add(curPath.get(i));
-					}
-				}
-				if (!nodelist1.isEmpty())
-					resVector.add(nodelist1);
-			}
-		}
-		if (!nodelist.isEmpty()) {
-			resVector.add(nodelist);
-		}
-		return resVector;
-	}
-
-	public void tracePrint() {
-		System.out.println("===============printing trace here===============");
-		for (Map.Entry<Integer, Template> integerTemplateEntry : this.traceline.entrySet()) {
-			System.out.println("" + integerTemplateEntry.getValue());
-		}
-		for (Map.Entry<Integer, HashMap<String, Template>> integerHashMapEntry : this.loopline.entrySet()) {
-			System.out.println("" + integerHashMapEntry.getValue());
-		}
-	}
-	public void emptyState() {
-		for (GrammarTreeNode t : this.totalOrderVector) {
-			t.emptyState();
-		}
-	}
-
-	public String toProgram() {
-		String resString = "";
-		while (curState < totalOrderVector.size()) {
-			resString = this.totalOrderVector.get(curState).toProgram();
-			if (!resString.contains("null")) {
-				this.program = resString;
-				return resString;
-			} else {
-				this.totalOrderVector.get(curState).emptyState();//some segments may work
-				curState++;
-			}
-		}
-		this.program = "null";
-		return "null";
-	}
-
-	public long size() {
-		long size = 0;
-		for (Template t : this.totalOrderVector) {
-			size += t.size();
-		}
-		return size;
-	}
-
-	@Override
-	public GrammarTreeNode mergewith(GrammarTreeNode a) {
-		Traces t = (Traces) a;
-
-		return this.mergewith(t);
-	}
-
-	@Override
-	public String getNodeType() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public double getScore() {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	@Override
-	public String getrepString() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public String getProgram() {
-		return this.program;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/UtilTools.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/UtilTools.java
deleted file mode 100644
index 9a6b07558..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/UtilTools.java
+++ /dev/null
@@ -1,450 +0,0 @@
-package edu.isi.karma.cleaning;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Random;
-import java.util.Vector;
-
-import au.com.bytecode.opencsv.CSVWriter;
-import edu.isi.karma.cleaning.features.RecordClassifier;
-
-public class UtilTools {
-	public static int index = 0;
-	public static Vector<String> results = new Vector<String>();
-
-	private UtilTools() {
-	}
-
-	@SuppressWarnings({ "unchecked", "rawtypes" })
-	public static Map sortByComparator(Map unsortMap) {
-		List list = new LinkedList(unsortMap.entrySet());
-		// sort list based on comparator
-		Collections.sort(list, new Comparator() {
-			public int compare(Object o1, Object o2) {
-				return ((Comparable) ((Map.Entry) (o1)).getValue())
-						.compareTo(((Map.Entry) (o2)).getValue());
-			}
-		});
-		// put sorted list into map again
-		// LinkedHashMap make sure order in which keys were inserted
-		Map sortedMap = new LinkedHashMap();
-		for (Iterator it = list.iterator(); it.hasNext();) {
-			Map.Entry entry = (Map.Entry) it.next();
-			sortedMap.put(entry.getKey(), entry.getValue());
-		}
-		return sortedMap;
-	}
-
-	// math operators
-
-	// inner product
-	public static double product(double[] a, double[] b) {
-		double sum = 0;
-		for (int i = 0; i < a.length; i++) {
-			sum += a[i] * b[i];
-		}
-		return sum;
-	}
-
-	// sum over vectors
-	public static double[] sum(Collection<double[]> vec) {
-		Iterator<double[]> iter = vec.iterator();
-		if (vec.size() <= 0)
-			return null;
-		double[] res = new double[iter.next().length];
-		while (iter.hasNext()) {
-			double[] tmp = iter.next();
-			for (int i = 0; i < res.length; i++) {
-				res[i] += tmp[i];
-			}
-		}
-		return res;
-	}
-
-	// init array using one element
-	public static double[] initArray(double[] array, double a) {
-		double[] res = new double[array.length];
-		for (int i = 0; i < array.length; i++) {
-			res[i] = a;
-		}
-		return res;
-	}
-
-	// scalar multiply vector
-	public static double[] produce(double coeff, double[] vec) {
-		double[] res = new double[vec.length];
-		for (int i = 0; i < vec.length; i++) {
-			res[i] = coeff * vec[i];
-		}
-		return res;
-	}
-
-	public static double distance(double[] a, double[] b, double[] w) {
-		double res = 0.0;
-		for (int i = 0; i < a.length; i++) {
-			res += Math.pow(a[i] - b[i], 2) * w[i];
-		}
-		return Math.sqrt(res);
-	}
-
-	public static double distance(double[] a, double[] b) {
-		double res = 0.0;
-		for (int i = 0; i < a.length; i++) {
-			res += Math.pow(a[i] - b[i], 2);
-		}
-		return Math.sqrt(res);
-	}
-
-	public static Vector<Integer> getStringPos(int tokenpos,
-			Vector<TNode> example) {
-
-		Vector<Integer> poss = new Vector<Integer>();
-		if (tokenpos < 0)
-			return poss;
-		int pos = 0;
-		int strleng = 0;
-		for (int i = 0; i < example.size(); i++) {
-			strleng += example.get(i).text.length();
-		}
-		for (int i = 0; i < tokenpos; i++) {
-			pos += example.get(i).text.length();
-		}
-		poss.add(pos); // forward position
-		poss.add(pos - strleng); // backward position
-		return poss;
-	}
-
-	public static Vector<GrammarTreeNode> convertSegVector(Vector<Segment> x) {
-		Vector<GrammarTreeNode> res = new Vector<GrammarTreeNode>();
-		for (Segment e : x) {
-			res.add(e);
-		}
-		return res;
-	}
-
-	public static int multinominalSampler(double[] probs) {
-		Random r = new Random();
-		double x = r.nextDouble();
-		if (x <= probs[0]) {
-			return 0;
-		}
-		x -= probs[0];
-		for (int i = 1; i < probs.length; i++) {
-			if (x <= probs[i]) {
-				return i;
-			}
-			x -= probs[i];
-		}
-		return 0;
-	}
-
-	public static int randChoose(int n) {
-		Random r = new Random();
-		return r.nextInt(n);
-	}
-
-	public static String print(Vector<TNode> x) {
-		String str = "";
-		if (x == null)
-			return "null";
-		for (TNode t : x)
-			if (t.text.compareTo("ANYTOK") == 0)
-				str += t.getType();
-			else
-				str += t.text;
-		return str;
-	}
-
-	public static boolean samesteplength(Vector<Integer> s) {
-		if (s.size() <= 1)
-			return false;
-		if (s.size() == 2) {
-			if (s.get(1) - s.get(0) >= 1) {
-				return true;
-			} else {
-				return false;
-			}
-		}
-		int span = s.get(1) - s.get(0);
-		for (int i = 2; i < s.size(); i++) {
-			if ((s.get(i) - s.get(i - 1)) != span)
-				return false;
-		}
-		return true;
-	}
-
-	public static void StringColorCode(String org, String res,
-			HashMap<String, String> dict) throws Exception {
-		int segmentCnt = 0;
-		Vector<int[]> allUpdates = new Vector<int[]>();
-		String pat = "((?<=\\{_L\\})|(?=\\{_L\\}))";
-		String pat1 = "((?<=\\{_S\\})|(?=\\{_S\\}))";
-		String orgdis = "";
-		String tardis = "";
-		String tar = "";
-		String[] st = res.split(pat);
-		boolean inloop = false;
-		for (String token : st) {
-			if (token.compareTo("{_L}") == 0 && !inloop) {
-				inloop = true;
-				continue;
-			}
-			if (token.compareTo("{_L}") == 0 && inloop) {
-				inloop = false;
-				continue;
-			}
-			String[] st1 = token.split(pat1);
-			for (String str : st1) {
-				if (str.compareTo("{_S}") == 0 || str.compareTo("{_S}") == 0) {
-					continue;
-				}
-				if (str.indexOf("{_C}") != -1) {
-					String[] pos = str.split("\\{_C\\}");
-					int[] poses = { Integer.valueOf(pos[0]),
-							Integer.valueOf(pos[1]), segmentCnt };
-					boolean findPos = false;
-					for (int i = 0; i < allUpdates.size(); i++) {
-						int[] cur = allUpdates.get(i);
-						if (poses[0] <= cur[0]) {
-							findPos = true;
-							allUpdates.add(i, poses);
-							break; // avoid infinite adding
-						}
-					}
-					if (!findPos) {
-						allUpdates.add(poses);
-					}
-					String tmp = org.substring(Integer.valueOf(pos[0]),
-							Integer.valueOf(pos[1]));
-					String tarseg = pos.length == 3 ? pos[2] : tmp;
-
-					if (inloop) {
-
-						tardis += String.format(
-								"<span class=\"a%d\">%s</span>", segmentCnt,
-								tarseg);
-						// orgdis +=
-						// String.format("<span class=\"a%d\">%s</span>",
-						// segmentCnt,tarseg);
-						tar += tarseg;
-					} else {
-						tardis += String.format(
-								"<span class=\"a%d\">%s</span>", segmentCnt,
-								tarseg);
-						// orgdis +=
-						// String.format("<span class=\"a%d\">%s</span>",
-						// segmentCnt,tarseg);
-						segmentCnt++;
-						tar += tarseg;
-					}
-
-				} else {
-					tardis += String.format("<span class=\"ins\">%s</span>",
-							str);
-					tar += str;
-				}
-			}
-		}
-		int pre = 0;
-		for (int[] update : allUpdates) {
-			if (update[0] >= pre) {
-				orgdis += org.substring(pre, update[0]);
-				orgdis += String.format("<span class=\"a%d\">%s</span>",
-						update[2], org.substring(update[0], update[1]));
-				pre = update[1];
-			}
-		}
-		if (org.length() > pre)
-			orgdis += org.substring(pre);
-		dict.put("Org", org);
-		dict.put("Tar", tar);
-		dict.put("Orgdis", orgdis);
-		dict.put("Tardis", tardis);
-	}
-
-	public static String escape(String s) {
-		s = s.replaceAll("\\\\", "\\\\\\\\\\\\\\\\");
-		HashMap<String, String> dict = new HashMap<String, String>();
-		dict.put("\\(", "\\\\(");
-		dict.put("\\)", "\\\\)");
-		dict.put("\\+", "\\\\+");
-		dict.put("\\.", "\\\\.");
-		dict.put("\\?", "\\\\?");
-		dict.put("\\$", "\\\\\\$");
-		dict.put("\\*", "\\\\*");
-		dict.put("\\^", "\\\\^");
-		dict.put("\\]", "\\\\]");
-		dict.put("\\[", "\\\\[");
-		dict.put("\\/", "\\\\/");
-		dict.put("\\'", "\\\\'");
-		dict.put("\\|", "\\\\|");
-		dict.put("\\\"", "\\\\\"");
-		for (Entry<String, String> stringStringEntry : dict.entrySet()) {
-			s = s.replaceAll(stringStringEntry.getKey(), stringStringEntry.getValue());
-		}
-		return s;
-	}
-
-	public static Vector<TNode> subtokenseqs(int a, int b, Vector<TNode> org) {
-		Vector<TNode> xNodes = new Vector<TNode>();
-		if (a < 0 || b >= org.size() || a > b) {
-			return null;
-		} else {
-			for (int i = a; i <= b; i++) {
-				xNodes.add(org.get(i));
-			}
-			return xNodes;
-		}
-	}
-
-	public static void clearTmpVars() {
-		results.clear();
-		index = 0;
-	}
-
-	public static Vector<String> buildDict(Collection<String> data) {
-		HashMap<String, Integer> mapHashSet = new HashMap<String, Integer>();
-		for (String pair : data) {
-			String s1 = pair;
-			if (s1.contains("<_START>")) {
-				s1 = s1.replace("<_START>", "");
-			}
-			if (s1.contains("<_END>")) {
-				s1 = s1.replace("<_END>", "");
-			}
-			Ruler r = new Ruler();
-			r.setNewInput(s1);
-			Vector<TNode> v = r.vec;
-			HashSet<String> curRow = new HashSet<String>();
-			for (TNode t : v) {
-				String k = t.text;
-				k = k.replaceAll("[0-9]+", "DIGITs");
-				// filter punctuation
-				if (k.trim().length() == 1 && !Character.isLetterOrDigit(k.charAt(0))) {
-					continue;
-				}
-				if (k.trim().length() == 0)
-					continue;
-				// only consider K once in one row
-				if (curRow.contains(k)) {
-					continue;
-				} else {
-					curRow.add(k);
-				}
-				if (mapHashSet.containsKey(k)) {
-					mapHashSet.put(k, mapHashSet.get(k) + 1);
-				} else {
-					mapHashSet.put(k, 1);
-				}
-			}
-		}
-		// prune infrequent terms
-		int thresdhold = (int) (data.size() * 0.10);
-		Iterator<Entry<String, Integer>> iter = mapHashSet.entrySet()
-				.iterator();
-		while (iter.hasNext()) {
-			Entry<String, Integer> e = iter.next();
-			if (e.getValue() < thresdhold) {
-				iter.remove();
-			}
-		}
-		Vector<String> res = new Vector<String>();
-		res.addAll(mapHashSet.keySet());
-		return res;
-	}
-
-	public static String formatExp(String[] e) {
-		String res = String.format("%s|%s", e[0], e[1]);
-		return res;
-	}
-
-	// test whether a covers b
-	public static boolean iscovered(String a, String b) {
-		String[] elems = b.split("\\*");
-		boolean covered = true;
-		for (String e : elems) {
-			if (a.indexOf(e) == -1) {
-				covered = false;
-				break;
-			}
-		}
-		return covered;
-	}
-
-	public static String createkey(ArrayList<String[]> examples) {
-		ArrayList<String> tmp = new ArrayList<String>();
-		for (String[] ele : examples) {
-			String t = UtilTools.formatExp(ele);
-			tmp.add(t);
-		}
-		Collections.sort(tmp);
-		String key = "";
-		for (String e : tmp) {
-			key += e + "*";
-		}
-		return key;
-	}
-
-	public static ArrayList<String[]> extractExamplesinPartition(
-			Collection<Partition> pars) {
-		ArrayList<String[]> examples = new ArrayList<String[]>();
-		for (Partition par : pars) {
-			for (int i = 0; i < par.orgNodes.size(); i++) {
-				String[] exp = { UtilTools.print(par.orgNodes.get(i)),
-						UtilTools.print(par.tarNodes.get(i)) };
-				examples.add(exp);
-			}
-		}
-		return examples;
-	}
-
-	public static void clusterData(
-			Collection<String[]> data, RecordClassifier rcf) {
-		HashMap<String, ArrayList<String[]>> res = new HashMap<String, ArrayList<String[]>>();
-		for (String[] elem : data) {
-			String[] n = { elem[0], elem[1] };
-			String lab = rcf.getLabel(elem[0]);
-			if (res.containsKey(lab)) {
-				res.get(lab).add(n);
-			} else {
-				ArrayList<String[]> x = new ArrayList<String[]>();
-				x.add(n);
-				res.put(lab, x);
-			}
-		}
-		for (Entry<String, ArrayList<String[]>> stringArrayListEntry : res.entrySet()) {
-			ArrayList<String[]> cdata = stringArrayListEntry.getValue();
-			File f = new File("./log/" + stringArrayListEntry.getKey() + ".csv");
-			CSVWriter cWriter;
-			try {
-				cWriter = new CSVWriter(new FileWriter(f));
-
-				for (String[] line : cdata) {
-					cWriter.writeNext(line);
-				}
-				cWriter.close();
-			} catch (IOException e) {
-				// TODO Auto-generated catch block
-				e.printStackTrace();
-			}
-		}
-	}
-	public static Vector<TNode> convertStringtoTNodes(String s1){
-		Ruler r = new Ruler();
-		r.setNewInput(s1);;
-		return r.vec;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/CntFeature.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/CntFeature.java
deleted file mode 100644
index b42487be2..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/CntFeature.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package edu.isi.karma.cleaning.features;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.Ruler;
-import edu.isi.karma.cleaning.TNode;
-
-public class CntFeature implements Feature {
-	String name = "";
-	double score = 0.0;
-	Vector<TNode> pa;
-
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public CntFeature(ArrayList<Vector<TNode>> v, ArrayList<Vector<TNode>> n,
-			Vector<TNode> t) {
-		pa = t;
-		score = calFeatures(v, n);
-	}
-
-	// x is the old y is the new example
-	public double calFeatures(ArrayList<Vector<TNode>> x,
-			ArrayList<Vector<TNode>> y) {
-		HashMap<Integer, Integer> tmp = new HashMap<Integer, Integer>();
-		for (int i = 0; i < y.size(); i++) {
-			int cnt = 0;
-			Vector<TNode> z = x.get(i);
-			Vector<TNode> z1 = y.get(i);
-			int bpos = 0;
-			int p = 0;
-			int bpos1 = 0;
-			int p1 = 0;
-			int cnt1 = 0;
-			while (p != -1) {
-				p = Ruler.Search(z, pa, bpos);
-				if (p == -1)
-					break;
-				bpos = p + 1;
-				cnt++;
-			}
-			while (p1 != -1) {
-				p1 = Ruler.Search(z1, pa, bpos1);
-				if (p1 == -1)
-					break;
-				bpos1 = p1 + 1;
-				cnt1++;
-			}
-			// use the minus value to compute homogenenity
-			// cnt = cnt - cnt1;
-			cnt = cnt1;
-			if (tmp.containsKey(cnt)) {
-				tmp.put(cnt, tmp.get(cnt) + 1);
-			} else {
-				tmp.put(cnt, 1);
-			}
-		}
-		Integer a[] = new Integer[tmp.keySet().size()];
-		tmp.values().toArray(a);
-		int b[] = new int[a.length];
-		for (int i = 0; i < a.length; i++) {
-			b[i] = a[i].intValue();
-		}
-		double res = RegularityFeatureSet.calShannonEntropy(b) * 1.0
-				/ Math.log(x.size());
-		return res;
-	}
-
-	public String getName() {
-
-		return this.name;
-	}
-
-	public double getScore() {
-
-		return score;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/Data2Features.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/Data2Features.java
deleted file mode 100644
index 052daeed3..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/Data2Features.java
+++ /dev/null
@@ -1,103 +0,0 @@
-package edu.isi.karma.cleaning.features;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Vector;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import au.com.bytecode.opencsv.CSVWriter;
-
-public class Data2Features {
-
-	private static Logger logger = LoggerFactory.getLogger(Data2Features.class);
-
-	private Data2Features() {
-	}
-
-	// convert the csv file to arff file
-	// return the fpath of arff file
-	/*
-	 * public static void Data2arff(String csvpath, String arfpath) { try {
-	 * CSVLoader loader = new CSVLoader(); loader.setSource(new File(csvpath));
-	 * Instances data = loader.getDataSet(); // save ARFF ArffSaver saver = new
-	 * ArffSaver(); saver.setInstances(data); saver.setFile(new File(arfpath));
-	 * saver.setDestination(new File(arfpath)); saver.writeBatch(); } catch
-	 * (Exception ex) { ex.printStackTrace(); } }
-	 */
-
-	public static void Testdata2CSV(Vector<String> tests, String fpath,
-			RecordFeatureSet rf) {
-		try {
-			CSVWriter writer = new CSVWriter(new FileWriter(new File(fpath)));
-			// get attribute names
-			// get attribute names
-			Collection<String> attrStrings = rf.getFeatureNames();
-			String[] attr_names = attrStrings.toArray(new String[attrStrings
-					.size() + 1]);
-			attr_names[attr_names.length - 1] = "label";
-			writer.writeNext(attr_names);
-			for (String Record : tests) {
-				Vector<String> row = new Vector<String>();
-				Collection<Feature> cf = rf.computeFeatures(Record, "");
-				Feature[] x = cf.toArray(new Feature[cf.size()]);
-				// row.add(f.getName());
-				for (int k = 0; k < cf.size(); k++) {
-					row.add(String.valueOf(x[k].getScore()));
-				}
-				row.add("");
-				String[] dataEntry = row.toArray(new String[row.size()]);
-				writer.writeNext(dataEntry);
-			}
-			writer.flush();
-			writer.close();
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-	}
-
-	// class: records convert them into csv file
-	public static void Traindata2CSV(
-			HashMap<String, Vector<String>> class2Records, String fpath,
-			RecordFeatureSet rf) {
-		try {
-			CSVWriter writer = new CSVWriter(new FileWriter(new File(fpath)));
-			Vector<String> vsStrings = new Vector<String>();
-			for (Vector<String> vecs : class2Records.values()) {
-				vsStrings.addAll(vecs);
-			}
-			// get attribute names
-			Collection<String> attrStrings = rf.getFeatureNames();
-			String[] attr_names = attrStrings.toArray(new String[attrStrings
-					.size() + 1]);
-			attr_names[attr_names.length - 1] = "label";
-			writer.writeNext(attr_names);
-			for (Map.Entry<String, Vector<String>> stringVectorEntry : class2Records.entrySet()) {
-
-				for (String Record : stringVectorEntry.getValue()) {
-					Vector<String> row = new Vector<String>();
-					Collection<Feature> cf = rf.computeFeatures(Record, stringVectorEntry.getKey());
-					Feature[] x = cf.toArray(new Feature[cf.size()]);
-					// row.add(f.getName());
-					for (int k = 0; k < cf.size(); k++) {
-						row.add(String.valueOf(x[k].getScore()));
-					}
-					row.add(stringVectorEntry.getKey()); // change this according to the dataset.
-					String[] dataEntry = row.toArray(new String[row.size()]);
-					writer.writeNext(dataEntry);
-				}
-
-			}
-			writer.flush();
-			writer.close();
-		} catch (Exception ex) {
-			logger.error("" + Arrays.toString(ex.getStackTrace()));
-		}
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/DataRanking.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/DataRanking.java
deleted file mode 100644
index 1a3b334c3..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/DataRanking.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package edu.isi.karma.cleaning.features;
-
-import java.util.Vector;
-
-public class DataRanking {
-	public Vector<Double> coreVector = new Vector<Double>();
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/Feature.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/Feature.java
deleted file mode 100644
index aa3b78c0a..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/Feature.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-/**
- * 
- */
-package edu.isi.karma.cleaning.features;
-
-/**
- * @author szekely
- * 
- */
-public interface Feature {
-
-	/**
-	 * @return the name of this feature.
-	 */
-	public String getName();
-
-	/**
-	 * @return the score of this feature on a set of strings.
-	 */
-	public double getScore();
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/FeatureSet.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/FeatureSet.java
deleted file mode 100644
index 2d01e8c46..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/FeatureSet.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-/**
- * 
- */
-package edu.isi.karma.cleaning.features;
-
-import java.util.Collection;
-
-/**
- * @author szekely
- * 
- */
-public interface FeatureSet {
-
-	/**
-	 * @param examples
-	 *            , the set of strings on which we want to compute features.
-	 * @return the features for the set of strings.
-	 */
-	public Collection<Feature> computeFeatures(Collection<String> examples,
-			Collection<String> oexamples);
-
-	/**
-	 * @return the name of all the features.
-	 */
-	public Collection<String> getFeatureNames();
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/MovFeature.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/MovFeature.java
deleted file mode 100644
index 571179a6e..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/MovFeature.java
+++ /dev/null
@@ -1,89 +0,0 @@
-package edu.isi.karma.cleaning.features;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.Ruler;
-import edu.isi.karma.cleaning.TNode;
-
-public class MovFeature implements Feature {
-	String name = "";
-	double score = 0.0;
-	Vector<TNode> pa;
-
-	public MovFeature(ArrayList<Vector<TNode>> v, ArrayList<Vector<TNode>> n,
-			Vector<TNode> t) {
-		pa = t;
-		score = calFeatures(v, n);
-	}
-
-	// x is the old y is the new example
-	public double calFeatures(ArrayList<Vector<TNode>> x,
-			ArrayList<Vector<TNode>> y) {
-		HashMap<Integer, Integer> tmp = new HashMap<Integer, Integer>();
-		for (int i = 0; i < x.size(); i++) {
-			int cnt = 0;
-			Vector<TNode> z = x.get(i);
-			Vector<TNode> z1 = y.get(i);
-			int bpos = 0;
-			int p = 0;
-			int bpos1 = 0;
-			int p1 = 0;
-			int cnt1 = 0;
-			while (p != -1) {
-				p = Ruler.Search(z, pa, bpos);
-				if (p == -1)
-					break;
-				bpos = p + 1;
-				cnt++;
-			}
-			while (p1 != -1) {
-				p1 = Ruler.Search(z1, pa, bpos1);
-				if (p1 == -1)
-					break;
-				bpos1 = p1 + 1;
-				cnt1++;
-			}
-			// use the minus value to compute homogenenity
-			cnt = cnt - cnt1;
-			int direction = 0;// indicate the moving direction 0 left 1 right 2
-								// still
-			if (cnt < 0) {
-				direction = 1;
-			} else if (cnt > 0) {
-				direction = 0;
-			} else {
-				direction = 2;
-			}
-			if (tmp.containsKey(direction)) {
-				tmp.put(direction, tmp.get(direction) + 1);
-			} else {
-				tmp.put(direction, 1);
-			}
-		}
-		Integer a[] = new Integer[tmp.keySet().size()];
-		tmp.values().toArray(a);
-		int b[] = new int[a.length];
-		for (int i = 0; i < a.length; i++) {
-			b[i] = a[i].intValue();
-		}
-		return RegularityFeatureSet.calShannonEntropy(b) * 1.0
-				/ Math.log(x.size());
-	}
-
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	public String getName() {
-		// TODO Auto-generated method stub
-		return this.name;
-	}
-
-	public double getScore() {
-		// TODO Auto-generated method stub
-		return this.score;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordClassifier.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordClassifier.java
deleted file mode 100644
index e8cb61806..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordClassifier.java
+++ /dev/null
@@ -1,578 +0,0 @@
-package edu.isi.karma.cleaning.features;
-
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-
-import libsvm.svm;
-import libsvm.svm_model;
-import libsvm.svm_node;
-import libsvm.svm_parameter;
-import libsvm.svm_print_interface;
-import libsvm.svm_problem;
-
-import org.apache.commons.lang.ArrayUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import au.com.bytecode.opencsv.CSVWriter;
-/*import de.bwaldvogel.liblinear.Feature;
- import de.bwaldvogel.liblinear.FeatureNode;
- import de.bwaldvogel.liblinear.Linear;
- import de.bwaldvogel.liblinear.Model;
- import de.bwaldvogel.liblinear.parameterseter;
- import de.bwaldvogel.liblinear.Problem;
- import de.bwaldvogel.liblinear.SolverType;*/
-import edu.isi.karma.cleaning.PartitionClassifierType;
-import edu.isi.karma.cleaning.UtilTools;
-
-public class RecordClassifier implements PartitionClassifierType {
-	Logger ulogger = LoggerFactory.getLogger(RecordClassifier.class);
-	RecordFeatureSet rf;
-	svm_model model;
-	ArrayList<svm_node[]> trainData = new ArrayList<svm_node[]>();
-	ArrayList<String> rawData = new ArrayList<String>();
-	ArrayList<Double> targets = new ArrayList<Double>();
-	int exampleCnt = 0;
-	HashMap<String, Double> labelMapping = new HashMap<String, Double>();
-	public double[] maxValues;
-	public double[] minValues;
-	public int ctype = svm_parameter.C_SVC; 
-	public RecordClassifier() {
-		this.rf = new RecordFeatureSet();
-	}
-
-	public RecordClassifier(RecordFeatureSet rf) {
-		this.rf = rf;
-	}
-	public RecordClassifier(RecordFeatureSet rf, int type) {
-		this.rf = rf;
-		ctype = type;
-	}
-	public void init() {
-		this.trainData = new ArrayList<svm_node[]>();
-		this.targets = new ArrayList<Double>();
-		labelMapping = new HashMap<String, Double>();
-		exampleCnt = 0;
-		model = null;
-		this.minValues = null;
-		this.maxValues = null;
-		this.rf.init();
-	}
-
-	public void addTrainingData(String v, double[] value, String label) {
-		// convert value to feature vector
-		rawData.add(v);
-		svm_node[] testNodes = new svm_node[value.length];
-		for (int k = 0; k < testNodes.length; k++) {
-			svm_node node = new svm_node();
-			node.index = k;
-			node.value = value[k];
-			testNodes[k] = node;
-		}
-		this.trainData.add(testNodes);
-		// convert label to a double class label
-		if (labelMapping.containsKey(label)) {
-			this.targets.add(labelMapping.get(label));
-		} else {
-			double lb = 0;
-			if (!this.labelMapping.isEmpty()) {
-				lb = Collections.max(labelMapping.values()) + 1;
-			}
-			this.labelMapping.put(label, lb);
-			this.targets.add(lb);
-		}
-	}
-
-	public void addTrainingData(String value, String label) {
-		// convert value to feature vector
-		rawData.add(value);
-		Collection<Feature> cfeat = rf.computeFeatures(value, "");
-		Feature[] x = cfeat.toArray(new Feature[cfeat.size()]);
-		// row.add(f.getName());
-		svm_node[] testNodes = new svm_node[cfeat.size()];
-		for (int k = 0; k < cfeat.size(); k++) {
-			svm_node node = new svm_node();
-			node.index = k;
-			node.value = x[k].getScore();
-			testNodes[k] = node;
-		}
-		this.trainData.add(testNodes);
-		// convert label to a double class label
-		if (labelMapping.containsKey(label)) {
-			this.targets.add(labelMapping.get(label));
-		} else {
-			double lb = 0;
-			if (!this.labelMapping.isEmpty()) {
-				lb = Collections.max(labelMapping.values()) + 1;
-			}
-			this.labelMapping.put(label, lb);
-			this.targets.add(lb);
-		}
-	}
-
-	public void printTraindata(svm_node[][] data) {
-		String res = "";
-		String line = Arrays.toString(this.rf.getFeatureNames().toArray(
-				new String[this.rf.getFeatureNames().size()]));
-		res += line + "\n";
-		for (svm_node[] l : data) {
-			String tmp = "";
-			for (svm_node n : l) {
-				tmp += n.index + ":" + n.value + " ";
-			}
-			tmp = tmp.substring(0, tmp.length() - 1);
-			res += tmp + "\n";
-		}
-	}
-
-	// duplicate data to avoid the situation that one instance per class (svm
-	// doesn't support prob estimation for this case)
-	public void duplicateData() {
-		int size = trainData.size();
-		for (int i = 0; i < size; i++) {
-			// insert row into traindata
-			svm_node[] row = trainData.get(i);
-			trainData.add(row);
-			// insert target into the target values
-			Double val = targets.get(i);
-			targets.add(val);
-		}
-	}
-
-	// used to balance unbalanced data.
-	public HashMap<Double, Double> adjustunbalancedData() {
-		HashMap<Double, Double> class2weight = new HashMap<Double, Double>();
-		for (Double b : targets) {
-			if (class2weight.containsKey(b)) {
-				class2weight.put(b, class2weight.get(b) + 1);
-			} else {
-				class2weight.put(b, 1.0);
-			}
-		}
-		Double maxNumber = Collections.max(class2weight.values());
-		for (Map.Entry<Double, Double> doubleDoubleEntry : class2weight.entrySet()) {
-			class2weight.put(doubleDoubleEntry.getKey(), maxNumber / doubleDoubleEntry.getValue() * 1.0);
-		}
-		return class2weight;
-	}
-
-	public void dignose() {
-		String s = Arrays.toString(this.rf.vocabs);
-		ulogger.info("Diagnose info....Vocbulary learned: " + s);
-	}
-
-	public void rescale(svm_node[] tmp) {
-		double[] maxvals = this.maxValues;
-		double[] minvals = this.minValues;
-		for (int i = 0; i < tmp.length; i++) {
-			if (maxvals[i] > minvals[i]) {
-				tmp[i].value = (tmp[i].value - minvals[i]) * 1.0
-						/ (maxvals[i] - minvals[i]);
-			} else {
-				tmp[i].value = 0;
-			}
-		}
-	}
-
-	public void convertToCSVfile() {
-		ArrayList<String[]> xArrayList = new ArrayList<String[]>();
-		String[] attrname = new String[rf.getFeatureNames().size() + 1];
-		String[] names = rf.getFeatureNames().toArray(
-				new String[attrname.length - 1]);
-		// add attribute names
-		System.arraycopy(names, 0, attrname, 0, names.length);
-		attrname[attrname.length - 1] = "label";
-		xArrayList.add(attrname);
-		for (svm_node[] tmp : trainData) {
-			String[] row = new String[tmp.length + 1];
-			for (int i = 0; i < tmp.length; i++) {
-				row[i] = tmp[i].value + "";
-			}
-			row[row.length - 1] = "c" + targets.get(trainData.indexOf(tmp));
-			xArrayList.add(row);
-		}
-		try {
-			CSVWriter cr = new CSVWriter(new FileWriter(
-					"/Users/bowu/Research/testdata/tmp/data.csv"));
-			for (String[] line : xArrayList) {
-				cr.writeNext(line);
-			}
-			cr.close();
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-	}
-
-	public void NormalizeTrainingData() {
-		int featuresize = rf.getFeatureNames().size();
-		double[] maxvals = new double[featuresize];
-		maxvals = UtilTools.initArray(maxvals, -1);
-		double[] minvals = new double[featuresize];
-		minvals = UtilTools.initArray(minvals, Double.MAX_VALUE);
-		for (svm_node[] tmp : trainData) {
-			for (int i = 0; i < tmp.length; i++) {
-				if (tmp[i].value > maxvals[i]) {
-					maxvals[i] = tmp[i].value;
-				}
-				if (tmp[i].value < minvals[i]) {
-					minvals[i] = tmp[i].value;
-				}
-			}
-		}
-		minValues = minvals;
-		maxValues = maxvals;
-
-		for (svm_node[] tmp : trainData) {
-			for (int i = 0; i < tmp.length; i++) {
-				if (maxvals[i] > minvals[i]) {
-					tmp[i].value = (tmp[i].value - minvals[i]) * 1.0
-							/ (maxvals[i] - minvals[i]);
-				} else {
-					tmp[i].value = 0;
-				}
-			}
-		}
-	}
-
-	public void parameterselectionandScale() {
-		this.NormalizeTrainingData();
-		this.gridSearch();
-	}
-
-	public double getAccuracy() {
-		int totalCnt = trainData.size();
-		int errorCnt = 0;
-		for (int i = 0; i < trainData.size(); i++) {
-			svm_node[] tdata = trainData.get(i);
-			double tar = targets.get(i);
-			double v = svm.svm_predict(model, tdata);
-			if (v != tar) {
-				errorCnt++;
-			}
-		}
-		return (totalCnt - errorCnt) * 1.0 / totalCnt;
-
-	}
-
-	@Override
-	public String learnClassifer() {
-		//dignose();
-		this.parameterselectionandScale();
-		return "";
-	}
-
-	public void gridSearch() {
-		double[][] gammas = { { 0.001,0.005, 0.01, 0.03, 0.05,0.1,0.5},
-				{ 0.06, 0.07, 0.08, 0.09, 0.1 } };
-		double[][] c = { { 0.5, 0.6, 0.7, 0.8, 0.9, 1.0 },
-				{ 2.0, 3.0, 4.0, 5.0, 6.0 } };
-		double maxAcc = -1;
-		double optG = 0.5;
-		double optC = 1;
-		// coarse level search
-		double[] gInd = {
-				(gammas[0][0] + gammas[0][gammas[0].length - 1]) * 1.0 / 2,
-				(gammas[1][0] + gammas[1][gammas[1].length - 1]) * 1.0 / 2 };
-		double[] cInd = { (c[0][0] + c[0][c[0].length - 1]) * 1.0 / 2,
-				(c[1][0] + c[1][c[1].length - 1]) * 1.0 / 2 };
-		int gIndex = -1;
-		int cIndex = -1;
-		for (int i = 0; i < gInd.length; i++) {
-			for (int j = 0; j < cInd.length; j++) {
-				double acc = cross_verify(gInd[i], cInd[j]);
-				if (acc > maxAcc) {
-					maxAcc = acc;
-					gIndex = i;
-					cIndex = j;
-
-				}
-			}
-		}
-		maxAcc = -1;
-		// fine level search
-		for (int i = 0; i < gammas[gIndex].length; i++) {
-			for (int j = 0; j < c[cIndex].length; j++) {
-				double acc = cross_verify(gammas[gIndex][i], c[cIndex][j]);
-				if (acc > maxAcc) {
-					maxAcc = acc;
-					optC = c[cIndex][j];
-					optG = gammas[gIndex][i];
-				}
-			}
-		}
-		// retain on all the data
-		//System.out.println(String.format("Gamma: %f, C: %f, Acc: %f", optG,optC, maxAcc));
-		this.model = internallearnClassifer(optG, optC, trainData, targets);
-		return;
-	}
-
-	public double cross_verify(double gamma, double c) {
-		double acc = 0.0;
-		int fold = 5;
-		HashMap<Double, ArrayList<Integer>> labPos = new HashMap<Double, ArrayList<Integer>>();
-		for (int i = 0; i < targets.size(); i++) {
-			Double l = targets.get(i);
-			if (labPos.containsKey(l)) {
-				labPos.get(l).add(i);
-			} else {
-				ArrayList<Integer> pos = new ArrayList<Integer>();
-				pos.add(i);
-				labPos.put(l, pos);
-			}
-		}
-
-		for (int i = 0; i < fold; i++) {
-			ArrayList<svm_node[]> tmpTrain = new ArrayList<svm_node[]>();
-			ArrayList<svm_node[]> tmpTest = new ArrayList<svm_node[]>();
-			ArrayList<Double> tmpTraintar = new ArrayList<Double>();
-			ArrayList<Double> tmpTesttar = new ArrayList<Double>();
-			for (Map.Entry<Double, ArrayList<Integer>> doubleArrayListEntry : labPos.entrySet()) {
-				int datasize = doubleArrayListEntry.getValue().size();
-				if (datasize < fold) {
-					// add its own data until reach the fold number
-					int times = fold / datasize;
-					@SuppressWarnings("unchecked")
-					ArrayList<Integer> ditems = (ArrayList<Integer>) doubleArrayListEntry.getValue().clone();
-					for (int t = 1; t < times+1; t++) {
-						doubleArrayListEntry.getValue().addAll(ditems);
-					}
-					datasize = doubleArrayListEntry.getValue().size();
-				}
-				for (int k = 0; k < datasize; k++) {
-					int itemIndex = doubleArrayListEntry.getValue().get(k);
-					if (k % fold == i) {
-						tmpTest.add(trainData.get(itemIndex));
-						tmpTesttar.add(targets.get(itemIndex));
-					} else {
-						tmpTrain.add(trainData.get(itemIndex));
-						tmpTraintar.add(targets.get(itemIndex));
-					}
-				}
-			}
-			svm_model m = internallearnClassifer(gamma, c, tmpTrain,
-					tmpTraintar);
-			acc += getAccuracy(m, tmpTest, tmpTesttar);
-		}
-		return acc * 1.0 / fold;
-	}
-
-	public double getAccuracy(svm_model m, ArrayList<svm_node[]> tData,
-			ArrayList<Double> tars) {
-		if (tData.isEmpty()) {
-			return 0;
-		}
-		int errorCnt = 0;
-		for (int i = 0; i < tData.size(); i++) {
-			double v = svm.svm_predict(m, tData.get(i));
-			if (v != tars.get(i)) {
-				errorCnt++;
-			}
-		}
-		return 1 - errorCnt * 1.0 / tData.size();
-	}
-
-	public svm_model internallearnClassifer(double gamma, double c,
-			ArrayList<svm_node[]> tData, ArrayList<Double> tars) {
-		// duplicateData();
-		this.convertToCSVfile();
-		svm_problem problem = new svm_problem();
-		problem.l = tData.size();
-		problem.x = tData.toArray(new svm_node[tData.size()][]); // feature
-																	// nodes
-		problem.y = ArrayUtils
-				.toPrimitive(tars.toArray(new Double[tars.size()])); // target
-																		// values
-		svm_parameter parameters = new svm_parameter();
-
-		parameters.gamma = gamma;
-		parameters.svm_type = ctype;
-		parameters.kernel_type = svm_parameter.RBF;
-		parameters.degree = 3;
-		parameters.coef0 = 0;
-		parameters.nu = 0.5;
-		parameters.cache_size = 100;
-		parameters.C = c;
-		parameters.eps = 1e-5;
-		parameters.p = 0.1;
-		parameters.shrinking = 1;
-		parameters.probability = 1;
-
-		HashMap<Double, Double> wtsdict = adjustunbalancedData();
-		parameters.nr_weight = wtsdict.keySet().size();
-		int ptr = 0;
-		int[] wts_labels = new int[parameters.nr_weight];
-		double[] wts = new double[parameters.nr_weight];
-		for (Map.Entry<Double, Double> doubleDoubleEntry : wtsdict.entrySet()) {
-			wts_labels[ptr] = doubleDoubleEntry.getKey().intValue();
-			wts[ptr] = doubleDoubleEntry.getValue();
-			ptr++;
-		}
-		parameters.weight_label = wts_labels;
-		parameters.weight = wts;
-
-		svm.svm_set_print_string_function(new svm_print_interface() {
-			public void print(String s) {
-			}
-		});
-		svm.rand.setSeed(0);
-		svm_model model = svm.svm_train(problem, parameters);
-		return model;
-	}
-
-	@Override
-	public String getLabel(String value) {
-		Collection<Feature> cfeat = rf.computeFeatures(value, "");
-		Feature[] x = cfeat.toArray(new Feature[cfeat.size()]);
-		// row.add(f.getName());
-		svm_node[] testNodes = new svm_node[cfeat.size()];
-		for (int k = 0; k < cfeat.size(); k++) {
-			svm_node node = new svm_node();
-			node.index = k;
-			node.value = x[k].getScore();
-			testNodes[k] = node;
-		}
-		/* temp test */
-
-		// double[] prob_estimates = new
-		// double[this.labelMapping.keySet().size()];
-		rescale(testNodes);
-		double v = svm.svm_predict(model, testNodes);
-		// find string lable
-		return findLable(v);
-	}
-
-	public String findLable(double v) {
-		String label = "";
-		for (String key : labelMapping.keySet()) {
-			if (labelMapping.get(key) == v) {
-				label = key;
-			}
-		}
-		if (label.compareTo("") == 0) {
-			ulogger.info("Double Label doesn't exist!");
-		}
-		return label;
-	}
-
-	public void selfVerify2() {
-		for (int i = 0; i < this.trainData.size(); i++) {
-			System.out.println("Label: " + this.rawData.get(i) + ", "
-					+ this.getLabel(this.rawData.get(i)));
-			System.out.println("Test1:" + this.printLine(trainData.get(i)));
-			System.out.println("Model: "
-					+ svm.svm_predict(model, this.trainData.get(i)));
-		}
-	}
-
-	public String printLine(svm_node[] line) {
-		String x = "";
-		for (int i = 0; i < line.length; i++) {
-			x += line[i].value + ",";
-		}
-		x = x.substring(0, x.length() - 1);
-		return x;
-	}
-
-	public boolean selfVerify() {
-		boolean res = true;
-		for (int i = 0; i < trainData.size(); i++) {
-			svm_node[] tdata = trainData.get(i);
-			double tar = targets.get(i);
-			double v = svm.svm_predict(model, tdata);
-			if (v != tar) {
-				return false;
-			}
-		}
-		return res;
-	}
-
-	public void testOnFile() {
-		String[] vocbs = { "x","DIGITs" };
-		String fpath1 = "/Users/bowu/Research/testdata/tmp/data.txt";
-		String fpath2 = "/Users/bowu/Research/testdata/tmp/labels.txt";
-		try {
-			BufferedReader br1 = new BufferedReader(new FileReader(fpath1));
-			BufferedReader br2 = new BufferedReader(new FileReader(fpath2));
-			String line = "";
-			ArrayList<String> data = new ArrayList<String>();
-			ArrayList<String> labels = new ArrayList<String>();
-			while ((line = br1.readLine()) != null) {
-				if (line.trim().length() > 0) {
-					data.add(line);
-				}
-			}
-			while ((line = br2.readLine()) != null) {
-				if (line.trim().length() > 0) {
-					labels.add(line);
-				}
-			}
-			RecordFeatureSet rfs = new RecordFeatureSet();
-			rfs.addVocabulary(vocbs);
-			this.rf = rfs;
-			for (int i = 0; i < data.size(); i++) {
-				addTrainingData(data.get(i), "c" + labels.get(i));
-			}
-			learnClassifer();
-			String[] test = { "4 x 9\"",
-					"H: 58 x  W: 25\"",
-					"15\" x 18\"",
-					"14.75\" H x 11\" W",
-					"Framed at 21.75\" H x 24.25\" W",
-					"49.5\" x 9\""};
-			for (int i = 0; i < test.length; i++) {
-				System.out.println(String.format("%s, %s ", test[i],
-						getLabel(test[i])));
-			}
-			selfVerify();
-			br1.close();
-			br2.close();
-		} catch (Exception ex) {
-			ex.printStackTrace();
-		}
-	}
-
-	public static void main(String[] args) {
-		// RecordFeatureSet rfs = new RecordFeatureSet();
-		// String[] vocbs = { "D", "E", "G", "(", ")", "H", ".", "in", "I",
-		// "DIGITs", "W", "cm", "P", "x" };
-		// // String[] vocbs ={};
-		// rfs.addVocabulary(vocbs);
-		// RecordClassifier rcf = new RecordClassifier(rfs);
-		// rcf.addTrainingData(
-		// "11.75 in|15.5 in HIGH x 15.75 in|19.75 in WIDE(29.84 cm|39.37 cm HIGH x 40.00 cm|50.16 cm WIDE)",
-		// "c1");
-		// rcf.addTrainingData(
-		// "7.25 in|11.5 in HIGH x 9.25 in|13 in WIDE(18.41 cm|29.21 cm HIGH x 23.49 cm|33.02 cm WIDE)",
-		// "c1");
-		// rcf.addTrainingData(
-		// "9.75 in|16 in HIGH x 13.75 in|19.5 in WIDE(24.76 cm|40.64 cm HIGH x 34.92 cm|49.53 cm WIDE)",
-		// "c1");
-		// rcf.addTrainingData("20 in. HIGH x 24 in. WIDE", "c2");
-		// rcf.addTrainingData("26 in. HIGH x 22.5 in. WIDE", "c2");
-		// rcf.addTrainingData("10.25 in. HIGH x 8.5 in. WIDE", "c2");
-		// rcf.addTrainingData("59.75 in WIDE(151.76 cm WIDE)", "c3");
-		// rcf.addTrainingData("29.75 in HIGH(75.56 cm HIGH)", "c4");
-		// rcf.learnClassifer();
-		// for (String val : rcf.rawData) {
-		// System.out.println("class: " + rcf.getLabel(val));
-		// }
-		//
-		// System.out.println("self verifying....");
-		// System.out.println(rcf.selfVerify());
-		// // System.out.println("class: "+rcf.getLabel("."));
-		// // System.out.println("class: "+rcf.getLabel("&$"));
-		RecordFeatureSet rfs1 = new RecordFeatureSet();
-		String[] vocbs1 = { "by", "G", "L", "M", "K", "ade", "DIGITs" };
-		rfs1.addVocabulary(vocbs1);
-		RecordClassifier rcf1 = new RecordClassifier(rfs1);
-		rcf1.testOnFile();
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordCntFeatures.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordCntFeatures.java
deleted file mode 100644
index 21a053955..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordCntFeatures.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.features;
-
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class RecordCntFeatures implements Feature {
-	public String name = "";
-	public String value = "";
-	public String tar = "";
-	public double score = 0.0;
-
-	public RecordCntFeatures(String name, String value, String tar) {
-		this.name = "attr_" + name;
-		this.value = value;
-		this.tar = tar;
-		score = this.computerScore();
-	}
-
-	public double computerScore() {
-		Matcher m = Pattern.compile(tar).matcher(value);
-		int count = 0;
-		while(m.find())
-		{
-			count++;
-		}
-		return count;
-	}
-
-	@Override
-	public String getName() {
-		return this.name;
-	}
-
-	@Override
-	public double getScore() {
-		return this.score;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordDistributionFeatures.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordDistributionFeatures.java
deleted file mode 100644
index 193829e09..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordDistributionFeatures.java
+++ /dev/null
@@ -1,18 +0,0 @@
-package edu.isi.karma.cleaning.features;
-
-public class RecordDistributionFeatures implements Feature {
-	public String name = "";
-	public String value = "";
-	public String tar = "";
-	public double score = 0.0;
-	@Override
-	public String getName() {
-		return null;
-	}
-
-	@Override
-	public double getScore() {
-		return 0;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordFeatureSet.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordFeatureSet.java
deleted file mode 100644
index a444bd610..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordFeatureSet.java
+++ /dev/null
@@ -1,130 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.features;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Vector;
-
-public class RecordFeatureSet {
-	public String record;
-	public HashSet<String> labels = new HashSet<String>();
-	public String[] xStrings = { "=","\\|","#", ";", ",", "!", "~", "@", "\\$", "%", "\\^",
-			"&", "\\*", "\\(", "\\)", "_", "-", "\\{", "\\}", "\\[", "\\]", "\\\"", "\\\'", ":",
-			"\\?", "<", ">", "\\.", "/", "\\\\", "\\d+", "[A-Z]+", "[a-z]+", "[\\s]" };
-	//public String[] xStrings = {"\\d+"};
-	public String[] vocabs = {};
-	public String[] getLabels()
-	{
-		return labels.toArray(new String[labels.size()]);
-	}
-
-	public RecordFeatureSet() {
-
-	}
-	public void init()
-	{
-		this.labels = new HashSet<String>();
-	}
-	public void removeFeatures(ArrayList<Integer> fs)
-	{
-		ArrayList<String> xList = new ArrayList<String>();
-		for(int i = 0; i<xStrings.length; i++)
-		{
-			boolean found = false;
-			for(int j = 0; j < fs.size(); j++)
-			{
-				if(i == fs.get(j))
-				{
-					found = true;
-					break;
-				}
-			}
-			if(!found)
-				xList.add(xStrings[i]);
-		}
-		xStrings = xList.toArray(new String[xList.size()]);
-	}
-	public void addVocabulary(String[] vocb)
-	{
-		if(vocb == null)
-		{
-			return;
-		}
-		//update xString to constain new Vocabs
-		ArrayList<String> res = new ArrayList<String>();
-		for(String syb: xStrings)
-		{
-			res.add(syb);
-		}
-		for (String s : vocb) {
-			boolean find = false;
-			for(String syb:res)
-			{
-				if(s.indexOf(syb)!= -1)
-				{
-					find = true;
-					break;
-				}
-			}
-			if(!find)
-				res.add(s);
-		}
-		this.xStrings = res.toArray(new String[res.size()]);
-	}
-	public Collection<Feature> computeFeatures(String record, String label) {
-		Vector<Feature> xCollection = new Vector<Feature>();
-		for (String c : xStrings) {
-			Feature f = new RecordCntFeatures(c, record, c);
-			xCollection.add(f);
-		}
-		if (!labels.contains(label)) {
-			this.labels.add(label);
-		}
-		return xCollection;
-	}
-
-	public Collection<String> getFeatureNames() {
-		Vector<String> x = new Vector<String>();
-		for (String s : xStrings) {
-			if (s.compareTo("\"") == 0) {
-				s = "Quote";
-			}
-			if (s.compareTo(",") == 0) {
-				s = "Comma";
-			}
-			if (s.compareTo("\\\"") == 0) {
-				s = "DbQuto";
-			}
-			if (s.compareTo("\\\'") == 0) {
-				s = "SgQuto";
-			}
-			x.add("attr_" + s);
-		}
-		return x;
-	}
-
-	public static void main(String[] args) {
-
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordPerFeatures.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordPerFeatures.java
deleted file mode 100644
index 1c8f58adb..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordPerFeatures.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.features;
-
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class RecordPerFeatures implements Feature {
-
-	public String name = "";
-	public double score = 0.0;
-	public String value = "";
-	public String tar = "";
-
-	public RecordPerFeatures(String name, String value, String tar) {
-		this.name = "attr_" + name;
-		this.value = value;
-		this.tar = tar;
-		this.score = this.computeScore();
-	}
-
-	public double computeScore() {
-		int cnt1 = 0;
-		Pattern p = Pattern.compile(tar);
-		Matcher m = p.matcher(this.value);
-		while (m.find()) {
-			cnt1 += m.group().length();
-		}
-		if (value.length() != 0) {
-			return cnt1 * 1.0 / value.length();
-		} else {
-			return 10000;
-		}
-	}
-
-	@Override
-	public String getName() {
-		return name;
-	}
-
-	@Override
-	public double getScore() {
-		return score;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordTextFeature.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordTextFeature.java
deleted file mode 100644
index 0575411f1..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RecordTextFeature.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-package edu.isi.karma.cleaning.features;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.Ruler;
-import edu.isi.karma.cleaning.TNode;
-
-//only to test whether a substring exist
-public class RecordTextFeature implements Feature {
-	public double score = 1.0;
-	public String text = "";
-	public Vector<TNode> nodes = new Vector<TNode>();
-	public String value = "";
-
-	public RecordTextFeature(String text, String value) {
-		this.text = text;
-		this.value = value;
-		Ruler ruler = new Ruler();
-		ruler.setNewInput(value);
-		nodes = ruler.vec;
-		this.score = computeScore();
-	}
-	public double computeScore()
-	{
-		int cnt = 0;
-		for(TNode t:nodes)
-		{
-			if(t.text.compareTo(text)==0)
-			{
-				cnt += 1;
-			}
-		}
-		return cnt;
-	}
-
-	@Override
-	public String getName() {
-		// TODO Auto-generated method stub
-		return "attr_" + text;
-	}
-
-	@Override
-	public double getScore() {
-		// TODO Auto-generated method stub
-		return this.score;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RegularityFeatureSet.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RegularityFeatureSet.java
deleted file mode 100644
index e11c30025..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/RegularityFeatureSet.java
+++ /dev/null
@@ -1,190 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.cleaning.features;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Vector;
-
-import org.antlr.runtime.ANTLRStringStream;
-import org.antlr.runtime.CharStream;
-import org.antlr.runtime.Token;
-
-import edu.isi.karma.cleaning.TNode;
-import edu.isi.karma.cleaning.Tokenizer;
-
-public class RegularityFeatureSet implements FeatureSet {
-
-	public ArrayList<Vector<TNode>> tokenseqs;
-	public ArrayList<Vector<TNode>> otokenseqs;
-	public Vector<String> fnames;
-	public static String[] targets = { "#", ";", ",", "!", "~", "@", "$", "%",
-			"^", "&", "*", "(", ")", "_", "-", "{", "}", "[", "]", "\"", "\'",
-			":", "?", "<", ">", ".", "bnk", "syb", "wrd", "num" };
-
-	public RegularityFeatureSet() {
-		tokenseqs = new ArrayList<Vector<TNode>>();
-		otokenseqs = new ArrayList<Vector<TNode>>();
-		fnames = new Vector<String>();
-	}
-
-	public Vector<TNode> tokenizer(String Org) {
-		CharStream cs = new ANTLRStringStream(Org);
-		Tokenizer tk = new Tokenizer(cs);
-		Token t;
-		t = tk.nextToken();
-		Vector<TNode> x = new Vector<TNode>();
-		while (t.getType() != -1) {
-			int mytype = -1;
-			if (t.getType() == 15) {
-				mytype = TNode.UWRDTYP;
-			} else if (t.getType() == 4) {
-				mytype = TNode.BNKTYP;
-			} else if (t.getType() == 10) {
-				mytype = TNode.NUMTYP;
-			} else if (t.getType() == 12) {
-				mytype = TNode.SYBSTYP;
-			} else if (t.getType() == 9) {
-				mytype = TNode.LWRDTYP;
-			}
-			TNode tx = new TNode(mytype, t.getText());
-			x.add(tx);
-			t = tk.nextToken();
-		}
-		return x;
-	}
-
-	public Collection<Feature> computeFeatures(Collection<String> examples,
-			Collection<String> oexamples) {
-		Vector<Feature> r = new Vector<Feature>();
-
-		for (String s : examples) {
-			Vector<TNode> x = this.tokenizer(s);
-			this.tokenseqs.add(x);
-		}
-		for (String s : oexamples) {
-			Vector<TNode> x = this.tokenizer(s);
-			this.otokenseqs.add(x);
-		}
-		// counting feature
-		String[] symbol = { "#", ";", ",", "!", "~", "@", "$", "%", "^", "&",
-				"*", "(", ")", "_", "-", "{", "}", "[", "]", "\"", "'", ":",
-				"?", "<", ">", "." };
-		Vector<CntFeature> cntfs = new Vector<CntFeature>(symbol.length);
-		// moving feature
-		Vector<MovFeature> movfs = new Vector<MovFeature>(symbol.length);
-		for (int i = 0; i < symbol.length; i++) {
-			TNode t = new TNode(TNode.SYBSTYP, symbol[i]);
-			Vector<TNode> li = new Vector<TNode>();
-			li.add(t);
-			cntfs.add(i, new CntFeature(this.otokenseqs, this.tokenseqs, li));
-			cntfs.get(i).setName("entr_cnt_" + symbol[i]);
-			movfs.add(i, new MovFeature(this.otokenseqs, this.tokenseqs, li));
-			movfs.get(i).setName("entr_mov" + symbol[i]);
-		}
-		// count the blank, symbol wrd and number token
-		TNode t = new TNode(TNode.BNKTYP, TNode.ANYTOK);
-		Vector<TNode> li = new Vector<TNode>();
-		li.add(t);
-		CntFeature cf = new CntFeature(this.otokenseqs, this.tokenseqs, li);
-		cf.setName("entr_cnt_bnk");
-		TNode t1 = new TNode(TNode.SYBSTYP, TNode.ANYTOK);
-		Vector<TNode> li1 = new Vector<TNode>();
-		li1.add(t1);
-		CntFeature cf1 = new CntFeature(this.otokenseqs, this.tokenseqs, li1);
-		cf1.setName("entr_cnt_syb");
-		TNode t2 = new TNode(TNode.LWRDTYP, TNode.ANYTOK);
-		Vector<TNode> li2 = new Vector<TNode>();
-		li2.add(t2);
-		CntFeature cf2 = new CntFeature(this.otokenseqs, this.tokenseqs, li2);
-		cf2.setName("entr_cnt_lwrd");
-		TNode t3 = new TNode(TNode.NUMTYP, TNode.ANYTOK);
-		Vector<TNode> li3 = new Vector<TNode>();
-		li3.add(t3);
-		CntFeature cf3 = new CntFeature(this.otokenseqs, this.tokenseqs, li3);
-		cf3.setName("entr_cnt_num");
-		/*
-		 * TNode t4 = new TNode(TNode.UWRDTYP,TNode.ANYTOK); Vector<TNode> li4 =
-		 * new Vector<TNode>(); li3.add(t4); CntFeature cf4 = new
-		 * CntFeature(this.otokenseqs,this.tokenseqs,li4);
-		 * cf3.setName("entr_cnt_num");
-		 */
-		cntfs.add(cf);
-		cntfs.add(cf1);
-		cntfs.add(cf2);
-		cntfs.add(cf3);
-		// cntfs.add(cf4);
-		r.addAll(cntfs);
-		r.addAll(movfs);
-		for (int i = 0; i < r.size(); i++) {
-			fnames.add(r.get(i).getName());
-		}
-		return r;
-	}
-
-	public static void buildEntropy(double a, int[] buk) {
-		int buks[] = buk;
-		if (a >= 0.0 && a < 0.1) {
-			buks[0] += 1;
-		} else if (a >= 0.1 && a < 0.2) {
-			buks[1] += 1;
-		} else if (a >= 0.2 && a < 0.3) {
-			buks[2] += 1;
-		} else if (a >= 0.3 && a < 0.4) {
-			buks[3] += 1;
-		} else if (a >= 0.4 && a < 0.5) {
-			buks[4] += 1;
-		} else if (a >= 0.5 && a < 0.6) {
-			buks[5] += 1;
-		} else if (a >= 0.6 && a < 0.7) {
-			buks[6] += 1;
-		} else if (a >= 0.7 && a < 0.8) {
-			buks[7] += 1;
-		} else if (a >= 0.8 && a < 0.9) {
-			buks[8] += 1;
-		} else if (a >= 0.9 && a <= 1.0) {
-			buks[9] += 1;
-		}
-	}
-
-	public static double calShannonEntropy(int[] a) {
-		int cnt = 0;
-		for (int c : a) {
-			cnt += c;
-		}
-		if (cnt == 0)
-			return Math.log(10);//
-		double entropy = 0.0;
-		for (int i = 0; i < a.length; i++) {
-			double freq = a[i] * 1.0 / cnt;
-			if (freq == 0)
-				continue;
-			entropy -= freq * Math.log(freq);
-		}
-		return entropy;
-	}
-
-	public Collection<String> getFeatureNames() {
-
-		return fnames;
-
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/VarianceFeatureSet.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/VarianceFeatureSet.java
deleted file mode 100644
index 458540348..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/features/VarianceFeatureSet.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.cleaning.features;
-
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.Vector;
-
-class Varfeature implements Feature {
-
-	String name = "";
-	double score = 0.0;
-
-	public Varfeature(double a, double b, String fname) {
-		score = a - b;
-		name = fname + "_var";
-	}
-
-	public String getName() {
-
-		return this.name;
-	}
-
-	public double getScore() {
-
-		return score;
-	}
-
-}
-
-public class VarianceFeatureSet implements FeatureSet {
-
-	public VarianceFeatureSet() {
-	}
-
-	public Collection<Feature> computeFeatures(Collection<String> oldexamples,
-			Collection<String> newexamples) {
-
-		Vector<Feature> fs = new Vector<Feature>();
-		RegularityFeatureSet rf1 = new RegularityFeatureSet();
-		Collection<Feature> x = rf1.computeFeatures(oldexamples, newexamples);
-		RegularityFeatureSet rf2 = new RegularityFeatureSet();
-		Collection<Feature> y = rf2.computeFeatures(oldexamples, newexamples);
-		Iterator<Feature> i1 = x.iterator();
-		Iterator<Feature> i2 = y.iterator();
-		while (i1.hasNext() && i2.hasNext()) {
-			Feature f1 = i1.next();
-			Feature f2 = i2.next();
-			if (f1.getName().compareTo(f2.getName()) == 0) {
-				Varfeature vf = new Varfeature(f1.getScore(), f2.getScore(),
-						f1.getName());
-				fs.add(vf);
-			}
-		}
-		return fs;
-	}
-
-	public Collection<String> getFeatureNames() {
-
-		return null;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/CaptializeAll.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/CaptializeAll.java
deleted file mode 100644
index 78f2b3865..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/CaptializeAll.java
+++ /dev/null
@@ -1,50 +0,0 @@
-package edu.isi.karma.cleaning.internalfunlibrary;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.TNode;
-import edu.isi.karma.cleaning.UtilTools;
-
-public class CaptializeAll implements TransformFunction {
-
-	@Override
-	public boolean convertable(Vector<TNode> sour, Vector<TNode> dest) {
-		String target = UtilTools.print(dest);
-		// if exact match succeed, return false;
-		if(UtilTools.print(sour).compareTo(target) == 0)
-			return false;
-		String tran = this.convert(sour);
-		if(target.compareTo(tran) == 0)
-		{
-			return true;
-		}
-		else
-		{
-			return false;
-		}
-	}
-
-	@Override
-	public String convert(Vector<TNode> sour) {
-		String ret = "";
-		try {
-			for (TNode t : sour) {
-				ret += Character.toUpperCase(t.text.charAt(0))
-						+ t.text.substring(1).toLowerCase();
-			}
-			if(ret.compareTo(UtilTools.print(sour)) == 0)
-			{
-				return null;
-			}
-			return ret;
-		} catch (Exception e) {
-			return null;
-		}
-	}
-
-	@Override
-	public int getId() {
-		return InternalTransformationLibrary.Functions.Cap.getValue();
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/ExactEqual.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/ExactEqual.java
deleted file mode 100644
index 2c607ad1d..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/ExactEqual.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package edu.isi.karma.cleaning.internalfunlibrary;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.TNode;
-import edu.isi.karma.cleaning.UtilTools;
-
-public class ExactEqual implements TransformFunction {
-
-	@Override
-	public boolean convertable(Vector<TNode> sour, Vector<TNode> dest) {
-		if (UtilTools.print(sour).compareTo(UtilTools.print(dest)) == 0) {
-			return true;
-		} else {
-			return false;
-		}
-	}
-
-	@Override
-	public String convert(Vector<TNode> sour) {
-		return UtilTools.print(sour);
-	}
-
-	@Override
-	public int getId() {
-		// TODO Auto-generated method stub
-		return InternalTransformationLibrary.Functions.Exact.getValue();
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/FirstLettersOfWords.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/FirstLettersOfWords.java
deleted file mode 100644
index cc4550217..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/FirstLettersOfWords.java
+++ /dev/null
@@ -1,50 +0,0 @@
-package edu.isi.karma.cleaning.internalfunlibrary;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.TNode;
-import edu.isi.karma.cleaning.UtilTools;
-
-public class FirstLettersOfWords implements TransformFunction {
-
-	@Override
-	public boolean convertable(Vector<TNode> sour, Vector<TNode> dest) {
-		String ts = UtilTools.print(dest);
-		if(UtilTools.print(sour).compareTo(ts) == 0){
-			return false;
-		}
-		String ss = this.convert(sour);
-		if(ss.compareTo(ts) == 0)
-		{
-			return true;
-		}
-		else
-		{
-			return false;
-		}
-	}
-
-	@Override
-	public String convert(Vector<TNode> sour) {
-		String ret = "";
-		try {
-			for (TNode t : sour) {
-				ret += t.text.substring(0, 1);
-			}
-			if(ret.compareTo(UtilTools.print(sour)) == 0)
-			{
-				return null;
-			}
-			return ret;
-		} catch (Exception ex) {
-			return null;
-		}
-	}
-
-	@Override
-	public int getId() {
-		// TODO Auto-generated method stub
-		return InternalTransformationLibrary.Functions.Firstletter.getValue();
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/InternalTransformationLibrary.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/InternalTransformationLibrary.java
deleted file mode 100644
index c6b3b60e9..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/InternalTransformationLibrary.java
+++ /dev/null
@@ -1,58 +0,0 @@
-package edu.isi.karma.cleaning.internalfunlibrary;
-
-import java.util.Collection;
-import java.util.HashMap;
-
-public class InternalTransformationLibrary {
-	public static enum Functions {
-		NonExist(-1), Cap(1), Exact(2), Uppercase(3), Lowercase(4), Firstletter(5);
-		private final int id;
-
-		Functions(int id) {
-			this.id = id;
-		}
-
-		public int getValue() {
-			return this.id;
-		}
-	}
-
-	public HashMap<Integer, TransformFunction> funcs = new HashMap<Integer, TransformFunction>();
-	public InternalTransformationLibrary() {
-		// add all the functions
-		ExactEqual equal = new ExactEqual();
-		funcs.put(equal.getId(), equal);
-		CaptializeAll cap = new CaptializeAll();
-		funcs.put(cap.getId(), cap);
-		FirstLettersOfWords fword = new FirstLettersOfWords();
-		funcs.put(fword.getId(), fword);
-		LowerCaseAll lca = new LowerCaseAll();
-		funcs.put(lca.getId(), lca);
-		UpperCaseAll uca = new UpperCaseAll();
-		funcs.put(uca.getId(), uca);
-	}
-	public static String getName(int id){
-		for(Functions val:Functions.values()){
-			if(id == val.getValue()){
-				return val.name();
-			}
-		}
-		return "";
-	}
-	public Collection<Integer> getAllIDs() {
-		return funcs.keySet();
-	}
-
-	public Collection<TransformFunction> getAllFuncs() {
-		return funcs.values();
-	}
-
-	public TransformFunction getFunc(Integer Id) {
-		if (funcs.containsKey(Id)) {
-			return funcs.get(Id);
-		} else {
-			return null;
-		}
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/LowerCaseAll.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/LowerCaseAll.java
deleted file mode 100644
index 1c63b3541..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/LowerCaseAll.java
+++ /dev/null
@@ -1,45 +0,0 @@
-package edu.isi.karma.cleaning.internalfunlibrary;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.TNode;
-import edu.isi.karma.cleaning.UtilTools;
-
-public class LowerCaseAll implements TransformFunction {
-
-	@Override
-	public boolean convertable(Vector<TNode> sour, Vector<TNode> dest) {
-		String ts = UtilTools.print(dest);
-		if(UtilTools.print(sour).compareTo(ts) == 0)
-			return false;
-		String ss = this.convert(sour);
-		if(ss.compareTo(ts) == 0)
-		{
-			return true;
-		}
-		else{
-			return false;
-		}
-	}
-
-	@Override
-	public String convert(Vector<TNode> sour) {
-		String ret = "";
-		for(TNode t: sour){
-			ret += t.text.toLowerCase();
-		}
-		if(ret.compareTo(UtilTools.print(sour)) == 0)
-		{
-			return null;
-		}
-		return ret;
-	
-	}
-
-	@Override
-	public int getId() {
-		// TODO Auto-generated method stub
-		return InternalTransformationLibrary.Functions.Lowercase.getValue();
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/TransformFunction.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/TransformFunction.java
deleted file mode 100644
index a0bd30b8b..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/TransformFunction.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package edu.isi.karma.cleaning.internalfunlibrary;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.TNode;
-
-public interface TransformFunction {
-	public boolean convertable(Vector<TNode> sour, Vector<TNode> dest);
-	public String convert(Vector<TNode> sour);
-	public int getId();
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/UpperCaseAll.java b/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/UpperCaseAll.java
deleted file mode 100644
index 835ec9a1a..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/cleaning/internalfunlibrary/UpperCaseAll.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package edu.isi.karma.cleaning.internalfunlibrary;
-
-import java.util.Vector;
-
-import edu.isi.karma.cleaning.TNode;
-import edu.isi.karma.cleaning.UtilTools;
-
-public class UpperCaseAll implements TransformFunction {
-
-	@Override
-	public boolean convertable(Vector<TNode> sour, Vector<TNode> dest) {
-		String ts = UtilTools.print(dest);
-		if(UtilTools.print(sour).compareTo(ts) == 0)
-			return false;
-		String ss = this.convert(sour);
-		if(ss.compareTo(ts) == 0)
-		{
-			return true;
-		}
-		else{
-			return false;
-		}
-	}
-
-	@Override
-	public String convert(Vector<TNode> sour) {
-		String ret = "";
-		for(TNode t: sour){
-			ret += t.text.toUpperCase();
-		}
-		if(ret.compareTo(UtilTools.print(sour)) == 0)
-		{
-			return null;
-		}
-		return ret;
-	
-	}
-
-	@Override
-	public int getId() {
-		// TODO Auto-generated method stub
-		return InternalTransformationLibrary.Functions.Uppercase.getValue();
-	}
-
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformation.java b/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformation.java
deleted file mode 100644
index 31e11d5b7..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformation.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.rep.cleaning;
-
-import edu.isi.karma.cleaning.InterpreterType;
-import edu.isi.karma.cleaning.ProgramRule;
-
-
-
-public class RamblerTransformation implements Transformation {
-	public String signature = "";
-	private ProgramRule prog;
-	public RamblerTransformation(ProgramRule prog)
-	{ 
-		this.prog = prog;
-		this.signature = prog.signString;
-	}
-	public String transform(String value) {
-		InterpreterType worker = prog.getRuleForValue(value);
-		String s = worker.execute(value);
-		if(s.contains("_FATAL_ERROR_"))
-			return value;
-		else
-			return s;
-	}	
-	public String getId() {
-		// TODO Auto-generated method stub
-		return this.signature;
-	}
-	public int hashCode()
-	{
-		return this.signature.hashCode();
-	}
-	public boolean equals(Object other) 
-	{
-		RamblerTransformation e = (RamblerTransformation)other;
-		if(e.signature.compareTo(this.signature)==0)
-		{
-			return true;
-		}
-		return false;
-	}
-	public String getClassLabel(String value)
-	{
-		return prog.getClassForValue(value);
-	}
-	@Override
-	public String transform_debug(String value) {
-		InterpreterType worker = prog.getRuleForValue(value);
-		if(value.length()==0)
-			return "";
-		String s = worker.execute_debug(value);
-		return s;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformationExample.java b/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformationExample.java
deleted file mode 100644
index fd6347d95..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformationExample.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.rep.cleaning;
-
-
-public class RamblerTransformationExample implements TransformationExample {
-
-	private String before = "";
-	private String after = "";
-	private String nodeID = "";
-	public RamblerTransformationExample(String before,String after,String nodeID)
-	{
-		this.before = before;
-		this.after = after;
-		this.nodeID = nodeID;
-	}
-	public String getNodeId() {
-		// TODO Auto-generated method stub
-		return this.nodeID;
-	}
-
-	public String getBefore() {
-		// TODO Auto-generated method stub
-		return this.before;
-	}
-
-	public String getAfter() {
-		// TODO Auto-generated method stub
-		return this.after;
-	}
-	public void setBefore(String before)
-	{
-		this.before = before;
-	}
-	public void setAfter(String after)
-	{
-		this.after = after;
-	}
-	public void setNodeId(String NodeId)
-	{
-		this.nodeID = NodeId;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformationInputs.java b/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformationInputs.java
deleted file mode 100644
index 662253a16..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformationInputs.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.rep.cleaning;
-
-import java.util.Collection;
-
-import edu.isi.karma.cleaning.DataPreProcessor;
-import edu.isi.karma.cleaning.Messager;
-
-
-public class RamblerTransformationInputs implements TransformationInputs {
-
-	private Collection<TransformationExample> examples;
-	private ValueCollection inputValues;
-	public DataPreProcessor dpp = null;
-	public Messager msg = null;
-	//private Transformation preferedTransformation;
-	public RamblerTransformationInputs(Collection<TransformationExample> examples,ValueCollection inputValues, DataPreProcessor dpp, Messager msg)
-	{
-		this.examples = examples;
-		this.inputValues = inputValues;
-		this.dpp = dpp;
-		this.msg = msg;
-	}
-	public Collection<TransformationExample> getExamples() {
-		// TODO Auto-generated method stub
-		return this.examples;
-	}
-	public ValueCollection getInputValues() {
-		// TODO Auto-generated method stub
-		return this.inputValues;
-	}
-	public void setPreferredRule(Transformation t) {
-		// TODO Auto-generated method stub
-		//this.preferedTransformation = t;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformationOutput.java b/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformationOutput.java
deleted file mode 100644
index cc0b6eb92..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerTransformationOutput.java
+++ /dev/null
@@ -1,160 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.rep.cleaning;
-
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Vector;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.TimeUnit;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import edu.isi.karma.cleaning.ProgSynthesis;
-import edu.isi.karma.cleaning.ProgramRule;
-
-public class RamblerTransformationOutput implements TransformationOutput {
-	private static Logger logger = LoggerFactory.getLogger(RamblerTransformationOutput.class);
-	private RamblerTransformationInputs input;
-	private HashMap<String, Transformation> transformations;
-	public boolean nullRule = false;
-	public String contextId;
-	public RamblerTransformationOutput(RamblerTransformationInputs input, String contextId) {
-		
-		this.input = input;
-		this.contextId = contextId;
-		transformations = new HashMap<String, Transformation>();
-		ExecutorService executor = Executors.newFixedThreadPool(1);
-		final Future<?> worker = executor.submit(new Runnable() {
-			public void run() {
-				try {
-					learnTransformation();
-				} catch (Exception ex) {
-					logger.error(ex.toString());
-				}
-			}
-		});
-		try {
-			worker.get(3000, TimeUnit.SECONDS);
-		} catch (Exception e) {
-			nullRule = true;
-			transformations.clear();
-		}
-		
-	}
-
-	private void learnTransformation() throws Exception {
-		Collection<TransformationExample> exs = input.getExamples();
-		Vector<String[]> exps = new Vector<String[]>();
-		Iterator<TransformationExample> iter = exs.iterator();
-		while (iter.hasNext()) {
-			TransformationExample t = iter.next();
-			String[] tmp = { t.getBefore(), t.getAfter() };
-			exps.add(tmp);
-		}
-		ProgSynthesis psProgSynthesis = new ProgSynthesis(contextId);
-		psProgSynthesis.inite(exps, input.dpp, input.msg);
-		// add time out here
-		Collection<ProgramRule> rules = null;
-		//rules = psProgSynthesis.adaptive_main();
-		rules = psProgSynthesis.run_main();
-		input.msg.updateCM_Constr(psProgSynthesis.partiCluster.getConstraints());
-		input.msg.updateWeights(psProgSynthesis.partiCluster.weights);
-
-		if (rules == null || rules.isEmpty()) {
-			ProgramRule r = new ProgramRule(ProgramRule.IDENTITY, contextId);
-			r.nullRule = true;
-			this.nullRule = true;
-			rules = new Vector<ProgramRule>();
-			rules.add(r);
-			// return;+
-		}
-		Iterator<ProgramRule> iterator = rules.iterator();
-		while (iterator.hasNext()) {
-			RamblerTransformation r = new RamblerTransformation(iterator.next());
-			if (!transformations.containsKey(r.signature)) {
-				transformations.put(r.signature, r);
-			}
-		}
-		// RamblerTransformation r = new
-		// RamblerTransformation(psProgSynthesis.getBestRule());
-		// transformations.put("BESTRULE",r);
-	}
-
-	public HashMap<String, Transformation> getTransformations() {
-		// TODO Auto-generated method stub
-		return transformations;
-	}
-
-	public ValueCollection getTransformedValues(String TransformatinId) {
-		Transformation t = transformations.get(TransformatinId);
-		ValueCollection v = input.getInputValues();
-		ValueCollection vo = new RamblerValueCollection();
-		Collection<String> keys = v.getNodeIDs();
-		Iterator<String> iter = keys.iterator();
-		while (iter.hasNext()) {
-			String k = iter.next();
-			String val = v.getValue(k);
-			if (val.length() > 0)
-				val = t.transform(val);
-			else
-				val = "";
-			vo.setValue(k, val);
-			// logger.debug(k+","+val);
-		}
-		return vo;
-	}
-
-	public Collection<String> getRecommandedNextExample() {
-		return null;
-	}
-
-	@Override
-	public ValueCollection getTransformedValues_debug(String TransformationId) {
-		Transformation t = transformations.get(TransformationId);
-		ValueCollection v = input.getInputValues();
-		ValueCollection vo = new RamblerValueCollection();
-		Collection<String> keys = v.getNodeIDs();
-		Iterator<String> iter = keys.iterator();
-		while (iter.hasNext()) {
-			String k = iter.next();
-			String orgval = v.getValue(k);
-			String cLabel = "";
-			String val = "";
-			if (orgval.length() > 0) {
-				val = t.transform_debug(orgval);
-				cLabel = t.getClassLabel(orgval);
-			} else {
-				val = "";
-				cLabel = t.getClassLabel(val);
-			}
-			vo.setValue(k, val);
-			vo.setKeyClass(k, cLabel);
-			// logger.debug(k+","+val);
-		}
-		return vo;
-	}
-
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerValueCollection.java b/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerValueCollection.java
deleted file mode 100644
index 386e21f45..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/RamblerValueCollection.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.rep.cleaning;
-
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
-
-import org.json.JSONObject;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-
-public class RamblerValueCollection implements ValueCollection {
-	private static Logger logger = LoggerFactory.getLogger(RamblerValueCollection.class);
-	private HashMap<String,String> data;
-	private HashMap<String, String> keyClass = new HashMap<String, String>();
-	public RamblerValueCollection(HashMap<String,String> data)
-	{
-		this.data = data;
-	}
-	public RamblerValueCollection()
-	{
-		data = new HashMap<String,String>();
-	}
-	public void setKeyClass(String key,String cLabel)
-	{
-		keyClass.put(key, cLabel);
-	}
-	public String getClass(String key)
-	{
-		if(keyClass.containsKey(key))
-		{
-			return keyClass.get(key);
-		}
-		else {
-			return "";
-		}
-	}
-	public void setValue(String id, String val)
-	{
-		if(data.containsKey(id))
-		{
-			data.put(id, val);
-		}
-		else
-		{
-			data.put(id, val);
-		}
-	}
-	public String getValue(String id) {
-		// TODO Auto-generated method stub
-		if(data.containsKey(id))
-		{
-			return data.get(id);
-		}
-		else
-			return "";
-	}
-
-	public Collection<String> getValues() {
-		// TODO Auto-generated method stub
-		return data.values();
-	}
-
-	public Collection<String> getNodeIDs() {
-		// TODO Auto-generated method stub
-		return data.keySet();
-	}
-
-	public JSONObject getJson() {
-		// TODO Auto-generated method stub
-		try
-		{
-			JSONObject jb = new JSONObject();
-			Set<String> ss = data.keySet();
-			for(Map.Entry<String, String> stringStringEntry : data.entrySet())
-			{
-				String val = stringStringEntry.getValue();
-				jb.put(stringStringEntry.getKey(), val);
-			}
-			return jb;
-		}
-		catch(Exception ex)
-		{
-			logger.error(""+ex.toString());
-			return null;
-		}
-	}
-	public String representation()
-	{
-		String result = "";
-		Set<String> res = data.keySet();
-		for(Map.Entry<String, String> stringStringEntry : data.entrySet())
-		{
-			result += stringStringEntry.getValue();
-			result += " ";
-		}
-		return result;
-	}
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/Transformation.java b/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/Transformation.java
deleted file mode 100644
index 9d82364d2..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/Transformation.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.rep.cleaning;
-
-public interface Transformation {
-	public abstract String transform(String value);
-	public abstract String transform_debug(String value);
-	public abstract String getId();
-	public abstract String getClassLabel(String value);
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/TransformationExample.java b/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/TransformationExample.java
deleted file mode 100644
index a51a9c91d..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/TransformationExample.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.rep.cleaning;
-
-public interface TransformationExample {
-	public abstract String getNodeId();
-	public abstract String getBefore();
-	public abstract String getAfter();
-	public abstract void setNodeId(String s);
-	public abstract void setBefore(String s);
-	public abstract void setAfter(String s);
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/TransformationInputs.java b/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/TransformationInputs.java
deleted file mode 100644
index 474a4ab52..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/TransformationInputs.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.rep.cleaning;
-
-import java.util.Collection;
-
-public interface TransformationInputs {
-	public abstract Collection<TransformationExample> getExamples();
-	public abstract ValueCollection getInputValues();
-	public abstract void setPreferredRule(Transformation t);
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/TransformationOutput.java b/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/TransformationOutput.java
deleted file mode 100644
index ca90ccdc7..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/TransformationOutput.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.rep.cleaning;
-
-import java.util.Collection;
-import java.util.HashMap;
-
-public interface TransformationOutput {
-	public abstract HashMap<String,Transformation> getTransformations();
-	public abstract ValueCollection getTransformedValues(String TransformatinId);
-	public abstract ValueCollection getTransformedValues_debug(String TransformationId);
-	public abstract Collection<String> getRecommandedNextExample();
-}
diff --git a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/ValueCollection.java b/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/ValueCollection.java
deleted file mode 100644
index 5467cd7d6..000000000
--- a/karma-cleaning/src/main/java/edu/isi/karma/rep/cleaning/ValueCollection.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-package edu.isi.karma.rep.cleaning;
-
-import java.util.Collection;
-
-import org.json.JSONObject;
-
-public interface ValueCollection {
-	public abstract String getValue(String id);
-	public abstract Collection<String> getValues();
-	public abstract Collection<String> getNodeIDs();
-	public abstract void setValue(String id, String val);
-	public abstract JSONObject getJson();
-	public abstract String representation();
-	public abstract void setKeyClass(String key,String cLabel);
-	public abstract String getClass(String key);
-}
diff --git a/karma-commands/commands-alignment-openrdf/src/main/java/edu/isi/karma/kr2rml/KR2RMLMappingWriter.java b/karma-commands/commands-alignment-openrdf/src/main/java/edu/isi/karma/kr2rml/KR2RMLMappingWriter.java
index ae827d252..a2566a46b 100644
--- a/karma-commands/commands-alignment-openrdf/src/main/java/edu/isi/karma/kr2rml/KR2RMLMappingWriter.java
+++ b/karma-commands/commands-alignment-openrdf/src/main/java/edu/isi/karma/kr2rml/KR2RMLMappingWriter.java
@@ -126,7 +126,7 @@ private void initializeTripleStore() throws RepositoryException {
 	
 	protected void initializeURIs()
 	{
-		repoURIs = new HashMap<String, URI>();
+		repoURIs = new HashMap<>();
 		for (String uri : Uris.Uris) {
 			repoURIs.put(uri, f.createURI(uri));
 		}				
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/AugmentDataCommand.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/AugmentDataCommand.java
index 6cceecb8b..8aa8dfa4c 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/AugmentDataCommand.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/AugmentDataCommand.java
@@ -73,7 +73,7 @@ public AugmentDataCommand(String id, String model, String dataRepoUrl, String wo
 		newhNodeId = hNodeId;
 		this.incoming = incoming;
 		this.sameAsPredicate = sameAsPredicate;
-		appliedCommands = new Stack<Command>();
+		appliedCommands = new Stack<>();
 		addTag(CommandTag.Transformation);
 	}
 
@@ -121,13 +121,13 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			return c;
 		}
 		HNode hnode = factory.getHNode(hNodeId);
-		List<String> hNodeIds = new LinkedList<String>();
+		List<String> hNodeIds = new LinkedList<>();
 		hNodeIds.add(hNodeId);
 		inputColumns.addAll(hNodeIds);
-		List<Table> dataTables = new ArrayList<Table>();
+		List<Table> dataTables = new ArrayList<>();
 		CloneTableUtils.getDatatable(worksheet.getDataTable(), factory.getHTable(hnode.getHTableId()), dataTables, selection);
-		Map<String, String> rowHashToSubjectURI = new HashMap<String, String>();
-		Map<String, List<String>> SubjectURIToRowId = new HashMap<String, List<String>>();
+		Map<String, String> rowHashToSubjectURI = new HashMap<>();
+		Map<String, List<String>> SubjectURIToRowId = new HashMap<>();
 		for(Table t : dataTables) {
 			for(Row r : t.getRows(0, t.getNumRows(), selection)) {
 				Node n = r.getNode(hNodeId);
@@ -155,11 +155,11 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		TripleStoreUtil util = new TripleStoreUtil();
 
 		//String modelContext = worksheet.getMetadataContainer().getWorksheetProperties().getPropertyValue(Property.modelContext);
-		List<String> subjects = new LinkedList<String>();
+		List<String> subjects = new LinkedList<>();
 		subjects.addAll(rowHashToSubjectURI.values());
-		List<String> predicates = new LinkedList<String>();
-		List<String> otherClasses = new LinkedList<String>();
-		Map<String, List<String>> results = new HashMap<String, List<String>>();
+		List<String> predicates = new LinkedList<>();
+		List<String> otherClasses = new LinkedList<>();
+		Map<String, List<String>> results = new HashMap<>();
 
 		URIFormatter uriFormatter = new URIFormatter(workspace.getOntologyManager(), new ErrorReport());
 		if(sameAsPredicate!= null && !sameAsPredicate.trim().isEmpty())
@@ -177,14 +177,14 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 
 		while (!subjects.isEmpty()) {
 			ListIterator<String> subjectsIterator = subjects.listIterator();
-			LinkedList<String> tempSubjects = new LinkedList<String>();
+			LinkedList<String> tempSubjects = new LinkedList<>();
 			while(tempSubjects.size() < limit && !subjects.isEmpty())
 			{
 				tempSubjects.add(subjectsIterator.next());
 				subjectsIterator.remove();
 			}
 			try {
-				Map<String, List<String>> temp = null;
+				Map<String, List<String>> temp;
 				if (!incoming)
 					temp = util.getObjectsForSubjectsAndPredicates(dataRepoUrl, null, tempSubjects , predicates, otherClasses, sameAsPredicate);
 				else
@@ -258,7 +258,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 				edu.isi.karma.rep.alignment.Node n = alignment.getNodeById(columnUri);
 
 				semanticType.put(ClientJsonKeys.isPrimary.name(), "true");
-				Set<edu.isi.karma.rep.alignment.Node> oldNodes = new HashSet<edu.isi.karma.rep.alignment.Node>(); 
+				Set<edu.isi.karma.rep.alignment.Node> oldNodes = new HashSet<>(); 
 				if(resultClass.get(i).trim().isEmpty())
 				{
 					semanticType.put(ClientJsonKeys.DomainId.name(), n.getId());
@@ -285,7 +285,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 					JSONArray newEdges = new JSONArray();
 					JSONObject newEdge = new JSONObject();
 					String sourceId = n.getId();
-					Set<edu.isi.karma.rep.alignment.Node> tempnodes = new HashSet<edu.isi.karma.rep.alignment.Node>();
+					Set<edu.isi.karma.rep.alignment.Node> tempnodes = new HashSet<>();
 					tempnodes.addAll(alignment.getNodesByUri(resultClass.get(i)));
 					tempnodes.removeAll(oldNodes);
 
@@ -340,13 +340,13 @@ private void addMappingToResults(Map<String, List<String>> results, Map<String,
 		List<String> resultObjects = results.get("resultObjects");
 		List<String> resultClasses = results.get("resultClasses");
 		if (resultSubjects == null)
-			resultSubjects = new LinkedList<String>();
+			resultSubjects = new LinkedList<>();
 		if (resultPredicates == null)
-			resultPredicates = new LinkedList<String>();
+			resultPredicates = new LinkedList<>();
 		if (resultObjects == null)
-			resultObjects = new LinkedList<String>();
+			resultObjects = new LinkedList<>();
 		if (resultClasses == null)
-			resultClasses = new LinkedList<String>();
+			resultClasses = new LinkedList<>();
 		resultSubjects.addAll(temp.get("resultSubjects"));
 		resultPredicates.addAll(temp.get("resultPredicates"));
 		resultObjects.addAll(temp.get("resultObjects"));
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/FetchR2RMLModelsListCommand.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/FetchR2RMLModelsListCommand.java
index 68a71f644..3217b8082 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/FetchR2RMLModelsListCommand.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/FetchR2RMLModelsListCommand.java
@@ -77,8 +77,8 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			List<String> model_Times = metadata.get("model_publishtimes");
 			List<String> model_Contexts = metadata.get("model_contexts");
 			List<String> model_inputColumns = metadata.get("model_inputcolumns");
-			final List<JSONObject> list = new ArrayList<JSONObject>();
-			Set<String> worksheetcolumns = new HashSet<String>();
+			final List<JSONObject> list = new ArrayList<>();
+			Set<String> worksheetcolumns = new HashSet<>();
 			if (worksheetId != null && !worksheetId.trim().isEmpty()) {
 				HTable htable = factory.getWorksheet(worksheetId).getHeaders();
 				getHNodesForWorksheet(htable, worksheetcolumns, factory);
@@ -90,7 +90,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			Iterator<String> inputitr = model_inputColumns.iterator();
 			while(nameitr.hasNext() && urlitr.hasNext() && timeitr.hasNext() && contextitr.hasNext() && inputitr.hasNext()) {
 				JSONObject obj = new JSONObject();
-				Set<String> inputs = new HashSet<String>();
+				Set<String> inputs = new HashSet<>();
 				obj.put("name", nameitr.next());
 				obj.put("url",  urlitr.next());
 				obj.put("publishTime", timeitr.next());
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetAlternativeLinksCommand.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetAlternativeLinksCommand.java
index bcc0081d9..7bfdfb214 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetAlternativeLinksCommand.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetAlternativeLinksCommand.java
@@ -89,7 +89,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		final Alignment alignment = AlignmentManager.Instance().getAlignment(alignmentId);
 //		OntologyManager ontMgr = workspace.getOntologyManager();
 		
-		Map<String, Label> linkList = new HashMap<String, Label>();
+		Map<String, Label> linkList = new HashMap<>();
 		if (linksRange == ALTERNATIVE_LINKS_RANGE.allObjectProperties) {
 			linkList = workspace.
 					getOntologyManager().getObjectProperties();
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetClassesCommand.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetClassesCommand.java
index 9f92ca07d..9202f960d 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetClassesCommand.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetClassesCommand.java
@@ -106,7 +106,7 @@ public void generateJson(String prefix, PrintWriter pw,
 		}
 
 		if (nodeSet == null) {
-			nodeSet = new HashMap<Node,Boolean>();
+			nodeSet = new HashMap<>();
 		}
 		final Map<Node,Boolean> finalNodeSet = nodeSet;
 
@@ -167,7 +167,7 @@ private Map<Node,Boolean> getAllClasses(Workspace workspace) {
 	private Map<Node,Boolean> getClassesInModel(Workspace workspace) {
 		final Alignment alignment = AlignmentManager.Instance().getAlignment(
 				workspace.getId(), worksheetId);
-		Map<Node,Boolean> nodeSet = new HashMap<Node,Boolean>();
+		Map<Node,Boolean> nodeSet = new HashMap<>();
 		Set<Node> treeNodes = alignment.getSteinerTree().vertexSet();
 		if (treeNodes != null) {
 			for (Node n : treeNodes) {
@@ -198,12 +198,12 @@ private Map<Node,Boolean> getClassesWithProperty(Workspace workspace, String pro
 	}
 
 	private Map<Node, Boolean> getNodesUsingAlignment(Workspace workspace, Set<Label> nodeLabels) {
-		Map<Node,Boolean> nodeSet = new HashMap<Node,Boolean>();
+		Map<Node,Boolean> nodeSet = new HashMap<>();
 		
 		final Alignment alignment = AlignmentManager.Instance().getAlignment(
 				workspace.getId(), worksheetId);
 
-		final Set<String> steinerTreeNodeIds = new HashSet<String>();
+		final Set<String> steinerTreeNodeIds = new HashSet<>();
 
 		if (alignment != null && !alignment.isEmpty()) {
 			for (Node node: alignment.getSteinerTree().vertexSet()) {
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetPropertiesCommand.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetPropertiesCommand.java
index 6d2976409..69f9e55a8 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetPropertiesCommand.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/GetPropertiesCommand.java
@@ -122,7 +122,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			}
 		} else if(propertiesRange == INTERNAL_PROP_RANGE.existingProperties) {
 			Alignment alignment = AlignmentManager.Instance().getAlignment(workspace.getId(), worksheetId);
-			Set<String> steinerTreeNodeIds = new HashSet<String>();
+			Set<String> steinerTreeNodeIds = new HashSet<>();
 			if (alignment != null && !alignment.isEmpty()) {
 				DirectedWeightedMultigraph<Node, LabeledLink> steinerTree = alignment.getSteinerTree(); 
 				for (Node node: steinerTree.vertexSet()) {
@@ -131,7 +131,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 					}
 				}
 				
-				List<LabeledLink> specializedLinks = new ArrayList<LabeledLink>();
+				List<LabeledLink> specializedLinks = new ArrayList<>();
 				Set<LabeledLink> temp = null;
 				temp = alignment.getLinksByType(LinkType.DataPropertyLink);
 				if (temp != null) specializedLinks.addAll(temp);
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SetSemanticTypeCommand.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SetSemanticTypeCommand.java
index b2e70dada..821bdab45 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SetSemanticTypeCommand.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SetSemanticTypeCommand.java
@@ -132,10 +132,10 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		oldGraph = (DirectedWeightedMultigraph<Node, DefaultLink>)alignment.getGraph().clone();
 
 		/*** Add the appropriate nodes and links in alignment graph ***/
-		List<SemanticType> typesList = new ArrayList<SemanticType>();
+		List<SemanticType> typesList = new ArrayList<>();
 		for (int i = 0; i < typesArr.length(); i++) {
 			try {
-				LabeledLink newLink = null;
+				LabeledLink newLink;
 				JSONObject type = typesArr.getJSONObject(i);
 				
 				String sourceId = "";
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestAutoModelCommand.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestAutoModelCommand.java
index c3aee7a88..7e9678a74 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestAutoModelCommand.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestAutoModelCommand.java
@@ -116,7 +116,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		Node classNode = alignment.addInternalNode(internalNodeLabel);
 		
 		// Create column nodes for all columns 
-		List<HNode> sortedLeafHNodes = new ArrayList<HNode>();
+		List<HNode> sortedLeafHNodes = new ArrayList<>();
 		worksheet.getHeaders().getSortedLeafHNodes(sortedLeafHNodes);
 		for (HNode hNode : sortedLeafHNodes){
 			String columnName = hNode.getColumnName().trim().replaceAll(" ", "_");
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestAutoModelCommandFactory.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestAutoModelCommandFactory.java
index 2f37c1e4e..72e513a15 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestAutoModelCommandFactory.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestAutoModelCommandFactory.java
@@ -107,7 +107,7 @@ public Command createCommand(JSONArray inputJson, String model, Workspace worksp
 			JSONObject value = (JSONObject) typeObj
 					.get(ClientJsonKeys.value.name());
 
-			SemanticType type = null;
+			SemanticType type;
 			String domain = (String) value
 					.get(SemanticType.ClientJsonKeys.DomainUri.name());
 			String fullType = (String) value
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestModelCommand.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestModelCommand.java
index 40d278958..ceec22c0e 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestModelCommand.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestModelCommand.java
@@ -135,7 +135,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 
 			initialGraph = (DirectedWeightedMultigraph<Node, DefaultLink>)alignment.getGraph().clone();
 			
-			List<HNode> orderedNodeIds = new ArrayList<HNode>();
+			List<HNode> orderedNodeIds = new ArrayList<>();
 			worksheet.getHeaders().getSortedLeafHNodes(orderedNodeIds);
 			
 			List<String> visibleHNodeIds = null;
@@ -175,7 +175,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		}
 
 		steinerNodes = alignment.computeSteinerNodes();
-		ModelLearner modelLearner = null;
+		ModelLearner modelLearner;
 
 		if (modelingConfiguration.getKnownModelsAlignment()) 
 			modelLearner = new ModelLearner(alignment.getGraphBuilder(), steinerNodes);
@@ -193,7 +193,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		
 //		logger.info(GraphUtil.labeledGraphToString(model.getGraph()));
 		
-		List<SemanticType> semanticTypes = new LinkedList<SemanticType>();
+		List<SemanticType> semanticTypes = new LinkedList<>();
 		alignment.updateAlignment(model, semanticTypes);
 		logger.info(GraphUtil.labeledGraphToString(alignment.getSteinerTree()));
 
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestModelCommandFactory.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestModelCommandFactory.java
index 41c3d11af..76866cb14 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestModelCommandFactory.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/SuggestModelCommandFactory.java
@@ -73,7 +73,7 @@ public Command createCommand(JSONArray inputJson, String model, Workspace worksp
 			JSONObject typeObj = (JSONObject) inputJson.get(++i);
 			JSONObject value = (JSONObject) typeObj.get(ClientJsonKeys.value.name());
 			
-			SemanticType type = null;
+			SemanticType type;
 			String domain = (String) value.get(SemanticType.ClientJsonKeys.DomainUri.name());
 			String fullType = (String) value.get(SemanticType.ClientJsonKeys.FullType.name());
 			
diff --git a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/UnassignSemanticTypeCommand.java b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/UnassignSemanticTypeCommand.java
index a2178d90a..d5704c30e 100644
--- a/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/UnassignSemanticTypeCommand.java
+++ b/karma-commands/commands-alignment/src/main/java/edu/isi/karma/controller/command/alignment/UnassignSemanticTypeCommand.java
@@ -143,10 +143,10 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		}
 
 		// Remove the nodes (if any) from the outlier tag
-		Collection<edu.isi.karma.rep.Node> nodes = new ArrayList<edu.isi.karma.rep.Node>();
+		Collection<edu.isi.karma.rep.Node> nodes = new ArrayList<>();
 		//TODO What does that mean? 
 		worksheet.getDataTable().collectNodes(currentPath, nodes, SuperSelectionManager.DEFAULT_SELECTION);
-		Set<String> nodeIds = new HashSet<String>();
+		Set<String> nodeIds = new HashSet<>();
 		for (edu.isi.karma.rep.Node node : nodes) {
 			nodeIds.add(node.getId());
 		}
diff --git a/karma-commands/commands-bloom/src/main/java/edu/isi/karma/controller/command/alignment/SearchForDataToAugmentCommand.java b/karma-commands/commands-bloom/src/main/java/edu/isi/karma/controller/command/alignment/SearchForDataToAugmentCommand.java
index 59fb3bc65..11cdc5b81 100644
--- a/karma-commands/commands-bloom/src/main/java/edu/isi/karma/controller/command/alignment/SearchForDataToAugmentCommand.java
+++ b/karma-commands/commands-bloom/src/main/java/edu/isi/karma/controller/command/alignment/SearchForDataToAugmentCommand.java
@@ -90,7 +90,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		HashMap<String, List<String>> result = null;
 		nodeUri = nodeUri.trim();
 		Map<String, Label> parents = workspace.getOntologyManager().getSuperClasses(nodeUri, true);
-		Set<String> classes = new HashSet<String>(parents.keySet());
+		Set<String> classes = new HashSet<>(parents.keySet());
 		classes.add(nodeUri);
 		StringBuilder builder = new StringBuilder();
 		nodeUri = builder.append("<").append(nodeUri).append(">").toString();
@@ -100,7 +100,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			LOG.error("Unable to find predicates for triples maps with same class as: " + nodeUri, e);
 		}
 		final JSONArray array = new JSONArray();
-		List<JSONObject> objects = new ArrayList<JSONObject>();
+		List<JSONObject> objects = new ArrayList<>();
 		List<String> concatenatedPredicateObjectMapsList = result.get("predicateObjectMaps");
 		List<String> predicates = result.get("predicates");
 		List<String> otherClasses = result.get("otherClasses");
@@ -118,10 +118,10 @@ public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
 			});
 		}
 		HNode hnode = factory.getHNode(hNodeId);
-		List<Table> dataTables = new ArrayList<Table>();
+		List<Table> dataTables = new ArrayList<>();
 		CloneTableUtils.getDatatable(worksheet.getDataTable(), factory.getHTable(hnode.getHTableId()), dataTables, selection);
 		KR2RMLBloomFilter uris = new KR2RMLBloomFilter(KR2RMLBloomFilter.defaultVectorSize, KR2RMLBloomFilter.defaultnbHash, Hash.JENKINS_HASH);
-		Set<String> uriSet = new HashSet<String>();
+		Set<String> uriSet = new HashSet<>();
 		for(Table t : dataTables) {
 			for(Row r : t.getRows(0, t.getNumRows(), selection)) {
 				Node n = r.getNode(hNodeId);
@@ -142,15 +142,15 @@ public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
 				}
 			}
 		}
-		Set<String> maps = new HashSet<String>();
-		Map<String, String> bloomfilterMapping = new HashMap<String, String>();
+		Set<String> maps = new HashSet<>();
+		Map<String, String> bloomfilterMapping = new HashMap<>();
 		try{
 			for (String concatenatedPredicateObjectMaps : concatenatedPredicateObjectMapsList) {
-				List<String> predicateObjectMaps = new ArrayList<String>(Arrays.asList(concatenatedPredicateObjectMaps.split(",")));
+				List<String> predicateObjectMaps = new ArrayList<>(Arrays.asList(concatenatedPredicateObjectMaps.split(",")));
 				maps.addAll(predicateObjectMaps);
 				if (maps.size() > limit) {
 					bloomfilterMapping.putAll(util.getBloomFiltersForMaps(tripleStoreUrl, null, maps));
-					maps = new HashSet<String>();
+					maps = new HashSet<>();
 				}
 			}
 			if (!maps.isEmpty())
@@ -162,7 +162,7 @@ public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
 		{
 
 			String concatenatedPredicateObjectMaps = concatenatedPredicateObjectMapsListItr.next();
-			List<String> predicateObjectMaps = new ArrayList<String>(Arrays.asList(concatenatedPredicateObjectMaps.split(",")));
+			List<String> predicateObjectMaps = new ArrayList<>(Arrays.asList(concatenatedPredicateObjectMaps.split(",")));
 			String predicate =  predicatesItr.next();
 			String otherClass = otherClassesItr.next();
 			try {
diff --git a/karma-commands/commands-bloom/src/main/java/edu/isi/karma/controller/command/alignment/SearchForDataToAugmentIncomingCommand.java b/karma-commands/commands-bloom/src/main/java/edu/isi/karma/controller/command/alignment/SearchForDataToAugmentIncomingCommand.java
index 16ad143d8..bf1847aa6 100644
--- a/karma-commands/commands-bloom/src/main/java/edu/isi/karma/controller/command/alignment/SearchForDataToAugmentIncomingCommand.java
+++ b/karma-commands/commands-bloom/src/main/java/edu/isi/karma/controller/command/alignment/SearchForDataToAugmentIncomingCommand.java
@@ -90,7 +90,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		HashMap<String, List<String>> result = null;
 		nodeUri = nodeUri.trim();
 		Map<String, Label> parents = workspace.getOntologyManager().getSuperClasses(nodeUri, true);
-		Set<String> classes = new HashSet<String>(parents.keySet());
+		Set<String> classes = new HashSet<>(parents.keySet());
 		classes.add(nodeUri);
 		StringBuilder builder = new StringBuilder();
 		nodeUri = builder.append("<").append(nodeUri).append(">").toString();
@@ -100,7 +100,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			LOG.error("Unable to find predicates for triples maps with same class as: " + nodeUri, e);
 		}
 		final JSONArray array = new JSONArray();
-		List<JSONObject> objects = new ArrayList<JSONObject>();
+		List<JSONObject> objects = new ArrayList<>();
 		List<String> concatenatedPredicateObjectMapsList = result.get("refObjectMaps");
 		List<String> predicates = result.get("predicates");
 		List<String> otherClasses = result.get("otherClasses");
@@ -109,10 +109,10 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		Iterator<String> otherClassesItr = otherClasses.iterator();
 		String hNodeId = FetchHNodeIdFromAlignmentCommand.gethNodeId(AlignmentManager.Instance().constructAlignmentId(workspace.getId(), worksheetId), columnUri);
 		HNode hnode = factory.getHNode(hNodeId);
-		List<Table> dataTables = new ArrayList<Table>();
+		List<Table> dataTables = new ArrayList<>();
 		CloneTableUtils.getDatatable(worksheet.getDataTable(), factory.getHTable(hnode.getHTableId()), dataTables, selection);
 		KR2RMLBloomFilter uris = new KR2RMLBloomFilter(KR2RMLBloomFilter.defaultVectorSize, KR2RMLBloomFilter.defaultnbHash, Hash.JENKINS_HASH);
-		Set<String> uriSet = new HashSet<String>();
+		Set<String> uriSet = new HashSet<>();
 		for(Table t : dataTables) {
 			for(Row r : t.getRows(0, t.getNumRows(), selection)) {
 				Node n = r.getNode(hNodeId);
@@ -133,15 +133,15 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 				}
 			}
 		}
-		Set<String> maps = new HashSet<String>();
-		Map<String, String> bloomfilterMapping = new HashMap<String, String>();
+		Set<String> maps = new HashSet<>();
+		Map<String, String> bloomfilterMapping = new HashMap<>();
 		try{
 			for (String concatenatedPredicateObjectMaps : concatenatedPredicateObjectMapsList) {
-				List<String> predicateObjectMaps = new ArrayList<String>(Arrays.asList(concatenatedPredicateObjectMaps.split(",")));
+				List<String> predicateObjectMaps = new ArrayList<>(Arrays.asList(concatenatedPredicateObjectMaps.split(",")));
 				maps.addAll(predicateObjectMaps);
 				if (maps.size() > limit) {
 					bloomfilterMapping.putAll(util.getBloomFiltersForMaps(tripleStoreUrl, null, maps));
-					maps = new HashSet<String>();
+					maps = new HashSet<>();
 				}
 			}
 			if (!maps.isEmpty())
@@ -152,7 +152,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		while(concatenatedPredicateObjectMapsListItr.hasNext() && predicatesItr.hasNext() && otherClassesItr.hasNext())
 		{
 			String concatenatedPredicateObjectMaps = concatenatedPredicateObjectMapsListItr.next();
-			List<String> predicateObjectMaps = new ArrayList<String>(Arrays.asList(concatenatedPredicateObjectMaps.split(",")));
+			List<String> predicateObjectMaps = new ArrayList<>(Arrays.asList(concatenatedPredicateObjectMaps.split(",")));
 			String predicate =  predicatesItr.next();
 			String otherClass = otherClassesItr.next();
 			try {
diff --git a/karma-commands/commands-bloom/src/main/java/edu/isi/karma/er/helper/BloomFilterTripleStoreUtil.java b/karma-commands/commands-bloom/src/main/java/edu/isi/karma/er/helper/BloomFilterTripleStoreUtil.java
index 1baff30f0..98f1ebb56 100644
--- a/karma-commands/commands-bloom/src/main/java/edu/isi/karma/er/helper/BloomFilterTripleStoreUtil.java
+++ b/karma-commands/commands-bloom/src/main/java/edu/isi/karma/er/helper/BloomFilterTripleStoreUtil.java
@@ -37,8 +37,8 @@ public boolean processBloomFilters(String modelContext,
 		boolean result = true;
 		try{
 		result &= updateTripleStore(obj, bloomfilterMapping, modelRepoUrl, modelContext);
-		Map<String, String> verification = new HashMap<String, String>();
-		Set<String> triplemaps = new HashSet<String>(Arrays.asList(obj.getString("ids").split(",")));
+		Map<String, String> verification = new HashMap<>();
+		Set<String> triplemaps = new HashSet<>(Arrays.asList(obj.getString("ids").split(",")));
 		boolean verify = verify(verification, triplemaps,modelRepoUrl ,modelContext,obj);
 		if (!verify) {
 			result &= updateTripleStore(obj, verification, modelRepoUrl, modelContext);
@@ -83,9 +83,9 @@ public boolean verify(Map<String, String> verification, Set<String> triplemaps,
 	}
 
 	public boolean updateTripleStore(JSONObject obj, Map<String, String> bloomfilterMapping, String modelRepoUrl, String modelContext) throws KarmaException, IOException {
-		Set<String> triplemaps = new HashSet<String>(Arrays.asList(obj.getString("ids").split(",")));
+		Set<String> triplemaps = new HashSet<>(Arrays.asList(obj.getString("ids").split(",")));
 		bloomfilterMapping.putAll(getBloomFiltersForMaps(modelRepoUrl, modelContext, triplemaps));
-		Map<String, KR2RMLBloomFilter> bfs = new HashMap<String, KR2RMLBloomFilter>();
+		Map<String, KR2RMLBloomFilter> bfs = new HashMap<>();
 		for (String tripleUri : triplemaps) {
 			String serializedBloomFilter = obj.getString(tripleUri);
 			KR2RMLBloomFilter bf = new KR2RMLBloomFilter();
@@ -99,7 +99,7 @@ public Map<String, String> getBloomFiltersForMaps(String tripleStoreURL, String
 		tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
 		testTripleStoreConnection(tripleStoreURL);
 
-		Map<String, String> bloomfilters = new HashMap<String, String>();
+		Map<String, String> bloomfilters = new HashMap<>();
 		try {
 
 			StringBuilder query = new StringBuilder();
@@ -129,7 +129,7 @@ public Map<String, String> getBloomFiltersForMaps(String tripleStoreURL, String
 			logger.debug("query: " + queryString);
 
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("query", queryString);
 			formparams.put("queryLn", "SPARQL");
 
@@ -191,7 +191,7 @@ public void deleteBloomFiltersForMaps(String tripleStoreURL, String context, Col
 			logger.debug("query: " + queryString);
 
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("update", queryString);
 
 			String responseString = HTTPUtil.executeHTTPPostRequest(
diff --git a/karma-commands/commands-bloom/src/main/java/edu/isi/karma/kr2rml/writer/KR2RMLBloomFilterManager.java b/karma-commands/commands-bloom/src/main/java/edu/isi/karma/kr2rml/writer/KR2RMLBloomFilterManager.java
index f3219ff7b..a5926ed62 100644
--- a/karma-commands/commands-bloom/src/main/java/edu/isi/karma/kr2rml/writer/KR2RMLBloomFilterManager.java
+++ b/karma-commands/commands-bloom/src/main/java/edu/isi/karma/kr2rml/writer/KR2RMLBloomFilterManager.java
@@ -22,12 +22,12 @@ public class KR2RMLBloomFilterManager {
 	protected R2RMLMappingIdentifier mappingIdentifier;
 	public KR2RMLBloomFilterManager(R2RMLMappingIdentifier mappingIdentifier)
 	{
-		idToBloomFilter = new ConcurrentHashMap<String, KR2RMLBloomFilter>();
+		idToBloomFilter = new ConcurrentHashMap<>();
 		this.mappingIdentifier = mappingIdentifier;
 	}
 	public KR2RMLBloomFilterManager(JSONObject serializedManager) throws IOException
 	{
-		idToBloomFilter = new ConcurrentHashMap<String, KR2RMLBloomFilter>();
+		idToBloomFilter = new ConcurrentHashMap<>();
 		String idsConcatenated = serializedManager.getString("ids");
 		String[] ids = idsConcatenated.split(",");
 		for(String id : ids)
diff --git a/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/FetchTransformingDataCommand.java b/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/FetchTransformingDataCommand.java
index 1eea3e30f..dfc45f369 100644
--- a/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/FetchTransformingDataCommand.java
+++ b/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/FetchTransformingDataCommand.java
@@ -55,7 +55,7 @@ public CommandType getCommandType() {
 	}
 
 	public HashSet<Integer> obtainIndexs(int size) {
-		HashSet<Integer> inds = new HashSet<Integer>();
+		HashSet<Integer> inds = new HashSet<>();
 		// select 30% or 50
 		int sample_size = size;
 		if (sample_size >= 500) {
@@ -84,7 +84,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 				System.currentTimeMillis(), worksheetId);
 		logger.info(Msg);
 		// Get the HNode
-		HashMap<String, HashMap<String, String>> rows = new HashMap<String, HashMap<String, String>>();
+		HashMap<String, HashMap<String, String>> rows = new HashMap<>();
 		HNodePath selectedPath = null;
 		List<HNodePath> columnPaths = wk.getHeaders().getAllPaths();
 		for (HNodePath path : columnPaths) {
@@ -93,7 +93,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			}
 		}
 		// random nodes
-		Collection<Node> nodes = new ArrayList<Node>();
+		Collection<Node> nodes = new ArrayList<>();
 		wk.getDataTable().collectNodes(selectedPath, nodes, selection);
 		HashSet<Integer> indSet = this.obtainIndexs(nodes.size());
 		int index = 0;
@@ -102,7 +102,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			if (indSet.contains(index)) {
 				String id = node.getId();
 				String originalVal = node.getValue().asString();
-				HashMap<String, String> x = new HashMap<String, String>();
+				HashMap<String, String> x = new HashMap<>();
 				x.put("Org", originalVal);
 				x.put("Tar", originalVal);
 				x.put("Orgdis", originalVal);
diff --git a/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/GenerateCleaningRulesCommand.java b/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/GenerateCleaningRulesCommand.java
index 21856166d..36e459153 100644
--- a/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/GenerateCleaningRulesCommand.java
+++ b/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/GenerateCleaningRulesCommand.java
@@ -61,7 +61,7 @@
 public class GenerateCleaningRulesCommand extends WorksheetSelectionCommand {
 	final String hNodeId;
 	private Vector<TransformationExample> examples;
-	private HashSet<String> nodeIds = new HashSet<String>();
+	private HashSet<String> nodeIds = new HashSet<>();
 	RamblerTransformationInputs inputs;
 	public String compResultString = "";
 	private static Logger logger = LoggerFactory.getLogger(GenerateCleaningRulesCommand.class);
@@ -78,7 +78,7 @@ public GenerateCleaningRulesCommand(String id, String model, String worksheetId,
 	}
 
 	private HashSet<String> parseNodeIds(String Ids) {
-		HashSet<String> tSet = new HashSet<String>();
+		HashSet<String> tSet = new HashSet<>();
 		try {
 			JSONArray jsa = new JSONArray(Ids);
 			for (int i = 0; i < jsa.length(); i++) {
@@ -92,7 +92,7 @@ private HashSet<String> parseNodeIds(String Ids) {
 	}
 
 	public static Vector<TransformationExample> parseExample(String example) {
-		Vector<TransformationExample> x = new Vector<TransformationExample>();
+		Vector<TransformationExample> x = new Vector<>();
 		try {
 			JSONArray jsa = new JSONArray(example);
 			for (int i = 0; i < jsa.length(); i++) {
@@ -148,8 +148,8 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		String msg = String.format("Gen rule start,Time,%d, Worksheet,%s",System.currentTimeMillis(),worksheetId);
 		logger.info(msg);
 		// Get the HNode
-		HashMap<String, String> rows = new HashMap<String, String>();
-		HashMap<String, Integer> amb = new HashMap<String, Integer>();
+		HashMap<String, String> rows = new HashMap<>();
+		HashMap<String, Integer> amb = new HashMap<>();
 		HNodePath selectedPath = null;
 		List<HNodePath> columnPaths = wk.getHeaders().getAllPaths();
 		for (HNodePath path : columnPaths) {
@@ -158,7 +158,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			}
 		}
 		
-		Collection<Node> nodes = new ArrayList<Node>();
+		Collection<Node> nodes = new ArrayList<>();
 		wk.getDataTable().collectNodes(selectedPath, nodes, selection);
 		for (Node node : nodes) {
 			String id = node.getId();
@@ -170,7 +170,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			calAmbScore(id, originalVal, amb);
 		}
 		RamblerValueCollection vc = new RamblerValueCollection(rows);
-		HashMap<String, Vector<String[]>> expFeData = new HashMap<String, Vector<String[]>>();
+		HashMap<String, Vector<String[]>> expFeData = new HashMap<>();
 		Messager mg = null;
 		if(wk.getMsg()!= null)
 		{
@@ -199,7 +199,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		RamblerTransformationOutput rtf = null;
 		// initialize the vocabulary
 		Iterator<String> iterx = inputs.getInputValues().getValues().iterator();
-		Vector<String> v = new Vector<String>();
+		Vector<String> v = new Vector<>();
 		int vb_cnt = 0;
 		while(iterx.hasNext() && vb_cnt < 30)
 		{
@@ -217,17 +217,17 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		}
 		Iterator<String> iter = rtf.getTransformations().keySet().iterator();
 		// id:{org: tar: orgdis: tardis: }
-		HashMap<String, HashMap<String, String>> resdata = new HashMap<String, HashMap<String, String>>();
-		HashSet<String> keys = new HashSet<String>();
+		HashMap<String, HashMap<String, String>> resdata = new HashMap<>();
+		HashSet<String> keys = new HashSet<>();
 		while (iter.hasNext()) {
 			String tpid = iter.next();
 			ValueCollection rvco = rtf.getTransformedValues_debug(tpid);
 			if (rvco == null)
 				continue;
 			// constructing displaying data
-			HashMap<String, String[]> xyzHashMap = new HashMap<String, String[]>();
+			HashMap<String, String[]> xyzHashMap = new HashMap<>();
 			for (String key : rvco.getNodeIDs()) {
-				HashMap<String, String> dict = new HashMap<String, String>();
+				HashMap<String, String> dict = new HashMap<>();
 				// add to the example selection
 				boolean isExp = false;
 				String org = vc.getValue(key);
@@ -255,7 +255,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 				for (TransformationExample exp : examples) {
 					if (exp.getNodeId().compareTo(key) == 0) {
 						if (!expFeData.containsKey(classLabel)) {
-							Vector<String[]> vstr = new Vector<String[]>();
+							Vector<String[]> vstr = new Vector<>();
 							String[] texp = {dict.get("Org"), pretar};
 							vstr.add(texp);
 							expFeData.put(classLabel, vstr);
@@ -348,7 +348,7 @@ public void updateCandiScore(ValueCollection rvco,
 			if (values.containsKey(id)) {
 				dict = values.get(id);
 			} else {
-				dict = new HashMap<String, Integer>();
+				dict = new HashMap<>();
 				values.put(id, dict);
 			}
 			if (dict.containsKey(value)) {
@@ -366,7 +366,7 @@ public HashMap<String, Double> getScore(HashMap<String, Integer> dicts,
 		int topKsize = 1;
 		if (sw)
 			topKsize = Integer.MAX_VALUE;
-		HashMap<String, Double> topK = new HashMap<String, Double>();
+		HashMap<String, Double> topK = new HashMap<>();
 		Iterator<String> iditer = dicts.keySet().iterator();
 		while (iditer.hasNext()) {
 			String id = iditer.next();
diff --git a/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/InvokeCleaningServiceCommand.java b/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/InvokeCleaningServiceCommand.java
index 333b048a8..91997cfdf 100644
--- a/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/InvokeCleaningServiceCommand.java
+++ b/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/InvokeCleaningServiceCommand.java
@@ -99,7 +99,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 				selectedPath = path;
 			}
 		}
-		Collection<Node> nodes = new ArrayList<Node>();
+		Collection<Node> nodes = new ArrayList<>();
 		workspace.getFactory().getWorksheet(worksheetId).getDataTable()
 				.collectNodes(selectedPath, nodes, selection);
 
@@ -133,7 +133,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 
 			URI u = null;
 			u = new URI(url);
-			List<NameValuePair> formparams = new ArrayList<NameValuePair>();
+			List<NameValuePair> formparams = new ArrayList<>();
 			formparams.add(new BasicNameValuePair("json", jsonString));
 
 			httppost = new HttpPost(u);
diff --git a/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/SubmitCleaningCommand.java b/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/SubmitCleaningCommand.java
index 0586f0b26..05af56120 100644
--- a/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/SubmitCleaningCommand.java
+++ b/karma-commands/commands-cleaning/src/main/java/edu/isi/karma/controller/command/cleaning/SubmitCleaningCommand.java
@@ -72,7 +72,7 @@ public class SubmitCleaningCommand extends WorksheetSelectionCommand {
 
 	private static Logger logger = LoggerFactory
 			.getLogger(SubmitCleaningCommand.class);
-	private Vector<TransformationExample> examples = new Vector<TransformationExample>();
+	private Vector<TransformationExample> examples = new Vector<>();
 
 	public SubmitCleaningCommand(String id, String model, String hNodeId, String worksheetId,
 			String Examples, String selectionId) {
@@ -160,12 +160,12 @@ public UpdateContainer doIt(Workspace workspace) {
 		String Msg = String.format("submit end, Time,%d, Worksheet,%s",
 				System.currentTimeMillis(), worksheetId);
 		logger.info(Msg);
-		String colnameString = "";
+		String colnameString;
 		UpdateContainer c = new UpdateContainer();
 		HNodePath selectedPath = null;
 		try {
 			// obtain transformed results
-			HashMap<String, String> rows = new HashMap<String, String>();
+			HashMap<String, String> rows = new HashMap<>();
 			colnameString = obtainTransformedResultsAndFindNewColumnName(
 					workspace, rows);
 			createAndExecuteNewAddColumnCommand(workspace, colnameString);
@@ -242,7 +242,7 @@ private void findNewHNodeIdAndHNodeAsDerived(Workspace workspace,
 	private ValueCollection getValueCollectionFromRamblerTranformationOutput(
 			RamblerTransformationOutput rtf) {
 		Iterator<String> iter = rtf.getTransformations().keySet().iterator();
-		Vector<ValueCollection> vvc = new Vector<ValueCollection>();
+		Vector<ValueCollection> vvc = new Vector<>();
 		String tpid = iter.next();
 		ValueCollection rvco = rtf.getTransformedValues(tpid);
 		vvc.add(rvco);
@@ -289,7 +289,7 @@ private String obtainTransformedResultsAndFindNewColumnName(
 
 			}
 		}
-		Collection<Node> nodes = new ArrayList<Node>();
+		Collection<Node> nodes = new ArrayList<>();
 		SuperSelection selection = getSuperSelection(workspace);
 		workspace.getFactory().getWorksheet(worksheetId).getDataTable()
 				.collectNodes(selectedPath, nodes, selection);
diff --git a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/CommandHistoryUtil.java b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/CommandHistoryUtil.java
index f13981238..aee51d075 100644
--- a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/CommandHistoryUtil.java
+++ b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/CommandHistoryUtil.java
@@ -25,10 +25,10 @@
 import java.util.*;
 
 public class CommandHistoryUtil {
-	private final List<Command> commands = new ArrayList<Command>();
+	private final List<Command> commands = new ArrayList<>();
 	private Workspace workspace;
 	private String worksheetId;
-	HashMap<String, CommandFactory> commandFactoryMap;
+	Map<String, CommandFactory> commandFactoryMap;
 	static Logger logger = Logger.getLogger(CommandHistoryUtil.class);
 
 	public CommandHistoryUtil(List<Command> commands, Workspace workspace, String worksheetId) {
@@ -73,7 +73,7 @@ private Map<Command, List<Command> > generateGraph() {
 
 	public Set<String> generateInputColumns() {
 		Map<Command, List<Command> > dag = generateGraph();
-		Set<String> inputColumns = new HashSet<String>();
+		Set<String> inputColumns = new HashSet<>();
 		for (Command t : commands) {
 			if (t.getCommandName().equals("SetSemanticTypeCommand") || t.getCommandName().equals("SetMetaPropertyCommand")) {
 				inputColumns.addAll(getParents(t, dag));
@@ -83,7 +83,7 @@ public Set<String> generateInputColumns() {
 	}
 
 	public Set<String> generateOutputColumns() {
-		Set<String> outputColumns = new HashSet<String>();
+		Set<String> outputColumns = new HashSet<>();
 		for (Command t : commands) {
 			if (t.getOutputColumns() != null)
 				outputColumns.addAll(t.getOutputColumns());
@@ -94,7 +94,7 @@ public Set<String> generateOutputColumns() {
 
 	private Set<String> getParents(Command c, Map<Command, List<Command> >dag) {
 		List<Command> parents = dag.get(c);
-		Set<String> terminalColumns = new HashSet<String>();
+		Set<String> terminalColumns = new HashSet<>();
 		if (parents == null || parents.size() == 0)
 			terminalColumns.addAll(c.getInputColumns());
 		else {
diff --git a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/HistoryJSONEditor.java b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/HistoryJSONEditor.java
index 4dfb48567..f1ee5a62f 100644
--- a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/HistoryJSONEditor.java
+++ b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/HistoryJSONEditor.java
@@ -41,7 +41,7 @@ public void deleteExistingTransformationCommands() {
 				}
 				else {
 					JSONArray array = new JSONArray(tmp);
-					Set<String> newOutputColumns = new HashSet<String>();
+					Set<String> newOutputColumns = new HashSet<>();
 					for (int j = 0; j < array.length(); j++) {
 						JSONObject obj = new JSONObject(array.get(j).toString());
 						newOutputColumns.add(obj.get("value").toString());
@@ -76,7 +76,7 @@ public void deleteExistingTransformationAndModelingCommands() {
 				}
 				else {
 					JSONArray array = new JSONArray(tmp);
-					Set<String> newOutputColumns = new HashSet<String>();
+					Set<String> newOutputColumns = new HashSet<>();
 					for (int j = 0; j < array.length(); j++) {
 						JSONObject obj = new JSONObject(array.get(j).toString());
 						newOutputColumns.add(obj.get("value").toString());
diff --git a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/AlignmentSVGVisualizationUpdate.java b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/AlignmentSVGVisualizationUpdate.java
index 3998fa8cd..58807f8ec 100644
--- a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/AlignmentSVGVisualizationUpdate.java
+++ b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/AlignmentSVGVisualizationUpdate.java
@@ -115,6 +115,14 @@ public boolean equals(Object o) {
 		return false;
 	}
 
+	@Override
+	public int hashCode() {
+		int result = this.worksheetId != null ? this.worksheetId.hashCode() : 0;
+		result = 31 * result + (this.alignmentGraph != null ? this.alignmentGraph.hashCode() : 0);
+		result = 31 * result + (this.alignment != null ? this.alignment.hashCode() : 0);
+		return result;
+	}
+
 	@Override
 	public void generateJson(String prefix, PrintWriter pw,
 			VWorkspace vWorkspace) {
@@ -151,8 +159,8 @@ public void generateJsonForForceLayout(String prefix, PrintWriter pw,
 			JSONArray linksArr = new JSONArray();
 			JSONArray edgeLinksArr = new JSONArray();
 
-			HashMap<Node, Integer> verticesIndex = new HashMap<Node, Integer>();
-			HashMap<String, ColumnNode> columnNodes = new HashMap<>();
+			Map<Node, Integer> verticesIndex = new HashMap<>();
+			Map<String, ColumnNode> columnNodes = new HashMap<>();
 
 			if (alignmentGraph != null
 					&& !alignmentGraph.vertexSet().isEmpty()) {
@@ -331,7 +339,7 @@ public void generateJsonForNormalLayout(String prefix, PrintWriter pw,
 			DisplayModel dm = new DisplayModel(alignmentGraph, vWorksheet
 					.getWorksheet().getHeaders());
 			HashMap<Node, Integer> nodeHeightsMap = dm.getNodesLevel();
-			HashMap<Node, Set<ColumnNode>> nodeCoverage = dm.getNodesSpan();
+			Map<Node, Set<ColumnNode>> nodeCoverage = dm.getNodesSpan();
 			/** Identify the max height **/
 			int maxTreeHeight = 0;
 			for (Map.Entry<Node, Integer> nodeIntegerEntry : nodeHeightsMap.entrySet()) {
@@ -340,14 +348,14 @@ public void generateJsonForNormalLayout(String prefix, PrintWriter pw,
 				}
 			}
 			/*** Add the nodes and the links from the Steiner tree ***/
-			List<String> hNodeIdsAdded = new ArrayList<String>();
+			List<String> hNodeIdsAdded = new ArrayList<>();
 			JSONArray nodesArr = new JSONArray();
 			JSONArray linksArr = new JSONArray();
 			if (alignmentGraph != null
 					&& !alignmentGraph.vertexSet().isEmpty()) {
 				/** Add the nodes **/
 				Set<Node> nodes = alignmentGraph.vertexSet();
-				HashMap<Node, Integer> verticesIndex = new HashMap<Node, Integer>();
+				Map<Node, Integer> verticesIndex = new HashMap<>();
 				int nodesIndexcounter = 0;
 				for (Node node : nodes) {
 					/**
diff --git a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/AllWorksheetHeadersUpdate.java b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/AllWorksheetHeadersUpdate.java
index ef710c98d..1f43fe392 100644
--- a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/AllWorksheetHeadersUpdate.java
+++ b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/AllWorksheetHeadersUpdate.java
@@ -96,4 +96,10 @@ public boolean equals(Object o) {
 		return false;
 	}
 
+	@Override
+	public int hashCode() {
+		int result = this.worksheetId != null ? this.worksheetId.hashCode() : 0;
+		result = 31 * result + (this.deleteAfterGenerate ? 1 : 0);
+		return result;
+	}
 }
diff --git a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/RegenerateWorksheetUpdate.java b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/RegenerateWorksheetUpdate.java
index b5cce0de7..a2d0ab2bc 100644
--- a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/RegenerateWorksheetUpdate.java
+++ b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/RegenerateWorksheetUpdate.java
@@ -70,4 +70,8 @@ public boolean equals(Object o) {
 		return false;
 	}
 
+	@Override
+	public int hashCode() {
+		return this.worksheetId != null ? this.worksheetId.hashCode() : 0;
+	}
 }
diff --git a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetCleaningUpdate.java b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetCleaningUpdate.java
index 63f58a5ed..967c66687 100644
--- a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetCleaningUpdate.java
+++ b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetCleaningUpdate.java
@@ -76,11 +76,11 @@ public void generateJson(String prefix, PrintWriter pw,
 		List<HNodePath> columnPaths = worksheet.getHeaders().getAllPaths();
 		ColumnMetadata colMetadata = worksheet.getMetadataContainer().getColumnMetadata();
 
-		List<String> columnsInvoked = new ArrayList<String>();
+		List<String> columnsInvoked = new ArrayList<>();
 
 		for (HNodePath path:columnPaths) {
 			String leafHNodeId = path.getLeaf().getId();
-			List<Node> nodes = new ArrayList<Node>(Math.max(1000, worksheet.getDataTable().getNumRows()));
+			List<Node> nodes = new ArrayList<>(Math.max(1000, worksheet.getDataTable().getNumRows()));
 			worksheet.getDataTable().collectNodes(path, nodes, selection);
 			final int sampleSize = (nodes.size() > 1000) ? 1000 : nodes.size();
 			columnsInvoked.add(leafHNodeId);
@@ -101,7 +101,7 @@ public void generateJson(String prefix, PrintWriter pw,
 						}
 					}
 					else {
-						Set<Integer> randomNums = new HashSet<Integer>();
+						Set<Integer> randomNums = new HashSet<>();
 						Random gen = new Random();
 						for (int i = 0; i < sampleSize; i++) {
 							int r = gen.nextInt(nodes.size());
@@ -129,7 +129,7 @@ public void generateJson(String prefix, PrintWriter pw,
 													.getContextParameters(WorkspaceKarmaHomeRegistry.getInstance().getKarmaHome(workspaceId))
 													.getParameterValue(ContextParameter.CLEANING_SERVICE_URL);
 				
-					Map<String, String> formParams = new HashMap<String, String>();
+					Map<String, String> formParams = new HashMap<>();
 					formParams.put(JsonKeys.json.name(), requestJsonArray.toString());
 					String reqResponse = HTTPUtil.executeHTTPPostRequest(cleaningServiceURL, null,
 							null, formParams);
@@ -226,4 +226,12 @@ public boolean equals(Object o) {
 		}
 		return false;
 	}
+
+	@Override
+	public int hashCode() {
+		int result = this.worksheetId != null ? this.worksheetId.hashCode() : 0;
+		result = 31 * result + (this.forceUpdates ? 1 : 0);
+		result = 31 * result + (this.selection != null ? this.selection.hashCode() : 0);
+		return result;
+	}
 }
diff --git a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetDeleteUpdate.java b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetDeleteUpdate.java
index 6bc4b6c9a..fd4a74ae0 100644
--- a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetDeleteUpdate.java
+++ b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetDeleteUpdate.java
@@ -52,5 +52,9 @@ public boolean equals(Object o) {
 		}
 		return false;
 	}
-	
+
+	@Override
+	public int hashCode() {
+		return this.worksheetId != null ? this.worksheetId.hashCode() : 0;
+	}
 }
diff --git a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetSuperSelectionListUpdate.java b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetSuperSelectionListUpdate.java
index 3688f38a1..b1855f7f1 100644
--- a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetSuperSelectionListUpdate.java
+++ b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/update/WorksheetSuperSelectionListUpdate.java
@@ -52,4 +52,8 @@ public boolean equals(Object o) {
 		return false;
 	}
 
+	@Override
+	public int hashCode() {
+		return this.worksheetId != null ? this.worksheetId.hashCode() : 0;
+	}
 }
diff --git a/karma-commands/commands-import/import-csv/src/main/java/edu/isi/karma/controller/update/CSVImportPreviewUpdate.java b/karma-commands/commands-import/import-csv/src/main/java/edu/isi/karma/controller/update/CSVImportPreviewUpdate.java
index d40997c89..aefea0688 100644
--- a/karma-commands/commands-import/import-csv/src/main/java/edu/isi/karma/controller/update/CSVImportPreviewUpdate.java
+++ b/karma-commands/commands-import/import-csv/src/main/java/edu/isi/karma/controller/update/CSVImportPreviewUpdate.java
@@ -92,7 +92,7 @@ public CSVImportPreviewUpdate(char delimiterChar, char quoteChar,
 	@Override
 	public void generateJson(String prefix, PrintWriter pw,
 			VWorkspace vWorkspace) {
-		Scanner scanner;
+		Scanner scanner = null;
 		int rowCount = 0;
 		int previewRowCounter = 0;
 
@@ -120,7 +120,7 @@ public void generateJson(String prefix, PrintWriter pw,
 					CSVReader reader = new CSVReader(new StringReader(line),
 							delimiter, quoteCharacter, escapeCharacter);
 					String[] rowValues = reader.readNext();
-					List<String> headers = new ArrayList<String>();
+					List<String> headers = new ArrayList<>();
 					if (rowValues == null || rowValues.length == 0) {
 						logger.error("No data found in the Header row!");
 						rowCount++;
@@ -151,7 +151,7 @@ public void generateJson(String prefix, PrintWriter pw,
 					CSVReader reader = new CSVReader(new StringReader(line),
 							delimiter, quoteCharacter, escapeCharacter);
 					String[] rowValues = reader.readNext();
-					List<String> vals = new ArrayList<String>();
+					List<String> vals = new ArrayList<>();
 					if (rowValues != null) {
 						for (int i = 0; i < rowValues.length; i++) {
 							vals.add(rowValues[i]);
@@ -181,6 +181,9 @@ public void generateJson(String prefix, PrintWriter pw,
 			logger.error("Error occured while reading the file!", e);
 		} catch (JSONException e) {
 			logger.error("Error occured while writing to JSON", e);
+		} finally {
+			if(scanner != null)
+				scanner.close();
 		}
 	}
 	
diff --git a/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/database/DatabaseTableImport.java b/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/database/DatabaseTableImport.java
index e4f7a558f..12c02d713 100644
--- a/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/database/DatabaseTableImport.java
+++ b/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/database/DatabaseTableImport.java
@@ -96,13 +96,13 @@ public Worksheet generateWorksheetForAllRows() throws SQLException, ClassNotFoun
         return generateWorksheet(dbUtil, data);
     }
 
-    private Worksheet generateWorksheet(AbstractJDBCUtil dbUtil, ArrayList<ArrayList<String>> data)
+    private Worksheet generateWorksheet(AbstractJDBCUtil dbUtil, List<ArrayList<String>> data)
     {
 	    /**
 	     * Add the headers *
 	     */
 	    HTable headers = getWorksheet().getHeaders();
-	    List<String> headersList = new ArrayList<String>();
+	    List<String> headersList = new ArrayList<>();
 	    for (int i = 0; i < data.get(0).size(); i++)
 	    {
 		    HNode hNode = null;
@@ -117,7 +117,7 @@ private Worksheet generateWorksheet(AbstractJDBCUtil dbUtil, ArrayList<ArrayList
 	    for (int i = 1; i < data.size(); i++)
 	    {
 		    Row row = dataTable.addRow(getFactory());
-		    ArrayList<String> rowData = data.get(i);
+		    List<String> rowData = data.get(i);
 		    for (int j = 0; j < rowData.size(); j++)
 		    {
 			    row.setValue(headersList.get(j), rowData.get(j), getFactory());
diff --git a/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/database/SQLImport.java b/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/database/SQLImport.java
index fdd39992c..6be2b0e71 100644
--- a/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/database/SQLImport.java
+++ b/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/database/SQLImport.java
@@ -87,10 +87,10 @@ private Worksheet generateWorksheet(AbstractJDBCUtil dbUtil, ArrayList<ArrayList
 	     * Add the headers *
 	     */
 	    HTable headers = getWorksheet().getHeaders();
-	    List<String> headersList = new ArrayList<String>();
+	    List<String> headersList = new ArrayList<>();
 	    for (int i = 0; i < data.get(0).size(); i++)
 	    {
-		    HNode hNode = null;
+		    HNode hNode;
 		    hNode = headers.addHNode(data.get(0).get(i), HNodeType.Regular, getWorksheet(), getFactory());
 		    headersList.add(hNode.getId());
 	    }
diff --git a/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/mdb/MDBFileExport.java b/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/mdb/MDBFileExport.java
index f10a07565..8378a5e82 100644
--- a/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/mdb/MDBFileExport.java
+++ b/karma-commands/commands-import/import-database/src/main/java/edu/isi/karma/imp/mdb/MDBFileExport.java
@@ -62,7 +62,7 @@ public String publishMDB(String csvFileName) throws FileNotFoundException {
 		logger.info("MDB file exported. Location:"
 				+ outputFile);
 
-		HashMap<String, String> modeledColumnTable = new HashMap<String, String>();
+		HashMap<String, String> modeledColumnTable = new HashMap<>();
 		for (SemanticType type : worksheet.getSemanticTypes().getListOfTypes()) {
 			modeledColumnTable.put(type.getHNodeId(),"");
 		}
@@ -76,8 +76,8 @@ public String publishMDB(String csvFileName) throws FileNotFoundException {
 			
 			TableBuilder tb = new TableBuilder(worksheet.getTitle().replaceAll("\\.", "_"));
 			
-			List<HNode> sortedLeafHNodes = new ArrayList<HNode>();
-			List<String> hNodeIdList = new ArrayList<String>();
+			List<HNode> sortedLeafHNodes = new ArrayList<>();
+			List<String> hNodeIdList = new ArrayList<>();
 			worksheet.getHeaders().getSortedLeafHNodes(sortedLeafHNodes);
 			for (HNode hNode : sortedLeafHNodes) {
 				if (modeledColumnTable.containsKey(hNode.getId())) {
diff --git a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/FeatureTable.java b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/FeatureTable.java
index e232d9f81..fbaa96add 100644
--- a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/FeatureTable.java
+++ b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/FeatureTable.java
@@ -26,7 +26,7 @@
 
 public class FeatureTable {
 	
-	private Map<String, String> popupData = new HashMap<String, String>();
+	private Map<String, String> popupData = new HashMap<>();
 
 	public FeatureTable() {
 		super();
diff --git a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/LineString.java b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/LineString.java
index 904cd6a73..e39ab1cfc 100644
--- a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/LineString.java
+++ b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/LineString.java
@@ -28,7 +28,7 @@
 
 public class LineString {
 	private final List<Coordinate> coordinatesList;
-	private Map<String, String> popupData = new HashMap<String, String>();
+	private Map<String, String> popupData = new HashMap<>();
 
 	public LineString(List<Coordinate> posList) {
 		super();
diff --git a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/Point.java b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/Point.java
index 07dc2fd68..92041a0fa 100644
--- a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/Point.java
+++ b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/Point.java
@@ -27,7 +27,7 @@ public class Point {
 	private final double latitude;
 	private final double longitude;
 
-	private Map<String, String> popupData = new HashMap<String, String>();
+	private Map<String, String> popupData = new HashMap<>();
 
 	public Point(double longitude, double latitude) {
 		this.longitude = longitude;
diff --git a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/SpatialReferenceSystemTransformationUtil.java b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/SpatialReferenceSystemTransformationUtil.java
index 48ef4f287..f7d704ab3 100644
--- a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/SpatialReferenceSystemTransformationUtil.java
+++ b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/SpatialReferenceSystemTransformationUtil.java
@@ -55,7 +55,7 @@ public static Geometry Transform(Geometry inGeom,
 		if(sourceCRS.equals(targetCRS))
 			return inGeom;
 		
-		MathTransform transform = null;
+		MathTransform transform;
 		
 		try {
 			transform = CRS.findMathTransform(sourceCRS, targetCRS, true);
@@ -102,8 +102,8 @@ public static String Transform(String inGeomWKT, String fromSRID,
 		if (!toSRID.contains(":"))
 			toSRID = "EPSG:" + toSRID;
 
-		CoordinateReferenceSystem sourceCRS = null;
-		CoordinateReferenceSystem targetCRS = null;
+		CoordinateReferenceSystem sourceCRS;
+		CoordinateReferenceSystem targetCRS;
 		try {
 			sourceCRS = CRS.decode(fromSRID, true);
 			targetCRS = CRS.decode(toSRID, true);
@@ -115,7 +115,7 @@ public static String Transform(String inGeomWKT, String fromSRID,
 			return inGeomWKT;
 		}
 
-		MathTransform transform = null;
+		MathTransform transform;
 		try {
 			transform = CRS.findMathTransform(sourceCRS, targetCRS, true);
 		} catch (FactoryException e) {
@@ -123,7 +123,7 @@ public static String Transform(String inGeomWKT, String fromSRID,
 			return inGeomWKT;
 		}
 
-		Geometry outGeom = null;
+		Geometry outGeom;
 		try {
 			outGeom = JTS.transform(JTSGeometry, transform);
 		} catch (MismatchedDimensionException e) {
diff --git a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/WorksheetGeospatialContent.java b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/WorksheetGeospatialContent.java
index d255cb15b..94df8aed7 100644
--- a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/WorksheetGeospatialContent.java
+++ b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/WorksheetGeospatialContent.java
@@ -58,10 +58,10 @@
 public class WorksheetGeospatialContent {
 	private Worksheet worksheet;
 	private SuperSelection selection;
-	private List<edu.isi.karma.geospatial.Point> points = new ArrayList<edu.isi.karma.geospatial.Point>();
-	private List<edu.isi.karma.geospatial.LineString> lines = new ArrayList<edu.isi.karma.geospatial.LineString>();
-	private List<Polygon> polygons = new ArrayList<Polygon>();
-	private List<FeatureTable> polygonTable = new ArrayList<FeatureTable>();
+	private List<edu.isi.karma.geospatial.Point> points = new ArrayList<>();
+	private List<edu.isi.karma.geospatial.LineString> lines = new ArrayList<>();
+	private List<Polygon> polygons = new ArrayList<>();
+	private List<FeatureTable> polygonTable = new ArrayList<>();
 	
 	private static String SRID_PROPERTY = ContextParametersRegistry.getInstance().getDefault()
 			.getParameterValue(ContextParameter.SRID_PROPERTY);
@@ -101,7 +101,7 @@ public WorksheetGeospatialContent(Worksheet worksheet, SuperSelection sel) {
 
 	private void populateGeospatialData() {
 		
-		List<String> coordinateHNodeIds = new ArrayList<String>();
+		List<String> coordinateHNodeIds = new ArrayList<>();
 		CoordinateCase currentCase = CoordinateCase.NOT_PRESENT;
 		boolean latFound = false;
 		boolean lngFound = false;
@@ -210,7 +210,7 @@ private void populateLines(List<String> coordinateHNodeIds,
 		        LineString JTSLine = (LineString)reader.read(posList);
 		        if(JTSLine == null) continue;
 		        int lineLength = JTSLine.getNumPoints();
-				List<Coordinate> coordsList = new ArrayList<Coordinate>();
+				List<Coordinate> coordsList = new ArrayList<>();
 				for (int i=0;i<lineLength;i++) {
 					
 					Coordinate coord = new Coordinate(JTSLine.getPointN(i).getX(),JTSLine.getPointN(i).getY());
@@ -320,9 +320,9 @@ private ArrayList<Row> getRows() {
 
 	private Map<String, String> getColumnMap() {
 		// Prepare a map of the column names that we use for descriptions
-		List<HNode> sortedLeafHNodes = new ArrayList<HNode>();
+		List<HNode> sortedLeafHNodes = new ArrayList<>();
 		worksheet.getHeaders().getSortedLeafHNodes(sortedLeafHNodes);
-		Map<String, String> columnNameMap = new HashMap<String, String>();
+		Map<String, String> columnNameMap = new HashMap<>();
 		for (HNode hNode : sortedLeafHNodes) {
 			columnNameMap.put(hNode.getId(), hNode.getColumnName());
 		}
@@ -381,7 +381,7 @@ public File publishKML() throws FileNotFoundException {
 			final LinearRing outerlinearring = new LinearRing();
 			outerboundary.setLinearRing(outerlinearring);
 
-			List<Coordinate> outercoord = new ArrayList<Coordinate>();
+			List<Coordinate> outercoord = new ArrayList<>();
 			outerlinearring.setCoordinates(outercoord);
 			for (int i=0;i<polygon.getExteriorRing().getNumPoints();i++) {
 				outercoord.add(new Coordinate(polygon.getExteriorRing().getPointN(i).getX(),polygon.getExteriorRing().getPointN(i).getY()));
@@ -396,7 +396,7 @@ public File publishKML() throws FileNotFoundException {
 				final LinearRing innerlinearring = new LinearRing();
 				innerboundary.setLinearRing(innerlinearring);
 	
-				List<Coordinate> innercoord = new ArrayList<Coordinate>();
+				List<Coordinate> innercoord = new ArrayList<>();
 				innerlinearring.setCoordinates(innercoord);
 				int numOfPoints = polygon.getInteriorRingN(i).getNumPoints();
 				for(int j=0;j<numOfPoints;j++)
diff --git a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/WorksheetToFeatureCollection.java b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/WorksheetToFeatureCollection.java
index 09599a1bb..32008f523 100644
--- a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/WorksheetToFeatureCollection.java
+++ b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/geospatial/WorksheetToFeatureCollection.java
@@ -100,14 +100,14 @@ public class WorksheetToFeatureCollection {
 	private Worksheet worksheet;
 	private OntologyManager om;
 
-	List<SimpleFeature> pointFeatureList = new ArrayList<SimpleFeature>();
-	List<SimpleFeature> lineFeatureList = new ArrayList<SimpleFeature>();
-	List<SimpleFeature> polygonFeatureList = new ArrayList<SimpleFeature>();
-	List<AttributeDescriptor> featureSchema = new ArrayList<AttributeDescriptor>();
-	List<String> geomHNodeIdList = new ArrayList<String>();
-	List<String> modeledHNodeIds = new ArrayList<String>();
-
-	private HashMap<String, String> kmlStyles = new HashMap<String, String>();
+	List<SimpleFeature> pointFeatureList = new ArrayList<>();
+	List<SimpleFeature> lineFeatureList = new ArrayList<>();
+	List<SimpleFeature> polygonFeatureList = new ArrayList<>();
+	List<AttributeDescriptor> featureSchema = new ArrayList<>();
+	List<String> geomHNodeIdList = new ArrayList<>();
+	List<String> modeledHNodeIds = new ArrayList<>();
+
+	private HashMap<String, String> kmlStyles = new HashMap<>();
 	private int kmlStylesCounter = 0;
 	private String[] kmlPushPings = {
 			"http://maps.google.com/mapfiles/kml/pushpin/blue-pushpin.png",
@@ -182,14 +182,14 @@ public WorksheetToFeatureCollection(Workspace workspace, Worksheet worksheet, On
 
 	private boolean isSubClassOf(String subClassUri, String superClassUri,
 			boolean recursive) {
-		boolean isSub = false;
+		boolean isSub;
 		isSub = this.om.isSubClass(subClassUri, superClassUri, recursive);
 		return isSub;
 	}
 
 	private boolean isSubPropertyOf(String subPropertyUri,
 			String superPropertyUri, boolean recursive) {
-		boolean isSub = false;
+		boolean isSub;
 		isSub = this.om.isSubProperty(subPropertyUri, superPropertyUri,
 				recursive);
 		return isSub;
@@ -223,7 +223,7 @@ pointFeatureLatHNodeId, getRows(), pointFeatureList,
 					"", getRows(), polygonFeatureList, Polygon.class);
 	}
 	private void prepareFeatureSchema() {
-		List<String> spatialHNodeIds = new ArrayList<String>();
+		List<String> spatialHNodeIds = new ArrayList<>();
 
 		for (SemanticType type : worksheet.getSemanticTypes().getListOfTypes()) {
 			/*
@@ -285,8 +285,9 @@ private void prepareFeatureSchema() {
 			modeledHNodeIds.add(0, type.getHNodeId());
 		}
 
+
 		if (!spatialHNodeIds.isEmpty()) {
-			List<HNode> sortedLeafHNodes = new ArrayList<HNode>();
+			List<HNode> sortedLeafHNodes = new ArrayList<>();
 			worksheet.getHeaders().getSortedLeafHNodes(sortedLeafHNodes);
 			for (HNode hNode : sortedLeafHNodes) {
 
@@ -316,8 +317,8 @@ private void populateSimpleFeatures(
 
 		for (Row row : rows) {
 			try {
-				Geometry JTSGeometry = null;
-				String posList = null;
+				Geometry JTSGeometry;
+				String posList;
 				if (geometry2HNodeId == "") {
 					posList = row.getNode(geometryHNodeId).getValue()
 							.asString();
@@ -347,7 +348,7 @@ else if(!posList.contains("(")) { // assuming the lon, lat case ... we might nee
 				if (JTSGeometry == null) 
 					continue;
 
-				String srid = "";
+				String srid;
 				if (SRIDHNodeId != "")
 					srid = row.getNode(SRIDHNodeId).getValue().asString();
 				else
@@ -486,7 +487,7 @@ public File saveShapefile(List<SimpleFeature> features,
 			throws FileNotFoundException, Exception {
 		File outputFile = new File(spatialDataFolder + fileName + ".shp");
 		
-		List<SimpleFeature> remainingFeatures = new ArrayList<SimpleFeature>();
+		List<SimpleFeature> remainingFeatures = new ArrayList<>();
 		
 		try {
 			/*
@@ -494,7 +495,7 @@ public File saveShapefile(List<SimpleFeature> features,
 			 */
 			ShapefileDataStoreFactory dataStoreFactory = new ShapefileDataStoreFactory();
 
-			Map<String, Serializable> params = new HashMap<String, Serializable>();
+			Map<String, Serializable> params = new HashMap<>();
 			params.put("url", outputFile.toURI().toURL());
 			params.put("create spatial index", Boolean.TRUE);
 
@@ -523,7 +524,7 @@ public File saveShapefile(List<SimpleFeature> features,
 				if(crs2==null)
 					continue;
 				
-				if(!crs.equals(crs2)) {
+				if(crs != null && !crs.equals(crs2)) {
 					remainingFeatures.add(feature);
 					features.remove(i);
 					i--;
@@ -690,7 +691,7 @@ public File publishKML(String spatialDataFolder, String fileName)
 					.Transform((Geometry) lineFeature.getAttribute(GEOM),
 							sourceCRS, targetCRS);
 
-			List<Coordinate> coordsList = new ArrayList<Coordinate>();
+			List<Coordinate> coordsList = new ArrayList<>();
 			double pointX = 0, pointY = 0;
 			for (int i = 0; i < line.getNumPoints(); i++) {
 				Coordinate coord = new Coordinate(
@@ -751,7 +752,7 @@ public File publishKML(String spatialDataFolder, String fileName)
 			final LinearRing outerlinearring = new LinearRing();
 			outerboundary.setLinearRing(outerlinearring);
 
-			List<Coordinate> outercoord = new ArrayList<Coordinate>();
+			List<Coordinate> outercoord = new ArrayList<>();
 			outerlinearring.setCoordinates(outercoord);
 			double pointX = 0, pointY = 0;
 			int pointCounter = 0;
@@ -771,7 +772,7 @@ public File publishKML(String spatialDataFolder, String fileName)
 				final LinearRing innerlinearring = new LinearRing();
 				innerboundary.setLinearRing(innerlinearring);
 
-				List<Coordinate> innercoord = new ArrayList<Coordinate>();
+				List<Coordinate> innercoord = new ArrayList<>();
 				innerlinearring.setCoordinates(innercoord);
 				int numOfPoints = polygon.getInteriorRingN(i).getNumPoints();
 				for (int j = 0; j < numOfPoints; j++) {
@@ -803,7 +804,7 @@ public File publishKML(String spatialDataFolder, String fileName)
 		final StringWriter out = new StringWriter();
 		kml.marshal(out);
 		String test = out.toString();
-		Writer outUTF8 = null;
+		Writer outUTF8;
 		try {
 			outUTF8 = new BufferedWriter(new OutputStreamWriter(
 					new FileOutputStream(outputFile), "UTF8"));
diff --git a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/webserver/SpatialReferenceSystemServiceHandler.java b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/webserver/SpatialReferenceSystemServiceHandler.java
index 5302c128b..199b7aaed 100644
--- a/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/webserver/SpatialReferenceSystemServiceHandler.java
+++ b/karma-commands/commands-import/import-spatial/src/main/java/edu/isi/karma/webserver/SpatialReferenceSystemServiceHandler.java
@@ -30,7 +30,7 @@ public void doGet(HttpServletRequest request,
 		logger.debug("Request Path Info: " + request.getPathInfo());
 		logger.debug("Request Param: " + request.getQueryString());
 		
-		String jsonOutput=null;
+		String jsonOutput;
 
 		String inGeomWKT = request.getParameter("geometry");
 		String fromSRID = request.getParameter("srid");
diff --git a/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/alignment/GenerateR2RMLModelCommand.java b/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/alignment/GenerateR2RMLModelCommand.java
index 4cbc60806..f25b4705c 100644
--- a/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/alignment/GenerateR2RMLModelCommand.java
+++ b/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/alignment/GenerateR2RMLModelCommand.java
@@ -196,7 +196,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			return new UpdateContainer(new ErrorUpdate(
 					"Please align the worksheet before generating R2RML Model!"));
 		}
-		Set<LabeledLink> links = new HashSet<LabeledLink>();
+		Set<LabeledLink> links = new HashSet<>();
 		if (alignment.getSteinerTree() != null) {
 			for (LabeledLink link : alignment.getSteinerTree().edgeSet()) {
 				if ((link.getStatus() == LinkStatus.Normal || link.getStatus() == LinkStatus.PreferredByUI) && (link.getType() == LinkType.ObjectPropertyLink)) {
diff --git a/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/publish/PublishRDFCommand.java b/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/publish/PublishRDFCommand.java
index fdf4d4e42..de6cecd28 100644
--- a/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/publish/PublishRDFCommand.java
+++ b/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/publish/PublishRDFCommand.java
@@ -173,13 +173,13 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 
 		// Generate the KR2RML data structures for the RDF generation
 		final ErrorReport errorReport = new ErrorReport();
-		KR2RMLMappingGenerator mappingGen = null;
+		KR2RMLMappingGenerator mappingGen;
 		String url = worksheet.getMetadataContainer().getWorksheetProperties().getPropertyValue(Property.modelUrl);
 		String modelContext = worksheet.getMetadataContainer().getWorksheetProperties().getPropertyValue(Property.modelContext);
 		TripleStoreUtil utilObj = new TripleStoreUtil();
 		String modelRepoUrl = worksheet.getMetadataContainer().getWorksheetProperties().getPropertyValue(Property.modelRepository);
 		modelRepoUrl = modelRepoUrl == null || modelRepoUrl.isEmpty()? TripleStoreUtil.defaultModelsRepoUrl : modelRepoUrl;
-		Map<String, String> bloomfilterMapping = new HashMap<String, String>();
+		Map<String, String> bloomfilterMapping = new HashMap<>();
 		boolean result = true;
 		try{
 			mappingGen = new KR2RMLMappingGenerator(workspace, worksheet,
@@ -214,9 +214,9 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 
 		StringWriter sw = new StringWriter();
 		// Generate the RDF using KR2RML data structures
-		long start = 0;
+		long start;
 		try {
-			List<KR2RMLRDFWriter> writers = new ArrayList<KR2RMLRDFWriter>();
+			List<KR2RMLRDFWriter> writers = new ArrayList<>();
 			File f = new File(rdfFileLocalPath);
 			File parentDir = f.getParentFile();
 			parentDir.mkdirs();
diff --git a/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/worksheet/ExportCSVCommandFactory.java b/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/worksheet/ExportCSVCommandFactory.java
index 394143cce..4e4ca97d8 100644
--- a/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/worksheet/ExportCSVCommandFactory.java
+++ b/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/worksheet/ExportCSVCommandFactory.java
@@ -49,13 +49,13 @@ public Command createCommand(HttpServletRequest request,
 		String graphUrl = request.getParameter(Arguments.graphUrl.name());
 		String nodeId = request.getParameter(Arguments.rootNodeId.name());
 		String colList = request.getParameter(Arguments.columnList.name());
-		ArrayList<HashMap<String, String>> cols = new ArrayList<HashMap<String, String>>();
+		ArrayList<HashMap<String, String>> cols = new ArrayList<>();
 		try {
 			
 			JSONObject arr = new JSONObject(colList);
 			for(int i=0; i<arr.keySet().size(); i++) {
 				JSONObject obj = arr.getJSONObject(String.valueOf(i));
-				HashMap<String, String> map = new HashMap<String, String>();
+				HashMap<String, String> map = new HashMap<>();
 				map.put("url", obj.getString("url"));
 				map.put("name", obj.getString("name"));
 				cols.add(map);
diff --git a/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/worksheet/FetchColumnCommand.java b/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/worksheet/FetchColumnCommand.java
index 9bed89a48..234e825ad 100644
--- a/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/worksheet/FetchColumnCommand.java
+++ b/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/controller/command/worksheet/FetchColumnCommand.java
@@ -181,7 +181,7 @@ public UpdateContainer doIt(Workspace workspace) {
 			if (sData == null | sData.isEmpty()) {
 				logger.error("Empty response object from query : " + query);
 			}
-			HashMap<String,String> cols = new HashMap<String,String>();
+			HashMap<String,String> cols = new HashMap<>();
 			try {
 				JSONObject obj1 = new JSONObject(sData);
 				JSONArray arr = obj1.getJSONObject("results").getJSONArray("bindings");
diff --git a/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/er/helper/ExportCSVUtil.java b/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/er/helper/ExportCSVUtil.java
index 73cec14d4..aacff4465 100644
--- a/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/er/helper/ExportCSVUtil.java
+++ b/karma-commands/commands-publish-alignment-openrdf/src/main/java/edu/isi/karma/er/helper/ExportCSVUtil.java
@@ -71,7 +71,7 @@ private ExportCSVUtil() {
 	public static HashMap<String, String> generateCSVQuery(Workspace workspace, final String worksheetId, final String rootNodeId,
 			final ArrayList<HashMap<String, String>> columnList, final String graphUrl) {
 	
-		HashMap<String, String> retVal = new HashMap<String, String>();
+		HashMap<String, String> retVal = new HashMap<>();
 		Worksheet worksheet = workspace.getWorksheet(worksheetId);
 		// Get the alignment for this Worksheet
 		Alignment alignment = AlignmentManager.Instance().getAlignment(AlignmentManager.
@@ -151,7 +151,7 @@ public static HashMap<String, String> generateCSVQuery(Workspace workspace, fina
 	
 	public static HashMap<String, String> generateCSVFile(Workspace workspace, final String worksheetId, final String rootNodeId,
 			final ArrayList<HashMap<String, String>> columnList, final String graphUrl, final String tripleStoreUrl, final String csvFilePath) {
-		HashMap<String, String> retVal = new HashMap<String, String>();
+		HashMap<String, String> retVal = new HashMap<>();
 		HashMap<String, String> query = generateCSVQuery(workspace, worksheetId, rootNodeId, columnList, graphUrl);
 		try {
 			if(query.containsKey("Error")) {
diff --git a/karma-commands/commands-publish/src/main/java/edu/isi/karma/model/serialization/DataSourceLoader.java b/karma-commands/commands-publish/src/main/java/edu/isi/karma/model/serialization/DataSourceLoader.java
index cdb02cd4f..9e18ffdf0 100644
--- a/karma-commands/commands-publish/src/main/java/edu/isi/karma/model/serialization/DataSourceLoader.java
+++ b/karma-commands/commands-publish/src/main/java/edu/isi/karma/model/serialization/DataSourceLoader.java
@@ -124,7 +124,7 @@ public void deleteSourceByUri(String uri) {
     @Override
 	public List<Source> getSourcesAbstractInfo(Integer sourceLimit) {
 		
-		List<Source> sourceList = new ArrayList<Source>();
+		List<Source> sourceList = new ArrayList<>();
 		
 		Model model = Repository.Instance().getModel();
 		
@@ -204,7 +204,7 @@ public List<Source> getSourcesAbstractInfo(Integer sourceLimit) {
 	public List<Source> getSourcesDetailedInfo(Integer sourceLimit) {
 
 		List<Source> sourceList = getSourcesAbstractInfo(sourceLimit);
-		List<Source> sourceListCompleteInfo = new ArrayList<Source>();
+		List<Source> sourceListCompleteInfo = new ArrayList<>();
 		for (Source s : sourceList) {
 			sourceListCompleteInfo.add(getSourceByUri(s.getUri()));
 		}
@@ -228,8 +228,8 @@ public Map<DataSource, Map<String, String>> getDataSourcesByIOPattern(edu.isi.ka
 			return null;
 		}
 		
-		Map<DataSource, Map<String, String>> sourcesAndMappings = 
-			new HashMap<DataSource, Map<String,String>>();
+		Map<DataSource, Map<String, String>> sourcesAndMappings =
+				new HashMap<>();
 		
 		Map<String, Map<String, String>> sourceIdsAndMappings =
 			semanticModel.findInJenaModel(Repository.Instance().getModel(), sourceLimit);
@@ -260,8 +260,8 @@ public Map<DataSource, Map<String, String>> getDataSourcesContainedInModel(edu.i
 		
 		List<Source> sourceList = getSourcesDetailedInfo(sourceLimit);
 		
-		Map<DataSource, Map<String, String>> sourcesAndMappings = 
-			new HashMap<DataSource, Map<String,String>>();
+		Map<DataSource, Map<String, String>> sourcesAndMappings =
+				new HashMap<>();
 
 		Model jenaModel = semanticModel.getJenaModel();
 		for (Source source : sourceList) {
@@ -346,7 +346,7 @@ private List<String> getVariables(Model model, Resource source_resource) {
 		
 		Property has_variable_property = model.getProperty(Namespaces.KARMA + "hasVariable");
 	
-		List<String> variables = new ArrayList<String>();
+		List<String> variables = new ArrayList<>();
 		NodeIterator nodeIterator = null;
 		RDFNode node = null;
 
@@ -371,7 +371,7 @@ private List<Attribute> getAttributes(Model model, Resource source_resource) {
 		
 		Property has_attribute_property = model.getProperty(Namespaces.KARMA + "hasAttribute");
 	
-		List<Attribute> attList = new ArrayList<Attribute>();
+		List<Attribute> attList = new ArrayList<>();
 		
 		NodeIterator nodeIterator = null;
 		RDFNode node = null;
@@ -439,7 +439,7 @@ private edu.isi.karma.rep.model.Model getSemanticModel(Model model, Resource sou
 
 		edu.isi.karma.rep.model.Model semanticModel = 
 			new edu.isi.karma.rep.model.Model(modelNode.asResource().getLocalName());
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 		
 
 		// hasAtom
diff --git a/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/MutatingPythonTransformationCommand.java b/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/MutatingPythonTransformationCommand.java
index 35b6ee576..dbc6739a3 100644
--- a/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/MutatingPythonTransformationCommand.java
+++ b/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/MutatingPythonTransformationCommand.java
@@ -62,7 +62,7 @@ public abstract class MutatingPythonTransformationCommand extends
 	private static Logger logger = LoggerFactory.getLogger(MutatingPythonTransformationCommand.class);
 	
 	protected final String newColumnName;
-	protected List<Node> affectedNodes = new LinkedList<Node>();
+	protected List<Node> affectedNodes = new LinkedList<>();
 	protected boolean isJSONOutput = false;
 	public MutatingPythonTransformationCommand(String id, String model, String newColumnName,
 			String transformationCode, String worksheetId, String hNodeId,
@@ -128,9 +128,9 @@ private JSONArray getMultiCellValueEditInputJSON(JSONArray rowsArray, String new
 	}
 	
 	protected Map<String, String> gatherTransformedResults(Workspace workspace, String hNodeId) {
-		Map<String, String> rowToValueMapping = new HashMap<String, String>();
+		Map<String, String> rowToValueMapping = new HashMap<>();
 		HNodePath hNodePath = workspace.getFactory().getHNode(hNodeId).getHNodePath(workspace.getFactory());
-		List<Node> nodes = new ArrayList<Node>();
+		List<Node> nodes = new ArrayList<>();
 		workspace.getWorksheet(worksheetId).getDataTable().collectNodes(hNodePath, nodes, getSuperSelection(workspace));
 		for (Node node : nodes) {
 			rowToValueMapping.put(node.getBelongsToRow().getId(), node.getValue().asString());
diff --git a/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/PythonTransformationCommand.java b/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/PythonTransformationCommand.java
index 8baf2ed78..c4038925b 100755
--- a/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/PythonTransformationCommand.java
+++ b/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/PythonTransformationCommand.java
@@ -128,11 +128,11 @@ protected void generateTransformedValues(Workspace workspace,
 		PythonInterpreter interpreter = repo.getInterpreter();
 
 		repo.initializeInterpreter(interpreter);
-		Collection<Node> nodes = new ArrayList<Node>(Math.max(1000, worksheet
+		Collection<Node> nodes = new ArrayList<>(Math.max(1000, worksheet
 				.getDataTable().getNumRows()));
 		worksheet.getDataTable().collectNodes(hNode.getHNodePath(f), nodes, selection);
 
-		Map<String, String> rowToValueMap = new HashMap<String, String>();
+		Map<String, String> rowToValueMap = new HashMap<>();
 
 		int counter = 0;
 		long starttime = System.currentTimeMillis();
diff --git a/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/SubmitPythonTransformationCommand.java b/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/SubmitPythonTransformationCommand.java
index e6393cff3..4c71f5b91 100644
--- a/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/SubmitPythonTransformationCommand.java
+++ b/karma-commands/commands-python/src/main/java/edu/isi/karma/controller/command/transformation/SubmitPythonTransformationCommand.java
@@ -191,7 +191,7 @@ protected  void saveOrResetColumnValues(Workspace workspace, ExecutionController
 	private void removeNestedTable(Workspace workspace) {
 		HNode hNode = workspace.getFactory().getHNode(pythonNodeId);
 		hNode.removeNestedTable();
-		List<Node> nodes = new ArrayList<Node>();
+		List<Node> nodes = new ArrayList<>();
 		workspace.getWorksheet(worksheetId).getDataTable().collectNodes(hNode.getHNodePath(workspace.getFactory()), nodes, getSuperSelection(workspace.getWorksheet(worksheetId)));
 		for (Node node : nodes) {
 			node.setNestedTable(null, workspace.getFactory());
@@ -248,8 +248,8 @@ protected void saveColumnValues(Workspace workspace) {
 		RepFactory f = workspace.getFactory();
 		HNode hNode = f.getHNode(pythonNodeId);
 
-		this.originalColumnValues = new ArrayList<String>();
-		Collection<Node> nodes = new ArrayList<Node>();
+		this.originalColumnValues = new ArrayList<>();
+		Collection<Node> nodes = new ArrayList<>();
 		worksheet.getDataTable().collectNodes(hNode.getHNodePath(f), nodes, selection);
 		for(Node node : nodes) {
 			originalColumnValues.add(node.serializeToJSON(selection, f).toString());
diff --git a/karma-commands/commands-python/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingGenerator.java b/karma-commands/commands-python/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingGenerator.java
index 93ac4fcd3..6a6506447 100644
--- a/karma-commands/commands-python/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingGenerator.java
+++ b/karma-commands/commands-python/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingGenerator.java
@@ -201,7 +201,7 @@ private void calculateColumnNodesCoveredByBlankNodes() throws KarmaException {
 				SubjectMap subjMap = r2rmlMapping.getSubjectMapIndex().get(treeNode.getId());
 				
 				if (subjMap.isBlankNode()) {
-					List<String> columnsCovered = new ArrayList<String>();
+					List<String> columnsCovered = new ArrayList<>();
 					Set<LabeledLink> links = dm.getOutgoingEdgesOf(treeNode);
 					Iterator<LabeledLink> linkIterator = links.iterator();
 					while(linkIterator.hasNext())
@@ -283,7 +283,7 @@ else if (link instanceof ColumnSubClassLink) {
 								subj.addRdfsType(typeTermSet2);
 							}
 							
-							List<String> columnsCovered = new LinkedList<String>();
+							List<String> columnsCovered = new LinkedList<>();
 							for(TemplateTerm term : subj.getTemplate().getAllColumnNameTermElements())
 							{
 								columnsCovered.add(term.getTemplateTermValue());
@@ -471,7 +471,7 @@ private void saveLinkFromColumnNameToPredicateObjectMap(String columnName, Predi
 		
 		List<PredicateObjectMap> pomList = r2rmlMapping.getAuxInfo().getColumnNameToPredObjLinks().get(columnName);  
 		if (pomList == null) {
-			pomList = new ArrayList<PredicateObjectMap>();
+			pomList = new ArrayList<>();
 		}
 		pomList.add(poMap);
 		r2rmlMapping.getAuxInfo().getColumnNameToPredObjLinks().put(columnName, pomList);
diff --git a/karma-commands/commands-python/src/main/java/edu/isi/karma/transformation/tokenizer/PythonTransformationAsURITokenizer.java b/karma-commands/commands-python/src/main/java/edu/isi/karma/transformation/tokenizer/PythonTransformationAsURITokenizer.java
index dbac2d743..e59c07db0 100644
--- a/karma-commands/commands-python/src/main/java/edu/isi/karma/transformation/tokenizer/PythonTransformationAsURITokenizer.java
+++ b/karma-commands/commands-python/src/main/java/edu/isi/karma/transformation/tokenizer/PythonTransformationAsURITokenizer.java
@@ -18,8 +18,8 @@ public class PythonTransformationAsURITokenizer {
 	private static List<String> acceptedTokens;
 	private static final Map<String, Pattern> patterns;
 	static {
-		patterns = new HashMap<String, Pattern>();
-		acceptedTokens = new LinkedList<String>();
+		patterns = new HashMap<>();
+		acceptedTokens = new LinkedList<>();
 		acceptedTokens.add(getValue);
 		acceptedTokens.add(literal);;
 		for(String acceptedToken : acceptedTokens)
@@ -40,7 +40,7 @@ public static List<PythonTransformationToken> tokenize(PythonTransformationComma
 	}
 	public static List<PythonTransformationToken> tokenize(String transformationCode)
 	{	
-		 List<PythonTransformationToken> tokens = new  LinkedList<PythonTransformationToken>();
+		 List<PythonTransformationToken> tokens = new LinkedList<>();
 		if(transformationCode == null || transformationCode.isEmpty())
 		{	
 			return tokens;
diff --git a/karma-commands/commands-update-jdbc/src/main/java/edu/isi/karma/controller/update/DatabaseTablePreviewUpdate.java b/karma-commands/commands-update-jdbc/src/main/java/edu/isi/karma/controller/update/DatabaseTablePreviewUpdate.java
index 3d59f05ce..9dd4389ad 100644
--- a/karma-commands/commands-update-jdbc/src/main/java/edu/isi/karma/controller/update/DatabaseTablePreviewUpdate.java
+++ b/karma-commands/commands-update-jdbc/src/main/java/edu/isi/karma/controller/update/DatabaseTablePreviewUpdate.java
@@ -23,6 +23,7 @@
 import java.io.PrintWriter;
 import java.sql.SQLException;
 import java.util.ArrayList;
+import java.util.List;
 
 import org.json.JSONArray;
 import org.json.JSONException;
@@ -69,7 +70,7 @@ public void generateJson(String prefix, PrintWriter pw,
 		try {
 			AbstractJDBCUtil dbUtil = JDBCUtilFactory.getInstance(dbType);
 			
-			ArrayList<ArrayList<String>> data = dbUtil.getDataForLimitedRows(dbType, hostname, 
+			List<ArrayList<String>> data = dbUtil.getDataForLimitedRows(dbType, hostname, 
 					portnumber, username, password, tableName, dBorSIDName, 10);
 			
 			JSONStringer jsonStr = new JSONStringer();
diff --git a/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/command/service/InvokeServiceCommand.java b/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/command/service/InvokeServiceCommand.java
index 47681c7bb..4cd7cad19 100644
--- a/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/command/service/InvokeServiceCommand.java
+++ b/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/command/service/InvokeServiceCommand.java
@@ -102,14 +102,14 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			initialGraph = (DirectedWeightedMultigraph<Node, DefaultLink>)alignment.getGraph().clone();
 		}
 		
-		List<String> requestURLStrings = new ArrayList<String>();
+		List<String> requestURLStrings = new ArrayList<>();
 		List<Row> rows = wk.getDataTable().getRows(0, wk.getDataTable().getNumRows(), selection);
 		if (rows == null || rows.isEmpty()) {
 			logger.error("Data table does not have any row.");
 			return new UpdateContainer(new ErrorUpdate("Data table does not have any row."));	
 		}
 		
-		List<String> requestIds = new ArrayList<String>();
+		List<String> requestIds = new ArrayList<>();
 		for (int i = 0; i < rows.size(); i++) {
 			requestIds.add(rows.get(i).getId());
 			requestURLStrings.add(rows.get(i).getNode(hNodeId).getValue().asString());
@@ -150,7 +150,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		}
 		
 		// Create new vWorksheet using the new header order
-		List<HNodePath> columnPaths = new ArrayList<HNodePath>();
+		List<HNodePath> columnPaths = new ArrayList<>();
 		for (HNode node : wk.getHeaders().getSortedHNodes()) {
 			HNodePath path = new HNodePath(node);
 			columnPaths.add(path);
diff --git a/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/command/service/PopulateCommand.java b/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/command/service/PopulateCommand.java
index 7f7308617..4e30de784 100644
--- a/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/command/service/PopulateCommand.java
+++ b/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/command/service/PopulateCommand.java
@@ -160,7 +160,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 				"Error occured while populating the source. Cannot find any services to be invoked according to this source model."));
 		}
 		
-		List<String> requestIds = new ArrayList<String>();
+		List<String> requestIds = new ArrayList<>();
 		Map<String, String> serviceToSourceAttMapping =  servicesAndMappings.get(service);
 		List<String> requestURLStrings = getUrlStrings(service, source, wk, serviceToSourceAttMapping, requestIds);
 		if (requestURLStrings == null || requestURLStrings.isEmpty()) {
@@ -189,7 +189,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		}
 		
 		// Create new vWorksheet using the new header order
-		List<HNodePath> columnPaths = new ArrayList<HNodePath>();
+		List<HNodePath> columnPaths = new ArrayList<>();
 		for (HNode node : wk.getHeaders().getSortedHNodes()) {
 			HNodePath path = new HNodePath(node);
 			columnPaths.add(path);
@@ -210,7 +210,7 @@ private List<String> getUrlStrings(WebService service, DataSource source,
 			Worksheet wk, Map<String, String> serviceToSourceAttMapping, 
 			List<String> requestIds) {
 		SuperSelection selection = getSuperSelection(wk);
-		List<String> requestURLStrings = new ArrayList<String>();
+		List<String> requestURLStrings = new ArrayList<>();
 		List<Row> rows = wk.getDataTable().getRows(0, wk.getDataTable().getNumRows(), selection);
 		if (rows == null || rows.isEmpty()) {
 			logger.error("Data table does not have any row.");
@@ -219,7 +219,7 @@ private List<String> getUrlStrings(WebService service, DataSource source,
 		
 		Map<String, String> attIdToValue = null;
 		for (int i = 0; i < rows.size(); i++) {
-			attIdToValue = new HashMap<String, String>();
+			attIdToValue = new HashMap<>();
 			for (Map.Entry<String, String> stringStringEntry : serviceToSourceAttMapping.entrySet()) {
 				String sourceAttId = stringStringEntry.getValue();
 				Attribute sourceAtt = source.getAttribute(sourceAttId);
@@ -259,7 +259,7 @@ public UpdateContainer undoIt(Workspace workspace) {
 		UpdateContainer c = new UpdateContainer();
 		
 		// Create new vWorksheet using the new header order
-		List<HNodePath> columnPaths = new ArrayList<HNodePath>();
+		List<HNodePath> columnPaths = new ArrayList<>();
 		for (HNode node : worksheetBeforeInvocation.getHeaders().getSortedHNodes()) {
 			HNodePath path = new HNodePath(node);
 			columnPaths.add(path);
diff --git a/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/update/AdditionalRowsUpdate.java b/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/update/AdditionalRowsUpdate.java
index 1aeb08e0a..127c94d0e 100644
--- a/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/update/AdditionalRowsUpdate.java
+++ b/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/update/AdditionalRowsUpdate.java
@@ -72,7 +72,7 @@ public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
 			JSONArray rowsJson = new JSONArray();
 			if(!additionalRows.isEmpty()) {
 				Row row = additionalRows.get(0);
-				ArrayList<VHNode> nodeList = getNestedNodeList(row, vWorksheet.getHeaderViewNodes());
+				List<VHNode> nodeList = getNestedNodeList(row, vWorksheet.getHeaderViewNodes());
 				rowsJson = upd.getRowsJsonArray(additionalRows, vWorksheet, 
 							nodeList,
 							vWorkspace.getPreferences().getIntViewPreferenceValue(
diff --git a/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/update/CleaningResultUpdate.java b/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/update/CleaningResultUpdate.java
index a29c2bed5..7100001e1 100644
--- a/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/update/CleaningResultUpdate.java
+++ b/karma-commands/commands-update/src/main/java/edu/isi/karma/controller/update/CleaningResultUpdate.java
@@ -15,10 +15,10 @@
 
 public class CleaningResultUpdate extends AbstractUpdate {
 
-	private HashMap<String,HashMap<String, String>> map = new HashMap<String, HashMap<String,String>>();
+	private HashMap<String,HashMap<String, String>> map = new HashMap<>();
 	private String hNodeId = "";
 	private String varString;
-	private Set<String> topkey = new HashSet<String>();
+	private Set<String> topkey = new HashSet<>();
 	public enum JsonKeys {
 		worksheetId, hNodeId, result
 	}
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/AddColumnCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/AddColumnCommand.java
index cfebbc99a..09f814184 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/AddColumnCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/AddColumnCommand.java
@@ -176,7 +176,7 @@ private void populateRowsWithDefaultValues(Worksheet worksheet, RepFactory facto
 				selectedPath = path;
 			}
 		}
-		Collection<Node> nodes = new ArrayList<Node>(Math.max(1000, worksheet.getDataTable().getNumRows()));
+		Collection<Node> nodes = new ArrayList<>(Math.max(1000, worksheet.getDataTable().getNumRows()));
 		worksheet.getDataTable().collectNodes(selectedPath, nodes, selection);	
 		for (Node node : nodes) {
 			node.setValue(this.defaultValue, NodeStatus.original, factory);
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/AddValuesCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/AddValuesCommand.java
index 08c7a9785..b15ce5c21 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/AddValuesCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/AddValuesCommand.java
@@ -91,7 +91,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		inputColumns.clear();
 		outputColumns.clear();
 		Object para = JSONUtil.createJson(this.getInputParameterJson());
-		String addValues = null;	
+		String addValues;	
 		HNode ndid = null;
 		try{
 			if (para instanceof JSONArray) {
@@ -164,7 +164,7 @@ private HNode addColumn(Workspace workspace, Worksheet worksheet, String newColu
 
 		//add new column to this table
 		//add column after the column with hNodeId
-		HNode ndid = null;
+		HNode ndid;
 		if (newColumnName != null && !newColumnName.trim().isEmpty()) {
 			if (hTable.getHNodeFromColumnName(newColumnName) != null) {
 				ndid = hTable.getHNodeFromColumnName(newColumnName);
@@ -213,7 +213,7 @@ private void populateRowsWithDefaultValues(Worksheet worksheet, RepFactory facto
 					selectedPath = path;
 			}
 		}
-		Collection<Node> nodes = new ArrayList<Node>(Math.max(1000, worksheet.getDataTable().getNumRows()));
+		Collection<Node> nodes = new ArrayList<>(Math.max(1000, worksheet.getDataTable().getNumRows()));
 		worksheet.getDataTable().collectNodes(selectedPath, nodes, selection);	
 		for (Node node : nodes) {
 			for (int i = 0; i < array.length(); i++) {
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/ExtractEntitiesCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/ExtractEntitiesCommand.java
index ae1315e0c..de4d1e7cd 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/ExtractEntitiesCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/ExtractEntitiesCommand.java
@@ -130,7 +130,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		SuperSelection selection = getSuperSelection(worksheet);
 		
 		String[] entities = entitiesToBeExt.split(",");
-		HashSet<String> entitiesReqd = new HashSet<String>();
+		HashSet<String> entitiesReqd = new HashSet<>();
 		
 		entitiesReqd.addAll(Arrays.asList(entities));
 
@@ -140,7 +140,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		RepFactory repFactory = workspace.getFactory();
 		HTable ht = repFactory.getHTable(repFactory.getHNode(hNodeId).getHTableId());
 		
-		List<Table> tables = new ArrayList<Table>();
+		List<Table> tables = new ArrayList<>();
 		
 		CloneTableUtils.getDatatable(worksheet.getDataTable(), ht, tables, selection);
 		for(Table table : tables) {
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/FoldCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/FoldCommand.java
index bad98ce17..1fb111c10 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/FoldCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/FoldCommand.java
@@ -37,7 +37,7 @@ public class FoldCommand extends WorksheetSelectionCommand {
 	//add column to this table
 	private String hTableId;
 	Command cmd;
-	private List<HNode> hnodes = new ArrayList<HNode>();
+	private List<HNode> hnodes = new ArrayList<>();
 	//the id of the new column that was created
 	//needed for undo
 	private String newHNodeId;
@@ -104,9 +104,9 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		ArrayList<Row> rows = worksheet.getDataTable().getRows(0, worksheet.getDataTable().getNumRows(), selection);
 		if (htable != worksheet.getHeaders()) {
 			HTable parentHT = htable.getParentHNode().getHTable(Repfactory);
-			List<Table> parentTables = new ArrayList<Table>();
+			List<Table> parentTables = new ArrayList<>();
 			CloneTableUtils.getDatatable(worksheet.getDataTable(), parentHT,parentTables, selection);
-			ArrayList<Row> parentRows = new ArrayList<Row>();
+			ArrayList<Row> parentRows = new ArrayList<>();
 			rows.clear();
 			for (Table tmp : parentTables) {
 				for (Row row : tmp.getRows(0, tmp.getNumRows(), selection)) {
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GenerateClusterValuesCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GenerateClusterValuesCommand.java
index e217f5727..63d2c1b43 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GenerateClusterValuesCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GenerateClusterValuesCommand.java
@@ -75,7 +75,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 				selectedPath = path;
 			}
 		}
-		Collection<Node> nodes = new ArrayList<Node>();
+		Collection<Node> nodes = new ArrayList<>();
 		workspace.getFactory().getWorksheet(worksheetId).getDataTable()
 				.collectNodes(selectedPath, nodes, selection);
 
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GlueCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GlueCommand.java
index 39e4f9039..06305bb1b 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GlueCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GlueCommand.java
@@ -94,7 +94,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		hNodeName.clear();
 		RepFactory factory = workspace.getFactory();
 		Worksheet oldws = workspace.getWorksheet(worksheetId);
-		List<HNode> hnodes = new ArrayList<HNode>();
+		List<HNode> hnodes = new ArrayList<>();
 		JSONArray checked = new JSONArray(hNodeIdList);
 		HTable ht;
 		if (hNodeId.compareTo("") != 0)
@@ -149,9 +149,9 @@ public UpdateContainer undoIt(Workspace workspace) {
 	private void glueNestedTable(Worksheet worksheet, Workspace workspace, HTable ht, List<HNode> hnodes, RepFactory factory) {
 		SuperSelection selection = getSuperSelection(worksheet);
 		HTable parentHT = ht.getParentHNode().getHTable(factory);
-		List<Table> parentTables = new ArrayList<Table>();
+		List<Table> parentTables = new ArrayList<>();
 		CloneTableUtils.getDatatable(worksheet.getDataTable(), parentHT,parentTables, selection);
-		ArrayList<Row> parentRows = new ArrayList<Row>();
+		ArrayList<Row> parentRows = new ArrayList<>();
 		for (Table tmp : parentTables) {
 			for (Row row : tmp.getRows(0, tmp.getNumRows(), selection)) {
 				parentRows.add(row);
@@ -161,7 +161,7 @@ private void glueNestedTable(Worksheet worksheet, Workspace workspace, HTable ht
 		outputColumns.add(newNode.getId());
 		newhNodeId = newNode.getId();
 		HTable newht = newNode.addNestedTable(newNode.getColumnName(), worksheet, factory);
-		List<HNode> childHNodes = new ArrayList<HNode>();
+		List<HNode> childHNodes = new ArrayList<>();
 		for (HNode hnode : hnodes) {
 			if (hnode.hasNestedTable()) {
 				for (HNode hn : hnode.getNestedTable().getHNodes()) {
@@ -197,7 +197,7 @@ private void glueTopLevel(Worksheet oldws, Workspace workspace, List<HNode> hnod
 		newhNodeId = newNode.getId();
 		outputColumns.add(newhNodeId);
 		HTable newht = newNode.addNestedTable(newNode.getColumnName(), oldws, factory);
-		List<HNode> childHNodes = new ArrayList<HNode>();
+		List<HNode> childHNodes = new ArrayList<>();
 		for (HNode hnode : hnodes) {
 			if (hnode.hasNestedTable()) {
 				for (HNode hn : hnode.getNestedTable().getHNodes()) {
@@ -234,7 +234,7 @@ private void generateRows(List<HNode> hNodes, SuperSelection selection, Row row,
 					max = size;
 				}
 			}
-			List<Row> newRows = new ArrayList<Row>();
+			List<Row> newRows = new ArrayList<>();
 			for (int i = 0; i < max; i++)
 				newRows.add(nestedTable.addRow(factory));
 			for (HNode hnode : hNodes) {
@@ -252,12 +252,12 @@ private void generateRows(List<HNode> hNodes, SuperSelection selection, Row row,
 			}
 		}
 		else {
-			List<List<Row>> tablesToCross = new ArrayList<List<Row>>();
+			List<List<Row>> tablesToCross = new ArrayList<>();
 			for (HNode hnode : hNodes) {
 				if (!hnode.hasNestedTable())
 					continue;
 				Node tmp = row.getNeighbor(hnode.getId());
-				ArrayList<Row> rowsInTable = new ArrayList<Row>();
+				ArrayList<Row> rowsInTable = new ArrayList<>();
 				tablesToCross.add(rowsInTable);
 				for (Row nestedRow : tmp.getNestedTable().getRows(0, tmp.getNestedTable().getNumRows(), selection)) {
 					rowsInTable.add(nestedRow);
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GroupByCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GroupByCommand.java
index 110ece123..fe267c00d 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GroupByCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/GroupByCommand.java
@@ -86,9 +86,9 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		RepFactory factory = workspace.getFactory();
 		Worksheet oldws = workspace.getWorksheet(worksheetId);
 		Object para = JSONUtil.createJson(this.getInputParameterJson());
-		List<String> hnodeIDs = new ArrayList<String>();
-		List<HNode> keyhnodes = new ArrayList<HNode>();
-		List<HNode> valuehnodes = new ArrayList<HNode>();
+		List<String> hnodeIDs = new ArrayList<>();
+		List<HNode> keyhnodes = new ArrayList<>();
+		List<HNode> valuehnodes = new ArrayList<>();
 		JSONArray checked = (JSONArray) JSONUtil.createJson(CommandInputJSONUtil.getStringValue("values", (JSONArray)para));
 		HTable ht;
 		if (hNodeId.compareTo("") != 0)
@@ -176,12 +176,12 @@ private Worksheet groupByTopLevel(Worksheet oldws, Workspace workspace, List<Str
 		HTable newht =  newws.getHeaders();
 		ArrayList<Row> rows = oldws.getDataTable().getRows(0, oldws.getDataTable().getNumRows(), selection);
 		HTable oldht =  oldws.getHeaders();
-		Map<String, ArrayList<String>> hash = new TreeMap<String, ArrayList<String>>();
+		Map<String, ArrayList<String>> hash = new TreeMap<>();
 		for (Row row : rows) {
 			String hashValue = HashValueManager.getHashValue(row, hnodeIDs);
 			ArrayList<String> ids = hash.get(hashValue);
 			if (ids == null)
-				ids = new ArrayList<String>();
+				ids = new ArrayList<>();
 			ids.add(row.getId());
 			hash.put(hashValue, ids);
 		}
@@ -205,9 +205,9 @@ private Worksheet groupByTopLevel(Worksheet oldws, Workspace workspace, List<Str
 	private void groupByNestedTable(Worksheet oldws, Workspace workspace, HTable ht, List<String> hnodeIDs, List<HNode> keyhnodes, List<HNode> valuehnodes, RepFactory factory) {
 		SuperSelection selection = getSuperSelection(oldws);
 		HTable parentHT = ht.getParentHNode().getHTable(factory);
-		List<Table> parentTables = new ArrayList<Table>();
+		List<Table> parentTables = new ArrayList<>();
 		CloneTableUtils.getDatatable(oldws.getDataTable(), parentHT,parentTables, selection);
-		ArrayList<Row> parentRows = new ArrayList<Row>();
+		ArrayList<Row> parentRows = new ArrayList<>();
 		for (Table tmp : parentTables) {
 			for (Row row : tmp.getRows(0, tmp.getNumRows(), selection)) {
 				parentRows.add(row);
@@ -234,12 +234,12 @@ private void groupByNestedTable(Worksheet oldws, Workspace workspace, HTable ht,
 				}	
 			}
 			ArrayList<Row> rows = t.getRows(0, t.getNumRows(), selection);
-			Map<String, ArrayList<String>> hash = new TreeMap<String, ArrayList<String>>();
+			Map<String, ArrayList<String>> hash = new TreeMap<>();
 			for (Row row : rows) {
 				String hashValue = HashValueManager.getHashValue(row, hnodeIDs);
 				ArrayList<String> ids = hash.get(hashValue);
 				if (ids == null)
-					ids = new ArrayList<String>();
+					ids = new ArrayList<>();
 				ids.add(row.getId());
 				hash.put(hashValue, ids);
 			}	
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MergeClusterValuesCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MergeClusterValuesCommand.java
index cd10ff0f5..649a7b1ff 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MergeClusterValuesCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MergeClusterValuesCommand.java
@@ -26,7 +26,7 @@
 public class MergeClusterValuesCommand extends WorksheetSelectionCommand {
 	private String hNodeId;
 	@SuppressWarnings("unused")
-	private Map<String, String> oldRowValueMap = new HashMap<String, String>();	
+	private Map<String, String> oldRowValueMap = new HashMap<>();	
 	MultipleValueEditColumnCommand edit;
 			
 	public MergeClusterValuesCommand(String id, String model, String hNodeId,
@@ -71,7 +71,7 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 				selectedPath = path;
 			}
 		}
-		Collection<Node> nodes = new ArrayList<Node>();
+		Collection<Node> nodes = new ArrayList<>();
 		workspace.getFactory().getWorksheet(worksheetId).getDataTable()
 				.collectNodes(selectedPath, nodes, selection);
 
@@ -101,10 +101,10 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 					mainSelectedPath = path;
 				}
 			}
-			Collection<Node> mainNodes = new ArrayList<Node>();
+			Collection<Node> mainNodes = new ArrayList<>();
 			workspace.getFactory().getWorksheet(mainWorksheetId).getDataTable().collectNodes(mainSelectedPath, mainNodes, selection);
 			int i = 0;
-			Map<String, String> rowValueMap = new TreeMap<String, String>();
+			Map<String, String> rowValueMap = new TreeMap<>();
 			
 			UpdateContainer c = new UpdateContainer();
 				for (Node node : mainNodes) {
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MultipleValueEditColumnCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MultipleValueEditColumnCommand.java
index 7cc7ca8d5..db2f7b7dc 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MultipleValueEditColumnCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MultipleValueEditColumnCommand.java
@@ -20,7 +20,7 @@
 public class MultipleValueEditColumnCommand extends WorksheetCommand {
 	private String hNodeID;
 	private Map<String, String> newRowValueMap;
-	private Map<String, String> oldRowValueMap = new HashMap<String, String>();
+	private Map<String, String> oldRowValueMap = new HashMap<>();
 
 	private static Logger logger = LoggerFactory.getLogger(MultipleValueEditColumnCommand.class);
 	
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MultipleValueEditColumnCommandFactory.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MultipleValueEditColumnCommandFactory.java
index ceda39785..09ac86aca 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MultipleValueEditColumnCommandFactory.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/MultipleValueEditColumnCommandFactory.java
@@ -31,7 +31,7 @@ public Command createCommand(JSONArray inputJson, String model, Workspace worksp
 		String worksheetId = CommandInputJSONUtil.getStringValue(Arguments.worksheetId.name(), inputJson);
 		JSONArray rows = CommandInputJSONUtil.getJSONArrayValue(Arguments.rows.name(), inputJson);
 		
-		Map<String, String> rowValueMap = new HashMap<String, String>();
+		Map<String, String> rowValueMap = new HashMap<>();
 		for (int i=0; i<rows.length(); i++) {
 			JSONObject rowObj = rows.getJSONObject(i);
 			rowValueMap.put(rowObj.getString(Arguments.rowID.name()), 
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SetWorksheetPropertiesCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SetWorksheetPropertiesCommand.java
index 8efdc38aa..333726457 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SetWorksheetPropertiesCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SetWorksheetPropertiesCommand.java
@@ -85,7 +85,7 @@ public CommandType getCommandType() {
 	public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		worksheet = workspace.getWorksheet(worksheetId);
 		
-		JSONObject propertiesJson = null;
+		JSONObject propertiesJson;
 		try {
 			propertiesJson = new JSONObject(properties);
 			WorksheetProperties props = worksheet.getMetadataContainer().getWorksheetProperties();
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SplitByCommaCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SplitByCommaCommand.java
index cd2eaf157..73454e655 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SplitByCommaCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SplitByCommaCommand.java
@@ -47,8 +47,8 @@ public class SplitByCommaCommand extends WorksheetSelectionCommand {
 	private HNode hNode;
 	private String splitValueHNodeId;
 
-	private HashMap<Node, CellValue> oldNodeValueMap = new HashMap<Node, CellValue>();
-	private HashMap<Node, NodeStatus> oldNodeStatusMap = new HashMap<Node, NodeStatus>();
+	private HashMap<Node, CellValue> oldNodeValueMap = new HashMap<>();
+	private HashMap<Node, NodeStatus> oldNodeStatusMap = new HashMap<>();
 
 //	private final Logger logger = LoggerFactory.getLogger(this.getClass());
 
@@ -136,7 +136,7 @@ public UpdateContainer undoIt(Workspace workspace) {
 		columnPaths.set(oldPathIndex, selectedPath);
 
 		// Populate the column with old values
-		Collection<Node> nodes = new ArrayList<Node>();
+		Collection<Node> nodes = new ArrayList<>();
 		wk.getDataTable().collectNodes(selectedPath, nodes, selection);
 
 		for (Node node : nodes) {
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SplitColumnByDelimiter.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SplitColumnByDelimiter.java
index 5d410c262..68a859f78 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SplitColumnByDelimiter.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/SplitColumnByDelimiter.java
@@ -86,7 +86,7 @@ public void split(HashMap<Node, CellValue> oldNodeValueMap,
 		}
 
 		// Convert the delimiter into character primitive type
-		char delimiterChar = ',';
+		char delimiterChar;
 		if (delimiter.equalsIgnoreCase("space"))
 			delimiterChar = ' ';
 		else if (delimiter.equalsIgnoreCase("tab"))
@@ -95,7 +95,7 @@ else if (delimiter.equalsIgnoreCase("tab"))
 			delimiterChar = new Character(delimiter.charAt(0));
 		}
 
-		Collection<Node> nodes = new ArrayList<Node>();
+		Collection<Node> nodes = new ArrayList<>();
 		worksheet.getDataTable().collectNodes(selectedPath, nodes, selection);
 
 		//pedro: 2012-10-09
@@ -167,7 +167,7 @@ else if (delimiter.equalsIgnoreCase("tab"))
 	public void empty() {
 		RepFactory factory = workspace.getFactory();
 		HTable ht = factory.getHTable(factory.getHNode(hNodeId).getHTableId());
-		List<Table> tables = new ArrayList<Table>();
+		List<Table> tables = new ArrayList<>();
 		
 		CloneTableUtils.getDatatable(worksheet.getDataTable(), ht, tables, selection);
 		for (Table t : tables) {
@@ -181,8 +181,9 @@ public void empty() {
 	public void split() throws IOException {
 		RepFactory factory = workspace.getFactory();
 		HTable ht = factory.getHTable(factory.getHNode(hNodeId).getHTableId());
-		List<Table> tables = new ArrayList<Table>();
-		char delimiterChar = ',';
+		List<Table> tables = new ArrayList<>();
+		char delimiterChar;
+
 		if (delimiter.equalsIgnoreCase("space"))
 			delimiterChar = ' ';
 		else if (delimiter.equalsIgnoreCase("tab"))
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/UnfoldCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/UnfoldCommand.java
index a82487a74..dc048e2c3 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/UnfoldCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/UnfoldCommand.java
@@ -159,12 +159,12 @@ public void setKeyName(String keyName) {
 	}
 
 	private void unfoldNestedLevel(Worksheet oldws, HTable ht, String keyHNodeid, String valueHNodeid, RepFactory factory) {
-		ArrayList<HNode> topHNodes = new ArrayList<HNode>(ht.getHNodes());
+		ArrayList<HNode> topHNodes = new ArrayList<>(ht.getHNodes());
 		SuperSelection selection = getSuperSelection(oldws);
 		HTable parentHT = ht.getParentHNode().getHTable(factory);
-		List<Table> parentTables = new ArrayList<Table>();
+		List<Table> parentTables = new ArrayList<>();
 		CloneTableUtils.getDatatable(oldws.getDataTable(), parentHT,parentTables, selection);
-		ArrayList<Row> parentRows = new ArrayList<Row>();
+		ArrayList<Row> parentRows = new ArrayList<>();
 		for (Table tmp : parentTables) {
 			for (Row row : tmp.getRows(0, tmp.getNumRows(), selection)) {
 				parentRows.add(row);
@@ -177,8 +177,8 @@ private void unfoldNestedLevel(Worksheet oldws, HTable ht, String keyHNodeid, St
 		HTable newHT = newNode.addNestedTable("Unfold: " + ht.getHNode(keyHNodeid).getColumnName(), oldws, factory);
 		HNode key = ht.getHNode(keyHNodeid);
 		HNode value = ht.getHNode(valueHNodeid);
-		List<HNode> hnodes = new ArrayList<HNode>();
-		List<String> hnodeIds = new ArrayList<String>();
+		List<HNode> hnodes = new ArrayList<>();
+		List<String> hnodeIds = new ArrayList<>();
 		if (!notOtherColumn) {
 			for (HNode h : topHNodes) {
 				if (h.getId().compareTo(value.getId()) != 0 && h.getId().compareTo(key.getId()) != 0) {
@@ -190,7 +190,7 @@ private void unfoldNestedLevel(Worksheet oldws, HTable ht, String keyHNodeid, St
 		for (Entry<String, String> entry : CloneTableUtils.cloneHTable(newHT, oldws, factory, hnodes, false).entrySet()) {
 			outputColumns.add(entry.getValue());
 		}
-		List<Row> resultRows = new ArrayList<Row>();
+		List<Row> resultRows = new ArrayList<>();
 		for (Row parentRow: parentRows) {
 			Table t = null;
 			for (Node node : parentRow.getNodes()) {
@@ -199,8 +199,8 @@ private void unfoldNestedLevel(Worksheet oldws, HTable ht, String keyHNodeid, St
 					break;
 				}	
 			}
-			Map<String, String> keyMapping = new HashMap<String, String>();
-			Map<String, String> HNodeidMapping = new HashMap<String, String>();
+			Map<String, String> keyMapping = new HashMap<>();
+			Map<String, String> HNodeidMapping = new HashMap<>();
 			ArrayList<Row> rows = t.getRows(0, t.getNumRows(), selection);
 			for (Row row : rows) {
 				Node n = row.getNode(key.getId());
@@ -218,12 +218,12 @@ private void unfoldNestedLevel(Worksheet oldws, HTable ht, String keyHNodeid, St
 				else
 					HNodeidMapping.put(stringStringEntry.getValue(), hn.getId());
 			}
-			Map<String, ArrayList<String>> hash = new HashMap<String, ArrayList<String>>();
+			Map<String, ArrayList<String>> hash = new HashMap<>();
 			for (Row row : rows) {
 				String hashValue = HashValueManager.getHashValue(row, hnodeIds);
 				ArrayList<String> ids = hash.get(hashValue);
 				if (ids == null)
-					ids = new ArrayList<String>();
+					ids = new ArrayList<>();
 				ids.add(row.getId());
 				hash.put(hashValue, ids);
 				//System.out.println("Hash: " + HashValueManager.getHashValue(row, hnodeIDs));
@@ -262,12 +262,12 @@ private Worksheet unfoldTopLevel(Worksheet oldws, String keyHNodeid, String valu
 		Worksheet newws = factory.createWorksheet("Unfold: " + oldws.getTitle(), workspace, oldws.getEncoding());
 		SuperSelection selection = getSuperSelection(oldws);
 		newws.getMetadataContainer().getWorksheetProperties().setPropertyValue(Property.sourceType, oldws.getMetadataContainer().getWorksheetProperties().getPropertyValue(Property.sourceType));
-		ArrayList<HNode> topHNodes = new ArrayList<HNode>(oldws.getHeaders().getHNodes());
+		ArrayList<HNode> topHNodes = new ArrayList<>(oldws.getHeaders().getHNodes());
 		ArrayList<Row> rows = oldws.getDataTable().getRows(0, oldws.getDataTable().getNumRows(), selection);
 		HNode key = oldws.getHeaders().getHNode(keyHNodeid);
 		HNode value = oldws.getHeaders().getHNode(valueHNodeid);
-		List<HNode> hnodes = new ArrayList<HNode>();
-		List<String> hnodeIds = new ArrayList<String>();
+		List<HNode> hnodes = new ArrayList<>();
+		List<String> hnodeIds = new ArrayList<>();
 		if (!notOtherColumn) {
 			for (HNode h : topHNodes) {
 				if (h.getId().compareTo(value.getId()) != 0 && h.getId().compareTo(key.getId()) != 0) {
@@ -277,8 +277,8 @@ private Worksheet unfoldTopLevel(Worksheet oldws, String keyHNodeid, String valu
 			}
 		}
 		CloneTableUtils.cloneHTable(newws.getHeaders(), newws, factory, hnodes, false);
-		Map<String, String> keyMapping = new HashMap<String, String>();
-		Map<String, String> HNodeidMapping = new HashMap<String, String>();
+		Map<String, String> keyMapping = new HashMap<>();
+		Map<String, String> HNodeidMapping = new HashMap<>();
 		for (Row row : rows) {
 			Node n = row.getNode(key.getId());
 			keyMapping.put(HashValueManager.getHashValue(oldws, n.getId(), factory), n.getValue().asString());
@@ -290,16 +290,17 @@ private Worksheet unfoldTopLevel(Worksheet oldws, String keyHNodeid, String valu
 			HNodeidMapping.put(stringStringEntry.getValue(), n.getId());
 		}
 
-		Map<String, ArrayList<String>> hash = new TreeMap<String, ArrayList<String>>();
+		Map<String, ArrayList<String>> hash = new TreeMap<>();
 		for (Row row : rows) {
 			String hashValue = HashValueManager.getHashValue(row, hnodeIds);
 			ArrayList<String> ids = hash.get(hashValue);
 			if (ids == null)
-				ids = new ArrayList<String>();
+				ids = new ArrayList<>();
 			ids.add(row.getId());
 			hash.put(hashValue, ids);
 		}
-		List<Row> resultRows = new ArrayList<Row>();
+
+		List<Row> resultRows = new ArrayList<>();
 		for (Entry<String, ArrayList<String>> stringArrayListEntry : hash.entrySet()) {
 			ArrayList<String> r = stringArrayListEntry.getValue();
 			Row lastRow = CloneTableUtils.cloneDataTable(factory.getRow(r.get(0)), newws.getDataTable(), 
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/ClearSelectionCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/ClearSelectionCommand.java
index b196516c2..f79cb629c 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/ClearSelectionCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/ClearSelectionCommand.java
@@ -28,7 +28,7 @@ public ClearSelectionCommand(String id, String model, String worksheetId, String
 		super(id, model, worksheetId, selectionId);
 		this.hNodeId = hNodeId;
 		this.type = type;
-		oldSelections = new HashMap<String, Selection>();
+		oldSelections = new HashMap<>();
 		addTag(CommandTag.Selection);
 	}
 
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/RefreshSelectionCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/RefreshSelectionCommand.java
index 8232405b9..1d139b534 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/RefreshSelectionCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/RefreshSelectionCommand.java
@@ -104,7 +104,7 @@ public UpdateContainer getErrorUpdate(String msg) {
 	}
 
 	private List<Command> gatherAllOperateSelectionCommands(List<Command> commands, Workspace workspace) {
-		List<Command> operationCommands = new ArrayList<Command>();
+		List<Command> operationCommands = new ArrayList<>();
 		for (Command c : commands) {
 			if (c instanceof OperateSelectionCommand) {
 				OperateSelectionCommand t = (OperateSelectionCommand)c;
diff --git a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/RefreshSuperSelectionCommand.java b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/RefreshSuperSelectionCommand.java
index 28ae14ea5..449ed60a6 100644
--- a/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/RefreshSuperSelectionCommand.java
+++ b/karma-commands/commands-worksheet/src/main/java/edu/isi/karma/controller/command/worksheet/selection/RefreshSuperSelectionCommand.java
@@ -73,7 +73,7 @@ public CommandType getCommandType() {
 	public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		Worksheet worksheet = workspace.getWorksheet(worksheetId);
 		SuperSelection currentSel = getSuperSelection(worksheet);
-		List<SelectionWithPriority> selections = new ArrayList<SelectionWithPriority>();
+		List<SelectionWithPriority> selections = new ArrayList<>();
 		for (Selection sel : currentSel.getAllSelection()) {
 			HTable ht = workspace.getFactory().getHTable(sel.getHTableId());
 			selections.add(new SelectionWithPriority(sel, hTableDepth(ht, workspace.getFactory())));
diff --git a/karma-common/src/main/java/edu/isi/karma/config/ModelingConfigurationRegistry.java b/karma-common/src/main/java/edu/isi/karma/config/ModelingConfigurationRegistry.java
index 0a86be86e..949f7aaa8 100644
--- a/karma-common/src/main/java/edu/isi/karma/config/ModelingConfigurationRegistry.java
+++ b/karma-common/src/main/java/edu/isi/karma/config/ModelingConfigurationRegistry.java
@@ -5,7 +5,7 @@
 public class ModelingConfigurationRegistry {
 	private static ModelingConfigurationRegistry singleton = new ModelingConfigurationRegistry();
 
-	private final ConcurrentHashMap<String, ModelingConfiguration> contextIdToModelingConfiguration = new ConcurrentHashMap<String, ModelingConfiguration>();
+	private final ConcurrentHashMap<String, ModelingConfiguration> contextIdToModelingConfiguration = new ConcurrentHashMap<>();
 
 	public static ModelingConfigurationRegistry getInstance() {
 		return singleton;
diff --git a/karma-common/src/main/java/edu/isi/karma/config/UIConfigurationRegistry.java b/karma-common/src/main/java/edu/isi/karma/config/UIConfigurationRegistry.java
index 6278e1633..fc1515117 100644
--- a/karma-common/src/main/java/edu/isi/karma/config/UIConfigurationRegistry.java
+++ b/karma-common/src/main/java/edu/isi/karma/config/UIConfigurationRegistry.java
@@ -5,7 +5,7 @@
 public class UIConfigurationRegistry {
 	private static UIConfigurationRegistry singleton = new UIConfigurationRegistry();
 
-	private final ConcurrentHashMap<String, UIConfiguration> contextIdToUIConfiguration = new ConcurrentHashMap<String, UIConfiguration>();
+	private final ConcurrentHashMap<String, UIConfiguration> contextIdToUIConfiguration = new ConcurrentHashMap<>();
 
 	public static UIConfigurationRegistry getInstance() {
 		return singleton;
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/command/Command.java b/karma-common/src/main/java/edu/isi/karma/controller/command/Command.java
index 5c95dc29d..2002ecec8 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/command/Command.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/command/Command.java
@@ -62,12 +62,12 @@ public abstract class Command extends Entity implements ICommand
 	 * Flag to tell if the command history should be written after this command
 	 * has been executed
 	 */
-	protected Set<String> inputColumns = new HashSet<String>();
-	protected Set<String> outputColumns = new HashSet<String>();
+	protected Set<String> inputColumns = new HashSet<>();
+	protected Set<String> outputColumns = new HashSet<>();
 	/**
 	 * List of tags for the command
 	 */
-	private List<CommandTag> tags = new ArrayList<CommandTag>();
+	private List<CommandTag> tags = new ArrayList<>();
 
 	private static final List<CommandTag> commandTagPriority = new ArrayList<>();
 
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/command/selection/MiniSelection.java b/karma-common/src/main/java/edu/isi/karma/controller/command/selection/MiniSelection.java
index 78216520a..a9bea8f11 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/command/selection/MiniSelection.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/command/selection/MiniSelection.java
@@ -70,7 +70,7 @@ public void addInputColumns(String hNodeId) {
 
 	private void populateSelection() {
 		final ServletContextParameterMap contextParameters = ContextParametersRegistry.getInstance().getContextParameters(workspace.getContextId());
-		List<Table> tables = new ArrayList<Table>();
+		List<Table> tables = new ArrayList<>();
 		Worksheet worksheet = workspace.getWorksheet(worksheetId);
 		CloneTableUtils.getDatatable(worksheet.getDataTable(), workspace.getFactory().getHTable(hTableId), tables, SuperSelectionManager.DEFAULT_SELECTION);
 		String selectionId = String.format("%d_%d_%s", System.currentTimeMillis(), Thread.currentThread().getId(), this.superSelectionName);//Thread.currentThread().getId() + this.superSelectionName;
@@ -99,7 +99,7 @@ private void populateSelection() {
 	private boolean evaluatePythonExpression(Row r, PyCode code, PythonInterpreter interpreter) {
 		evalColumns.clear();
 		try {
-			ArrayList<Node> nodes = new ArrayList<Node>(r.getNodes());
+			ArrayList<Node> nodes = new ArrayList<>(r.getNodes());
 			Node node = nodes.get(0);
 			interpreter.getLocals().__setitem__("nodeid", new PyString(node.getId()));
 			PyObject output = interpreter.eval(code);
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/command/selection/Selection.java b/karma-common/src/main/java/edu/isi/karma/controller/command/selection/Selection.java
index f4d39119e..707f85ac1 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/command/selection/Selection.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/command/selection/Selection.java
@@ -28,7 +28,7 @@ public enum Tag {
 	protected SelectionStatus status;
 	protected Workspace workspace;
 	protected String worksheetId;
-	protected List<Tag> tags = new ArrayList<Tag>();
+	protected List<Tag> tags = new ArrayList<>();
 	protected String hTableId;
 	protected String Id;
 	protected Map<Row, Boolean> selectedRowsCache;
@@ -48,9 +48,9 @@ public enum Tag {
 		{
 			this.superSelectionName = "";
 		}
-		selectedRowsCache = new HashMap<Row, Boolean>();
-		evalColumns = new HashSet<String>();
-		selectedRowsColumns = new HashSet<String>();
+		selectedRowsCache = new HashMap<>();
+		evalColumns = new HashSet<>();
+		selectedRowsColumns = new HashSet<>();
 		hasSelectedRowsMethod = false;
 	}
 		
@@ -104,11 +104,11 @@ public RowStatus getSelectedStatus(Row row) {
 	public abstract void updateSelection();
 	
 	public Set<String> getInputColumns() {
-		return new HashSet<String>(evalColumns);
+		return new HashSet<>(evalColumns);
 	}
 	
 	public Set<String> getSelectedRowsColumns() {
-		return new HashSet<String>(selectedRowsColumns);
+		return new HashSet<>(selectedRowsColumns);
 	}
 	
 	public String getParentSuperSelection() {
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SelectionManager.java b/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SelectionManager.java
index 54693eb3c..61fb7db2e 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SelectionManager.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SelectionManager.java
@@ -7,7 +7,7 @@
 import java.util.concurrent.ConcurrentHashMap;
 
 public class SelectionManager {
-	private Map<String, List<Selection> > selectionMapping = new ConcurrentHashMap<String, List<Selection> >();
+	private Map<String, List<Selection> > selectionMapping = new ConcurrentHashMap<>();
 	public static String defaultCode = "return False";
 	
 	public void removeSelection(Selection sel) {
@@ -17,7 +17,7 @@ public void removeSelection(Selection sel) {
 	}
 	
 	public List<Selection> getAllDefinedSelection() {
-		List<Selection> selections = new ArrayList<Selection>();
+		List<Selection> selections = new ArrayList<>();
 		for (Entry<String, List<Selection> > entry : selectionMapping.entrySet()) {
 			List<Selection> sels = entry.getValue();
 			if (sels != null)
@@ -30,7 +30,7 @@ public void addSelection(Selection sel) {
 		String hTableId = sel.getHTableId();
 		List<Selection> selections = selectionMapping.get(hTableId);
 		if (selections == null)
-			selections = new ArrayList<Selection>();
+			selections = new ArrayList<>();
 		selections.add(sel);
 		selectionMapping.put(hTableId, selections);
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SuperSelection.java b/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SuperSelection.java
index dcdcd938e..658905545 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SuperSelection.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SuperSelection.java
@@ -12,7 +12,7 @@ public class SuperSelection {
 	private String name;
 	
 	public SuperSelection(String name) {
-		selections = new HashSet<Selection>();
+		selections = new HashSet<>();
 		this.name = name;
 	}
 
@@ -72,6 +72,6 @@ public Selection getSelection(String hTableId) {
 	}
 	
 	public Set<Selection> getAllSelection() {
-		return new HashSet<Selection>(selections);
+		return new HashSet<>(selections);
 	}
 }
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SuperSelectionManager.java b/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SuperSelectionManager.java
index df84e510e..fb2cb7fd8 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SuperSelectionManager.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/command/selection/SuperSelectionManager.java
@@ -10,7 +10,7 @@
 public class SuperSelectionManager {
 	public static final String DEFAULT_SELECTION_NAME = "DEFAULT_SELECTION";
 	public static final String DEFAULT_SELECTION_TEST_NAME = "DEFAULT_TEST";
-	private Map<String, SuperSelection> selectionMapping = new HashMap<String, SuperSelection>();
+	private Map<String, SuperSelection> selectionMapping = new HashMap<>();
 	public static final SuperSelection DEFAULT_SELECTION = new SuperSelection(DEFAULT_SELECTION_NAME);
 	public SuperSelectionManager() {
 		selectionMapping.put(DEFAULT_SELECTION_NAME, DEFAULT_SELECTION);
@@ -54,6 +54,6 @@ public SuperSelection getSuperSelection(String name) {
 	}
 	
 	public List<SuperSelection> getAllDefinedSelection() {
-		return new ArrayList<SuperSelection>(selectionMapping.values());
+		return new ArrayList<>(selectionMapping.values());
 	}
  }
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/command/service/ServiceTableUtil.java b/karma-common/src/main/java/edu/isi/karma/controller/command/service/ServiceTableUtil.java
index bb740f653..089d4423a 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/command/service/ServiceTableUtil.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/command/service/ServiceTableUtil.java
@@ -48,26 +48,17 @@ private ServiceTableUtil() {
 
 
 	public static void populateEmptyWorksheet(Table table, Worksheet worksheet, RepFactory factory) {
-
 		logger.info("Populating an empty worksheet with the service data ...");
-
-		List<String> hNodeIdList = new ArrayList<String>();
-		hNodeIdList = addHeaders(table.getHeaders(), worksheet, factory);
-
+		List<String> hNodeIdList = addHeaders(table.getHeaders(), worksheet, factory);
 		edu.isi.karma.rep.Table dataTable = worksheet.getDataTable();
 		addRows(table.getValues(), worksheet, factory, hNodeIdList, dataTable);
 
 	}
 	
 	public static void populateWorksheet(Table table, Worksheet worksheet, RepFactory factory, SuperSelection sel) {
-		
 		logger.info("Populating existing worksheet with the service data ...");
-		
-		List<String> oldHNodeIdList = new ArrayList<String>(worksheet.getHeaders().getHNodeIds());
-
-		List<String> hNodeIdList = new ArrayList<String>();
-		hNodeIdList = addHeaders(table.getHeaders(), worksheet, factory);
-
+		List<String> oldHNodeIdList = new ArrayList<>(worksheet.getHeaders().getHNodeIds());
+		List<String> hNodeIdList = addHeaders(table.getHeaders(), worksheet, factory);
 		edu.isi.karma.rep.Table dataTable = worksheet.getDataTable();
 		updateRows(table.getValues(), table.getRowIds(), worksheet, factory, oldHNodeIdList, hNodeIdList, dataTable, sel);
 
@@ -75,7 +66,7 @@ public static void populateWorksheet(Table table, Worksheet worksheet, RepFactor
 	
 	private static List<String> addHeaders(List<Attribute> tableHeader, Worksheet worksheet, RepFactory factory) {
 		HTable headers = worksheet.getHeaders();
-		List<String> headersList = new ArrayList<String>();
+		List<String> headersList = new ArrayList<>();
 		
 		for (int i = 0; i < tableHeader.size(); i++) {
 			Attribute att = tableHeader.get(i);
@@ -109,11 +100,11 @@ private static void updateRows(List<List<String>> tableValues, List<String> tabl
 		
 		int rowsCount = dataTable.getNumRows();
 		List<Row> oldRows = dataTable.getRows(0, rowsCount, sel);
-		List<HashMap<String, String>> oldRowValues = new ArrayList<HashMap<String,String>>();
-		List<String> oldRowIds = new ArrayList<String>();
+		List<HashMap<String, String>> oldRowValues = new ArrayList<>();
+		List<String> oldRowIds = new ArrayList<>();
 		
 		for (Row r : oldRows) {
-			HashMap<String, String> vals = new HashMap<String, String>();
+			HashMap<String, String> vals = new HashMap<>();
 			for (Node n : r.getNodes()) {
 				vals.put(n.getHNodeId(), n.getValue().asString());
 			}
@@ -121,8 +112,8 @@ private static void updateRows(List<List<String>> tableValues, List<String> tabl
 			oldRowIds.add(r.getId());
 		}
 		
-		HashMap<String, String> currentRow = null;
-		String currentRowId = "";
+		HashMap<String, String> currentRow;
+		String currentRowId;
 		
 		int addedRowsCount = 0; 
 		for (int i = 0; i < oldRowValues.size(); i++) {
@@ -141,7 +132,7 @@ private static void updateRows(List<List<String>> tableValues, List<String> tabl
 				
 				addedRowsCount ++;
 				
-				Row row = null;
+				Row row;
 				if (addedRowsCount <= rowsCount)
 					row = dataTable.getRows(addedRowsCount - 1, 1, sel).get(0);
 				else 
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/history/CommandHistory.java b/karma-common/src/main/java/edu/isi/karma/controller/history/CommandHistory.java
index 91f130157..d5b9c5bad 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/history/CommandHistory.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/history/CommandHistory.java
@@ -71,7 +71,7 @@ public class CommandHistory implements Cloneable{
 
 	private final Logger logger = LoggerFactory.getLogger(this.getClass().getSimpleName());
 
-	private static HashMap<String, IHistorySaver> historySavers = new HashMap<>();
+	private static Map<String, IHistorySaver> historySavers = new HashMap<>();
 
 	private final static Set<CommandConsolidator> consolidators = new HashSet<>();
 
@@ -198,7 +198,8 @@ public UpdateContainer doCommand(Command command, Workspace workspace, boolean s
 
 	private void writeHistoryPerWorksheet(Workspace workspace, IHistorySaver historySaver) throws Exception {
 		String workspaceId = workspace.getId();
-		HashMap<String, JSONArray> comMap = new HashMap<String, JSONArray>();
+		Map<String, JSONArray> comMap = new HashMap<>();
+
 		for(ICommand command : _getHistory()) {
 			if(command.isSavedInHistory() &&
 					(command.hasTag(CommandTag.Modeling)
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/history/WorksheetCommandHistoryExecutor.java b/karma-common/src/main/java/edu/isi/karma/controller/history/WorksheetCommandHistoryExecutor.java
index 5f6ac8f4e..b700f02c6 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/history/WorksheetCommandHistoryExecutor.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/history/WorksheetCommandHistoryExecutor.java
@@ -220,7 +220,7 @@ public UpdateContainer normalizeCommandHistoryJsonInput(Workspace workspace, Str
 				String predicate = link.getString("predicate");
 				Object object = link.get("object");
 				
-				String objectHNodeId = null, subjectHNodeId = null;
+				String objectHNodeId, subjectHNodeId;
 				if(subject instanceof JSONArray) {
 					subjectHNodeId = generateHNodeId((JSONArray)subject, hTable, addIfNonExist, uc);
 				} else {
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/update/SemanticTypesUpdate.java b/karma-common/src/main/java/edu/isi/karma/controller/update/SemanticTypesUpdate.java
index bf569b34a..11322cfa3 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/update/SemanticTypesUpdate.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/update/SemanticTypesUpdate.java
@@ -222,7 +222,7 @@ private boolean isMetaProperty(Label type, ColumnNode alignmentColumnNode) {
 	}
 
 	private Map<String, SemanticTypeNode> createDomainNodeMap() {
-		Map<String, SemanticTypeNode> hNodeIdToDomainNodeMap = new HashMap<String, SemanticTypeNode>();
+		Map<String, SemanticTypeNode> hNodeIdToDomainNodeMap = new HashMap<>();
 		Set<Node> alignmentColumnNodes = alignment.getNodesByType(NodeType.ColumnNode);
 		if (alignmentColumnNodes == null)
 			return hNodeIdToDomainNodeMap;
@@ -233,7 +233,7 @@ private Map<String, SemanticTypeNode> createDomainNodeMap() {
 				if (incomingLink!= null && incomingLink.getSource() instanceof InternalNode) {
 					String hNodeId = ((ColumnNode)cNode).getHNodeId();
 					if(incomingLink instanceof DataPropertyOfColumnLink || incomingLink instanceof ObjectPropertySpecializationLink) {
-						String id = null;
+						String id;
 						if(incomingLink instanceof DataPropertyOfColumnLink)
 							id = ((DataPropertyOfColumnLink)incomingLink).getSpecializedLinkId();
 						else 
@@ -253,7 +253,7 @@ private Map<String, SemanticTypeNode> createDomainNodeMap() {
 
 	private Map<String, ColumnNode> createColumnNodeMap() {
 		Set<Node> alignmentColumnNodes = alignment.getNodesByType(NodeType.ColumnNode);
-		Map<String, ColumnNode> hNodeIdToColumnNodeMap = new HashMap<String, ColumnNode>();
+		Map<String, ColumnNode> hNodeIdToColumnNodeMap = new HashMap<>();
 		if (alignmentColumnNodes == null)
 			return hNodeIdToColumnNodeMap;
 		for (Node cNode : alignmentColumnNodes) {
diff --git a/karma-common/src/main/java/edu/isi/karma/controller/update/UpdateContainer.java b/karma-common/src/main/java/edu/isi/karma/controller/update/UpdateContainer.java
index cdd52e01c..20ac2ce1b 100644
--- a/karma-common/src/main/java/edu/isi/karma/controller/update/UpdateContainer.java
+++ b/karma-common/src/main/java/edu/isi/karma/controller/update/UpdateContainer.java
@@ -42,7 +42,7 @@
  */
 public class UpdateContainer {
 
-	private final List<AbstractUpdate> updates = new LinkedList<AbstractUpdate>();
+	private final List<AbstractUpdate> updates = new LinkedList<>();
 
 	public enum JsonKeys {
 		elements, workspaceId
@@ -60,7 +60,7 @@ public void add(AbstractUpdate update) {
 	}
 
 	public void append(UpdateContainer updateContainer) {
-		Set<AbstractUpdate> needToDeleted = new HashSet<AbstractUpdate>();
+		Set<AbstractUpdate> needToDeleted = new HashSet<>();
 		for (AbstractUpdate update : updateContainer.updates) {
 			for (AbstractUpdate update2 : updates) {
 				if (update2.equals(update)) {
diff --git a/karma-common/src/main/java/edu/isi/karma/er/helper/CloneTableUtils.java b/karma-common/src/main/java/edu/isi/karma/er/helper/CloneTableUtils.java
index 335ac49a8..d6db66de7 100644
--- a/karma-common/src/main/java/edu/isi/karma/er/helper/CloneTableUtils.java
+++ b/karma-common/src/main/java/edu/isi/karma/er/helper/CloneTableUtils.java
@@ -35,7 +35,7 @@ public static Map<String, String> cloneHTable(HTable newHTable, Worksheet newWor
 			if (hnode.hasNestedTable()) {
 				HTable oldNested = hnode.getNestedTable();
 				HTable newNested = newHNode.addNestedTable(hnode.getNestedTable().getTableName(), newWorksheet, factory);
-				tmp.putAll(cloneHTable(newNested, newWorksheet, factory, new ArrayList<HNode>(oldNested.getHNodes()), false));
+				tmp.putAll(cloneHTable(newNested, newWorksheet, factory, new ArrayList<>(oldNested.getHNodes()), false));
 			}
 		}
 		return tmp;
diff --git a/karma-common/src/main/java/edu/isi/karma/er/helper/PythonRepository.java b/karma-common/src/main/java/edu/isi/karma/er/helper/PythonRepository.java
index 0ec4d005f..11bcedf00 100644
--- a/karma-common/src/main/java/edu/isi/karma/er/helper/PythonRepository.java
+++ b/karma-common/src/main/java/edu/isi/karma/er/helper/PythonRepository.java
@@ -18,9 +18,9 @@
 public class PythonRepository {
 
 	private static Logger logger = LoggerFactory.getLogger(PythonRepository.class);
-	private ConcurrentHashMap<String, PyCode> scripts = new ConcurrentHashMap<String, PyCode>();
-	private ConcurrentHashMap<String, PyCode> libraryScripts = new ConcurrentHashMap<String, PyCode>();
-	private ConcurrentHashMap<String, Long> fileNameTolastTimeRead = new ConcurrentHashMap<String, Long>();
+	private ConcurrentHashMap<String, PyCode> scripts = new ConcurrentHashMap<>();
+	private ConcurrentHashMap<String, PyCode> libraryScripts = new ConcurrentHashMap<>();
+	private ConcurrentHashMap<String, Long> fileNameTolastTimeRead = new ConcurrentHashMap<>();
 	private List<String> localKeys = Arrays.asList("workspaceid", "selectionName", "command", "worksheetId", "selection", "nodeid");
 	private boolean libraryHasBeenLoaded = false;
 	private boolean reloadLibrary = true;
@@ -38,7 +38,7 @@ public PythonRepository(boolean reloadLibrary, String repositoryPath)
 
 	private void initialize()
 	{
-		scripts = new ConcurrentHashMap<String, PyCode>();
+		scripts = new ConcurrentHashMap<>();
 		initialLocals = new PyStringMap();
 		interpreter = PythonInterpreter.threadLocalStateInterpreter(initialLocals);
 		
@@ -56,7 +56,7 @@ private void initialize()
 
 	public PyCode compileAndAddToRepositoryAndExec(PythonInterpreter interpreter, String statement)
 	{
-		PyCode py  = null;
+		PyCode py;
 		if(!scripts.containsKey(statement))
 		{
 			py = compileAndAddToRepository(interpreter,statement);
@@ -69,7 +69,7 @@ public PyCode compileAndAddToRepositoryAndExec(PythonInterpreter interpreter, St
 	}
 	public PyCode compileAndAddToRepository(PythonInterpreter interpreter,
 			String statement) {
-		PyCode py  = null;
+		PyCode py;
 		if(!scripts.containsKey(statement))
 		{
 			py = compile(interpreter, statement);
@@ -167,8 +167,8 @@ public boolean accept(File dir, String name) {
 
 	public synchronized void resetLibrary()
 	{
-		libraryScripts = new ConcurrentHashMap<String, PyCode>();
-		fileNameTolastTimeRead = new ConcurrentHashMap<String,Long>();		
+		libraryScripts = new ConcurrentHashMap<>();
+		fileNameTolastTimeRead = new ConcurrentHashMap<>();		
 		libraryHasBeenLoaded = false;
 
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/er/helper/PythonRepositoryRegistry.java b/karma-common/src/main/java/edu/isi/karma/er/helper/PythonRepositoryRegistry.java
index 4731e2d3c..3b3dc1cd8 100644
--- a/karma-common/src/main/java/edu/isi/karma/er/helper/PythonRepositoryRegistry.java
+++ b/karma-common/src/main/java/edu/isi/karma/er/helper/PythonRepositoryRegistry.java
@@ -7,7 +7,7 @@ public class PythonRepositoryRegistry {
 
 	private static PythonRepositoryRegistry singleton = new PythonRepositoryRegistry();
 
-	private final Map<String, PythonRepository> karmaHomeToPythonRepository = new ConcurrentHashMap<String, PythonRepository>();
+	private final Map<String, PythonRepository> karmaHomeToPythonRepository = new ConcurrentHashMap<>();
 
 	public static PythonRepositoryRegistry getInstance() {
 		return singleton;
diff --git a/karma-common/src/main/java/edu/isi/karma/er/helper/SPARQLGeneratorUtil.java b/karma-common/src/main/java/edu/isi/karma/er/helper/SPARQLGeneratorUtil.java
index d63976255..25819f838 100644
--- a/karma-common/src/main/java/edu/isi/karma/er/helper/SPARQLGeneratorUtil.java
+++ b/karma-common/src/main/java/edu/isi/karma/er/helper/SPARQLGeneratorUtil.java
@@ -61,17 +61,17 @@ public ParentMapingInfo(TriplesMap triple, Predicate predicate) {
 	
 	private String generate_sparql(TriplesMap node, String node_symbol, String graph) {
 		
-		ArrayList<Object> queue = new ArrayList<Object>();
+		ArrayList<Object> queue = new ArrayList<>();
 		queue.add(node);
 		StringBuffer query = new StringBuffer();
 		this.var_count = 1;
-		this.prefix_list = new HashMap<String, String>();
+		this.prefix_list = new HashMap<>();
 		this.select_params = new StringBuffer();
-		HashMap<TriplesMap, String> markedTriples = new HashMap<TriplesMap, String>();
+		HashMap<TriplesMap, String> markedTriples = new HashMap<>();
 		
-		this.ParentMapingInfoList = new HashMap<String, SPARQLGeneratorUtil.ParentMapingInfo>();
+		this.ParentMapingInfoList = new HashMap<>();
 		
-		HashMap<Predicate, String> predicateList = new HashMap<Predicate, String>();
+		HashMap<Predicate, String> predicateList = new HashMap<>();
 		
 		// using a BFS approach, we traverse the tree from the root node and add triples/predicates to the queue
 		while(!queue.isEmpty()) {
@@ -203,21 +203,21 @@ public String get_query(TriplesMap root, ArrayList<HashMap<String, String>> colu
 	 * */
 	public String get_query(TriplesMap root, ArrayList<HashMap<String, String>> columns, boolean distinct_query) {
 		
-		ArrayList<Object> queue = new ArrayList<Object>();
+		ArrayList<Object> queue = new ArrayList<>();
 		queue.add(root);
 		StringBuffer query = new StringBuffer();
 		this.var_count = 1;
-		this.prefix_list = new HashMap<String, String>();
+		this.prefix_list = new HashMap<>();
 		this.select_params = new StringBuffer();
 //		ArrayList<String> select_param = new ArrayList<String>();
-		HashMap<TriplesMap, String> markedTriples = new HashMap<TriplesMap, String>();
+		HashMap<TriplesMap, String> markedTriples = new HashMap<>();
 		
-		ArrayList<String> visited_columns = new ArrayList<String>();
-		this.ParentMapingInfoList = new HashMap<String, SPARQLGeneratorUtil.ParentMapingInfo>();
+		ArrayList<String> visited_columns = new ArrayList<>();
+		this.ParentMapingInfoList = new HashMap<>();
 		
 		// save the column predicate url and the column name to be dislayed
-		HashMap<Predicate, String> predicateList = new HashMap<Predicate, String>();
-		HashMap<String, String> columnList = new HashMap<String, String>();
+		HashMap<Predicate, String> predicateList = new HashMap<>();
+		HashMap<String, String> columnList = new HashMap<>();
 		if(columns != null && !columns.isEmpty()) {
 //			for (String k : columns) {
 //				int index = 0;
@@ -383,7 +383,7 @@ else if (currentObj instanceof RefObjectMap) {
 	 }
 	
 	private String checkParentMarked(TriplesMap triple, HashMap<TriplesMap, String> markedTriples, String var1) {
-		Stack<String> stk = new Stack<String>(); 
+		Stack<String> stk = new Stack<>(); 
 		ParentMapingInfo parentTriple = this.ParentMapingInfoList.get(triple.getSubject().getId());
 		boolean markedParent = false;
 		int count = 1;
diff --git a/karma-common/src/main/java/edu/isi/karma/er/helper/TripleStoreUtil.java b/karma-common/src/main/java/edu/isi/karma/er/helper/TripleStoreUtil.java
index 1261da51e..2aa43b00e 100644
--- a/karma-common/src/main/java/edu/isi/karma/er/helper/TripleStoreUtil.java
+++ b/karma-common/src/main/java/edu/isi/karma/er/helper/TripleStoreUtil.java
@@ -96,7 +96,7 @@ public enum RDF_Types {
 	static {
 		initialize();
 
-		mime_types = new HashMap<String, String>();
+		mime_types = new HashMap<>();
 		mime_types.put(RDF_Types.TriG.name(), "application/x-trig");
 		mime_types.put(RDF_Types.BinaryRDF.name(), "application/x-binary-rdf");
 		mime_types.put(RDF_Types.TriX.name(), "application/trix");
@@ -120,7 +120,7 @@ public static boolean initialize() {
 		HttpGet httpget;
 		HttpResponse response;
 		HttpEntity entity;
-		List<String> repositories = new ArrayList<String>();
+		List<String> repositories = new ArrayList<>();
 
 		try {
 			// query the list of repositories
@@ -225,7 +225,7 @@ public boolean testURIExists(String tripleStoreURL, String context, String uri)
 			logger.debug("query: " + queryString);
 
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("query", queryString);
 			formparams.put("queryLn", "SPARQL");
 
@@ -249,11 +249,11 @@ public Map<String, List<String>> getObjectsForSubjectsAndPredicates(String tripl
 
 		tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
 		testTripleStoreConnection(tripleStoreURL);
-		Map<String, List<String>> results = new HashMap<String,List<String>>();
-		List<String> resultSubjects = new LinkedList<String>();
-		List<String> resultPredicates = new LinkedList<String>();
-		List<String> resultObjects = new LinkedList<String>();
-		List<String> resultClasses = new LinkedList<String>();
+		Map<String, List<String>> results = new HashMap<>();
+		List<String> resultSubjects = new LinkedList<>();
+		List<String> resultPredicates = new LinkedList<>();
+		List<String> resultObjects = new LinkedList<>();
+		List<String> resultClasses = new LinkedList<>();
 		results.put("resultSubjects", resultSubjects);
 		results.put("resultPredicates", resultPredicates);
 		results.put("resultObjects", resultObjects);
@@ -339,7 +339,7 @@ public Map<String, List<String>> getObjectsForSubjectsAndPredicates(String tripl
 			logger.debug("query: " + queryString);
 
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("query", queryString);
 			formparams.put("queryLn", "SPARQL");
 
@@ -377,11 +377,11 @@ public Map<String, List<String>> getSubjectsForPredicatesAndObjects(String tripl
 
 		tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
 		testTripleStoreConnection(tripleStoreURL);
-		Map<String, List<String>> results = new HashMap<String,List<String>>();
-		List<String> resultSubjects = new LinkedList<String>();
-		List<String> resultPredicates = new LinkedList<String>();
-		List<String> resultObjects = new LinkedList<String>();
-		List<String> resultClasses = new LinkedList<String>();
+		Map<String, List<String>> results = new HashMap<>();
+		List<String> resultSubjects = new LinkedList<>();
+		List<String> resultPredicates = new LinkedList<>();
+		List<String> resultObjects = new LinkedList<>();
+		List<String> resultClasses = new LinkedList<>();
 		results.put("resultSubjects", resultSubjects);
 		results.put("resultPredicates", resultPredicates);
 		results.put("resultObjects", resultObjects);
@@ -461,7 +461,7 @@ public Map<String, List<String>> getSubjectsForPredicatesAndObjects(String tripl
 			logger.debug("query: " + queryString);
 
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("query", queryString);
 			formparams.put("queryLn", "SPARQL");
 
@@ -519,7 +519,7 @@ public void deleteMappingFromTripleStore(String tripleStoreURL, String context,
 			logger.debug("query: " + queryString);
 
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("update", queryString);
 
 			String responseString = HTTPUtil.executeHTTPPostRequest(
@@ -607,7 +607,7 @@ public String getMappingFromTripleStore(String tripleStoreURL, String context, S
 			logger.debug("query: " + queryString);
 
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("query", queryString);
 			formparams.put("queryLn", "SPARQL");
 
@@ -651,9 +651,9 @@ public HashMap<String, List<String>> getPredicatesForParentTriplesMapsWithSameCl
 		tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
 		testTripleStoreConnection(tripleStoreURL);
 
-		List<String> predicates = new LinkedList<String>();
-		List<String> matchingRefObjMaps = new LinkedList<String>();
-		List<String> otherClasses = new LinkedList<String>();
+		List<String> predicates = new LinkedList<>();
+		List<String> matchingRefObjMaps = new LinkedList<>();
+		List<String> otherClasses = new LinkedList<>();
 		try {
 
 			StringBuilder query = new StringBuilder();
@@ -691,7 +691,7 @@ public HashMap<String, List<String>> getPredicatesForParentTriplesMapsWithSameCl
 			logger.debug("query: " + queryString);
 
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("query", queryString);
 			formparams.put("queryLn", "SPARQL");
 
@@ -721,7 +721,7 @@ public HashMap<String, List<String>> getPredicatesForParentTriplesMapsWithSameCl
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 		}
-		HashMap<String, List<String>> values = new HashMap<String, List<String>>();
+		HashMap<String, List<String>> values = new HashMap<>();
 		values.put("predicates", predicates);
 		values.put("refObjectMaps", matchingRefObjMaps);
 		values.put("otherClasses", otherClasses);
@@ -734,9 +734,9 @@ public HashMap<String, List<String>> getPredicatesForTriplesMapsWithSameClass(St
 		tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
 		testTripleStoreConnection(tripleStoreURL);
 
-		List<String> predicates = new LinkedList<String>();
-		List<String> matchingPOMs = new LinkedList<String>();
-		List<String> otherClasses = new LinkedList<String>();
+		List<String> predicates = new LinkedList<>();
+		List<String> matchingPOMs = new LinkedList<>();
+		List<String> otherClasses = new LinkedList<>();
 		try {
 
 			StringBuilder query = new StringBuilder();
@@ -775,7 +775,7 @@ public HashMap<String, List<String>> getPredicatesForTriplesMapsWithSameClass(St
 			logger.debug("query: " + queryString);
 
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("query", queryString);
 			formparams.put("queryLn", "SPARQL");
 
@@ -805,7 +805,7 @@ public HashMap<String, List<String>> getPredicatesForTriplesMapsWithSameClass(St
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 		}
-		HashMap<String, List<String>> values = new HashMap<String, List<String>>();
+		HashMap<String, List<String>> values = new HashMap<>();
 		values.put("predicates", predicates);
 		values.put("predicateObjectMaps", matchingPOMs);
 		values.put("otherClasses", otherClasses);
@@ -848,11 +848,11 @@ public HashMap<String, List<String>> getMappingsWithMetadata(String TripleStoreU
 		TripleStoreURL = normalizeTripleStoreURL(TripleStoreURL);
 		testTripleStoreConnection(TripleStoreURL);
 
-		List<String> times = new ArrayList<String>();
-		List<String> names = new ArrayList<String>();
-		List<String> urls = new ArrayList<String>();
-		List<String> inputColumns = new ArrayList<String>();
-		List<String> contexts = new ArrayList<String>();
+		List<String> times = new ArrayList<>();
+		List<String> names = new ArrayList<>();
+		List<String> urls = new ArrayList<>();
+		List<String> inputColumns = new ArrayList<>();
+		List<String> contexts = new ArrayList<>();
 		try {
 
 			StringBuilder query = new StringBuilder();
@@ -872,7 +872,7 @@ public HashMap<String, List<String>> getMappingsWithMetadata(String TripleStoreU
 			logger.debug("query: " + queryString);
 
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("query", queryString);
 			formparams.put("queryLn", "SPARQL");
 
@@ -903,7 +903,7 @@ public HashMap<String, List<String>> getMappingsWithMetadata(String TripleStoreU
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 		}
-		HashMap<String, List<String>> values = new HashMap<String, List<String>>();
+		HashMap<String, List<String>> values = new HashMap<>();
 		values.put("model_publishtimes", times);
 		values.put("model_names", names);
 		values.put("model_urls", urls);
@@ -920,8 +920,8 @@ public HashMap<String, List<String>> getMappingsWithMetadata(String TripleStoreU
 	 * */
 	public HashMap<String, List<String>> fetchModelNames(String TripleStoreURL) throws KarmaException {
 
-		List<String> names = new ArrayList<String>();
-		List<String> urls = new ArrayList<String>();
+		List<String> names = new ArrayList<>();
+		List<String> urls = new ArrayList<>();
 
 		TripleStoreURL = normalizeTripleStoreURL(TripleStoreURL);
 		testTripleStoreConnection(TripleStoreURL);
@@ -930,7 +930,7 @@ public HashMap<String, List<String>> fetchModelNames(String TripleStoreURL) thro
 			String queryString = "PREFIX km-dev:<http://isi.edu/integration/karma/dev#> SELECT ?y ?z where { ?x km-dev:sourceName ?y . ?x km-dev:serviceUrl ?z . } ORDER BY ?y ?z";
 			logger.debug("query: " + queryString);
 
-			Map<String, String> formparams = new HashMap<String, String>();
+			Map<String, String> formparams = new HashMap<>();
 			formparams.put("query", queryString);
 			formparams.put("queryLn", "SPARQL");
 			String responseString = HTTPUtil.executeHTTPPostRequest(
@@ -952,7 +952,7 @@ public HashMap<String, List<String>> fetchModelNames(String TripleStoreURL) thro
 			logger.error(e.getMessage());
 			e.printStackTrace();
 		}
-		HashMap<String, List<String>> values = new HashMap<String, List<String>>();
+		HashMap<String, List<String>> values = new HashMap<>();
 		values.put("model_names", names);
 		values.put("model_urls", urls);
 		return values;
@@ -980,7 +980,7 @@ protected boolean saveToStore(HttpEntity entity, String tripleStoreURL,
 			String context, boolean replaceFlag, 
 			String rdfType, String baseURL) throws KarmaException {
 		boolean retVal = false;
-		HttpResponse response = null;
+		HttpResponse response;
 
 		tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
 		testTripleStoreConnection(tripleStoreURL);
@@ -1111,7 +1111,7 @@ public static String invokeSparqlQuery(String query, String tripleStoreUrl,
 			String acceptContentType, String contextType)
 					throws ClientProtocolException, IOException, JSONException {
 
-		Map<String, String> formParams = new HashMap<String, String>();
+		Map<String, String> formParams = new HashMap<>();
 		formParams.put("query", query);
 		formParams.put("queryLn", "SPARQL");
 
@@ -1140,7 +1140,7 @@ public static boolean create_repo(String repo_name, String repo_desc,
 		try {
 			HttpPost httppost = new HttpPost(defaultWorkbenchUrl
 					+ "/NONE/create");
-			List<NameValuePair> formparams = new ArrayList<NameValuePair>();
+			List<NameValuePair> formparams = new ArrayList<>();
 			formparams.add(new BasicNameValuePair("Repository ID", repo_name));
 			formparams
 			.add(new BasicNameValuePair("Repository title", repo_name));
@@ -1184,7 +1184,7 @@ public List<String> getContexts(String url) {
 			url = defaultModelsRepoUrl;
 		}
 		url += "/contexts";
-		List<String> graphs = new ArrayList<String>();
+		List<String> graphs = new ArrayList<>();
 
 		String responseString;
 		try {
diff --git a/karma-common/src/main/java/edu/isi/karma/imp/avro/AvroImport.java b/karma-common/src/main/java/edu/isi/karma/imp/avro/AvroImport.java
index b6a18ee2f..a4fa404be 100644
--- a/karma-common/src/main/java/edu/isi/karma/imp/avro/AvroImport.java
+++ b/karma-common/src/main/java/edu/isi/karma/imp/avro/AvroImport.java
@@ -66,14 +66,14 @@ public AvroImport (File file, String worksheetName, Workspace workspace,
 	@Override
 	public Worksheet generateWorksheet() throws JSONException, IOException,
 			KarmaException {
-		DataFileReader<Void> schemareader = new DataFileReader<Void>(file, new GenericDatumReader<Void>());
+		DataFileReader<Void> schemareader = new DataFileReader<>(file, new GenericDatumReader<Void>());
 		Schema schema = schemareader.getSchema();
 		schemareader.close();
-		DataFileReader<GenericRecord> reader = new DataFileReader<GenericRecord>(file, new GenericDatumReader<GenericRecord>(schema));
+		DataFileReader<GenericRecord> reader = new DataFileReader<>(file, new GenericDatumReader<GenericRecord>(schema));
 		ByteArrayOutputStream baos = new ByteArrayOutputStream();
 		baos.write('[');
 		baos.write('\n');
-		GenericDatumWriter<GenericRecord> writer = new GenericDatumWriter<GenericRecord>(reader.getSchema());
+		GenericDatumWriter<GenericRecord> writer = new GenericDatumWriter<>(reader.getSchema());
 		while(reader.hasNext())
 		{
 			
diff --git a/karma-common/src/main/java/edu/isi/karma/imp/csv/CSVFileExport.java b/karma-common/src/main/java/edu/isi/karma/imp/csv/CSVFileExport.java
index 4196009ed..8207b0c36 100644
--- a/karma-common/src/main/java/edu/isi/karma/imp/csv/CSVFileExport.java
+++ b/karma-common/src/main/java/edu/isi/karma/imp/csv/CSVFileExport.java
@@ -31,6 +31,7 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -64,7 +65,8 @@ public String publishCSV() throws FileNotFoundException {
 				filename;
 		logger.info("CSV file exported. Location:"
 				+ outputFile);
-		HashMap<String, String> modeledColumnTable = new HashMap<String, String>();
+
+		Map<String, String> modeledColumnTable = new HashMap<>();
 		for (SemanticType type : worksheet.getSemanticTypes().getListOfTypes()) {
 			modeledColumnTable.put(type.getHNodeId(),"");
 		}
@@ -74,8 +76,8 @@ public String publishCSV() throws FileNotFoundException {
 			return "";
 		StringBuilder sb = new StringBuilder();
 		ArrayList<Row> rows =  worksheet.getDataTable().getRows(0, numRows, SuperSelectionManager.DEFAULT_SELECTION);
-		List<HNode> sortedLeafHNodes = new ArrayList<HNode>();
-		List<String> hNodeIdList = new ArrayList<String>();
+		List<HNode> sortedLeafHNodes = new ArrayList<>();
+		List<String> hNodeIdList = new ArrayList<>();
 		worksheet.getHeaders().getSortedLeafHNodes(sortedLeafHNodes);
 		for (HNode hNode : sortedLeafHNodes) {
 			if(modeledColumnTable.containsKey(hNode.getId())) {
diff --git a/karma-common/src/main/java/edu/isi/karma/imp/csv/CSVImport.java b/karma-common/src/main/java/edu/isi/karma/imp/csv/CSVImport.java
index abbe2e7c1..63ecebd26 100644
--- a/karma-common/src/main/java/edu/isi/karma/imp/csv/CSVImport.java
+++ b/karma-common/src/main/java/edu/isi/karma/imp/csv/CSVImport.java
@@ -68,7 +68,7 @@ public Worksheet generateWorksheet() throws IOException, KarmaException {
 
         // Index for row currently being read
         int rowCount = 0;
-        Map<Integer, String> hNodeIdList = new HashMap<Integer, String>();
+        Map<Integer, String> hNodeIdList = new HashMap<>();
 
         // If no row is present for the column headers
         if (headerRowIndex == 0) {
@@ -122,7 +122,7 @@ protected BufferedReader getLineReader() throws IOException {
     private Map<Integer, String> addHeaders(Worksheet worksheet, RepFactory fac,
             String line, BufferedReader br) throws IOException {
         HTable headers = worksheet.getHeaders();
-        Map<Integer, String> headersMap = new HashMap<Integer, String>();
+        Map<Integer, String> headersMap = new HashMap<>();
 
         CSVReader reader = new CSVReader(new StringReader(line), delimiter,
                 quoteCharacter, escapeCharacter);
@@ -183,7 +183,7 @@ private boolean addRow(Worksheet worksheet, RepFactory fac, String line,
     private Map<Integer, String> addEmptyHeaders(Worksheet worksheet,
             RepFactory fac, BufferedReader br) throws IOException {
         HTable headers = worksheet.getHeaders();
-        Map<Integer, String> headersMap = new HashMap<Integer, String>();
+        Map<Integer, String> headersMap = new HashMap<>();
 
         
         br.mark(1000000);
diff --git a/karma-common/src/main/java/edu/isi/karma/imp/json/JsonImportValues.java b/karma-common/src/main/java/edu/isi/karma/imp/json/JsonImportValues.java
index 99be21003..a34fffc2f 100644
--- a/karma-common/src/main/java/edu/isi/karma/imp/json/JsonImportValues.java
+++ b/karma-common/src/main/java/edu/isi/karma/imp/json/JsonImportValues.java
@@ -35,7 +35,7 @@ public class JsonImportValues {
 	private RepFactory factory;
 	private Worksheet worksheet;
 	private JSONArray columnsJson;
-	private Map<String, Boolean> columnsCache = new HashMap<String, Boolean>();
+	private Map<String, Boolean> columnsCache = new HashMap<>();
 	public JsonImportValues(int maxNumLines, int numObjects, RepFactory factory, 
 			Worksheet worksheet, JSONArray columnsJson) {
 		this.maxNumLines = maxNumLines;
@@ -341,7 +341,7 @@ public HTable addNestedHTable(HNode hNode, String key, Row row) {
 					worksheet, factory);
 
 			// Check for all the nodes that have value and nested tables
-			Collection<Node> nodes = new ArrayList<Node>();
+			Collection<Node> nodes = new ArrayList<>();
 			worksheet.getDataTable().collectNodes(
 					hNode.getHNodePath(factory), nodes, SuperSelectionManager.DEFAULT_SELECTION);
 			for (Node node : nodes) {
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/ContextGenerator.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/ContextGenerator.java
index 024065d0a..a8f66af64 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/ContextGenerator.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/ContextGenerator.java
@@ -19,7 +19,7 @@
 public class ContextGenerator {
 	private Model model;
 	private boolean isGenerateAtIdType;
-	Map<String, Set<ContextObject>> contextMapping = new HashMap<String, Set<ContextObject>>();
+	Map<String, Set<ContextObject>> contextMapping = new HashMap<>();
 	private abstract class ContextObject {
 		public String prefix;
 		public String URI;
@@ -96,7 +96,7 @@ public JSONObject generateContext() {
 						String prefix = shortForm.substring(0, shortForm.lastIndexOf(":"));
 						Set<ContextObject> existPrefixes = contextMapping.get(postfix);
 						if (existPrefixes == null) {
-							existPrefixes = new HashSet<ContextObject>();
+							existPrefixes = new HashSet<>();
 						}
 						existPrefixes.add(new ClassContextObject(prefix, fullURI));
 						contextMapping.put(postfix, existPrefixes);
@@ -122,7 +122,7 @@ public JSONObject generateContext() {
 						String prefix = shortForm.substring(0, shortForm.lastIndexOf(":"));
 						Set<ContextObject> existPrefixes = contextMapping.get(postfix);
 						if (existPrefixes == null) {
-							existPrefixes = new HashSet<ContextObject>();
+							existPrefixes = new HashSet<>();
 						}
 						existPrefixes.add(new PredicateContextObject(prefix, fullURI, dataType));
 						contextMapping.put(postfix, existPrefixes);
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/KR2RMLWorksheetRDFGenerator.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/KR2RMLWorksheetRDFGenerator.java
index 1f256e67a..37f04eb2c 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/KR2RMLWorksheetRDFGenerator.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/KR2RMLWorksheetRDFGenerator.java
@@ -79,9 +79,9 @@ public class KR2RMLWorksheetRDFGenerator {
 	protected KR2RMLMappingColumnNameHNodeTranslator translator;
 	protected ConcurrentHashMap<String, String> hNodeToContextUriMap;
 	protected List<KR2RMLRDFWriter> outWriters;
-	protected List<String> tripleMapToKill = new ArrayList<String>();
-	protected List<String> tripleMapToStop = new ArrayList<String>();
-	protected List<String> POMToKill = new ArrayList<String>();
+	protected List<String> tripleMapToKill = new ArrayList<>();
+	protected List<String> tripleMapToStop = new ArrayList<>();
+	protected List<String> POMToKill = new ArrayList<>();
 	private Logger logger = LoggerFactory.getLogger(KR2RMLWorksheetRDFGenerator.class);
 	private URIFormatter uriFormatter;
 	private RootStrategy strategy;
@@ -156,10 +156,10 @@ private void initializeMemberVariables(Worksheet worksheet,
 		this.outputFileName = outputFileName;
 		this.errorReport = errorReport;
 		this.uriFormatter = new URIFormatter(kr2rmlMapping.getPrefixes(), errorReport);
-		this.hNodeToContextUriMap = new ConcurrentHashMap<String, String>();
+		this.hNodeToContextUriMap = new ConcurrentHashMap<>();
 		this.addColumnContextInformation = addColumnContextInformation;
 		this.translator = new KR2RMLMappingColumnNameHNodeTranslator(factory, worksheet);
-		this.outWriters = new LinkedList<KR2RMLRDFWriter>();
+		this.outWriters = new LinkedList<>();
 	}
 
 	@SuppressWarnings({ "rawtypes", "unchecked" })
@@ -173,7 +173,7 @@ public void generateRDF(boolean closeWriterAfterGeneration) throws IOException {
 
 
 
-			Map<TriplesMapGraph, List<String>> graphTriplesMapsProcessingOrder = new HashMap<TriplesMapGraph, List<String>>();
+			Map<TriplesMapGraph, List<String>> graphTriplesMapsProcessingOrder = new HashMap<>();
 			for(TriplesMapGraph graph : kr2rmlMapping.getAuxInfo().getTriplesMapGraph().getGraphs())
 			{
 				TriplesMapGraph copyGraph = graph.copyGraph();
@@ -186,7 +186,7 @@ public void generateRDF(boolean closeWriterAfterGeneration) throws IOException {
 				try{
 					DFSTriplesMapGraphDAGifier dagifier = new DFSTriplesMapGraphDAGifier();
 					
-					List<String> triplesMapsProcessingOrder = new LinkedList<String>();
+					List<String> triplesMapsProcessingOrder = new LinkedList<>();
 					triplesMapsProcessingOrder = dagifier.dagify(copyGraph, strategy);
 					graphTriplesMapsProcessingOrder.put(copyGraph, triplesMapsProcessingOrder);
 				}catch (Exception e)
@@ -214,7 +214,7 @@ public void generateRDF(boolean closeWriterAfterGeneration) throws IOException {
 			}
 			int i=1;
 			TriplesMapPlanExecutor e = new TriplesMapPlanExecutor(false);
-			Map<TriplesMap, TriplesMapWorkerPlan> triplesMapToWorkerPlan = new HashMap<TriplesMap, TriplesMapWorkerPlan>() ;
+			Map<TriplesMap, TriplesMapWorkerPlan> triplesMapToWorkerPlan = new HashMap<>() ;
 			for(TriplesMap triplesMap : kr2rmlMapping.getTriplesMapList())
 			{
 				try{
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/ShortHandURIGenerator.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/ShortHandURIGenerator.java
index 03b433dda..4fa25b444 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/ShortHandURIGenerator.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/ShortHandURIGenerator.java
@@ -8,8 +8,8 @@
 
 public class ShortHandURIGenerator {
 
-	private Set<Prefix> prefixes = new HashSet<Prefix>();
-	private Map<String, Prefix> prefixMapping = new ConcurrentHashMap<String, Prefix>();
+	private Set<Prefix> prefixes = new HashSet<>();
+	private Map<String, Prefix> prefixMapping = new ConcurrentHashMap<>();
 
 	public ShortHandURI getShortHand(String URI) {
 		Prefix p = prefixMapping.get(URI);
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/SubjectMap.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/SubjectMap.java
index a4eded493..14122a21e 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/SubjectMap.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/SubjectMap.java
@@ -36,7 +36,7 @@ public class SubjectMap extends TermMap {
 	public SubjectMap(String id) {
 		super(id);
 		this.template = new TemplateTermSet();
-		this.rdfsTypes = new ArrayList<TemplateTermSet>();
+		this.rdfsTypes = new ArrayList<>();
 		this.isBlankNode = false;
 		this.setAsSteinerTreeRootNode(false);
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/URIFormatter.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/URIFormatter.java
index 71db0f662..951f48369 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/URIFormatter.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/URIFormatter.java
@@ -38,7 +38,7 @@ public URIFormatter()
 	{
 		reportErrors = false;
 		replacePrefixesWithNamespaces = false;
-		prefixToNamespaceMap = new HashMap<String, String>();
+		prefixToNamespaceMap = new HashMap<>();
 		errorReport = null;
 	}
 
@@ -46,7 +46,7 @@ public URIFormatter(OntologyManager ontMgr, ErrorReport errorReport)
 	{
 		reportErrors = true;
 		replacePrefixesWithNamespaces = true;
-		prefixToNamespaceMap = new HashMap<String, String>();
+		prefixToNamespaceMap = new HashMap<>();
 		populatePrefixToNamespaceMap(ontMgr);
 		this.errorReport = errorReport;
 	}
@@ -54,7 +54,7 @@ public URIFormatter(List<Prefix> prefixes, ErrorReport errorReport)
 	{
 		reportErrors = true;
 		replacePrefixesWithNamespaces = true;
-		prefixToNamespaceMap = new HashMap<String, String>();
+		prefixToNamespaceMap = new HashMap<>();
 		populatePrefixToNamespaceMap(prefixes);
 		this.errorReport = errorReport;
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/formatter/KR2RMLColumnNameFormatter.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/formatter/KR2RMLColumnNameFormatter.java
index 75e926f73..ea59df28f 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/formatter/KR2RMLColumnNameFormatter.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/formatter/KR2RMLColumnNameFormatter.java
@@ -25,8 +25,8 @@
 
 public abstract class KR2RMLColumnNameFormatter {
 
-	protected Map<String, String> formattedColumnNames = new HashMap<String, String>();
-	protected Map<String, String> formattingRemovedColumnNames = new HashMap<String, String>();
+	protected Map<String, String> formattedColumnNames = new HashMap<>();
+	protected Map<String, String> formattingRemovedColumnNames = new HashMap<>();
 	
 	public String getFormattedColumnName(String columnName) {
 		if(!isFormattedColumnNameMemoized(columnName))
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMapping.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMapping.java
index dfe7c1955..ab0214fad 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMapping.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMapping.java
@@ -49,8 +49,8 @@ public KR2RMLMapping(R2RMLMappingIdentifier id, KR2RMLVersion version)
 		super(id);
 		this.version = version;
 		this.auxInfo = new KR2RMLMappingAuxillaryInformation();	
-		this.subjectMapIndex = new HashMap<String, SubjectMap>();
-		this.triplesMapIndex = new HashMap<String, TriplesMap>();
+		this.subjectMapIndex = new HashMap<>();
+		this.triplesMapIndex = new HashMap<>();
 	}
 
 	public KR2RMLVersion getVersion()
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingAuxillaryInformation.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingAuxillaryInformation.java
index 8b05e7f64..0382d91ef 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingAuxillaryInformation.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingAuxillaryInformation.java
@@ -41,11 +41,11 @@ public class KR2RMLMappingAuxillaryInformation {
 	
 	public KR2RMLMappingAuxillaryInformation() {
 		this.triplesMapGraphMerger = new TriplesMapGraphMerger();
-		this.blankNodesUriPrefixMap = new HashMap<String, String>();
-		this.blankNodesColumnCoverage = new HashMap<String, List<String>>();
-		this.columnNameToPredObjMLinks = new HashMap<String, List<PredicateObjectMap>>();
-		this.subjectMapIdToTemplateAnchor = new HashMap<String, String>();
-		this.graphNodeIdToTriplesMapIdMap = new HashMap<String, String>();
+		this.blankNodesUriPrefixMap = new HashMap<>();
+		this.blankNodesColumnCoverage = new HashMap<>();
+		this.columnNameToPredObjMLinks = new HashMap<>();
+		this.subjectMapIdToTemplateAnchor = new HashMap<>();
+		this.graphNodeIdToTriplesMapIdMap = new HashMap<>();
 	}
 
 	public TriplesMapGraphMerger getTriplesMapGraph() {
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingColumnNameHNodeTranslator.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingColumnNameHNodeTranslator.java
index bd56f2e89..a56d86c96 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingColumnNameHNodeTranslator.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/KR2RMLMappingColumnNameHNodeTranslator.java
@@ -41,8 +41,8 @@ public class KR2RMLMappingColumnNameHNodeTranslator {
 	
 	private RepFactory factory;
 	private Worksheet worksheet;
-	private Map<String, String> hNodeIdToColumnName = new HashMap<String, String>();
-	private Map<String, String> columnNameToHNodeId  = new HashMap<String, String>();
+	private Map<String, String> hNodeIdToColumnName = new HashMap<>();
+	private Map<String, String> columnNameToHNodeId  = new HashMap<>();
 	
 	public KR2RMLMappingColumnNameHNodeTranslator(RepFactory factory, Worksheet worksheet)
 	{
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/R2RMLMapping.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/R2RMLMapping.java
index 20e73d4fa..0dfb16ec5 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/R2RMLMapping.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/R2RMLMapping.java
@@ -29,8 +29,8 @@
 
 public class R2RMLMapping {
 	
-	private List<TriplesMap> triplesMapList = new ArrayList<TriplesMap>();
-	private List<Prefix> prefixes = new ArrayList<Prefix>();
+	private List<TriplesMap> triplesMapList = new ArrayList<>();
+	private List<Prefix> prefixes = new ArrayList<>();
 	private R2RMLMappingIdentifier id;
 	
 	public R2RMLMapping(R2RMLMappingIdentifier id) {
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/WorksheetR2RMLJenaModelParser.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/WorksheetR2RMLJenaModelParser.java
index f82c10240..aa006086c 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/WorksheetR2RMLJenaModelParser.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/mapping/WorksheetR2RMLJenaModelParser.java
@@ -133,7 +133,7 @@ public KR2RMLMapping parse() throws IOException, KarmaException, JSONException
 		Property modelVersionNameProp = model.getProperty(Uris.KM_MODEL_VERSION_URI);
 		Statement s = model.getProperty(mappingResource, modelVersionNameProp);
 		
-		KR2RMLVersion version = null;
+		KR2RMLVersion version;
 		try 
 		{
 			version = new KR2RMLVersion(s.getString());
@@ -172,7 +172,7 @@ public KR2RMLMapping parse() throws IOException, KarmaException, JSONException
 	private void createGraphNodeToTriplesNodeMap(KR2RMLMapping kr2rmlMapping) throws FileNotFoundException, UnsupportedEncodingException{
 		
 		StmtIterator itr = model.listStatements(null, model.getProperty(Uris.KM_NODE_ID_URI), (RDFNode)null);
-		Resource subject = null;
+		Resource subject;
 		Map<String,String> graphNodeIdToTriplesMapIdMap = kr2rmlMapping.getAuxInfo().getGraphNodeIdToTriplesMapIdMap();
 		while (itr.hasNext()) {
 			Statement subjMapToNodeIdStmt = itr.next();
@@ -193,7 +193,7 @@ private SourceTypes getSourceType(Resource mappingResource)
 	{
 		Property sourceNameProp = model.getProperty(Uris.KM_SOURCE_TYPE_URI);
 		Statement s = model.getProperty(mappingResource, sourceNameProp);
-		String sourceType = null;
+		String sourceType;
 		if(s != null)
 		{
 			RDFNode node = s.getObject();
@@ -289,7 +289,7 @@ private void createPredicateObjectMaps(Resource mappingResource, KR2RMLMapping k
 	}
 
 	private List<Resource> createSubjectMaps(Resource mappingResource, KR2RMLMapping kr2rmlMapping) throws JSONException {
-		List<Resource> subjectMapResources = new ArrayList<Resource>();
+		List<Resource> subjectMapResources = new ArrayList<>();
 		Property hasTrMapUri = model.getProperty(Uris.KM_HAS_TRIPLES_MAP_URI);
 		
 		// Get all the triple maps
@@ -476,7 +476,7 @@ private void addColumnNameToPredObjectMapLink(ObjectMap objMap, PredicateObjectM
 				List<PredicateObjectMap> existingPomList = kr2rmlMapping.getAuxInfo().
 						getColumnNameToPredObjLinks().get(columnNameWithoutFormatting);  
 				if (existingPomList == null) {
-					existingPomList = new ArrayList<PredicateObjectMap>();
+					existingPomList = new ArrayList<>();
 				}
 				existingPomList.add(pom);
 				kr2rmlMapping.getAuxInfo().getColumnNameToPredObjLinks().put(columnNameWithoutFormatting, existingPomList);
@@ -514,7 +514,7 @@ private SubjectMap addSubjectMapForTripleMap(Resource trMapRes, KR2RMLMapping kr
 				String template = templNode.toString();
 				subjTemplTermSet = TemplateTermSetBuilder.constructTemplateTermSetFromR2rmlTemplateString(
 						template, kr2rmlMapping.getColumnNameFormatter());
-				List<String> columnsCovered = new LinkedList<String>();
+				List<String> columnsCovered = new LinkedList<>();
 				for(TemplateTerm term : subjTemplTermSet.getAllColumnNameTermElements())
 				{
 					columnsCovered.add(term.getTemplateTermValue());
@@ -579,7 +579,7 @@ private void calculateColumnNodesCoveredByBlankNodes(KR2RMLMapping kr2rmlMapping
 		for (Resource subjMapRes:subjectMapResources) {
 			
 			if (model.contains(subjMapRes, termTypeProp, blankNodeRes)) {
-				List<String> columnsCovered = new ArrayList<String>();
+				List<String> columnsCovered = new ArrayList<>();
 				Resource blankNodeSubjRes = blankNodeSubjMapItr.next();
 				
 				SubjectMap subjMap = kr2rmlMapping.getSubjectMapIndex().get(blankNodeSubjRes.getId().getLabelString());
@@ -590,7 +590,7 @@ private void calculateColumnNodesCoveredByBlankNodes(KR2RMLMapping kr2rmlMapping
 							bnodePrefixItr.next().toString());
 				}
 				
-				TriplesMap mytm = null;
+				TriplesMap mytm;
 				for(TriplesMap tm : kr2rmlMapping.getTriplesMapList())
 				{
 					if(tm.getSubject().getId().equalsIgnoreCase(subjMap.getId()))
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/ConstantPredicateObjectMappingPlan.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/ConstantPredicateObjectMappingPlan.java
index f96f3314a..998bf3b00 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/ConstantPredicateObjectMappingPlan.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/ConstantPredicateObjectMappingPlan.java
@@ -49,7 +49,7 @@ protected void generateInternal(TemplateTermSet subjectMapTemplate,
 			throws HNodeNotFoundKarmaException {
 		
 		this.pom = pom;
-		combinedSubjectObjectTermsToPaths = new HashMap<ColumnTemplateTerm, HNodePath>();
+		combinedSubjectObjectTermsToPaths = new HashMap<>();
 		combinedSubjectObjectTermsToPaths.putAll(subjectTermsToPaths);
 		this.isLiteral = true;
 		TemplateTermSet literalTemplate = pom.getObject().getRdfLiteralType();
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/DFSTriplesMapGraphDAGifier.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/DFSTriplesMapGraphDAGifier.java
index 37c4b02b2..fceae77c5 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/DFSTriplesMapGraphDAGifier.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/DFSTriplesMapGraphDAGifier.java
@@ -37,15 +37,15 @@ public class DFSTriplesMapGraphDAGifier implements TriplesMapGraphDAGifier {
 	@Override
 	public List<String> dagify(TriplesMapGraph graph, RootStrategy rootStrategy) {
 	
-		HashSet<String> triplesMapsIds = new HashSet<String>();
+		HashSet<String> triplesMapsIds = new HashSet<>();
 
 		if(graph.getTriplesMapIds().isEmpty())
 		{
-			return new LinkedList<String>();
+			return new LinkedList<>();
 		}
 		if(graph.getTriplesMapIds().size() == 1)
 		{
-			List<String> results = new LinkedList<String>();
+			List<String> results = new LinkedList<>();
 			results.addAll(graph.getTriplesMapIds());
 			return results;
 		}
@@ -69,10 +69,10 @@ public List<String> dagify(TriplesMapGraph graph, RootStrategy rootStrategy) {
 		return spilledNodes;
 	}
 
-	private List<String> cleanGraph(HashSet<String> triplesMapsIds,
+	private List<String> cleanGraph(Set<String> triplesMapsIds,
 			TriplesMapGraph newGraph, String rootTriplesMapId) {
 		boolean modifications = true;
-		List<String> spilledTriplesMaps = new LinkedList<String>();
+		List<String> spilledTriplesMaps = new LinkedList<>();
 		
 		while(!triplesMapsIds.isEmpty() && modifications)
 		{
@@ -94,7 +94,7 @@ private List<String> cleanGraph(HashSet<String> triplesMapsIds,
 				}
 				if(links.size() <= 1 || allLinksAreIncoming(triplesMapId, links))
 				{
-					List<TriplesMapLink> tempLinks = new LinkedList<TriplesMapLink>();
+					List<TriplesMapLink> tempLinks = new LinkedList<>();
 					tempLinks.addAll(links);
 					// leave the root alone unless it's empty!
 					if(triplesMapId.compareTo(rootTriplesMapId) == 0)
@@ -149,8 +149,8 @@ private void dfs(TriplesMapGraph graph, String rootTriplesMapId, Set<String> vis
 		final String localTriplesMapId = triplesMapId;
 		visited.add(triplesMapId);
 		List<TriplesMapLink> links = graph.getAllNeighboringTriplesMap(triplesMapId);
-		List<String> nodesToVisit = new LinkedList<String>();
-		List<TriplesMapLink> sortedLinks = new LinkedList<TriplesMapLink>();
+		List<String> nodesToVisit = new LinkedList<>();
+		List<TriplesMapLink> sortedLinks = new LinkedList<>();
 		sortedLinks.addAll(links);
 		Collections.sort(sortedLinks, new Comparator<TriplesMapLink>(){
 
@@ -206,7 +206,7 @@ else if(o1IsSource && !o2IsSource)
 	}
 	private void dfs(TriplesMapGraph graph, String rootTriplesMapId)
 	{
-		Set<String> visited = new HashSet<String>();
+		Set<String> visited = new HashSet<>();
 		dfs(graph, rootTriplesMapId, visited, rootTriplesMapId);
 	}
 
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/PredicateObjectMappingPlan.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/PredicateObjectMappingPlan.java
index 2e20f84cd..898472db4 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/PredicateObjectMappingPlan.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/PredicateObjectMappingPlan.java
@@ -69,13 +69,13 @@ protected void generateInternal(TemplateTermSet subjectMapTemplate,
 			throws HNodeNotFoundKarmaException {
 		
 		this.pom = pom;
-		combinedSubjectObjectTermsToPaths = new HashMap<ColumnTemplateTerm, HNodePath>();
+		combinedSubjectObjectTermsToPaths = new HashMap<>();
 		combinedSubjectObjectTermsToPaths.putAll(subjectTermsToPaths);
-		Map<ColumnTemplateTerm, HNodePath> objectTermsToPaths = new HashMap<ColumnTemplateTerm, HNodePath>();
+		Map<ColumnTemplateTerm, HNodePath> objectTermsToPaths = new HashMap<>();
 		
 		populateTermsToPathForSubject(objectTermsToPaths, objectTemplateTermSetPopulator.getTerms());
 		combinedSubjectObjectTermsToPaths.putAll(objectTermsToPaths);
-		LinkedList<ColumnTemplateTerm> objectColumnTerms = new LinkedList<ColumnTemplateTerm>();
+		LinkedList<ColumnTemplateTerm> objectColumnTerms = new LinkedList<>();
 		objectColumnTerms.addAll(objectTemplateTermSetPopulator.getTerms().getAllColumnNameTermElements());
 		complicatedPlan = new SinglyAnchoredTemplateTermSetPopulatorPlan(combinedSubjectObjectTermsToPaths, objectColumnTerms, subjectMapTemplate.getAllColumnNameTermElements(), selection);
 		generatePredicatesForPom(pom);
@@ -83,14 +83,14 @@ protected void generateInternal(TemplateTermSet subjectMapTemplate,
 
 	protected void generatePredicatesForPom(PredicateObjectMap pom) throws HNodeNotFoundKarmaException {
 		this.pom = pom;
-		List<ColumnTemplateTerm> subjectAndObjectTemplateTerms = new LinkedList<ColumnTemplateTerm>();
+		List<ColumnTemplateTerm> subjectAndObjectTemplateTerms = new LinkedList<>();
 		subjectAndObjectTemplateTerms.addAll(this.combinedSubjectObjectTermsToPaths.keySet());
-		LinkedList<ColumnTemplateTerm> predicateColumnTemplateTerms = new LinkedList<ColumnTemplateTerm>();
+		LinkedList<ColumnTemplateTerm> predicateColumnTemplateTerms = new LinkedList<>();
 		predicateColumnTemplateTerms.addAll(pom.getPredicate().getTemplate().getAllColumnNameTermElements());
 		predicateTemplateTermSetPopulator = new TemplateTermSetPopulator(pom.getPredicate().getTemplate(), new StringBuilder(), uriFormatter, true, true);
-		Map<ColumnTemplateTerm, HNodePath> combinedSubjectObjectPredicateTermsToPaths = new HashMap<ColumnTemplateTerm, HNodePath>();
+		Map<ColumnTemplateTerm, HNodePath> combinedSubjectObjectPredicateTermsToPaths = new HashMap<>();
 		combinedSubjectObjectPredicateTermsToPaths.putAll(combinedSubjectObjectTermsToPaths);
-		Map<ColumnTemplateTerm, HNodePath> predicateTermsToPaths = new HashMap<ColumnTemplateTerm, HNodePath>();
+		Map<ColumnTemplateTerm, HNodePath> predicateTermsToPaths = new HashMap<>();
 		
 		populateTermsToPathForSubject(predicateTermsToPaths, pom.getPredicate().getTemplate());
 		combinedSubjectObjectTermsToPaths.putAll(predicateTermsToPaths);
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/SubjectMapPlan.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/SubjectMapPlan.java
index 60e3fce47..c777804af 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/SubjectMapPlan.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/SubjectMapPlan.java
@@ -55,7 +55,7 @@ public SubjectMapPlan(TriplesMap triplesMap, KR2RMLMapping kr2rmlMapping,
 	}
 	public SubjectMap configureSubjectMapPlan(TriplesMap triplesMap)
 			throws HNodeNotFoundKarmaException {
-		subjectTermsToPaths = new HashMap<ColumnTemplateTerm, HNodePath>();
+		subjectTermsToPaths = new HashMap<>();
 		SubjectMap subjMap = triplesMap.getSubject();
 		subjectMapTTSPopulator = generateTemplateTermSetPopulatorForSubjectMap(subjMap);
 		populateTermsToPathForSubject(subjectTermsToPaths, subjectMapTTSPopulator.getTerms());
@@ -65,7 +65,7 @@ public SubjectMap configureSubjectMapPlan(TriplesMap triplesMap)
 	
 	public List<PopulatedTemplateTermSet> execute(Row r)
 	{
-		List<PopulatedTemplateTermSet> subjects = new LinkedList<PopulatedTemplateTermSet>();
+		List<PopulatedTemplateTermSet> subjects = new LinkedList<>();
 		subjects.addAll(subjectMapTTSPopulator.populate(r, subjectPlan));
 		return subjects;
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMap.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMap.java
index 3ec2c6637..1c26d5f20 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMap.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMap.java
@@ -32,7 +32,7 @@ public class TriplesMap {
 	
 	private final String id;
 	private SubjectMap subject;
-	private List<PredicateObjectMap> predicateObjectMaps = new ArrayList<PredicateObjectMap>();
+	private List<PredicateObjectMap> predicateObjectMaps = new ArrayList<>();
 	private final static String TRIPLES_MAP_PREFIX = "TriplesMap";
 	
 	public TriplesMap(String id, SubjectMap subject) {
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapGraph.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapGraph.java
index 9b629c028..f6ef00be7 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapGraph.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapGraph.java
@@ -35,9 +35,9 @@ public class TriplesMapGraph {
 	private Map<String, TriplesMap> triplesMapIndex;
 
 	public TriplesMapGraph() {
-		this.links = new HashSet<TriplesMapLink>();
-		this.neighboringTriplesMapCache = new HashMap<String, List<TriplesMapLink>>();
-		this.triplesMapIndex = new HashMap<String, TriplesMap>();
+		this.links = new HashSet<>();
+		this.neighboringTriplesMapCache = new HashMap<>();
+		this.triplesMapIndex = new HashMap<>();
 	}
 
 	public Set<TriplesMapLink> getLinks() {
@@ -49,7 +49,7 @@ public void addTriplesMap(TriplesMap triplesMap)
 		triplesMapIndex.put(triplesMap.getId(), triplesMap);
 		List<TriplesMapLink> neighbouringLinks = neighboringTriplesMapCache.get(triplesMap.getId());
 		if (neighbouringLinks == null) {
-			neighbouringLinks = new LinkedList<TriplesMapLink>();
+			neighbouringLinks = new LinkedList<>();
 			neighboringTriplesMapCache.put(triplesMap.getId(), neighbouringLinks);
 		}
 	}
@@ -77,7 +77,7 @@ private void updateCache(TriplesMapLink link) {
 		// Add source neighboring links to the cache
 		List<TriplesMapLink> sourceNeighbouringLinks = neighboringTriplesMapCache.get(link.getSourceMap().getId());
 		if (sourceNeighbouringLinks == null) {
-			sourceNeighbouringLinks = new LinkedList<TriplesMapLink>();
+			sourceNeighbouringLinks = new LinkedList<>();
 		}
 		sourceNeighbouringLinks.add(link);
 		triplesMapIndex.put(link.getSourceMap().getId(),link.getSourceMap());
@@ -86,7 +86,7 @@ private void updateCache(TriplesMapLink link) {
 		// Add target neighboring links to the cache
 		List<TriplesMapLink> targetNeighbouringLinks = neighboringTriplesMapCache.get(link.getTargetMap().getId());
 		if (targetNeighbouringLinks == null) {
-			targetNeighbouringLinks = new LinkedList<TriplesMapLink>();
+			targetNeighbouringLinks = new LinkedList<>();
 		}
 		targetNeighbouringLinks.add(link);
 		triplesMapIndex.put(link.getTargetMap().getId(),link.getTargetMap());
@@ -95,13 +95,13 @@ private void updateCache(TriplesMapLink link) {
 
 	public List<TriplesMapLink> getAllNeighboringTriplesMap(String triplesMapId) {
 		if (neighboringTriplesMapCache.get(triplesMapId) == null)
-			return new LinkedList<TriplesMapLink>();
+			return new LinkedList<>();
 
 		return neighboringTriplesMapCache.get(triplesMapId);
 	}
 
 	public List<String> removeLink(TriplesMapLink link) {
-		List<String> removedTriplesMaps = new LinkedList<String>();
+		List<String> removedTriplesMaps = new LinkedList<>();
 		links.remove(link);
 		removedTriplesMaps.addAll(removeLinkFromCache(link, link.getTargetMap().getId()));
 		removedTriplesMaps.addAll(removeLinkFromCache(link, link.getSourceMap().getId()));
@@ -109,7 +109,7 @@ public List<String> removeLink(TriplesMapLink link) {
 	}
 
 	private List<String> removeLinkFromCache(TriplesMapLink link, String mapId) {
-		List<String> removedTriplesMaps = new LinkedList<String>();
+		List<String> removedTriplesMaps = new LinkedList<>();
 		List<TriplesMapLink> targetLinks = neighboringTriplesMapCache.get(mapId);
 		targetLinks.remove(link);
 		if(targetLinks.isEmpty())
@@ -137,7 +137,7 @@ public TriplesMap getTriplesMap(String triplesMapId)
 
 	public List<String> removeTriplesMap(String triplesMapId) {
 
-		List<String> removedTriplesMaps = new LinkedList<String>();
+		List<String> removedTriplesMaps = new LinkedList<>();
 		List<TriplesMapLink> targetLinks = neighboringTriplesMapCache.get(triplesMapId);
 		if(targetLinks != null)
 		{
@@ -187,7 +187,7 @@ public TriplesMapGraph shallowCopyGraph() {
 		newGraph.links.addAll(links);
 		for (Entry<String, List<TriplesMapLink>> entry : neighboringTriplesMapCache.entrySet()) {
 			
-			newGraph.neighboringTriplesMapCache.put(entry.getKey(), new LinkedList<TriplesMapLink>(entry.getValue()));
+			newGraph.neighboringTriplesMapCache.put(entry.getKey(), new LinkedList<>(entry.getValue()));
 		}
 		newGraph.triplesMapIndex.putAll(triplesMapIndex);
 		return newGraph;
@@ -196,8 +196,8 @@ public void killTriplesMap(List<String> tripleMapToKill, RootStrategy strategy)
 		if (tripleMapToKill.isEmpty()) {
 			return;
 		}
-		List<TriplesMapLink> remainedLinks = new LinkedList<TriplesMapLink>();
-		Set<String> visited = new HashSet<String>();
+		List<TriplesMapLink> remainedLinks = new LinkedList<>();
+		Set<String> visited = new HashSet<>();
 		killTriplesMap(strategy.findRoot(this), tripleMapToKill, remainedLinks, visited);
 		links.clear();
 		neighboringTriplesMapCache.clear();
@@ -209,7 +209,7 @@ public void killTriplesMap(List<String> tripleMapToKill, RootStrategy strategy)
 
 	private void killTriplesMap(String rootId, List<String> tripleMapToKill, List<TriplesMapLink> remainedLinks, Set<String> visited) {
 		visited.add(rootId);
-		Set<String> next = new HashSet<String>();
+		Set<String> next = new HashSet<>();
 		List<TriplesMapLink> links = neighboringTriplesMapCache.get(rootId);
 		if (links != null) {
 			for (TriplesMapLink link : links) {
@@ -230,8 +230,8 @@ public void killPredicateObjectMap(List<String> POMToKill, RootStrategy strategy
 		if (POMToKill.isEmpty()) {
 			return;
 		}
-		List<TriplesMapLink> remainedLinks = new LinkedList<TriplesMapLink>();
-		Set<String> visited = new HashSet<String>();
+		List<TriplesMapLink> remainedLinks = new LinkedList<>();
+		Set<String> visited = new HashSet<>();
 		killPredicateObjectMap(strategy.findRoot(this), POMToKill, remainedLinks, visited);
 		links.clear();
 		neighboringTriplesMapCache.clear();
@@ -243,7 +243,7 @@ public void killPredicateObjectMap(List<String> POMToKill, RootStrategy strategy
 
 	private void killPredicateObjectMap(String rootId, List<String> POMToKill, List<TriplesMapLink> remainedLinks, Set<String> visited) {
 		visited.add(rootId);
-		Set<String> next = new HashSet<String>();
+		Set<String> next = new HashSet<>();
 		List<TriplesMapLink> links = neighboringTriplesMapCache.get(rootId);
 		if (links != null) {
 			for (TriplesMapLink link : links) {
@@ -264,8 +264,8 @@ public void stopTriplesMap(List<String> tripleMapToStop, RootStrategy strategy)
 		if (tripleMapToStop.isEmpty()) {
 			return;
 		}
-		List<TriplesMapLink> remainedLinks = new LinkedList<TriplesMapLink>();
-		Set<String> visited = new HashSet<String>();
+		List<TriplesMapLink> remainedLinks = new LinkedList<>();
+		Set<String> visited = new HashSet<>();
 		stopTriplesMap(strategy.findRoot(this), tripleMapToStop, remainedLinks, visited);
 		links.clear();
 		neighboringTriplesMapCache.clear();
@@ -280,7 +280,7 @@ private void stopTriplesMap(String rootId, List<String> tripleMapToStop, List<Tr
 		if (tripleMapToStop.contains(rootId)) {
 			return;
 		}
-		Set<String> next = new HashSet<String>();
+		Set<String> next = new HashSet<>();
 		List<TriplesMapLink> links = neighboringTriplesMapCache.get(rootId);
 		if (links != null) {
 			for (TriplesMapLink link : links) {
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapGraphMerger.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapGraphMerger.java
index bedd71790..fdf9b0d5e 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapGraphMerger.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapGraphMerger.java
@@ -30,7 +30,7 @@ public class TriplesMapGraphMerger {
 	
 	public TriplesMapGraphMerger()
 	{
-		graphs = new LinkedList<TriplesMapGraph>();
+		graphs = new LinkedList<>();
 	}
 	
 	public TriplesMapGraph getTriplesMapGraph(String triplesMapId)
@@ -60,7 +60,7 @@ public void addLink(TriplesMapLink link)
 			graphs.add(graph);
 			return;
 		}
-		List<TriplesMapGraph> graphsForMerging = new LinkedList<TriplesMapGraph>();
+		List<TriplesMapGraph> graphsForMerging = new LinkedList<>();
 		Iterator<TriplesMapGraph> iter = graphs.iterator();
 		while(iter.hasNext())
 		{
@@ -75,7 +75,7 @@ public void addLink(TriplesMapLink link)
 		}
 		iter = graphsForMerging.iterator();
 		TriplesMapGraph mergedGraph = iter.next();
-		TriplesMapGraph graphToMerge = null;
+		TriplesMapGraph graphToMerge;
 		while(iter.hasNext())
 		{
 			graphToMerge = iter.next();
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapPlanExecutor.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapPlanExecutor.java
index d1e69fcc4..3759953ad 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapPlanExecutor.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapPlanExecutor.java
@@ -61,8 +61,7 @@ public ErrorReport execute(final TriplesMapPlan plan)
 			
 			if(submitPlansIndividually)
 			{
-				List<Future<Boolean>> results = new LinkedList<Future<Boolean>>();
-				results = service.invokeAll(plan.workers);
+				List<Future<Boolean>> results = service.invokeAll(plan.workers);
 				for(Future<Boolean> result : results)
 				{
 					result.get(1, TimeUnit.MINUTES);
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapPlanGenerator.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapPlanGenerator.java
index 1bb195925..75566e3a4 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapPlanGenerator.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapPlanGenerator.java
@@ -40,7 +40,7 @@ public class TriplesMapPlanGenerator {
 	private static Logger LOG = LoggerFactory.getLogger(TriplesMapPlanGenerator.class);
 	
 	private Map<TriplesMap, TriplesMapWorkerPlan> triplesMapToWorkerPlan;
-	private Set<String> unprocessedTriplesMapsIds = new HashSet<String>();
+	private Set<String> unprocessedTriplesMapsIds = new HashSet<>();
 	private Row r;
 	private List<KR2RMLRDFWriter> outWriters;
 	
@@ -53,8 +53,8 @@ public TriplesMapPlanGenerator(Map<TriplesMap, TriplesMapWorkerPlan> triplesMapT
 
 	public TriplesMapPlan generatePlan(TriplesMapGraphMerger tmf, RootStrategy strategy)
 	{
-		List<TriplesMapWorker> workers = new LinkedList<TriplesMapWorker>();
-		Map<String, List<PopulatedTemplateTermSet>>triplesMapSubjects = new ConcurrentHashMap<String, List<PopulatedTemplateTermSet>>();
+		List<TriplesMapWorker> workers = new LinkedList<>();
+		Map<String, List<PopulatedTemplateTermSet>>triplesMapSubjects = new ConcurrentHashMap<>();
 		TriplesMapPlan plan = new TriplesMapPlan(workers, r, triplesMapSubjects);
 		
 		List<TriplesMapGraph> graphs = tmf.getGraphs();
@@ -68,8 +68,8 @@ public TriplesMapPlan generatePlan(TriplesMapGraphMerger tmf, RootStrategy strat
 
 	public TriplesMapPlan generatePlan(TriplesMapGraph graph, List<String> triplesMapProcessingOrder, RootStrategy strategy)
 	{
-		List<TriplesMapWorker> workers = new LinkedList<TriplesMapWorker>();
-		Map<String, List<PopulatedTemplateTermSet>>triplesMapSubjects = new ConcurrentHashMap<String, List<PopulatedTemplateTermSet>>();
+		List<TriplesMapWorker> workers = new LinkedList<>();
+		Map<String, List<PopulatedTemplateTermSet>>triplesMapSubjects = new ConcurrentHashMap<>();
 		TriplesMapPlan plan = new TriplesMapPlan(workers, r, triplesMapSubjects);
 		Map<TriplesMap, TriplesMapWorker> mapToWorker = generatePlan(graph, plan, strategy);
 		for(String triplesMapId : triplesMapProcessingOrder)
@@ -100,7 +100,7 @@ private Map<TriplesMap, TriplesMapWorker> generatePlan(TriplesMapGraph graph, Tr
 	{
 		unprocessedTriplesMapsIds.addAll(graph.getTriplesMapIds());
 		//add strategy
-		Map<TriplesMap, TriplesMapWorker> mapToWorker = new HashMap<TriplesMap, TriplesMapWorker>();
+		Map<TriplesMap, TriplesMapWorker> mapToWorker = new HashMap<>();
 		if(strategy == null)
 		{
 			strategy = new SteinerTreeRootStrategy(new WorksheetDepthRootStrategy());
@@ -141,7 +141,7 @@ private void generateTriplesMapWorker(
 		List<TriplesMapLink> links = graph.getAllNeighboringTriplesMap(map.getId());
 		
 		
-		List<TriplesMapWorker> workersDependentOn = new LinkedList<TriplesMapWorker>();
+		List<TriplesMapWorker> workersDependentOn = new LinkedList<>();
 		for(TriplesMapLink link : links)
 		{
 			if((link.getSourceMap() == map && !link.isFlipped()) || (link.getTargetMap() == map && link.isFlipped()))
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapWorker.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapWorker.java
index 5691ff447..916c34f5e 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapWorker.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapWorker.java
@@ -54,7 +54,7 @@ public TriplesMapWorker(TriplesMap triplesMap, List<TriplesMapWorker> workersDep
 		this.latch = new CountDownLatch(workersDependentOn.size());
 		this.triplesMap = triplesMap;
 		this.plan = plan;
-		this.dependentTriplesMapWorkers = new LinkedList<TriplesMapWorker>();
+		this.dependentTriplesMapWorkers = new LinkedList<>();
 		this.r = r;
 		this.outWriters = outWriters;
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapWorkerPlan.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapWorkerPlan.java
index d4feeb402..a7112d643 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapWorkerPlan.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/planning/TriplesMapWorkerPlan.java
@@ -88,7 +88,7 @@ public void generate() throws HNodeNotFoundKarmaException
 	{ 
 		subjectMapPlan = new SubjectMapPlan(triplesMap, kr2rmlMapping,uriFormatter, factory, translator, selection);
 		
-		internalLinksPlans = new LinkedList<PredicateObjectMappingPlan>();
+		internalLinksPlans = new LinkedList<>();
 		
 		List<TriplesMapLink> links = null;
 		for(TriplesMapGraph graph : graphTriplesMapsProcessingOrder.keySet())
@@ -106,7 +106,7 @@ public void generate() throws HNodeNotFoundKarmaException
 						link.getTargetMap().getId().compareTo(triplesMap.getId()) == 0 && link.isFlipped())
 				{
 					PredicateObjectMap pom = link.getPredicateObjectMapLink();
-					TriplesMap objectTriplesMap = null;
+					TriplesMap objectTriplesMap;
 					if(link.isFlipped())
 					{
 						objectTriplesMap = link.getSourceMap();
@@ -132,8 +132,8 @@ public void generate() throws HNodeNotFoundKarmaException
 			}
 		}
 		
-		columnLinksPlans = new LinkedList<PredicateObjectMappingPlan>();
-		constantLinksPlans = new LinkedList<PredicateObjectMappingPlan>();
+		columnLinksPlans = new LinkedList<>();
+		constantLinksPlans = new LinkedList<>();
 		// Subject 
 		// Generate triples for specifying the types
 		for (TemplateTermSet typeTerm:triplesMap.getSubject().getRdfsType()) {
@@ -163,7 +163,7 @@ public void generate() throws HNodeNotFoundKarmaException
 				continue;
 			}
 			try{
-				PredicateObjectMappingPlan pomPlan = null;
+				PredicateObjectMappingPlan pomPlan;
 				if(pom.getObject().getTemplate().getAllColumnNameTermElements().isEmpty())
 				{
 					pomPlan = new ConstantPredicateObjectMappingPlan(subjectMapPlan.getTemplate(), pom, kr2rmlMapping,subjectMapPlan.getSubjectTermsToPaths(), uriFormatter, factory, translator, selection);
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/ConstantTemplateTermSetPopulatorPlan.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/ConstantTemplateTermSetPopulatorPlan.java
index 9aab9b16f..691712fa2 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/ConstantTemplateTermSetPopulatorPlan.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/ConstantTemplateTermSetPopulatorPlan.java
@@ -17,11 +17,11 @@ public ConstantTemplateTermSetPopulatorPlan(SuperSelection sel) {
 
 	public Map<PopulatedTemplateTermSet, List<PartiallyPopulatedTermSet>> execute(Row topRow, List<PopulatedTemplateTermSet> anchors)
 	{
-		Map<PopulatedTemplateTermSet, List<PartiallyPopulatedTermSet>> results = new HashMap<PopulatedTemplateTermSet, List<PartiallyPopulatedTermSet>>();
+		Map<PopulatedTemplateTermSet, List<PartiallyPopulatedTermSet>> results = new HashMap<>();
 		
 			for(PopulatedTemplateTermSet anchor: anchors)
 			{
-				List<PartiallyPopulatedTermSet> references = new LinkedList<PartiallyPopulatedTermSet>();
+				List<PartiallyPopulatedTermSet> references = new LinkedList<>();
 				references.add(new PartiallyPopulatedTermSet());
 				results.put(anchor, references);
 			}
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/DoublyAnchoredTemplateTermSetPopulator.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/DoublyAnchoredTemplateTermSetPopulator.java
index 22dcc1d36..1e897f911 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/DoublyAnchoredTemplateTermSetPopulator.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/DoublyAnchoredTemplateTermSetPopulator.java
@@ -48,14 +48,14 @@ public List<PartiallyPopulatedTermSet> execute(Row topRow, PopulatedTemplateTerm
 		
 		if(columnTerms == null || columnTerms.isEmpty())
 		{
-			List<PartiallyPopulatedTermSet> predicates = new LinkedList<PartiallyPopulatedTermSet>();
+			List<PartiallyPopulatedTermSet> predicates = new LinkedList<>();
 			predicates.add(new PartiallyPopulatedTermSet());
 			return predicates;
 		}
 		List<PartiallyPopulatedTermSet> independentResults = this.execute(topRow);
 		
 		
-		List<List<PartiallyPopulatedTermSet>> toMerge = new LinkedList<List<PartiallyPopulatedTermSet>>();
+		List<List<PartiallyPopulatedTermSet>> toMerge = new LinkedList<>();
 		if(!independentResults.isEmpty())
 		{
 			toMerge.add(independentResults);
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/DynamicTemplateTermSetPopulatorStrategy.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/DynamicTemplateTermSetPopulatorStrategy.java
index a6d18b3fa..27353bc1b 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/DynamicTemplateTermSetPopulatorStrategy.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/DynamicTemplateTermSetPopulatorStrategy.java
@@ -40,7 +40,7 @@ public DynamicTemplateTermSetPopulatorStrategy(HNodePath targetPath, HNodePath p
 	}
 	@Override
 	public Collection<Node> getNodes(Row topRow, Row currentRow, SuperSelection sel) {
-		Collection<Node> nodes = new LinkedList<Node>();
+		Collection<Node> nodes = new LinkedList<>();
 		currentRow.collectNodes(relativePath, nodes, sel);
 		return nodes;
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/MemoizedTemplateTermSetPopulatorStrategy.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/MemoizedTemplateTermSetPopulatorStrategy.java
index fbb3086b2..2324f303b 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/MemoizedTemplateTermSetPopulatorStrategy.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/MemoizedTemplateTermSetPopulatorStrategy.java
@@ -47,7 +47,7 @@ public Collection<Node> getNodes(Row topRow, Row currentRow, SuperSelection sel)
 			{
 				if(nodes == null || topRow != this.topRow)
 				{
-					nodes = new LinkedList<Node>();
+					nodes = new LinkedList<>();
 					topRow.collectNodes(path, nodes, sel);
 					this.topRow = topRow;
 				}
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/PartiallyPopulatedTermSet.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/PartiallyPopulatedTermSet.java
index 8d44dc402..f03d8429d 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/PartiallyPopulatedTermSet.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/PartiallyPopulatedTermSet.java
@@ -31,11 +31,11 @@ public class PartiallyPopulatedTermSet {
 	
 	PartiallyPopulatedTermSet()
 	{
-		termsToNode = new HashMap<ColumnTemplateTerm, Node>();
+		termsToNode = new HashMap<>();
 	}
 	PartiallyPopulatedTermSet(ColumnTemplateTerm term, Node node)
 	{
-		termsToNode = new HashMap<ColumnTemplateTerm, Node>();
+		termsToNode = new HashMap<>();
 		termsToNode.put(term, node);
 	}
 	
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/SinglyAnchoredTemplateTermSetPopulatorPlan.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/SinglyAnchoredTemplateTermSetPopulatorPlan.java
index 137eb6bb2..5620dcccb 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/SinglyAnchoredTemplateTermSetPopulatorPlan.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/SinglyAnchoredTemplateTermSetPopulatorPlan.java
@@ -52,15 +52,15 @@ private void generateComplicated() {
 		{
 			return;
 		}
-		nestedPlans = new HashMap<ColumnTemplateTerm, TemplateTermSetPopulatorPlan>();
-		LinkedList<ColumnTemplateTerm> columnTermsLocal = new LinkedList<ColumnTemplateTerm>();
+		nestedPlans = new HashMap<>();
+		LinkedList<ColumnTemplateTerm> columnTermsLocal = new LinkedList<>();
 		columnTermsLocal.addAll(columnTerms);
 		sortColumnTermsByHNodePathDepth(columnTermsLocal);
 		Map<ColumnTemplateTerm, ColumnTemplateTerm> termsToTermDependentOn = generateTermsToTermDependentOn(columnTermsLocal, comparisonTerms);
 		
 		//Now we should have a column terms mapped to their closest affinity in the other group.
-		Map<ColumnTemplateTerm, List<ColumnTemplateTerm>> otherToGenerate = new HashMap<ColumnTemplateTerm, List<ColumnTemplateTerm>>();
-		List<ColumnTemplateTerm> independentNestedTerms = new LinkedList<ColumnTemplateTerm>();
+		Map<ColumnTemplateTerm, List<ColumnTemplateTerm>> otherToGenerate = new HashMap<>();
+		List<ColumnTemplateTerm> independentNestedTerms = new LinkedList<>();
 		for(Entry<ColumnTemplateTerm, ColumnTemplateTerm> termToTermDependentOn : termsToTermDependentOn.entrySet())
 		{
 			ColumnTemplateTerm dependentTerm = termToTermDependentOn.getValue();
@@ -82,7 +82,7 @@ private void generateComplicated() {
 		for(Entry<ColumnTemplateTerm, List<ColumnTemplateTerm>> other : otherToGenerate.entrySet())
 		{
 			TemplateTermSetPopulatorWorker parentWorker = new TemplateTermSetPopulatorWorker(other.getKey(), termToPath.get(other.getKey()), null, selection);
-			Map<ColumnTemplateTerm, HNodePath> truncatedTermToPath = new HashMap<ColumnTemplateTerm, HNodePath>();
+			Map<ColumnTemplateTerm, HNodePath> truncatedTermToPath = new HashMap<>();
 			for(Entry<ColumnTemplateTerm, HNodePath> terms : termToPath.entrySet())
 			{
 				truncatedTermToPath.put(terms.getKey(), HNodePath.findPathBetweenLeavesWithCommonHead(termToPath.get(other.getKey()), terms.getValue()));
@@ -91,7 +91,7 @@ private void generateComplicated() {
 			nestedPlans.put(other.getKey(), plan);
 		}
 		
-		Map<ColumnTemplateTerm, ColumnTemplateTerm> parentTermsToTermDependentOn = new HashMap<ColumnTemplateTerm, ColumnTemplateTerm>();
+		Map<ColumnTemplateTerm, ColumnTemplateTerm> parentTermsToTermDependentOn = new HashMap<>();
 		
 		columnTermsLocal.addAll(independentNestedTerms);
 		sortColumnTermsByHNodePathDepth(columnTermsLocal);
@@ -103,12 +103,12 @@ private void generateComplicated() {
 	
 	public Map<PopulatedTemplateTermSet, List<PartiallyPopulatedTermSet>> execute(Row topRow, List<PopulatedTemplateTermSet> anchors)
 	{
-		Map<PopulatedTemplateTermSet, List<PartiallyPopulatedTermSet>> results = new HashMap<PopulatedTemplateTermSet, List<PartiallyPopulatedTermSet>>();
+		Map<PopulatedTemplateTermSet, List<PartiallyPopulatedTermSet>> results = new HashMap<>();
 		if(columnTerms == null || columnTerms.isEmpty())
 		{
 			for(PopulatedTemplateTermSet anchor: anchors)
 			{
-				List<PartiallyPopulatedTermSet> references = new LinkedList<PartiallyPopulatedTermSet>();
+				List<PartiallyPopulatedTermSet> references = new LinkedList<>();
 				references.add(new PartiallyPopulatedTermSet());
 				results.put(anchor, references);
 			}
@@ -119,7 +119,7 @@ public Map<PopulatedTemplateTermSet, List<PartiallyPopulatedTermSet>> execute(Ro
 		
 		for(PopulatedTemplateTermSet anchor: anchors)
 		{
-			List<List<PartiallyPopulatedTermSet>> toMerge = new LinkedList<List<PartiallyPopulatedTermSet>>();
+			List<List<PartiallyPopulatedTermSet>> toMerge = new LinkedList<>();
 			if(!independentResults.isEmpty())
 			{
 				toMerge.add(independentResults);
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSet.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSet.java
index 586383e47..014b74cd1 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSet.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSet.java
@@ -40,7 +40,7 @@ public class TemplateTermSet {
 	private final List<TemplateTerm> termSet;
 	
 	public TemplateTermSet() {
-		termSet = new LinkedList<TemplateTerm>();
+		termSet = new LinkedList<>();
 	}
 	
 	public void addTemplateTermToSet(TemplateTerm term) {
@@ -52,7 +52,7 @@ public List<TemplateTerm> getAllTerms() {
 	}
 	
 	public List<ColumnTemplateTerm> getAllColumnNameTermElements() {
-		List<ColumnTemplateTerm> cnList = new ArrayList<ColumnTemplateTerm>();
+		List<ColumnTemplateTerm> cnList = new ArrayList<>();
 		for (TemplateTerm term:termSet) {
 			if (term instanceof ColumnTemplateTerm) {
 				cnList.add((ColumnTemplateTerm)term);
@@ -94,7 +94,7 @@ public String getR2rmlTemplateString(RepFactory factory, KR2RMLColumnNameFormatt
 			} else if (term instanceof ColumnTemplateTerm) {
 				HNode hNode = factory.getHNode(term.getTemplateTermValue());
 				if (hNode != null) {
-					String colNameStr = "";
+					String colNameStr;
 					try {
 						JSONArray colNameArr = hNode.getJSONArrayRepresentation(factory);
 						if (colNameArr.length() == 1) {
@@ -133,7 +133,7 @@ public String getColumnNameR2RMLRepresentation(RepFactory factory, KR2RMLColumnN
 			} else if (term instanceof ColumnTemplateTerm) {
 				HNode hNode = factory.getHNode(term.getTemplateTermValue());
 				if (hNode != null) {
-					String colNameStr = "";
+					String colNameStr;
 					try {
 						JSONArray colNameArr = hNode.getJSONArrayRepresentation(factory);
 						if (colNameArr.length() == 1) {
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulator.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulator.java
index 6a7dbf3fe..2bc702c50 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulator.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulator.java
@@ -89,12 +89,12 @@ public List<PopulatedTemplateTermSet> generatePopulatedTemplatesFromPartials(Lis
 	}
 	protected List<PopulatedTemplateTermSet> generatePopulatedTemplates(List<PartiallyPopulatedTermSet> partials, StringBuilder output,
 			List<TemplateTerm> terms) {
-		List<PopulatedTemplateTermSet> templates = new LinkedList<PopulatedTemplateTermSet>();
+		List<PopulatedTemplateTermSet> templates = new LinkedList<>();
 		
 		for(PartiallyPopulatedTermSet partial : partials)
 		{
 			StringBuilder uri = new StringBuilder();
-			Map<ColumnTemplateTerm, Node> references = new HashMap<ColumnTemplateTerm, Node>();
+			Map<ColumnTemplateTerm, Node> references = new HashMap<>();
 			boolean allTermsSatisifed = true;
 			boolean atLeastOneTermSatisified = false;
 			for(TemplateTerm term : terms)
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulatorPlan.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulatorPlan.java
index 504b10762..ad583ffff 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulatorPlan.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulatorPlan.java
@@ -41,9 +41,9 @@
 
 public class TemplateTermSetPopulatorPlan {
 	
-	protected Map<ColumnTemplateTerm, TemplateTermSetPopulatorWorker> independentWorkers = new HashMap<ColumnTemplateTerm, TemplateTermSetPopulatorWorker>();
-	protected Map<ColumnTemplateTerm, TemplateTermSetPopulatorWorker> workers = new HashMap<ColumnTemplateTerm, TemplateTermSetPopulatorWorker>();
-	protected Map<ColumnTemplateTerm, List<TemplateTermSetPopulatorWorker>> workerDependencyPlaceholder = new HashMap<ColumnTemplateTerm, List<TemplateTermSetPopulatorWorker>>();
+	protected Map<ColumnTemplateTerm, TemplateTermSetPopulatorWorker> independentWorkers = new HashMap<>();
+	protected Map<ColumnTemplateTerm, TemplateTermSetPopulatorWorker> workers = new HashMap<>();
+	protected Map<ColumnTemplateTerm, List<TemplateTermSetPopulatorWorker>> workerDependencyPlaceholder = new HashMap<>();
 	protected Map<ColumnTemplateTerm, HNodePath> termToPath;
 	protected TemplateTermSetPopulatorWorker firstWorker;
 	protected LinkedList<ColumnTemplateTerm> columnTerms;
@@ -51,7 +51,7 @@ public class TemplateTermSetPopulatorPlan {
 	protected SuperSelection selection;
 	private static final List<ColumnAffinity> affinities;
 	static {
-		affinities = new LinkedList<ColumnAffinity>();
+		affinities = new LinkedList<>();
 		affinities.add(RowColumnAffinity.INSTANCE);
 		affinities.add(ParentRowColumnAffinity.INSTANCE);
 		affinities.add(CommonParentRowColumnAffinity.INSTANCE);
@@ -63,7 +63,7 @@ protected TemplateTermSetPopulatorPlan(SuperSelection sel)
 	public TemplateTermSetPopulatorPlan(Map<ColumnTemplateTerm, HNodePath> termToPath, Collection<ColumnTemplateTerm> columnTerms, SuperSelection sel)
 	{
 		this.termToPath = termToPath;
-		this.columnTerms = new LinkedList<ColumnTemplateTerm>();
+		this.columnTerms = new LinkedList<>();
 		this.comparisonTerms = this.columnTerms;
 		this.columnTerms.addAll(columnTerms);
 		this.firstWorker = null;
@@ -73,7 +73,7 @@ public TemplateTermSetPopulatorPlan(Map<ColumnTemplateTerm, HNodePath> termToPat
 	public TemplateTermSetPopulatorPlan(Map<ColumnTemplateTerm, HNodePath> termToPath, Collection<ColumnTemplateTerm> columnTerms, TemplateTermSetPopulatorWorker firstWorker, SuperSelection sel)
 	{
 		this.termToPath = termToPath;
-		this.columnTerms = new LinkedList<ColumnTemplateTerm>();
+		this.columnTerms = new LinkedList<>();
 		this.comparisonTerms = this.columnTerms;
 		this.columnTerms.addAll(columnTerms);
 		this.firstWorker = firstWorker;
@@ -95,7 +95,7 @@ public TemplateTermSetPopulatorPlan(
 
 	private void generate()
 	{
-		LinkedList<ColumnTemplateTerm> columnTermsLocal = new LinkedList<ColumnTemplateTerm>();
+		LinkedList<ColumnTemplateTerm> columnTermsLocal = new LinkedList<>();
 		columnTermsLocal.addAll(columnTerms);
 		sortColumnTermsByHNodePathDepth(columnTermsLocal);
 		Map<ColumnTemplateTerm, ColumnTemplateTerm> termsToTermDependentOn = generateTermsToTermDependentOn(columnTermsLocal, comparisonTerms);
@@ -128,7 +128,7 @@ protected void generateWorkers(
 	}
 
 	protected Map<ColumnTemplateTerm, ColumnTemplateTerm> generateTermsToTermDependentOn(LinkedList<ColumnTemplateTerm> columnTermsLocal, List<ColumnTemplateTerm> comparisonTermsLocal) {
-		Map<ColumnTemplateTerm, ColumnTemplateTerm> termsToTermDependentOn = new HashMap<ColumnTemplateTerm, ColumnTemplateTerm>();
+		Map<ColumnTemplateTerm, ColumnTemplateTerm> termsToTermDependentOn = new HashMap<>();
 		while(!columnTermsLocal.isEmpty())
 		{
 			
@@ -189,7 +189,7 @@ private TemplateTermSetPopulatorWorker generateWorker(
 
 	private TemplateTermSetPopulatorStrategy generateStrategy(
 			ColumnTemplateTerm currentTerm, ColumnTemplateTerm dependentTerm) {
-		TemplateTermSetPopulatorStrategy strategy = null;
+		TemplateTermSetPopulatorStrategy strategy;
 		if(dependentTerm == null && firstWorker == null) 
 		{
 			strategy = new MemoizedTemplateTermSetPopulatorStrategy(termToPath.get(currentTerm));
@@ -225,7 +225,7 @@ private void manageDependencies(ColumnTemplateTerm currentTerm,
 
 	private void generateDependency(ColumnTemplateTerm dependentTerm,
 			TemplateTermSetPopulatorWorker worker) {
-		TemplateTermSetPopulatorWorker dependentOnWorker = null;
+		TemplateTermSetPopulatorWorker dependentOnWorker;
 		dependentOnWorker = workers.get(dependentTerm);
 		if(dependentOnWorker != null)
 		{
@@ -292,7 +292,7 @@ public List<PartiallyPopulatedTermSet> execute(Row topRow)
 	{
 		if(columnTerms == null || columnTerms.isEmpty())
 		{
-			List<PartiallyPopulatedTermSet> predicates = new LinkedList<PartiallyPopulatedTermSet>();
+			List<PartiallyPopulatedTermSet> predicates = new LinkedList<>();
 			predicates.add(new PartiallyPopulatedTermSet());
 			return predicates;
 		}
@@ -300,7 +300,7 @@ public List<PartiallyPopulatedTermSet> execute(Row topRow)
 		{
 			return firstWorker.work(topRow);
 		}
-		return new LinkedList<PartiallyPopulatedTermSet>();
+		return new LinkedList<>();
 	}
 	public List<PartiallyPopulatedTermSet> executeComplicated(Row topRow, Node value) {
 		return firstWorker.work(topRow, value);
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulatorWorker.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulatorWorker.java
index e665b0988..2611a3176 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulatorWorker.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/template/TemplateTermSetPopulatorWorker.java
@@ -45,7 +45,7 @@ public TemplateTermSetPopulatorWorker(	ColumnTemplateTerm term,
 		this.path = path;
 		this.strategy = strategy;
 		this.selection = sel;
-		dependentWorkers = new LinkedList<TemplateTermSetPopulatorWorker>();
+		dependentWorkers = new LinkedList<>();
 	}
 	
 	public void addDependentWorker(TemplateTermSetPopulatorWorker worker)
@@ -60,7 +60,7 @@ public List<PartiallyPopulatedTermSet> work(Row topRow)
 	}
 	protected List<PartiallyPopulatedTermSet> work(Row topRow, Row currentRow)
 	{
-		List<PartiallyPopulatedTermSet> results = new LinkedList<PartiallyPopulatedTermSet>();
+		List<PartiallyPopulatedTermSet> results = new LinkedList<>();
 		Collection<Node> nodes = strategy.getNodes(topRow, currentRow, selection);
 		
 		for(Node n : nodes)
@@ -85,7 +85,7 @@ protected List<PartiallyPopulatedTermSet> work(Row topRow, Row currentRow)
 	}
 
 	protected List<PartiallyPopulatedTermSet> work(Row topRow, Node n) {
-		List<List<PartiallyPopulatedTermSet>> partialResults = new LinkedList<List<PartiallyPopulatedTermSet>>();
+		List<List<PartiallyPopulatedTermSet>> partialResults = new LinkedList<>();
 		for(TemplateTermSetPopulatorWorker dependentWorker: dependentWorkers)
 		{
 			partialResults.add(dependentWorker.work(topRow, n.getBelongsToRow()));
@@ -96,7 +96,7 @@ protected List<PartiallyPopulatedTermSet> work(Row topRow, Node n) {
 	}
 	
 	protected static List<PartiallyPopulatedTermSet> combinePartialResults(List<List<PartiallyPopulatedTermSet>> partialResults) {
-		List<PartiallyPopulatedTermSet> combinedResults = new LinkedList<PartiallyPopulatedTermSet>();
+		List<PartiallyPopulatedTermSet> combinedResults = new LinkedList<>();
 		
 		if(!partialResults.isEmpty())
 		{
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/AvroKR2RMLRDFWriter.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/AvroKR2RMLRDFWriter.java
index e905a7132..b4dfd3bc2 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/AvroKR2RMLRDFWriter.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/AvroKR2RMLRDFWriter.java
@@ -38,7 +38,7 @@
 public class AvroKR2RMLRDFWriter extends SFKR2RMLRDFWriter<GenericRecord> {
 
 	private static Logger LOG = LoggerFactory.getLogger(AvroKR2RMLRDFWriter.class);
-	protected Map<String, Schema> triplesMapIdToSchema = new HashMap<String, Schema>();
+	protected Map<String, Schema> triplesMapIdToSchema = new HashMap<>();
 	protected RepFactory rep;
 	protected Schema rootSchema;
 	private OutputStream output; 
@@ -69,8 +69,8 @@ public void setProcessingOrder(Map<TriplesMapGraph, List<String>> triplesMapProc
 		String rootTriplesMapId = this.rootTriplesMapIds.iterator().next();
 		rootSchema = triplesMapIdToSchema.get(rootTriplesMapId);
 
-		datumWriter = new GenericDatumWriter<GenericRecord>(rootSchema);
-		dfw = new DataFileWriter<GenericRecord>(datumWriter);
+		datumWriter = new GenericDatumWriter<>(rootSchema);
+		dfw = new DataFileWriter<>(datumWriter);
 		dfw.create(rootSchema, output);
 		
 		
@@ -81,7 +81,7 @@ protected Schema getSchemaForTriplesMap(TriplesMapGraph graph, String triplesMap
 		TriplesMap map = graph.getTriplesMap(triplesMapId);
 		RecordBuilder<Schema> rb = SchemaBuilder.record("subjr"+(id++));
 		
-		Set<String> currentPredicates = new HashSet<String>(); 
+		Set<String> currentPredicates = new HashSet<>(); 
 		FieldAssembler<Schema> fieldAssembler = rb.fields();
 		for(PredicateObjectMap pom : map.getPredicateObjectMaps())
 		{
@@ -213,7 +213,7 @@ protected void addValueToMap(PredicateObjectMap pom, GenericRecord subject, Obje
 		String mapPredicateName = pom.getPredicate().getId().replaceAll("[^\\w]", "_");
 		if(object instanceof String)
 		{
-			Map<String, String> values = null;
+			Map<String, String> values;
 			if(subject.get(mapPredicateName)== null)
 			{
 				subject.put(mapPredicateName, new ConcurrentHashMap<String, String>());
@@ -223,7 +223,7 @@ protected void addValueToMap(PredicateObjectMap pom, GenericRecord subject, Obje
 		}
 		else if(object instanceof GenericRecord)
 		{
-			Map<String, GenericRecord> values = null;
+			Map<String, GenericRecord> values;
 			if(subject.get(mapPredicateName)== null)
 			{
 				subject.put(mapPredicateName, new ConcurrentHashMap<String, GenericRecord>());
@@ -253,7 +253,7 @@ protected void addValueToArray(PredicateObjectMap pom, GenericRecord subject, Ob
 				}
 				else if(currentObj instanceof GenericRecord)
 				{
-					array = new GenericData.Array<GenericRecord>(subject.getSchema().getField(shortHandPredicateURI).schema().getTypes().get(0), new LinkedList<GenericRecord>());
+					array = new GenericData.Array<>(subject.getSchema().getField(shortHandPredicateURI).schema().getTypes().get(0), new LinkedList<GenericRecord>());
 					array.add((GenericRecord)object);
 					array.add((GenericRecord)currentObj);
 				}
@@ -261,7 +261,7 @@ else if(currentObj instanceof GenericRecord)
 			else
 			{
 					GenericRecord objectToAdd = (GenericRecord)object;
-					array = new GenericData.Array<GenericRecord>(objectToAdd.getSchema(), new LinkedList<GenericRecord>());
+					array = new GenericData.Array<>(objectToAdd.getSchema(), new LinkedList<GenericRecord>());
 					array.add(objectToAdd);
 				
 			}
@@ -278,7 +278,7 @@ else if(object instanceof String)
 				}
 				else if(currentObj instanceof String)
 				{
-					strings = new GenericData.Array<String>(SchemaBuilder.array().items().stringType(), new LinkedList<String>());
+					strings = new GenericData.Array<>(SchemaBuilder.array().items().stringType(), new LinkedList<String>());
 					strings.add((String)object);
 					strings.add((String)currentObj);
 				}
@@ -286,7 +286,7 @@ else if(currentObj instanceof String)
 			else
 			{
 					String objectToAdd = (String)object;
-					strings = new GenericData.Array<String>(SchemaBuilder.array().items().stringType(), new LinkedList<String>());
+					strings = new GenericData.Array<>(SchemaBuilder.array().items().stringType(), new LinkedList<String>());
 					strings.add(objectToAdd);
 				
 			}
@@ -297,7 +297,7 @@ else if(currentObj instanceof String)
 	
 	@Override
 	public void finishRow() {
-		for(ConcurrentHashMap<String, GenericRecord> records : this.rootObjectsByTriplesMapId.values())
+		for(Map<String, GenericRecord> records : this.rootObjectsByTriplesMapId.values())
 		{
 			
 			for(GenericRecord record : records.values()){ 
@@ -350,7 +350,7 @@ protected void collapseSameType(GenericRecord obj) {
 				collapseSameType((GenericRecord)value);
 			if (value instanceof GenericArray) {
 				GenericArray array = (GenericArray)value;
-				Set<Object> valuesHash = new HashSet<Object>();
+				Set<Object> valuesHash = new HashSet<>();
 				boolean unmodified = true;
 				for (int i = 0; i < array.size(); i++) {
 					Object o = array.get(i);
@@ -363,7 +363,7 @@ protected void collapseSameType(GenericRecord obj) {
 				}
 				if(!unmodified)
 				{
-					GenericArray<Object> newValues = new GenericData.Array<Object>(array.getSchema(), valuesHash);
+					GenericArray<Object> newValues = new GenericData.Array<>(array.getSchema(), valuesHash);
 					obj.put(f.name(), newValues);
 				}
 			}
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/JSONKR2RMLRDFWriter.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/JSONKR2RMLRDFWriter.java
index e729b56ad..6415511cd 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/JSONKR2RMLRDFWriter.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/JSONKR2RMLRDFWriter.java
@@ -228,7 +228,7 @@ protected void collapseSameType(JSONObject obj) {
 			if (value instanceof JSONArray) {
 				JSONArray array = (JSONArray)value;
 				JSONArray newArray = new JSONArray();
-				Map<String, Object> types = new HashMap<String, Object>();
+				Map<String, Object> types = new HashMap<>();
 				int length = array.length();
 				for (int i = 0; i < length; i++) {
 					Object o = array.get(i);
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/N3KR2RMLRDFWriter.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/N3KR2RMLRDFWriter.java
index 748be9bd9..f0a5555f6 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/N3KR2RMLRDFWriter.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/N3KR2RMLRDFWriter.java
@@ -46,14 +46,14 @@ public N3KR2RMLRDFWriter(URIFormatter uriFormatter, OutputStream outputStream)
 	{
 		this.outWriter = new PrintWriter(outputStream);
 		this.uriFormatter = uriFormatter;
-		generatedTriples = new ConcurrentHashMap<String, String>();
+		generatedTriples = new ConcurrentHashMap<>();
 		baseURI = null;
 	}
 	public N3KR2RMLRDFWriter(URIFormatter uriFormatter, PrintWriter writer)
 	{
 		this.outWriter =writer;
 		this.uriFormatter = uriFormatter;
-		generatedTriples = new ConcurrentHashMap<String, String>();
+		generatedTriples = new ConcurrentHashMap<>();
 	}
 
 	private void outputTriple(String triple)
@@ -144,7 +144,7 @@ public void finishRow()
 			outWriter.println(value);
 		}
 		outWriter.println("");
-		generatedTriples = new ConcurrentHashMap<String, String>();
+		generatedTriples = new ConcurrentHashMap<>();
 	}
 	@Override
 	public void flush() {
diff --git a/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/SFKR2RMLRDFWriter.java b/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/SFKR2RMLRDFWriter.java
index 9f9a6d330..7640e98de 100644
--- a/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/SFKR2RMLRDFWriter.java
+++ b/karma-common/src/main/java/edu/isi/karma/kr2rml/writer/SFKR2RMLRDFWriter.java
@@ -18,12 +18,12 @@ public abstract class SFKR2RMLRDFWriter<E> extends KR2RMLRDFWriter {
 	protected boolean firstObject = true;
 	protected ConcurrentHashMap<String, ConcurrentHashMap<String, E>> generatedObjectsByTriplesMapId;
 	protected ConcurrentHashMap<String, E> generatedObjectsWithoutTriplesMap;
-	protected ConcurrentHashMap<String, ConcurrentHashMap<String, E>> rootObjectsByTriplesMapId = new ConcurrentHashMap<String, ConcurrentHashMap<String,E>>();
+	protected ConcurrentHashMap<String, ConcurrentHashMap<String, E>> rootObjectsByTriplesMapId = new ConcurrentHashMap<>();
 	protected ShortHandURIGenerator shortHandURIGenerator = new ShortHandURIGenerator();
 	protected String rootTriplesMapId; 
 	protected Set<String> rootTriplesMapIds;
 	protected String baseURI = "";
-	private static Set<String> numericLiteralTypes = new HashSet<String>();
+	private static Set<String> numericLiteralTypes = new HashSet<>();
 	static {
 		numericLiteralTypes.add("http://www.w3.org/2001/XMLSchema#decimal");
 		numericLiteralTypes.add("http://www.w3.org/2001/XMLSchema#integer");
@@ -45,9 +45,9 @@ public abstract class SFKR2RMLRDFWriter<E> extends KR2RMLRDFWriter {
 	}
 	public SFKR2RMLRDFWriter (PrintWriter outWriter) {
 		this.outWriter = outWriter;
-		generatedObjectsWithoutTriplesMap = new ConcurrentHashMap<String, E>();
-		generatedObjectsByTriplesMapId = new ConcurrentHashMap<String, ConcurrentHashMap<String, E>>();
-		rootTriplesMapIds = new HashSet<String>();
+		generatedObjectsWithoutTriplesMap = new ConcurrentHashMap<>();
+		generatedObjectsByTriplesMapId = new ConcurrentHashMap<>();
+		rootTriplesMapIds = new HashSet<>();
 		this.rootObjectsByTriplesMapId.put("", new ConcurrentHashMap<String, E>());
 		initializeOutput();
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/metadata/KarmaMetadataManager.java b/karma-common/src/main/java/edu/isi/karma/metadata/KarmaMetadataManager.java
index 7c557cb35..361089b1d 100644
--- a/karma-common/src/main/java/edu/isi/karma/metadata/KarmaMetadataManager.java
+++ b/karma-common/src/main/java/edu/isi/karma/metadata/KarmaMetadataManager.java
@@ -16,7 +16,7 @@ public class KarmaMetadataManager {
 	public KarmaMetadataManager(ServletContextParameterMap contextParameters) throws KarmaException
 	{
 		createDirectoryForMetadata(contextParameters);
-		metadataTypes = new HashMap<KarmaMetadataType, KarmaMetadata>();
+		metadataTypes = new HashMap<>();
 		
 	}
 	private void createDirectoryForMetadata(ServletContextParameterMap contextParameters) throws KarmaException {
diff --git a/karma-common/src/main/java/edu/isi/karma/metadata/KarmaUserMetadata.java b/karma-common/src/main/java/edu/isi/karma/metadata/KarmaUserMetadata.java
index 4a6fd8d03..9b947b2b5 100644
--- a/karma-common/src/main/java/edu/isi/karma/metadata/KarmaUserMetadata.java
+++ b/karma-common/src/main/java/edu/isi/karma/metadata/KarmaUserMetadata.java
@@ -70,7 +70,7 @@ protected void createFile(
 	
 	private static void renameExistingFolder(String userDirPath, ContextParameter parameter, String directory) {
 		
-		HashMap<ContextParameter, String> oldNames = new HashMap<ContextParameter, String>();
+		HashMap<ContextParameter, String> oldNames = new HashMap<>();
 		oldNames.put(ContextParameter.ALIGNMENT_GRAPH_DIRECTORY, "AlignmentGraph");
 		oldNames.put(ContextParameter.JSON_MODELS_DIR, "JSON");
 		oldNames.put(ContextParameter.R2RML_USER_DIR, "R2RML");
diff --git a/karma-common/src/main/java/edu/isi/karma/metadata/SemanticTypeModelMetadata.java b/karma-common/src/main/java/edu/isi/karma/metadata/SemanticTypeModelMetadata.java
index 6330a6bef..68c8d19c4 100644
--- a/karma-common/src/main/java/edu/isi/karma/metadata/SemanticTypeModelMetadata.java
+++ b/karma-common/src/main/java/edu/isi/karma/metadata/SemanticTypeModelMetadata.java
@@ -23,7 +23,7 @@ public SemanticTypeModelMetadata(ServletContextParameterMap contextParameters) t
 	
 	@Override
 	public void setup(UpdateContainer uc, Workspace workspace) {
-		File modelFile = null;
+		File modelFile;
 		modelFile = new File(contextParameters.getParameterValue(ContextParameter.SEMTYPE_MODEL_DIRECTORY));
 		/* Read and populate CRF Model from a file */
 		if(!modelFile.exists())
diff --git a/karma-common/src/main/java/edu/isi/karma/metadata/TextualSemanticTypeModelMetadata.java b/karma-common/src/main/java/edu/isi/karma/metadata/TextualSemanticTypeModelMetadata.java
index c9c680765..13428250c 100644
--- a/karma-common/src/main/java/edu/isi/karma/metadata/TextualSemanticTypeModelMetadata.java
+++ b/karma-common/src/main/java/edu/isi/karma/metadata/TextualSemanticTypeModelMetadata.java
@@ -23,7 +23,7 @@ public TextualSemanticTypeModelMetadata(ServletContextParameterMap contextParame
 	
 	@Override
 	public void setup(UpdateContainer uc, Workspace workspace) {
-		File modelFile = null;
+		File modelFile;
 		modelFile = new File(contextParameters.getParameterValue(ContextParameter.TEXTUAL_SEMTYPE_MODEL_DIRECTORY));
 		/* Read and populate CRF Model from a file */
 		if(!modelFile.exists())
diff --git a/karma-common/src/main/java/edu/isi/karma/model/serialization/WebServiceLoader.java b/karma-common/src/main/java/edu/isi/karma/model/serialization/WebServiceLoader.java
index 18d2b1d8c..388ebc582 100644
--- a/karma-common/src/main/java/edu/isi/karma/model/serialization/WebServiceLoader.java
+++ b/karma-common/src/main/java/edu/isi/karma/model/serialization/WebServiceLoader.java
@@ -123,11 +123,11 @@ public void deleteSourceByUri(String uri) {
     @Override
 	public List<Source> getSourcesAbstractInfo(Integer serviceLimit) {
 		
-		List<Source> serviceList = new ArrayList<Source>();
+		List<Source> serviceList = new ArrayList<>();
 		
 		Model model = Repository.Instance().getModel();
 		
-		String service_id = "";
+		String service_id;
 		String service_name = "";
 		String service_address = "";
 		
@@ -209,7 +209,7 @@ public List<Source> getSourcesAbstractInfo(Integer serviceLimit) {
 	public List<Source> getSourcesDetailedInfo(Integer serviceLimit) {
 
 		List<Source> serviceList = getSourcesAbstractInfo(serviceLimit);
-		List<Source> serviceListCompleteInfo = new ArrayList<Source>();
+		List<Source> serviceListCompleteInfo = new ArrayList<>();
 		for (Source s : serviceList) {
 			serviceListCompleteInfo.add(getSourceByUri(s.getUri()));
 		}
@@ -297,8 +297,8 @@ public Map<WebService, Map<String, String>> getServicesByInputPattern(edu.isi.ka
 			return null;
 		}
 		
-		Map<WebService, Map<String, String>> servicesAndMappings = 
-			new HashMap<WebService, Map<String,String>>();
+		Map<WebService, Map<String, String>> servicesAndMappings =
+				new HashMap<>();
 		
 		Map<String, Map<String, String>> serviceIdsAndMappings = 
 			semanticModel.findInServiceInputs(Repository.Instance().getModel(), serviceLimit);
@@ -331,8 +331,8 @@ public Map<WebService, Map<String, String>> getServicesByOutputPattern(edu.isi.k
 			return null;
 		}
 		
-		Map<WebService, Map<String, String>> servicesAndMappings = 
-			new HashMap<WebService, Map<String,String>>();
+		Map<WebService, Map<String, String>> servicesAndMappings =
+				new HashMap<>();
 		
 		Map<String, Map<String, String>> serviceIdsAndMappings = 
 			semanticModel.findInServiceOutputs(Repository.Instance().getModel(), serviceLimit);
@@ -362,8 +362,8 @@ public Map<WebService, Map<String, String>> getServicesWithInputContainedInModel
 		
 		List<Source> serviceList = getSourcesDetailedInfo(serviceLimit);
 		
-		Map<WebService, Map<String, String>> servicesAndMappings = 
-			new HashMap<WebService, Map<String,String>>();
+		Map<WebService, Map<String, String>> servicesAndMappings =
+				new HashMap<>();
 
 		Model jenaModel = semanticModel.getJenaModel();
 		for (Source service : serviceList) {
@@ -405,8 +405,8 @@ public Map<WebService, Map<String, String>> getServicesWithOutputContainedInMode
 		
 		List<Source> serviceList = getSourcesDetailedInfo(serviceLimit);
 		
-		Map<WebService, Map<String, String>> servicesAndMappings = 
-			new HashMap<WebService, Map<String,String>>();
+		Map<WebService, Map<String, String>> servicesAndMappings =
+				new HashMap<>();
 
 		Model jenaModel = semanticModel.getJenaModel();
 		for (Source service : serviceList) {
@@ -445,8 +445,8 @@ public WebService importSourceFromJenaModel(Model model) {
 		logger.debug("model size: " + model.getGraph().size());
 
 		String service_name = "";
-		String service_uri = "";
-		String service_id = "";
+		String service_uri;
+		String service_id;
 		String service_address = "";
 		String service_method = "";
 
@@ -466,8 +466,8 @@ public WebService importSourceFromJenaModel(Model model) {
 
 		Resource service_resource = model.getResource(service_uri);
 		
-		NodeIterator nodeIterator = null;
-		RDFNode node = null;
+		NodeIterator nodeIterator;
+		RDFNode node;
 
 		// service name
 		nodeIterator = model.listObjectsOfProperty(service_resource, has_name_property);
@@ -493,7 +493,7 @@ public WebService importSourceFromJenaModel(Model model) {
 		} else
 			logger.debug("service does not have a method.");
 
-		List<String> variables = null;
+		List<String> variables;
 		List<Attribute> inputAttributes = null;
 		List<Attribute> outputAttributes = null;
 		edu.isi.karma.rep.model.Model inputModel = null;
@@ -533,10 +533,9 @@ public WebService importSourceFromJenaModel(Model model) {
 	private List<String> getVariables(Model model, Resource service_resource) {
 		
 		Property has_variable_property = model.getProperty(Namespaces.KARMA + "hasVariable");
-	
-		List<String> variables = new ArrayList<String>();
-		NodeIterator nodeIterator = null;
-		RDFNode node = null;
+		List<String> variables = new ArrayList<>();
+		NodeIterator nodeIterator;
+		RDFNode node;
 
 		// hasAttribute
 		nodeIterator = model.listObjectsOfProperty(service_resource, has_variable_property);
@@ -561,10 +560,10 @@ private List<Attribute> getAttributes(Model model, Resource io_resource, String
 		Property has_mandatory_attribute_property = model.getProperty(Namespaces.KARMA + "hasMandatoryAttribute");
 		Property has_optional_attribute_property = model.getProperty(Namespaces.KARMA + "hasOptionalAttribute");
 
-		List<Attribute> attList = new ArrayList<Attribute>();
+		List<Attribute> attList = new ArrayList<>();
 		
-		NodeIterator nodeIterator = null;
-		RDFNode node = null;
+		NodeIterator nodeIterator;
+		RDFNode node;
 
 		// hasAttribute
 		nodeIterator = model.listObjectsOfProperty(io_resource, has_attribute_property);
@@ -611,7 +610,7 @@ private List<Attribute> getAttributes(Model model, Resource io_resource, String
 	
 	private Attribute getAttribute(Model model, Resource att_resource, String ioType, AttributeRequirement requirement) {
 		
-		String att_id = "";
+		String att_id;
 		String att_name = "";
 		String att_groundedIn = "";
 
@@ -622,8 +621,8 @@ private Attribute getAttribute(Model model, Resource att_resource, String ioType
 		att_id = att_resource.getLocalName();
 		logger.debug("attribute id: " + att_id);
 
-		NodeIterator nodeIterator = null;
-		RDFNode node = null;
+		NodeIterator nodeIterator;
+		RDFNode node;
 		
 
 		// attribute name
@@ -642,7 +641,7 @@ private Attribute getAttribute(Model model, Resource att_resource, String ioType
 		} else
 			logger.debug("attribute does not have agroundedIn value.");
 
-		Attribute att = null;
+		Attribute att;
 		if (att_groundedIn.length() > 0)
 			att = new Attribute(att_id, att_resource.getNameSpace(), att_name, ioType, requirement, att_groundedIn );
 		else
@@ -657,9 +656,9 @@ private edu.isi.karma.rep.model.Model getSemanticModel(Model model, Resource io_
 		Property has_model_property = model.getProperty(Namespaces.KARMA + "hasModel");
 		Property has_atom_property = model.getProperty(Namespaces.KARMA + "hasAtom");
 		
-		NodeIterator nodeIterator = null;
-		RDFNode modelNode = null;
-		RDFNode atomNode = null;
+		NodeIterator nodeIterator;
+		RDFNode modelNode;
+		RDFNode atomNode;
 
 		// hasModel
 		nodeIterator = model.listObjectsOfProperty(io_resource, has_model_property);
@@ -670,7 +669,7 @@ private edu.isi.karma.rep.model.Model getSemanticModel(Model model, Resource io_
 
 		edu.isi.karma.rep.model.Model semanticModel = 
 			new edu.isi.karma.rep.model.Model(modelNode.asResource().getLocalName());
-		List<Atom> atoms = new ArrayList<Atom>();
+		List<Atom> atoms = new ArrayList<>();
 		
 
 		// hasAtom
@@ -695,8 +694,8 @@ private Atom getAtom(Model model, Resource atom_resource) {
 		
 		Property rdf_type = model.getProperty(Namespaces.RDF + "type");
 
-		NodeIterator nodeIterator = null;
-		RDFNode node = null;
+		NodeIterator nodeIterator;
+		RDFNode node;
 
 		String classAtomUri = Namespaces.SWRL + "ClassAtom";
 		String propertyAtomUri = Namespaces.SWRL + "IndividualPropertyAtom";
@@ -723,11 +722,11 @@ else if (node.asResource().getURI().equalsIgnoreCase(propertyAtomUri)) {
 	
 	private ClassAtom getClassAtom(Model model, Resource atom_resource) {
 		
-		String predicateUri = null;
-		String predicatePrefix = null;
-		String predicateNs = null;
+		String predicateUri;
+		String predicatePrefix;
+		String predicateNs;
 		
-		String argument1Id = null;
+		String argument1Id;
 		String argument1Type = null;
 		
 		Resource attribute = ResourceFactory.createResource(Namespaces.KARMA + "Attribute");
@@ -737,8 +736,8 @@ private ClassAtom getClassAtom(Model model, Resource atom_resource) {
 		Property argument1_property = model.getProperty(Namespaces.SWRL + "argument1");
 
 
-		NodeIterator nodeIterator = null;
-		RDFNode node = null;
+		NodeIterator nodeIterator;
+		RDFNode node;
 
 		// atom class predicate
 		nodeIterator = model.listObjectsOfProperty(atom_resource, class_predicate_property);
@@ -779,12 +778,12 @@ else if (isInstanceOfTheClass(node.asResource(), variable))
 	
 	private IndividualPropertyAtom getPropertyAtom(Model model, Resource atom_resource) {
 		
-		String predicateUri = null;
-		String predicatePrefix = null;
-		String predicateNs = null;
+		String predicateUri;
+		String predicatePrefix;
+		String predicateNs;
 		
-		String argument1Id = null;
-		String argument2Id = null; 
+		String argument1Id;
+		String argument2Id; 
 
 		String argument1Type = null;
 		String argument2Type = null; 
@@ -796,8 +795,8 @@ private IndividualPropertyAtom getPropertyAtom(Model model, Resource atom_resour
 		Property argument1_property = model.getProperty(Namespaces.SWRL + "argument1");
 		Property argument2_property = model.getProperty(Namespaces.SWRL + "argument2");
 
-		NodeIterator nodeIterator = null;
-		RDFNode node = null;
+		NodeIterator nodeIterator;
+		RDFNode node;
 
 		// atom class predicate
 		nodeIterator = model.listObjectsOfProperty(atom_resource, property_predicate_property);
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/Uris.java b/karma-common/src/main/java/edu/isi/karma/modeling/Uris.java
index bfd142865..28233c212 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/Uris.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/Uris.java
@@ -116,7 +116,7 @@ public abstract class Uris {
 	// Linking related URIs
 	public static final String KM_LINKING_MATCHES_URI = Namespaces.KARMA_DEV + "possibleLinkingMatches";
 	
-	public static final List<String> Uris = new ArrayList<String>();
+	public static final List<String> Uris = new ArrayList<>();
 	static {
 		List<Field> staticFields = new ArrayList<>();
 	    Field[] allFields = Uris.class.getDeclaredFields();
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/Alignment.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/Alignment.java
index 69e79cbe0..29b87e4d3 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/Alignment.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/Alignment.java
@@ -26,6 +26,7 @@
 import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import org.jgrapht.UndirectedGraph;
@@ -92,7 +93,7 @@ public Alignment(OntologyManager ontologyManager) {
 		this.contextId = ontologyManager.getContextId();
 		this.ontologyManager = ontologyManager;
 		this.ontologyManager.subscribeListener(this);
-		this.sourceColumnNodes = new HashSet<ColumnNode>(); 
+		this.sourceColumnNodes = new HashSet<>(); 
 		ModelingConfiguration conf = ModelingConfigurationRegistry.getInstance().
 				getModelingConfiguration(ContextParametersRegistry.getInstance().getContextParameters(contextId).getKarmaHome());
 		if (conf.getKnownModelsAlignment()) {
@@ -137,7 +138,7 @@ public DirectedWeightedMultigraph<Node, LabeledLink> getSteinerTree() {
 		// GraphUtil.printGraph(this.steinerTree);
 		
 		if (this.steinerTree == null)
-			steinerTree = new DirectedWeightedMultigraph<Node, LabeledLink>(LabeledLink.class);
+			steinerTree = new DirectedWeightedMultigraph<>(LabeledLink.class);
 		
 		return this.steinerTree;
 	}
@@ -531,7 +532,7 @@ public List<LabeledLink> getPossibleLinks(String sourceId, String targetId) {
 	}
 
 	public Set<LabeledLink> getIncomingLinksInTree(String nodeId) {
-		Set<LabeledLink> results = new HashSet<LabeledLink>();
+		Set<LabeledLink> results = new HashSet<>();
 		
 		if (steinerTree == null)
 			return results;
@@ -555,7 +556,7 @@ public Set<LabeledLink> getIncomingLinksInTree(String nodeId) {
 	}
 	
 	public Set<LabeledLink> getOutgoingLinksInTree(String nodeId) {
-		Set<LabeledLink> results = new HashSet<LabeledLink>();
+		Set<LabeledLink> results = new HashSet<>();
 		
 		if (steinerTree == null)
 			return results;
@@ -700,7 +701,7 @@ private void updateLinksPreferredByUI() {
 	}
 	
 	public List<Node> computeSteinerNodes() {
-		Set<Node> steinerNodes = new HashSet<Node>();
+		Set<Node> steinerNodes = new HashSet<>();
 		
 		// Add column nodes and their domain
 		// it is better to set isForced flag when setting a semantic type
@@ -713,7 +714,7 @@ public List<Node> computeSteinerNodes() {
 					steinerNodes.add(n);
 				
 				if (n.getSemanticTypeStatus() == ColumnSemanticTypeStatus.UserAssigned) {
-					HashMap<SemanticType, LabeledLink> domainLinks = 
+					Map<SemanticType, LabeledLink> domainLinks = 
 							GraphUtil.getDomainLinks(this.graphBuilder.getGraph(), n, n.getUserSemanticTypes());
 					if (domainLinks != null) {
 						for (LabeledLink l : domainLinks.values()) {
@@ -745,14 +746,14 @@ public List<Node> computeSteinerNodes() {
 			}
 		}
 		
-		ArrayList<Node> result = new ArrayList<>();
+		List<Node> result = new ArrayList<>();
 		result.addAll(steinerNodes);
 		return result;
 	}
 	
 	public List<LabeledLink> suggestLinks(String nodeId) {
 		
-		List<LabeledLink> suggestedLinks = new LinkedList<LabeledLink>();
+		List<LabeledLink> suggestedLinks = new LinkedList<>();
 		
 		if (this.steinerTree == null) {
 			logger.error("the model is null.");
@@ -766,7 +767,7 @@ public List<LabeledLink> suggestLinks(String nodeId) {
 		}
 		
 		
-		Set<String> currentLinkIds = new HashSet<String>();
+		Set<String> currentLinkIds = new HashSet<>();
 		Set<LabeledLink> currentIncomingLinks, currentOutgoingLinks;
 		currentIncomingLinks = this.getIncomingLinksInTree(nodeId);
 		currentOutgoingLinks = this.getOutgoingLinksInTree(nodeId);
@@ -777,7 +778,7 @@ public List<LabeledLink> suggestLinks(String nodeId) {
 			for (LabeledLink l : currentOutgoingLinks)
 				currentLinkIds.add(l.getId());
 		
-		Set<LabeledLink> candidateLinks = new HashSet<LabeledLink>();
+		Set<LabeledLink> candidateLinks = new HashSet<>();
 		List<LabeledLink> incomingLinks, outgoingLinks;
 		incomingLinks = ModelLearningGraph.getInstance(ontologyManager, ModelLearningGraphType.Compact).
 				getGraphBuilder().getIncomingLinks(nodeId);
@@ -800,7 +801,7 @@ public List<LabeledLink> suggestLinks(String nodeId) {
 		}
 		
 		AlignmentScore currentScore = new AlignmentScore(modelCoherence, modelCost);
-		List<AlignmentScore> alignmentScores = new LinkedList<AlignmentScore>();
+		List<AlignmentScore> alignmentScores = new LinkedList<>();
 		for (LabeledLink l : candidateLinks) {
 			if (l.getModelIds() == null || l.getModelIds().isEmpty()) // ignore the links that are added by the user (not present in the known models)
 				continue;
@@ -820,7 +821,7 @@ public List<LabeledLink> suggestLinks(String nodeId) {
 
 	public List<LabeledLink> suggestAlternativeLinks(String linkId) {
 
-		List<LabeledLink> alternativeLinks = new LinkedList<LabeledLink>();
+		List<LabeledLink> alternativeLinks = new LinkedList<>();
 		
 		if (this.steinerTree == null) {
 			logger.error("the model is null.");
@@ -845,7 +846,7 @@ public List<LabeledLink> suggestAlternativeLinks(String linkId) {
 			return alternativeLinks;
 		}
 		
-		Set<LabeledLink> candidateLinks = new HashSet<LabeledLink>();
+		Set<LabeledLink> candidateLinks = new HashSet<>();
 		List<LabeledLink> incomingLinks, outgoingLinks;
 		incomingLinks = ModelLearningGraph.getInstance(ontologyManager, ModelLearningGraphType.Compact).
 				getGraphBuilder().getLinks(target.getId(), source.getId());
@@ -868,7 +869,7 @@ public List<LabeledLink> suggestAlternativeLinks(String linkId) {
 		}
 		
 		AlignmentScore currentScore = new AlignmentScore(modelCoherence, modelCost);
-		List<AlignmentScore> alignmentScores = new LinkedList<AlignmentScore>();
+		List<AlignmentScore> alignmentScores = new LinkedList<>();
 		for (LabeledLink l : candidateLinks) {
 			if (l.getModelIds() == null || l.getModelIds().isEmpty()) // ignore the links that are added by the user (not present in the known models)
 				continue;
@@ -938,7 +939,7 @@ private void learnFromOntology() {
 //		GraphPreProcess graphPreProcess = new GraphPreProcess(this.graphBuilder.getGraph(), 
 //				this.getLinksByStatus(LinkStatus.PreferredByUI),
 //				this.getLinksByStatus(LinkStatus.ForcedByUser));		
-		UndirectedGraph<Node, DefaultLink> undirectedGraph = new AsUndirectedGraph<Node, DefaultLink>(this.getGraph());
+		UndirectedGraph<Node, DefaultLink> undirectedGraph = new AsUndirectedGraph<>(this.getGraph());
 
 		logger.debug("computing steiner nodes ...");
 		List<Node> steinerNodes = this.computeSteinerNodes();
@@ -982,8 +983,8 @@ private void learnFromKnownSemanticModels() {
 			logger.error("could not learn any model for this source!");
 			if (this.steinerTree == null)
 			{
-				this.steinerTree = 
-						new DirectedWeightedMultigraph<Node, LabeledLink>(LabeledLink.class);
+				this.steinerTree =
+						new DirectedWeightedMultigraph<>(LabeledLink.class);
 			}
 			this.addForcedNodes();
 			this.addForcedLinks(); //add new semantic type to the tree
@@ -1037,12 +1038,11 @@ public void updateAlignment(SemanticModel model, List<SemanticType> semanticType
 		if (model == null) 
 			return;
 		
-		if (semanticTypes == null) semanticTypes = new LinkedList<SemanticType>();
+		if (semanticTypes == null) semanticTypes = new LinkedList<>();
 		
-		DirectedWeightedMultigraph<Node, LabeledLink> tree = 
-				new DirectedWeightedMultigraph<Node, LabeledLink>(LabeledLink.class);
-
-		HashMap<Node, Node> modelToAlignmentNode = new HashMap<Node, Node>();
+		DirectedWeightedMultigraph<Node, LabeledLink> tree =
+				new DirectedWeightedMultigraph<>(LabeledLink.class);
+		Map<Node, Node> modelToAlignmentNode = new HashMap<>();
 		for (Node n : model.getGraph().vertexSet()) {
 			if (n instanceof InternalNode) {
 
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/AlignmentManager.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/AlignmentManager.java
index 542cf6deb..7ce66af62 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/AlignmentManager.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/AlignmentManager.java
@@ -21,6 +21,7 @@
 package edu.isi.karma.modeling.alignment;
 
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
 
@@ -29,14 +30,14 @@
 import edu.isi.karma.rep.WorkspaceManager;
 
 public class AlignmentManager {
-	private static ConcurrentHashMap<String, Alignment> alignmentMap = null;
+	private static Map<String, Alignment> alignmentMap = null;
 	private static AlignmentManager _InternalInstance = null;
 	public static AlignmentManager Instance()
 	{
 		if (_InternalInstance == null)
 		{
 			_InternalInstance = new AlignmentManager();
-			alignmentMap = new ConcurrentHashMap<String, Alignment>();
+			alignmentMap = new ConcurrentHashMap<>();
 		}
 		return _InternalInstance;
 	}
@@ -80,7 +81,7 @@ public Alignment createAlignment(String workspaceId, String worksheetId, Ontolog
 	}
 
 	public void removeWorkspaceAlignments(String workspaceId) {
-		ArrayList<String> keysToBeRemoved = new ArrayList<String>();
+		List<String> keysToBeRemoved = new ArrayList<>();
 		for(String key:alignmentMap.keySet()) {
 			if(key.startsWith(workspaceId+":")) {
 				keysToBeRemoved.add(key);
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphBuilder.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphBuilder.java
index 7b66852aa..9dd2930e2 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphBuilder.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphBuilder.java
@@ -109,32 +109,32 @@ public GraphBuilder(OntologyManager ontologyManager, boolean addThingNode) {
 		this.ontologyManager = ontologyManager;
 		this.nodeIdFactory = new NodeIdFactory();
 
-		this.idToNodeMap = new HashMap<String, Node>();
-		this.idToLinkMap = new HashMap<String, LabeledLink>();
-		this.uriToNodesMap = new HashMap<String, Set<Node>>();
-		this.uriToLinksMap = new HashMap<String, Set<LabeledLink>>();
-		this.typeToNodesMap = new HashMap<NodeType, Set<Node>>();
-		this.typeToLinksMap = new HashMap<LinkType, Set<LabeledLink>>();
-		this.statusToLinksMap = new HashMap<LinkStatus, Set<LabeledLink>>();
+		this.idToNodeMap = new HashMap<>();
+		this.idToLinkMap = new HashMap<>();
+		this.uriToNodesMap = new HashMap<>();
+		this.uriToLinksMap = new HashMap<>();
+		this.typeToNodesMap = new HashMap<>();
+		this.typeToLinksMap = new HashMap<>();
+		this.statusToLinksMap = new HashMap<>();
 		
-		this.uriClosure = new HashMap<String, Set<String>>();
+		this.uriClosure = new HashMap<>();
 
-		this.graph = new DirectedWeightedMultigraph<Node, DefaultLink>(DefaultLink.class);
+		this.graph = new DirectedWeightedMultigraph<>(DefaultLink.class);
 		
-		this.visitedSourceTargetPairs = new HashSet<String>();
+		this.visitedSourceTargetPairs = new HashSet<>();
 			
-		this.modelIds = new HashSet<String>();
-		this.linkCountMap = new HashMap<String, Integer>();
-		this.nodeDataPropertyCount = new HashMap<String, Integer>();
-		this.semanticTypeMatches = new HashMap<String, Set<SemanticTypeMapping>>();
-		this.patternLinks = new HashMap<String, List<LabeledLink>>();
+		this.modelIds = new HashSet<>();
+		this.linkCountMap = new HashMap<>();
+		this.nodeDataPropertyCount = new HashMap<>();
+		this.semanticTypeMatches = new HashMap<>();
+		this.patternLinks = new HashMap<>();
 
-		this.nodeDataProperties= new HashMap<String,Set<Node>>(); 
+		this.nodeDataProperties= new HashMap<>(); 
 		
-		this.nodeIncomingLinks = new HashMap<String, Set<LabeledLink>>();
-		this.nodeOutgoingLinks = new HashMap<String, Set<LabeledLink>>();
+		this.nodeIncomingLinks = new HashMap<>();
+		this.nodeOutgoingLinks = new HashMap<>();
 		
-		this.forcedNodes = new HashSet<Node>();
+		this.forcedNodes = new HashSet<>();
 		if (addThingNode) 
 			this.initialGraph();
 		
@@ -274,7 +274,7 @@ public boolean addNodeAndUpdate(Node node, Set<Node> addedNodes) {
 			return result;
 
 		if (addedNodes == null) 
-			addedNodes = new HashSet<Node>();
+			addedNodes = new HashSet<>();
 		addedNodes.add(node);
 		if (node instanceof InternalNode) 
 			addClosureAndUpdateLinks((InternalNode)node, addedNodes);
@@ -296,7 +296,7 @@ public InternalNode copyNodeAndUpdate(Node node, boolean copyLinksToColumnNodes)
 	private void addClosureAndUpdateLinks(InternalNode node, Set<Node> addedNodes) {
 		
 		ModelingConfiguration modelingConfiguration = ModelingConfigurationRegistry.getInstance().getModelingConfiguration(ContextParametersRegistry.getInstance().getContextParameters(ontologyManager.getContextId()).getKarmaHome());
-		if (addedNodes == null) addedNodes = new HashSet<Node>();
+		if (addedNodes == null) addedNodes = new HashSet<>();
 		if (node instanceof InternalNode) {
 
 			long start = System.currentTimeMillis();
@@ -339,7 +339,7 @@ private void addClosureAndUpdateLinks(InternalNode node, Set<Node> addedNodes) {
 	public void addClosureAndUpdateLinks(Set<InternalNode> internalNodes, Set<Node> addedNodes) {
 		
 		logger.debug("<enter");
-		if (addedNodes == null) addedNodes = new HashSet<Node>();
+		if (addedNodes == null) addedNodes = new HashSet<>();
 
 		long start = System.currentTimeMillis();
 		float elapsedTimeSec;
@@ -401,14 +401,14 @@ public boolean addNode(Node node) {
 //		logger.info("Added in idToNodeMap:" + node.getId());
 		Set<Node> nodesWithSameUri = uriToNodesMap.get(node.getUri());
 		if (nodesWithSameUri == null) {
-			nodesWithSameUri = new HashSet<Node>();
+			nodesWithSameUri = new HashSet<>();
 			uriToNodesMap.put(node.getUri(), nodesWithSameUri);
 		}
 		nodesWithSameUri.add(node);
 		
 		Set<Node> nodesWithSameType = typeToNodesMap.get(node.getType());
 		if (nodesWithSameType == null) {
-			nodesWithSameType = new HashSet<Node>();
+			nodesWithSameType = new HashSet<>();
 			typeToNodesMap.put(node.getType(), nodesWithSameType);
 		}
 		nodesWithSameType.add(node);
@@ -540,14 +540,14 @@ public boolean addLink(Node source, Node target, DefaultLink link) {
 		
 		Set<LabeledLink> linksWithSameUri = uriToLinksMap.get(labeledLink.getUri());
 		if (linksWithSameUri == null) {
-			linksWithSameUri = new HashSet<LabeledLink>();
+			linksWithSameUri = new HashSet<>();
 			uriToLinksMap.put(labeledLink.getUri(), linksWithSameUri);
 		}
 		linksWithSameUri.add(labeledLink);
 				
 		Set<LabeledLink> linksWithSameType = typeToLinksMap.get(labeledLink.getType());
 		if (linksWithSameType == null) {
-			linksWithSameType = new HashSet<LabeledLink>();
+			linksWithSameType = new HashSet<>();
 			typeToLinksMap.put(labeledLink.getType(), linksWithSameType);
 		}
 		linksWithSameType.add(labeledLink);
@@ -555,7 +555,7 @@ public boolean addLink(Node source, Node target, DefaultLink link) {
 		if (labeledLink.getStatus() != LinkStatus.Normal) {
 			Set<LabeledLink> linksWithSameStatus = statusToLinksMap.get(labeledLink.getStatus());
 			if (linksWithSameStatus == null) { 
-				linksWithSameStatus = new HashSet<LabeledLink>();
+				linksWithSameStatus = new HashSet<>();
 				statusToLinksMap.put(labeledLink.getStatus(), linksWithSameStatus);
 			}
 		}
@@ -580,7 +580,7 @@ public boolean addLink(Node source, Node target, DefaultLink link) {
 			
 			Set<Node> dataPropertyColumnNodes = this.nodeDataProperties.get(key);
 			if (dataPropertyColumnNodes == null) {
-				dataPropertyColumnNodes = new HashSet<Node>();
+				dataPropertyColumnNodes = new HashSet<>();
 				this.nodeDataProperties.put(key, dataPropertyColumnNodes);
 			}
 			dataPropertyColumnNodes.add(target);
@@ -588,7 +588,7 @@ public boolean addLink(Node source, Node target, DefaultLink link) {
 			key = source.getUri() + link.getUri();
 			Set<SemanticTypeMapping> SemanticTypeMappings = this.semanticTypeMatches.get(key);
 			if (SemanticTypeMappings == null) {
-				SemanticTypeMappings = new HashSet<SemanticTypeMapping>();
+				SemanticTypeMappings = new HashSet<>();
 				this.semanticTypeMatches.put(key, SemanticTypeMappings);
 			}
 			SemanticTypeMappings.add(new SemanticTypeMapping(null, null, (InternalNode)source, labeledLink, (ColumnNode)target));
@@ -609,7 +609,7 @@ public void savePatternLink(LabeledLink l) {
 		String key = l.getSource().getUri() + l.getUri() + l.getTarget().getUri();
 		List<LabeledLink> links = this.patternLinks.get(key);
 		if (links == null) {
-			links = new LinkedList<LabeledLink>();
+			links = new LinkedList<>();
 			this.patternLinks.put(key, links);
 		}
 		links.add(l);
@@ -684,7 +684,7 @@ public void changeLinkStatus(LabeledLink link, LinkStatus newStatus) {
 		
 		Set<LabeledLink> linksWithNewStatus = this.statusToLinksMap.get(newStatus);
 		if (linksWithNewStatus == null) {
-			linksWithNewStatus = new HashSet<LabeledLink>();
+			linksWithNewStatus = new HashSet<>();
 			statusToLinksMap.put(newStatus, linksWithNewStatus);
 		}
 		linksWithNewStatus.add(graphLink);
@@ -801,7 +801,7 @@ public boolean removeNode(Node node) {
 	
 	public LinkFrequency getMoreFrequentLinkBetweenNodes(String sourceUri, String targetUri) {
 
-		List<String> possibleLinksFromSourceToTarget = new ArrayList<String>();
+		List<String> possibleLinksFromSourceToTarget = new ArrayList<>();
 
 		HashSet<String> objectPropertiesDirect;
 		HashSet<String> objectPropertiesIndirect;
@@ -932,7 +932,7 @@ public LinkFrequency getMoreFrequentLinkBetweenNodes(String sourceUri, String ta
 				selectedLinkUri = Uris.RDFS_SUBCLASS_URI;
 				type = 9;
 			} else {	// if (objectPropertiesWithoutDomainAndRange != null && objectPropertiesWithoutDomainAndRange.keySet().size() > 0) {
-				selectedLinkUri = new ArrayList<String>(objectPropertiesWithoutDomainAndRange.keySet()).get(0);
+				selectedLinkUri = new ArrayList<>(objectPropertiesWithoutDomainAndRange.keySet()).get(0);
 				type = 10;
 			}
 
@@ -1000,7 +1000,7 @@ private void updateLinkCountMap(DefaultLink link) {
 
 	private HashSet<String> getUriDirectConnections(String uri) {
 		
-		HashSet<String> uriDirectConnections = new HashSet<String>();
+		HashSet<String> uriDirectConnections = new HashSet<>();
 		
 		HashSet<String> opDomainClasses = null;
 		HashMap<String, Label> superClasses = null;
@@ -1026,9 +1026,9 @@ private Set<String> computeUriClosure(String uri) {
 		if (closure != null) 
 			return closure;
 	
-		closure = new HashSet<String>();
-		List<String> closedList = new ArrayList<String>();
-		HashMap<String, Set<String>> dependentUrisMap = new HashMap<String, Set<String>>();
+		closure = new HashSet<>();
+		List<String> closedList = new ArrayList<>();
+		HashMap<String, Set<String>> dependentUrisMap = new HashMap<>();
 		computeUriClosureRecursive(uri, closure, closedList, dependentUrisMap);
 		if (closedList.contains(uri) && !closure.contains(uri))
 			closure.add(uri);
@@ -1075,7 +1075,7 @@ private void computeUriClosureRecursive(String uri, Set<String> closure,
 				if (closedList.contains(c)) {
 					Set<String> dependentUris = dependentUrisMap.get(uri);
 					if (dependentUris == null) {
-						dependentUris = new HashSet<String>();
+						dependentUris = new HashSet<>();
 						dependentUrisMap.put(uri, dependentUris);
 					}
 					if (!dependentUris.contains(c)) dependentUris.add(c);
@@ -1083,7 +1083,7 @@ private void computeUriClosureRecursive(String uri, Set<String> closure,
 				}
 				if (!closure.contains(c)) closure.add(c);
 				if (!closedList.contains(c)) closedList.add(c);
-				Set<String> localClosure = new HashSet<String>();
+				Set<String> localClosure = new HashSet<>();
 				computeUriClosureRecursive(c, localClosure, closedList, dependentUrisMap);
 				for (String s : localClosure)
 					if (!closure.contains(s)) closure.add(s);
@@ -1096,7 +1096,7 @@ private void computeUriClosureRecursive(String uri, Set<String> closure,
 	
 	public List<Node> getNodeClosure(Node node) {
 		
-		List<Node> nodeClosure = new ArrayList<Node>();
+		List<Node> nodeClosure = new ArrayList<>();
 		if (node instanceof ColumnNode) return nodeClosure;
 		
 		String uri = node.getUri();
@@ -1122,7 +1122,7 @@ private void addNodeClosure(Node node, Set<Node> newAddedNodes) {
 
 		logger.debug("<enter");
 		
-		if (newAddedNodes == null) newAddedNodes = new HashSet<Node>();
+		if (newAddedNodes == null) newAddedNodes = new HashSet<>();
 		
 		String uri = node.getUri();
 		if (this.uriClosure.get(uri) != null) // the closure is already computed and added to the graph.
@@ -1152,7 +1152,7 @@ private void updateLinks() {
 		if (nodeSet == null || nodeSet.isEmpty())
 			return;
 		
-		List<Node> nodes = new ArrayList<Node>(nodeSet);
+		List<Node> nodes = new ArrayList<>(nodeSet);
 		logger.debug("number of internal nodes: " + nodes.size());
 		
 		Node source;
@@ -1301,7 +1301,7 @@ public List<LabeledLink> getPossibleLinks(String sourceId, String targetId) {
 	public List<LabeledLink> getPossibleLinks(String sourceId, String targetId, LinkType linkType, 
 			ObjectPropertyType objectProertyType) {
 		
-		List<LabeledLink> sortedLinks = new ArrayList<LabeledLink>();
+		List<LabeledLink> sortedLinks = new ArrayList<>();
 
 		Node source = this.idToNodeMap.get(sourceId);
 		Node target = this.idToNodeMap.get(targetId);
@@ -1361,7 +1361,7 @@ public List<LabeledLink> getPossibleLinks(String sourceId, String targetId, Link
 	
 	public List<LabeledLink> getLinks(String sourceId, String targetId) {
 		
-		List<LabeledLink> links  = new LinkedList<LabeledLink>();
+		List<LabeledLink> links  = new LinkedList<>();
 
 		Node source = this.getIdToNodeMap().get(sourceId);
 		if (source == null) return links;
@@ -1383,7 +1383,7 @@ public List<LabeledLink> getLinks(String sourceId, String targetId) {
 
 	public List<LabeledLink> getIncomingLinks(String nodeId) {
 		
-		List<LabeledLink> incomingLinks  = new LinkedList<LabeledLink>();
+		List<LabeledLink> incomingLinks  = new LinkedList<>();
 
 		Node node = this.getIdToNodeMap().get(nodeId);
 		if (node == null) return incomingLinks;
@@ -1402,7 +1402,7 @@ public List<LabeledLink> getIncomingLinks(String nodeId) {
 	
 	public List<LabeledLink> getOutgoingLinks(String nodeId) {
 		
-		List<LabeledLink> outgoingLinks  = new LinkedList<LabeledLink>();
+		List<LabeledLink> outgoingLinks  = new LinkedList<>();
 
 		Node node = this.getIdToNodeMap().get(nodeId);
 		if (node == null) return outgoingLinks;
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphBuilderTopK.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphBuilderTopK.java
index 80bde9e36..95e9d7f98 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphBuilderTopK.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphBuilderTopK.java
@@ -46,25 +46,25 @@ public class GraphBuilderTopK extends GraphBuilder {
 	
 	public GraphBuilderTopK(OntologyManager ontologyManager, boolean addThingNode) { 
 		super(ontologyManager, addThingNode);
-		if (topKGraph == null) topKGraph = new HashMap<SteinerNode, TreeSet<SteinerEdge>>();
-		if (topKGraphNodes == null) topKGraphNodes = new HashMap<String, SteinerNode>();
+		if (topKGraph == null) topKGraph = new HashMap<>();
+		if (topKGraphNodes == null) topKGraphNodes = new HashMap<>();
 	}
 	
 	public GraphBuilderTopK(OntologyManager ontologyManager, DirectedWeightedMultigraph<Node, DefaultLink> graph) {
 		super(ontologyManager, graph, true);
-		if (topKGraph == null) topKGraph = new HashMap<SteinerNode, TreeSet<SteinerEdge>>();
-		if (topKGraphNodes == null) topKGraphNodes = new HashMap<String, SteinerNode>();
+		if (topKGraph == null) topKGraph = new HashMap<>();
+		if (topKGraphNodes == null) topKGraphNodes = new HashMap<>();
 	}
 	
 	public HashMap<SteinerNode, TreeSet<SteinerEdge>> getTopKGraph() {
 		if (topKGraph == null)
-			topKGraph = new HashMap<SteinerNode, TreeSet<SteinerEdge>>();
+			topKGraph = new HashMap<>();
 		return topKGraph;
 	}
 
 	public HashMap<String, SteinerNode> getTopKGraphNodes() {
 		if (topKGraphNodes == null)
-			topKGraphNodes = new HashMap<String, SteinerNode>();
+			topKGraphNodes = new HashMap<>();
 		return topKGraphNodes;
 	}
 	
@@ -169,7 +169,7 @@ public List<DirectedWeightedMultigraph<Node, LabeledLink>> getTopKSteinerTrees(S
 //		for (Node n : steinerNodes)
 //			System.out.println(n instanceof ColumnNode ? ((ColumnNode)n).getColumnName() : n.getId());
 		
-		TreeSet<SteinerNode> terminals= new TreeSet<SteinerNode>();
+		TreeSet<SteinerNode> terminals= new TreeSet<>();
 		for (Node n : steinerNodes) {
 			if (onlyAddInternalNodes && !(n instanceof InternalNode)) {
 				continue;
@@ -211,8 +211,8 @@ public List<DirectedWeightedMultigraph<Node, LabeledLink>> getTopKSteinerTrees(S
 		CustomizedBANKS.graph = this.getTopKGraph();
 		CustomizedBANKS.nodes = this.getTopKGraphNodes();
 		
-		List<DirectedWeightedMultigraph<Node, LabeledLink>> results = new 
-				LinkedList<DirectedWeightedMultigraph<Node, LabeledLink>>();
+		List<DirectedWeightedMultigraph<Node, LabeledLink>> results = new
+				LinkedList<>();
 		
 		N.getTopKTrees(k);
 		DirectedWeightedMultigraph<Node, LabeledLink> processedTree = null;
@@ -274,7 +274,7 @@ public DirectedWeightedMultigraph<Node, LabeledLink> getLabeledSteinerTree(Resul
 			return null;
 		
 		WeightedMultigraph<Node, DefaultLink> tree =
-				new WeightedMultigraph<Node, DefaultLink>(DefaultLink.class);
+				new WeightedMultigraph<>(DefaultLink.class);
 		
 		if (initialTree.getFacts().isEmpty()) { //add all terminal nodes
 			for (SteinerNode t : terminals) {
@@ -282,7 +282,7 @@ public DirectedWeightedMultigraph<Node, LabeledLink> getLabeledSteinerTree(Resul
 			}
 		}
 		
-		HashSet<Node> visitedNodes = new HashSet<Node>();
+		HashSet<Node> visitedNodes = new HashSet<>();
 		Node source, target;
 		DefaultLink l; 
 		double weight;
@@ -392,7 +392,7 @@ public static void main(String[] args) throws Exception {
 		gbtk.addLink(n2, n3, e7, 0.5);
 		
 		
-		Set<Node> steinerNodes = new HashSet<Node>();
+		Set<Node> steinerNodes = new HashSet<>();
 		steinerNodes.add(n2);
 		steinerNodes.add(n3);
 		
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphPath.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphPath.java
index d4d079a7a..70b516830 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphPath.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphPath.java
@@ -36,13 +36,13 @@ public class GraphPath {
 	
 	
 	public GraphPath() {
-		this.edgeList = new LinkedList<DefaultLink>();
+		this.edgeList = new LinkedList<>();
 		this.startNode = null;
 		this.endNode = null;
 	}
 	
 	public GraphPath(GraphPath gp) {
-		this.edgeList = new LinkedList<DefaultLink>();
+		this.edgeList = new LinkedList<>();
 		for (DefaultLink l : gp.getLinks())
 			this.addLink(l);
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphPreProcess.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphPreProcess.java
index e77a37a51..292b0b9db 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphPreProcess.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphPreProcess.java
@@ -89,7 +89,7 @@ private void updateWeights() {
 	}
 
 	public UndirectedGraph<Node, DefaultLink> getUndirectedGraph() {	
-		return  new AsUndirectedGraph<Node, DefaultLink>(this.gPrime);
+		return new AsUndirectedGraph<>(this.gPrime);
 	}
 	
 }
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphUtil.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphUtil.java
index a382b1173..f8c4989fb 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphUtil.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphUtil.java
@@ -84,7 +84,7 @@ public static DirectedGraph<Node, DefaultLink> asDirectedGraph(UndirectedGraph<N
 			return null;
 		}		
 
-		DirectedGraph<Node, DefaultLink> g = new DirectedWeightedMultigraph<Node, DefaultLink>(DefaultLink.class);
+		DirectedGraph<Node, DefaultLink> g = new DirectedWeightedMultigraph<>(DefaultLink.class);
 		
 		for (Node v : undirectedGraph.vertexSet())
 			g.addVertex(v);
@@ -103,7 +103,7 @@ public static DirectedWeightedMultigraph<Node, DefaultLink> asDefaultGraph(Direc
 			return null;
 		}		
 
-		DirectedWeightedMultigraph<Node, DefaultLink> g = new DirectedWeightedMultigraph<Node, DefaultLink>(DefaultLink.class);
+		DirectedWeightedMultigraph<Node, DefaultLink> g = new DirectedWeightedMultigraph<>(DefaultLink.class);
 		
 		for (Node v : graph.vertexSet())
 			g.addVertex(v);
@@ -121,7 +121,7 @@ public static DirectedWeightedMultigraph<Node, LabeledLink> asLabeledGraph(Direc
 			return null;
 		}		
 
-		DirectedWeightedMultigraph<Node, LabeledLink> g = new DirectedWeightedMultigraph<Node, LabeledLink>(LabeledLink.class);
+		DirectedWeightedMultigraph<Node, LabeledLink> g = new DirectedWeightedMultigraph<>(LabeledLink.class);
 		
 		for (Node v : graph.vertexSet())
 			g.addVertex(v);
@@ -140,7 +140,7 @@ public static UndirectedGraph<Node, DefaultLink> asDefaultGraph(UndirectedGraph<
 			return null;
 		}		
 
-		UndirectedGraph<Node, DefaultLink> g = new WeightedMultigraph<Node, DefaultLink>(DefaultLink.class);
+		UndirectedGraph<Node, DefaultLink> g = new WeightedMultigraph<>(DefaultLink.class);
 		
 		for (Node v : graph.vertexSet())
 			g.addVertex(v);
@@ -158,7 +158,7 @@ public static WeightedMultigraph<Node, LabeledLink> asLabeledGraph(WeightedMulti
 			return null;
 		}		
 
-		WeightedMultigraph<Node, LabeledLink> g = new WeightedMultigraph<Node, LabeledLink>(LabeledLink.class);
+		WeightedMultigraph<Node, LabeledLink> g = new WeightedMultigraph<>(LabeledLink.class);
 		
 		for (Node v : graph.vertexSet())
 			g.addVertex(v);
@@ -274,8 +274,8 @@ public static String labeledGraphToString(Graph<Node, LabeledLink> graph) {
 	
 	public static List<GraphPath> getPaths(DirectedGraph<Node, DefaultLink> g, int length) {
 		
-		List<GraphPath> graphPaths = 
-				new LinkedList<GraphPath>();
+		List<GraphPath> graphPaths =
+				new LinkedList<>();
 
 		if (g == null)
 			return graphPaths;
@@ -291,8 +291,8 @@ public static List<GraphPath> getPaths(DirectedGraph<Node, DefaultLink> g, int l
 	
 	public static List<GraphPath> getOutgoingPaths(DirectedGraph<Node, DefaultLink> g, Node n, int length) {
 		
-		List<GraphPath> graphPaths = 
-				new LinkedList<GraphPath>();
+		List<GraphPath> graphPaths =
+				new LinkedList<>();
 
 		if (g == null || n == null || length <= 0 || !g.vertexSet().contains(n))
 			return graphPaths;
@@ -324,7 +324,7 @@ public static List<GraphPath> getOutgoingPaths(DirectedGraph<Node, DefaultLink>
 	
 	public static Set<Node> getOutNeighbors(DirectedGraph<Node, DefaultLink> g, Node n) {
 		
-		Set<Node> neighbors = new HashSet<Node>();
+		Set<Node> neighbors = new HashSet<>();
 		if (g == null || n == null || !g.vertexSet().contains(n))
 			return neighbors;
 		
@@ -341,7 +341,7 @@ public static Set<Node> getOutNeighbors(DirectedGraph<Node, DefaultLink> g, Node
 
 	public static Set<Node> getInNeighbors(DirectedGraph<Node, DefaultLink> g, Node n) {
 		
-		Set<Node> neighbors = new HashSet<Node>();
+		Set<Node> neighbors = new HashSet<>();
 		if (g == null || n == null || !g.vertexSet().contains(n))
 			return neighbors;
 		
@@ -357,7 +357,7 @@ public static Set<Node> getInNeighbors(DirectedGraph<Node, DefaultLink> g, Node
 	
 	public static Set<LabeledLink> getDomainLinksInLabeledGraph(DirectedGraph<Node, LabeledLink> g, ColumnNode n) {
 		
-		Set<LabeledLink> domainLinks = new HashSet<LabeledLink>();
+		Set<LabeledLink> domainLinks = new HashSet<>();
 		if (g == null || 
 				n == null || 
 				!g.vertexSet().contains(n))
@@ -375,7 +375,7 @@ public static Set<LabeledLink> getDomainLinksInLabeledGraph(DirectedGraph<Node,
 	
 	public static Set<LabeledLink> getDomainLinksInDefaultGraph(DirectedGraph<Node, DefaultLink> g, ColumnNode n) {
 		
-		Set<LabeledLink> domainLinks = new HashSet<LabeledLink>();
+		Set<LabeledLink> domainLinks = new HashSet<>();
 		if (g == null || 
 				n == null || 
 				!g.vertexSet().contains(n))
@@ -394,7 +394,7 @@ public static Set<LabeledLink> getDomainLinksInDefaultGraph(DirectedGraph<Node,
 	
 	public static HashMap<SemanticType, LabeledLink> getDomainLinks(DirectedGraph<Node, DefaultLink> g, ColumnNode n, List<SemanticType> semanticTypes) {
 		
-		HashMap<SemanticType, LabeledLink> domainLinks = new HashMap<SemanticType, LabeledLink>();
+		HashMap<SemanticType, LabeledLink> domainLinks = new HashMap<>();
 		if (g == null || 
 				n == null || 
 				semanticTypes == null ||
@@ -695,7 +695,7 @@ public static DirectedWeightedMultigraph<Node, DefaultLink> readGraph(JsonReader
 		Node n, source, target;
 		DefaultLink l;
 		Double[] weight = new Double[1];
-		HashMap<String, Node> idToNodes = new HashMap<String, Node>();
+		HashMap<String, Node> idToNodes = new HashMap<>();
 		
 		reader.beginObject();
 	    while (reader.hasNext()) {
@@ -773,7 +773,7 @@ private static Node readNode(JsonReader reader) throws IOException {
 			} else if (key.equals("userSelectedSemanticType") && reader.peek() != JsonToken.NULL) {
 				userSelectedSemanticType = readSemanticType(reader);
 			} else if (key.equals("suggestedSemanticTypes") && reader.peek() != JsonToken.NULL) {
-				learnedSemanticTypes = new ArrayList<SemanticType>();
+				learnedSemanticTypes = new ArrayList<>();
 				reader.beginArray();
 			    while (reader.hasNext()) {
 			    	SemanticType semanticType = readSemanticType(reader);
@@ -781,7 +781,7 @@ private static Node readNode(JsonReader reader) throws IOException {
 				}
 		    	reader.endArray();				
 			} else if (key.equals("userSemanticTypes") && reader.peek() != JsonToken.NULL) {
-				userSemanticTypes = new ArrayList<SemanticType>();
+				userSemanticTypes = new ArrayList<>();
 				reader.beginArray();
 			    while (reader.hasNext()) {
 			    	SemanticType semanticType = readSemanticType(reader);
@@ -789,7 +789,7 @@ private static Node readNode(JsonReader reader) throws IOException {
 				}
 		    	reader.endArray();				} 
 			else if (key.equals("learnedSemanticTypes") && reader.peek() != JsonToken.NULL) {
-				learnedSemanticTypes = new ArrayList<SemanticType>();
+				learnedSemanticTypes = new ArrayList<>();
 				reader.beginArray();
 			    while (reader.hasNext()) {
 			    	SemanticType semanticType = readSemanticType(reader);
@@ -810,7 +810,7 @@ else if (key.equals("learnedSemanticTypes") && reader.peek() != JsonToken.NULL)
     	} else if (type == NodeType.ColumnNode) {
     		n = new ColumnNode(id, hNodeId, columnName, rdfLiteralType);
     		if (userSemanticTypes == null && userSelectedSemanticType != null) {
-				userSemanticTypes = new ArrayList<SemanticType>();
+				userSemanticTypes = new ArrayList<>();
 				userSemanticTypes.add(userSelectedSemanticType);
     		}
     		if (userSemanticTypes != null) {
@@ -968,7 +968,7 @@ private static SemanticType readSemanticType(JsonReader reader) throws IOExcepti
 	
 	private static Set<String> readModelIds(JsonReader reader) throws IOException {
 		
-		Set<String> modelIds = new HashSet<String>();
+		Set<String> modelIds = new HashSet<>();
 		
 		reader.beginArray();
 	    while (reader.hasNext()) {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphVizUtil.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphVizUtil.java
index 00c0e0183..a7b6296b7 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphVizUtil.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/GraphVizUtil.java
@@ -136,7 +136,7 @@ private static org.kohsuke.graphviz.Graph convertToGraphviz(
 		//edgeStyle.attr("fontsize", "10");
 		edgeStyle.attr("fontcolor", "black");
 		
-		HashMap<Node, org.kohsuke.graphviz.Node> nodeIndex = new HashMap<Node, org.kohsuke.graphviz.Node>();
+		HashMap<Node, org.kohsuke.graphviz.Node> nodeIndex = new HashMap<>();
 		
 		for (DefaultLink e : graph.edgeSet()) {
 			
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/LinkIdFactory.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/LinkIdFactory.java
index a7f818ad1..6b9e18b56 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/LinkIdFactory.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/LinkIdFactory.java
@@ -25,7 +25,7 @@
 
 public class LinkIdFactory {
 
-	private HashMap<String, Integer> linksUris = new HashMap<String, Integer>();
+	private HashMap<String, Integer> linksUris = new HashMap<>();
 	public static final String separator = "---";
 
 //	public String getLinkId(String uri) {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/NodeIdFactory.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/NodeIdFactory.java
index 8f4f89b44..34091c018 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/NodeIdFactory.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/NodeIdFactory.java
@@ -25,7 +25,7 @@
 
 public class NodeIdFactory implements Cloneable {
 
-	private HashMap<String, Integer> nodeUris = new HashMap<String, Integer>();
+	private HashMap<String, Integer> nodeUris = new HashMap<>();
 	
 
 	public String getNodeId(String uri) {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/SemanticModel.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/SemanticModel.java
index a4c475dfc..017a46ea6 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/SemanticModel.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/SemanticModel.java
@@ -89,7 +89,7 @@ public SemanticModel(String id,
 		this.graph = graph;
 
 		this.sourceColumns = this.getColumnNodes();
-		this.mappingToSourceColumns = new HashMap<ColumnNode, ColumnNode>();
+		this.mappingToSourceColumns = new HashMap<>();
 		for (ColumnNode c : this.sourceColumns)
 			this.mappingToSourceColumns.put(c, c);
 	}
@@ -104,7 +104,7 @@ public SemanticModel(String id,
 		this.setUserTypesForColumnNodes();
 
 		this.sourceColumns = this.getColumnNodes();
-		this.mappingToSourceColumns = new HashMap<ColumnNode, ColumnNode>();
+		this.mappingToSourceColumns = new HashMap<>();
 		for (ColumnNode c : this.sourceColumns)
 			this.mappingToSourceColumns.put(c, c);
 	}
@@ -122,7 +122,7 @@ public SemanticModel(Workspace workspace, Worksheet worksheet,
 		this.setUserTypesForColumnNodes();
 		
 		this.sourceColumns = this.getColumnNodes();
-		this.mappingToSourceColumns = new HashMap<ColumnNode, ColumnNode>();
+		this.mappingToSourceColumns = new HashMap<>();
 		for (ColumnNode c : this.sourceColumns)
 			this.mappingToSourceColumns.put(c, c);
 	}
@@ -198,7 +198,7 @@ public void setMrr(Double mrr) {
 	}
 
 	public Set<InternalNode> getInternalNodes() {
-		Set<InternalNode> internalNodes = new HashSet<InternalNode>();
+		Set<InternalNode> internalNodes = new HashSet<>();
 		if (this.graph != null) {
 			for (Node n : this.graph.vertexSet())
 				if (n instanceof InternalNode)
@@ -208,7 +208,7 @@ public Set<InternalNode> getInternalNodes() {
 	}
 
 	public List<ColumnNode> getColumnNodes() {
-		List<ColumnNode> columnNodes = new LinkedList<ColumnNode>();
+		List<ColumnNode> columnNodes = new LinkedList<>();
 		if (this.graph != null) {
 			for (Node n : this.graph.vertexSet())
 				if (n instanceof ColumnNode)
@@ -274,7 +274,7 @@ public ModelEvaluation evaluate(SemanticModel baseModel, boolean ignoreSemanticT
 			return new ModelEvaluation(null, null, null, null);
 		
 		NodeIdFactory nodeIdFactory = new NodeIdFactory();
-		HashMap<Node,String> baseNodeIds = new HashMap<Node,String>();
+		HashMap<Node,String> baseNodeIds = new HashMap<>();
 		for (Node n : baseModel.getGraph().vertexSet()) {
 			if (n instanceof InternalNode)
 				baseNodeIds.put(n, nodeIdFactory.getNodeId(n.getUri()));
@@ -283,7 +283,7 @@ public ModelEvaluation evaluate(SemanticModel baseModel, boolean ignoreSemanticT
 		}
 		
 		Set<String> baseTriples = getTriples(baseModel.getGraph(), baseNodeIds, ignoreSemanticTypes, ignoreColumnNodes);
-		Set<String> targetTriples = null;
+		Set<String> targetTriples;
 		List<HashMap<Node,String>> targetNodeIdSets = getPossibleNodeIdSets();
 		if (targetNodeIdSets == null)
 			return null;
@@ -313,7 +313,7 @@ private Set<String> getTriples(DirectedWeightedMultigraph<Node, LabeledLink> g,
 			boolean ignoreSemanticTypes, boolean ignoreColumnNodes) {
 		
 		String separator = "|";
-		Set<String> triples = new HashSet<String>();
+		Set<String> triples = new HashSet<>();
 		if (g == null)
 			return triples;
 		
@@ -338,16 +338,16 @@ private Set<String> getTriples(DirectedWeightedMultigraph<Node, LabeledLink> g,
 	private List<HashMap<Node,String>> getPossibleNodeIdSets() {
 		
 		DirectedWeightedMultigraph<Node, LabeledLink> g = this.getGraph();
-		List<HashMap<Node,String>> nodeIdSets = new ArrayList<HashMap<Node,String>>();
+		List<HashMap<Node,String>> nodeIdSets = new ArrayList<>();
 		if (g == null)
 			return nodeIdSets;
 		
-		Set<Node> internalNodes = new HashSet<Node>();
+		Set<Node> internalNodes = new HashSet<>();
 		for (Node n : g.vertexSet()) 
 			if (n instanceof InternalNode) 
 				internalNodes.add(n);
 
-		Set<Node> columnNodes = new HashSet<Node>();
+		Set<Node> columnNodes = new HashSet<>();
 		for (Node n : g.vertexSet()) 
 			if (n instanceof ColumnNode) 
 				columnNodes.add(n);
@@ -371,11 +371,11 @@ private List<HashMap<Node,String>> getPossibleNodeIdSets() {
 //		System.out.println(numberOfPossibleSets);
 
 		for (int i = 0; i < numberOfPossibleSets; i++) {
-			HashMap<Node, String> nodeIds = new HashMap<Node,String>();
+			HashMap<Node, String> nodeIds = new HashMap<>();
 			NodeIdFactory nodeIdFactory = new NodeIdFactory();
 			
 			for (Node n : columnNodes) {
-				ColumnNode cn = null;
+				ColumnNode cn;
 				if (this.mappingToSourceColumns != null && 
 						(cn = this.mappingToSourceColumns.get((ColumnNode)n)) != null) {
 					nodeIds.put(n, cn.getId());
@@ -429,14 +429,14 @@ private List<HashMap<Node,String>> getPossibleNodeIdSets() {
 		for (String s : index.keySet()) {
 			Collection<Node> nodeGroup = index.get(s);
 			if (nodeGroup != null && nodeGroup.size() > 1) {
-				Set<String> ids = new HashSet<String>();
-				List<Node> nodes = new ArrayList<Node>();
+				Set<String> ids = new HashSet<>();
+				List<Node> nodes = new ArrayList<>();
 				nodes.addAll(nodeGroup);
 				for (Node n : nodes)
 					ids.add(nodeIdFactory.getNodeId(n.getLabel().getUri()));
 
 				Collection<List<String>> permutations = Collections2.permutations(ids);
-				List<List<String>> permList = new ArrayList<List<String>>();
+				List<List<String>> permList = new ArrayList<>();
 				permList.addAll(permutations);
 				
 				interval = interval / BigIntegerMath.factorial(nodeGroup.size()).intValue();
@@ -465,8 +465,8 @@ public ModelEvaluation evaluate_old(SemanticModel baseModel) {
 		Double distance = getDistance(baseModel);
 		
 		int maxLength = maxPathLengthForEvaluation;
-		List<GraphPath> basePaths = new LinkedList<GraphPath>();
-		List<GraphPath> modelPaths = new LinkedList<GraphPath>();
+		List<GraphPath> basePaths = new LinkedList<>();
+		List<GraphPath> modelPaths = new LinkedList<>();
 		List<GraphPath> gpList;
 		String pathStr;
 		for (int i = 1; i <= maxLength; i++) {
@@ -475,10 +475,10 @@ public ModelEvaluation evaluate_old(SemanticModel baseModel) {
 			gpList = GraphUtil.getPaths(GraphUtil.asDefaultGraph(this.graph), i);
 			if (gpList != null) modelPaths.addAll(gpList);
 		}
-		Set<String> basePathString = new HashSet<String>();
-		Set<String> modelPathString = new HashSet<String>();
+		Set<String> basePathString = new HashSet<>();
+		Set<String> modelPathString = new HashSet<>();
 		
-		Map<String, Integer> visitedPaths = new HashMap<String, Integer>();
+		Map<String, Integer> visitedPaths = new HashMap<>();
 		Integer count;
 		for (GraphPath gp : basePaths) {
 			pathStr = getPathString(baseModel, gp);
@@ -563,17 +563,17 @@ private Double getDistance(SemanticModel sm) {
 				linkDeletion = 0,
 				linkRelabeling = 0;
 		
-		HashMap<String, Integer> mainNodes = new HashMap<String, Integer>();
-		HashMap<String, Integer> targetNodes = new HashMap<String, Integer>();
+		HashMap<String, Integer> mainNodes = new HashMap<>();
+		HashMap<String, Integer> targetNodes = new HashMap<>();
 
-		HashMap<String, Integer> mainLinks = new HashMap<String, Integer>();
-		HashMap<String, Integer> targetLinks = new HashMap<String, Integer>();
+		HashMap<String, Integer> mainLinks = new HashMap<>();
+		HashMap<String, Integer> targetLinks = new HashMap<>();
 		
-		HashMap<String, Set<String>> mainNodePairToLinks = new HashMap<String, Set<String>>();
-		HashMap<String, Set<String>> targetNodePairToLinks = new HashMap<String, Set<String>>();
+		HashMap<String, Set<String>> mainNodePairToLinks = new HashMap<>();
+		HashMap<String, Set<String>> targetNodePairToLinks = new HashMap<>();
 
 		String key, sourceStr, targetStr, linkStr;
-		Integer count = 0;
+		Integer count;
 		
 		// Adding the nodes to the maps
 		for (Node n : mainModel.graph.vertexSet()) {
@@ -624,7 +624,7 @@ else if (target instanceof ColumnNode) {
 			else mainLinks.put(key, ++count);
 			
 			Set<String> links = mainNodePairToLinks.get(sourceStr + targetStr);
-			if (links == null) { links = new HashSet<String>(); mainNodePairToLinks.put(sourceStr + targetStr, links); }
+			if (links == null) { links = new HashSet<>(); mainNodePairToLinks.put(sourceStr + targetStr, links); }
 			links.add(linkStr);
 		}
 		for (LabeledLink l : targetModel.graph.edgeSet()) {
@@ -648,7 +648,7 @@ else if (target instanceof ColumnNode) {
 			else targetLinks.put(key, ++count);
 			
 			Set<String> links = targetNodePairToLinks.get(sourceStr + targetStr);
-			if (links == null) { links = new HashSet<String>(); targetNodePairToLinks.put(sourceStr + targetStr, links); }
+			if (links == null) { links = new HashSet<>(); targetNodePairToLinks.put(sourceStr + targetStr, links); }
 			links.add(linkStr);
 		}
 		
@@ -856,8 +856,8 @@ private static SemanticModel readModel(JsonReader reader) throws IOException {
 			} else if (key.equals("description") && reader.peek() != JsonToken.NULL) {
 				description = reader.nextString();
 			} else if (key.equals("sourceColumns") && reader.peek() != JsonToken.NULL) {
-				sourceColumns = new LinkedList<ColumnNode>();
-				sourceColumnIds = new HashMap<String, ColumnNode>();
+				sourceColumns = new LinkedList<>();
+				sourceColumnIds = new HashMap<>();
 				reader.beginArray();
 			    while (reader.hasNext()) {
 			    	ColumnNode cn = readSourceColumn(reader);
@@ -868,7 +868,7 @@ private static SemanticModel readModel(JsonReader reader) throws IOException {
 				}
 		    	reader.endArray();				
 			} else if (key.equals("mappingToSourceColumns") && reader.peek() != JsonToken.NULL) {
-				mappingToSourceColumnsIds = new HashMap<String, String>();
+				mappingToSourceColumnsIds = new HashMap<>();
 				Map <String, String> oneEntryMapping;
 				reader.beginArray();
 			    while (reader.hasNext()) {
@@ -885,7 +885,7 @@ private static SemanticModel readModel(JsonReader reader) throws IOException {
 		}
     	reader.endObject();
     	
-		Map<ColumnNode, ColumnNode> mappingToSourceColumns = new HashMap<ColumnNode, ColumnNode>();
+		Map<ColumnNode, ColumnNode> mappingToSourceColumns = new HashMap<>();
 		if (graph != null && mappingToSourceColumnsIds != null && !mappingToSourceColumnsIds.isEmpty()) {
 			for (Node n : graph.vertexSet()) {
 				if (n instanceof ColumnNode) {
@@ -948,7 +948,7 @@ private static Map<String, String> readMappingToSourceColumn(JsonReader reader)
 		}
     	reader.endObject();
     	
-    	Map<String, String> mapping = new HashMap<String, String>();
+    	Map<String, String> mapping = new HashMap<>();
     	mapping.put(id, sourceColumnId);
     	return mapping;
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/SteinerTree.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/SteinerTree.java
index 59f1edfdb..a5602797a 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/SteinerTree.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/SteinerTree.java
@@ -66,8 +66,8 @@ private Pseudograph<Node, DefaultLink> step1() {
 		
 		logger.debug("<enter");
 
-		Pseudograph<Node, DefaultLink> g = 
-			new Pseudograph<Node, DefaultLink>(DefaultLink.class);
+		Pseudograph<Node, DefaultLink> g =
+				new Pseudograph<>(DefaultLink.class);
 		
 		for (Node n : this.steinerNodes) {
 			g.addVertex(n);
@@ -76,7 +76,7 @@ private Pseudograph<Node, DefaultLink> step1() {
 		BellmanFordShortestPath<Node, DefaultLink> path;
 		
 		for (Node n1 : this.steinerNodes) {
-			path = new BellmanFordShortestPath<Node, DefaultLink>(this.graph, n1);
+			path = new BellmanFordShortestPath<>(this.graph, n1);
 			
 			for (Node n2 : this.steinerNodes) {
 				
@@ -110,16 +110,16 @@ private WeightedMultigraph<Node, DefaultLink> step2(Pseudograph<Node, DefaultLin
 		logger.debug("<enter");
 
 		KruskalMinimumSpanningTree<Node, DefaultLink> mst =
-            new KruskalMinimumSpanningTree<Node, DefaultLink>(g1);
+				new KruskalMinimumSpanningTree<>(g1);
 
 //    	logger.debug("Total MST Cost: " + mst.getSpanningTreeCost());
 
         Set<DefaultLink> edges = mst.getEdgeSet();
 
-		WeightedMultigraph<Node, DefaultLink> g2 = 
-			new WeightedMultigraph<Node, DefaultLink>(DefaultLink.class);
+		WeightedMultigraph<Node, DefaultLink> g2 =
+				new WeightedMultigraph<>(DefaultLink.class);
 		
-		List<DefaultLink> edgesSortedById = new ArrayList<DefaultLink>();
+		List<DefaultLink> edgesSortedById = new ArrayList<>();
 		
 		for (DefaultLink e : edges) 
 			edgesSortedById.add(e);
@@ -147,8 +147,8 @@ private WeightedMultigraph<Node, DefaultLink> step3(WeightedMultigraph<Node, Def
 		
 		logger.debug("<enter");
 
-		WeightedMultigraph<Node, DefaultLink> g3 = 
-			new WeightedMultigraph<Node, DefaultLink>(DefaultLink.class);
+		WeightedMultigraph<Node, DefaultLink> g3 =
+				new WeightedMultigraph<>(DefaultLink.class);
 		
 		Set<DefaultLink> edges = g2.edgeSet();
 		DijkstraShortestPath<Node, DefaultLink> path;
@@ -159,7 +159,7 @@ private WeightedMultigraph<Node, DefaultLink> step3(WeightedMultigraph<Node, Def
 			source = edge.getSource();
 			target = edge.getTarget();
 			
-			path = new DijkstraShortestPath<Node, DefaultLink>(this.graph, source, target);
+			path = new DijkstraShortestPath<>(this.graph, source, target);
 			List<DefaultLink> pathEdges = path.getPathEdgeList();
 			
 			if (pathEdges == null)
@@ -198,16 +198,16 @@ private WeightedMultigraph<Node, DefaultLink> step4(WeightedMultigraph<Node, Def
 		logger.debug("<enter");
 
 		KruskalMinimumSpanningTree<Node, DefaultLink> mst =
-            new KruskalMinimumSpanningTree<Node, DefaultLink>(g3);
+				new KruskalMinimumSpanningTree<>(g3);
 
 //    	logger.debug("Total MST Cost: " + mst.getSpanningTreeCost());
 
         Set<DefaultLink> edges = mst.getEdgeSet();
 
-		WeightedMultigraph<Node, DefaultLink> g4 = 
-			new WeightedMultigraph<Node, DefaultLink>(DefaultLink.class);
+		WeightedMultigraph<Node, DefaultLink> g4 =
+				new WeightedMultigraph<>(DefaultLink.class);
 		
-		List<DefaultLink> edgesSortedById = new ArrayList<DefaultLink>();
+		List<DefaultLink> edgesSortedById = new ArrayList<>();
 		
 		for (DefaultLink e : edges) 
 			edgesSortedById.add(e);
@@ -237,7 +237,7 @@ private WeightedMultigraph<Node, DefaultLink> step5(WeightedMultigraph<Node, Def
 
 		WeightedMultigraph<Node, DefaultLink> g5 = g4; 
 
-		List<Node> nonSteinerLeaves = new ArrayList<Node>();
+		List<Node> nonSteinerLeaves = new ArrayList<>();
 		
 		Set<Node> vertexSet = g4.vertexSet();
 		for (Node vertex : vertexSet) {
@@ -279,7 +279,7 @@ private void runAlgorithm() {
 //		GraphUtil.printGraph(g1);
 		
 		if (g1.vertexSet().size() < 2) {
-			this.tree = new WeightedMultigraph<Node, DefaultLink>(DefaultLink.class);
+			this.tree = new WeightedMultigraph<>(DefaultLink.class);
 			for (Node n : g1.vertexSet()) this.tree.addVertex(n);
 			return;
 		}
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/TreePostProcess.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/TreePostProcess.java
index 3c2297036..18e09a548 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/TreePostProcess.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/TreePostProcess.java
@@ -92,7 +92,7 @@ public Node getRoot() {
 	
 	private static List<Node> findPossibleRoots(DirectedWeightedMultigraph<Node, DefaultLink> tree) {
 
-		List<Node> possibleRoots = new ArrayList<Node>();
+		List<Node> possibleRoots = new ArrayList<>();
 
 		// If tree contains the Thing, we return it as the root
 		for (Node v: tree.vertexSet()) { 
@@ -102,14 +102,14 @@ private static List<Node> findPossibleRoots(DirectedWeightedMultigraph<Node, Def
 		}
 
 		int maxReachableNodes = -1;
-		int reachableNodes = -1;
+		int reachableNodes;
 		
-		List<Node> vertexList = new ArrayList<Node>();
-		List<Integer> reachableNodesList = new ArrayList<Integer>();
+		List<Node> vertexList = new ArrayList<>();
+		List<Integer> reachableNodesList = new ArrayList<>();
 		
 		for (Node v: tree.vertexSet()) {
-			BreadthFirstIterator<Node, DefaultLink> i = 
-				new BreadthFirstIterator<Node, DefaultLink>(tree, v);
+			BreadthFirstIterator<Node, DefaultLink> i =
+					new BreadthFirstIterator<>(tree, v);
 			
 			reachableNodes = -1;
 			while (i.hasNext()) {
@@ -152,7 +152,7 @@ private void buildOutputTree(boolean allowedChangingGraph) {
 
 		List<LabeledLink> temp1 = null;
 //		List<LabeledLink> temp2 = null;
-		List<LabeledLink> possibleLinks = new ArrayList<LabeledLink>();
+		List<LabeledLink> possibleLinks = new ArrayList<>();
 		
 		for (DefaultLink link : links) {
 			if (link instanceof CompactLink) {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/CandidateSteinerSets.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/CandidateSteinerSets.java
index 56c2773ff..71e59fda4 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/CandidateSteinerSets.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/CandidateSteinerSets.java
@@ -42,7 +42,7 @@ public class CandidateSteinerSets {
 	private String contextId;
 	public CandidateSteinerSets(int maxNumberOfSteinerNodes, String contextId) {
 		this.contextId = contextId;
-		this.steinerSets = new ArrayList<SteinerNodes>();
+		this.steinerSets = new ArrayList<>();
 	}
 	
 	public int numberOfCandidateSets() {
@@ -55,11 +55,11 @@ public List<SteinerNodes> getSteinerSets() {
 	
 	public void updateSteinerSets(Set<SemanticTypeMapping> mappings) {
 		
-		List<SteinerNodes> newSteinerNodes = new ArrayList<SteinerNodes>();
+		List<SteinerNodes> newSteinerNodes = new ArrayList<>();
 		if (mappings == null || mappings.isEmpty()) 
 			return;
 
-		List<SemanticTypeMapping> sortedMappings = new ArrayList<SemanticTypeMapping>(mappings);
+		List<SemanticTypeMapping> sortedMappings = new ArrayList<>(mappings);
 		Collections.sort(sortedMappings);
 
 		
@@ -112,7 +112,7 @@ public void updateSteinerSets(Set<SemanticTypeMapping> mappings) {
 	
 	public void updateSteinerSets(InternalNode n) {
 		
-		List<SteinerNodes> newSteinerNodes = new ArrayList<SteinerNodes>();
+		List<SteinerNodes> newSteinerNodes = new ArrayList<>();
 		if (n == null) 
 			return;
 		
@@ -166,8 +166,8 @@ private List<SteinerNodes> getTopKSteinerSets(List<SteinerNodes> steinerSets, in
 		
 		logger.info("number of steiner sets before computing pareto optimal: " + steinerSets.size());
 		
-		List<SteinerNodes> paretoFrontierSteinerSets = 
-				new ArrayList<SteinerNodes>();
+		List<SteinerNodes> paretoFrontierSteinerSets =
+				new ArrayList<>();
 		
 		if (steinerSets == null || steinerSets.isEmpty() || k <= 0)
 			return paretoFrontierSteinerSets;
@@ -191,7 +191,7 @@ private List<SteinerNodes> getTopKSteinerSets(List<SteinerNodes> steinerSets, in
 		
 		logger.info("number of steiner sets after computing pareto optimal: " + paretoFrontierSteinerSets.size());
 
-		List<SteinerNodes> results = new ArrayList<SteinerNodes>();
+		List<SteinerNodes> results = new ArrayList<>();
 		for (int i = 0; i < ModelingConfigurationRegistry.getInstance().getModelingConfiguration(contextId).getMappingBranchingFactor() && i < paretoFrontierSteinerSets.size(); i++) {
 			if (i == 0) {
 				System.out.println(paretoFrontierSteinerSets.get(i).getScoreDetailsString());
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/Coherence.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/Coherence.java
index f804eeba9..93e69e9d9 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/Coherence.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/Coherence.java
@@ -23,21 +23,21 @@ public abstract class Coherence {
 	public Coherence() {
 		this.items = new ArrayList<>();
 		this.itemsCount = 0;
-		this.patternSize = new HashMap<String, Integer>();
-		this.patternGuid = new HashMap<String, String>();
+		this.patternSize = new HashMap<>();
+		this.patternGuid = new HashMap<>();
 		this.maxPatterns = new String[NUM_OF_MAX_SIZE_PATTERNS];
 		this.numOfElementsInMaxPatterns = 0;
-		this.patternIndex = new HashMap<String, Integer>();
+		this.patternIndex = new HashMap<>();
 	}
 	
 	public Coherence(Coherence coherence) {
-		this.items = new ArrayList<CoherenceItem>(coherence.getItems());
+		this.items = new ArrayList<>(coherence.getItems());
 		this.itemsCount = coherence.itemsCount;
-		this.patternSize = new HashMap<String, Integer>(coherence.patternSize);
-		this.patternGuid = new HashMap<String, String>(coherence.patternGuid);
+		this.patternSize = new HashMap<>(coherence.patternSize);
+		this.patternGuid = new HashMap<>(coherence.patternGuid);
 		this.maxPatterns = coherence.maxPatterns.clone();
 		this.numOfElementsInMaxPatterns = coherence.numOfElementsInMaxPatterns;
-		this.patternIndex = new HashMap<String, Integer>(coherence.patternIndex);
+		this.patternIndex = new HashMap<>(coherence.patternIndex);
 	}
 	
 	public List<CoherenceItem> getItems() {
@@ -59,7 +59,7 @@ public Map<String, String> getPatternGuid() {
 	}
 
 	public List<Integer> getCoherenceList() {
-		List<Integer> coherenceList = new ArrayList<Integer>(patternSize.values());
+		List<Integer> coherenceList = new ArrayList<>(patternSize.values());
 		Collections.sort(coherenceList, Collections.reverseOrder());
 		coherenceList = coherenceList.subList(0, Math.min(coherenceList.size(), 5));
 		return coherenceList;
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/Confidence.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/Confidence.java
index bc1cf8486..03b6dbf8e 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/Confidence.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/Confidence.java
@@ -9,11 +9,11 @@ public class Confidence {
 	private List<Double> values;
 	
 	public Confidence() {
-		this.values = new ArrayList<Double>();
+		this.values = new ArrayList<>();
 	}
 	
 	public Confidence(Confidence confidence) {
-		this.values = new ArrayList<Double>(confidence.getValues());
+		this.values = new ArrayList<>(confidence.getValues());
 	}
 
 	public List<Double> getValues() {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearner.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearner.java
index 4a8a5e041..e443152c3 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearner.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearner.java
@@ -188,10 +188,10 @@ private GraphBuilder cloneGraphBuilder(GraphBuilder graphBuilder) {
 	public List<SortableSemanticModel> hypothesize(boolean useCorrectTypes, int numberOfCandidates) throws Exception {
 
 		ModelingConfiguration modelingConfiguration = ModelingConfigurationRegistry.getInstance().getModelingConfiguration(ContextParametersRegistry.getInstance().getContextParameters(ontologyManager.getContextId()).getKarmaHome());
-		List<SortableSemanticModel> sortableSemanticModels = new ArrayList<SortableSemanticModel>();
-		Set<Node> addedNodes = new HashSet<Node>(); //They should be deleted from the graph after computing the semantic models
+		List<SortableSemanticModel> sortableSemanticModels = new ArrayList<>();
+		Set<Node> addedNodes = new HashSet<>(); //They should be deleted from the graph after computing the semantic models
 
-		List<ColumnNode> columnNodes = new LinkedList<ColumnNode>();
+		List<ColumnNode> columnNodes = new LinkedList<>();
 		for (Node n : steinerNodes)
 			if (n instanceof ColumnNode)
 				columnNodes.add((ColumnNode)n);
@@ -204,8 +204,8 @@ public List<SortableSemanticModel> hypothesize(boolean useCorrectTypes, int numb
 				candidateSteinerSets.getSteinerSets().isEmpty()) {
 			logger.error("there is no candidate set of steiner nodes.");
 			
-			DirectedWeightedMultigraph<Node, LabeledLink> tree = 
-					new DirectedWeightedMultigraph<Node, LabeledLink>(LabeledLink.class);
+			DirectedWeightedMultigraph<Node, LabeledLink> tree =
+					new DirectedWeightedMultigraph<>(LabeledLink.class);
 			
 			for (Node n : steinerNodes)
 				tree.addVertex(n);
@@ -238,9 +238,9 @@ public List<SortableSemanticModel> hypothesize(boolean useCorrectTypes, int numb
 			} 
 			else 
 			{
-				topKSteinerTrees = new LinkedList<DirectedWeightedMultigraph<Node, LabeledLink>>();
+				topKSteinerTrees = new LinkedList<>();
 				SteinerTree steinerTree = new SteinerTree(
-						new AsUndirectedGraph<Node, DefaultLink>(this.graphBuilder.getGraph()), Lists.newLinkedList(sn.getNodes()));
+						new AsUndirectedGraph<>(this.graphBuilder.getGraph()), Lists.newLinkedList(sn.getNodes()));
 				WeightedMultigraph<Node, DefaultLink> t = steinerTree.getDefaultSteinerTree();
 				TreePostProcess treePostProcess = new TreePostProcess(this.graphBuilder, t);
 				if (treePostProcess.getTree() != null)
@@ -303,11 +303,11 @@ private CandidateSteinerSets getCandidateSteinerSets(List<Node> steinerNodes, in
 		CandidateSteinerSets candidateSteinerSets = new CandidateSteinerSets(maxNumberOfSteinerNodes, ontologyManager.getContextId());
 
 		if (addedNodes == null) 
-			addedNodes = new HashSet<Node>();
+			addedNodes = new HashSet<>();
 
 		Set<SemanticTypeMapping> tempSemanticTypeMappings;
-		HashMap<ColumnNode, List<SemanticType>> columnSemanticTypes = new HashMap<ColumnNode, List<SemanticType>>();
-		HashMap<String, Integer> semanticTypesCount = new HashMap<String, Integer>();
+		HashMap<ColumnNode, List<SemanticType>> columnSemanticTypes = new HashMap<>();
+		HashMap<String, Integer> semanticTypesCount = new HashMap<>();
 		List<SemanticType> candidateSemanticTypes;
 		String domainUri = "", propertyUri = "";
 
@@ -362,7 +362,7 @@ private CandidateSteinerSets getCandidateSteinerSets(List<Node> steinerNodes, in
 						GraphUtil.getDomainLinks(this.graphBuilder.getGraph(), cn, cn.getUserSemanticTypes());
 				if (domainLinks != null && !domainLinks.isEmpty()) {
 					for (SemanticType st : cn.getUserSemanticTypes()) {
-						semanticTypeMappings = new HashSet<SemanticTypeMapping>();
+						semanticTypeMappings = new HashSet<>();
 						LabeledLink domainLink = domainLinks.get(st);
 						if (domainLink == null || domainLink.getSource() == null || !(domainLink.getSource() instanceof InternalNode))
 							continue;
@@ -373,7 +373,7 @@ private CandidateSteinerSets getCandidateSteinerSets(List<Node> steinerNodes, in
 					}
 				}
 			} else {
-				semanticTypeMappings = new HashSet<SemanticTypeMapping>();
+				semanticTypeMappings = new HashSet<>();
 				for (SemanticType semanticType: candidateSemanticTypes) {
 	
 					logger.info("\t" + semanticType.getConfidenceScore() + " :" + semanticType.getModelLabelString());
@@ -436,9 +436,9 @@ private Set<SemanticTypeMapping> findSemanticTypeInGraph(ColumnNode sourceColumn
 		logger.debug("finding matches for semantic type in the graph ... ");
 
 		if (addedNodes == null)
-			addedNodes = new HashSet<Node>();
+			addedNodes = new HashSet<>();
 
-		Set<SemanticTypeMapping> mappings = new HashSet<SemanticTypeMapping>();
+		Set<SemanticTypeMapping> mappings = new HashSet<>();
 
 		if (semanticType == null) {
 			logger.error("semantic type is null.");
@@ -533,7 +533,7 @@ private SemanticTypeMapping addSemanticTypeStruct(ColumnNode sourceColumn, Seman
 		logger.debug("adding semantic type to the graph ... ");
 
 		if (addedNodes == null) 
-			addedNodes = new HashSet<Node>();
+			addedNodes = new HashSet<>();
 
 		if (semanticType == null) {
 			logger.error("semantic type is null.");
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearner_Old.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearner_Old.java
index 282a5aa3d..0daf1b398 100755
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearner_Old.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearner_Old.java
@@ -164,7 +164,7 @@ private boolean isGraphUpToDate() {
 
 	public List<SortableSemanticModel_Old> hypothesize(boolean useCorrectTypes, int numberOfCRFCandidates) {
 
-		Set<Node> addedNodes = new HashSet<Node>(); //They should be deleted from the graph after computing the semantic models
+		Set<Node> addedNodes = new HashSet<>(); //They should be deleted from the graph after computing the semantic models
 
 		logger.info("finding candidate steiner sets ... ");
 		CandidateSteinerSets candidateSteinerSets = getCandidateSteinerSets(columnNodes, useCorrectTypes, numberOfCRFCandidates, addedNodes);
@@ -186,7 +186,7 @@ public List<SortableSemanticModel_Old> hypothesize(boolean useCorrectTypes, int
 
 
 		logger.info("computing steiner trees ...");
-		List<SortableSemanticModel_Old> sortableSemanticModels = new ArrayList<SortableSemanticModel_Old>();
+		List<SortableSemanticModel_Old> sortableSemanticModels = new ArrayList<>();
 		int count = 1;
 		for (SteinerNodes sn : candidateSteinerSets.getSteinerSets()) {
 			logger.debug("computing steiner tree for steiner nodes set " + count + " ...");
@@ -212,7 +212,7 @@ public List<SortableSemanticModel_Old> hypothesize(boolean useCorrectTypes, int
 //		logger.info("results are ready ...");
 //		return sortableSemanticModels;
 
-		List<SortableSemanticModel_Old> uniqueModels = new ArrayList<SortableSemanticModel_Old>();
+		List<SortableSemanticModel_Old> uniqueModels = new ArrayList<>();
 		SortableSemanticModel_Old current, previous;
 		if (sortableSemanticModels != null) {
 			if (!sortableSemanticModels.isEmpty())
@@ -239,10 +239,10 @@ private DirectedWeightedMultigraph<Node, LabeledLink> computeSteinerTree(Set<Nod
 		}
 
 		//		System.out.println(steinerNodes.size());
-		List<Node> steinerNodeList = new ArrayList<Node>(steinerNodes); 
+		List<Node> steinerNodeList = new ArrayList<>(steinerNodes); 
 
 		long start = System.currentTimeMillis();
-		UndirectedGraph<Node, DefaultLink> undirectedGraph = new AsUndirectedGraph<Node, DefaultLink>(this.graphBuilder.getGraph());
+		UndirectedGraph<Node, DefaultLink> undirectedGraph = new AsUndirectedGraph<>(this.graphBuilder.getGraph());
 
 		logger.debug("computing steiner tree ...");
 		SteinerTree steinerTree = new SteinerTree(undirectedGraph, steinerNodeList);
@@ -276,11 +276,11 @@ private CandidateSteinerSets getCandidateSteinerSets(List<ColumnNode> columnNode
 		CandidateSteinerSets candidateSteinerSets = new CandidateSteinerSets(maxNumberOfSteinerNodes, ontologyManager.getContextId());
 
 		if (addedNodes == null) 
-			addedNodes = new HashSet<Node>();
+			addedNodes = new HashSet<>();
 
 		Set<SemanticTypeMapping> tempSemanticTypeMappings;
-		HashMap<ColumnNode, List<SemanticType>> columnSemanticTypes = new HashMap<ColumnNode, List<SemanticType>>();
-		HashMap<String, Integer> semanticTypesCount = new HashMap<String, Integer>();
+		HashMap<ColumnNode, List<SemanticType>> columnSemanticTypes = new HashMap<>();
+		HashMap<String, Integer> semanticTypesCount = new HashMap<>();
 		List<SemanticType> candidateSemanticTypes;
 		String domainUri = "", propertyUri = "";
 
@@ -312,7 +312,7 @@ private CandidateSteinerSets getCandidateSteinerSets(List<ColumnNode> columnNode
 
 			logger.info("===== Column: " + n.getColumnName());
 
-			Set<SemanticTypeMapping> semanticTypeMappings = new HashSet<SemanticTypeMapping>();
+			Set<SemanticTypeMapping> semanticTypeMappings = new HashSet<>();
 			for (SemanticType semanticType: candidateSemanticTypes) {
 
 				logger.info("\t===== Semantic Type: " + semanticType.getModelLabelString());
@@ -364,9 +364,9 @@ private Set<SemanticTypeMapping> findSemanticTypeInGraph(ColumnNode sourceColumn
 		logger.debug("finding matches for semantic type in the graph ... ");
 
 		if (addedNodes == null)
-			addedNodes = new HashSet<Node>();
+			addedNodes = new HashSet<>();
 
-		Set<SemanticTypeMapping> mappings = new HashSet<SemanticTypeMapping>();
+		Set<SemanticTypeMapping> mappings = new HashSet<>();
 
 		if (semanticType == null) {
 			logger.error("semantic type is null.");
@@ -461,7 +461,7 @@ private SemanticTypeMapping addSemanticTypeStruct(ColumnNode sourceColumn, Seman
 		logger.debug("adding semantic type to the graph ... ");
 
 		if (addedNodes == null) 
-			addedNodes = new HashSet<Node>();
+			addedNodes = new HashSet<>();
 
 		if (semanticType == null) {
 			logger.error("semantic type is null.");
@@ -524,15 +524,15 @@ private SemanticTypeMapping addSemanticTypeStruct(ColumnNode sourceColumn, Seman
 
 	private void updateWeights() {
 
-		List<DefaultLink> oldLinks = new ArrayList<DefaultLink>();
+		List<DefaultLink> oldLinks = new ArrayList<>();
 
-		List<Node> sources = new ArrayList<Node>();
-		List<Node> targets = new ArrayList<Node>();
-		List<LabeledLink> newLinks = new ArrayList<LabeledLink>();
-		List<Double> weights = new ArrayList<Double>();
+		List<Node> sources = new ArrayList<>();
+		List<Node> targets = new ArrayList<>();
+		List<LabeledLink> newLinks = new ArrayList<>();
+		List<Double> weights = new ArrayList<>();
 
-		HashMap<String, LinkFrequency> sourceTargetLinkFrequency = 
-				new HashMap<String, LinkFrequency>();
+		HashMap<String, LinkFrequency> sourceTargetLinkFrequency =
+				new HashMap<>();
 
 		LinkFrequency lf1, lf2;
 
@@ -685,7 +685,7 @@ public static void test() throws Exception {
 		//		if (true)
 		//			return;
 
-		List<SemanticModel> trainingData = new ArrayList<SemanticModel>();
+		List<SemanticModel> trainingData = new ArrayList<>();
 
 		OntologyManager ontologyManager = new OntologyManager(contextParameters.getId());
 		File ff = new File(Params.ONTOLOGY_DIR);
@@ -807,8 +807,8 @@ public static void test() throws Exception {
 								hypothesisList;
 				}
 
-				Map<String, SemanticModel> models = 
-						new TreeMap<String, SemanticModel>();
+				Map<String, SemanticModel> models =
+						new TreeMap<>();
 
 				// export to json
 				//				if (topHypotheses != null)
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraph.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraph.java
index b8a1a3a45..97f156b92 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraph.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraph.java
@@ -54,7 +54,7 @@ public abstract class ModelLearningGraph {
 
 	private static Logger logger = LoggerFactory.getLogger(ModelLearningGraph.class);
 	
-	private static ConcurrentHashMap<OntologyManager, ModelLearningGraph> instances = new ConcurrentHashMap<OntologyManager, ModelLearningGraph>();
+	private static ConcurrentHashMap<OntologyManager, ModelLearningGraph> instances = new ConcurrentHashMap<>();
 	protected OntologyManager ontologyManager;
 	protected GraphBuilder graphBuilder;
 	protected NodeIdFactory nodeIdFactory; 
@@ -191,7 +191,7 @@ public void initializeFromJsonRepository() {
 			this.graphBuilder = new GraphBuilderTopK(ontologyManager, false);
 		this.nodeIdFactory = new NodeIdFactory();
 		
-		Set<InternalNode> addedNodes = new HashSet<InternalNode>();
+		Set<InternalNode> addedNodes = new HashSet<>();
 		Set<InternalNode> temp;
 		File ff = new File(contextParameters.getParameterValue(ContextParameter.JSON_MODELS_DIR));
 		if (ff.exists()) {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphCompact.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphCompact.java
index e87de8eb5..68067fa57 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphCompact.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphCompact.java
@@ -72,9 +72,9 @@ private void addInternalNodes(SemanticModel model, Set<InternalNode> addedNodes)
 		if (model == null || model.getGraph() == null) 
 			return;
 		
-		if (addedNodes == null) addedNodes = new HashSet<InternalNode>();
+		if (addedNodes == null) addedNodes = new HashSet<>();
 
-		HashMap<String, Integer> uriCount = new HashMap<String, Integer>();
+		HashMap<String, Integer> uriCount = new HashMap<>();
 		for (Node n : model.getGraph().vertexSet()) {
 			if (n instanceof InternalNode) {
 				Integer count = uriCount.get(n.getUri());
@@ -99,14 +99,14 @@ private void addInternalNodes(SemanticModel model, Set<InternalNode> addedNodes)
 	
 	private HashMap<Node,Node> getInternalNodeMapping(SemanticModel model) {
 		
-		HashMap<Node,Node> internalNodeMapping = 
-				new HashMap<Node,Node>();
+		HashMap<Node,Node> internalNodeMapping =
+				new HashMap<>();
 		
-		HashMap<String, List<Node>> uriMatchedNodes = 
-				new HashMap<String, List<Node>>();
+		HashMap<String, List<Node>> uriMatchedNodes =
+				new HashMap<>();
 		
 		String uri;
-		List<Node> sortedNodes = new ArrayList<Node>();
+		List<Node> sortedNodes = new ArrayList<>();
 		for (Node n : model.getGraph().vertexSet()) {
 			sortedNodes.add(n);
 		}
@@ -116,7 +116,7 @@ private HashMap<Node,Node> getInternalNodeMapping(SemanticModel model) {
 				uri = n.getUri();
 				List<Node> sortedMatchedNodes = uriMatchedNodes.get(uri);
 				if (sortedMatchedNodes == null) {
-					sortedMatchedNodes = new ArrayList<Node>();
+					sortedMatchedNodes = new ArrayList<>();
 					Set<Node> matchedNodes = this.graphBuilder.getUriToNodesMap().get(uri);
 					if (matchedNodes != null) sortedMatchedNodes.addAll(matchedNodes);
 					Collections.sort(sortedMatchedNodes, new NodeSupportingModelsComparator());
@@ -145,9 +145,9 @@ private HashMap<Node,Node> getColumnNodeMapping(SemanticModel model,
 		if (internalNodeMapping == null || internalNodeMapping.isEmpty()) 
 			return null;
 
-		HashMap<String,List<Node>> dataPropertyColumnNodes = new HashMap<String,List<Node>>();
+		HashMap<String,List<Node>> dataPropertyColumnNodes = new HashMap<>();
 		
-		HashMap<Node,Node> columnNodeMapping = new HashMap<Node,Node>();
+		HashMap<Node,Node> columnNodeMapping = new HashMap<>();
 		
 		for (Node n : model.getGraph().vertexSet()) {
 			if (n instanceof ColumnNode) {
@@ -167,7 +167,7 @@ private HashMap<Node,Node> getColumnNodeMapping(SemanticModel model,
 						sortedMatchedNodes = dataPropertyColumnNodes.get(key);
 					} else {
 						Set<Node> matchedColumnNodes = this.graphBuilder.getNodeDataProperties().get(key);
-						sortedMatchedNodes = new ArrayList<Node>();
+						sortedMatchedNodes = new ArrayList<>();
 						if (matchedColumnNodes != null) sortedMatchedNodes.addAll(matchedColumnNodes);
 						Collections.sort(sortedMatchedNodes, new NodeSupportingModelsComparator());
 						dataPropertyColumnNodes.put(key, sortedMatchedNodes);
@@ -202,7 +202,7 @@ private void addLinks(SemanticModel model,
 		Node source, target;
 		Node n1, n2;
 
-		HashMap<Node,Node> mapping = new HashMap<Node,Node>();
+		HashMap<Node,Node> mapping = new HashMap<>();
 		if (internalNodeMapping != null) mapping.putAll(internalNodeMapping);
 		if (columnNodeMapping != null) mapping.putAll(columnNodeMapping);
 		
@@ -324,7 +324,7 @@ public Set<InternalNode> addModel(SemanticModel model, PatternWeightSystem weigh
 		this.totalNumberOfKnownModels ++;
 
 		// add the model  nodes that are not in the graph
-		Set<InternalNode> addedInternalNodes = new HashSet<InternalNode>();
+		Set<InternalNode> addedInternalNodes = new HashSet<>();
 		this.addInternalNodes(model, addedInternalNodes);
 		HashMap<Node, Node> internalNodeMapping = this.getInternalNodeMapping(model);
 
@@ -338,7 +338,7 @@ public Set<InternalNode> addModel(SemanticModel model, PatternWeightSystem weigh
 
 	public Set<InternalNode> addLodPattern(SemanticModel model) {
 		
-		Set<InternalNode> addedNodes = new HashSet<InternalNode>();
+		Set<InternalNode> addedNodes = new HashSet<>();
 		
 		if (model == null) 
 			return addedNodes;
@@ -351,15 +351,15 @@ public Set<InternalNode> addLodPattern(SemanticModel model) {
 		String sourceUri, targetUri, linkUri; 
 		String id, key;
 		
-		Set<String> mappedLinks = new HashSet<String>();
-		Set<String> mappedNodes = new HashSet<String>();
+		Set<String> mappedLinks = new HashSet<>();
+		Set<String> mappedNodes = new HashSet<>();
 
-		HashMap<Node,Node> mapping = new HashMap<Node,Node>();
+		HashMap<Node,Node> mapping = new HashMap<>();
 		
-		HashMap<String, List<Node>> uriMatchedNodes = new HashMap<String, List<Node>>();
+		HashMap<String, List<Node>> uriMatchedNodes = new HashMap<>();
 
-		List<LabeledLink> sortedLinks = new ArrayList<LabeledLink>();
-		List<LabeledLink> idSortedLinks = new ArrayList<LabeledLink>();
+		List<LabeledLink> sortedLinks = new ArrayList<>();
+		List<LabeledLink> idSortedLinks = new ArrayList<>();
 		idSortedLinks.addAll(model.getGraph().edgeSet());
 		Collections.sort(idSortedLinks);
 		for (LabeledLink l : idSortedLinks) {
@@ -461,7 +461,7 @@ public Set<InternalNode> addLodPattern(SemanticModel model) {
 				
 				List<Node> sortedMatchedNodes = uriMatchedNodes.get(sourceUri);
 				if (sortedMatchedNodes == null) {
-					sortedMatchedNodes = new LinkedList<Node>();
+					sortedMatchedNodes = new LinkedList<>();
 					Set<Node> matchedNodes = this.graphBuilder.getUriToNodesMap().get(sourceUri);
 					if (matchedNodes != null && !matchedNodes.isEmpty()) {
 						sortedMatchedNodes.addAll(matchedNodes);
@@ -516,7 +516,7 @@ public Set<InternalNode> addLodPattern(SemanticModel model) {
 //				}
 				List<Node> sortedMatchedNodes = uriMatchedNodes.get(targetUri);
 				if (sortedMatchedNodes == null) {
-					sortedMatchedNodes = new LinkedList<Node>();
+					sortedMatchedNodes = new LinkedList<>();
 					Set<Node> matchedNodes = this.graphBuilder.getUriToNodesMap().get(targetUri);
 					if (matchedNodes != null && !matchedNodes.isEmpty()) {
 						sortedMatchedNodes.addAll(matchedNodes);
@@ -622,7 +622,7 @@ public static void main(String[] args) throws Exception {
 
 		ModelLearningGraph ml = ModelLearningGraph.getEmptyInstance(ontologyManager, ModelLearningGraphType.Compact);
 		int i = 0;
-		Set<InternalNode> addedNodes = new HashSet<InternalNode>();
+		Set<InternalNode> addedNodes = new HashSet<>();
 		Set<InternalNode> temp;
 		for (SemanticModel sm : semanticModels) {
 			i++;
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphCompact_Old.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphCompact_Old.java
index 162083053..81b53afc8 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphCompact_Old.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphCompact_Old.java
@@ -78,10 +78,10 @@ private HashMap<Node,Set<Node>> addInternalNodes(SemanticModel model, Set<Intern
 		if (model == null || model.getGraph() == null) 
 			return null;
 		
-		HashMap<Node,Set<Node>> internalNodeMatches = new HashMap<Node,Set<Node>>();
-		if (addedNodes == null) addedNodes = new HashSet<InternalNode>();
+		HashMap<Node,Set<Node>> internalNodeMatches = new HashMap<>();
+		if (addedNodes == null) addedNodes = new HashSet<>();
 
-		HashMap<String, Integer> uriCount = new HashMap<String, Integer>();
+		HashMap<String, Integer> uriCount = new HashMap<>();
 		for (Node n : model.getGraph().vertexSet()) {
 			if (n instanceof InternalNode) {
 				Integer count = uriCount.get(n.getUri());
@@ -120,12 +120,12 @@ private HashMap<Node,Set<Node>> addColumnNodes(SemanticModel model,
 		if (model == null || model.getGraph() == null) 
 			return null;
 
-		if (modelNodeDomains == null) modelNodeDomains = new HashMap<Node,Set<LabeledLink>>();
-		if (graphNodeDomains == null) graphNodeDomains = new HashMap<Node,Set<LabeledLink>>();
+		if (modelNodeDomains == null) modelNodeDomains = new HashMap<>();
+		if (graphNodeDomains == null) graphNodeDomains = new HashMap<>();
 		
-		HashMap<Node,Set<Node>> columnNodeMatches = new HashMap<Node,Set<Node>>();
+		HashMap<Node,Set<Node>> columnNodeMatches = new HashMap<>();
 		
-		HashMap<String, Integer> dataPropertyCount = new HashMap<String, Integer>(); // key = domainUri + propertyUri
+		HashMap<String, Integer> dataPropertyCount = new HashMap<>(); // key = domainUri + propertyUri
 		for (Node n : model.getGraph().vertexSet()) {
 			if (n instanceof ColumnNode) {
 				Set<LabeledLink> domainLinks = GraphUtil.getDomainLinksInLabeledGraph(model.getGraph(), (ColumnNode)n);
@@ -145,7 +145,7 @@ private HashMap<Node,Set<Node>> addColumnNodes(SemanticModel model,
 		}
 		
 		for (Node n : model.getGraph().vertexSet()) {
-			Set<Node> matches = new HashSet<Node>();
+			Set<Node> matches = new HashSet<>();
 			if (n instanceof ColumnNode) {
 				Set<LabeledLink> domainLinks = modelNodeDomains.get(n);
 				if (domainLinks == null || domainLinks.isEmpty())
@@ -211,7 +211,7 @@ private List<HashMap<Node,Node>> updateMapping(List<HashMap<Node,Node>> mappings
 		
 //		System.out.println("node: " + node.getId());
 		
-		List<HashMap<Node,Node>> newMappings = new LinkedList<HashMap<Node,Node>>();
+		List<HashMap<Node,Node>> newMappings = new LinkedList<>();
 		
 		Set<Node> matchedNodes = null;
 		if (node instanceof InternalNode && internalNodeMatches != null) 
@@ -229,7 +229,7 @@ else if (node instanceof ColumnNode && columnNodeMatches != null)
 
 		if (mappings.isEmpty()) {
 			for (Node n : matchedNodes) {
-				HashMap<Node,Node> nodeMap = new HashMap<Node,Node>();
+				HashMap<Node,Node> nodeMap = new HashMap<>();
 				nodeMap.put(node, n);
 				newMappings.add(nodeMap);
 //				System.out.println("\t\t" + n.getId());
@@ -237,7 +237,7 @@ else if (node instanceof ColumnNode && columnNodeMatches != null)
 		} else {
 			for (int i = 0; i < mappings.size(); i++) {
 				HashMap<Node,Node> nodeMap = mappings.get(i);
-				Set<Node> correspondingMatches = new HashSet<Node>();
+				Set<Node> correspondingMatches = new HashSet<>();
 				for (Node n : matchedNodes) {
 					if (n instanceof ColumnNode) {
 						Set<LabeledLink> modelDomainLinks = modelNodeDomains.get(node);
@@ -251,7 +251,7 @@ else if (node instanceof ColumnNode && columnNodeMatches != null)
 							}
 						}
 						Set<LabeledLink> graphDomainLinks = graphNodeDomains.get(n);
-						Set<Node> domainNodes = new HashSet<Node>();
+						Set<Node> domainNodes = new HashSet<>();
 						if (graphDomainLinks != null) {
 							for (LabeledLink l : graphDomainLinks) {
 								if (l.getSource() != null) {
@@ -270,9 +270,9 @@ else if (node instanceof ColumnNode && columnNodeMatches != null)
 							continue;
 						
 					}
-					HashMap<Node,Node> newMapping = new HashMap<Node,Node>(nodeMap);
+					HashMap<Node,Node> newMapping = new HashMap<>(nodeMap);
 					newMapping.put(node, n);
-					if (new HashSet<Node>(newMapping.values()).size() != size)
+					if (new HashSet<>(newMapping.values()).size() != size)
 						continue;
 
 //					for (Node nnn : newMapping.values()) {
@@ -295,7 +295,7 @@ private List<HashMap<Node,Node>> findMappings(SemanticModel model,
 		if (model == null || model.getGraph() == null) 
 			return null;
 		
-		List<HashMap<Node,Node>> mappings = new LinkedList<HashMap<Node,Node>>();
+		List<HashMap<Node,Node>> mappings = new LinkedList<>();
 
 //		logger.info("max mapping size: " + MAX_MAPPING_SIZE);
 		
@@ -350,7 +350,7 @@ public Set<InternalNode> addModel(SemanticModel model, PatternWeightSystem weigh
 		}
 		
 		// add the model  nodes that are not in the graph
-		Set<InternalNode> addedInternalNodes = new HashSet<InternalNode>();
+		Set<InternalNode> addedInternalNodes = new HashSet<>();
 		HashMap<Node, Set<Node>> internalNodeMatches = addInternalNodes(model, addedInternalNodes);
 //		if (modelId.equalsIgnoreCase("s21-s-met.json"))
 //		for (Entry<Node, Set<Node>> entry : internalNodeMatches.entrySet()) {
@@ -359,8 +359,8 @@ public Set<InternalNode> addModel(SemanticModel model, PatternWeightSystem weigh
 //				System.out.println("\t" + n.getId());
 //			}
 //		}
-		HashMap<Node,Set<LabeledLink>> modelNodeDomains = new HashMap<Node,Set<LabeledLink>>();
-		HashMap<Node,Set<LabeledLink>> graphNodeDomains = new HashMap<Node,Set<LabeledLink>>();
+		HashMap<Node,Set<LabeledLink>> modelNodeDomains = new HashMap<>();
+		HashMap<Node,Set<LabeledLink>> graphNodeDomains = new HashMap<>();
 		HashMap<Node, Set<Node>> columnNodeMatches = addColumnNodes(model, modelNodeDomains, graphNodeDomains);
 //		if (modelId.equalsIgnoreCase("s21-s-met.json"))
 //		for (Entry<Node, Set<Node>> entry : columnNodeMatches.entrySet()) {
@@ -488,7 +488,7 @@ public static void main(String[] args) throws Exception {
 
 		ModelLearningGraph ml = ModelLearningGraph.getEmptyInstance(ontologyManager, ModelLearningGraphType.Compact);
 		int i = 0;
-		Set<InternalNode> addedNodes = new HashSet<InternalNode>();
+		Set<InternalNode> addedNodes = new HashSet<>();
 		Set<InternalNode> temp;
 		for (SemanticModel sm : semanticModels) {
 			i++;
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphSparse.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphSparse.java
index bf21e8166..516cfe9ca 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphSparse.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelLearningGraphSparse.java
@@ -94,7 +94,7 @@ public Set<InternalNode> addModel(SemanticModel model, PatternWeightSystem weigh
 			return null;
 		}
 
-		visitedNodes = new HashMap<Node, Node>();
+		visitedNodes = new HashMap<>();
 
 		for (LabeledLink e : model.getGraph().edgeSet()) {
 
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelReader.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelReader.java
index e2ffcd5e3..28229d056 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelReader.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/ModelReader.java
@@ -57,7 +57,7 @@ public static List<SemanticModel> importSemanticModelsFromJsonFiles(String path,
 		File ff = new File(path);
 		File[] files = ff.listFiles();
 		
-		List<SemanticModel> semanticModels = new ArrayList<SemanticModel>();
+		List<SemanticModel> semanticModels = new ArrayList<>();
 		
 		for (File f : files) {
 			if (f.getName().endsWith(fileExtension)) {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/SteinerNodes.java b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/SteinerNodes.java
index 5ceb7e327..22fdf29b2 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/SteinerNodes.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/alignment/learner/SteinerNodes.java
@@ -52,9 +52,9 @@ public class SteinerNodes implements Comparable<SteinerNodes> {
 	private String contextId;
 	public SteinerNodes(String contextId) {
 		this.contextId = contextId;
-		this.nodes = new HashSet<Node>();
-		this.mappingToSourceColumns = new HashMap<ColumnNode, ColumnNode>();
-		this.columnNodeInfo = new HashMap<ColumnNode, SemanticTypeMapping>();
+		this.nodes = new HashSet<>();
+		this.mappingToSourceColumns = new HashMap<>();
+		this.columnNodeInfo = new HashMap<>();
 		this.semanticTypesCount = 0;
 		this.confidence = new Confidence();
 		this.nodeCoherence = new NodeCoherence();
@@ -65,9 +65,9 @@ public SteinerNodes(String contextId) {
 	
 	public SteinerNodes(SteinerNodes steinerNodes,String contextId) {
 		this.contextId = contextId;
-		this.nodes = new HashSet<Node>(steinerNodes.getNodes());
-		this.mappingToSourceColumns = new HashMap<ColumnNode, ColumnNode>(steinerNodes.getMappingToSourceColumns());
-		this.columnNodeInfo = new HashMap<ColumnNode, SemanticTypeMapping>(steinerNodes.getColumnNodeInfo());
+		this.nodes = new HashSet<>(steinerNodes.getNodes());
+		this.mappingToSourceColumns = new HashMap<>(steinerNodes.getMappingToSourceColumns());
+		this.columnNodeInfo = new HashMap<>(steinerNodes.getColumnNodeInfo());
 		this.confidence = new Confidence(steinerNodes.getConfidence());
 		this.nodeCoherence = new NodeCoherence(steinerNodes.getCoherence());
 //		this.frequency = steinerNodes.getFrequency();
@@ -235,7 +235,7 @@ private double getSizeReduction() {
 	
 	private double getArithmeticMean(double[] input) {
 		
-		double result = 0.0;
+		double result;
 		if (input == null)
 			return 0.0;
 		
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/ontology/AutoOntology.java b/karma-common/src/main/java/edu/isi/karma/modeling/ontology/AutoOntology.java
index ed203f0df..00ee66f18 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/ontology/AutoOntology.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/ontology/AutoOntology.java
@@ -54,7 +54,7 @@ public AutoOntology(Worksheet worksheet) {
 	}
 	public void Build(String path) throws IOException {
 		
-		List<HNode> sortedLeafHNodes = new ArrayList<HNode>();
+		List<HNode> sortedLeafHNodes = new ArrayList<>();
 		worksheet.getHeaders().getSortedLeafHNodes(sortedLeafHNodes);
 		OntModel autoOntology = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );
 		String ns = Namespaces.KARMA;
@@ -71,7 +71,7 @@ public void Build(String path) throws IOException {
 		op.addDomain(topClass);
 //		op.addRange(thingClass);
 		
-		Writer outUTF8 =null;
+		Writer outUTF8;
 		try {
 			outUTF8 = new BufferedWriter(new OutputStreamWriter(
 					new FileOutputStream(path), "UTF8"));
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyCache.java b/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyCache.java
index 3b9ff4b29..598c1ac33 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyCache.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyCache.java
@@ -227,53 +227,53 @@ public void init() {
 	}
 
 	private void allocateDataStructures() {
-		this.classes = new HashMap<String, Label>();
-		this.properties = new HashMap<String, Label>();
-		this.dataProperties = new HashMap<String, Label>();
-		this.objectProperties = new HashMap<String, Label>();
+		this.classes = new HashMap<>();
+		this.properties = new HashMap<>();
+		this.dataProperties = new HashMap<>();
+		this.objectProperties = new HashMap<>();
 		
-		this.dataPropertiesWithoutDomain = new HashMap<String, Label>();
-		this.objectPropertiesWithOnlyDomain = new HashMap<String, Label>();
-		this.objectPropertiesWithOnlyRange = new HashMap<String, Label>();
-		this.objectPropertiesWithoutDomainAndRange = new HashMap<String, Label>();
+		this.dataPropertiesWithoutDomain = new HashMap<>();
+		this.objectPropertiesWithOnlyDomain = new HashMap<>();
+		this.objectPropertiesWithOnlyRange = new HashMap<>();
+		this.objectPropertiesWithoutDomainAndRange = new HashMap<>();
 		
 //		this.classHierarchy = new OntologyTreeNode(new Label(Uris.THING_URI, Namespaces.OWL, Prefixes.OWL), null, null);
 //		this.dataPropertyHierarchy = new OntologyTreeNode(new Label("Data Properties"), null, null);
 //		this.objectPropertyHierarchy = new OntologyTreeNode(new Label("Object Properties"), null, null);
 
-		this.directSubClasses = new HashMap<String, HashMap<String, Label>>();
-		this.indirectSubClasses = new HashMap<String, HashMap<String, Label>>();
-		this.directSuperClasses = new HashMap<String, HashMap<String, Label>>();
-		this.indirectSuperClasses = new HashMap<String, HashMap<String, Label>>();
-		this.directSubClassCheck = new HashSet<String>();
-		this.indirectSubClassCheck = new HashSet<String>();
+		this.directSubClasses = new HashMap<>();
+		this.indirectSubClasses = new HashMap<>();
+		this.directSuperClasses = new HashMap<>();
+		this.indirectSuperClasses = new HashMap<>();
+		this.directSubClassCheck = new HashSet<>();
+		this.indirectSubClassCheck = new HashSet<>();
 //		this.directSubclassSuperclassPairs = new ArrayList<SubclassSuperclassPair>();
 //		this.indirectSubclassSuperclassPairs = new ArrayList<SubclassSuperclassPair>();
 		
-		this.directSubProperties = new HashMap<String, HashMap<String, Label>>();
-		this.indirectSubProperties = new HashMap<String, HashMap<String, Label>>();
-		this.directSuperProperties = new HashMap<String, HashMap<String, Label>>();
-		this.indirectSuperProperties = new HashMap<String, HashMap<String, Label>>();
-		this.directSubPropertyCheck = new HashSet<String>();
-		this.indirectSubPropertyCheck = new HashSet<String>();
+		this.directSubProperties = new HashMap<>();
+		this.indirectSubProperties = new HashMap<>();
+		this.directSuperProperties = new HashMap<>();
+		this.indirectSuperProperties = new HashMap<>();
+		this.directSubPropertyCheck = new HashSet<>();
+		this.indirectSubPropertyCheck = new HashSet<>();
 		
-		this.propertyInverse = new HashMap<String, Label>();
-		this.propertyInverseOf = new HashMap<String, Label>();
+		this.propertyInverse = new HashMap<>();
+		this.propertyInverseOf = new HashMap<>();
 		
-		this.propertyDirectDomains = new HashMap<String, HashSet<String>>();
-		this.propertyIndirectDomains = new HashMap<String, HashSet<String>>();
-		this.propertyDirectRanges = new HashMap<String, HashSet<String>>();
-		this.propertyIndirectRanges = new HashMap<String, HashSet<String>>();
+		this.propertyDirectDomains = new HashMap<>();
+		this.propertyIndirectDomains = new HashMap<>();
+		this.propertyDirectRanges = new HashMap<>();
+		this.propertyIndirectRanges = new HashMap<>();
 		
-		this.directOutDataProperties = new HashMap<String, HashSet<String>>();
-		this.indirectOutDataProperties = new HashMap<String, HashSet<String>>();
-		this.directOutObjectProperties = new HashMap<String, HashSet<String>>();
-		this.indirectOutObjectProperties = new HashMap<String, HashSet<String>>();
-		this.directInObjectProperties = new HashMap<String, HashSet<String>>();
-		this.indirectInObjectProperties = new HashMap<String, HashSet<String>>();
+		this.directOutDataProperties = new HashMap<>();
+		this.indirectOutDataProperties = new HashMap<>();
+		this.directOutObjectProperties = new HashMap<>();
+		this.indirectOutObjectProperties = new HashMap<>();
+		this.directInObjectProperties = new HashMap<>();
+		this.indirectInObjectProperties = new HashMap<>();
 		
-		this.domainRangeToDirectProperties = new HashMap<String, HashSet<String>>();
-		this.domainRangeToIndirectProperties = new HashMap<String, HashSet<String>>();
+		this.domainRangeToDirectProperties = new HashMap<>();
+		this.domainRangeToIndirectProperties = new HashMap<>();
 //		this.domainRangeToDomainlessProperties = new HashMap<String, List<String>>();
 //		this.domainRangeToRangelessProperties = new HashMap<String, List<String>>();
 		
@@ -772,7 +772,7 @@ private void processSchemaOrgOntology() {
 
 	private void buildSubClassesMaps() {
 		
-		HashMap<String, Label> allClassesExceptThing = new HashMap<String, Label>();
+		HashMap<String, Label> allClassesExceptThing = new HashMap<>();
 		for (Entry<String, Label> entry : this.classes.entrySet())
 			if (!entry.getKey().equalsIgnoreCase(Uris.THING_URI))
 				allClassesExceptThing.put(entry.getKey(), entry.getValue());
@@ -791,7 +791,7 @@ private void buildSubClassesMaps() {
 				
 				directSubClassesLocal = this.ontHandler.getSubClasses(c, false);
 				allSubClassesLocal = this.ontHandler.getSubClasses(c, true);
-				indirectSubClassesLocal = new HashMap<String, Label>();
+				indirectSubClassesLocal = new HashMap<>();
 				for (Entry<String, Label> entry : allSubClassesLocal.entrySet())
 					if (!directSubClassesLocal.containsKey(entry.getKey()))
 						indirectSubClassesLocal.put(entry.getKey(), entry.getValue());
@@ -837,7 +837,7 @@ private void buildSuperClassesMaps() {
 			this.directSuperClasses.put(c, directSuperClassesLocal);
 			
 			allSuperClassesLocal = this.ontHandler.getSuperClasses(c, true);
-			indirectSuperClassesLocal = new HashMap<String, Label>();
+			indirectSuperClassesLocal = new HashMap<>();
 			for (Entry<String, Label> entry : allSuperClassesLocal.entrySet())
 				if (!directSuperClassesLocal.containsKey(entry.getKey()))
 					indirectSuperClassesLocal.put(entry.getKey(), entry.getValue());
@@ -849,7 +849,7 @@ private void buildSuperClassesMaps() {
 			
 			HashMap<String, Label> superClasses = this.indirectSuperClasses.get(stringHashMapEntry.getKey());
 			if (superClasses == null) {
-				superClasses = new HashMap<String, Label>();
+				superClasses = new HashMap<>();
 				this.indirectSuperClasses.put(stringHashMapEntry.getKey(), superClasses); 
 			}
 			if (!stringHashMapEntry.getKey().equalsIgnoreCase(Uris.THING_URI) && !superClasses.containsKey(Uris.THING_URI))
@@ -869,7 +869,7 @@ private void buildSubPropertiesMaps() {
 			directSubPropertiesLocal = this.ontHandler.getSubProperties(p, false);
 			
 			allSubPropertiesLocal = this.ontHandler.getSubProperties(p, true);
-			indirectSubPropertiesLocal = new HashMap<String, Label>();
+			indirectSubPropertiesLocal = new HashMap<>();
 			for (Entry<String, Label> entry : allSubPropertiesLocal.entrySet())
 				if (!directSubPropertiesLocal.containsKey(entry.getKey()))
 					indirectSubPropertiesLocal.put(entry.getKey(), entry.getValue());
@@ -898,7 +898,7 @@ private void buildSuperPropertiesMaps() {
 			this.directSuperProperties.put(p, directSuperPropertiesLocal);
 			
 			allSuperPropertiesLocal = this.ontHandler.getSuperProperties(p, true);
-			indirectSuperPropertiesLocal = new HashMap<String, Label>();
+			indirectSuperPropertiesLocal = new HashMap<>();
 			for (Entry<String, Label> entry : allSuperPropertiesLocal.entrySet())
 				if (!directSuperPropertiesLocal.containsKey(entry.getKey()))
 					indirectSuperPropertiesLocal.put(entry.getKey(), entry.getValue());
@@ -933,16 +933,16 @@ private void buildDataPropertiesMaps() {
 		
 		for (String propertyUri : this.dataProperties.keySet()) {
 			
-			directDomains = new HashSet<OntResource>();
-			directDomainsUris = new HashSet<String>();
-			indirectDomainsUris = new HashSet<String>();
-			allDomains = new HashSet<OntResource>();
-			allDomainsUris = new HashSet<String>();
-			directRanges = new HashSet<OntResource>();
-			directRangesUris = new HashSet<String>();
-			indirectRangesUris = new HashSet<String>();
-			allRanges = new HashSet<OntResource>();
-			allRangesUris = new HashSet<String>();
+			directDomains = new HashSet<>();
+			directDomainsUris = new HashSet<>();
+			indirectDomainsUris = new HashSet<>();
+			allDomains = new HashSet<>();
+			allDomainsUris = new HashSet<>();
+			directRanges = new HashSet<>();
+			directRangesUris = new HashSet<>();
+			indirectRangesUris = new HashSet<>();
+			allRanges = new HashSet<>();
+			allRangesUris = new HashSet<>();
 			
 			OntProperty property = this.ontHandler.getOntModel().getOntProperty(propertyUri);
 			if (property == null || !property.isURIResource())
@@ -965,7 +965,7 @@ private void buildDataPropertiesMaps() {
 			for (OntResource domain : directDomains) {
 				temp = directOutDataProperties.get(domain.getURI());
 				if (temp == null) {
-					temp = new HashSet<String>();
+					temp = new HashSet<>();
 					directOutDataProperties.put(domain.getURI(), temp);
 				}
 				temp.add(property.getURI());
@@ -973,7 +973,7 @@ private void buildDataPropertiesMaps() {
 
 			// all domains
 			if (directDomainsUris.contains(Uris.THING_URI))
-				allDomainsUris = new HashSet<String>(this.classes.keySet());
+				allDomainsUris = new HashSet<>(this.classes.keySet());
 			else {
 				for (OntResource domain : directDomains) {
 					allDomains.add(domain);
@@ -997,7 +997,7 @@ private void buildDataPropertiesMaps() {
 			for (String domainUri : indirectDomainsUris) {
 				temp = indirectOutDataProperties.get(domainUri);
 				if (temp == null) { 
-					temp = new HashSet<String>();
+					temp = new HashSet<>();
 					indirectOutDataProperties.put(domainUri, temp);
 				}
 				temp.add(property.getURI());
@@ -1063,16 +1063,16 @@ private void buildObjectPropertiesMaps() {
 			if (property == null || !property.isURIResource())
 				continue;
 						
-			directDomains = new HashSet<OntResource>();
-			directDomainsUris = new HashSet<String>();
-			indirectDomainsUris = new HashSet<String>();
-			allDomains = new HashSet<OntResource>();
-			allDomainsUris = new HashSet<String>();
-			directRanges = new HashSet<OntResource>();
-			directRangesUris = new HashSet<String>();
-			indirectRangesUris = new HashSet<String>();
-			allRanges = new HashSet<OntResource>();
-			allRangesUris = new HashSet<String>();
+			directDomains = new HashSet<>();
+			directDomainsUris = new HashSet<>();
+			indirectDomainsUris = new HashSet<>();
+			allDomains = new HashSet<>();
+			allDomainsUris = new HashSet<>();
+			directRanges = new HashSet<>();
+			directRangesUris = new HashSet<>();
+			indirectRangesUris = new HashSet<>();
+			allRanges = new HashSet<>();
+			allRangesUris = new HashSet<>();
 			
 //			count ++;
 //			if (count % 1000 == 0)
@@ -1099,7 +1099,7 @@ private void buildObjectPropertiesMaps() {
 			for (OntResource domain : directDomains) {
 				temp = directOutObjectProperties.get(domain.getURI());
 				if (temp == null) {
-					temp = new HashSet<String>();
+					temp = new HashSet<>();
 					directOutObjectProperties.put(domain.getURI(), temp);
 				}
 				temp.add(property.getURI());
@@ -1107,7 +1107,7 @@ private void buildObjectPropertiesMaps() {
 
 			// all domains
 			if (directDomainsUris.contains(Uris.THING_URI))
-				allDomainsUris = new HashSet<String>(this.classes.keySet());
+				allDomainsUris = new HashSet<>(this.classes.keySet());
 			else {
 				for (OntResource domain : directDomains) {
 					allDomains.add(domain);
@@ -1131,7 +1131,7 @@ private void buildObjectPropertiesMaps() {
 			for (String domainUri : indirectDomainsUris) {
 				temp = indirectOutObjectProperties.get(domainUri);
 				if (temp == null) { 
-					temp = new HashSet<String>();
+					temp = new HashSet<>();
 					indirectOutObjectProperties.put(domainUri, temp);
 				}
 				temp.add(property.getURI());
@@ -1157,7 +1157,7 @@ private void buildObjectPropertiesMaps() {
 			for (OntResource range : directRanges) {
 				temp = directInObjectProperties.get(range.getURI());
 				if (temp == null) {
-					temp = new HashSet<String>();
+					temp = new HashSet<>();
 					directInObjectProperties.put(range.getURI(), temp);
 				}
 				temp.add(property.getURI());
@@ -1165,7 +1165,7 @@ private void buildObjectPropertiesMaps() {
 			
 			// all ranges
 			if (directRangesUris.contains(Uris.THING_URI))
-				allRangesUris = new HashSet<String>(this.classes.keySet());
+				allRangesUris = new HashSet<>(this.classes.keySet());
 			else {
 				for (OntResource range : directRanges) {
 					allRanges.add(range);
@@ -1189,7 +1189,7 @@ private void buildObjectPropertiesMaps() {
 			for (String rangeUri : indirectRangesUris) {
 				temp = indirectInObjectProperties.get(rangeUri);
 				if (temp == null) {
-					temp = new HashSet<String>();
+					temp = new HashSet<>();
 					indirectInObjectProperties.put(rangeUri, temp);
 				}
 				temp.add(property.getURI());
@@ -1200,7 +1200,7 @@ private void buildObjectPropertiesMaps() {
 					temp = 
 						domainRangeToDirectProperties.get(domain + range);
 					if (temp == null) {
-						temp = new HashSet<String>();
+						temp = new HashSet<>();
 						domainRangeToDirectProperties.put(domain + range, temp);
 					}
 					temp.add(property.getURI());
@@ -1212,7 +1212,7 @@ private void buildObjectPropertiesMaps() {
 					if (directDomainsUris.contains(domain) && directRangesUris.contains(range)) continue;
 					temp = domainRangeToIndirectProperties.get(domain + range);
 					if (temp == null) {
-						temp = new HashSet<String>();
+						temp = new HashSet<>();
 						domainRangeToIndirectProperties.put(domain + range, temp);
 					}
 					temp.add(property.getURI());
@@ -1330,7 +1330,7 @@ private void updateMapsWithSubpropertyDefinitions() {
 		// iterate over all properties
 		for (String p : this.properties.keySet()) {
 			
-			allSuperPropertiesLocal = new HashSet<String>();
+			allSuperPropertiesLocal = new HashSet<>();
 			
 			Set<String> directSuperPropertiesLocal = this.directSuperProperties.get(p).keySet();
 			Set<String> indirectSuperPropertiesLocal = this.indirectSuperProperties.get(p).keySet();
@@ -1343,20 +1343,20 @@ private void updateMapsWithSubpropertyDefinitions() {
 			
 			HashSet<String> directDomains = this.propertyDirectDomains.get(p);
 			HashSet<String> indirectDomains = this.propertyIndirectDomains.get(p);
-			HashSet<String> allDomains = new HashSet<String>();
+			HashSet<String> allDomains = new HashSet<>();
 			if (directDomains != null) allDomains.addAll(directDomains);
 			if (indirectDomains != null) allDomains.addAll(indirectDomains);
 
 			HashSet<String> directRanges = this.propertyDirectRanges.get(p);
 			HashSet<String> indirectRanges = this.propertyIndirectRanges.get(p);
-			HashSet<String> allRanges = new HashSet<String>();
+			HashSet<String> allRanges = new HashSet<>();
 			if (directRanges != null) allRanges.addAll(directRanges);
 			if (indirectRanges != null) allRanges.addAll(indirectRanges);
 
 			for (String d : allDomains) {
 				temp = indirectOutObjectProperties.get(d);
 				if (temp == null) {
-					temp = new HashSet<String>();
+					temp = new HashSet<>();
 					indirectOutObjectProperties.put(d,  temp);
 				}
 				for (String superP : allSuperPropertiesLocal) {
@@ -1367,7 +1367,7 @@ private void updateMapsWithSubpropertyDefinitions() {
 			for (String r : allRanges) {
 				temp = indirectInObjectProperties.get(r);
 				if (temp == null) {
-					temp = new HashSet<String>();
+					temp = new HashSet<>();
 					indirectInObjectProperties.put(r,  temp);
 				}
 				for (String superP : allSuperPropertiesLocal) {
@@ -1379,7 +1379,7 @@ private void updateMapsWithSubpropertyDefinitions() {
 				for (String range : allRanges) {
 					temp = domainRangeToIndirectProperties.get(domain + range);
 					if (temp == null) {
-						temp = new HashSet<String>();
+						temp = new HashSet<>();
 						domainRangeToIndirectProperties.put(domain + range, temp);
 					}
 					for (String superP : allSuperPropertiesLocal) {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyHandler.java b/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyHandler.java
index 61bffab2c..abf99df79 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyHandler.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyHandler.java
@@ -97,7 +97,7 @@ public Label getResourceLabel(Resource r) {
 	 * @return
 	 */
 	public HashSet<String> getResourcesUris(HashSet<OntResource> resources) {
-		HashSet<String> resourcesURIs = new HashSet<String>();
+		HashSet<String> resourcesURIs = new HashSet<>();
 		if (resources != null)
 			for (OntResource r: resources) {
 				resourcesURIs.add(r.getURI());
@@ -111,7 +111,7 @@ public HashSet<String> getResourcesUris(HashSet<OntResource> resources) {
 	 * @return
 	 */
 	public HashMap<String, Label> getResourcesLabels(HashSet<OntResource> resources) {
-		HashMap<String, Label> resourcesLabels = new HashMap<String, Label>();
+		HashMap<String, Label> resourcesLabels = new HashMap<>();
 		if (resources != null)
 			for (OntResource r: resources) {
 				resourcesLabels.put(r.getURI(), getResourceLabel(r));
@@ -212,7 +212,7 @@ public void getParents(OntResource r, HashSet<OntResource> resources, boolean re
 		OntProperty p = null;
 		
 		if (resources == null) 
-			resources = new HashSet<OntResource>();
+			resources = new HashSet<>();
 
 		if (r == null)
 			return;
@@ -241,7 +241,7 @@ else if  (r.isProperty())
                 	if (recursive)
                 		getParents(superC, resources, recursive);
                 } else {
-                	HashSet<OntResource> members = new HashSet<OntResource>();
+                	HashSet<OntResource> members = new HashSet<>();
                 	getMembers(superC, members, false);
                 	for (OntResource or : members) {
                 		resources.add(or);
@@ -297,7 +297,7 @@ public void getChildren(OntResource r, HashSet<OntResource> resources, boolean r
 		OntProperty p = null;
 		
 		if (resources == null) 
-			resources = new HashSet<OntResource>();
+			resources = new HashSet<>();
 
 		if (r == null)
 			return;
@@ -326,7 +326,7 @@ else if  (r.isProperty())
                 	if (recursive)
                 		getChildren(subC, resources, recursive);
                 } else {
-                	HashSet<OntResource> members = new HashSet<OntResource>();
+                	HashSet<OntResource> members = new HashSet<>();
                 	getMembers(subC, members, false);
                 	for (OntResource or : members) {
                 		resources.add(or);
@@ -378,7 +378,7 @@ else if  (r.isProperty())
 	public void getMembers(OntResource r, HashSet<OntResource> resources, boolean recursive) {
 
 		if (resources == null) 
-			resources = new HashSet<OntResource>();
+			resources = new HashSet<>();
 
 		if (r == null)
 			return;
@@ -431,9 +431,9 @@ else if (c.isUnionClass()) { // in form of unionOf or intersectionOf
 	 */
 	public HashMap<String, Label> getSubClasses(String classUri, boolean recursive) {
 
-		HashSet<OntResource> resources = new HashSet<OntResource>();
+		HashSet<OntResource> resources = new HashSet<>();
 		OntResource r = ontModel.getOntClass(classUri);
-		if (r == null) return new HashMap<String, Label>();
+		if (r == null) return new HashMap<>();
 		getChildren(r, resources, recursive);
 		return getResourcesLabels(resources);
 	}
@@ -446,9 +446,9 @@ public HashMap<String, Label> getSubClasses(String classUri, boolean recursive)
 	 */
 	public HashMap<String, Label> getSuperClasses(String classUri, boolean recursive) {
 		
-		HashSet<OntResource> resources = new HashSet<OntResource>();
+		HashSet<OntResource> resources = new HashSet<>();
 		OntResource r = ontModel.getOntClass(classUri);
-		if (r == null) return new HashMap<String, Label>();
+		if (r == null) return new HashMap<>();
 		getParents(r, resources, recursive);
 		return getResourcesLabels(resources);
 	}
@@ -461,9 +461,9 @@ public HashMap<String, Label> getSuperClasses(String classUri, boolean recursive
 	 */
 	public HashMap<String, Label> getSubProperties(String propertyUri, boolean recursive) {
 
-		HashSet<OntResource> resources = new HashSet<OntResource>();
+		HashSet<OntResource> resources = new HashSet<>();
 		OntResource r = ontModel.getOntProperty(propertyUri);
-		if (r == null) return new HashMap<String, Label>();
+		if (r == null) return new HashMap<>();
 		getChildren(r, resources, recursive);
 		return getResourcesLabels(resources);
 	}
@@ -476,9 +476,9 @@ public HashMap<String, Label> getSubProperties(String propertyUri, boolean recur
 	 */
 	public HashMap<String, Label> getSuperProperties(String propertyUri, boolean recursive) {
 
-		HashSet<OntResource> resources = new HashSet<OntResource>();
+		HashSet<OntResource> resources = new HashSet<>();
 		OntResource r = ontModel.getOntProperty(propertyUri);
-		if (r == null) return new HashMap<String, Label>();
+		if (r == null) return new HashMap<>();
 		getParents(r, resources, recursive);
 		return getResourcesLabels(resources);
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyManager.java b/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyManager.java
index 8b39e0151..d4c4fae4a 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyManager.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/ontology/OntologyManager.java
@@ -52,7 +52,7 @@ public OntologyManager(String contextId) {
 		this.contextId = contextId;
 		ontHandler = new OntologyHandler();
 		ontCache = new OntologyCache(ontHandler, contextId);
-		ontUpdateListeners = new ArrayList<OntologyUpdateListener>();	
+		ontUpdateListeners = new ArrayList<>();	
 	}
 	
 	public String getContextId()
@@ -249,8 +249,8 @@ public Label getUriLabel(String uri) {
 	
 	public HashSet<String> getPossibleUris(String sourceUri, String targetUri) {
 
-		HashSet<String> linkUris = 
-				new HashSet<String>();
+		HashSet<String> linkUris =
+				new HashSet<>();
 
 		HashSet<String> objectPropertiesDirect;
 		HashSet<String> objectPropertiesIndirect;
@@ -365,7 +365,7 @@ else if (recursive)
 	 */
 	public HashSet<String> getDomainsOfProperty(String propertyUri, boolean recursive) {
 
-		HashSet<String> results = new HashSet<String>();
+		HashSet<String> results = new HashSet<>();
 		HashSet<String> direct = null;
 		HashSet<String> indirect = null;
 		
@@ -387,7 +387,7 @@ public HashSet<String> getDomainsOfProperty(String propertyUri, boolean recursiv
 	 */
 	public HashSet<String> getRangesOfProperty(String propertyUri, boolean recursive) {
 
-		HashSet<String> results = new HashSet<String>();
+		HashSet<String> results = new HashSet<>();
 		HashSet<String> direct = null;
 		HashSet<String> indirect = null;
 		
@@ -411,7 +411,7 @@ public HashSet<String> getRangesOfProperty(String propertyUri, boolean recursive
 	public HashSet<String> getDomainsGivenRange(String rangeUri, boolean recursive) {
 		
 		HashSet<String> objectProperties = ontCache.getDirectInObjectProperties().get(rangeUri);
-		HashSet<String> results = new HashSet<String>();
+		HashSet<String> results = new HashSet<>();
 		HashSet<String> direct = null;
 		HashSet<String> indirect = null;
 		
@@ -454,7 +454,7 @@ public Map<String, Label> getObjectPropertiesByDomainRange(String domainUri, Str
 					objectProperties = propRecursive;
 			}
 		}
-		HashMap<String, Label> results = new HashMap<String, Label>();
+		HashMap<String, Label> results = new HashMap<>();
 		HashSet<String> direct = null;
 		HashSet<String> indirect = null;
 		
@@ -496,7 +496,7 @@ public Map<String, Label> getObjectPropertiesByDomainRange(String domainUri, Str
 	
 	
 	public Map<String, Label> getObjectPropertiesByDomain(String domainUri, boolean recursive) {
-		HashSet<String> all = new HashSet<String>();
+		HashSet<String> all = new HashSet<>();
 		HashSet<String> objectProperties = ontCache.getDirectOutObjectProperties().get(domainUri);
 		if(objectProperties != null)
 			all.addAll(objectProperties);
@@ -505,7 +505,7 @@ public Map<String, Label> getObjectPropertiesByDomain(String domainUri, boolean
 			if(propRecursive != null)
 				all.addAll(propRecursive);
 		}
-		HashMap<String, Label> results = new HashMap<String, Label>();
+		HashMap<String, Label> results = new HashMap<>();
 		
 		for (String op : all) {
 			results.put(op, ontCache.getPropertyLabel(op));
@@ -515,7 +515,7 @@ public Map<String, Label> getObjectPropertiesByDomain(String domainUri, boolean
 	}
 	
 	public Map<String, Label> getObjectPropertiesByRange(String rangeUri, boolean recursive) {
-		HashSet<String> all = new HashSet<String>();
+		HashSet<String> all = new HashSet<>();
 		HashSet<String> objectProperties = ontCache.getDirectInObjectProperties().get(rangeUri);
 		if(objectProperties != null)
 			all.addAll(objectProperties);
@@ -524,7 +524,7 @@ public Map<String, Label> getObjectPropertiesByRange(String rangeUri, boolean re
 			if(propRecursive != null)
 				all.addAll(propRecursive);
 		}
-		HashMap<String, Label> results = new HashMap<String, Label>();
+		HashMap<String, Label> results = new HashMap<>();
 		
 		for (String op : all) {
 			results.put(op, ontCache.getPropertyLabel(op));
@@ -534,7 +534,7 @@ public Map<String, Label> getObjectPropertiesByRange(String rangeUri, boolean re
 	}
 	
 	public Map<String, Label> getDataPropertiesByDomain(String domainUri, boolean recursive) {
-		HashSet<String> all = new HashSet<String>();
+		HashSet<String> all = new HashSet<>();
 		HashSet<String> dataProperties = ontCache.getDirectOutDataProperties().get(domainUri);
 		if(dataProperties != null)
 			all.addAll(dataProperties);
@@ -543,7 +543,7 @@ public Map<String, Label> getDataPropertiesByDomain(String domainUri, boolean re
 			if(propRecursive != null)
 				all.addAll(propRecursive);
 		}
-		HashMap<String, Label> results = new HashMap<String, Label>();
+		HashMap<String, Label> results = new HashMap<>();
 		
 		for (String op : all) {
 			results.put(op, ontCache.getPropertyLabel(op));
@@ -554,7 +554,7 @@ public Map<String, Label> getDataPropertiesByDomain(String domainUri, boolean re
 	
 	public Map<String, String> getPrefixMap () {
 		Map<String, String> nsMap = ontHandler.getOntModel().getNsPrefixMap();
-		Map<String, String> prefixMap = new HashMap<String, String>();
+		Map<String, String> prefixMap = new HashMap<>();
 		
 		for(Map.Entry<String, String> stringStringEntry : nsMap.entrySet()) {
 			if (!stringStringEntry.getKey().equals("") && !prefixMap.containsKey(stringStringEntry.getValue()))
@@ -574,7 +574,7 @@ public HashMap<String, Label> getSubClasses(String classUri, boolean recursive)
 		HashMap<String, Label> direct = ontCache.getDirectSubClasses().get(classUri);
 		if (!recursive) return direct;
 		
-		HashMap<String, Label> all = new HashMap<String, Label>();
+		HashMap<String, Label> all = new HashMap<>();
 		HashMap<String, Label> indirect = ontCache.getIndirectSubClasses().get(classUri);
 		if (direct != null) all.putAll(direct);
 		if (indirect != null) all.putAll(indirect);
@@ -592,7 +592,7 @@ public HashMap<String, Label> getSuperClasses(String classUri, boolean recursive
 		HashMap<String, Label> direct = ontCache.getDirectSuperClasses().get(classUri);
 		if (!recursive) return direct;
 		
-		HashMap<String, Label> all = new HashMap<String, Label>();
+		HashMap<String, Label> all = new HashMap<>();
 		HashMap<String, Label> indirect = ontCache.getIndirectSuperClasses().get(classUri);
 		if (direct != null) all.putAll(direct);
 		if (indirect != null) all.putAll(indirect);
@@ -610,7 +610,7 @@ public HashMap<String, Label> getSubProperties(String propertyUri, boolean recur
 		HashMap<String, Label> direct = ontCache.getDirectSubProperties().get(propertyUri);
 		if (!recursive) return direct;
 		
-		HashMap<String, Label> all = new HashMap<String, Label>();
+		HashMap<String, Label> all = new HashMap<>();
 		HashMap<String, Label> indirect = ontCache.getIndirectSubProperties().get(propertyUri);
 		if (direct != null) all.putAll(direct);
 		if (indirect != null) all.putAll(indirect);
@@ -629,7 +629,7 @@ public HashMap<String, Label> getSuperProperties(String propertyUri, boolean rec
 		HashMap<String, Label> direct = ontCache.getDirectSuperProperties().get(propertyUri);
 		if (!recursive) return direct;
 		
-		HashMap<String, Label> all = new HashMap<String, Label>();
+		HashMap<String, Label> all = new HashMap<>();
 		HashMap<String, Label> indirect = ontCache.getIndirectSuperProperties().get(propertyUri);
 		if (direct != null) all.putAll(direct);
 		if (indirect != null) all.putAll(indirect);
@@ -694,7 +694,7 @@ public HashSet<String> getObjectPropertiesWithOnlyDomain(String domainUri) {
 		
 		HashSet<String> directOutProperties;
 		HashSet<String> indirectOutProperties;
-		HashSet<String> results = new HashSet<String>();
+		HashSet<String> results = new HashSet<>();
 
 		directOutProperties = this.ontCache.getDirectOutObjectProperties().get(domainUri);
 		if (directOutProperties != null)
@@ -717,7 +717,7 @@ public HashSet<String> getObjectPropertiesWithOnlyRange(String rangeUri) {
 		
 		HashSet<String> directInProperties;
 		HashSet<String> indirectInProperties;
-		HashSet<String> results = new HashSet<String>();
+		HashSet<String> results = new HashSet<>();
 		
 		directInProperties = this.ontCache.getDirectInObjectProperties().get(rangeUri);
 		if (directInProperties != null)
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/semantictypes/SemanticTypeColumnModel.java b/karma-common/src/main/java/edu/isi/karma/modeling/semantictypes/SemanticTypeColumnModel.java
index e13cc06a4..5fc1cfe1b 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/semantictypes/SemanticTypeColumnModel.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/semantictypes/SemanticTypeColumnModel.java
@@ -42,7 +42,7 @@
 
 public class SemanticTypeColumnModel implements Jsonizable {
 
-	private final HashMap<String, Double> scoreMap = new HashMap<String, Double>();
+	private final HashMap<String, Double> scoreMap = new HashMap<>();
 
 	public SemanticTypeColumnModel(List<SemanticTypeLabel> labels) {
 		for (int i = 0; i < labels.size(); i++) {
@@ -110,7 +110,7 @@ public JSONObject getAsJSONObject(OntologyManager ontMgr, Alignment alignment) t
 		JSONArray arr = new JSONArray();
 		
 		/** Create a set of node ids of internal nodes of Steiner Tree **/
-		Set<String> steinerTreeNodeIds = new HashSet<String>();
+		Set<String> steinerTreeNodeIds = new HashSet<>();
 		if (alignment != null && !alignment.isEmpty()) {
 			for (Node node: alignment.getSteinerTree().vertexSet()) {
 				if (node.getType() == NodeType.InternalNode) {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/semantictypes/SemanticTypeUtil.java b/karma-common/src/main/java/edu/isi/karma/modeling/semantictypes/SemanticTypeUtil.java
index 0013cc355..9ffd8250e 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/semantictypes/SemanticTypeUtil.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/semantictypes/SemanticTypeUtil.java
@@ -83,19 +83,19 @@ public static ArrayList<String> getTrainingExamples(Workspace workspace, Workshe
 			HNodePath path, SuperSelection sel) {
 		if(!getSemanticTypeTrainingEnabled() || path == null)
 		{
-			return new ArrayList<String>();
+			return new ArrayList<>();
 		}
 		final ServletContextParameterMap contextParameters = ContextParametersRegistry.getInstance().getContextParameters(workspace.getContextId());
 		int TRAINING_EXAMPLE_MAX_COUNT = Integer
 		.parseInt(contextParameters
 				.getParameterValue(ContextParameter.TRAINING_EXAMPLE_MAX_COUNT));
-		ArrayList<Node> nodes = new ArrayList<Node>(Math.max(100, worksheet.getDataTable().getNumRows()));
+		ArrayList<Node> nodes = new ArrayList<>(Math.max(100, worksheet.getDataTable().getNumRows()));
 		worksheet.getDataTable().collectNodes(path, nodes, sel);
 
 		Random r = new Random();
-		ArrayList<String> subset = new ArrayList<String>(TRAINING_EXAMPLE_MAX_COUNT);
+		ArrayList<String> subset = new ArrayList<>(TRAINING_EXAMPLE_MAX_COUNT);
 		if (nodes.size() > TRAINING_EXAMPLE_MAX_COUNT *2) {
-			HashSet<Integer> seenValues = new HashSet<Integer>(TRAINING_EXAMPLE_MAX_COUNT);
+			HashSet<Integer> seenValues = new HashSet<>(TRAINING_EXAMPLE_MAX_COUNT);
 			// SubList method of ArrayList causes ClassCast exception
 			int attempts = 0;
 			while(subset.size() < TRAINING_EXAMPLE_MAX_COUNT && attempts < Math.min(nodes.size(), TRAINING_EXAMPLE_MAX_COUNT*2))
@@ -130,7 +130,7 @@ private class TrainingFactory extends Thread {
 		private Condition taskAvailable;
 		
 		TrainingFactory() {
-			this.tasks = new ArrayList<TrainingJob>();
+			this.tasks = new ArrayList<>();
 			this.lock = new ReentrantLock();
 			this.taskAvailable = this.lock.newCondition();
 			this.start();
@@ -233,7 +233,7 @@ public SemanticTypeColumnModel predictColumnSemanticType(Workspace workspace, Wo
 		}
 
 		/** Remove the labels that are not in the ontology or are already used as the semantic type **/
-		List<SemanticTypeLabel> removeLabels = new ArrayList<SemanticTypeLabel>();
+		List<SemanticTypeLabel> removeLabels = new ArrayList<>();
 		String domainUri, typeUri;
 		Label domain, type;
 		for (int i=0; i<result.size(); i++) {
@@ -276,7 +276,7 @@ public SemanticTypeColumnModel predictColumnSemanticType(Workspace workspace, Wo
 	public List<SemanticType> getSuggestedTypes(OntologyManager ontologyManager, 
 			ColumnNode columnNode, SemanticTypeColumnModel columnModel) {
 		
-		ArrayList<SemanticType> suggestedSemanticTypes = new ArrayList<SemanticType>();
+		ArrayList<SemanticType> suggestedSemanticTypes = new ArrayList<>();
 		if (columnModel == null)
 			return suggestedSemanticTypes;
 		
@@ -307,7 +307,7 @@ public List<SemanticType> getSuggestedTypes(OntologyManager ontologyManager,
 	}
 	
 	public ArrayList<SemanticType> getColumnSemanticSuggestions(Workspace workspace, Worksheet worksheet, ColumnNode columnNode, int numSuggestions, SuperSelection sel) {
-		ArrayList<SemanticType> suggestedSemanticTypes = new ArrayList<SemanticType>();
+		ArrayList<SemanticType> suggestedSemanticTypes = new ArrayList<>();
 		logger.info("Column Semantic Suggestions for:" + columnNode.getColumnName());
 		if(workspace != null && worksheet != null) {
 			OntologyManager ontologyManager = workspace.getOntologyManager();
@@ -367,20 +367,20 @@ public ArrayList<SemanticType> getColumnSemanticSuggestions(Workspace workspace,
 	 */
 	public static void identifyOutliers(Worksheet worksheet, String predictedType, HNodePath path, Tag outlierTag,
 			ISemanticTypeModelHandler modelHandler, SuperSelection sel) {
-		Collection<Node> nodes = new ArrayList<Node>();
+		Collection<Node> nodes = new ArrayList<>();
 		worksheet.getDataTable().collectNodes(path, nodes, sel);
 
 		// Identify the top semantic type for each node
 		// It it does not matches the predicted type, it is a outlier.
-		Set<String> allNodeIds = new HashSet<String>();
-		Set<String> outlierNodeIds = new HashSet<String>();
+		Set<String> allNodeIds = new HashSet<>();
+		Set<String> outlierNodeIds = new HashSet<>();
 
 		int outlierCounter = 0;
 		for (Node node : nodes) {
 			allNodeIds.add(node.getId());
 
 			// Compute the semantic type for the node value
-			List<String> examples = new ArrayList<String>();
+			List<String> examples = new ArrayList<>();
 
 			String nodeVal = node.getValue().asString();
 			if (nodeVal != null && !nodeVal.equals("")) {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ApprSteinerTree.java b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ApprSteinerTree.java
index 64ae11e1d..b8eeaa189 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ApprSteinerTree.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ApprSteinerTree.java
@@ -41,10 +41,10 @@ public ApprSteinerTree(Set<SteinerNode>terminalNodes, Set<SteinerNode>treeNodes)
 	 * @return copy of this ApprSteinerTree
 	 */
 	public ApprSteinerTree clone(){
-		Set<SteinerNode> newTerminals= new TreeSet<SteinerNode>();
+		Set<SteinerNode> newTerminals= new TreeSet<>();
 		
-		Set<SteinerNode> newTreeNodes= new TreeSet<SteinerNode>();
-		Map<String,SteinerNode> hms=new HashMap<String,SteinerNode>();
+		Set<SteinerNode> newTreeNodes= new TreeSet<>();
+		Map<String,SteinerNode> hms= new HashMap<>();
 		
 		// copy nodes (only nodeIds: SteinerNode.copy())
 		for(SteinerNode n: treeNodes){
@@ -80,7 +80,7 @@ public ApprSteinerTree clone(){
 	 * @return TreeSet<SteinerNode> of all nodes that have degree >= 3 and the terminals
 	 */
 	public Set<SteinerNode> getFixedNodes(){
-		Set<SteinerNode> fixedNodes= new TreeSet<SteinerNode>();
+		Set<SteinerNode> fixedNodes= new TreeSet<>();
 		// first add all terminals
 		fixedNodes.addAll(terminalNodes);
 		
@@ -99,7 +99,7 @@ public Set<SteinerNode> getFixedNodes(){
 	 * @return the subtrees resulting from the removal of p
 	 */
 	public List<Set<SteinerNode>> getNodeSetPartitioning(LoosePath p){
-		List<Set<SteinerNode>> listOfPartitions = new ArrayList<Set<SteinerNode>>();
+		List<Set<SteinerNode>> listOfPartitions = new ArrayList<>();
 		SteinerNode n1 = p.getFirstNode();
 		SteinerNode n2 = p.getLastNode();
 		for(SteinerNode node:treeNodes){
@@ -120,8 +120,8 @@ public List<Set<SteinerNode>> getNodeSetPartitioning(LoosePath p){
 	 * @return the nodes reached by the BFS
 	 */
 	public Set<SteinerNode> getNodesInBreadthFirstFrom(SteinerNode node, SteinerEdge exceptForEdge){
-		Set<SteinerNode> ts = new TreeSet<SteinerNode>();
-		Queue<SteinerNode> queue=new LinkedList<SteinerNode>();
+		Set<SteinerNode> ts = new TreeSet<>();
+		Queue<SteinerNode> queue= new LinkedList<>();
 		queue.offer(node);
 		while(!queue.isEmpty()){
 			SteinerNode n=queue.poll();
@@ -148,7 +148,7 @@ public Set<SteinerNode> getNodesInBreadthFirstFrom(SteinerNode node, SteinerEdge
 	 * @return PriorityQueue of all loose paths connected to fixedNode
 	 */
 	public PriorityQueue<LoosePath> getLoosePaths(SteinerNode fixedNode){
-		PriorityQueue<LoosePath> loosePaths=new PriorityQueue<LoosePath>();
+		PriorityQueue<LoosePath> loosePaths= new PriorityQueue<>();
 		
 		for(SteinerEdge edge: fixedNode.edges){
 			SteinerEdge e2=edge;
@@ -161,7 +161,7 @@ public PriorityQueue<LoosePath> getLoosePaths(SteinerNode fixedNode){
 			else{
 				n1.addEdge(n2, false, edge.getEdgeLabel(), edge.weight());
 			}
-			LinkedList<SteinerNode> pathNodes = new LinkedList<SteinerNode>();
+			LinkedList<SteinerNode> pathNodes = new LinkedList<>();
 			pathNodes.add(n1);pathNodes.add(n2);
 			// following a loose path
 			while(!n.isFixedNode()&&!terminalNodes.contains(n)){
@@ -192,7 +192,7 @@ public PriorityQueue<LoosePath> getLoosePaths(SteinerNode fixedNode){
 	 * @return priority queue of all loose paths in a tree (ranked by their scores) 
 	 */
 	public Set<LoosePath> getLoosePaths(){
-		Set<LoosePath> loosePaths= new TreeSet<LoosePath>();
+		Set<LoosePath> loosePaths= new TreeSet<>();
 		for(SteinerNode node: treeNodes){
 			if(node.isFixedNode()||terminalNodes.contains(node)){
 				loosePaths.addAll(getLoosePaths(node));
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/BANKSfromMM_Old.java b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/BANKSfromMM_Old.java
index 486abc8b6..9cdb99f2b 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/BANKSfromMM_Old.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/BANKSfromMM_Old.java
@@ -10,6 +10,7 @@
 import java.util.Map;
 import java.util.PriorityQueue;
 import java.util.Queue;
+import java.util.Set;
 import java.util.TreeSet;
 
 //import org.slf4j.Logger;
@@ -24,7 +25,7 @@ public class BANKSfromMM_Old extends TopKSteinertrees {
 
 	private int iteratorCounter=0;
 	
-	private HashMap<SteinerNode,SteinerNode> recurseNodeMap;
+	private Map<SteinerNode,SteinerNode> recurseNodeMap;
 	private List<HashMap<SteinerNode,SteinerNode>> shortestNodeIndex;
 	private List<HashMap<SteinerNode,SortedSteinerNodes>> duplicateIndex;
 	private String contextId;
@@ -37,12 +38,12 @@ public BANKSfromMM_Old(String contextId) {
 	}
 	
 	class SortedSteinerNodes{
-		TreeSet<SteinerNode> set;
+		Set<SteinerNode> set;
 		SortedSteinerNodes(){
-			set= new TreeSet<SteinerNode>(new Comparator<SteinerNode>(){
-				public int compare(SteinerNode n1, SteinerNode n2){
-					if(n1.distancesToSources[0]>n2.distancesToSources[0]) return 1;
-					else if(n1.distancesToSources[0]<n2.distancesToSources[0])return -1;
+			set= new TreeSet<>(new Comparator<SteinerNode>() {
+				public int compare(SteinerNode n1, SteinerNode n2) {
+					if (n1.distancesToSources[0] > n2.distancesToSources[0]) return 1;
+					else if (n1.distancesToSources[0] < n2.distancesToSources[0]) return -1;
 					else return 0;
 				}
 			});
@@ -60,10 +61,10 @@ class BANKSIterator{
 		double distanceToSource;
 		BANKSIterator(){
 			id=iteratorCounter;
-			banksIterator= new PriorityQueue<SteinerNode>(10, new Comparator<SteinerNode>(){
-				public int compare(SteinerNode n1, SteinerNode n2){
-					if(n1.distancesToSources[0]>n2.distancesToSources[0]) return 1;
-					else if(n1.distancesToSources[0]<n2.distancesToSources[0])return -1;
+			banksIterator= new PriorityQueue<>(10, new Comparator<SteinerNode>() {
+				public int compare(SteinerNode n1, SteinerNode n2) {
+					if (n1.distancesToSources[0] > n2.distancesToSources[0]) return 1;
+					else if (n1.distancesToSources[0] < n2.distancesToSources[0]) return -1;
 					else return 0;
 				}
 			});
@@ -85,23 +86,23 @@ public BANKSfromMM_Old(TreeSet<SteinerNode> terminals, Integer recursiveLevel, I
 		this.recursiveLevel = recursiveLevel;
 		this.maxPermutations = maxPermutations;
 		
-		banksIterators=new PriorityQueue<BANKSIterator>(terminals.size(), new Comparator<BANKSIterator>(){
-			public int compare(BANKSIterator it1, BANKSIterator it2){
-				if(it1.distanceToSource>it2.distanceToSource) return 1;
-				else if (it1.distanceToSource<it2.distanceToSource) return -1;
+		banksIterators= new PriorityQueue<>(terminals.size(), new Comparator<BANKSIterator>() {
+			public int compare(BANKSIterator it1, BANKSIterator it2) {
+				if (it1.distanceToSource > it2.distanceToSource) return 1;
+				else if (it1.distanceToSource < it2.distanceToSource) return -1;
 				else return 0;
 			}
 		});
 		
-		shortestNodeIndex = new ArrayList<HashMap<SteinerNode, SteinerNode>>();
-		duplicateIndex = new ArrayList<HashMap<SteinerNode,SortedSteinerNodes>>();
+		shortestNodeIndex = new ArrayList<>();
+		duplicateIndex = new ArrayList<>();
 		
 		for(int i=0; i<terminalNodes.size();i++){
 			banksIterators.offer(new BANKSIterator());
 			shortestNodeIndex.add(new HashMap<SteinerNode,SteinerNode>());
 		}
 		
-		recurseNodeMap = new HashMap<SteinerNode, SteinerNode>();
+		recurseNodeMap = new HashMap<>();
 		
 	}
 	
@@ -119,7 +120,7 @@ private List<HashMap<Integer, SteinerNode>> getPermutation(
 		}
 		
 		SortedSteinerNodes sortedNodes = duplicateIndex.get(queueId).get(searchNode);
-		List<SteinerNode> steinerNodes = new LinkedList<SteinerNode>();
+		List<SteinerNode> steinerNodes = new LinkedList<>();
 		Iterator<SteinerNode> nodeIterator = sortedNodes.set.iterator();
 		for (int i = 0; i < sortedNodes.set.size() && i < max; i++) {
 			SteinerNode n = nodeIterator.next();
@@ -127,13 +128,13 @@ private List<HashMap<Integer, SteinerNode>> getPermutation(
 				steinerNodes.add(n);
 		}
 		
-		List<HashMap<Integer, SteinerNode>> newSearchNodeInQueues = 
-				new LinkedList<HashMap<Integer, SteinerNode>>();
+		List<HashMap<Integer, SteinerNode>> newSearchNodeInQueues =
+				new LinkedList<>();
 		
 		for (HashMap<Integer, SteinerNode> map : searchNodeInQueues) {
 			for (SteinerNode n : steinerNodes) {
-				HashMap<Integer, SteinerNode> newMap = 
-						new HashMap<Integer, SteinerNode>(map);
+				HashMap<Integer, SteinerNode> newMap =
+						new HashMap<>(map);
 				newMap.put(queueId, n);
 				newSearchNodeInQueues.add(newMap);
 			}
@@ -148,11 +149,11 @@ private int getApprTree(SteinerNode ancestor, List<Map<String, SteinerNode>> pro
 		if (this.recurseNodeMap.containsKey(ancestor)) 
 			searchNode = this.recurseNodeMap.get(ancestor);
 
-		List<HashMap<Integer, SteinerNode>> searchNodeInQueues = 
-				new LinkedList<HashMap<Integer, SteinerNode>>();
+		List<HashMap<Integer, SteinerNode>> searchNodeInQueues =
+				new LinkedList<>();
 
-		HashMap<Integer, SteinerNode> mainQueueMap = 
-				new HashMap<Integer, SteinerNode>();
+		HashMap<Integer, SteinerNode> mainQueueMap =
+				new HashMap<>();
 		mainQueueMap.put(queueId, ancestor);
 		searchNodeInQueues.add(mainQueueMap);
 
@@ -189,13 +190,13 @@ private int getApprTree(SteinerNode ancestor, List<Map<String, SteinerNode>> pro
 	 */
 	private void getApprTree(
 			SteinerNode ancestor, 
-			HashMap<Integer, SteinerNode> searchNodeInQueues, 
+			Map<Integer, SteinerNode> searchNodeInQueues, 
 			List<Map<String, SteinerNode>> processedNodes, 
 			int queueId) throws Exception{
-		TreeSet<SteinerNode> steinerNodes = new TreeSet<SteinerNode>();
-		Map<String , SteinerNode> treeNodes= new HashMap<String, SteinerNode>();
+		TreeSet<SteinerNode> steinerNodes = new TreeSet<>();
+		Map<String , SteinerNode> treeNodes= new HashMap<>();
 		
-		SteinerNode replacedNode = null;
+		SteinerNode replacedNode;
 		if (this.recurseNodeMap.containsKey(ancestor)) {
 			replacedNode = this.recurseNodeMap.get(ancestor);
 			treeNodes.put(replacedNode.name,new SteinerNode(replacedNode.name));
@@ -280,14 +281,14 @@ public void buildConnectivityGraph(int k) throws Exception{
 		boolean debug = false;
 		
 		//nodes polled from queues
-		List<Map<String, SteinerNode>> processedNodes= 
-				new ArrayList<Map<String, SteinerNode>>();
-		List<Map<String, SteinerNode>> processedNodesHelper= 
-				new ArrayList<Map<String, SteinerNode>>();
+		List<Map<String, SteinerNode>> processedNodes=
+				new ArrayList<>();
+		List<Map<String, SteinerNode>> processedNodesHelper=
+				new ArrayList<>();
 
 		
-		List<HashMap<String, Integer>> recursesForNodesInQueue = 
-				new ArrayList<HashMap<String, Integer>>();
+		List<HashMap<String, Integer>> recursesForNodesInQueue =
+				new ArrayList<>();
 		
 		//mark nodes in the iterators as visited
 		int j=0;
@@ -302,8 +303,8 @@ public void buildConnectivityGraph(int k) throws Exception{
 				visitedNodes.get(j).put(n.name(),n);
 				shortestNodeIndex.get(j).put(n, n);
 				
-				HashMap<SteinerNode, SortedSteinerNodes> map = 
-						new HashMap<SteinerNode, SortedSteinerNodes>();
+				HashMap<SteinerNode, SortedSteinerNodes> map =
+						new HashMap<>();
 				
 				SortedSteinerNodes treeSet = new SortedSteinerNodes();
 				treeSet.set.add(n);
@@ -349,10 +350,10 @@ public void buildConnectivityGraph(int k) throws Exception{
 					
 					if (count>k) break;
 					
-					Queue<SteinerEdge> rs= new PriorityQueue<SteinerEdge>(10, new Comparator<SteinerEdge>(){
-						public int compare(SteinerEdge e1, SteinerEdge e2){
-							if(e1.weight()>e2.weight()) return 1;
-							else if (e1.weight()<e2.weight()) return -1;
+					Queue<SteinerEdge> rs= new PriorityQueue<>(10, new Comparator<SteinerEdge>() {
+						public int compare(SteinerEdge e1, SteinerEdge e2) {
+							if (e1.weight() > e2.weight()) return 1;
+							else if (e1.weight() < e2.weight()) return -1;
 							else return 0;
 						}
 					});
@@ -362,7 +363,7 @@ public int compare(SteinerEdge e1, SteinerEdge e2){
 					while(!rs.isEmpty()){
 						
 						accessedEdges++;
-						SteinerNode newNode=null;
+						SteinerNode newNode;
 						
 						// getting (creating) neighbor of n
 						SteinerEdge e= rs.poll();
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/CustomizedBANKS.java b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/CustomizedBANKS.java
index 81920239f..dcf60bc3f 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/CustomizedBANKS.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/CustomizedBANKS.java
@@ -10,6 +10,7 @@
 import java.util.Map;
 import java.util.PriorityQueue;
 import java.util.Queue;
+import java.util.Set;
 import java.util.TreeSet;
 
 import edu.isi.karma.config.ModelingConfiguration;
@@ -24,7 +25,7 @@ public class CustomizedBANKS extends TopKSteinertrees {
 	private int iteratorCounter=0;
 	private ModelCoherence modelCoherence;
 	
-	private HashMap<SteinerNode,SteinerNode> recurseNodeMap;
+	private Map<SteinerNode,SteinerNode> recurseNodeMap;
 	private List<HashMap<SteinerNode,SteinerNode>> shortestNodeIndex;
 	private List<HashMap<SteinerNode,SortedSteinerNodes>> duplicateIndex;
 	private String contextId;
@@ -37,12 +38,12 @@ public CustomizedBANKS() {
 	}
 	
 	class SortedSteinerNodes{
-		TreeSet<SteinerNode> set;
+		Set<SteinerNode> set;
 		SortedSteinerNodes(){
-			set= new TreeSet<SteinerNode>(new Comparator<SteinerNode>(){
-				public int compare(SteinerNode n1, SteinerNode n2){
-					if(n1.distancesToSources[0]>n2.distancesToSources[0]) return 1;
-					else if(n1.distancesToSources[0]<n2.distancesToSources[0])return -1;
+			set= new TreeSet<>(new Comparator<SteinerNode>() {
+				public int compare(SteinerNode n1, SteinerNode n2) {
+					if (n1.distancesToSources[0] > n2.distancesToSources[0]) return 1;
+					else if (n1.distancesToSources[0] < n2.distancesToSources[0]) return -1;
 					else return 0;
 				}
 			});
@@ -62,7 +63,7 @@ class BANKSIterator{
 		SteinerEdge predecessorLink;
 		BANKSIterator(ModelCoherence modelCoherence){
 			id=iteratorCounter;
-			banksIterator= new PriorityQueue<SteinerNode>(10, new SteinerNodeComparator(modelCoherence));
+			banksIterator= new PriorityQueue<>(10, new SteinerNodeComparator(modelCoherence));
 //			banksIterator= new PriorityQueue<SteinerNode>(10, new Comparator<SteinerNode>(){
 //				public int compare(SteinerNode n1, SteinerNode n2){
 //					if(n1.distancesToSources[0]>n2.distancesToSources[0]) return 1;
@@ -91,7 +92,7 @@ public CustomizedBANKS(TreeSet<SteinerNode> terminals, Integer recursiveLevel, I
 		if (maxPermutations != null)
 			this.maxPermutations = maxPermutations;
 		
-		banksIterators=new PriorityQueue<BANKSIterator>(terminals.size(), new BANKSIteratorComparator(this.modelCoherence));
+		banksIterators= new PriorityQueue<>(terminals.size(), new BANKSIteratorComparator(this.modelCoherence));
 		
 //		banksIterators=new PriorityQueue<BANKSIterator>(terminals.size(), new Comparator<BANKSIterator>(){
 //			public int compare(BANKSIterator it1, BANKSIterator it2){
@@ -101,15 +102,15 @@ public CustomizedBANKS(TreeSet<SteinerNode> terminals, Integer recursiveLevel, I
 //			}
 //		});
 		
-		shortestNodeIndex = new ArrayList<HashMap<SteinerNode, SteinerNode>>();
-		duplicateIndex = new ArrayList<HashMap<SteinerNode,SortedSteinerNodes>>();
+		shortestNodeIndex = new ArrayList<>();
+		duplicateIndex = new ArrayList<>();
 		
 		for(int i=0; i<terminalNodes.size();i++){
 			banksIterators.offer(new BANKSIterator(this.modelCoherence));
 			shortestNodeIndex.add(new HashMap<SteinerNode,SteinerNode>());
 		}
 		
-		recurseNodeMap = new HashMap<SteinerNode, SteinerNode>();
+		recurseNodeMap = new HashMap<>();
 		
 	}
 	
@@ -127,7 +128,7 @@ private List<HashMap<Integer, SteinerNode>> getPermutation(
 		}
 		
 		SortedSteinerNodes sortedNodes = duplicateIndex.get(queueId).get(searchNode);
-		List<SteinerNode> steinerNodes = new LinkedList<SteinerNode>();
+		List<SteinerNode> steinerNodes = new LinkedList<>();
 		Iterator<SteinerNode> nodeIterator = sortedNodes.set.iterator();
 		for (int i = 0; i < sortedNodes.set.size() && i < max; i++) {
 			SteinerNode n = nodeIterator.next();
@@ -135,13 +136,13 @@ private List<HashMap<Integer, SteinerNode>> getPermutation(
 				steinerNodes.add(n);
 		}
 		
-		List<HashMap<Integer, SteinerNode>> newSearchNodeInQueues = 
-				new LinkedList<HashMap<Integer, SteinerNode>>();
+		List<HashMap<Integer, SteinerNode>> newSearchNodeInQueues =
+				new LinkedList<>();
 		
 		for (HashMap<Integer, SteinerNode> map : searchNodeInQueues) {
 			for (SteinerNode n : steinerNodes) {
-				HashMap<Integer, SteinerNode> newMap = 
-						new HashMap<Integer, SteinerNode>(map);
+				HashMap<Integer, SteinerNode> newMap =
+						new HashMap<>(map);
 				newMap.put(queueId, n);
 				newSearchNodeInQueues.add(newMap);
 			}
@@ -156,11 +157,11 @@ private int getApprTree(SteinerNode ancestor, List<Map<String, SteinerNode>> pro
 		if (this.recurseNodeMap.containsKey(ancestor)) 
 			searchNode = this.recurseNodeMap.get(ancestor);
 
-		List<HashMap<Integer, SteinerNode>> searchNodeInQueues = 
-				new LinkedList<HashMap<Integer, SteinerNode>>();
+		List<HashMap<Integer, SteinerNode>> searchNodeInQueues =
+				new LinkedList<>();
 
-		HashMap<Integer, SteinerNode> mainQueueMap = 
-				new HashMap<Integer, SteinerNode>();
+		HashMap<Integer, SteinerNode> mainQueueMap =
+				new HashMap<>();
 		mainQueueMap.put(queueId, ancestor);
 		searchNodeInQueues.add(mainQueueMap);
 
@@ -199,11 +200,11 @@ private int getApprTree(SteinerNode ancestor, List<Map<String, SteinerNode>> pro
 	 */
 	private void getApprTree(
 			SteinerNode ancestor, 
-			HashMap<Integer, SteinerNode> searchNodeInQueues, 
+			Map<Integer, SteinerNode> searchNodeInQueues, 
 			List<Map<String, SteinerNode>> processedNodes, 
 			int queueId) throws Exception{
-		TreeSet<SteinerNode> steinerNodes = new TreeSet<SteinerNode>();
-		Map<String , SteinerNode> treeNodes= new HashMap<String, SteinerNode>();
+		TreeSet<SteinerNode> steinerNodes = new TreeSet<>();
+		Map<String , SteinerNode> treeNodes= new HashMap<>();
 		
 		SteinerNode replacedNode = null;
 		if (this.recurseNodeMap.containsKey(ancestor)) {
@@ -286,14 +287,14 @@ public void buildConnectivityGraph(int k) throws Exception{
 		boolean debug = false;
 		
 		//nodes polled from queues
-		List<Map<String, SteinerNode>> processedNodes= 
-				new ArrayList<Map<String, SteinerNode>>();
-		List<Map<String, SteinerNode>> processedNodesHelper= 
-				new ArrayList<Map<String, SteinerNode>>();
+		List<Map<String, SteinerNode>> processedNodes=
+				new ArrayList<>();
+		List<Map<String, SteinerNode>> processedNodesHelper=
+				new ArrayList<>();
 
 		
-		List<HashMap<String, Integer>> recursesForNodesInQueue = 
-				new ArrayList<HashMap<String, Integer>>();
+		List<HashMap<String, Integer>> recursesForNodesInQueue =
+				new ArrayList<>();
 		
 		//mark nodes in the iterators as visited
 		int j=0;
@@ -308,8 +309,8 @@ public void buildConnectivityGraph(int k) throws Exception{
 				visitedNodes.get(j).put(n.name(),n);
 				shortestNodeIndex.get(j).put(n, n);
 				
-				HashMap<SteinerNode, SortedSteinerNodes> map = 
-						new HashMap<SteinerNode, SortedSteinerNodes>();
+				HashMap<SteinerNode, SortedSteinerNodes> map =
+						new HashMap<>();
 				
 				SortedSteinerNodes treeSet = new SortedSteinerNodes();
 				treeSet.set.add(n);
@@ -361,10 +362,10 @@ public void buildConnectivityGraph(int k) throws Exception{
 					
 					if (count>k) break;
 					
-					Queue<SteinerEdge> rs= new PriorityQueue<SteinerEdge>(10, new Comparator<SteinerEdge>(){
-						public int compare(SteinerEdge e1, SteinerEdge e2){
-							if(e1.weight()>e2.weight()) return 1;
-							else if (e1.weight()<e2.weight()) return -1;
+					Queue<SteinerEdge> rs= new PriorityQueue<>(10, new Comparator<SteinerEdge>() {
+						public int compare(SteinerEdge e1, SteinerEdge e2) {
+							if (e1.weight() > e2.weight()) return 1;
+							else if (e1.weight() < e2.weight()) return -1;
 							else return 0;
 						}
 					});
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/Graph.java b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/Graph.java
index c7f8ba62e..143208279 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/Graph.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/Graph.java
@@ -23,13 +23,13 @@ public class Graph<V, E extends Edge<V>> {
 	public int INF = Integer.MAX_VALUE;
 	
 	public Graph () {
-		nodes = new HashMap<String, V> ();
-		edges = new HashSet<E> ();
+		nodes = new HashMap<>();
+		edges = new HashSet<>();
 	}
 	
 	public HashSet<E> edges () { return edges; }
 
-	public HashSet<V> nodes () { return new HashSet<V> (nodes.values()); }
+	public HashSet<V> nodes () { return new HashSet<> (nodes.values()); }
 	
 	public void addNode (V v) {
 		nodes.put(v.toString(), v);
@@ -69,8 +69,8 @@ public boolean loadGraph ()
 	public String toString () {
     if(edges.isEmpty()) return("<Empty graph>");
     StringBuilder b=new StringBuilder();
-    Set<Edge> goodEdges = new TreeSet<Edge>();
-    Set<Edge> badEdges = new TreeSet<Edge>();
+    Set<Edge> goodEdges = new TreeSet<>();
+    Set<Edge> badEdges = new TreeSet<>();
     for(Edge e : edges) {
     	if(goodEdges.contains(e)){badEdges.add(e); continue;}
     	goodEdges.add(e);
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/LoosePath.java b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/LoosePath.java
index 9056f5781..85c927593 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/LoosePath.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/LoosePath.java
@@ -26,14 +26,14 @@ public LoosePath(LinkedList<SteinerNode> pathNodes){
 	
 	
 	public Set<SteinerNode> getNodes(){
-		Set<SteinerNode> nodeSet= new TreeSet<SteinerNode>();
+		Set<SteinerNode> nodeSet= new TreeSet<>();
 		nodeSet.addAll(pathNodes);
 		return nodeSet;
 	}
 	
 	// copying this loose path
 	public SteinerSubTree clone(){
-		LinkedList<SteinerNode> l= new LinkedList<SteinerNode>();
+		LinkedList<SteinerNode> l= new LinkedList<>();
 		for(SteinerNode n: pathNodes){
 			l.add(n.copy());
 		}
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ModelCoherence.java b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ModelCoherence.java
index 531e4d965..c93400151 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ModelCoherence.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ModelCoherence.java
@@ -20,9 +20,9 @@ public class ModelCoherence {
 	public ModelCoherence(int size, int k) {
 		this.k = k;
 		this.modelFrequency = new ModelFrequencyPair[size];
-		this.modelIndex = new HashMap<String,Integer>();
-		this.topKModels = new ArrayList<ModelFrequencyPair>();
-		this.visitedLinks = new HashSet<String>();
+		this.modelIndex = new HashMap<>();
+		this.topKModels = new ArrayList<>();
+		this.visitedLinks = new HashSet<>();
 	}
 
 	public void update(SteinerEdge e) {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ResultGraph.java b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ResultGraph.java
index 0cf8d5909..602d48bf9 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ResultGraph.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/ResultGraph.java
@@ -9,7 +9,7 @@ public class ResultGraph {
 	private List<Fact> facts;
 	
 	public ResultGraph() {
-		this.facts = new LinkedList<Fact>();
+		this.facts = new LinkedList<>();
 	}
 	
 	public Double getScore() {
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/SteinerNode.java b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/SteinerNode.java
index f76011153..33005f2f8 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/SteinerNode.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/SteinerNode.java
@@ -34,7 +34,7 @@ public class SteinerNode extends Entity {
 	
 	public SteinerNode(String id){
 		super(id);
-		edges=new TreeSet<SteinerEdge>();		
+		edges= new TreeSet<>();		
 	}
 	
 	/**
@@ -98,7 +98,7 @@ public String getEdgeLabelToNode(SteinerNode n){
 	 * @return all neighbors of this steiner node
 	 */
 	public TreeSet<SteinerNode> getNeighbors(){
-		TreeSet<SteinerNode> ts = new TreeSet<SteinerNode>();
+		TreeSet<SteinerNode> ts = new TreeSet<>();
 		for(SteinerEdge e: edges){
 			if(e.sourceNode.equals(this))
 				ts.add(e.sinkNode);
@@ -115,7 +115,7 @@ public TreeSet<SteinerNode> getNeighbors(){
 	 * through exceptForEdge
 	 */
 	public TreeSet<SteinerNode> getNeighbors(SteinerEdge exceptForEdge){
-		TreeSet<SteinerNode> ts = new TreeSet<SteinerNode>();
+		TreeSet<SteinerNode> ts = new TreeSet<>();
 		if(exceptForEdge==null){
 			return getNeighbors();
 		}
@@ -160,14 +160,14 @@ public void addEdge(SteinerNode n, boolean isSourceNode, String l, float weight)
 	 *
 	 */
 	public void deleteEdges(){
-		edges= new TreeSet<SteinerEdge>();
+		edges= new TreeSet<>();
 	}
 	
 	/**
 	 * @param e steiner edge to be removed
 	 */
 	public void deleteEdge(SteinerEdge e){
-		Set<SteinerEdge> badEdges= new TreeSet<SteinerEdge>();
+		Set<SteinerEdge> badEdges= new TreeSet<>();
 		for(SteinerEdge e1: edges)
 			if(e1.sinkNode.equals(e.sinkNode)&& e1.sourceNode.equals(e.sourceNode))
 				badEdges.add(e1);
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/SteinerSubTree.java b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/SteinerSubTree.java
index a5bacbab8..274a437cf 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/SteinerSubTree.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/SteinerSubTree.java
@@ -18,7 +18,7 @@ public abstract class SteinerSubTree implements Comparable<SteinerSubTree>, Clon
 	
 	
 	public SteinerSubTree() {
-		nodes= new TreeSet<SteinerNode>();
+		nodes= new TreeSet<>();
 		score=0;
 	}
 	
@@ -37,7 +37,7 @@ public double getScore(){
 	 * @return all edges of this subtree
 	 */
 	public Set<SteinerEdge> getEdges(){
-		Set<SteinerEdge> stEdges = new TreeSet<SteinerEdge>();
+		Set<SteinerEdge> stEdges = new TreeSet<>();
 		for(SteinerNode n: getNodes())
 			for(SteinerEdge e: n.edges)
 				stEdges.add(e);
diff --git a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/TopKSteinertrees.java b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/TopKSteinertrees.java
index 13861ca61..ad60394ef 100644
--- a/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/TopKSteinertrees.java
+++ b/karma-common/src/main/java/edu/isi/karma/modeling/steiner/topk/TopKSteinertrees.java
@@ -38,7 +38,7 @@ public abstract class TopKSteinertrees {
 	public static Map<String, SteinerNode> nodes;
 	
 	//maps node names to ids
-	public static Map<String, Integer> nodeToId= new HashMap<String, Integer>();
+	public static Map<String, Integer> nodeToId= new HashMap<>();
 
 	
 	
@@ -89,7 +89,7 @@ public void writeGraphForSTAR(String fileName) throws IOException{
 		new File(folder).mkdir();
 		
 		FileWriter fw= new FileWriter(folder+fileName+"STAR.txt");
-		TreeSet<SteinerEdge> ts = new TreeSet<SteinerEdge>();
+		TreeSet<SteinerEdge> ts = new TreeSet<>();
 		for(Map.Entry<SteinerNode, TreeSet<SteinerEdge>> steinerNodeTreeSetEntry : graph.entrySet()){
 			for(SteinerEdge e: steinerNodeTreeSetEntry.getValue()){
 				if(ts.contains(e))continue;
@@ -109,8 +109,8 @@ public void writeGraphForSTAR(String fileName) throws IOException{
 	 * @throws IOException
 	 */
 	public void loadGraphFromFiles(boolean uniformWeights)throws IOException{
-		graph= new HashMap<SteinerNode, TreeSet<SteinerEdge>>();
-		nodes = new HashMap<String, SteinerNode>();
+		graph= new HashMap<>();
+		nodes = new HashMap<>();
 		//FileReader fr = new FileReader("d:\\DBLPgraph\\IMDBSTAR.txt");
 		FileReader fr = new FileReader("d:\\DBLPgraph\\dblpgraphNeighS.txt");
 		//FileReader fr = new FileReader("d:\\DBLPgraph\\DBLPSTAR.txt");
@@ -134,7 +134,7 @@ public void loadGraphFromFiles(boolean uniformWeights)throws IOException{
 				nodes.put(arr[3], new SteinerNode(arr[3]));
 				graph.put(nodes.get(arr[3]), new TreeSet<SteinerEdge>());
 			}
-			SteinerEdge e=null;
+			SteinerEdge e;
 			if(!uniformWeights){
 				Random r= new Random();
 				arr[1]=String.valueOf(r.nextFloat());
@@ -154,8 +154,8 @@ public void loadGraphFromFiles(boolean uniformWeights)throws IOException{
 	}
 	
 	public void loadGraphFromFile(String filename)throws IOException{
-		graph= new HashMap<SteinerNode, TreeSet<SteinerEdge>>();
-		nodes = new HashMap<String, SteinerNode>();
+		graph= new HashMap<>();
+		nodes = new HashMap<>();
 		//FileReader fr = new FileReader("d:\\DBLPgraph\\IMDBSTAR.txt");
 		FileReader fr = new FileReader(filename);
 		//FileReader fr = new FileReader("d:\\DBLPgraph\\DBLPSTAR.txt");
@@ -179,7 +179,7 @@ public void loadGraphFromFile(String filename)throws IOException{
 				nodes.put(arr[3], new SteinerNode(arr[3]));
 				graph.put(nodes.get(arr[3]), new TreeSet<SteinerEdge>());
 			}
-			SteinerEdge e=null;
+			SteinerEdge e;
 			if(isArg1) e= new SteinerEdge(nodes.get(arr[3]), arr[0].intern(), nodes.get(arr[2]) ,Float.valueOf(arr[1])); 
 			else e= new SteinerEdge(nodes.get(arr[2]), arr[0].intern(), nodes.get(arr[3]),Float.valueOf(arr[1]));
 				
@@ -214,7 +214,7 @@ public void loadGraphFromFile(String filename)throws IOException{
 	public TopKSteinertrees() {
 		// TODO Auto-generated constructor stub
 		// added by mohsen
-		this.addedSteinerTrees = new LinkedList<ApprSteinerTree>();
+		this.addedSteinerTrees = new LinkedList<>();
 	}
 	
 	
@@ -227,14 +227,14 @@ public TopKSteinertrees() {
 	 */
 	public TopKSteinertrees(TreeSet<SteinerNode> terminals)throws Exception {
 		terminalNodes=terminals;
-		iterators=new ArrayList<Queue<SteinerNode>>(terminals.size());
-		visitedNodes= new ArrayList<HashMap<String, SteinerNode>>();
-		forbiddenNodes = new HashMap<String, SteinerNode>();
-		almostForbiddenNodes = new HashMap<String, SteinerNode>();
-		resultQueue=new LinkedList<ResultGraph>();
+		iterators= new ArrayList<>(terminals.size());
+		visitedNodes= new ArrayList<>();
+		forbiddenNodes = new HashMap<>();
+		almostForbiddenNodes = new HashMap<>();
+		resultQueue= new LinkedList<>();
 		
 		// added by mohsen
-		this.addedSteinerTrees = new LinkedList<ApprSteinerTree>();
+		this.addedSteinerTrees = new LinkedList<>();
 
 		//for each terminal set an iterator
 		for(int i=0; i< terminals.size(); i++){
@@ -260,8 +260,8 @@ public TopKSteinertrees(TreeSet<SteinerNode> terminals)throws Exception {
 	 * @throws Exception 
 	 */
 	public void getTaxonomicTree(SteinerNode ancestor) throws Exception{
-		TreeSet<SteinerNode> treeNodes = new TreeSet<SteinerNode>();
-		Map<String , SteinerNode> taxonomicTreeNodes= new HashMap<String, SteinerNode>();
+		TreeSet<SteinerNode> treeNodes = new TreeSet<>();
+		Map<String , SteinerNode> taxonomicTreeNodes= new HashMap<>();
 		taxonomicTreeNodes.put(ancestor.getNodeId(),new SteinerNode(ancestor.getNodeId()));
 		for(Map<String, SteinerNode> pnM:  visitedNodes){
 			SteinerNode newNode=pnM.get(ancestor.getNodeId());
@@ -295,7 +295,7 @@ public void getTaxonomicTree(SteinerNode ancestor) throws Exception{
 	 * @param map
 	 */
 	protected void clean (Map<String, SteinerNode> map){
-		LinkedList<SteinerNode> outliers = new LinkedList<SteinerNode>();
+		LinkedList<SteinerNode> outliers = new LinkedList<>();
 		for(SteinerNode n: map.values())
 			if(!terminalNodes.contains(n)&& n.getDegree()==1)
 				outliers.add(n);
@@ -355,8 +355,8 @@ protected ApprSteinerTree getApprTreeFrom(SteinerNode v, Map<String, SteinerNode
 			}
 		}
 		v=v.predecessor;
-		Map<String, SteinerNode> resultSet= new HashMap<String,SteinerNode>();
-		Map<String, SteinerNode> treeNodeSet= new HashMap<String,SteinerNode>();
+		Map<String, SteinerNode> resultSet= new HashMap<>();
+		Map<String, SteinerNode> treeNodeSet= new HashMap<>();
 		for(SteinerNode n: initialSet1){resultSet.put(n.name(), n);treeNodeSet.put(n.name(), new SteinerNode(n.name()));}
 		for(SteinerNode n: initialSet2){resultSet.put(n.name(), n);treeNodeSet.put(n.name(), new SteinerNode(n.name()));}
 		//follow the predecessors of v until a predecessor
@@ -369,7 +369,7 @@ protected ApprSteinerTree getApprTreeFrom(SteinerNode v, Map<String, SteinerNode
 			v = newNode;
 		}
 		// make sure all edges are ok!
-		TreeSet<SteinerEdge> copyOfEdges= new TreeSet<SteinerEdge>();
+		TreeSet<SteinerEdge> copyOfEdges= new TreeSet<>();
 		for(SteinerNode n: resultSet.values()){
 			copyOfEdges.addAll(n.edges);
 		}
@@ -377,7 +377,7 @@ protected ApprSteinerTree getApprTreeFrom(SteinerNode v, Map<String, SteinerNode
 			treeNodeSet.get(e.sourceNode.name()).addEdge(
 					treeNodeSet.get(e.sinkNode.name()), false, e.getEdgeLabel(), e.weight());
 		}
-		Set<SteinerNode> treeNodes= new TreeSet<SteinerNode>();
+		Set<SteinerNode> treeNodes= new TreeSet<>();
 		treeNodes.addAll(treeNodeSet.values());
 		//D.p(resultSet.values());
 		return new ApprSteinerTree(terminalNodes, treeNodes);
@@ -397,7 +397,7 @@ protected ApprSteinerTree getApprTreeFrom(SteinerNode v, Map<String, SteinerNode
 	protected ApprSteinerTree getApprTreeFrom(SteinerNode v, Map<String, SteinerNode>visitedNodes1, 
 			 Map<String, SteinerNode>visitedNodes2, Set<SteinerNode>initialSet1, 
 			 Set<SteinerNode>initialSet2){
-		Map<String, SteinerNode> resultSet= new HashMap<String,SteinerNode>();
+		Map<String, SteinerNode> resultSet= new HashMap<>();
 		for(SteinerNode n: initialSet1)resultSet.put(n.name(), n);
 		for(SteinerNode n: initialSet2)resultSet.put(n.name(), n);
 		SteinerNode newNode= v.predecessor;
@@ -423,7 +423,7 @@ protected ApprSteinerTree getApprTreeFrom(SteinerNode v, Map<String, SteinerNode
 		}
 		//make sure all edges are ok!
 		for(SteinerNode node: resultSet.values()){
-			TreeSet<SteinerEdge> copyOfEdges= new TreeSet<SteinerEdge>();
+			TreeSet<SteinerEdge> copyOfEdges= new TreeSet<>();
 			copyOfEdges.addAll(node.edges);
 			for(SteinerEdge e: copyOfEdges){
 				node.edges.remove(e);
@@ -431,7 +431,7 @@ protected ApprSteinerTree getApprTreeFrom(SteinerNode v, Map<String, SteinerNode
 						e.getEdgeLabel(), resultSet.get(e.sinkNode.name()),e.weight()));
 			}
 		}
-		Set<SteinerNode> treeNodes= new TreeSet<SteinerNode>();
+		Set<SteinerNode> treeNodes= new TreeSet<>();
 		treeNodes.addAll(resultSet.values());
 		//D.p(resultSet.values());
 		return new ApprSteinerTree(terminalNodes, treeNodes);
diff --git a/karma-common/src/main/java/edu/isi/karma/rdf/RdfGenerator.java b/karma-common/src/main/java/edu/isi/karma/rdf/RdfGenerator.java
index e927ea730..b1af576db 100644
--- a/karma-common/src/main/java/edu/isi/karma/rdf/RdfGenerator.java
+++ b/karma-common/src/main/java/edu/isi/karma/rdf/RdfGenerator.java
@@ -75,10 +75,10 @@ protected void applyHistoryToWorksheet(Workspace workspace, Worksheet worksheet,
 		WorksheetCommandHistoryExecutor wchr = new WorksheetCommandHistoryExecutor(worksheet.getId(), workspace);
 		try
 		{
-			List<CommandTag> tags = new ArrayList<CommandTag>();
+			List<CommandTag> tags = new ArrayList<>();
 			tags.add(CommandTag.Transformation);
 			
-			List<CommandTag> ignoreTags = new ArrayList<CommandTag>();
+			List<CommandTag> ignoreTags = new ArrayList<>();
 			ignoreTags.add(CommandTag.IgnoreInBatch);
 			wchr.executeCommandsByTags(tags, 
 					ignoreTags,
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/ColumnMetadata.java b/karma-common/src/main/java/edu/isi/karma/rep/ColumnMetadata.java
index 293d0abc9..550643c86 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/ColumnMetadata.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/ColumnMetadata.java
@@ -39,15 +39,15 @@ public class ColumnMetadata {
 	private Map<String, Boolean>	    columnOnError;
 	public ColumnMetadata() {
 		super();
-		this.columnPreferredLengths = new HashMap<String, Integer>();
+		this.columnPreferredLengths = new HashMap<>();
 //		this.columnTypes 			= new HashMap<String, ColumnMetadata.COLUMN_TYPE>();
 //		this.invalidNodeIds 		= new HashMap<String, List<String>>();
-		this.columnHistogramData	= new HashMap<String, JSONObject>();
-		this.columnPythonTransform  = new HashMap<String, String>();
-		this.columnPreviousCommandId = new HashMap<String, String>();
-		this.columnDerivedFrom = new HashMap<String, String>();
-		this.columnDataStructure = new HashMap<String, DataStructure>();
-		this.columnOnError = new HashMap<String, Boolean>();
+		this.columnHistogramData	= new HashMap<>();
+		this.columnPythonTransform  = new HashMap<>();
+		this.columnPreviousCommandId = new HashMap<>();
+		this.columnDerivedFrom = new HashMap<>();
+		this.columnDataStructure = new HashMap<>();
+		this.columnOnError = new HashMap<>();
 	}
 	
 	public enum DataStructure {
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/HNode.java b/karma-common/src/main/java/edu/isi/karma/rep/HNode.java
index bcaaae755..31184170b 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/HNode.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/HNode.java
@@ -70,7 +70,7 @@ public enum HNodeType {
 		this.columnName = columnName;
 		this.automaticallyAdded = automaticallyAdded;
 		this.type = type;
-		this.commandsApplied = new HashMap<String, HashSet<HNode>>();
+		this.commandsApplied = new HashMap<>();
 	}
 
 	public String getColumnName() {
@@ -214,7 +214,7 @@ public int compareTo(HNode other) {
 	public JSONArray getJSONArrayRepresentation(RepFactory f)
 			throws JSONException {
 		JSONArray arr = new JSONArray();
-		Stack<HNode> st = new Stack<HNode>();
+		Stack<HNode> st = new Stack<>();
 		st.push(this);
 		HTable t = f.getHTable(hTableId);
 		HNode parentNode = t.getParentHNode();
@@ -234,7 +234,7 @@ public JSONArray getJSONArrayRepresentation(RepFactory f)
 	}
 	
 	public List<HNode> getHNodesAccessibleList(RepFactory f) {
-		List<HNode> hNodeList = new ArrayList<HNode>();
+		List<HNode> hNodeList = new ArrayList<>();
 		HTable table = this.getHTable(f);
 		
 		while (table != null) {
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/HNodePath.java b/karma-common/src/main/java/edu/isi/karma/rep/HNodePath.java
index 2bd062a3d..ea67f0633 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/HNodePath.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/HNodePath.java
@@ -39,7 +39,7 @@
 public class HNodePath {
 
 	private static final Logger LOG = LoggerFactory.getLogger(HNodePath.class);
-	private List<HNode> hNodes = new LinkedList<HNode>();
+	private List<HNode> hNodes = new LinkedList<>();
 	private Object msger = null;//used for holding session cleaning data
 	private Object dpp = null; // data preprocessing for cleaning
 	public HNodePath() {
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/HTable.java b/karma-common/src/main/java/edu/isi/karma/rep/HTable.java
index 1b94af7c4..6dd61fb9b 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/HTable.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/HTable.java
@@ -48,9 +48,9 @@ public class HTable extends RepEntity {
 	private String tableName;
 
 	// My columns: map of HNodeId to HNode
-	private final Map<String, HNode> nodes = new HashMap<String, HNode>();
+	private final Map<String, HNode> nodes = new HashMap<>();
 
-	private ArrayList<String> orderedNodeIds = new ArrayList<String>();
+	private ArrayList<String> orderedNodeIds = new ArrayList<>();
 
 	
 	// mariam
@@ -184,7 +184,7 @@ public HNode addHNode(String columnName, boolean automaticallyAdded, HNodeType t
 	}
 
 	public List<HNode> getSortedHNodes() {
-		List<HNode> allHNodes = new LinkedList<HNode>();
+		List<HNode> allHNodes = new LinkedList<>();
 		for (String hNodeId : orderedNodeIds) {
 			allHNodes.add(nodes.get(hNodeId));
 		}
@@ -289,7 +289,7 @@ public void prettyPrint(String prefix, PrintWriter pw, RepFactory factory) {
 	}
 
 	public List<HNodePath> getAllPaths() {
-		List<HNodePath> x = new LinkedList<HNodePath>();
+		List<HNodePath> x = new LinkedList<>();
 		for (HNode hn : getSortedHNodes()) {
 			x.add(new HNodePath(hn));
 		}
@@ -297,7 +297,7 @@ public List<HNodePath> getAllPaths() {
 	}
 
 	private List<HNodePath> expandPaths(List<HNodePath> paths) {
-		List<HNodePath> x = new LinkedList<HNodePath>();
+		List<HNodePath> x = new LinkedList<>();
 		for (HNodePath p : paths) {
 			if (p.getLeaf().getNestedTable() != null) {
 				HTable nestedHTable = p.getLeaf().getNestedTable();
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/HashValueManager.java b/karma-common/src/main/java/edu/isi/karma/rep/HashValueManager.java
index a7252d305..05ee7ba78 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/HashValueManager.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/HashValueManager.java
@@ -11,7 +11,8 @@
 import edu.isi.karma.controller.command.selection.SuperSelectionManager;
 
 public class HashValueManager {
-	private static Map<String, Map<String, String>> hashTable = new ConcurrentHashMap<String, Map<String, String>>();
+
+	private static Map<String, Map<String, String>> hashTable = new ConcurrentHashMap<>();
 
 	private HashValueManager() {
 	}
@@ -22,7 +23,7 @@ private static void computeHashValue(Row row, List<String> HNodeIds) {
 			if (n.hasNestedTable()) {
 				Table nestedTable = n.getNestedTable();
 				for (Row nestedRow : nestedTable.getRows(0, nestedTable.getNumRows(), SuperSelectionManager.DEFAULT_SELECTION)) {
-					List<String> ids = new ArrayList<String>();
+					List<String> ids = new ArrayList<>();
 					for (Node node : nestedRow.getNodes()) {
 						ids.add(node.getHNodeId());
 					}
@@ -32,7 +33,7 @@ private static void computeHashValue(Row row, List<String> HNodeIds) {
 			else {
 				Map<String, String> tmp = hashTable.get(row.getId());
 				if (tmp == null) 
-					tmp = new ConcurrentHashMap<String, String>();
+					tmp = new ConcurrentHashMap<>();
 				String value = n.getValue().asString();
 				value = DigestUtils.shaHex(value);
 				tmp.put(n.getId(), value);
@@ -48,13 +49,13 @@ public static String getHashValue(Row row, List<String> HNodeIds) {
 	}
 	
 	private static String getHashValueRecurse(Row row, List<String> HNodeIds) {
-		List<String> hashString = new ArrayList<String>();
+		List<String> hashString = new ArrayList<>();
 		for (String HNodeid : HNodeIds) {
 			Node n = row.getNode(HNodeid);
 			if (n.hasNestedTable()) {
 				Table nestedTable = n.getNestedTable();
 				for (Row nestedRow : nestedTable.getRows(0, nestedTable.getNumRows(), SuperSelectionManager.DEFAULT_SELECTION)) {
-					List<String> ids = new ArrayList<String>();
+					List<String> ids = new ArrayList<>();
 					for (Node node : nestedRow.getNodes()) {
 						ids.add(node.getHNodeId());
 					}
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/RepFactory.java b/karma-common/src/main/java/edu/isi/karma/rep/RepFactory.java
index bf5e47cd5..813949351 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/RepFactory.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/RepFactory.java
@@ -35,12 +35,12 @@
 public class RepFactory {
 
 
-	private final Map<String, HNode> hNodes = new ConcurrentHashMap<String, HNode>(100);
-	private final Map<String, HTable> hTables = new ConcurrentHashMap<String, HTable>(10);
-	private final Map<String, Worksheet> worksheets = new ConcurrentHashMap<String, Worksheet>(10);
-	private final Map<String, Table> tables = new ConcurrentHashMap<String, Table>(10);
-	private final Map<String, Row> rows = new ConcurrentHashMap<String, Row>(1000);
-	private final Map<String, Node> nodes = new ConcurrentHashMap<String, Node>(10000);
+	private final Map<String, HNode> hNodes = new ConcurrentHashMap<>(100);
+	private final Map<String, HTable> hTables = new ConcurrentHashMap<>(10);
+	private final Map<String, Worksheet> worksheets = new ConcurrentHashMap<>(10);
+	private final Map<String, Table> tables = new ConcurrentHashMap<>(10);
+	private final Map<String, Row> rows = new ConcurrentHashMap<>(1000);
+	private final Map<String, Node> nodes = new ConcurrentHashMap<>(10000);
 	private int id = 0;
 	
 	public Worksheet createWorksheet(String tableName, Workspace workspace, String encoding) {
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/Row.java b/karma-common/src/main/java/edu/isi/karma/rep/Row.java
index 31b67afd3..32901d940 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/Row.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/Row.java
@@ -45,7 +45,7 @@ public class Row extends RepEntity implements Neighbor {
 
 	// My nodes, columns containing cells or nested tables, a map from HNode ids
 	// to Node.
-	private final Map<String, Node> nodes = new HashMap<String, Node>();
+	private final Map<String, Node> nodes = new HashMap<>();
 
 	// mariam
 	/**
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/Table.java b/karma-common/src/main/java/edu/isi/karma/rep/Table.java
index 8f6dc2983..3d20a929d 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/Table.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/Table.java
@@ -51,7 +51,7 @@ public class Table extends RepEntity {
 	private final String hTableId;
 
 	// My rows.
-	private List<Row> rows = new ArrayList<Row>();
+	private List<Row> rows = new ArrayList<>();
 	
 	// mariam
 	/**
@@ -157,7 +157,7 @@ public Row getRow(int index)
 	 *         are out of bounds.
 	 */
 	public ArrayList<Row> getRows(int startIndex, int count, SuperSelection sel) {
-		ArrayList<Row> result = new ArrayList<Row>();
+		ArrayList<Row> result = new ArrayList<>();
 		Iterator<Row> itr = rows.iterator();
 		int sum = 0, index = 0;
 		while(itr.hasNext()) {
@@ -195,7 +195,7 @@ public void prettyPrint(String prefix, PrintWriter pw, RepFactory factory) {
 	 */
 	public boolean collectNodes(HNodePath path, Collection<Node> nodes, SuperSelection sel) {
 		if (nodes == null) {
-			nodes = new ArrayList<Node>();
+			nodes = new ArrayList<>();
 		}
 		return collectNodes(path, nodes, rows, sel);
 	}
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/Workspace.java b/karma-common/src/main/java/edu/isi/karma/rep/Workspace.java
index 63c57e739..00ed04f93 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/Workspace.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/Workspace.java
@@ -60,7 +60,7 @@ public class Workspace extends Entity {
 	/**
 	 * Record all the worksheets defined in this workspace.
 	 */
-	private final Map<String, Worksheet> worksheets = new ConcurrentHashMap<String, Worksheet>();
+	private final Map<String, Worksheet> worksheets = new ConcurrentHashMap<>();
 	
 	/**
 	 * Saves all the tagging information
@@ -128,7 +128,7 @@ public Worksheet getWorksheet(String id) {
 	}
 
 	public Collection<Worksheet> getWorksheets() {
-		return new ArrayList<Worksheet>(worksheets.values());
+		return new ArrayList<>(worksheets.values());
 	}
 
 	public RepFactory getFactory() {
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/WorkspaceManager.java b/karma-common/src/main/java/edu/isi/karma/rep/WorkspaceManager.java
index 4854ecd25..065314a8e 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/WorkspaceManager.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/WorkspaceManager.java
@@ -39,7 +39,7 @@ public class WorkspaceManager {
 	
 	private AtomicInteger nextId = new AtomicInteger(1);
 	
-	private final Map<String, Workspace> workspaces = new ConcurrentHashMap<String, Workspace>();
+	private final Map<String, Workspace> workspaces = new ConcurrentHashMap<>();
 	
 	private static WorkspaceManager singleton = new WorkspaceManager();
 	
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/alignment/ColumnNode.java b/karma-common/src/main/java/edu/isi/karma/rep/alignment/ColumnNode.java
index 971ef19e8..e80502ead 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/alignment/ColumnNode.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/alignment/ColumnNode.java
@@ -69,7 +69,7 @@ public void setLearnedSemanticTypes(List<SemanticType> learnedSemanticTypes) {
 				sum += st.getConfidenceScore() != null ? st.getConfidenceScore().doubleValue() : 0.0;
 			}
 			double confidence;
-			this.learnedSemanticTypes = new ArrayList<SemanticType>();
+			this.learnedSemanticTypes = new ArrayList<>();
 			for (SemanticType st : learnedSemanticTypes) {
 				confidence = st.getConfidenceScore() != null ? st.getConfidenceScore() : 0.0;
 				SemanticType semType = new SemanticType(st.getHNodeId(), 
@@ -111,7 +111,7 @@ public void setRdfLiteralType(Label rdfLiteralType) {
 	
 	public List<SemanticType> getUserSemanticTypes() {
 		if (userSemanticTypes == null)
-			this.userSemanticTypes = new ArrayList<SemanticType>();
+			this.userSemanticTypes = new ArrayList<>();
 		return Collections.unmodifiableList(userSemanticTypes);
 	}
 
@@ -127,7 +127,7 @@ public void assignUserType(SemanticType newType) {
 			return;
 		
 		if (userSemanticTypes == null)
-			this.userSemanticTypes = new ArrayList<SemanticType>();
+			this.userSemanticTypes = new ArrayList<>();
 		
 		//FIXME: when user invokes SetSemanticType, we should unassign the old one, otherwise
 		// we don't know if user wants to add more types or replace the existing one
@@ -157,7 +157,7 @@ public void unassignUserType(SemanticType semanticType) {
 				}
 			}
 		}
-		if (tobeDeletedIndex != -1) {
+		if (tobeDeletedIndex != -1 && userSemanticTypes != null) {
 			userSemanticTypes.remove(tobeDeletedIndex);
 		}
 		if (userSemanticTypes == null || userSemanticTypes.isEmpty())
@@ -166,7 +166,7 @@ public void unassignUserType(SemanticType semanticType) {
 
 	public List<SemanticType> getTopKLearnedSemanticTypes(int k) {
 		
-		List<SemanticType> semanticTypes = new ArrayList<SemanticType>();
+		List<SemanticType> semanticTypes = new ArrayList<>();
 		if (this.learnedSemanticTypes == null || this.learnedSemanticTypes.isEmpty())
 			return semanticTypes;
 		
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/alignment/DisplayModel.java b/karma-common/src/main/java/edu/isi/karma/rep/alignment/DisplayModel.java
index 278a00c71..d4b32a145 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/alignment/DisplayModel.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/alignment/DisplayModel.java
@@ -51,8 +51,8 @@ public class DisplayModel {
 	public DisplayModel(DirectedWeightedMultigraph<Node, LabeledLink> model) {
 		this.models = new ArrayList<>();
 		this.computeModels(model);
-		this.nodesLevel = new HashMap<Node, Integer>();
-		this.nodesSpan = new HashMap<Node, Set<ColumnNode>>();
+		this.nodesLevel = new HashMap<>();
+		this.nodesSpan = new HashMap<>();
 		this.hTable = null;
 		
 		for(DirectedWeightedMultigraph<Node, LabeledLink> subModel : models) {
@@ -64,8 +64,8 @@ public DisplayModel(DirectedWeightedMultigraph<Node, LabeledLink> model) {
 	public DisplayModel(DirectedWeightedMultigraph<Node, LabeledLink> model, HTable hTable) {
 		this.models = new ArrayList<>();
 		this.computeModels(model);
-		this.nodesLevel = new HashMap<Node, Integer>();
-		this.nodesSpan = new HashMap<Node, Set<ColumnNode>>();
+		this.nodesLevel = new HashMap<>();
+		this.nodesSpan = new HashMap<>();
 		this.hTable = hTable;
 
 		int modelNum = 1;
@@ -107,7 +107,7 @@ public DisplayModel(DirectedWeightedMultigraph<Node, LabeledLink> model, HTable
 		
 		//Remove missing Levels
 		int newMaxLevel = getMaxLevel(false);
-		HashMap<Integer, Set<Node>> nodesAtLevel = getLevelToNodes(null, false);
+		Map<Integer, Set<Node>> nodesAtLevel = getLevelToNodes(null, false);
 		for(int i=maxLevel; i<newMaxLevel; i++) {
 			Set<Node> nodes = nodesAtLevel.get(i);
 			if(nodes == null || nodes.isEmpty()) {
@@ -156,7 +156,7 @@ public HashMap<Node, Set<ColumnNode>> getNodesSpan() {
 	private static HashMap<Node, Integer> inDegreeInSet(DirectedWeightedMultigraph<Node, LabeledLink> g, 
 			Set<Node> nodes, boolean includeSelfLinks) {
 		
-		HashMap<Node, Integer> nodeToInDegree = new HashMap<Node, Integer>();
+		HashMap<Node, Integer> nodeToInDegree = new HashMap<>();
 		if (g == null || nodes == null) return nodeToInDegree;
 		for (Node n : nodes) {
 			Set<LabeledLink> incomingLinks = g.incomingEdgesOf(n);
@@ -180,7 +180,7 @@ private static HashMap<Node, Integer> inDegreeInSet(DirectedWeightedMultigraph<N
 	private static HashMap<Node, Integer> outDegreeInSet(DirectedWeightedMultigraph<Node, LabeledLink> g, 
 			Set<Node> nodes, boolean includeSelfLinks) {
 		
-		HashMap<Node, Integer> nodeToOutDegree = new HashMap<Node, Integer>();
+		HashMap<Node, Integer> nodeToOutDegree = new HashMap<>();
 		if (g == null || nodes == null) return nodeToOutDegree;
 		for (Node n : nodes) {
 			Set<LabeledLink> outgoingLinks = g.outgoingEdgesOf(n);
@@ -213,7 +213,7 @@ public boolean isModelEmpty() {
 	}
 	
 	private Set<Node> getAllColumnNodes(DirectedWeightedMultigraph<Node, LabeledLink> model) {
-		Set<Node> columnNodes = new HashSet<Node>();
+		Set<Node> columnNodes = new HashSet<>();
 		for (Node u : model.vertexSet()) {
 			if (u instanceof ColumnNode)
 				columnNodes.add(u);
@@ -251,7 +251,7 @@ private void levelingCyclicGraph(DirectedWeightedMultigraph<Node, LabeledLink> m
 		Set<Node> markedNodes = new HashSet<>();
 		markedNodes.addAll(columnNodes);
 		
-		Queue<Node> q = new LinkedList<Node>();
+		Queue<Node> q = new LinkedList<>();
 		int maxLevel = model.vertexSet().size();
 				
 		for (Node u : model.vertexSet()) {
@@ -286,7 +286,7 @@ private void levelingCyclicGraph(DirectedWeightedMultigraph<Node, LabeledLink> m
 			}
 		}
 		
-		HashMap<Integer, Set<Node>> levelToNodes = getLevelToNodes(model, false);
+		Map<Integer, Set<Node>> levelToNodes = getLevelToNodes(model, false);
 		
 		// find in/out degree in each level
 		int k = 0;
@@ -348,8 +348,8 @@ private void levelingCyclicGraph(DirectedWeightedMultigraph<Node, LabeledLink> m
 	public HashMap<Integer, Set<Node>> getLevelToNodes(DirectedWeightedMultigraph<Node, LabeledLink> model, 
 			boolean considerColumnNodes) {
 
-		HashMap<Integer, Set<Node>> levelToNodes = 
-				new HashMap<Integer, Set<Node>>();
+		HashMap<Integer, Set<Node>> levelToNodes =
+				new HashMap<>();
 		
 		if (this.nodesLevel == null)
 			return levelToNodes;
@@ -357,7 +357,7 @@ public HashMap<Integer, Set<Node>> getLevelToNodes(DirectedWeightedMultigraph<No
 		for (Entry<Node, Integer> entry : nodesLevel.entrySet()) {
 			Set<Node> nodes = levelToNodes.get(entry.getValue());
 			if (nodes == null) {
-				nodes = new HashSet<Node>();
+				nodes = new HashSet<>();
 				levelToNodes.put(entry.getValue(), nodes);
 			}
 			
@@ -415,12 +415,12 @@ private void computeNodeSpan(DirectedWeightedMultigraph<Node, LabeledLink> model
 		
 		// Add empty set for all internal nodes
 		for (Node n : model.vertexSet()) {
-			Set<ColumnNode> columnNodes = new HashSet<ColumnNode>();
+			Set<ColumnNode> columnNodes = new HashSet<>();
 			nodesSpan.put(n, columnNodes);
 		}
 		
-		HashMap<Integer, Set<Node>> levelToNodes = getLevelToNodes(model, true);
-		Set<ColumnNode> allColumnNodes = new HashSet<ColumnNode>();
+		Map<Integer, Set<Node>> levelToNodes = getLevelToNodes(model, true);
+		Set<ColumnNode> allColumnNodes = new HashSet<>();
 		
 		int i = getMaxLevel(true);
 		while (i >= 0) {
@@ -435,7 +435,7 @@ private void computeNodeSpan(DirectedWeightedMultigraph<Node, LabeledLink> model
 						continue;
 					}
 					
-					List<Node> neighborsInLowerLevel = new ArrayList<Node>();
+					List<Node> neighborsInLowerLevel = new ArrayList<>();
 					
 					// finding the nodes connected to n (incoming & outgoing) from a lower level
 					Set<LabeledLink> outgoingLinks = model.outgoingEdgesOf(n);
@@ -482,8 +482,8 @@ private boolean overlap(Node n1, Node n2) {
 		if (n1Span == null || n2Span == null)
 			return false;
 
-		Set<String> n1NodeIds = new HashSet<String>();
-		Set<String> n2NodeIds = new HashSet<String>();
+		Set<String> n1NodeIds = new HashSet<>();
+		Set<String> n2NodeIds = new HashSet<>();
 		
 		for (ColumnNode c : n1Span)
 			if (c != null)
@@ -494,10 +494,10 @@ private boolean overlap(Node n1, Node n2) {
 				n2NodeIds.add(c.getHNodeId());
 
 		
-		List<Integer> n1SpanPositions = new ArrayList<Integer>();
-		List<Integer> n2SpanPositions = new ArrayList<Integer>();
-		
-		ArrayList<HNode> orderedNodeIds = new ArrayList<HNode>();
+		List<Integer> n1SpanPositions = new ArrayList<>();
+		List<Integer> n2SpanPositions = new ArrayList<>();
+		List<HNode> orderedNodeIds = new ArrayList<>();
+
 		this.hTable.getSortedLeafHNodes(orderedNodeIds);
 		if (orderedNodeIds != null)
 		for (int i = 0; i < orderedNodeIds.size(); i++) {
@@ -526,7 +526,7 @@ private boolean overlap(Node n1, Node n2) {
 	
 	private HashMap<Node, Integer> getNodeOverlap(Set<Node> nodes) {
 		
-		HashMap<Node, Integer> nodesOverlap = new HashMap<Node, Integer>();
+		HashMap<Node, Integer> nodesOverlap = new HashMap<>();
 		
 		int count;
 		for (Node n1 : nodes) {
@@ -549,7 +549,7 @@ private void updateNodeLevelsConsideringOverlaps(DirectedWeightedMultigraph<Node
 		
 		int maxLevel = model.vertexSet().size();
 
-		HashMap<Integer, Set<Node>> levelToNodes = getLevelToNodes(model, false);
+		Map<Integer, Set<Node>> levelToNodes = getLevelToNodes(model, false);
 
 		// find in/out degree in each level
 		int k = 0;
@@ -668,7 +668,7 @@ private void computeModels(DirectedWeightedMultigraph<Node, LabeledLink> model)
 		for(Node n : model.vertexSet()) {
 			DirectedWeightedMultigraph<Node, LabeledLink> nodeModel = findModel(n);
 			if(nodeModel == null) {
-				nodeModel = new DirectedWeightedMultigraph<Node, LabeledLink>(LabeledLink.class); 
+				nodeModel = new DirectedWeightedMultigraph<>(LabeledLink.class); 
 				this.models.add(nodeModel);
 				nodeModel.addVertex(n);
 			}
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/alignment/LabeledLink.java b/karma-common/src/main/java/edu/isi/karma/rep/alignment/LabeledLink.java
index 9fc32cc9a..658917a97 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/alignment/LabeledLink.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/alignment/LabeledLink.java
@@ -69,7 +69,7 @@ private void init() {
 		this.label = new Label(l);
 		this.status = LinkStatus.Normal;
 		this.keyInfo = LinkKeyInfo.None;
-		this.modelIds = new HashSet<String>();
+		this.modelIds = new HashSet<>();
 	}
 	
 	public Label getLabel() {
@@ -118,7 +118,7 @@ public void setKeyType(LinkKeyInfo keyType) {
 	
 	public Set<String> getModelIds() {
 		if (this.modelIds == null)
-			return new HashSet<String>();
+			return new HashSet<>();
 		return modelIds;
 	}
 
@@ -157,7 +157,7 @@ else if (this instanceof ObjectPropertySpecializationLink)
 			logger.error("cannot instanciate a link from the type: " + this.getType().toString());
 		
 		newLink.setStatus(this.getStatus());
-		newLink.setModelIds(new HashSet<String>(this.getModelIds()));
+		newLink.setModelIds(new HashSet<>(this.getModelIds()));
 		newLink.setKeyType(this.getKeyType());
 		
 		return newLink;
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/alignment/Node.java b/karma-common/src/main/java/edu/isi/karma/rep/alignment/Node.java
index 89c279669..8e3dd97a6 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/alignment/Node.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/alignment/Node.java
@@ -63,7 +63,7 @@ private void init() {
 		Label l = null;
 		this.label = new Label(l);
 		this.type = NodeType.None;
-		this.modelIds = new HashSet<String>();
+		this.modelIds = new HashSet<>();
 	}
 	
 	public String getId() {
@@ -104,7 +104,7 @@ public NodeType getType() {
 	
 	public Set<String> getModelIds() {
 		if (this.modelIds == null)
-			return new HashSet<String>();
+			return new HashSet<>();
 		return modelIds;
 	}
 
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/alignment/SemanticTypes.java b/karma-common/src/main/java/edu/isi/karma/rep/alignment/SemanticTypes.java
index e23677327..2318e8337 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/alignment/SemanticTypes.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/alignment/SemanticTypes.java
@@ -31,8 +31,8 @@
 
 public class SemanticTypes implements Jsonizable {
 	// Map from the HNodeIds (for each column) to the semantic type
-	private Map<String, SemanticType> types = new HashMap<String, SemanticType>();
-	private Map<String, SynonymSemanticTypes> synonymTypes = new HashMap<String, SynonymSemanticTypes>();
+	private Map<String, SemanticType> types = new HashMap<>();
+	private Map<String, SynonymSemanticTypes> synonymTypes = new HashMap<>();
 
 	public Map<String, SemanticType> getTypes() {
 		return types;
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/metadata/SourceInformation.java b/karma-common/src/main/java/edu/isi/karma/rep/metadata/SourceInformation.java
index 87631a6e7..5cfe9f6c6 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/metadata/SourceInformation.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/metadata/SourceInformation.java
@@ -6,7 +6,7 @@
 import java.util.Map;
 
 public class SourceInformation {
-	private Map<InfoAttribute, String> attributeValueMap = new HashMap<InfoAttribute, String>();
+	private Map<InfoAttribute, String> attributeValueMap = new HashMap<>();
 	
 	public enum InfoAttribute {
 		/*** Database source information attributes ***/
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/metadata/Tag.java b/karma-common/src/main/java/edu/isi/karma/rep/metadata/Tag.java
index 9e2ed5502..f8a556082 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/metadata/Tag.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/metadata/Tag.java
@@ -36,7 +36,7 @@ public Tag(TagName label, Color color) {
 		super();
 		this.label = label;
 		this.color = color;
-		nodeIdList = new HashSet<String>();
+		nodeIdList = new HashSet<>();
 	}
 	
 	public Color getColor() {
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/metadata/TagsContainer.java b/karma-common/src/main/java/edu/isi/karma/rep/metadata/TagsContainer.java
index b61d18d18..015bf0ef7 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/metadata/TagsContainer.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/metadata/TagsContainer.java
@@ -32,7 +32,7 @@ public static enum Color {
 		Blue, Red, Green
 	}
 
-	private Set<Tag> tags = new HashSet<Tag>();
+	private Set<Tag> tags = new HashSet<>();
 
 	public Set<Tag> getTags() {
 		return tags;
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/metadata/WorksheetProperties.java b/karma-common/src/main/java/edu/isi/karma/rep/metadata/WorksheetProperties.java
index bc81e5d8f..d07e9135f 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/metadata/WorksheetProperties.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/metadata/WorksheetProperties.java
@@ -52,7 +52,7 @@ public enum SourceTypes {
 	}
 	
 	public WorksheetProperties() {
-		propertyValueMap = new HashMap<Property, String>();
+		propertyValueMap = new HashMap<>();
 	}
 
 	public void setPropertyValue(Property property, String value) {
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/model/Model.java b/karma-common/src/main/java/edu/isi/karma/rep/model/Model.java
index 6f0c5259e..4ee2b40e8 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/model/Model.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/model/Model.java
@@ -60,7 +60,7 @@ public class Model {
 
 	public Model(String id) {
 		this.id = id;
-		atoms = new ArrayList<Atom>();
+		atoms = new ArrayList<>();
 	}
 	
 //	public Model(String id, String type) {
@@ -195,10 +195,10 @@ public Map<String, Map<String, String>> findInJenaModel(
 	private Map<String, Map<String, String>> findSemanticModelInJenaModel( 
 			com.hp.hpl.jena.rdf.model.Model jenaModel, String ioType, Integer limit) {
 
-		Map<String, Map<String, String>> IdsAndMappings = 
-			new HashMap<String, Map<String,String>>();
+		Map<String, Map<String, String>> IdsAndMappings =
+				new HashMap<>();
 		
-		List<String> argList = new ArrayList<String>();
+		List<String> argList = new ArrayList<>();
 		String queryString = "";
 		if (ioType.equalsIgnoreCase(IOType.INPUT)) 
 			queryString = this.getSparqlToMatchServiceInputs(argList);
@@ -265,10 +265,10 @@ else if (ioType.equalsIgnoreCase(IOType.OUTPUT))
 	public List<Map<String, String>> findModelDataInJenaData( 
 			com.hp.hpl.jena.rdf.model.Model jenaModel, Integer limit) {
 
-		List<Map<String, String>> attValueList = 
-			new ArrayList<Map<String,String>>();
+		List<Map<String, String>> attValueList =
+				new ArrayList<>();
 		
-		List<String> argList = new ArrayList<String>();
+		List<String> argList = new ArrayList<>();
 		String queryString = "";
 		queryString = this.getSparqlDataQuery(argList);
 		
@@ -297,8 +297,8 @@ public List<Map<String, String>> findModelDataInJenaData(
 			for ( ; results.hasNext() ; )
 			{
 				QuerySolution soln = results.nextSolution() ;
-				Map<String, String> attValues = 
-					new HashMap<String, String>();
+				Map<String, String> attValues =
+						new HashMap<>();
 				
 				for (String arg : argList) {
 					RDFNode argNode = soln.get(arg) ;
@@ -345,7 +345,7 @@ public String getSparqlDataQuery(List<String> argList) {
 		String queryString = "";
 		
 		// map of NS --> Prefix
-		Map<String, String> nsToPrefixMapping = new HashMap<String, String>();
+		Map<String, String> nsToPrefixMapping = new HashMap<>();
 		nsToPrefixMapping.put(Namespaces.RDF, Prefixes.RDF);
 		
 		String select_header = "SELECT \n";
@@ -359,7 +359,7 @@ public String getSparqlDataQuery(List<String> argList) {
 		String argument2Var = "";
 
 		if (argList == null) 
-			argList = new ArrayList<String>();
+			argList = new ArrayList<>();
 		
 		for (int i = 0; i < this.getAtoms().size(); i++) {
 			Atom atom = this.getAtoms().get(i);
@@ -441,7 +441,7 @@ public String getSparqlConstructQuery(List<String> argList) {
 		String queryString = "";
 		
 		// map of NS --> Prefix
-		Map<String, String> nsToPrefixMapping = new HashMap<String, String>();
+		Map<String, String> nsToPrefixMapping = new HashMap<>();
 		nsToPrefixMapping.put(Namespaces.RDF, Prefixes.RDF);
 		
 		String construct_header = "CONSTRUCT { \n";
@@ -455,7 +455,7 @@ public String getSparqlConstructQuery(List<String> argList) {
 		String argument2Var = "";
 
 		if (argList == null) 
-			argList = new ArrayList<String>();
+			argList = new ArrayList<>();
 		
 		for (int i = 0; i < this.getAtoms().size(); i++) {
 			Atom atom = this.getAtoms().get(i);
@@ -548,7 +548,7 @@ private String getSparqlQuery(String ioType, List<String> argList) {
 		String queryString = "";
 		
 		// map of NS --> Prefix
-		Map<String, String> nsToPrefixMapping = new HashMap<String, String>();
+		Map<String, String> nsToPrefixMapping = new HashMap<>();
 		nsToPrefixMapping.put(Namespaces.KARMA, Prefixes.KARMA);
 		nsToPrefixMapping.put(Namespaces.SWRL, Prefixes.SWRL);
 		nsToPrefixMapping.put(Namespaces.HRESTS, Prefixes.HRESTS);
@@ -579,7 +579,7 @@ else if (ioType.equalsIgnoreCase(IOType.INPUT))
 		String argument2Var = "";
 
 		if (argList == null) 
-			argList = new ArrayList<String>();
+			argList = new ArrayList<>();
 
 		for (int i = 0; i < m.getAtoms().size(); i++) {
 			Atom atom = m.getAtoms().get(i);
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/sources/DataSource.java b/karma-common/src/main/java/edu/isi/karma/rep/sources/DataSource.java
index aa4b6206a..aec937529 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/sources/DataSource.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/sources/DataSource.java
@@ -25,6 +25,7 @@
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import org.jgrapht.graph.DirectedWeightedMultigraph;
 import org.slf4j.Logger;
@@ -50,36 +51,36 @@ public class DataSource extends Source {
 	private Model model;
 	private List<String> variables;
 
-	HashMap<String, Attribute> attIdToAttMap;
+	Map<String, Attribute> attIdToAttMap;
 
 	public DataSource(String id) {
 		super(id);
-		variables = new ArrayList<String>();
-		attributes = new ArrayList<Attribute>();
-		attIdToAttMap = new HashMap<String, Attribute>();
+		variables = new ArrayList<>();
+		attributes = new ArrayList<>();
+		attIdToAttMap = new HashMap<>();
 	}
 	
 	public DataSource(String id, String name) {
 		super(id, name);
-		variables = new ArrayList<String>();
-		attributes = new ArrayList<Attribute>();
-		attIdToAttMap = new HashMap<String, Attribute>();
+		variables = new ArrayList<>();
+		attributes = new ArrayList<>();
+		attIdToAttMap = new HashMap<>();
 	}
 	
 	public DataSource(String name, DirectedWeightedMultigraph<Node, LabeledLink> treeModel) {
 		super(new RandomGUID().toString());
 		this.setName(name);
-		variables = new ArrayList<String>();
-		attributes = new ArrayList<Attribute>();
-		attIdToAttMap = new HashMap<String, Attribute>();
+		variables = new ArrayList<>();
+		attributes = new ArrayList<>();
+		attIdToAttMap = new HashMap<>();
 		this.updateModel(treeModel);
 	}
 	
 	public DataSource(DirectedWeightedMultigraph<Node, LabeledLink> treeModel) {
 		super(new RandomGUID().toString());
-		variables = new ArrayList<String>();
-		attributes = new ArrayList<Attribute>();
-		attIdToAttMap = new HashMap<String, Attribute>();
+		variables = new ArrayList<>();
+		attributes = new ArrayList<>();
+		attIdToAttMap = new HashMap<>();
 		this.updateModel(treeModel);
 	}
 
@@ -128,9 +129,8 @@ private void updateModel(DirectedWeightedMultigraph<Node, LabeledLink> treeModel
 			return;
 		
 		Model m = new Model("model");
-		
-		HashMap<String, Argument> vertexIdToArgument = new HashMap<String, Argument>();
-		List<Attribute> attributeList = new ArrayList<Attribute>();
+		Map<String, Argument> vertexIdToArgument = new HashMap<>();
+		List<Attribute> attributeList = new ArrayList<>();
 		
 		// get the column name associated to the hNodeIds to assign to attribute names 
 		// set the rdf ids of all the vertices.
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/sources/Invocation.java b/karma-common/src/main/java/edu/isi/karma/rep/sources/Invocation.java
index d71af23a3..eb05ca8af 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/sources/Invocation.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/sources/Invocation.java
@@ -109,8 +109,8 @@ private static String getId(String name, HashMap<String, Integer> nameCounter) {
 	private void updateResponse() {
 		
 		Table results = new Table();
-		List<String> columns = new ArrayList<String>();
-        HashMap<String, Integer> attributeNameCounter = new HashMap<String, Integer>();
+		List<String> columns = new ArrayList<>();
+        HashMap<String, Integer> attributeNameCounter = new HashMap<>();
 
         logger.info("output type is: " + response.getType());
         if (response.getType() == null) {
@@ -224,7 +224,7 @@ public void joinInputAndOutput() {
     	
 		jointInputAndOutput = new Table(this.response.getTable());
 		
-		List<String> inputValues = new ArrayList<String>();
+		List<String> inputValues = new ArrayList<>();
 		if (this.request.getAttributes() != null)
 		for (int j = this.request.getAttributes().size() - 1; j >= 0; j--) {
 			
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/sources/InvocationManager.java b/karma-common/src/main/java/edu/isi/karma/rep/sources/InvocationManager.java
index 80c68ac87..8d4a733e5 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/sources/InvocationManager.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/sources/InvocationManager.java
@@ -69,7 +69,7 @@ public InvocationManager(String urlColumnName, List<String> idList, List<String>
 			throw new KarmaException("Cannot model a service without any request example.");
 		
 		this.serviceData = null;
-		this.invocations = new ArrayList<Invocation>();
+		this.invocations = new ArrayList<>();
 		
 		json = new JsonArray();
 		jsonUrl = new JsonArray();
@@ -85,16 +85,16 @@ public InvocationManager(String urlColumnName, List<String> idList, List<String>
 	public InvocationManager(String urlColumnName, String requestURLString) 
 	throws MalformedURLException, KarmaException {
 		this.urlColumnName = (urlColumnName == null || urlColumnName.trim().length() == 0) ? "url" : urlColumnName;
-		this.idList = new ArrayList<String>();
+		this.idList = new ArrayList<>();
 		this.idList.add("1");
-		List<String> requestURLList = new ArrayList<String>();
+		List<String> requestURLList = new ArrayList<>();
 		requestURLList.add(requestURLString);
 		requestURLs = URLManager.getURLsFromStrings(requestURLList);
 		if (requestURLs == null || requestURLs.isEmpty())
 			throw new KarmaException("Cannot model a service without any request example.");
 		
 		this.serviceData = null;
-		this.invocations = new ArrayList<Invocation>();
+		this.invocations = new ArrayList<>();
 		
 		json = new JsonArray();
 		jsonUrl = new JsonArray();
@@ -119,7 +119,7 @@ private void invokeAndGetResponse() {
 			invocation.invokeAPI();
 			invocations.add(invocation);
 		}
-		List<Table> invocationData = new ArrayList<Table>();
+		List<Table> invocationData = new ArrayList<>();
 		for (Invocation inv : this.invocations) {
 			populateJsonArraysFromInvocation(inv);
 			invocationData.add(inv.getJointInputAndOutput());
@@ -208,11 +208,11 @@ public Table getServiceData(boolean includeURL, boolean includeInputAttributes,
 		List<List<String>> values = this.serviceData.getValues();
 
 		Table newTable = new Table();
-		List<Attribute> newHeader = new ArrayList<Attribute>();
-		List<List<String>> newValues = new ArrayList<List<String>>();
-		List<String> newRowIds = new ArrayList<String>(this.serviceData.getRowIds());
+		List<Attribute> newHeader = new ArrayList<>();
+		List<List<String>> newValues = new ArrayList<>();
+		List<String> newRowIds = new ArrayList<>(this.serviceData.getRowIds());
 		
-		List<Integer> includingColumns = new ArrayList<Integer>();
+		List<Integer> includingColumns = new ArrayList<>();
 		
 		if (headers != null) {
 			if (includeURL && !headers.isEmpty())
@@ -230,7 +230,7 @@ public Table getServiceData(boolean includeURL, boolean includeInputAttributes,
 			newHeader.add(headers.get(colIndex));
 		}
 		for (List<String> vals : values) {
-			List<String> rowVals = new ArrayList<String>();
+			List<String> rowVals = new ArrayList<>();
 			for (Integer colIndex : includingColumns)
 				rowVals.add(vals.get(colIndex));
 			newValues.add(rowVals);
@@ -254,7 +254,7 @@ public String getServiceJson(boolean includeInputAttributes) {
 	}
 	
 	private List<Attribute> getInputAttributes() {
-		List<Attribute> inAttributes = new ArrayList<Attribute>();
+		List<Attribute> inAttributes = new ArrayList<>();
 		
 		Table serviceTable = getServiceData();
 		for (Attribute p : serviceTable.getHeaders()) {
@@ -267,7 +267,7 @@ private List<Attribute> getInputAttributes() {
 	}
 	
 	private List<Attribute> getOutputAttributes() {
-		List<Attribute> outAttributes = new ArrayList<Attribute>();
+		List<Attribute> outAttributes = new ArrayList<>();
 		
 		Table serviceTable = getServiceData();
 		for (Attribute p : serviceTable.getHeaders()) {
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/sources/Request.java b/karma-common/src/main/java/edu/isi/karma/rep/sources/Request.java
index c2ca59c95..8acf68b95 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/sources/Request.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/sources/Request.java
@@ -39,7 +39,7 @@ public Request(Request request) {
 		this.type = request.type;
 		this.url = request.url;
 		this.endPoint = request.endPoint;
-		this.attributes = new ArrayList<Attribute>(request.getAttributes());
+		this.attributes = new ArrayList<>(request.getAttributes());
 	}
 	
 	public Request(URL url) {
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/sources/Response.java b/karma-common/src/main/java/edu/isi/karma/rep/sources/Response.java
index b98b0c80c..def485a90 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/sources/Response.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/sources/Response.java
@@ -61,7 +61,7 @@ public List<Attribute> getAttributes() {
 		return this.attributes;
 	}
 	private void buildAttributeListFromTable() {
-		this.attributes = new ArrayList<Attribute>();
+		this.attributes = new ArrayList<>();
 		if (table == null)
 			return;
 		for (Attribute p : table.getHeaders()) {
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/sources/Table.java b/karma-common/src/main/java/edu/isi/karma/rep/sources/Table.java
index f2855ef78..d7a889f78 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/sources/Table.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/sources/Table.java
@@ -37,15 +37,15 @@ public class Table {
 	private List<String> rowIds;
 	
 	public Table() {
-		headers = new ArrayList<Attribute>();
-		values = new ArrayList<List<String>>();
-		rowIds = new ArrayList<String>();
+		headers = new ArrayList<>();
+		values = new ArrayList<>();
+		rowIds = new ArrayList<>();
 	}
 	
 	public Table(Table table) {
-		this.headers = new ArrayList<Attribute>(table.headers);
-		this.values = new ArrayList<List<String>>(table.values);
-		this.rowIds = new ArrayList<String>(table.rowIds);
+		this.headers = new ArrayList<>(table.headers);
+		this.values = new ArrayList<>(table.values);
+		this.rowIds = new ArrayList<>(table.rowIds);
 	}
 	
 	public int getRowsCount() {
@@ -145,8 +145,8 @@ private boolean sameHeaders(Table t) {
 		if (this.getColumnsCount() != t.getColumnsCount())
 			return false;
 		
-		List<String> attNames = new ArrayList<String>();
-		List<String> tAttNames = new ArrayList<String>();
+		List<String> attNames = new ArrayList<>();
+		List<String> tAttNames = new ArrayList<>();
 		
 		for (Attribute att : this.getHeaders()) 
 			attNames.add(att.getName());
@@ -171,22 +171,22 @@ public void cartesianProductOrUnionIfSameHeaders(Table t) {
     	else if (t1Cols == 0) {
     		
     		if (this.headers == null)
-    			this.headers = new ArrayList<Attribute>();
+    			this.headers = new ArrayList<>();
     		
     		for (Attribute att : t.getHeaders())
     			this.headers.add(new Attribute(att));
 
     		if (this.values == null)
-    			this.values = new ArrayList<List<String>>();
+    			this.values = new ArrayList<>();
 
     		if (t.getValues() != null)
     			for (List<String> v : t.getValues())
     				if (v != null)
-    					values.add(new ArrayList<String>(v));
+    					values.add(new ArrayList<>(v));
     	} else {
     		
     		if (sameHeaders(t)) {
-    			List<Table> tables = new ArrayList<Table>();
+    			List<Table> tables = new ArrayList<>();
     			tables.add(this);
     			tables.add(t);
     			Table result = union(tables);
@@ -202,11 +202,11 @@ else if (t1Cols == 0) {
         	int t2Rows = t.getRowsCount();
         	int totalRows = t1Rows == 0 || t2Rows == 0 ? t1Rows + t2Rows : t1Rows * t2Rows;
         	
-        	List<List<String>> values = new ArrayList<List<String>>();
+        	List<List<String>> values = new ArrayList<>();
 
     		for (int i = 0; i < totalRows; i++) {
         		
-        		List<String> row = new ArrayList<String>();
+        		List<String> row = new ArrayList<>();
         		
         		for (int j = 0; j < t1Cols; j++) {
         			int index = t1Rows == 0 ? -1 : i % t1Rows;
@@ -243,17 +243,16 @@ public static Table union(List<Table> srcTables) {
     		return null;
     	
     	Table resultTable = new Table();
-    	
-		String attributeId = "";
-		List<String> uniqueAttributeIDs = new ArrayList<String>();
+		String attributeId;
+		List<String> uniqueAttributeIDs = new ArrayList<>();
 		
-		List<List<Attribute>> srcAttributes = new ArrayList<List<Attribute>>();
-		List<List<List<String>>> srcValues = new ArrayList<List<List<String>>>();
-		List<List<String>> srcRowIds = new ArrayList<List<String>>();
+		List<List<Attribute>> srcAttributes = new ArrayList<>();
+		List<List<List<String>>> srcValues = new ArrayList<>();
+		List<List<String>> srcRowIds = new ArrayList<>();
 		
-		List<Attribute> resultAttributes = new ArrayList<Attribute>();
-		List<List<String>> resultValues = new ArrayList<List<String>>();
-		List<String> resultRowIds = new ArrayList<String>();
+		List<Attribute> resultAttributes = new ArrayList<>();
+		List<List<String>> resultValues = new ArrayList<>();
+		List<String> resultRowIds = new ArrayList<>();
 		
 		for (Table t : srcTables) {
 			srcAttributes.add(t.getHeaders());
@@ -272,10 +271,11 @@ public static Table union(List<Table> srcTables) {
 			}
 		}
 		
-		List<Attribute> rawAttributes = null;
-		List<String> rawAttributeIDs = new ArrayList<String>();
-		List<String> rawValues = null;
-		String singleValue = null;
+		List<Attribute> rawAttributes;
+		List<String> rawAttributeIDs = new ArrayList<>();
+		List<String> rawValues;
+		String singleValue;
+
 		for (int i = 0; i < srcAttributes.size(); i++) {
 			
 			rawAttributes = srcAttributes.get(i);
@@ -286,7 +286,7 @@ public static Table union(List<Table> srcTables) {
 //			logger.debug("table " + i);
 			for (int j = 0; j < srcValues.get(i).size(); j++) {
 				
-				List<String> populatedValues = new ArrayList<String>();
+				List<String> populatedValues = new ArrayList<>();
 				rawValues = srcValues.get(i).get(j);
 				
 //				logger.debug("\t row " + j);
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/sources/URLManager.java b/karma-common/src/main/java/edu/isi/karma/rep/sources/URLManager.java
index 0502b971f..518bbfc50 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/sources/URLManager.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/sources/URLManager.java
@@ -47,7 +47,7 @@ private URLManager() {
 
 	public static List<URL> getURLsFromJSON(String requestURLsJSONArray) throws JSONException, MalformedURLException {
 
-		List<URL> urls = new ArrayList<URL>();
+		List<URL> urls = new ArrayList<>();
 		JSONArray jsonArray = new JSONArray(requestURLsJSONArray);
 		
 //		String firstEndpoint = "";
@@ -66,7 +66,7 @@ public static List<URL> getURLsFromJSON(String requestURLsJSONArray) throws JSON
 	public static List<URL> getURLsFromStrings(List<String> requestURLStrings) 
 	throws MalformedURLException, KarmaException {
 
-		List<URL> urls = new ArrayList<URL>();
+		List<URL> urls = new ArrayList<>();
 		
 		String firstEndpoint = "";
 		for (int i = 0; i < requestURLStrings.size(); i++) {
@@ -181,14 +181,12 @@ public static List<Attribute> getQueryAttributes(URL url) {
 	    try {
 	    	
 	    	String urlString = url.toString();
-	    	
-	        Map<String, List<String>> attributes = new HashMap<String, List<String>>();
-	        
-	        List<Attribute> attributeList = new ArrayList<Attribute>();
-	        HashMap<String, Integer> attributeNameCounter = new HashMap<String, Integer>();
-	        String attributeName = "";
-	        String attributeId = "";
-	        String attributeValue = "";
+	        Map<String, List<String>> attributes = new HashMap<>();
+	        List<Attribute> attributeList = new ArrayList<>();
+	        HashMap<String, Integer> attributeNameCounter = new HashMap<>();
+	        String attributeName;
+	        String attributeId;
+	        String attributeValue;
 	        
 	        String[] urlParts = urlString.split("\\?");
 	        if (urlParts.length > 1) {
@@ -207,7 +205,7 @@ public static List<Attribute> getQueryAttributes(URL url) {
 	
 		                List<String> values = attributes.get(key);
 		                if (values == null) {
-		                    values = new ArrayList<String>();
+		                    values = new ArrayList<>();
 		                    attributes.put(key, values);
 		                }
 		                values.add(value);
@@ -267,10 +265,10 @@ private static String getId(String name, HashMap<String, Integer> nameCounter) {
 	 * @throws MalformedURLException 
 	 */
 	public static List<String>  extractAttributeNames(List<String> urlList) throws MalformedURLException {
-		List<String> attributesNameList = new ArrayList<String>();
+		List<String> attributesNameList = new ArrayList<>();
 
-		Attribute p = null;
-		String key = null;
+		Attribute p;
+		String key;
 		for (int i = 0; i < urlList.size(); i++) {
 			//System.out.println(urlList.get(i));
 			List<Attribute> attributeList = getQueryAttributes(urlList.get(i));
@@ -288,11 +286,11 @@ public static List<String>  extractAttributeNames(List<String> urlList) throws M
 	
 	
 	public static List<List<String>>  attributeValuesInTable(List<String> urlList, List<String> attributeNames) throws MalformedURLException {
-		List<List<String>> allAttributes = new ArrayList<List<String>>();
+		List<List<String>> allAttributes = new ArrayList<>();
 
-		Attribute p = null;
-		String key = null;
-		int index = -1;
+		Attribute p;
+		String key;
+		int index;
 		
 		for (int i = 0; i < urlList.size(); i++) {
 			//System.out.println(urlList.get(i));
@@ -316,11 +314,11 @@ public static List<List<String>>  attributeValuesInTable(List<String> urlList, L
 	}
 	
 	public static List<List<String>>  attributeValuesInSets(List<String> urlList, List<String> attributeNames) throws MalformedURLException {
-		List<List<String>> allAttributes = new ArrayList<List<String>>();
+		List<List<String>> allAttributes = new ArrayList<>();
 
-		Attribute p = null;
-		String key = null;
-		int index = -1;
+		Attribute p;
+		String key;
+		int index;
 		
 		for (int j = 0; j < attributeNames.size(); j++) {
 			allAttributes.add(new ArrayList<String>());
@@ -418,7 +416,7 @@ public static String createApiLink(String apiEndPoint, List<String> attributeNam
 		if (!invocationURL.endsWith("?"))
 			invocationURL += "?";
 
-		String value = "";
+		String value;
 		for (int i = 0; i < attributeNames.size(); i++) {
 			value = attributeValues.get(i).trim();
 			
diff --git a/karma-common/src/main/java/edu/isi/karma/rep/sources/WebService.java b/karma-common/src/main/java/edu/isi/karma/rep/sources/WebService.java
index 933c3ce40..d1f206595 100644
--- a/karma-common/src/main/java/edu/isi/karma/rep/sources/WebService.java
+++ b/karma-common/src/main/java/edu/isi/karma/rep/sources/WebService.java
@@ -75,11 +75,11 @@ public class WebService extends Source {
 	public WebService(String id, URL urlExample) {
 		super(id, URLManager.getOperationName(urlExample));
 		this.urlExample= urlExample;
-		this.hNodeIdToAttribute = new HashMap<String, Attribute>();
-		this.variables = new ArrayList<String>();
-		this.inputAttributes = new ArrayList<Attribute>();
-		this.outputAttributes = new ArrayList<Attribute>();
-		this.attIdToAttMap = new HashMap<String, Attribute>();
+		this.hNodeIdToAttribute = new HashMap<>();
+		this.variables = new ArrayList<>();
+		this.inputAttributes = new ArrayList<>();
+		this.outputAttributes = new ArrayList<>();
+		this.attIdToAttMap = new HashMap<>();
 	}
 	
 	public WebService(String id, String name, URL urlExample) {
@@ -87,35 +87,35 @@ public WebService(String id, String name, URL urlExample) {
 		this.urlExample= urlExample;
 		this.setMethod(HttpMethods.GET.name());
 		this.urlExample = urlExample;
-		this.inputAttributes = new ArrayList<Attribute>();
-		this.outputAttributes = new ArrayList<Attribute>();
-		this.attIdToAttMap = new HashMap<String, Attribute>();
+		this.inputAttributes = new ArrayList<>();
+		this.outputAttributes = new ArrayList<>();
+		this.attIdToAttMap = new HashMap<>();
 	}
 	
 	public WebService(String id, String addressTemplate) {
 		super(id);
 		this.address= addressTemplate;
-		this.inputAttributes = new ArrayList<Attribute>();
-		this.outputAttributes = new ArrayList<Attribute>();
-		this.attIdToAttMap = new HashMap<String, Attribute>();
+		this.inputAttributes = new ArrayList<>();
+		this.outputAttributes = new ArrayList<>();
+		this.attIdToAttMap = new HashMap<>();
 	}
 	
 	public WebService(String id, String name, String addressTemplate) {
 		super(id);
 		this.setName(name);
 		this.address= addressTemplate;
-		this.inputAttributes = new ArrayList<Attribute>();
-		this.outputAttributes = new ArrayList<Attribute>();
-		this.attIdToAttMap = new HashMap<String, Attribute>();
+		this.inputAttributes = new ArrayList<>();
+		this.outputAttributes = new ArrayList<>();
+		this.attIdToAttMap = new HashMap<>();
 	}
 
 	public WebService(String id, String name, URL urlExample, String method) {
 		super(id, name);
 		this.urlExample = urlExample;
 		this.setMethod(method);
-		this.inputAttributes = new ArrayList<Attribute>();
-		this.outputAttributes = new ArrayList<Attribute>();
-		this.attIdToAttMap = new HashMap<String, Attribute>();
+		this.inputAttributes = new ArrayList<>();
+		this.outputAttributes = new ArrayList<>();
+		this.attIdToAttMap = new HashMap<>();
 	}
 
 	public String getOperationName() {
@@ -143,7 +143,7 @@ public String getPopulatedAddress(Map<String, String> attIdToValue, List<Attribu
 		String populatedAddress = address;
 		
 		if (missingAttributes == null)
-			missingAttributes = new ArrayList<Attribute>();
+			missingAttributes = new ArrayList<>();
 		
 		for (Attribute att : this.inputAttributes) {
 			
@@ -339,16 +339,16 @@ public void updateModel(DirectedWeightedMultigraph<Node, LabeledLink> treeModel)
 		if (treeModel == null)
 			return;
 		
-		List<Node> inputAttributesNodes = new ArrayList<Node>();
-		List<Node> outputAttributesNodes = new ArrayList<Node>();
+		List<Node> inputAttributesNodes = new ArrayList<>();
+		List<Node> outputAttributesNodes = new ArrayList<>();
 		
-		HashMap<String, Argument> vertexIdToArgument = new HashMap<String, Argument>();
+		HashMap<String, Argument> vertexIdToArgument = new HashMap<>();
 
 		this.hNodeIdToAttribute.clear();
 		buildHNodeId2AttributeMapping();
 		
 		// set the rdf ids of all the vertices. The rdf id of leaf vertices are the attribute ids. 
-		String hNodeId = "";
+		String hNodeId;
 		for (Node n : treeModel.vertexSet()) {
 			if (n instanceof ColumnNode) {
 				logger.debug("Node " + n.getLocalId() + " is a column node.");
@@ -378,8 +378,8 @@ public void updateModel(DirectedWeightedMultigraph<Node, LabeledLink> treeModel)
 		}
 
 		
-		List<String> inputModelVertexes = new ArrayList<String>();
-		List<String> inputModelEdges = new ArrayList<String>();		
+		List<String> inputModelVertexes = new ArrayList<>();
+		List<String> inputModelEdges = new ArrayList<>();		
 		
 		Model inputModel = getInputModel(treeModel, inputAttributesNodes, 
 				inputModelVertexes, inputModelEdges,
@@ -403,8 +403,8 @@ private Model getInputModel(DirectedWeightedMultigraph<Node, LabeledLink> treeMo
 			return null;
 				
 		logger.debug("compute the steiner tree from the alignment tree with input nodes as steiner nodes ...");
-		UndirectedGraph<Node, LabeledLink> undirectedGraph = 
-			new AsUndirectedGraph<Node, LabeledLink>(treeModel);
+		UndirectedGraph<Node, LabeledLink> undirectedGraph =
+				new AsUndirectedGraph<>(treeModel);
 		List<Node> steinerNodes = inputNodes;
 		SteinerTree steinerTree = new SteinerTree(GraphUtil.asDefaultGraph(undirectedGraph), steinerNodes);
 		
@@ -438,7 +438,7 @@ private Model getInputModel(DirectedWeightedMultigraph<Node, LabeledLink> treeMo
 				continue;
 			
 			Label propertyPredicate = new Label(e.getLabel().getUri(), e.getLabel().getNs(), e.getLabel().getPrefix());
-			IndividualPropertyAtom propertyAtom = null;
+			IndividualPropertyAtom propertyAtom;
 			
 //			// has_subclass is from source to target, we substitute this with a rdfs:subClassOf from target to source
 //			if (propertyPredicate.getUriString().equalsIgnoreCase(ModelingParams.HAS_SUBCLASS_URI)){
@@ -494,7 +494,7 @@ private Model getOutputModel(DirectedWeightedMultigraph<Node, LabeledLink> treeM
 				continue;
 			
 			Label propertyPredicate = new Label(e.getLabel().getUri(), e.getLabel().getNs(), e.getLabel().getPrefix());
-			IndividualPropertyAtom propertyAtom = null;
+			IndividualPropertyAtom propertyAtom;
 			
 			// has_subclass is from source to target, we substitute this with a rdfs:subClassOf from target to source
 //			if (propertyPredicate.getUriString().equalsIgnoreCase(ModelingParams.HAS_SUBCLASS_URI)){
diff --git a/karma-common/src/main/java/edu/isi/karma/service/json/ArrayValue.java b/karma-common/src/main/java/edu/isi/karma/service/json/ArrayValue.java
index cff4633df..bb2f32c22 100644
--- a/karma-common/src/main/java/edu/isi/karma/service/json/ArrayValue.java
+++ b/karma-common/src/main/java/edu/isi/karma/service/json/ArrayValue.java
@@ -24,7 +24,7 @@
 import java.util.List;
 
 public class ArrayValue extends Value{
-	private List<Element> elements = new ArrayList<Element>();
+	private List<Element> elements = new ArrayList<>();
 
 	public List<Element> getElements() {
 		return elements;
diff --git a/karma-common/src/main/java/edu/isi/karma/service/json/Element.java b/karma-common/src/main/java/edu/isi/karma/service/json/Element.java
index 0e3b049ed..fa22637b7 100644
--- a/karma-common/src/main/java/edu/isi/karma/service/json/Element.java
+++ b/karma-common/src/main/java/edu/isi/karma/service/json/Element.java
@@ -140,13 +140,13 @@ private void getFlatTable(Element root, Table t) {
     	
     	if (root.valueType == ValueType.SINGLE) { 
     		innerT.getHeaders().add(new Attribute(root.getKey(), root.getKey()));
-    		List<String> v = new ArrayList<String>();
+    		List<String> v = new ArrayList<>();
     		v.add(((SingleValue)root.getValue()).getValueString());
     		innerT.getValues().add(v);
     		t.cartesianProductOrUnionIfSameHeaders(innerT);
     		return;
     	} else {
-    		List<String> v = new ArrayList<String>();
+    		List<String> v = new ArrayList<>();
 			for (Element child : ((ArrayValue)root.getValue()).getElements()) 
 			{
 				if (child.valueType == ValueType.SINGLE) {
diff --git a/karma-common/src/main/java/edu/isi/karma/service/json/JsonManager.java b/karma-common/src/main/java/edu/isi/karma/service/json/JsonManager.java
index 2b0fdaad7..9d4ad3a65 100644
--- a/karma-common/src/main/java/edu/isi/karma/service/json/JsonManager.java
+++ b/karma-common/src/main/java/edu/isi/karma/service/json/JsonManager.java
@@ -175,7 +175,7 @@ public static void union(List<List<String>> srcColumns, List<List<List<String>>>
 			rawNames = srcColumns.get(i);
 			for (int j = 0; j < srcValues.get(i).size(); j++) {
 				
-				List<String> populatedValues = new ArrayList<String>();
+				List<String> populatedValues = new ArrayList<>();
 				rawValues = srcValues.get(i).get(j);
 				
 				for (int k = 0; k < columns.size(); k++) {
@@ -215,7 +215,7 @@ public static void union(List<List<String>> srcColumns, List<List<String>> srcTy
 			rawNames = srcColumns.get(i);
 			for (int j = 0; j < srcValues.get(i).size(); j++) {
 				
-				List<String> populatedValues = new ArrayList<String>();
+				List<String> populatedValues = new ArrayList<>();
 				rawValues = srcValues.get(i).get(j);
 				
 				for (int k = 0; k < columns.size(); k++) {
@@ -241,10 +241,10 @@ public static void getJsonFlat(String json, List<String> columns, List<List<Stri
     	Table t = element.getFlatTable();
 
     	if (columns == null)
-    		columns = new ArrayList<String>();
+    		columns = new ArrayList<>();
     	
     	if (values == null)
-    		values = new ArrayList<List<String>>();
+    		values = new ArrayList<>();
     	
     	if (t.getColumnsCount() > 0) {
 	    	for (Attribute att : t.getHeaders())
@@ -306,8 +306,8 @@ public static String jsonToCSV(String json) {
 
 	public static String jsonToCSV(String json, Character separator, Character quotechar, Character endlinechar) {
 		
-        List<String> columns = new ArrayList<String>();
-        List<List<String>> values = new ArrayList<List<String>>();
+        List<String> columns = new ArrayList<>();
+        List<List<String>> values = new ArrayList<>();
         
         getJsonFlat(json, columns, values);
         
diff --git a/karma-common/src/main/java/edu/isi/karma/util/HTTPUtil.java b/karma-common/src/main/java/edu/isi/karma/util/HTTPUtil.java
index 6a27d040a..caa1976da 100644
--- a/karma-common/src/main/java/edu/isi/karma/util/HTTPUtil.java
+++ b/karma-common/src/main/java/edu/isi/karma/util/HTTPUtil.java
@@ -69,7 +69,7 @@ public static String executeHTTPPostRequest(String serviceURL, String contentTyp
 					throws ClientProtocolException, IOException {
 		
 		// Prepare the message body parameters
-		List<NameValuePair> formParams = new ArrayList<NameValuePair>();
+		List<NameValuePair> formParams = new ArrayList<>();
 		for (Map.Entry<String, String> stringStringEntry : formParameters.entrySet()) {
 			formParams.add(new BasicNameValuePair(stringStringEntry.getKey(), stringStringEntry.getValue()));
 		}
diff --git a/karma-common/src/main/java/edu/isi/karma/util/Util.java b/karma-common/src/main/java/edu/isi/karma/util/Util.java
index 4650e3c50..62a08026f 100644
--- a/karma-common/src/main/java/edu/isi/karma/util/Util.java
+++ b/karma-common/src/main/java/edu/isi/karma/util/Util.java
@@ -43,15 +43,15 @@ private Util() {
 	 */
 	public static HashMap<String, Double> sortHashMap(
 			HashMap<String, Double> input) {
-		Map<String, Double> tempMap = new HashMap<String, Double>();
+		Map<String, Double> tempMap = new HashMap<>();
 		for (Map.Entry<String, Double> stringDoubleEntry : input.entrySet()) {
 			tempMap.put(stringDoubleEntry.getKey(), stringDoubleEntry.getValue());
 		}
 
-		List<String> mapKeys = new ArrayList<String>(tempMap.keySet());
-		List<Double> mapValues = new ArrayList<Double>(tempMap.values());
-		HashMap<String, Double> sortedMap = new LinkedHashMap<String, Double>();
-		TreeSet<Double> sortedSet = new TreeSet<Double>(mapValues);
+		List<String> mapKeys = new ArrayList<>(tempMap.keySet());
+		List<Double> mapValues = new ArrayList<>(tempMap.values());
+		HashMap<String, Double> sortedMap = new LinkedHashMap<>();
+		TreeSet<Double> sortedSet = new TreeSet<>(mapValues);
 		Object[] sortedArray = sortedSet.toArray();
 
 		int size = sortedArray.length;
diff --git a/karma-common/src/main/java/edu/isi/karma/view/VHNode.java b/karma-common/src/main/java/edu/isi/karma/view/VHNode.java
index e041bdad8..e867df2a2 100644
--- a/karma-common/src/main/java/edu/isi/karma/view/VHNode.java
+++ b/karma-common/src/main/java/edu/isi/karma/view/VHNode.java
@@ -45,7 +45,7 @@ public void setVisible(boolean visible) {
 	}
 
 	public ArrayList<String> getAllPaths() {
-		ArrayList<String> paths = new ArrayList<String>();
+		ArrayList<String> paths = new ArrayList<>();
 		paths.add(getNodePathSignature());
 		
 		
diff --git a/karma-common/src/main/java/edu/isi/karma/view/VWorksheet.java b/karma-common/src/main/java/edu/isi/karma/view/VWorksheet.java
index b18591dfb..a5b7dffb9 100644
--- a/karma-common/src/main/java/edu/isi/karma/view/VWorksheet.java
+++ b/karma-common/src/main/java/edu/isi/karma/view/VWorksheet.java
@@ -82,7 +82,7 @@ public class VWorksheet extends ViewEntity {
 	 * We create a TablePager for the top level table and every nested table we
 	 * see. It records how the table is scrolled.
 	 */
-	private Map<String, TablePager> tableId2TablePager = new HashMap<String, TablePager>();
+	private Map<String, TablePager> tableId2TablePager = new HashMap<>();
 	
 	private static Logger logger = LoggerFactory
 			.getLogger(VWorksheet.class);
diff --git a/karma-common/src/main/java/edu/isi/karma/view/VWorkspaceRegistry.java b/karma-common/src/main/java/edu/isi/karma/view/VWorkspaceRegistry.java
index 750df912c..7f8ab3c73 100644
--- a/karma-common/src/main/java/edu/isi/karma/view/VWorkspaceRegistry.java
+++ b/karma-common/src/main/java/edu/isi/karma/view/VWorkspaceRegistry.java
@@ -26,7 +26,7 @@
 
 public class VWorkspaceRegistry {
 
-	private static Map<String, VWorkspace> registry = new HashMap<String, VWorkspace>();
+	private static Map<String, VWorkspace> registry = new HashMap<>();
 
 	private static VWorkspaceRegistry instance = new VWorkspaceRegistry();
 	private VWorkspaceRegistry()
diff --git a/karma-common/src/main/java/edu/isi/karma/view/ViewFactory.java b/karma-common/src/main/java/edu/isi/karma/view/ViewFactory.java
index 816b402e3..5bb35aace 100644
--- a/karma-common/src/main/java/edu/isi/karma/view/ViewFactory.java
+++ b/karma-common/src/main/java/edu/isi/karma/view/ViewFactory.java
@@ -50,7 +50,7 @@ public ViewFactory() {
 
 	private int nextId = 1;
 
-	private Map<String, VWorksheet> vWorksheets = new HashMap<String, VWorksheet>();
+	private Map<String, VWorksheet> vWorksheets = new HashMap<>();
 
 	private String getId(String prefix) {
 		return prefix + (nextId++);
@@ -122,7 +122,7 @@ public VWorksheet getVWorksheetByWorksheetId(String worksheetId)
 	}
 	
 	public void addWorksheets(Collection<Worksheet> worksheets, VWorkspace vWorkspace) {
-		List<VWorksheet> newWorksheets = new LinkedList<VWorksheet>();
+		List<VWorksheet> newWorksheets = new LinkedList<>();
 		for (Worksheet w : worksheets) {
 			if (null == getVWorksheetByWorksheetId(w.getId())) {
 				newWorksheets
diff --git a/karma-common/src/main/java/edu/isi/karma/webserver/ExecutionController.java b/karma-common/src/main/java/edu/isi/karma/webserver/ExecutionController.java
index ce432f67d..73e724642 100644
--- a/karma-common/src/main/java/edu/isi/karma/webserver/ExecutionController.java
+++ b/karma-common/src/main/java/edu/isi/karma/webserver/ExecutionController.java
@@ -47,7 +47,7 @@ public class ExecutionController {
 
 	private static Logger logger = LoggerFactory
 			.getLogger(ExecutionController.class);
-	private static final HashMap<String, CommandFactory> commandFactoryMap = new HashMap<String, CommandFactory>();
+	private static final HashMap<String, CommandFactory> commandFactoryMap = new HashMap<>();
 	private final Workspace workspace;
 
 	static{
diff --git a/karma-common/src/main/java/edu/isi/karma/webserver/WorkspaceRegistry.java b/karma-common/src/main/java/edu/isi/karma/webserver/WorkspaceRegistry.java
index 16dd9f3fc..7c1280010 100644
--- a/karma-common/src/main/java/edu/isi/karma/webserver/WorkspaceRegistry.java
+++ b/karma-common/src/main/java/edu/isi/karma/webserver/WorkspaceRegistry.java
@@ -33,7 +33,7 @@ public class WorkspaceRegistry {
 
 	private static WorkspaceRegistry singleton = new WorkspaceRegistry();
 
-	private final Map<String, ExecutionController> workspaceId2ExecutionController = new ConcurrentHashMap<String, ExecutionController>();
+	private final Map<String, ExecutionController> workspaceId2ExecutionController = new ConcurrentHashMap<>();
 
 	public static WorkspaceRegistry getInstance() {
 		return singleton;
diff --git a/karma-jdbc/src/main/java/edu/isi/karma/rdf/DatabaseTableRDFGenerator.java b/karma-jdbc/src/main/java/edu/isi/karma/rdf/DatabaseTableRDFGenerator.java
index 858e68995..29399964d 100644
--- a/karma-jdbc/src/main/java/edu/isi/karma/rdf/DatabaseTableRDFGenerator.java
+++ b/karma-jdbc/src/main/java/edu/isi/karma/rdf/DatabaseTableRDFGenerator.java
@@ -172,7 +172,7 @@ private void generateRDF(String wkname, String query, List<KR2RMLRDFWriter> writ
 		
 		int counter = 0;
 		
-		ArrayList<String> rowValues = null;
+		List<String> rowValues = null;
 		while ((rowValues = dbUtil.parseResultSetRow(r)) != null) {
 			// Generate RDF and create a new worksheet for every DATABASE_TABLE_FETCH_SIZE rows
 			if(counter%DATABASE_TABLE_FETCH_SIZE == 0 && counter != 0) {
@@ -233,7 +233,8 @@ private void generateRDFFromWorksheet(Worksheet wk,
 	private List<String> addHeaders (Worksheet wk, List<String> columnNames,
 			RepFactory factory) {
 		HTable headers = wk.getHeaders();
-		ArrayList<String> headersList = new ArrayList<String>();
+		List<String> headersList = new ArrayList<>();
+
         for(int i=0; i< columnNames.size(); i++){
         	HNode hNode = null;
         	hNode = headers.addHNode(columnNames.get(i), HNodeType.Regular, wk, factory);
diff --git a/karma-jdbc/src/main/java/edu/isi/karma/util/AbstractJDBCUtil.java b/karma-jdbc/src/main/java/edu/isi/karma/util/AbstractJDBCUtil.java
index f3b9d98f7..af5e190fd 100644
--- a/karma-jdbc/src/main/java/edu/isi/karma/util/AbstractJDBCUtil.java
+++ b/karma-jdbc/src/main/java/edu/isi/karma/util/AbstractJDBCUtil.java
@@ -57,7 +57,7 @@ public abstract ArrayList<ArrayList<String>> getSQLQueryDataForLimitedRows(DBTyp
 	public abstract ArrayList<String> getListOfTables(Connection conn) throws SQLException, ClassNotFoundException;
 
 	protected Connection getConnection(String driver, String connectString) throws SQLException, ClassNotFoundException {
-		Connection localConn = null;
+		Connection localConn;
 		Class.forName(driver);
 		localConn = DriverManager.getConnection(connectString);
 		return localConn;
@@ -154,19 +154,19 @@ ArrayList<ArrayList<String>> getDataForQuery(Connection conn, String query) thro
 	private static boolean warnedSqlException = false;
 	
 	protected ArrayList<ArrayList<String>> parseResultSetIntoArrayListOfRows(ResultSet r) throws SQLException {
-		ArrayList<ArrayList<String>> vals = new ArrayList<ArrayList<String>>();
+		ArrayList<ArrayList<String>> vals = new ArrayList<>();
 
 		ResultSetMetaData meta = r.getMetaData();
 
 		// Add the column names
-		ArrayList<String> columnNamesRow = new ArrayList<String>();
+		ArrayList<String> columnNamesRow = new ArrayList<>();
 		for (int i = 1; i <= meta.getColumnCount(); i++) {
 			columnNamesRow.add(meta.getColumnName(i));
 		}
 		vals.add(columnNamesRow);
 		
 		// Add an ArrayList for each row
-		ArrayList<String> row = null;
+		ArrayList<String> row;
 		while ((row = parseResultSetRow(r)) != null) {
 			vals.add(row);
 		}
@@ -177,7 +177,7 @@ protected ArrayList<ArrayList<String>> parseResultSetIntoArrayListOfRows(ResultS
 	public ArrayList<String> parseResultSetRow(ResultSet r) throws SQLException {
 		if(r.next()) {
 			ResultSetMetaData meta = r.getMetaData();
-			ArrayList<String> row = new ArrayList<String>();
+			ArrayList<String> row = new ArrayList<>();
 			for (int i = 1; i <= meta.getColumnCount(); i++) {
 
 				String val;
@@ -207,7 +207,7 @@ public ArrayList<String> parseResultSetRow(ResultSet r) throws SQLException {
 	 * @throws ClassNotFoundException
 	 */
 	public boolean tableExists(String tableName, Connection conn) throws SQLException, ClassNotFoundException {
-		ArrayList<String> tn = getListOfTables(conn);
+		List<String> tn = getListOfTables(conn);
 
 		if (tn.contains(tableName)) {
 			return true;
@@ -226,7 +226,7 @@ public boolean tableExists(String tableName, Connection conn) throws SQLExceptio
 	 */
 	public List<String> getColumnNames(String db, String tableName, Connection conn) throws SQLException
 	{
-		List<String> columnNames = new ArrayList<String>(10);
+		List<String> columnNames = new ArrayList<>(10);
 		ResultSet rs = conn.getMetaData().getColumns(db, null, tableName, null);
 		while(rs.next())
 		{
@@ -245,7 +245,7 @@ public List<String> getColumnNames(String db, String tableName, Connection conn)
 	 */
 	public List<String> getColumnTypes(String db, String tableName, Connection conn) throws SQLException
 	{
-		List<String> columnTypes = new ArrayList<String>(10);
+		List<String> columnTypes = new ArrayList<>(10);
 		ResultSet rs = conn.getMetaData().getColumns(db, null, tableName, null);
 		while(rs.next())
 		{
diff --git a/karma-jdbc/src/main/java/edu/isi/karma/util/MySQLUtil.java b/karma-jdbc/src/main/java/edu/isi/karma/util/MySQLUtil.java
index 5ee382744..823d1b571 100644
--- a/karma-jdbc/src/main/java/edu/isi/karma/util/MySQLUtil.java
+++ b/karma-jdbc/src/main/java/edu/isi/karma/util/MySQLUtil.java
@@ -46,7 +46,7 @@ public class MySQLUtil extends AbstractJDBCUtil {
 	public ArrayList<String> getListOfTables(Connection conn) 
 			throws SQLException, ClassNotFoundException {
 		
-		ArrayList<String> tableNames = new ArrayList<String>();
+		ArrayList<String> tableNames = new ArrayList<>();
 		DatabaseMetaData dmd = conn.getMetaData();
 		ResultSet rs = dmd.getTables(null, null, null, new String[] {"TABLE","VIEW"});
 		while (rs.next())
diff --git a/karma-jdbc/src/main/java/edu/isi/karma/util/OracleUtil.java b/karma-jdbc/src/main/java/edu/isi/karma/util/OracleUtil.java
index b447ade66..6dae8dc8f 100644
--- a/karma-jdbc/src/main/java/edu/isi/karma/util/OracleUtil.java
+++ b/karma-jdbc/src/main/java/edu/isi/karma/util/OracleUtil.java
@@ -42,7 +42,7 @@ public class OracleUtil extends AbstractJDBCUtil {
 	@Override
 	public ArrayList<String> getListOfTables(Connection conn)
 			throws SQLException, ClassNotFoundException {
-		ArrayList<String> tableNames = new ArrayList<String>();
+		ArrayList<String> tableNames = new ArrayList<>();
 		
 		Statement stmt = conn.createStatement(); 
 	    ResultSet rs = stmt.executeQuery("select object_name from user_objects " +
@@ -52,6 +52,9 @@ public ArrayList<String> getListOfTables(Connection conn)
 	      String tableName = rs.getString(1);
 	      tableNames.add(tableName);
 	    }
+		rs.close();
+		stmt.close();
+		
 	    Collections.sort(tableNames);
 		return tableNames;
 	}
diff --git a/karma-jdbc/src/main/java/edu/isi/karma/util/PostGISUtil.java b/karma-jdbc/src/main/java/edu/isi/karma/util/PostGISUtil.java
index 0f7adf8fc..ba5f2e235 100644
--- a/karma-jdbc/src/main/java/edu/isi/karma/util/PostGISUtil.java
+++ b/karma-jdbc/src/main/java/edu/isi/karma/util/PostGISUtil.java
@@ -46,7 +46,7 @@ public class PostGISUtil extends AbstractJDBCUtil {
 	public ArrayList<String> getListOfTables(Connection conn) 
 			throws SQLException, ClassNotFoundException {
 		
-		ArrayList<String> tableNames = new ArrayList<String>();
+		ArrayList<String> tableNames = new ArrayList<>();
 		DatabaseMetaData dmd = conn.getMetaData();
 		ResultSet rs = dmd.getTables(null, null, null, new String[] {"TABLE"});
 		String schemaName, tableName;
diff --git a/karma-jdbc/src/main/java/edu/isi/karma/util/SQLServerUtil.java b/karma-jdbc/src/main/java/edu/isi/karma/util/SQLServerUtil.java
index bbea7c919..da00ec4e9 100644
--- a/karma-jdbc/src/main/java/edu/isi/karma/util/SQLServerUtil.java
+++ b/karma-jdbc/src/main/java/edu/isi/karma/util/SQLServerUtil.java
@@ -49,7 +49,7 @@ public class SQLServerUtil extends AbstractJDBCUtil {
 	public ArrayList<String> getListOfTables(Connection conn) 
 			throws SQLException, ClassNotFoundException {
 		
-		ArrayList<String> tableNames = new ArrayList<String>();
+		ArrayList<String> tableNames = new ArrayList<>();
 		DatabaseMetaData dmd = conn.getMetaData();
 		//Pedro: 2012/12/03 comment out to enable loading Views in Karma (on behalf of Maria)
 		//ResultSet rs = dmd.getTables(null, null, null, new String[] {"TABLE"});
@@ -121,7 +121,7 @@ public ArrayList<ArrayList<String>> getSQLQueryDataForLimitedRows(DBType dbType,
 
 	@Override
 	public String prepareName(String name) {
-		String s = name;
+		String s;
 		s = name.replace('-', '_');
 		s = "[" + s + "]";
 		return s;
@@ -159,7 +159,7 @@ protected String getConnectStringTemplate() {
 	 */
 	public List<String> getColumnNames(String db, String tableName, Connection conn) throws SQLException
 	{
-		List<String> columnNames = new ArrayList<String>(10);
+		List<String> columnNames = new ArrayList<>(10);
 		String schema = null;
 		int idx = tableName.indexOf(".");
 		if(idx != -1) {
@@ -184,7 +184,7 @@ public List<String> getColumnNames(String db, String tableName, Connection conn)
 	 */
 	public List<String> getColumnTypes(String db, String tableName, Connection conn) throws SQLException
 	{
-		List<String> columnTypes = new ArrayList<String>(10);
+		List<String> columnTypes = new ArrayList<>(10);
 		String schema = null;
 		int idx = tableName.indexOf(".");
 		if(idx != -1) {
diff --git a/karma-jdbc/src/main/java/edu/isi/karma/util/SybaseUtil.java b/karma-jdbc/src/main/java/edu/isi/karma/util/SybaseUtil.java
index f102529fe..ccf924501 100644
--- a/karma-jdbc/src/main/java/edu/isi/karma/util/SybaseUtil.java
+++ b/karma-jdbc/src/main/java/edu/isi/karma/util/SybaseUtil.java
@@ -35,7 +35,7 @@ protected String getConnectStringTemplate() {
 	}
 
 	public Connection getConnection(String driver, String url, String username, String pwd) throws SQLException, ClassNotFoundException {
-		Connection localConn = null;
+		Connection localConn;
 		Class.forName(driver);
 		localConn = DriverManager.getConnection(url, username, pwd);
 		return localConn;
@@ -59,7 +59,7 @@ public Connection getConnection(String hostname,
 	public ArrayList<String> getListOfTables(Connection conn) 
 			throws SQLException, ClassNotFoundException {
 		
-		ArrayList<String> tableNames = new ArrayList<String>();
+		ArrayList<String> tableNames = new ArrayList<>();
 		DatabaseMetaData dmd = conn.getMetaData();
 		ResultSet rs = dmd.getTables(null, null, null, new String[] {"TABLE","VIEW"});
 		while (rs.next())
@@ -120,7 +120,7 @@ public ArrayList<ArrayList<String>> getSQLQueryDataForLimitedRows(DBType dbType,
 	
 	@Override
 	public String prepareName(String name) {
-		String s = name;
+		String s;
 		s = name.replace('-', '_');
 		s = "`" + s + "`";
 		return s;
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/core/Context.java b/karma-jsonld/src/main/java/com/github/jsonldjava/core/Context.java
index 636021cc4..72b39f995 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/core/Context.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/core/Context.java
@@ -136,14 +136,14 @@ && getTermDefinition(activeProperty).containsKey("@language") && languageMapping
      */
     public Context parse(Object localContext, List<String> remoteContexts) throws JsonLdError {
         if (remoteContexts == null) {
-            remoteContexts = new ArrayList<String>();
+            remoteContexts = new ArrayList<>();
         }
         // 1. Initialize result to the result of cloning active context.
         Context result = this.clone(); // TODO: clone?
         // 2)
         if (!(localContext instanceof List)) {
             final Object temp = localContext;
-            localContext = new ArrayList<Object>();
+            localContext = new ArrayList<>();
             ((List<Object>) localContext).add(temp);
         }
         // 3)
@@ -237,7 +237,7 @@ else if (context instanceof String) {
             }
 
             // 3.7
-            final Map<String, Boolean> defined = new LinkedHashMap<String, Boolean>();
+            final Map<String, Boolean> defined = new LinkedHashMap<>();
             for (final String key : ((Map<String, Object>) context).keySet()) {
                 if ("@base".equals(key) || "@vocab".equals(key) || "@language".equals(key)) {
                     continue;
@@ -537,7 +537,7 @@ String compactIri(String iri, Object value, boolean relativeToVocab, boolean rev
             }
 
             // 2.2)
-            final List<String> containers = new ArrayList<String>();
+            final List<String> containers = new ArrayList<>();
             // 2.3)
             String typeLanguage = "@language";
             String typeLanguageValue = "@null";
@@ -659,7 +659,7 @@ else if (((Map<String, Object>) value).containsKey("@type")) {
                 typeLanguageValue = "@null";
             }
             // 2.10)
-            final List<String> preferredValues = new ArrayList<String>();
+            final List<String> preferredValues = new ArrayList<>();
             // 2.11)
             if ("@reverse".equals(typeLanguageValue)) {
                 preferredValues.add("@reverse");
@@ -771,7 +771,7 @@ else if (((Map<String, Object>) value).containsKey("@type")) {
      * @return A map from prefix string to IRI string
      */
     public Map<String, String> getPrefixes(boolean onlyCommonPrefixes) {
-        final Map<String, String> prefixes = new LinkedHashMap<String, String>();
+        final Map<String, String> prefixes = new LinkedHashMap<>();
         for (final Map.Entry<String, Object> stringObjectEntry : termDefinitions.entrySet()) {
             if (stringObjectEntry.getKey().contains(":")) {
                 continue;
@@ -807,7 +807,7 @@ public Context clone() {
         final Context rval = (Context) super.clone();
         // TODO: is this shallow copy enough? probably not, but it passes all
         // the tests!
-        rval.termDefinitions = new LinkedHashMap<String, Object>(this.termDefinitions);
+        rval.termDefinitions = new LinkedHashMap<>(this.termDefinitions);
         return rval;
     }
 
@@ -839,7 +839,7 @@ public Map<String, Object> getInverse() {
 
         // create term selections for each mapping in the context, ordererd by
         // shortest and then lexicographically least
-        final List<String> terms = new ArrayList<String>(termDefinitions.keySet());
+        final List<String> terms = new ArrayList<>(termDefinitions.keySet());
         Collections.sort(terms, new Comparator<String>() {
             @Override
             public int compare(String a, String b) {
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdApi.java b/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdApi.java
index 4a6c84e81..72b2a5c30 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdApi.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdApi.java
@@ -148,7 +148,7 @@ public Object compact(Context activeCtx, String activeProperty, Object element,
         // 2)
         if (element instanceof List) {
             // 2.1)
-            final List<Object> result = new ArrayList<Object>();
+            final List<Object> result = new ArrayList<>();
             // 2.2)
             for (final Object item : (List<Object>) element) {
                 // 2.2.1)
@@ -185,7 +185,7 @@ public Object compact(Context activeCtx, String activeProperty, Object element,
             // 6)
             final Map<String, Object> result = newMap();
             // 7)
-            final List<String> keys = new ArrayList<String>(elem.keySet());
+            final List<String> keys = new ArrayList<>(elem.keySet());
             Collections.sort(keys);
             for (final String expandedProperty : keys) {
                 final Object expandedValue = elem.get(expandedProperty);
@@ -201,7 +201,7 @@ public Object compact(Context activeCtx, String activeProperty, Object element,
                     }
                     // 7.1.2)
                     else {
-                        final List<String> types = new ArrayList<String>();
+                        final List<String> types = new ArrayList<>();
                         // 7.1.2.2)
                         for (final String expandedType : (List<String>) expandedValue) {
                             types.add(activeCtx.compactIri(expandedType, true));
@@ -234,14 +234,14 @@ public Object compact(Context activeCtx, String activeProperty, Object element,
                     // 7.2.2)
                     // Note: Must create a new set to avoid modifying the set we
                     // are iterating over
-                    for (final String property : new HashSet<String>(compactedValue.keySet())) {
+                    for (final String property : new HashSet<>(compactedValue.keySet())) {
                         final Object value = compactedValue.get(property);
                         // 7.2.2.1)
                         if (activeCtx.isReverseProperty(property)) {
                             // 7.2.2.1.1)
                             if (("@set".equals(activeCtx.getContainer(property)) || !compactArrays)
                                     && !(value instanceof List)) {
-                                final List<Object> tmp = new ArrayList<Object>();
+                                final List<Object> tmp = new ArrayList<>();
                                 tmp.add(value);
                                 result.put(property, tmp);
                             }
@@ -252,7 +252,7 @@ public Object compact(Context activeCtx, String activeProperty, Object element,
                             // 7.2.2.1.3)
                             else {
                                 if (!(result.get(property) instanceof List)) {
-                                    final List<Object> tmp = new ArrayList<Object>();
+                                    final List<Object> tmp = new ArrayList<>();
                                     tmp.add(result.put(property, tmp));
                                 }
                                 if (value instanceof List) {
@@ -302,11 +302,11 @@ else if ("@index".equals(expandedProperty) || "@value".equals(expandedProperty)
                             expandedValue, true, insideReverse);
                     // 7.5.2)
                     if (!result.containsKey(itemActiveProperty)) {
-                        result.put(itemActiveProperty, new ArrayList<Object>());
+                        result.put(itemActiveProperty, new ArrayList<>());
                     } else {
                         final Object value = result.get(itemActiveProperty);
                         if (!(value instanceof List)) {
-                            final List<Object> tmp = new ArrayList<Object>();
+                            final List<Object> tmp = new ArrayList<>();
                             tmp.add(value);
                             result.put(itemActiveProperty, tmp);
                         }
@@ -337,7 +337,7 @@ else if ("@index".equals(expandedProperty) || "@value".equals(expandedProperty)
                     if (isList) {
                         // 7.6.4.1)
                         if (!(compactedItem instanceof List)) {
-                            final List<Object> tmp = new ArrayList<Object>();
+                            final List<Object> tmp = new ArrayList<>();
                             tmp.add(compactedItem);
                             compactedItem = tmp;
                         }
@@ -392,7 +392,7 @@ else if (result.containsKey(itemActiveProperty)) {
                         } else {
                             List<Object> tmp;
                             if (!(mapObject.get(mapKey) instanceof List)) {
-                                tmp = new ArrayList<Object>();
+                                tmp = new ArrayList<>();
                                 tmp.add(mapObject.put(mapKey, tmp));
                             } else {
                                 tmp = (List<Object>) mapObject.get(mapKey);
@@ -408,7 +408,7 @@ else if (result.containsKey(itemActiveProperty)) {
                                 .equals(expandedProperty))
                                 && (!(compactedItem instanceof List));
                         if (check) {
-                            final List<Object> tmp = new ArrayList<Object>();
+                            final List<Object> tmp = new ArrayList<>();
                             tmp.add(compactedItem);
                             compactedItem = tmp;
                         }
@@ -417,7 +417,7 @@ else if (result.containsKey(itemActiveProperty)) {
                             result.put(itemActiveProperty, compactedItem);
                         } else {
                             if (!(result.get(itemActiveProperty) instanceof List)) {
-                                final List<Object> tmp = new ArrayList<Object>();
+                                final List<Object> tmp = new ArrayList<>();
                                 tmp.add(result.put(itemActiveProperty, tmp));
                             }
                             if (compactedItem instanceof List) {
@@ -492,7 +492,7 @@ public Object expand(Context activeCtx, String activeProperty, Object element)
         // 3)
         if (element instanceof List) {
             // 3.1)
-            final List<Object> result = new ArrayList<Object>();
+            final List<Object> result = new ArrayList<>();
             // 3.2)
             for (final Object item : (List<Object>) element) {
                 // 3.2.1)
@@ -527,7 +527,7 @@ else if (element instanceof Map) {
             // 6)
             Map<String, Object> result = newMap();
             // 7)
-            final List<String> keys = new ArrayList<String>(elem.keySet());
+            final List<String> keys = new ArrayList<>(elem.keySet());
             Collections.sort(keys);
             for (final String key : keys) {
                 final Object value = elem.get(key);
@@ -635,7 +635,7 @@ else if ("@list".equals(expandedProperty)) {
 
                         // NOTE: step not in the spec yet
                         if (!(expandedValue instanceof List)) {
-                            final List<Object> tmp = new ArrayList<Object>();
+                            final List<Object> tmp = new ArrayList<>();
                             tmp.add(expandedValue);
                             expandedValue = tmp;
                         }
@@ -669,7 +669,7 @@ else if ("@reverse".equals(expandedProperty)) {
                                 final Object item = stringObjectEntry.getValue();
                                 // 7.4.11.2.1)
                                 if (!result.containsKey(stringObjectEntry.getKey())) {
-                                    result.put(stringObjectEntry.getKey(), new ArrayList<Object>());
+                                    result.put(stringObjectEntry.getKey(), new ArrayList<>());
                                 }
                                 // 7.4.11.2.2)
                                 if (item instanceof List) {
@@ -708,7 +708,7 @@ else if ("@reverse".equals(expandedProperty)) {
                                     }
                                     // 7.4.11.3.3.1.2)
                                     if (!reverseMap.containsKey(property)) {
-                                        reverseMap.put(property, new ArrayList<Object>());
+                                        reverseMap.put(property, new ArrayList<>());
                                     }
                                     // 7.4.11.3.3.1.3)
                                     ((List<Object>) reverseMap.get(property)).add(item);
@@ -736,14 +736,14 @@ else if ("@explicit".equals(expandedProperty)
                 // 7.5
                 else if ("@language".equals(activeCtx.getContainer(key)) && value instanceof Map) {
                     // 7.5.1)
-                    expandedValue = new ArrayList<Object>();
+                    expandedValue = new ArrayList<>();
                     // 7.5.2)
                     for (final String language : ((Map<String, Object>) value).keySet()) {
                         Object languageValue = ((Map<String, Object>) value).get(language);
                         // 7.5.2.1)
                         if (!(languageValue instanceof List)) {
                             final Object tmp = languageValue;
-                            languageValue = new ArrayList<Object>();
+                            languageValue = new ArrayList<>();
                             ((List<Object>) languageValue).add(tmp);
                         }
                         // 7.5.2.2)
@@ -764,9 +764,9 @@ else if ("@language".equals(activeCtx.getContainer(key)) && value instanceof Map
                 // 7.6)
                 else if ("@index".equals(activeCtx.getContainer(key)) && value instanceof Map) {
                     // 7.6.1)
-                    expandedValue = new ArrayList<Object>();
+                    expandedValue = new ArrayList<>();
                     // 7.6.2)
-                    final List<String> indexKeys = new ArrayList<String>(
+                    final List<String> indexKeys = new ArrayList<>(
                             ((Map<String, Object>) value).keySet());
                     Collections.sort(indexKeys);
                     for (final String index : indexKeys) {
@@ -774,7 +774,7 @@ else if ("@index".equals(activeCtx.getContainer(key)) && value instanceof Map) {
                         // 7.6.2.1)
                         if (!(indexValue instanceof List)) {
                             final Object tmp = indexValue;
-                            indexValue = new ArrayList<Object>();
+                            indexValue = new ArrayList<>();
                             ((List<Object>) indexValue).add(tmp);
                         }
                         // 7.6.2.2)
@@ -804,7 +804,7 @@ else if ("@index".equals(activeCtx.getContainer(key)) && value instanceof Map) {
                             || !((Map<String, Object>) expandedValue).containsKey("@list")) {
                         Object tmp = expandedValue;
                         if (!(tmp instanceof List)) {
-                            tmp = new ArrayList<Object>();
+                            tmp = new ArrayList<>();
                             ((List<Object>) tmp).add(expandedValue);
                         }
                         expandedValue = newMap();
@@ -823,7 +823,7 @@ else if ("@index".equals(activeCtx.getContainer(key)) && value instanceof Map) {
                     // 7.10.3)
                     if (!(expandedValue instanceof List)) {
                         final Object tmp = expandedValue;
-                        expandedValue = new ArrayList<Object>();
+                        expandedValue = new ArrayList<>();
                         ((List<Object>) expandedValue).add(tmp);
                     }
                     // 7.10.4)
@@ -836,7 +836,7 @@ else if ("@index".equals(activeCtx.getContainer(key)) && value instanceof Map) {
                         }
                         // 7.10.4.2)
                         if (!reverseMap.containsKey(expandedProperty)) {
-                            reverseMap.put(expandedProperty, new ArrayList<Object>());
+                            reverseMap.put(expandedProperty, new ArrayList<>());
                         }
                         // 7.10.4.3)
                         if (item instanceof List) {
@@ -851,7 +851,7 @@ else if ("@index".equals(activeCtx.getContainer(key)) && value instanceof Map) {
                 else {
                     // 7.11.1)
                     if (!result.containsKey(expandedProperty)) {
-                        result.put(expandedProperty, new ArrayList<Object>());
+                        result.put(expandedProperty, new ArrayList<>());
                     }
                     // 7.11.2)
                     if (expandedValue instanceof List) {
@@ -903,7 +903,7 @@ else if (result.containsKey("@type")) {
             else if (result.containsKey("@type")) {
                 final Object rtype = result.get("@type");
                 if (!(rtype instanceof List)) {
-                    final List<Object> tmp = new ArrayList<Object>();
+                    final List<Object> tmp = new ArrayList<>();
                     tmp.add(rtype);
                     result.put("@type", tmp);
                 }
@@ -1019,11 +1019,11 @@ void generateNodeMap(Object element, Map<String, Object> nodeMap, String activeG
         if (elem.containsKey("@type")) {
             // 3.1)
             List<String> oldTypes;
-            final List<String> newTypes = new ArrayList<String>();
+            final List<String> newTypes = new ArrayList<>();
             if (elem.get("@type") instanceof List) {
                 oldTypes = (List<String>) elem.get("@type");
             } else {
-                oldTypes = new ArrayList<String>();
+                oldTypes = new ArrayList<>();
                 oldTypes.add((String) elem.get("@type"));
             }
             for (final String item : oldTypes) {
@@ -1055,7 +1055,7 @@ void generateNodeMap(Object element, Map<String, Object> nodeMap, String activeG
         // 5)
         else if (elem.containsKey("@list")) {
             // 5.1)
-            final Map<String, Object> result = newMap("@list", new ArrayList<Object>());
+            final Map<String, Object> result = newMap("@list", new ArrayList<>());
             // 5.2)
             // for (final Object item : (List<Object>) elem.get("@list")) {
             // generateNodeMap(item, nodeMap, activeGraph, activeSubject,
@@ -1153,7 +1153,7 @@ else if (activeProperty != null) {
                 generateNodeMap(elem.remove("@graph"), nodeMap, id, null, null, null);
             }
             // 6.11)
-            final List<String> keys = new ArrayList<String>(elem.keySet());
+            final List<String> keys = new ArrayList<>(elem.keySet());
             Collections.sort(keys);
             for (String property : keys) {
                 final Object value = elem.get(property);
@@ -1163,7 +1163,7 @@ else if (activeProperty != null) {
                 }
                 // 6.11.2)
                 if (!node.containsKey(property)) {
-                    node.put(property, new ArrayList<Object>());
+                    node.put(property, new ArrayList<>());
                 }
                 // 6.11.3)
                 generateNodeMap(value, nodeMap, activeGraph, id, property, null);
@@ -1189,7 +1189,7 @@ private String generateBlankNodeId(String property, Object elem) {
      *
      * http://www.w3.org/TR/json-ld-api/#generate-blank-node-identifier
      */
-    private final Map<String, String> blankNodeIdentifierMap = new LinkedHashMap<String, String>();
+    private final Map<String, String> blankNodeIdentifierMap = new LinkedHashMap<>();
 
     /**
      * Generates a blank node identifier for the given key using the algorithm
@@ -1287,11 +1287,11 @@ public List<Object> frame(Object input, List<Object> frame) throws JsonLdError {
         final FramingContext state = new FramingContext(this.opts);
 
         // use tree map so keys are sotred by default
-        final Map<String, Object> nodes = new TreeMap<String, Object>();
+        final Map<String, Object> nodes = new TreeMap<>();
         generateNodeMap(input, nodes);
         this.nodeMap = (Map<String, Object>) nodes.get("@default");
 
-        final List<Object> framed = new ArrayList<Object>();
+        final List<Object> framed = new ArrayList<>();
         // NOTE: frame validation is done by the function not allowing anything
         // other than list to me passed
         frame(state,
@@ -1329,11 +1329,11 @@ private void frame(FramingContext state, Map<String, Object> nodes, Map<String,
         final Boolean explicicOn = getFrameFlag(frame, "@explicit", state.explicit);
 
         // add matches to output
-        final List<String> ids = new ArrayList<String>(matches.keySet());
+        final List<String> ids = new ArrayList<>(matches.keySet());
         Collections.sort(ids);
         for (final String id : ids) {
             if (property == null) {
-                state.embeds = new LinkedHashMap<String, EmbedNode>();
+                state.embeds = new LinkedHashMap<>();
             }
 
             // start output
@@ -1387,7 +1387,7 @@ private void frame(FramingContext state, Map<String, Object> nodes, Map<String,
 
                 // iterate over subject properties
                 final Map<String, Object> element = (Map<String, Object>) matches.get(id);
-                List<String> props = new ArrayList<String>(element.keySet());
+                List<String> props = new ArrayList<>(element.keySet());
                 Collections.sort(props);
                 for (final String prop : props) {
 
@@ -1416,7 +1416,7 @@ private void frame(FramingContext state, Map<String, Object> nodes, Map<String,
                                 && ((Map<String, Object>) item).containsKey("@list")) {
                             // add empty list
                             final Map<String, Object> list = newMap();
-                            list.put("@list", new ArrayList<Object>());
+                            list.put("@list", new ArrayList<>());
                             addFrameOutput(state, output, prop, list);
 
                             // add list objects
@@ -1460,7 +1460,7 @@ else if (JsonLdUtils.isNodeReference(item)) {
                 }
 
                 // handle defaults
-                props = new ArrayList<String>(frame.keySet());
+                props = new ArrayList<>(frame.keySet());
                 Collections.sort(props);
                 for (final String prop : props) {
                     // skip keywords
@@ -1482,12 +1482,12 @@ else if (JsonLdUtils.isNodeReference(item)) {
                                     def = JsonLdUtils.clone(propertyFrame.get("@default"));
                                 }
                                 if (!(def instanceof List)) {
-                                    final List<Object> tmp = new ArrayList<Object>();
+                                    final List<Object> tmp = new ArrayList<>();
                                     tmp.add(def);
                                     def = tmp;
                                 }
                                 final Map<String, Object> tmp1 = newMap("@preserve", def);
-                                final List<Object> tmp2 = new ArrayList<Object>();
+                                final List<Object> tmp2 = new ArrayList<>();
                                 tmp2.add(tmp1);
                                 output.put(prop, tmp2);
                             }
@@ -1536,7 +1536,7 @@ private static void removeEmbed(FramingContext state, String id) {
         // remove existing embed
         if (JsonLdUtils.isNode(parent)) {
             // replace subject with reference
-            final List<Object> newvals = new ArrayList<Object>();
+            final List<Object> newvals = new ArrayList<>();
             final List<Object> oldvals = (List<Object>) ((Map<String, Object>) parent)
                     .get(property);
             for (final Object v : oldvals) {
@@ -1589,7 +1589,7 @@ private boolean filterNode(FramingContext state, Map<String, Object> node,
             }
             Object nodeTypes = node.get("@type");
             if (nodeTypes == null) {
-                nodeTypes = new ArrayList<Object>();
+                nodeTypes = new ArrayList<>();
             } else if (!(nodeTypes instanceof List)) {
                 throw new JsonLdError(Error.SYNTAX_ERROR, "node @type must be an array");
             }
@@ -1633,7 +1633,7 @@ private static void addFrameOutput(FramingContext state, Object parent, String p
         if (parent instanceof Map) {
             List<Object> prop = (List<Object>) ((Map<String, Object>) parent).get(property);
             if (prop == null) {
-                prop = new ArrayList<Object>();
+                prop = new ArrayList<>();
                 ((Map<String, Object>) parent).put(property, prop);
             }
             prop.add(output);
@@ -1769,7 +1769,7 @@ public boolean isWellFormedListNode() {
 
         // return this node without the usages variable
         public Map<String, Object> serialize() {
-            return new LinkedHashMap<String, Object>(this);
+            return new LinkedHashMap<>(this);
         }
     }
 
@@ -1784,9 +1784,9 @@ public Map<String, Object> serialize() {
      */
     public List<Object> fromRDF(final RDFDataset dataset) throws JsonLdError {
         // 1)
-        final Map<String, NodeMapNode> defaultGraph = new LinkedHashMap<String, NodeMapNode>();
+        final Map<String, NodeMapNode> defaultGraph = new LinkedHashMap<>();
         // 2)
-        final Map<String, Map<String, NodeMapNode>> graphMap = new LinkedHashMap<String, Map<String, NodeMapNode>>();
+        final Map<String, Map<String, NodeMapNode>> graphMap = new LinkedHashMap<>();
         graphMap.put("@default", defaultGraph);
 
         // 3/3.1)
@@ -1797,7 +1797,7 @@ public List<Object> fromRDF(final RDFDataset dataset) throws JsonLdError {
             // 3.2+3.4)
             Map<String, NodeMapNode> nodeMap;
             if (!graphMap.containsKey(name)) {
-                nodeMap = new LinkedHashMap<String, NodeMapNode>();
+                nodeMap = new LinkedHashMap<>();
                 graphMap.put(name, nodeMap);
             } else {
                 nodeMap = graphMap.get(name);
@@ -1869,8 +1869,8 @@ public List<Object> fromRDF(final RDFDataset dataset) throws JsonLdError {
                 String property = usage.property;
                 Map<String, Object> head = usage.value;
                 // 4.3.2)
-                final List<Object> list = new ArrayList<Object>();
-                final List<String> listNodes = new ArrayList<String>();
+                final List<Object> list = new ArrayList<>();
+                final List<String> listNodes = new ArrayList<>();
                 // 4.3.3)
                 while (RDF_REST.equals(property) && node.isWellFormedListNode()) {
                     // 4.3.3.1)
@@ -1917,18 +1917,18 @@ public List<Object> fromRDF(final RDFDataset dataset) throws JsonLdError {
         }
 
         // 5)
-        final List<Object> result = new ArrayList<Object>();
+        final List<Object> result = new ArrayList<>();
         // 6)
-        final List<String> ids = new ArrayList<String>(defaultGraph.keySet());
+        final List<String> ids = new ArrayList<>(defaultGraph.keySet());
         Collections.sort(ids);
         for (final String subject : ids) {
             final NodeMapNode node = defaultGraph.get(subject);
             // 6.1)
             if (graphMap.containsKey(subject)) {
                 // 6.1.1)
-                node.put("@graph", new ArrayList<Object>());
+                node.put("@graph", new ArrayList<>());
                 // 6.1.2)
-                final List<String> keys = new ArrayList<String>(graphMap.get(subject).keySet());
+                final List<String> keys = new ArrayList<>(graphMap.get(subject).keySet());
                 Collections.sort(keys);
                 for (final String s : keys) {
                     final NodeMapNode n = graphMap.get(subject).get(s);
@@ -2039,7 +2039,7 @@ private void replaceBlankNode(Map<String, Object> graph) {
      */
     public Object normalize(Map<String, Object> dataset) throws JsonLdError {
         // create quads and map bnodes to their associated quads
-        final List<Object> quads = new ArrayList<Object>();
+        final List<Object> quads = new ArrayList<>();
         final Map<String, Object> bnodes = newMap();
         for (String graphName : dataset.keySet()) {
             final List<Map<String, Object>> triples = (List<Map<String, Object>>) dataset
@@ -2073,7 +2073,7 @@ public Object normalize(Map<String, Object> dataset) throws JsonLdError {
                         if (!bnodes.containsKey(id)) {
                             bnodes.put(id, new LinkedHashMap<String, List<Object>>() {
                                 {
-                                    put("quads", new ArrayList<Object>());
+                                    put("quads", new ArrayList<>());
                                 }
                             });
                         }
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdProcessor.java b/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdProcessor.java
index 91dddc9d3..a243b60df 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdProcessor.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdProcessor.java
@@ -153,12 +153,12 @@ public static List<Object> expand(Object input, JsonLdOptions opts) throws JsonL
                 && ((Map) expanded).size() == 1) {
             expanded = ((Map<String, Object>) expanded).get("@graph");
         } else if (expanded == null) {
-            expanded = new ArrayList<Object>();
+            expanded = new ArrayList<>();
         }
 
         // normalize to an array
         if (!(expanded instanceof List)) {
-            final List<Object> tmp = new ArrayList<Object>();
+            final List<Object> tmp = new ArrayList<>();
             tmp.add(expanded);
             expanded = tmp;
         }
@@ -215,9 +215,9 @@ public static Object flatten(Object input, Object context, JsonLdOptions opts)
             // TODO: SPEC doesn't specify that this should only be added if it
             // doesn't exists
             if (!entry.containsKey("@graph")) {
-                entry.put("@graph", new ArrayList<Object>());
+                entry.put("@graph", new ArrayList<>());
             }
-            final List<String> keys = new ArrayList<String>(graph.keySet());
+            final List<String> keys = new ArrayList<>(graph.keySet());
             Collections.sort(keys);
             for (final String id : keys) {
                 final Map<String, Object> node = (Map<String, Object>) graph.get(id);
@@ -228,9 +228,9 @@ public static Object flatten(Object input, Object context, JsonLdOptions opts)
 
         }
         // 5)
-        final List<Object> flattened = new ArrayList<Object>();
+        final List<Object> flattened = new ArrayList<>();
         // 6)
-        final List<String> keys = new ArrayList<String>(defaultGraph.keySet());
+        final List<String> keys = new ArrayList<>(defaultGraph.keySet());
         Collections.sort(keys);
         for (final String id : keys) {
             final Map<String, Object> node = (Map<String, Object>) defaultGraph.get(id);
@@ -246,7 +246,7 @@ public static Object flatten(Object input, Object context, JsonLdOptions opts)
             Object compacted = new JsonLdApi(opts).compact(activeCtx, null, flattened,
                     opts.getCompactArrays());
             if (!(compacted instanceof List)) {
-                final List<Object> tmp = new ArrayList<Object>();
+                final List<Object> tmp = new ArrayList<>();
                 tmp.add(compacted);
                 compacted = tmp;
             }
@@ -311,7 +311,7 @@ public static Map<String, Object> frame(Object input, Object frame, JsonLdOption
 
         Object compacted = api.compact(activeCtx, null, framed);
         if (!(compacted instanceof List)) {
-            final List<Object> tmp = new ArrayList<Object>();
+            final List<Object> tmp = new ArrayList<>();
             tmp.add(compacted);
             compacted = tmp;
         }
@@ -493,7 +493,7 @@ public static Object toRDF(Object input, JsonLdTripleCallback callback, JsonLdOp
             if (input instanceof List) {
                 _input = (List<Map<String, Object>>) input;
             } else {
-                _input = new ArrayList<Map<String, Object>>();
+                _input = new ArrayList<>();
                 _input.add((Map<String, Object>) input);
             }
             for (final Map<String, Object> e : _input) {
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdUtils.java b/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdUtils.java
index 9354c5cea..e56d708b8 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdUtils.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/core/JsonLdUtils.java
@@ -111,7 +111,7 @@ static void mergeValue(Map<String, Object> obj, String key, Object value) {
         }
         List<Object> values = (List<Object>) obj.get(key);
         if (values == null) {
-            values = new ArrayList<Object>();
+            values = new ArrayList<>();
             obj.put(key, values);
         }
         if ("@list".equals(key)
@@ -131,7 +131,7 @@ static void mergeCompactedValue(Map<String, Object> obj, String key, Object valu
             return;
         }
         if (!(prop instanceof List)) {
-            final List<Object> tmp = new ArrayList<Object>();
+            final List<Object> tmp = new ArrayList<>();
             tmp.add(prop);
         }
         if (value instanceof List) {
@@ -217,7 +217,7 @@ static void addValue(Map<String, Object> subject, String property, Object value,
 
         if (isArray(value)) {
             if (((List) value).isEmpty() && propertyIsArray && !subject.containsKey(property)) {
-                subject.put(property, new ArrayList<Object>());
+                subject.put(property, new ArrayList<>());
             }
             for (final Object val : (List) value) {
                 addValue(subject, property, val, propertyIsArray, allowDuplicate);
@@ -228,7 +228,7 @@ static void addValue(Map<String, Object> subject, String property, Object value,
 
             // make property an array if value not present or always an array
             if (!isArray(subject.get(property)) && (!hasValue || propertyIsArray)) {
-                final List<Object> tmp = new ArrayList<Object>();
+                final List<Object> tmp = new ArrayList<>();
                 tmp.add(subject.get(property));
                 subject.put(property, tmp);
             }
@@ -241,7 +241,7 @@ static void addValue(Map<String, Object> subject, String property, Object value,
             // add new value as a set or single value
             Object tmp;
             if (propertyIsArray) {
-                tmp = new ArrayList<Object>();
+                tmp = new ArrayList<>();
                 ((List<Object>) tmp).add(value);
             } else {
                 tmp = value;
@@ -347,13 +347,13 @@ private static String prependBase(Object baseobj, String iri) {
      * @throws JsonLdError
      */
     static List<Object> expandLanguageMap(Map<String, Object> languageMap) throws JsonLdError {
-        final List<Object> rval = new ArrayList<Object>();
-        final List<String> keys = new ArrayList<String>(languageMap.keySet());
+        final List<Object> rval = new ArrayList<>();
+        final List<String> keys = new ArrayList<>(languageMap.keySet());
         Collections.sort(keys); // lexicographically sort languages
         for (final String key : keys) {
             List<Object> val;
             if (!isArray(languageMap.get(key))) {
-                val = new ArrayList<Object>();
+                val = new ArrayList<>();
                 val.add(languageMap.get(key));
             } else {
                 val = (List<Object>) languageMap.get(key);
@@ -509,7 +509,7 @@ else if (iri.indexOf("//") != 0) {
     static Object removePreserve(Context ctx, Object input, JsonLdOptions opts) throws JsonLdError {
         // recurse through arrays
         if (isArray(input)) {
-            final List<Object> output = new ArrayList<Object>();
+            final List<Object> output = new ArrayList<>();
             for (final Object i : (List<Object>) input) {
                 final Object result = removePreserve(ctx, i, opts);
                 // drop nulls from arrays
@@ -580,7 +580,7 @@ private static String _join(List<String> list, String joiner) {
      * @return
      */
     private static List<String> _split(String string, String delim) {
-        final List<String> rval = new ArrayList<String>(Arrays.asList(string.split(delim)));
+        final List<String> rval = new ArrayList<>(Arrays.asList(string.split(delim)));
         if (string.endsWith("/")) {
             // javascript .split includes a blank entry if the string ends with
             // the delimiter, java .split does not so we need to add it manually
@@ -713,7 +713,7 @@ static void removeValue(Map<String, Object> subject, String property, Map<String
     static void removeValue(Map<String, Object> subject, String property,
             Map<String, Object> value, boolean propertyIsArray) {
         // filter out value
-        final List<Object> values = new ArrayList<Object>();
+        final List<Object> values = new ArrayList<>();
         if (subject.get(property) instanceof List) {
             for (final Object e : (List) subject.get(property)) {
                 if (!value.equals(e)) {
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/core/NormalizeUtils.java b/karma-jsonld/src/main/java/com/github/jsonldjava/core/NormalizeUtils.java
index 96382edcd..70f50e3dc 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/core/NormalizeUtils.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/core/NormalizeUtils.java
@@ -33,10 +33,10 @@ public NormalizeUtils(List<Object> quads, Map<String, Object> bnodes, UniqueName
 
     // generates unique and duplicate hashes for bnodes
     public Object hashBlankNodes(Collection<String> unnamed_) throws JsonLdError {
-        List<String> unnamed = new ArrayList<String>(unnamed_);
-        List<String> nextUnnamed = new ArrayList<String>();
-        Map<String, List<String>> duplicates = new LinkedHashMap<String, List<String>>();
-        Map<String, String> unique = new LinkedHashMap<String, String>();
+        List<String> unnamed = new ArrayList<>(unnamed_);
+        List<String> nextUnnamed = new ArrayList<>();
+        Map<String, List<String>> duplicates = new LinkedHashMap<>();
+        Map<String, String> unique = new LinkedHashMap<>();
 
         // NOTE: not using the same structure as javascript here to avoid
         // possible stack overflows
@@ -45,7 +45,7 @@ public Object hashBlankNodes(Collection<String> unnamed_) throws JsonLdError {
             if (hui == unnamed.size()) {
                 // done, name blank nodes
                 Boolean named = false;
-                List<String> hashes = new ArrayList<String>(unique.keySet());
+                List<String> hashes = new ArrayList<>(unique.keySet());
                 Collections.sort(hashes);
                 for (final String hash : hashes) {
                     final String bnode = unique.get(hash);
@@ -62,16 +62,16 @@ public Object hashBlankNodes(Collection<String> unnamed_) throws JsonLdError {
                     // hashBlankNodes(unnamed);
                     hui = -1;
                     unnamed = nextUnnamed;
-                    nextUnnamed = new ArrayList<String>();
-                    duplicates = new LinkedHashMap<String, List<String>>();
-                    unique = new LinkedHashMap<String, String>();
+                    nextUnnamed = new ArrayList<>();
+                    duplicates = new LinkedHashMap<>();
+                    unique = new LinkedHashMap<>();
                     continue;
                 }
                 // name the duplicate hash bnods
                 else {
                     // names duplicate hash bnodes
                     // enumerate duplicate hash groups in sorted order
-                    hashes = new ArrayList<String>(duplicates.keySet());
+                    hashes = new ArrayList<>(duplicates.keySet());
                     Collections.sort(hashes);
 
                     // process each group
@@ -79,7 +79,7 @@ public Object hashBlankNodes(Collection<String> unnamed_) throws JsonLdError {
                         if (pgi == hashes.size()) {
                             // done, create JSON-LD array
                             // return createArray();
-                            final List<String> normalized = new ArrayList<String>();
+                            final List<String> normalized = new ArrayList<>();
 
                             // Note: At this point all bnodes in the set of RDF
                             // quads have been
@@ -138,7 +138,7 @@ public Object hashBlankNodes(Collection<String> unnamed_) throws JsonLdError {
 
                         // name each group member
                         final List<String> group = duplicates.get(hashes.get(pgi));
-                        final List<HashResult> results = new ArrayList<HashResult>();
+                        final List<HashResult> results = new ArrayList<>();
                         for (int n = 0;; n++) {
                             if (n == group.size()) {
                                 // name bnodes in hash order
@@ -188,7 +188,7 @@ public int compare(HashResult a, HashResult b) {
                 duplicates.get(hash).add(bnode);
                 nextUnnamed.add(bnode);
             } else if (unique.containsKey(hash)) {
-                final List<String> tmp = new ArrayList<String>();
+                final List<String> tmp = new ArrayList<>();
                 tmp.add(unique.get(hash));
                 tmp.add(bnode);
                 duplicates.put(hash, tmp);
@@ -229,7 +229,7 @@ private static HashResult hashPaths(String id, Map<String, Object> bnodes, Uniqu
             // create SHA-1 digest
             final MessageDigest md = MessageDigest.getInstance("SHA-1");
 
-            final Map<String, List<String>> groups = new LinkedHashMap<String, List<String>>();
+            final Map<String, List<String>> groups = new LinkedHashMap<>();
             List<String> groupHashes;
             final List<Object> quads = (List<Object>) ((Map<String, Object>) bnodes.get(id))
                     .get("quads");
@@ -237,7 +237,7 @@ private static HashResult hashPaths(String id, Map<String, Object> bnodes, Uniqu
             for (int hpi = 0;; hpi++) {
                 if (hpi == quads.size()) {
                     // done , hash groups
-                    groupHashes = new ArrayList<String>(groups.keySet());
+                    groupHashes = new ArrayList<>(groups.keySet());
                     Collections.sort(groupHashes);
                     for (int hgi = 0;; hgi++) {
                         if (hgi == groupHashes.size()) {
@@ -263,7 +263,7 @@ private static HashResult hashPaths(String id, Map<String, Object> bnodes, Uniqu
 
                             // build adjacent path
                             String path = "";
-                            final List<String> recurse = new ArrayList<String>();
+                            final List<String> recurse = new ArrayList<>();
                             for (final String bnode : permutation) {
                                 // use canonical name if available
                                 if (namer.isNamed(bnode)) {
@@ -393,7 +393,7 @@ private static HashResult hashPaths(String id, Map<String, Object> bnodes, Uniqu
                     if (groups.containsKey(groupHash)) {
                         groups.get(groupHash).add(bnode);
                     } else {
-                        final List<String> tmp = new ArrayList<String>();
+                        final List<String> tmp = new ArrayList<>();
                         tmp.add(bnode);
                         groups.put(groupHash, tmp);
                     }
@@ -432,7 +432,7 @@ private static String hashQuads(String id, Map<String, Object> bnodes, UniqueNam
         // serialize all of bnode's quads
         final List<Map<String, Object>> quads = (List<Map<String, Object>>) ((Map<String, Object>) bnodes
                 .get(id)).get("quads");
-        final List<String> nquads = new ArrayList<String>();
+        final List<String> nquads = new ArrayList<>();
         for (int i = 0; i < quads.size(); ++i) {
             nquads.add(toNQuad((RDFDataset.Quad) quads.get(i),
                     quads.get(i).get("name") != null ? (String) ((Map<String, Object>) quads.get(i)
@@ -504,7 +504,7 @@ public Permutator(List<String> list) {
             this.list = (List<String>) JsonLdUtils.clone(list);
             Collections.sort(this.list);
             this.done = false;
-            this.left = new LinkedHashMap<String, Boolean>();
+            this.left = new LinkedHashMap<>();
             for (final String i : this.list) {
                 this.left.put(i, true);
             }
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/core/RDFDataset.java b/karma-jsonld/src/main/java/com/github/jsonldjava/core/RDFDataset.java
index 20f31d49d..45dbddfae 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/core/RDFDataset.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/core/RDFDataset.java
@@ -354,7 +354,7 @@ public boolean isBlankNode() {
     public RDFDataset() {
         super();
         put("@default", new ArrayList<Quad>());
-        context = new LinkedHashMap<String, String>();
+        context = new LinkedHashMap<>();
         // put("@context", context);
     }
 
@@ -534,16 +534,16 @@ public void addQuad(final String subject, final String predicate, final String o
      */
     void graphToRDF(String graphName, Map<String, Object> graph) {
         // 4.2)
-        final List<Quad> triples = new ArrayList<Quad>();
+        final List<Quad> triples = new ArrayList<>();
         // 4.3)
-        final List<String> subjects = new ArrayList<String>(graph.keySet());
+        final List<String> subjects = new ArrayList<>(graph.keySet());
         // Collections.sort(subjects);
         for (final String id : subjects) {
             if (JsonLdUtils.isRelativeIri(id)) {
                 continue;
             }
             final Map<String, Object> node = (Map<String, Object>) graph.get(id);
-            final List<String> properties = new ArrayList<String>(node.keySet());
+            final List<String> properties = new ArrayList<>(node.keySet());
             Collections.sort(properties);
             for (String property : properties) {
                 final List<Object> values;
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/core/RDFDatasetUtils.java b/karma-jsonld/src/main/java/com/github/jsonldjava/core/RDFDatasetUtils.java
index 356f72f9f..06d30d90f 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/core/RDFDatasetUtils.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/core/RDFDatasetUtils.java
@@ -29,10 +29,11 @@ private RDFDatasetUtils() {
      */
     @Deprecated
     static List<Object> graphToRDF(Map<String, Object> graph, UniqueNamer namer) {
-        final List<Object> rval = new ArrayList<Object>();
+        final List<Object> rval = new ArrayList<>();
         for (final Map.Entry<String, Object> stringObjectEntry : graph.entrySet()) {
             final Map<String, Object> node = (Map<String, Object>) stringObjectEntry.getValue();
-            final List<String> properties = new ArrayList<String>(node.keySet());
+            final List<String> properties = new ArrayList<>(node.keySet());
+
             Collections.sort(properties);
             for (String property : properties) {
                 final Object items = node.get(property);
@@ -203,7 +204,7 @@ private static Object objectToRDF(Object item, UniqueNamer namer) {
     }
 
     public static String toNQuads(RDFDataset dataset) {
-        final List<String> quads = new ArrayList<String>();
+        final List<String> quads = new ArrayList<>();
         for (String graphName : dataset.graphNames()) {
             final List<RDFDataset.Quad> triples = dataset.getQuads(graphName);
             if ("@default".equals(graphName)) {
@@ -517,7 +518,7 @@ public static RDFDataset parseNQuads(String input) throws JsonLdError {
 
             // initialise graph in dataset
             if (!dataset.containsKey(name)) {
-                final List<RDFDataset.Quad> tmp = new ArrayList<RDFDataset.Quad>();
+                final List<RDFDataset.Quad> tmp = new ArrayList<>();
                 tmp.add(triple);
                 dataset.put(name, tmp);
             }
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/core/UniqueNamer.java b/karma-jsonld/src/main/java/com/github/jsonldjava/core/UniqueNamer.java
index 4c336034a..25211bf4c 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/core/UniqueNamer.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/core/UniqueNamer.java
@@ -18,7 +18,7 @@ public class UniqueNamer implements Cloneable {
     public UniqueNamer(String prefix) {
         this.prefix = prefix;
         this.counter = 0;
-        this.existing = new LinkedHashMap<String, String>();
+        this.existing = new LinkedHashMap<>();
     }
 
     /**
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/impl/TurtleRDFParser.java b/karma-jsonld/src/main/java/com/github/jsonldjava/impl/TurtleRDFParser.java
index 03ea6ff08..ad41ec35e 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/impl/TurtleRDFParser.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/impl/TurtleRDFParser.java
@@ -101,7 +101,7 @@ private Regex() {
 
     private class State {
         String baseIri = "";
-        Map<String, String> namespaces = new LinkedHashMap<String, String>();
+        Map<String, String> namespaces = new LinkedHashMap<>();
         String curSubject = null;
         String curPredicate = null;
 
@@ -116,7 +116,7 @@ private class State {
         // construction to make
         // first active bnode _:b1
 
-        private final Stack<Map<String, String>> stack = new Stack<Map<String, String>>();
+        private final Stack<Map<String, String>> stack = new Stack<>();
         public boolean expectingBnodeClose = false;
 
         public State(String input) throws JsonLdError {
@@ -299,7 +299,7 @@ else if (state.line.startsWith("(")) {
                 // match predicate
                 match = Regex.PREDICATE.matcher(state.line);
                 if (match.find()) {
-                    String iri = "";
+                    String iri;
                     if (match.group(1) != null) {
                         // matched IRI
                         iri = unescape(match.group(1));
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/impl/TurtleTripleCallback.java b/karma-jsonld/src/main/java/com/github/jsonldjava/impl/TurtleTripleCallback.java
index 64494cb68..22f68b586 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/impl/TurtleTripleCallback.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/impl/TurtleTripleCallback.java
@@ -44,12 +44,12 @@ public Object call(RDFDataset dataset) {
         for (final Entry<String, String> e : dataset.getNamespaces().entrySet()) {
             availableNamespaces.put(e.getValue(), e.getKey());
         }
-        usedNamespaces = new LinkedHashSet<String>();
+        usedNamespaces = new LinkedHashSet<>();
 
         final int tabs = 0;
 
-        final Map<String, List<Object>> refs = new LinkedHashMap<String, List<Object>>();
-        final Map<String, Map<String, List<Object>>> ttl = new LinkedHashMap<String, Map<String, List<Object>>>();
+        final Map<String, List<Object>> refs = new LinkedHashMap<>();
+        final Map<String, Map<String, List<Object>>> ttl = new LinkedHashMap<>();
 
         for (String graphName : dataset.keySet()) {
             final List<RDFDataset.Quad> triples = dataset.getQuads(graphName);
@@ -86,7 +86,7 @@ public Object call(RDFDataset dataset) {
                         if (thisSubject.containsKey(predicate)) {
                             thisPredicate = thisSubject.get(predicate);
                         } else {
-                            thisPredicate = new ArrayList<Object>();
+                            thisPredicate = new ArrayList<>();
                             thisSubject.put(predicate, thisPredicate);
                         }
                         prevPredicate = predicate;
@@ -96,13 +96,13 @@ public Object call(RDFDataset dataset) {
                     if (ttl.containsKey(subject)) {
                         thisSubject = ttl.get(subject);
                     } else {
-                        thisSubject = new LinkedHashMap<String, List<Object>>();
+                        thisSubject = new LinkedHashMap<>();
                         ttl.put(subject, thisSubject);
                     }
                     if (thisSubject.containsKey(predicate)) {
                         thisPredicate = thisSubject.get(predicate);
                     } else {
-                        thisPredicate = new ArrayList<Object>();
+                        thisPredicate = new ArrayList<>();
                         thisSubject.put(predicate, thisPredicate);
                     }
 
@@ -117,7 +117,7 @@ public Object call(RDFDataset dataset) {
                     if (o.startsWith("_:")) {
                         // add ref to o
                         if (!refs.containsKey(o)) {
-                            refs.put(o, new ArrayList<Object>());
+                            refs.put(o, new ArrayList<>());
                         }
                         refs.get(o).add(thisPredicate);
                     }
@@ -126,14 +126,14 @@ public Object call(RDFDataset dataset) {
             }
         }
 
-        final Map<String, List<Object>> collections = new LinkedHashMap<String, List<Object>>();
+        final Map<String, List<Object>> collections = new LinkedHashMap<>();
 
-        final List<String> subjects = new ArrayList<String>(ttl.keySet());
+        final List<String> subjects = new ArrayList<>(ttl.keySet());
         // find collections
         for (final String subj : subjects) {
             Map<String, List<Object>> preds = ttl.get(subj);
             if (preds != null && preds.containsKey(RDF_FIRST)) {
-                final List<Object> col = new ArrayList<Object>();
+                final List<Object> col = new ArrayList<>();
                 collections.put(subj, col);
                 while (true) {
                     final List<Object> first = preds.remove(RDF_FIRST);
@@ -174,7 +174,7 @@ public Object call(RDFDataset dataset) {
             Object object = ttl.remove(stringListEntry.getKey());
             if (collections.containsKey(stringListEntry.getKey())) {
                 object = new LinkedHashMap<String, List<Object>>();
-                final List<Object> tmp = new ArrayList<Object>();
+                final List<Object> tmp = new ArrayList<>();
                 tmp.add(collections.remove(stringListEntry.getKey()));
                 ((HashMap<String, Object>) object).put(COLS_KEY, tmp);
             }
@@ -187,7 +187,7 @@ public Object call(RDFDataset dataset) {
         for (final Entry<String, List<Object>> stringListEntry : collections.entrySet()) {
             final Map<String, List<Object>> subj = ttl.get(stringListEntry.getKey());
             if (!subj.containsKey(COLS_KEY)) {
-                subj.put(COLS_KEY, new ArrayList<Object>());
+                subj.put(COLS_KEY, new ArrayList<>());
             }
             subj.get(COLS_KEY).add(stringListEntry.getValue());
         }
@@ -232,7 +232,7 @@ private String generateObject(Object object, String sep, boolean hasNext, int in
             }
         } else {
             // must be an object
-            final Map<String, Map<String, List<Object>>> tmp = new LinkedHashMap<String, Map<String, List<Object>>>();
+            final Map<String, Map<String, List<Object>>> tmp = new LinkedHashMap<>();
             tmp.put("_:x", (Map<String, List<Object>>) object);
             obj = generateTurtle(tmp, indentation + 1, lineLength, true);
         }
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/utils/JarCacheStorage.java b/karma-jsonld/src/main/java/com/github/jsonldjava/utils/JarCacheStorage.java
index 04977867f..c8e013ba8 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/utils/JarCacheStorage.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/utils/JarCacheStorage.java
@@ -125,7 +125,7 @@ private Enumeration<URL> getResources() throws IOException {
      *
      * @see #getJarCache(URL)
      */
-    protected ConcurrentMap<URI, SoftReference<JsonNode>> jarCaches = new ConcurrentHashMap<URI, SoftReference<JsonNode>>();
+    protected ConcurrentMap<URI, SoftReference<JsonNode>> jarCaches = new ConcurrentHashMap<>();
 
     protected JsonNode getJarCache(URL url) throws IOException, JsonProcessingException {
 
@@ -153,7 +153,7 @@ protected JsonNode getJarCache(URL url) throws IOException, JsonProcessingExcept
         // Use putIfAbsent to ensure concurrent reads do not return different
         // JsonNode objects, for memory management purposes
         final SoftReference<JsonNode> putIfAbsent = jarCaches.putIfAbsent(uri,
-                new SoftReference<JsonNode>(tree));
+                new SoftReference<>(tree));
         if (putIfAbsent != null) {
             final JsonNode returnValue = putIfAbsent.get();
             if (returnValue != null) {
@@ -161,7 +161,7 @@ protected JsonNode getJarCache(URL url) throws IOException, JsonProcessingExcept
             } else {
                 // Force update the reference if the existing reference had
                 // been garbage collected
-                jarCaches.put(uri, new SoftReference<JsonNode>(tree));
+                jarCaches.put(uri, new SoftReference<>(tree));
             }
         }
         return tree;
@@ -173,7 +173,7 @@ protected HttpCacheEntry cacheEntry(URI requestedUri, URL baseURL, JsonNode cach
         log.debug("Cache hit for " + requestedUri);
         log.trace("{}", cacheNode);
 
-        final List<Header> responseHeaders = new ArrayList<Header>();
+        final List<Header> responseHeaders = new ArrayList<>();
         if (!cacheNode.has(HTTP.DATE_HEADER)) {
             responseHeaders
             .add(new BasicHeader(HTTP.DATE_HEADER, DateUtils.formatDate(new Date())));
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/utils/JsonLdUrl.java b/karma-jsonld/src/main/java/com/github/jsonldjava/utils/JsonLdUrl.java
index 464e3892e..de878fa4c 100755
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/utils/JsonLdUrl.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/utils/JsonLdUrl.java
@@ -119,13 +119,13 @@ public static String removeDotSegments(String path, boolean hasAuthority) {
         }
 
         // RFC 3986 5.2.4 (reworked)
-        final List<String> input = new ArrayList<String>(Arrays.asList(path.split("/")));
+        final List<String> input = new ArrayList<>(Arrays.asList(path.split("/")));
         if (path.endsWith("/")) {
             // javascript .split includes a blank entry if the string ends with
             // the delimiter, java .split does not so we need to add it manually
             input.add("");
         }
-        final List<String> output = new ArrayList<String>();
+        final List<String> output = new ArrayList<>();
         for (int i = 0; i < input.size(); i++) {
             if (".".equals(input.get(i)) || ("".equals(input.get(i)) && input.size() - i > 1)) {
                 // input.remove(0);
@@ -189,12 +189,12 @@ else if (iri.indexOf("//") != 0) {
         final JsonLdUrl rel = JsonLdUrl.parse(iri.substring(root.length()));
 
         // remove path segments that match
-        final List<String> baseSegments = new ArrayList<String>(Arrays.asList(base.normalizedPath
+        final List<String> baseSegments = new ArrayList<>(Arrays.asList(base.normalizedPath
                 .split("/")));
         if (base.normalizedPath.endsWith("/")) {
             baseSegments.add("");
         }
-        final List<String> iriSegments = new ArrayList<String>(Arrays.asList(rel.normalizedPath
+        final List<String> iriSegments = new ArrayList<>(Arrays.asList(rel.normalizedPath
                 .split("/")));
         if (rel.normalizedPath.endsWith("/")) {
             iriSegments.add("");
diff --git a/karma-jsonld/src/main/java/com/github/jsonldjava/utils/Obj.java b/karma-jsonld/src/main/java/com/github/jsonldjava/utils/Obj.java
index a7f371de3..9714450ed 100644
--- a/karma-jsonld/src/main/java/com/github/jsonldjava/utils/Obj.java
+++ b/karma-jsonld/src/main/java/com/github/jsonldjava/utils/Obj.java
@@ -11,7 +11,7 @@ public class Obj {
      * @return A new {@link Map} instance.
      */
     public static Map<String, Object> newMap() {
-        return new LinkedHashMap<String, Object>(2, 0.75f);
+        return new LinkedHashMap<>(2, 0.75f);
     }
 
     /**
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/N3Reducer.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/N3Reducer.java
index 237c506e6..59c227759 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/N3Reducer.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/N3Reducer.java
@@ -13,7 +13,7 @@ public class N3Reducer extends Reducer<Text,Text,Text,Text>{
 	protected void reduce(Text key, Iterable<Text> values, Context context) throws IOException, InterruptedException
 	{
 		Iterator<Text> iterator = values.iterator();
-		Set<String> allTriples = new HashSet<String>();
+		Set<String> allTriples = new HashSet<>();
 		while(iterator.hasNext())
 		{
 			String value = iterator.next().toString();
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/N3ToJSONReducer.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/N3ToJSONReducer.java
index da1cd66da..5edb9c3b4 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/N3ToJSONReducer.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/N3ToJSONReducer.java
@@ -24,7 +24,7 @@ public class N3ToJSONReducer extends Reducer<Text,Text,Text,Text>{
 	protected void reduce(Text key, Iterable<Text> values, Context context) throws IOException, InterruptedException
 	{	
 		Iterator<Text> iterator = values.iterator();
-		Set<String> allTriples = new HashSet<String>();
+		Set<String> allTriples = new HashSet<>();
 		while(iterator.hasNext())
 		{
 			String value = iterator.next().toString();
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/XMLElementExtractorMapper.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/XMLElementExtractorMapper.java
index 6d7ac9144..8cef45e14 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/XMLElementExtractorMapper.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/XMLElementExtractorMapper.java
@@ -33,8 +33,8 @@ public void map(Text key, BytesWritable value, Context context) throws IOExcepti
 		String ouputKey = key.toString();
 		reusableKey.set(ouputKey);
 		int start =0;
-		int end = 0;
-		int position = 0;
+		int end;
+		int position;
 		while(-1 != (position = makeSureTagIsValid(value.getBytes(), startTag, start)))
 		{
 			end = rawIndexOf(value.getBytes(), endTag, position);
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CollectJSONObject.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CollectJSONObject.java
index b367f4fa1..e85ace6a2 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CollectJSONObject.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CollectJSONObject.java
@@ -33,7 +33,7 @@ public Text evaluate(Text target, Text path) {
 	}
 
 	protected static String[] splitPath(String aPath) {
-		List<String> levelsCandidates = new LinkedList<String>();
+		List<String> levelsCandidates = new LinkedList<>();
 		int lastSplit = 0;
 		for(int i = 0; i < aPath.length() - 1; i++)
 		{
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CreateJSONFromSequenceFile.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CreateJSONFromSequenceFile.java
index 0b3dad661..35974abf7 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CreateJSONFromSequenceFile.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CreateJSONFromSequenceFile.java
@@ -50,7 +50,7 @@ public static void main(String[] args) throws IOException, InstantiationExceptio
 			String fileName = status.getPath().getName();
 			if (status.getLen() > 0) {
 				String outputFileName = outputPath + File.separator + fileName;// + ".json";
-				List<FSDataOutputStream> streams = new LinkedList<FSDataOutputStream>();
+				List<FSDataOutputStream> streams = new LinkedList<>();
 				if(cl.hasOption("splits"))
 				{
 					Integer splits = Integer.parseInt((String) cl.getOptionValue("splits"));
@@ -71,7 +71,7 @@ public static void main(String[] args) throws IOException, InstantiationExceptio
 	public static void createJSONFromSequenceFileFrom(Path input, List<FSDataOutputStream> streams) throws IOException, InstantiationException, IllegalAccessException, ClassNotFoundException {
 		Path inputPath = input;
 		Configuration conf = new Configuration();
-		List<PrintWriter> fws = new LinkedList<PrintWriter>();
+		List<PrintWriter> fws = new LinkedList<>();
 		for(FSDataOutputStream stream : streams)
 		{
 			PrintWriter fw = new PrintWriter(stream);
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CreateSequenceFile.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CreateSequenceFile.java
index 5146b0ebb..9df243baa 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CreateSequenceFile.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/CreateSequenceFile.java
@@ -7,6 +7,7 @@
 import java.io.InputStreamReader;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 import java.util.concurrent.Callable;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ExecutionException;
@@ -36,8 +37,7 @@
 import edu.isi.karma.rdf.CommandLineArgumentParser;
 
 public class CreateSequenceFile {
-
-	ConcurrentHashMap<String, SequenceFile.Writer> writers = new ConcurrentHashMap<String, SequenceFile.Writer>();
+	Map<String, Writer> writers = new ConcurrentHashMap<>();
 	boolean useKey = true;
 	boolean outputFileName = false;
 	String filePath = null;
@@ -52,7 +52,7 @@ public void execute() throws IOException, FileNotFoundException {
 		ExecutorService executor = Executors.newFixedThreadPool(4);
 		FileSystem hdfs = FileSystem.get(new Configuration());
 		RemoteIterator<LocatedFileStatus> itr = hdfs.listFiles(new Path(filePath), true);
-		List<Future<Boolean>> results = new LinkedList<Future<Boolean>>();
+		List<Future<Boolean>> results = new LinkedList<>();
 		while (itr.hasNext()) {
 			LocatedFileStatus status = itr.next();
 			String fileName = status.getPath().getName();
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/MergeJSON.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/MergeJSON.java
index cf38ce36f..bc899f600 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/MergeJSON.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/MergeJSON.java
@@ -33,7 +33,7 @@ public Text evaluate(Text target, Text source, Text path, Text Id) {
 	}
 	protected static String mergeJSON(String sourceString, String targetString,
 			String pathString, String atId) {
-		List<String> sourceStrings = new LinkedList<String>();
+		List<String> sourceStrings = new LinkedList<>();
 		sourceStrings.add(sourceString);
 		return mergeJSON(sourceStrings, targetString, pathString, atId);
 	}
@@ -43,7 +43,7 @@ protected static String mergeJSON(List<String> sourceStrings, String targetStrin
 		
 		JSONObject rootTargetObj = new JSONObject(targetString);
 		JSONObject targetResult = rootTargetObj;
-		ArrayList<String> pathElements = new ArrayList<String>();
+		ArrayList<String> pathElements = new ArrayList<>();
 		for(String element:array)
 		{
 			if(element.equals("$"))
@@ -74,7 +74,7 @@ private static void mergeJSON(String sourceString, JSONObject targetObj,
 	}
 	protected static List<JSONObject> collectObjectsFromJSONPath(List<String> pathElements, Object targetObj)
 	{
-		List<JSONObject> collectedObjects = new LinkedList<JSONObject>();
+		List<JSONObject> collectedObjects = new LinkedList<>();
 		collectObjectsFromJSONPath(collectedObjects, pathElements, targetObj);
 		return collectedObjects;
 	}
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/SplitAndCleanJSONArray.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/SplitAndCleanJSONArray.java
index 94c74f973..4ecd0e12b 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/SplitAndCleanJSONArray.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/function/SplitAndCleanJSONArray.java
@@ -25,7 +25,7 @@ public Object evaluate(DeferredObject[] arguments) throws HiveException
 	{
 		assert(arguments.length == 1);
 		Text arrayToCleanText = (Text)converters[0].convert(arguments[0].get());
-		List<Text> cleanedValues = new LinkedList<Text>();
+		List<Text> cleanedValues = new LinkedList<>();
 		if(arrayToCleanText == null)
 		{
 			return cleanedValues;
@@ -37,7 +37,7 @@ public Object evaluate(DeferredObject[] arguments) throws HiveException
 				arrayToClean = arrayToClean.substring(1,arrayToClean.length()-1);
 			}
 			
-			Set<Text> cleanedValuesSet = new HashSet<Text>();
+			Set<Text> cleanedValuesSet = new HashSet<>();
 			
 			String[] values = arrayToClean.split(",");
 			for(String value : values)
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/AvroBatchRecordReader.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/AvroBatchRecordReader.java
index e258c2e0c..baa140422 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/AvroBatchRecordReader.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/AvroBatchRecordReader.java
@@ -15,7 +15,7 @@ public class AvroBatchRecordReader<T> extends AvroRecordReaderBase<Text, Text, T
 	protected AvroBatchRecordReader(Schema readerSchema) {
 		super(readerSchema);
 	}
-	List<JSONObject> data = new LinkedList<JSONObject>();
+	List<JSONObject> data = new LinkedList<>();
 
 	@Override
 	public Text getCurrentKey() throws IOException, InterruptedException {
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/CSVBatchRecordReader.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/CSVBatchRecordReader.java
index 984b612c0..bc9c75822 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/CSVBatchRecordReader.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/CSVBatchRecordReader.java
@@ -23,7 +23,7 @@ public class CSVBatchRecordReader
 	recordReader;
 	protected String header = null;
 	private LongWritable key = null;
-	List<String> data = new LinkedList<String>();
+	List<String> data = new LinkedList<>();
 	private static final int batchSize = 10000;
 	public CSVBatchRecordReader()
 			throws IOException {
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/SequenceFileAsJSONRecordBatchReader.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/SequenceFileAsJSONRecordBatchReader.java
index 0761adb0f..21a9c0728 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/SequenceFileAsJSONRecordBatchReader.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/inputformat/SequenceFileAsJSONRecordBatchReader.java
@@ -23,12 +23,12 @@ public class SequenceFileAsJSONRecordBatchReader
 	private final SequenceFileRecordReader<WritableComparable<?>, Writable>
 	sequenceFileRecordReader;
 
-	List<JSONObject> data = new LinkedList<JSONObject>();
+	List<JSONObject> data = new LinkedList<>();
 	private static final int batchSize = 10000;
 	public SequenceFileAsJSONRecordBatchReader()
 			throws IOException {
 		sequenceFileRecordReader =
-				new SequenceFileRecordReader<WritableComparable<?>, Writable>();
+				new SequenceFileRecordReader<>();
 	}
 
 	public void initialize(InputSplit split, TaskAttemptContext context)
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/Neo4jCSVGenerator.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/Neo4jCSVGenerator.java
index eaf04a653..2fa6defdc 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/Neo4jCSVGenerator.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/Neo4jCSVGenerator.java
@@ -134,8 +134,8 @@ public class Neo4jCSVGenerator {
 //	}
 	
 	private static void printUsage() {
-		List<String> parameters = new ArrayList<String>();
-		List<String> descriptions = new ArrayList<String>();
+		List<String> parameters = new ArrayList<>();
+		List<String> descriptions = new ArrayList<>();
 		
 		parameters.add("-base");   
 		descriptions.add("path of the base folder, default is \".\"");
@@ -185,7 +185,7 @@ public static void main(String[] args) {
 			}
 		}
 		
-		HashMap<String, String> arguments = new HashMap<String, String>();
+		HashMap<String, String> arguments = new HashMap<>();
 		for (int i = 0; i < args.length; i+=2) {
 			if ( i + 1 < args.length) {
 				arguments.put(args[i].trim().toLowerCase(), args[i+1].trim());
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/TripleMapper.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/TripleMapper.java
index 9b37d424f..d382383f0 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/TripleMapper.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/TripleMapper.java
@@ -28,7 +28,7 @@ public void map(Text key, Text value, Context context)
 			triple = triple.substring(0, triple.length() - 5) + " .";
 		}
 
-		List<String> list = new ArrayList<String>();
+		List<String> list = new ArrayList<>();
 		Matcher m = Pattern.compile("([^\"]\\S*|\".+?\")\\s*").matcher(triple);
 		while (m.find())
 			list.add(m.group(1));
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/TripleReducer.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/TripleReducer.java
index 4ae523f66..e7e78a58e 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/TripleReducer.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/tripleparser/TripleReducer.java
@@ -29,7 +29,7 @@ public void reduce(Text key, Iterable<NullWritable> values, Context context)
 		String target;
 		
 		String object = parts[2]; 
-		String literalValue = "";
+		String literalValue;
 		
 		String prefix = "Literal:";
 		if (object.startsWith(prefix)) { // object is literal
diff --git a/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestJSONMapReduce.java b/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestJSONMapReduce.java
index 165a0fee5..260c664c6 100644
--- a/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestJSONMapReduce.java
+++ b/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestJSONMapReduce.java
@@ -66,13 +66,13 @@ public void testMapDisableNesting() throws IOException {
 	@Test
 	public void testReduce() throws IOException 
 	{
-		List<Pair<Text,List<Text>>> inputs = new LinkedList<Pair<Text,List<Text>>>();
+		List<Pair<Text,List<Text>>> inputs = new LinkedList<>();
 
-		List<Text> jasonTriples = new LinkedList<Text>();
+		List<Text> jasonTriples = new LinkedList<>();
 		jasonTriples.add(new Text(IOUtils.toString(TestN3MapReduce.class.getClassLoader().getResourceAsStream("jason.json"))));
 		jasonTriples.add(new Text(IOUtils.toString(TestN3MapReduce.class.getClassLoader().getResourceAsStream("jason3.json"))));
 
-		inputs.add(new Pair<Text,List<Text>>(new Text("http://lod.isi.edu/cs548/person/Slepicka"), jasonTriples));
+		inputs.add(new Pair<>(new Text("http://lod.isi.edu/cs548/person/Slepicka"), jasonTriples));
 		reduceDriver.withAllOutput(getPairsFromFile("output/jason.output.json"));
 		reduceDriver.withAll(inputs);
 		reduceDriver.runTest();
diff --git a/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestJSONMapReduceMultiRoots.java b/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestJSONMapReduceMultiRoots.java
index b25d228b5..9ce87779d 100644
--- a/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestJSONMapReduceMultiRoots.java
+++ b/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestJSONMapReduceMultiRoots.java
@@ -57,7 +57,7 @@ public void testMultiRoot() throws URISyntaxException, IOException{
 		
 		JSONArray jObj = new JSONArray(IOUtils.toString(TestJSONMapReduceMultiRoots.class.getClassLoader().getResourceAsStream("data/peoplev2.json")));
 		
-		List<Pair<Writable,Text>> inputs = new ArrayList<Pair<Writable,Text>>();
+		List<Pair<Writable,Text>> inputs = new ArrayList<>();
 		
 		for(int i=0;i<jObj.length();i++){
 			inputs.add(new Pair<Writable,Text>(new Text(jObj.getJSONObject(i).getString("url")), new Text(jObj.getString(i))));
diff --git a/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestN3MapReduce.java b/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestN3MapReduce.java
index e88678451..1a9b65f84 100644
--- a/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestN3MapReduce.java
+++ b/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestN3MapReduce.java
@@ -71,11 +71,11 @@ public void testMapWithBadInputTypeSpecified() throws IOException, URISyntaxExce
 	@Test
 	public void testReduce() throws IOException 
 	{
-		List<Pair<Text,List<Text>>> inputs = new LinkedList<Pair<Text,List<Text>>>();
-		List<Pair<Text,Text>> outputs = new LinkedList<Pair<Text,Text>>();
+		List<Pair<Text,List<Text>>> inputs = new LinkedList<>();
+		List<Pair<Text,Text>> outputs = new LinkedList<>();
 
-		List<Text> jasonTriples = new LinkedList<Text>();
-		List<Text> sufjanTriples = new LinkedList<Text>();
+		List<Text> jasonTriples = new LinkedList<>();
+		List<Text> sufjanTriples = new LinkedList<>();
 		jasonTriples.add(new Text("<http://ex.com/jason> foaf:firstName \"Jason\" ."));
 		jasonTriples.add(new Text("<http://ex.com/jason> foaf:lastName \"Slepicka\" ."));
 		jasonTriples.add(new Text("<http://ex.com/jason> foaf:lastName \"Slepicka\" ."));
@@ -85,11 +85,11 @@ public void testReduce() throws IOException
 		sufjanTriples.add(new Text("<http://ex.com/sufjan> foaf:lastName \"Slepicka\" ."));
 
 
-		inputs.add(new Pair<Text, List<Text>>(new Text("<http://ex.com/jason>"), jasonTriples));
-		inputs.add(new Pair<Text, List<Text>>(new Text("<http://ex.com/sufjan>"), sufjanTriples));
+		inputs.add(new Pair<>(new Text("<http://ex.com/jason>"), jasonTriples));
+		inputs.add(new Pair<>(new Text("<http://ex.com/sufjan>"), sufjanTriples));
 		reduceDriver.withAll(inputs);
-		outputs.add(new Pair<Text, Text>(new Text("<http://ex.com/jason>"), new Text("<http://ex.com/jason> foaf:lastName \"Slepicka\" .\n<http://ex.com/jason> foaf:firstName \"Jason\" .\n")));
-		outputs.add(new Pair<Text, Text>(new Text("<http://ex.com/sufjan>"), new Text("<http://ex.com/sufjan> foaf:lastName \"Slepicka\" .\n<http://ex.com/sufjan> foaf:firstName \"Sufjan\" .\n")));
+		outputs.add(new Pair<>(new Text("<http://ex.com/jason>"), new Text("<http://ex.com/jason> foaf:lastName \"Slepicka\" .\n<http://ex.com/jason> foaf:firstName \"Jason\" .\n")));
+		outputs.add(new Pair<>(new Text("<http://ex.com/sufjan>"), new Text("<http://ex.com/sufjan> foaf:lastName \"Slepicka\" .\n<http://ex.com/sufjan> foaf:firstName \"Sufjan\" .\n")));
 		reduceDriver.addAllOutput(outputs);
 		reduceDriver.runTest();
 
diff --git a/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestRDFMapReduce.java b/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestRDFMapReduce.java
index 2e0614528..d3c600b69 100644
--- a/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestRDFMapReduce.java
+++ b/karma-mr/src/test/java/edu/isi/karma/mapreduce/driver/TestRDFMapReduce.java
@@ -30,13 +30,13 @@ public List<Pair<Text,Text>> getPairsFromFile(String file) throws IOException
 	{
 		String fileText = IOUtils.toString(TestJSONMapReduce.class.getClassLoader().getResourceAsStream(file));
 		String[] serializedPairs = fileText.split("\\)(\r\n|\n)\\(");
-		List<Pair<Text,Text>> pairs = new LinkedList<Pair<Text,Text>>();
+		List<Pair<Text,Text>> pairs = new LinkedList<>();
 		for(String serializedPair : serializedPairs)
 		{
 			int firstComma = serializedPair.indexOf(",");
 			String key = serializedPair.substring(serializedPair.startsWith("(")?1: 0, firstComma);
 			String value = serializedPair.substring(firstComma + 2, serializedPair.length()-(serializedPair.endsWith(")")? 1:0));
-			pairs.add(new Pair<Text,Text>(new Text(key), new Text(value)));
+			pairs.add(new Pair<>(new Text(key), new Text(value)));
 		}
 		return pairs;
 	}
@@ -44,7 +44,7 @@ public List<Pair<Writable,Text>> getNullTextPairsFromFile(String file) throws IO
 	{
 		String fileText = IOUtils.toString(TestJSONMapReduce.class.getClassLoader().getResourceAsStream(file));
 		String[] values = fileText.split("(\r\n|\n)");
-		List<Pair<Writable,Text>> pairs = new LinkedList<Pair<Writable,Text>>();
+		List<Pair<Writable,Text>> pairs = new LinkedList<>();
 		for(String value : values)
 		{
 			pairs.add(new Pair<Writable,Text>(NullWritable.get(), new Text(value)));
@@ -54,16 +54,16 @@ public List<Pair<Writable,Text>> getNullTextPairsFromFile(String file) throws IO
 	public List<Pair<Text,List<Text>>> getReducerPairsFromFile(String file) throws IOException
 	{
 		List<Pair<Text, Text>> unsplitPairs = this.getPairsFromFile(file);
-		List<Pair<Text, List<Text>>> splitPairs = new LinkedList<Pair<Text, List<Text>>>();
+		List<Pair<Text, List<Text>>> splitPairs = new LinkedList<>();
 		for(Pair<Text, Text> unsplitPair : unsplitPairs)
 		{
-			List<Text> splitValues = new LinkedList<Text>();
+			List<Text> splitValues = new LinkedList<>();
 			String [] splits = unsplitPair.getSecond().toString().split("(\r\n|\n)");
 			for(String split : splits)
 			{
 				splitValues.add(new Text(split));
 			}
-			splitPairs.add(new Pair<Text,List<Text>>(unsplitPair.getFirst(), splitValues));
+			splitPairs.add(new Pair<>(unsplitPair.getFirst(), splitValues));
 			
 		}
 		return splitPairs;
diff --git a/karma-offline/src/main/java/edu/isi/karma/rdf/BaseRDFImpl.java b/karma-offline/src/main/java/edu/isi/karma/rdf/BaseRDFImpl.java
index 08ee0c4d7..a5a830a74 100644
--- a/karma-offline/src/main/java/edu/isi/karma/rdf/BaseRDFImpl.java
+++ b/karma-offline/src/main/java/edu/isi/karma/rdf/BaseRDFImpl.java
@@ -10,6 +10,7 @@
 import java.io.StringWriter;
 import java.net.MalformedURLException;
 import java.util.HashMap;
+import java.util.Map;
 import java.util.Properties;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -36,7 +37,7 @@ public abstract class BaseRDFImpl implements Serializable {
     protected boolean hasHeader = false;
     boolean readKarmaConfig = false;
     protected JSONArray jKarmaConfig = null;
-    protected HashMap<String, Pattern> urlPatterns=null;
+    protected Map<String, Pattern> urlPatterns=null;
     protected boolean disableNesting = false;
     public BaseRDFImpl(String propertyPath) {
         try {
diff --git a/karma-offline/src/main/java/edu/isi/karma/rdf/GenericRDFGenerator.java b/karma-offline/src/main/java/edu/isi/karma/rdf/GenericRDFGenerator.java
index 210acc328..9961da89c 100644
--- a/karma-offline/src/main/java/edu/isi/karma/rdf/GenericRDFGenerator.java
+++ b/karma-offline/src/main/java/edu/isi/karma/rdf/GenericRDFGenerator.java
@@ -78,10 +78,10 @@ public GenericRDFGenerator() {
 	
 	public GenericRDFGenerator(String selectionName) {
 		super(selectionName);
-		this.modelIdentifiers = new ConcurrentHashMap<String, R2RMLMappingIdentifier>();
-		this.readModelParsers = new ConcurrentHashMap<String, WorksheetR2RMLJenaModelParser>();
-		this.contextCache = new HashMap<String, JSONObject>();
-		this.contextIdentifiers = new HashMap<String, ContextIdentifier>();
+		this.modelIdentifiers = new ConcurrentHashMap<>();
+		this.readModelParsers = new ConcurrentHashMap<>();
+		this.contextCache = new HashMap<>();
+		this.contextIdentifiers = new HashMap<>();
 	}
 
 	public void addModel(R2RMLMappingIdentifier modelIdentifier) {
diff --git a/karma-offline/src/main/java/edu/isi/karma/rdf/OfflineRdfGenerator.java b/karma-offline/src/main/java/edu/isi/karma/rdf/OfflineRdfGenerator.java
index 9c946af84..1ede83b75 100644
--- a/karma-offline/src/main/java/edu/isi/karma/rdf/OfflineRdfGenerator.java
+++ b/karma-offline/src/main/java/edu/isi/karma/rdf/OfflineRdfGenerator.java
@@ -130,7 +130,7 @@ public class OfflineRdfGenerator {
 	public OfflineRdfGenerator(CommandLine cl)
 	{
 
-		this.writers = new LinkedList<KR2RMLRDFWriter>();
+		this.writers = new LinkedList<>();
 		parseCommandLineOptions(cl);	
 	}
 
@@ -243,10 +243,10 @@ else if(inputDelimiter.equalsIgnoreCase("space"))
 			rootTripleMap = "";
 		}
 		if (killTripleMap == null) {
-			this.killTripleMap = new ArrayList<String>();
+			this.killTripleMap = new ArrayList<>();
 		}
 		else {
-			this.killTripleMap = new ArrayList<String>(Arrays.asList(killTripleMap.split(",")));
+			this.killTripleMap = new ArrayList<>(Arrays.asList(killTripleMap.split(",")));
 			int size = this.killTripleMap.size();
 			for (int i = 0; i < size; i++) {
 				String t = this.killTripleMap.remove(0);
@@ -254,10 +254,10 @@ else if(inputDelimiter.equalsIgnoreCase("space"))
 			}
 		}
 		if (stopTripleMap == null) {
-			this.stopTripleMap = new ArrayList<String>();
+			this.stopTripleMap = new ArrayList<>();
 		}
 		else {
-			this.stopTripleMap = new ArrayList<String>(Arrays.asList(stopTripleMap.split(",")));
+			this.stopTripleMap = new ArrayList<>(Arrays.asList(stopTripleMap.split(",")));
 			int size = this.stopTripleMap.size();
 			for (int i = 0; i < size; i++) {
 				String t = this.stopTripleMap.remove(0);
@@ -265,10 +265,10 @@ else if(inputDelimiter.equalsIgnoreCase("space"))
 			}
 		}
 		if (POMToKill == null) {
-			this.POMToKill = new ArrayList<String>();
+			this.POMToKill = new ArrayList<>();
 		}
 		else {
-			this.POMToKill = new ArrayList<String>(Arrays.asList(POMToKill.split(",")));
+			this.POMToKill = new ArrayList<>(Arrays.asList(POMToKill.split(",")));
 			int size = this.POMToKill.size();
 			for (int i = 0; i < size; i++) {
 				String t = this.POMToKill.remove(0);
diff --git a/karma-offline/src/main/java/edu/isi/karma/rdf/RDFGeneratorRequest.java b/karma-offline/src/main/java/edu/isi/karma/rdf/RDFGeneratorRequest.java
index 8cb48fcf6..c847f357c 100644
--- a/karma-offline/src/main/java/edu/isi/karma/rdf/RDFGeneratorRequest.java
+++ b/karma-offline/src/main/java/edu/isi/karma/rdf/RDFGeneratorRequest.java
@@ -23,7 +23,7 @@ public class RDFGeneratorRequest {
 	private InputStream inputStream;
 	private InputType dataType;
 	private boolean addProvenance;
-	private List<KR2RMLRDFWriter> writers = new LinkedList<KR2RMLRDFWriter>();
+	private List<KR2RMLRDFWriter> writers = new LinkedList<>();
 	private String modelName;
 	private String sourceName;
 	private String contextName;
@@ -42,9 +42,9 @@ public RDFGeneratorRequest(String modelName, String sourceName)
 		this.inputFile = null;
 		this.inputStream = null;
 		this.contextName = null;
-		tripleMapToKill = new ArrayList<String>();
-		tripleMapToStop = new ArrayList<String>();
-		POMToKill = new ArrayList<String>();
+		tripleMapToKill = new ArrayList<>();
+		tripleMapToStop = new ArrayList<>();
+		POMToKill = new ArrayList<>();
 		contextParameters = null;
 	}
 
diff --git a/karma-offline/src/main/java/edu/isi/karma/rdf/bloom/AddSameAsToBloomFilters.java b/karma-offline/src/main/java/edu/isi/karma/rdf/bloom/AddSameAsToBloomFilters.java
index b7103b443..1ac88e0f1 100644
--- a/karma-offline/src/main/java/edu/isi/karma/rdf/bloom/AddSameAsToBloomFilters.java
+++ b/karma-offline/src/main/java/edu/isi/karma/rdf/bloom/AddSameAsToBloomFilters.java
@@ -45,9 +45,9 @@ public static void main(String[] args) throws KarmaException, IOException, Parse
         triplestoreURL = (String) cl.getOptionValue("triplestoreurl");
         predicate = (String) cl.getOptionValue("predicate");
         BloomFilterTripleStoreUtil utilObj = new BloomFilterTripleStoreUtil();
-        Set<String> predicates = new HashSet<String>();
+        Set<String> predicates = new HashSet<>();
         predicates.add(predicate);
-        List<String> predicateObjectMaps = new ArrayList<String>();
+        List<String> predicateObjectMaps = new ArrayList<>();
         for (String t : utilObj.getPredicatesForParentTriplesMapsWithSameClass(triplestoreURL, null, predicates).get("refObjectMaps")) {
         	predicateObjectMaps.addAll(Arrays.asList(t.split(",")));
         }
@@ -55,7 +55,7 @@ public static void main(String[] args) throws KarmaException, IOException, Parse
         	predicateObjectMaps.addAll(Arrays.asList(t.split(",")));
         }
         Map<String, String> serializedmapping = utilObj.getBloomFiltersForMaps(triplestoreURL, null, predicateObjectMaps);
-        Map<String, KR2RMLBloomFilter> mapping = new HashMap<String, KR2RMLBloomFilter>();
+        Map<String, KR2RMLBloomFilter> mapping = new HashMap<>();
         
         for (Entry<String, String> entry : serializedmapping.entrySet()) {
         	String key = entry.getKey();
diff --git a/karma-offline/src/main/java/edu/isi/karma/rdf/bloom/CombineBloomFiltersFromRDF.java b/karma-offline/src/main/java/edu/isi/karma/rdf/bloom/CombineBloomFiltersFromRDF.java
index 2781c8b99..ae3f7a491 100644
--- a/karma-offline/src/main/java/edu/isi/karma/rdf/bloom/CombineBloomFiltersFromRDF.java
+++ b/karma-offline/src/main/java/edu/isi/karma/rdf/bloom/CombineBloomFiltersFromRDF.java
@@ -49,8 +49,8 @@ public static void main(String[] args) throws IOException, KarmaException {
         if (filepath == null || triplestoreURL == null || context == null)
         	return;
 		File file = new File(filepath);
-		Map<String, BloomFilterWorker> workers = new HashMap<String, BloomFilterWorker>();
-		Map<String, KR2RMLBloomFilter> bfs = new HashMap<String, KR2RMLBloomFilter>();
+		Map<String, BloomFilterWorker> workers = new HashMap<>();
+		Map<String, KR2RMLBloomFilter> bfs = new HashMap<>();
 		long start = System.currentTimeMillis();
 		if (file.isDirectory()) {
 			File[] files = file.listFiles();
@@ -89,11 +89,11 @@ public static void main(String[] args) throws IOException, KarmaException {
 			}
 			BloomFilterTripleStoreUtil utilObj = new BloomFilterTripleStoreUtil();
 			Set<String> triplemaps = bfs.keySet();
-			Map<String, String> bloomfilterMapping = new HashMap<String, String>();
+			Map<String, String> bloomfilterMapping = new HashMap<>();
 			bloomfilterMapping.putAll(utilObj.getBloomFiltersForMaps(triplestoreURL, context, triplemaps));
 			utilObj.updateTripleStoreWithBloomFilters(bfs, bloomfilterMapping, triplestoreURL, context);
 			System.out.println("process time: " + (System.currentTimeMillis() - start));
-			Map<String, String> verification = new HashMap<String, String>();
+			Map<String, String> verification = new HashMap<>();
 			verification.putAll(utilObj.getBloomFiltersForMaps(triplestoreURL, context, triplemaps));
 			boolean verify = true;
 			for (Entry<String, String> entry : verification.entrySet()) {
diff --git a/karma-offline/src/test/java/edu/isi/karma/rdf/TestAvroRDFGenerator.java b/karma-offline/src/test/java/edu/isi/karma/rdf/TestAvroRDFGenerator.java
index 4be5a72fe..91cfb4d7e 100644
--- a/karma-offline/src/test/java/edu/isi/karma/rdf/TestAvroRDFGenerator.java
+++ b/karma-offline/src/test/java/edu/isi/karma/rdf/TestAvroRDFGenerator.java
@@ -90,7 +90,7 @@ public void testGenerateAvro1() {
 			StringWriter sw = new StringWriter();
 			PrintWriter pw = new PrintWriter(sw);
 			JSONKR2RMLRDFWriter jsonwriter = new JSONKR2RMLRDFWriter(pw);
-			List<KR2RMLRDFWriter> writers = new LinkedList<KR2RMLRDFWriter>();
+			List<KR2RMLRDFWriter> writers = new LinkedList<>();
 			writers.add(arvowriter);
 			writers.add(jsonwriter);
 			RDFGeneratorRequest request = new RDFGeneratorRequest("people-model", filename);
@@ -124,7 +124,7 @@ public void testGenerateAvro2() {
 			StringWriter sw = new StringWriter();
 			PrintWriter pw = new PrintWriter(sw);
 			JSONKR2RMLRDFWriter jsonwriter = new JSONKR2RMLRDFWriter(pw);
-			List<KR2RMLRDFWriter> writers = new LinkedList<KR2RMLRDFWriter>();
+			List<KR2RMLRDFWriter> writers = new LinkedList<>();
 			writers.add(arvowriter);
 			writers.add(jsonwriter);
 			RDFGeneratorRequest request = new RDFGeneratorRequest("people-avro-model", filename);
@@ -136,11 +136,11 @@ public void testGenerateAvro2() {
 			rdfGen.generateRDF(request);
 			fos.flush();
 			fos.close();
-			DataFileReader<Void> schemareader = new DataFileReader<Void>(tempAvroOutput, new GenericDatumReader<Void>());
+			DataFileReader<Void> schemareader = new DataFileReader<>(tempAvroOutput, new GenericDatumReader<Void>());
 			Schema schema = schemareader.getSchema();
 			
 			DatumReader<GenericRecord> datumReader = new GenericDatumReader<>(schema);
-			DataFileReader<GenericRecord> reader = new DataFileReader<GenericRecord>(tempAvroOutput, datumReader);
+			DataFileReader<GenericRecord> reader = new DataFileReader<>(tempAvroOutput, datumReader);
 			
 			int count = 0;
 			while(reader.hasNext())
@@ -162,8 +162,8 @@ public void testGenerateAvro3() {
 		try {
 			Parser parser = new Schema.Parser();
 			Schema peopleSchema = parser.parse(new File(getTestResource("people.avsc").toURI()));
-			GenericDatumWriter<GenericRecord> datumWriter = new GenericDatumWriter<GenericRecord>(peopleSchema);
-			DataFileWriter<GenericRecord> dfw = new DataFileWriter<GenericRecord>(datumWriter);
+			GenericDatumWriter<GenericRecord> datumWriter = new GenericDatumWriter<>(peopleSchema);
+			DataFileWriter<GenericRecord> dfw = new DataFileWriter<>(datumWriter);
 			File tempfile = File.createTempFile("karma-people", "avro");
 			
 			tempfile.deleteOnExit();
@@ -194,7 +194,7 @@ public void testGenerateAvro4() {
 			StringWriter sw = new StringWriter();
 			PrintWriter pw = new PrintWriter(sw);
 			JSONKR2RMLRDFWriter jsonwriter = new JSONKR2RMLRDFWriter(pw);
-			List<KR2RMLRDFWriter> writers = new LinkedList<KR2RMLRDFWriter>();
+			List<KR2RMLRDFWriter> writers = new LinkedList<>();
 			writers.add(arvowriter);
 			writers.add(jsonwriter);
 			RDFGeneratorRequest request = new RDFGeneratorRequest("people-array.avro-model", filename);
@@ -230,7 +230,7 @@ private GenericRecord generatePersonRecord(Schema peopleSchema, String name, Str
 		record.put("twitter", twitter);
 		Schema userIdArraySchema = peopleSchema.getField("userids").schema();
 		Schema userIdSchema = userIdArraySchema.getElementType();
-		GenericArray<GenericRecord> useridrecords = new GenericData.Array<GenericRecord>(userIdArraySchema, new LinkedList<GenericRecord>());
+		GenericArray<GenericRecord> useridrecords = new GenericData.Array<>(userIdArraySchema, new LinkedList<GenericRecord>());
 		
 		Random r = new Random();
 		for(int j = 0; j < 2; j++)
diff --git a/karma-offline/src/test/java/edu/isi/karma/rdf/TestJSONDagRDFGenerator.java b/karma-offline/src/test/java/edu/isi/karma/rdf/TestJSONDagRDFGenerator.java
index 1146a742f..9b1a703bc 100644
--- a/karma-offline/src/test/java/edu/isi/karma/rdf/TestJSONDagRDFGenerator.java
+++ b/karma-offline/src/test/java/edu/isi/karma/rdf/TestJSONDagRDFGenerator.java
@@ -98,7 +98,7 @@ private void testMenus() {
 	@Test
 	public void testGenerateRDFThreaded()
 	{
-		List<Future<Boolean>> results = new LinkedList<Future<Boolean>>();
+		List<Future<Boolean>> results = new LinkedList<>();
 		ExecutorService es  = Executors.newFixedThreadPool(4);
 		for(int i = 0; i < 4 ; i++)
 		{
diff --git a/karma-offline/src/test/java/edu/isi/karma/rdf/TestRdfGenerator.java b/karma-offline/src/test/java/edu/isi/karma/rdf/TestRdfGenerator.java
index 0fca691a7..824733349 100644
--- a/karma-offline/src/test/java/edu/isi/karma/rdf/TestRdfGenerator.java
+++ b/karma-offline/src/test/java/edu/isi/karma/rdf/TestRdfGenerator.java
@@ -81,13 +81,13 @@ protected void generateRdfFile(File inputFile, InputType inputType, String model
 
 	protected List<KR2RMLRDFWriter> createBasicWriter(PrintWriter pw) {
 		N3KR2RMLRDFWriter writer = new N3KR2RMLRDFWriter(new URIFormatter(), pw);
-		List<KR2RMLRDFWriter> writers = new LinkedList<KR2RMLRDFWriter>();
+		List<KR2RMLRDFWriter> writers = new LinkedList<>();
 		writers.add(writer);
 		return writers;
 	}
 	
 	protected HashSet<String> getFileContent(File file) {
-		HashSet<String> hashSet = new HashSet<String>();
+		HashSet<String> hashSet = new HashSet<>();
 		
 		try {
 			String encoding = EncodingDetector.detect(file);
@@ -112,7 +112,7 @@ protected HashSet<String> getFileContent(File file) {
 	
 
 	protected HashSet<String> getHashSet(String[] array) {
-		HashSet<String> hashSet = new HashSet<String>();
+		HashSet<String> hashSet = new HashSet<>();
 		for (int i = 0; i < array.length; i++) {
 			String line = array[i].trim();
 			if (line.length() > 0)
diff --git a/karma-offline/src/test/java/edu/isi/karma/rdf/TestSelection.java b/karma-offline/src/test/java/edu/isi/karma/rdf/TestSelection.java
index bcda3192a..5af0eebe7 100644
--- a/karma-offline/src/test/java/edu/isi/karma/rdf/TestSelection.java
+++ b/karma-offline/src/test/java/edu/isi/karma/rdf/TestSelection.java
@@ -129,7 +129,7 @@ public void testSelection2() throws IOException, KarmaException {
 		worksheet.getSuperSelectionManager().defineSelection("test").addSelection(sel);
 		StringWriter sw = new StringWriter();
 		PrintWriter pw = new PrintWriter(sw);
-		List<KR2RMLRDFWriter> writers = new ArrayList<KR2RMLRDFWriter>();
+		List<KR2RMLRDFWriter> writers = new ArrayList<>();
 		writers.add(new N3KR2RMLRDFWriter(new URIFormatter(), pw));
 		WorksheetR2RMLJenaModelParser modelParser = new WorksheetR2RMLJenaModelParser(modelIdentifier);
 		applyHistoryToWorksheet(workspace, worksheet, modelParser.parse());
@@ -153,10 +153,10 @@ private void applyHistoryToWorksheet(Workspace workspace, Worksheet worksheet,
 		WorksheetCommandHistoryExecutor wchr = new WorksheetCommandHistoryExecutor(worksheet.getId(), workspace);
 		try
 		{
-			List<CommandTag> tags = new ArrayList<CommandTag>();
+			List<CommandTag> tags = new ArrayList<>();
 			tags.add(CommandTag.Transformation);
 			
-			List<CommandTag> ignoreTags = new ArrayList<CommandTag>();
+			List<CommandTag> ignoreTags = new ArrayList<>();
 			ignoreTags.add(CommandTag.IgnoreInBatch);
 			
 			wchr.executeCommandsByTags(tags, 
diff --git a/karma-spark/src/main/java/edu/isi/karma/spark/JSONReducerDriver.java b/karma-spark/src/main/java/edu/isi/karma/spark/JSONReducerDriver.java
index 03d1c5a0a..418176bbb 100644
--- a/karma-spark/src/main/java/edu/isi/karma/spark/JSONReducerDriver.java
+++ b/karma-spark/src/main/java/edu/isi/karma/spark/JSONReducerDriver.java
@@ -111,7 +111,7 @@ public Tuple2<String, String> call(Tuple2<String, String> tuple)
 					key = obj.getString("@id");
 				}
 				
-				return new Tuple2<String, String>(key, value);
+				return new Tuple2<>(key, value);
 			}
 		}).reduceByKey(new Function2<String, String, String>() {
 			
diff --git a/karma-storm/src/main/java/edu/isi/karma/storm/bolt/KarmaReducerBolt.java b/karma-storm/src/main/java/edu/isi/karma/storm/bolt/KarmaReducerBolt.java
index bdcfbe23f..6f92e25de 100644
--- a/karma-storm/src/main/java/edu/isi/karma/storm/bolt/KarmaReducerBolt.java
+++ b/karma-storm/src/main/java/edu/isi/karma/storm/bolt/KarmaReducerBolt.java
@@ -39,7 +39,7 @@ public KarmaReducerBolt(Set<String> models, boolean outputId)
 	@Override
 	public void prepare(Map globalConf, TopologyContext context,
 			OutputCollector collector) {
-		allJsonToMerge = new HashMap<String, JSONToMerge>();
+		allJsonToMerge = new HashMap<>();
 		this.collector = collector;
 		
 	}
diff --git a/karma-storm/src/main/java/edu/isi/karma/storm/function/JSONToMerge.java b/karma-storm/src/main/java/edu/isi/karma/storm/function/JSONToMerge.java
index e1cebf003..0eb5fc2b3 100644
--- a/karma-storm/src/main/java/edu/isi/karma/storm/function/JSONToMerge.java
+++ b/karma-storm/src/main/java/edu/isi/karma/storm/function/JSONToMerge.java
@@ -16,9 +16,9 @@ public class JSONToMerge {
 	protected List<Tuple> tuplesToAck;
 	public JSONToMerge(int expectedSourcesToMerge)
 	{
-		this.tuplesToAck = new LinkedList<Tuple>();
+		this.tuplesToAck = new LinkedList<>();
 		this.expectedSourcesToMerge = expectedSourcesToMerge;
-		this.jsonBySource = new HashMap<String, String>(expectedSourcesToMerge);
+		this.jsonBySource = new HashMap<>(expectedSourcesToMerge);
 		this.lastUpdateTimestamp = System.currentTimeMillis();
 	}
 
diff --git a/karma-storm/src/test/java/edu/isi/karma/storm/TestBasicKarmaTopology.java b/karma-storm/src/test/java/edu/isi/karma/storm/TestBasicKarmaTopology.java
index d4e14fc76..2e1ead3c9 100644
--- a/karma-storm/src/test/java/edu/isi/karma/storm/TestBasicKarmaTopology.java
+++ b/karma-storm/src/test/java/edu/isi/karma/storm/TestBasicKarmaTopology.java
@@ -76,14 +76,14 @@ public void run(ILocalCluster cluster) throws Exception {
 							
 							builder.setBolt("karma-generate-json", new KarmaBolt(basicKarmaBoltProperties, null)).shuffleGrouping("karma-json-spout");
 
-							Set<String> sources = new HashSet<String>();
+							Set<String> sources = new HashSet<>();
 							sources.add(source);
 							KarmaReducerBolt reducerBolt = new KarmaReducerBolt(sources);
 							builder.setBolt("karma-reducer-json", reducerBolt).fieldsGrouping("karma-generate-json", new Fields("id"));
 							
 							String inputs = IOUtils.toString(getTestResource("input/people.json"));
 							JSONArray array = new JSONArray(inputs);
-							List<Values> values = new LinkedList<Values>();
+							List<Values> values = new LinkedList<>();
 							for(int i = 0; i < array.length(); i++)
 							{
 								JSONObject obj = array.getJSONObject(i);
diff --git a/karma-typer/src/main/java/edu/isi/karma/semantictypes/evaluation/EvaluateMRR.java b/karma-typer/src/main/java/edu/isi/karma/semantictypes/evaluation/EvaluateMRR.java
index 865fa5dba..43dce3147 100644
--- a/karma-typer/src/main/java/edu/isi/karma/semantictypes/evaluation/EvaluateMRR.java
+++ b/karma-typer/src/main/java/edu/isi/karma/semantictypes/evaluation/EvaluateMRR.java
@@ -16,6 +16,7 @@
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
+import java.util.List;
 
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
@@ -59,7 +60,8 @@ public static MRRItem calculateMRRValue(String inputFile, Integer numberOfCandid
 
 					// Reading correct Semantic labels and storing in an array list 
 					JSONArray userArray = (JSONArray) obj.get("userSemanticTypes");
-					ArrayList <String> correctTypes= new ArrayList<String>();
+					List<String> correctTypes= new ArrayList<>();
+
 					for(Object o1: userArray){
 						JSONObject userObj= (JSONObject) o1;
 						correctTypes.add(userObj.get("domain").toString() + userObj.get("type").toString());
@@ -67,7 +69,8 @@ public static MRRItem calculateMRRValue(String inputFile, Integer numberOfCandid
 
 					// Reading learned Semantic labels and storing in an array list 
 					JSONArray learnedArray = (JSONArray) obj.get("learnedSemanticTypes");
-					ArrayList <String> learnedTypes= new ArrayList<String>();
+					List<String> learnedTypes= new ArrayList<>();
+
 					if (learnedArray != null)
 					for(Object o2: learnedArray){
 						JSONObject learnedObj= (JSONObject) o2;
@@ -162,7 +165,8 @@ public static JSONObject calculateMRR(String inputFile){
 
 					// Reading correct Semantic labels and storing in an array list 
 					JSONArray userArray = (JSONArray) obj.get("userSemanticTypes");
-					ArrayList <String> correctTypes= new ArrayList<String>();
+					List<String> correctTypes= new ArrayList<>();
+
 					for(Object o1: userArray){
 						JSONObject userObj= (JSONObject) o1;
 						correctTypes.add(userObj.get("domain").toString() + userObj.get("type").toString());
@@ -170,7 +174,8 @@ public static JSONObject calculateMRR(String inputFile){
 
 					// Reading learned Semantic labels and storing in an array list 
 					JSONArray learnedArray = (JSONArray) obj.get("learnedSemanticTypes");
-					ArrayList <String> learnedTypes= new ArrayList<String>();
+					List<String> learnedTypes= new ArrayList<>();
+
 					for(Object o2: learnedArray){
 						JSONObject learnedObj= (JSONObject) o2;
 						learnedTypes.add(learnedObj.get("domain").toString() + learnedObj.get("type").toString()); 
diff --git a/karma-typer/src/main/java/edu/isi/karma/semantictypes/numeric/KSTest.java b/karma-typer/src/main/java/edu/isi/karma/semantictypes/numeric/KSTest.java
index 3263f1a26..b9d796ac7 100644
--- a/karma-typer/src/main/java/edu/isi/karma/semantictypes/numeric/KSTest.java
+++ b/karma-typer/src/main/java/edu/isi/karma/semantictypes/numeric/KSTest.java
@@ -14,7 +14,7 @@ public class KSTest {
 	public List<SemanticTypeLabel> predictLabelsForColumn(int numPredictions, Map<String, List<Double>> trainingLabelToExamplesMap,
 			List<Double> testExamples) {
 
-		List<SemanticTypeLabel> sortedPredictions = new ArrayList<SemanticTypeLabel>();	// descending order of p-Value
+		List<SemanticTypeLabel> sortedPredictions = new ArrayList<>();	// descending order of p-Value
 		KolmogorovSmirnovTest test = new KolmogorovSmirnovTest();
 	  	double pValue;
 	    
diff --git a/karma-typer/src/main/java/edu/isi/karma/semantictypes/typinghandler/HybridSTModelHandler.java b/karma-typer/src/main/java/edu/isi/karma/semantictypes/typinghandler/HybridSTModelHandler.java
index 4f6c9a697..c8324cbfd 100644
--- a/karma-typer/src/main/java/edu/isi/karma/semantictypes/typinghandler/HybridSTModelHandler.java
+++ b/karma-typer/src/main/java/edu/isi/karma/semantictypes/typinghandler/HybridSTModelHandler.java
@@ -90,7 +90,7 @@ public synchronized boolean addType(String label, List<String> examples) {
 		}
 		
 		label = label.trim();
-		ArrayList<String> cleanedExamples = new ArrayList<String>();
+		ArrayList<String> cleanedExamples = new ArrayList<>();
 		countNumeric = cleanedExamplesList(examples, cleanedExamples);
 		
 		// making sure that the condition where the examples list is not empty
@@ -288,7 +288,7 @@ public List<SemanticTypeLabel> predictType(List<String> examples,
 				logger.warn("KS test called");
 				
 				// extract distributions for each trained semantic label
-				Map<String, List<Double>> trainingLabelToExamplesMap = new HashMap<String, List<Double>>();
+				Map<String, List<Double>> trainingLabelToExamplesMap = new HashMap<>();
 				try {
 					IndexReader reader = DirectoryReader.open(FSDirectory.open(new File(
 							getIndexDirectory(isNumeric))));
@@ -296,7 +296,7 @@ public List<SemanticTypeLabel> predictType(List<String> examples,
 						for (int i=0; i<reader.maxDoc(); i++) {
 						    Document doc = reader.document(i);
 						    String label = doc.get(Indexer.LABEL_FIELD_NAME);
-						    List<Double> exampleList = new ArrayList<Double>(); 
+						    List<Double> exampleList = new ArrayList<>(); 
 						    String content = doc.get(Indexer.CONTENT_FIELD_NAME);
 						    for (String example: content.split(" ")) {
 						    	try {
@@ -316,7 +316,7 @@ public List<SemanticTypeLabel> predictType(List<String> examples,
 				}				
 
 				// extract test column distribution
-				List<Double> testExamples = new ArrayList<Double>();
+				List<Double> testExamples = new ArrayList<>();
 				for (String example: examples) {
 					if(example.matches(numericRegEx)) {
 						try {
@@ -467,7 +467,7 @@ private String getSanitizedString(String unsanitizedString) {
 	 * @return Returns list of allowed Characters
 	 */
 	private ArrayList<String> allowedCharacters() {
-		ArrayList<String> allowed = new ArrayList<String>();
+		ArrayList<String> allowed = new ArrayList<>();
 		// Adding A-Z
 		for (int c = 65; c <= 90; c++) {
 			allowed.add(String.valueOf((char) c));
@@ -503,7 +503,7 @@ private ArrayList<String> allowedCharacters() {
 
 	public List<String> cleanExamplesNumeric(List<String> exampleList)
 	{
-		List<String> cleanedExamples = new ArrayList<String>();
+		List<String> cleanedExamples = new ArrayList<>();
 		Iterator<String> itr = exampleList.iterator();
 		while(itr.hasNext()) {
 			String ex = itr.next();
diff --git a/karma-typer/src/main/java/edu/isi/karma/semantictypes/typinghandler/LuceneBasedSTModelHandler.java b/karma-typer/src/main/java/edu/isi/karma/semantictypes/typinghandler/LuceneBasedSTModelHandler.java
index 39f66e35c..d0abae695 100644
--- a/karma-typer/src/main/java/edu/isi/karma/semantictypes/typinghandler/LuceneBasedSTModelHandler.java
+++ b/karma-typer/src/main/java/edu/isi/karma/semantictypes/typinghandler/LuceneBasedSTModelHandler.java
@@ -70,7 +70,7 @@ public synchronized boolean addType(String label, List<String> examples) {
 		}
 		
 		label = label.trim();
-		ArrayList<String> cleanedExamples = new ArrayList<String>();
+		ArrayList<String> cleanedExamples = new ArrayList<>();
 		cleanedExamplesList(examples, cleanedExamples);
 		
 		// making sure that the condition where the examples list is not empty
@@ -317,7 +317,7 @@ private String getSanitizedString(String unsanitizedString) {
 	 * @return Returns list of allowed Characters
 	 */
 	private ArrayList<String> allowedCharacters() {
-		ArrayList<String> allowed = new ArrayList<String>();
+		ArrayList<String> allowed = new ArrayList<>();
 		// Adding A-Z
 		for (int c = 65; c <= 90; c++) {
 			allowed.add(String.valueOf((char) c));
diff --git a/karma-util/src/main/java/edu/isi/karma/imp/excel/ToCSV.java b/karma-util/src/main/java/edu/isi/karma/imp/excel/ToCSV.java
index fa54decca..66b1d5fcd 100644
--- a/karma-util/src/main/java/edu/isi/karma/imp/excel/ToCSV.java
+++ b/karma-util/src/main/java/edu/isi/karma/imp/excel/ToCSV.java
@@ -163,7 +163,7 @@ public class ToCSV {
 	private DataFormatter formatter = null;
 	private FormulaEvaluator evaluator = null;
 	private String separator = null;
-	private List<File> csvFiles = new ArrayList<File>();
+	private List<File> csvFiles = new ArrayList<>();
 
 	private static final String CSV_FILE_EXTENSION = ".csv";
 	private static final String DEFAULT_SEPARATOR = ",";
@@ -329,8 +329,8 @@ public void convertExcelToCSV(String strSource, String strDestination,
 			IllegalArgumentException, InvalidFormatException {
 		File source = new File(strSource);
 		File destination = new File(strDestination);
-		File[] filesList = null;
-		String destinationFilename = null;
+		File[] filesList;
+		String destinationFilename;
 
 		// Check that the source file/folder exists.
 		if (!source.exists()) {
@@ -475,10 +475,10 @@ private void openWorkbook(InputStream is) throws InvalidFormatException, IOExcep
 	 */
 	private void convertToCSV(File destination, String excelFileName)
 			throws FileNotFoundException, IOException {
-		Sheet sheet = null;
-		Row row = null;
-		int lastRowNum = 0;
-		this.csvData = new ArrayList<ArrayList<String>>();
+		Sheet sheet;
+		Row row;
+		int lastRowNum;
+		this.csvData = new ArrayList<>();
 
 		logger.info("Converting files contents to CSV format.");
 
@@ -520,9 +520,9 @@ private void convertToCSV(File destination, String excelFileName)
 
 	private void convertWorksheetToCSV(int wsIdx, Writer writer) throws IOException {
 		Sheet sheet = this.workbook.getSheetAt(wsIdx);
-		Row row = null;
-		int lastRowNum = 0;
-		this.csvData = new ArrayList<ArrayList<String>>();
+		Row row;
+		int lastRowNum;
+		this.csvData = new ArrayList<>();
 		this.maxRowWidth = -1;
 		
 		if(sheet != null && sheet.getPhysicalNumberOfRows() > 0) {
@@ -581,11 +581,11 @@ private void convertWorksheetToCSV(int wsIdx, Writer writer) throws IOException
 	 */
 	private void saveCSVFile(File file) throws FileNotFoundException,
 			IOException {
-		FileWriter fw = null;
+		FileWriter fw;
 		BufferedWriter bw = null;
-		ArrayList<String> line = null;
-		StringBuffer buffer = null;
-		String csvLineElement = null;
+		ArrayList<String> line;
+		StringBuffer buffer;
+		String csvLineElement;
 		try {
 
 			logger.info("Saving the CSV file [" + file.getName() + "]");
@@ -660,9 +660,9 @@ private void saveCSVFile(File file) throws FileNotFoundException,
 	 *            an Excel workbook.
 	 */
 	private void rowToCSV(Row row) {
-		Cell cell = null;
-		int lastCellNum = 0;
-		ArrayList<String> csvLine = new ArrayList<String>();
+		Cell cell;
+		int lastCellNum;
+		ArrayList<String> csvLine = new ArrayList<>();
 
 		// Check to ensure that a row was recovered from the sheet as it is
 		// possible that one or more rows between other populated rows could be
@@ -740,7 +740,7 @@ private void rowToCSV(Row row) {
 	 *         mark characters correctly escaped.
 	 */
 	private String escapeEmbeddedCharacters(String field) {
-		StringBuffer buffer = null;
+		StringBuffer buffer;
 
 		// If the fields contents should be formatted to confrom with Excel's
 		// convention....
@@ -810,7 +810,7 @@ public static void main(String[] args) {
 		// with matching names but different extensions - Test.xls and Test.xlsx
 		// for example - then the CSV file generated from one will overwrite
 		// that generated from the other.
-		ToCSV converter = null;
+		ToCSV converter;
 		try {
 			converter = new ToCSV();
 			if (args.length == 2) {
diff --git a/karma-util/src/main/java/edu/isi/karma/kr2rml/ErrorReport.java b/karma-util/src/main/java/edu/isi/karma/kr2rml/ErrorReport.java
index fdb80b122..681d9f7c7 100644
--- a/karma-util/src/main/java/edu/isi/karma/kr2rml/ErrorReport.java
+++ b/karma-util/src/main/java/edu/isi/karma/kr2rml/ErrorReport.java
@@ -40,7 +40,7 @@ public enum Priority {
 	}
 	
 	public ErrorReport() {
-		this.reports = new HashSet<ReportMessage>();
+		this.reports = new HashSet<>();
 	}
 	
 	public void addReportMessage(ReportMessage errMsg) {
diff --git a/karma-util/src/main/java/edu/isi/karma/util/RandomGUID.java b/karma-util/src/main/java/edu/isi/karma/util/RandomGUID.java
index 023da3ae0..781d26a15 100644
--- a/karma-util/src/main/java/edu/isi/karma/util/RandomGUID.java
+++ b/karma-util/src/main/java/edu/isi/karma/util/RandomGUID.java
@@ -166,7 +166,7 @@ private void getRandomGUID(boolean secure) {
 
         try {
             long time = System.currentTimeMillis();
-            long rand = 0;
+            long rand;
 
             if (secure) {
                 rand = mySecureRand.nextLong();
diff --git a/karma-util/src/main/java/edu/isi/karma/webserver/ContextParametersRegistry.java b/karma-util/src/main/java/edu/isi/karma/webserver/ContextParametersRegistry.java
index 89afc32ac..acae76983 100644
--- a/karma-util/src/main/java/edu/isi/karma/webserver/ContextParametersRegistry.java
+++ b/karma-util/src/main/java/edu/isi/karma/webserver/ContextParametersRegistry.java
@@ -6,7 +6,7 @@
 public class ContextParametersRegistry {
 	private static ContextParametersRegistry singleton = new ContextParametersRegistry();
 
-	private final ConcurrentHashMap<String, ServletContextParameterMap> karmaHomeToContextParameters = new ConcurrentHashMap<String, ServletContextParameterMap>();
+	private final ConcurrentHashMap<String, ServletContextParameterMap> karmaHomeToContextParameters = new ConcurrentHashMap<>();
 
 	public static ContextParametersRegistry getInstance() {
 		return singleton;
diff --git a/karma-util/src/main/java/edu/isi/karma/webserver/ServletContextParameterMap.java b/karma-util/src/main/java/edu/isi/karma/webserver/ServletContextParameterMap.java
index 3901a819a..2e1bdc326 100644
--- a/karma-util/src/main/java/edu/isi/karma/webserver/ServletContextParameterMap.java
+++ b/karma-util/src/main/java/edu/isi/karma/webserver/ServletContextParameterMap.java
@@ -29,7 +29,7 @@
 import org.slf4j.LoggerFactory;
 
 public class ServletContextParameterMap {
-	private Map<ContextParameter, String> valuesMap = new ConcurrentHashMap<ContextParameter, String>();
+	private Map<ContextParameter, String> valuesMap = new ConcurrentHashMap<>();
 
 	protected final String id;
 	
diff --git a/karma-util/src/main/java/edu/isi/karma/webserver/WorkspaceKarmaHomeRegistry.java b/karma-util/src/main/java/edu/isi/karma/webserver/WorkspaceKarmaHomeRegistry.java
index dfb0c5e61..fed23095a 100644
--- a/karma-util/src/main/java/edu/isi/karma/webserver/WorkspaceKarmaHomeRegistry.java
+++ b/karma-util/src/main/java/edu/isi/karma/webserver/WorkspaceKarmaHomeRegistry.java
@@ -6,7 +6,7 @@
 public class WorkspaceKarmaHomeRegistry {
 	private static WorkspaceKarmaHomeRegistry singleton = new WorkspaceKarmaHomeRegistry();
 
-	private final Map<String, String> workspaceToKarmaHome = new ConcurrentHashMap<String, String>();
+	private final Map<String, String> workspaceToKarmaHome = new ConcurrentHashMap<>();
 
 	public static WorkspaceKarmaHomeRegistry getInstance() {
 		return singleton;
diff --git a/karma-web-services/web-services-publish-es/src/main/java/edu/isi/karma/web/services/publish/es/ElasticSearchPublishServlet.java b/karma-web-services/web-services-publish-es/src/main/java/edu/isi/karma/web/services/publish/es/ElasticSearchPublishServlet.java
index d4dcb6253..92f70efe9 100644
--- a/karma-web-services/web-services-publish-es/src/main/java/edu/isi/karma/web/services/publish/es/ElasticSearchPublishServlet.java
+++ b/karma-web-services/web-services-publish-es/src/main/java/edu/isi/karma/web/services/publish/es/ElasticSearchPublishServlet.java
@@ -12,6 +12,7 @@
 import java.security.NoSuchAlgorithmException;
 import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.List;
 
 import javax.servlet.ServletContext;
 import javax.ws.rs.Consumes;
@@ -338,7 +339,8 @@ private RDFGeneratorRequest generateRDFRequest(String modelName, Model model, St
 	public static void initContextParameters(ServletContext ctx, ServletContextParameterMap contextParameters)
 	{
 		Enumeration<?> params = ctx.getInitParameterNames();
-		ArrayList<String> validParams = new ArrayList<String>();
+		List<String> validParams = new ArrayList<>();
+
 		for (ContextParameter param : ContextParameter.values()) {
 			validParams.add(param.name());
 		}
diff --git a/karma-web-services/web-services-rdf/src/main/java/edu/isi/karma/web/services/rdf/RDFGeneratorServlet.java b/karma-web-services/web-services-rdf/src/main/java/edu/isi/karma/web/services/rdf/RDFGeneratorServlet.java
index e64b4f2f7..0c2e9bbc5 100644
--- a/karma-web-services/web-services-rdf/src/main/java/edu/isi/karma/web/services/rdf/RDFGeneratorServlet.java
+++ b/karma-web-services/web-services-rdf/src/main/java/edu/isi/karma/web/services/rdf/RDFGeneratorServlet.java
@@ -289,7 +289,7 @@ else if(formParams.containsKey(FormParameters.RAW_DATA)
 			
 			String r2rmlURI = formParams.getFirst(FormParameters.R2RML_URL);
 			String r2rmlFileName = new File(r2rmlURI).getName();
-	        String contextFileName = null;
+	        String contextFileName;
 	       
 	        if(urlContext == null){
 	        	
@@ -312,7 +312,7 @@ else if(formParams.containsKey(FormParameters.RAW_DATA)
 			JSONTokener token = new JSONTokener(IOUtils.toInputStream(jsonContext)); 
 
 			ContextIdentifier contextId = new ContextIdentifier("generic-context", urlContext);
-			JSONKR2RMLRDFWriter writer =null;
+			JSONKR2RMLRDFWriter writer;
 			if (baseUri != null)
 				 writer = new JSONKR2RMLRDFWriter(pw,baseUri);
 			else
diff --git a/karma-web/src/main/java/edu/isi/karma/linkedapi/server/PostRequestManager.java b/karma-web/src/main/java/edu/isi/karma/linkedapi/server/PostRequestManager.java
index a652f0715..15423995e 100644
--- a/karma-web/src/main/java/edu/isi/karma/linkedapi/server/PostRequestManager.java
+++ b/karma-web/src/main/java/edu/isi/karma/linkedapi/server/PostRequestManager.java
@@ -118,7 +118,7 @@ private String getUrlString(WebService service, Map<String, String> inputAttValu
 		
 		List<Attribute> missingAttributes= null;
 		
-		missingAttributes = new ArrayList<Attribute>();
+		missingAttributes = new ArrayList<>();
 		String url = service.getPopulatedAddress(inputAttValues, missingAttributes);
 		
 		//FIXME: Authentication Data
@@ -166,7 +166,7 @@ public void addStatementsToJenaModel(WebService service, Model model,
 		model.setNsPrefix(Prefixes.RDFS, Namespaces.RDFS);
 		Property rdf_type = model.createProperty(Namespaces.RDF , "type");
 
-		Map<String, Resource> outputVariablesToResource = new HashMap<String, Resource>();
+		Map<String, Resource> outputVariablesToResource = new HashMap<>();
 		String predicateUri = "";
 		String argument1 = "";
 		String argument2 = "";
@@ -297,8 +297,8 @@ public void HandleRequest() throws IOException {
 			this.outputJenaModel.setNsPrefixes(this.inputJenaModel.getNsPrefixMap());
 		}
 		
-		Map<String, String> outputAttNameToAttIds = new HashMap<String, String>();
-		Map<String, String> outputAttValues = new HashMap<String, String>();
+		Map<String, String> outputAttNameToAttIds = new HashMap<>();
+		Map<String, String> outputAttValues = new HashMap<>();
 		
 		if (blankInput) { // service without input parameter
 			String invocationURL = getUrlString(service, new HashMap<String, String>());
diff --git a/karma-web/src/main/java/edu/isi/karma/webserver/RequestController.java b/karma-web/src/main/java/edu/isi/karma/webserver/RequestController.java
index 442c48003..7bc09b640 100644
--- a/karma-web/src/main/java/edu/isi/karma/webserver/RequestController.java
+++ b/karma-web/src/main/java/edu/isi/karma/webserver/RequestController.java
@@ -60,7 +60,7 @@ protected void doPost(HttpServletRequest request, HttpServletResponse response)
 		}
 
 		VWorkspace vWorkspace = VWorkspaceRegistry.getInstance().getVWorkspace(workspaceId);
-		String responseString = "";
+		String responseString;
 		boolean isPreview = Boolean.parseBoolean(request.getParameter("isPreview"));
 		boolean isUserInteraction = Boolean.parseBoolean(request.getParameter("isUserInteraction"));
 		boolean isExecute = Boolean.parseBoolean(request.getParameter("execute"));
diff --git a/karma-web/src/main/java/edu/isi/karma/webserver/ServerStart.java b/karma-web/src/main/java/edu/isi/karma/webserver/ServerStart.java
index 6d6447cb7..d89437951 100644
--- a/karma-web/src/main/java/edu/isi/karma/webserver/ServerStart.java
+++ b/karma-web/src/main/java/edu/isi/karma/webserver/ServerStart.java
@@ -41,7 +41,7 @@ public class ServerStart extends HttpServlet {
 	public static void initContextParameters(ServletContext ctx, ServletContextParameterMap contextParameters)
 	{
 		Enumeration<?> params = ctx.getInitParameterNames();
-		ArrayList<String> validParams = new ArrayList<String>();
+		ArrayList<String> validParams = new ArrayList<>();
 		for (ContextParameter param : ContextParameter.values()) {
 			validParams.add(param.name());
 		}
diff --git a/karma-web/src/main/webapp/css/cleaning.css b/karma-web/src/main/webapp/css/cleaning.css
deleted file mode 100644
index 0003c0b60..000000000
--- a/karma-web/src/main/webapp/css/cleaning.css
+++ /dev/null
@@ -1,118 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-.hover { background-color: #106166; color: #fff; cursor:pointer; }
-.page{ margin:5px;}
-
-
-span.ins {
-	background:#F7BE81;
-}
-span.a0 {
-	color:#1f77b4;
-}
-span.a1 {
-	color:#2ca02c;
-}
-span.a2 {
-	color:#d62728;
-}
-span.a3 {
-	color:#9467bd;
-}
-span.a4 {
-	color:#8c564b;
-}
-span.a5 {
-	color:#e377c2;
-}
-span.a6 {
-	color:#7f7f7f;
-}
-span.a7 {
-	color:#bcbd22;
-}
-span.a8 {
-	color:#17becf;
-}
-span.a9 {
-	color:#6600CC;
-}
-div.cleanExampleDiv {
-/*	border: solid #8C8C8C 1px;*/
-	display: block;
-	min-height: 16px;
-    min-width: 70px;
-	padding-left: 2px;
-}
-
-div.ambExampleDiv {
-/*	border: solid #8C8C8C 1px;*/
-	display: block;
-	min-height: 12px;
-	padding-left: 2px;
-	/*width: 150px;*/
-	background-color:#FDDDDF;
-}
-table.cleaningExampleDivTable td {
-	padding: 0px;
-}
-
-div.cleaningExampleBorderDiv {
-	border: solid #8C8C8C 1px;
-	min-height: 12px;
-	padding-left: 2px;
-}
-
-tr#buttonsAndRuleInfoRow td {
-	font-size: 20px;
-}
-
-
-div.undoEditButton {
-	float:right;
-	display: inline;
-	margin-left: 4px;
-	margin-top: 2px;
-	width: 15px;
-	height: 15px;
-}
-button.closeButton{
-	float:right;
-	display: inline;
-	width: 20px;
-	height: 20px;
-}
-button.editbutton{
-	display:table-cell;
-	vertical-align: middle;
-    text-align: center;
-	float:right;
-	width: 20px;
-	height: 20px;
-}
-.cleaningOverflowDiv {
-	max-height: 150px;
-	overflow: auto;
-}
-.cleaningOverflowDivLarge {
-	max-height: 450px;
-	overflow: auto;
-}
diff --git a/karma-web/src/main/webapp/css/cleaning_1.css b/karma-web/src/main/webapp/css/cleaning_1.css
deleted file mode 100644
index 9e63a7b22..000000000
--- a/karma-web/src/main/webapp/css/cleaning_1.css
+++ /dev/null
@@ -1,176 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * 	http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * 
- * This code was developed by the Information Integration Group as part 
- * of the Karma project at the Information Sciences Institute of the 
- * University of Southern California.  For more information, publications, 
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-span.hover { background-color: #106166; color: #fff; cursor:pointer; }
-span.page{ margin:5px;}
-table#cleaningExamplesTable {
-	border-width: 1px; 
-	border-spacing: 1px; 
-	border-collapse: collapse;
-	width: 680px;
-}
-
-table.info{
-	border:none;
-	font-size: 12px;
-}
-
-table#cleaningExamplesTable td{
-	font-size: 12px;
-	border: solid 1px;
-	height: 15px;
-	padding: 1px;
-	width: 350px;
-}
-table td.ruleResultsValue_begin{
-	font-size: 12px;
-	border: 1px solid;
-	height: 15px;
-	padding: 1px;
-}
-
-table#cleaningExamplesTable td.ruleResultsValue_rest{	
-	border: none;
-}
-table#cleaningExamplesTable button.suggestion{
-   font-size:11px;
-   font-family:Arial,sans-serif;
-   text-align:left;
-   color:#444444;
-   width:90px;
-   background-color:#FDDDDF;
-   border-style:none;
-}
-
-table#infoPanel {
-	visibility:hidden;
-}
-table#cleaningExamplesTable td.noBorder {
-	border: none;
-	width:10px;
-}
-table#cleaningExamplesTable td.noinnerBorder {
-	font-size: 12px;
-	border: none;
-	height: 15px;
-	padding: 1px;
-}
-
-table#infoPanel td.info {
-	font-size: 12px;
-	border: 1px solid;
-}
-table#infoPanel td.heading{
-	font-size:12px;
-	font-weight:900;
-}
-
-table#cleaningExamplesTable td.examplesDivider {
-	width:20px;
-	border: none;
-}
-
-table#cleaningExamplesTable td.cleaningTableHeading {
-	font-weight: 900;
-	padding-bottom:4px;
-}
-
-span.a0 {
-	color:#000000;
-}
-span.a1 {
-	color:#000000;
-}
-span.a2 {
-	color:#000000;
-}
-span.a3 {
-	color:#000000;
-}
-span.a4 {
-	color:#000000;
-}
-span.a5 {
-	color:#000000;
-}
-span.a6 {
-	color:#000000;
-}
-span.a7 {
-	color:#000000;
-}
-span.a8 {
-	color:#000000;
-}
-span.a9 {
-	color:#000000;
-}
-div.cleanExampleDiv {
-/*	border: solid #8C8C8C 1px;*/
-	display: block;
-	min-height: 12px;
-	padding-left: 2px;
-}
-
-div.ambExampleDiv {
-/*	border: solid #8C8C8C 1px;*/
-	display: block;
-	min-height: 12px;
-	padding-left: 2px;
-	/*width: 150px;*/
-	background-color:#FDDDDF;
-}
-table.cleaningExampleDivTable td {
-	padding: 0px;
-}
-
-div.cleaningExampleBorderDiv {
-	border: solid #8C8C8C 1px;
-	min-height: 12px;
-	padding-left: 2px;
-}
-
-tr#buttonsAndRuleInfoRow td {
-	font-size: 20px;
-}
-
-
-div.undoEditButton {
-	float:right;
-	display: inline;
-	margin-left: 4px;
-	margin-top: 2px;
-	width: 15px;
-	height: 15px;
-}
-button.closeButton{
-	float:right;
-	display: inline;
-	width: 15px;
-	height: 15px;
-}
-button.editbutton{
-	display:table-cell;
-	vertical-align: middle;
-    text-align: center;
-	float:right;
-	width: 15px;
-	height: 15px;
-}
diff --git a/karma-web/src/main/webapp/index.jsp b/karma-web/src/main/webapp/index.jsp
index 0fb7550aa..e050c8b7e 100755
--- a/karma-web/src/main/webapp/index.jsp
+++ b/karma-web/src/main/webapp/index.jsp
@@ -67,7 +67,6 @@ and related projects, please see: http://www.isi.edu/integration
         <link rel="stylesheet" type="text/css" href="./css/ServiceImport.css?<jsp:include page='version.jsp' />" />
         <link rel="stylesheet" type="text/css" href="./css/headerParsingExample.css?<jsp:include page='version.jsp' />" />
         <link rel="stylesheet" type="text/css" href="./css/AlignmentHeaders.css?<jsp:include page='version.jsp' />" />
-        <link rel="stylesheet" type="text/css" href="./css/cleaning.css?<jsp:include page='version.jsp' />" />
         <link rel="stylesheet" type="text/css" href="./css/alignment.css?<jsp:include page='version.jsp' />" />
         <link rel="stylesheet" type="text/css" href="./css/d3.css?<jsp:include page='version.jsp' />" />
         <link rel="stylesheet" type="text/css" href="./css/main.css?<jsp:include page='version.jsp' />" />
@@ -352,7 +351,6 @@ and related projects, please see: http://www.isi.edu/integration
         <script type="text/javascript" src="js/databaseImportDialog.js?<jsp:include page='version.jsp' />"></script>
         <script type="text/javascript" src="js/d3-model-manager.js?<jsp:include page='version.jsp' />"></script>
         <script type="text/javascript" src="js/fileImport.js?<jsp:include page='version.jsp' />"></script>
-        <script type="text/javascript" src="js/cleaning.js?<jsp:include page='version.jsp' />"></script>
         <script type="text/javascript" src="js/reset-options.js?<jsp:include page='version.jsp' />"></script>
         <script type="text/javascript" src="js/cleaning-charts.js?<jsp:include page='version.jsp' />"></script>
         <script type="text/javascript" src="js/showModel.js?<jsp:include page='version.jsp' />"></script>
diff --git a/karma-web/src/main/webapp/js/ServerResponseObjectParsing.js b/karma-web/src/main/webapp/js/ServerResponseObjectParsing.js
index a2656eea7..66903a985 100755
--- a/karma-web/src/main/webapp/js/ServerResponseObjectParsing.js
+++ b/karma-web/src/main/webapp/js/ServerResponseObjectParsing.js
@@ -610,14 +610,6 @@ function parse(data) {
 			} else {
 				$.sticky(element["numRowsNotInserted"] + " rows not saved in database! Check log file for details.");
 			}
-		} else if (element["updateType"] == "CleaningResultUpdate") {
-			if (element["result"] != null) {
-				if (element["result"][0] == null || element["result"][0]["top"].length == 0) {
-					alert("Cannot find any transformations! ");
-				}
-
-				TransformColumnDialog.getInstance().handleCleaningResultUpdate(element["result"]);
-			}
 		} else if (element["updateType"] == "InfoUpdate") {
 			$.sticky(element["Info"]);
 		} else if (element["updateType"] == "AlignmentSVGVisualizationUpdate") {
diff --git a/karma-web/src/main/webapp/js/cleaning.js b/karma-web/src/main/webapp/js/cleaning.js
deleted file mode 100755
index 5e1bb9eee..000000000
--- a/karma-web/src/main/webapp/js/cleaning.js
+++ /dev/null
@@ -1,373 +0,0 @@
-/*******************************************************************************
- * Copyright 2012 University of Southern California
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *  http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- * This code was developed by the Information Integration Group as part
- * of the Karma project at the Information Sciences Institute of the
- * University of Southern California.  For more information, publications,
- * and related projects, please see: http://www.isi.edu/integration
- ******************************************************************************/
-
-var TransformColumnDialog = (function() {
-	var instance = null;
-
-	function PrivateConstructor() {
-		var dialog = $("#transformColumnDialog");
-		var worksheetId, columnId;
-		var cleaningExamples, results, topkeys, transformedResult, nodeIds;
-
-		function init() {
-			//Initialize what happens when we show the dialog
-			dialog.on('show.bs.modal', function(e) {
-				hideError();
-				userExamples = [];
-				loadInitialData();
-			});
-
-			//Initialize handler for Save button
-			//var me = this;
-			$('#btnSave', dialog).on('click', function(e) {
-				e.preventDefault();
-				saveDialog(e);
-			});
-
-			$("button#generateCleaningRules", dialog).on('click', function(e) {
-				e.preventDefault();
-				handleGenerateCleaningRulesButton();
-			});
-		}
-
-		function hideError() {
-			$("div.error", dialog).hide();
-		}
-
-		function showError() {
-			$("div.error", dialog).show();
-		}
-
-		function saveDialog(e) {
-			console.log("Save clicked");
-			hide();
-
-			var selectedHNodeId = columnId;
-			//var transformedRes = transformedResult;
-			var info = generateInfoObject(worksheetId, selectedHNodeId, "SubmitCleaningCommand");
-			info["examples"] = JSON.stringify(cleaningExamples);
-
-			var newInfo = info['newInfo'];
-			newInfo.push(getParamObject("examples", cleaningExamples, "other"));
-			info["newInfo"] = JSON.stringify(newInfo);
-			showLoading(worksheetId);
-			var returned = sendRequest(info, worksheetId);
-		};
-
-		function loadInitialData() {
-			cleaningExamples = [];
-			results = [];
-			topkeys = [];
-
-			var values = fetchCleanningRawData();
-
-			// Populate the table of cleaning preview table
-			var cleaningTable = $("table#cleaningExamplesTable");
-			$("tr.nonHeading", cleaningTable).remove();
-			$("tr.suggestion", cleaningTable).remove();
-
-			nodeIds = [];
-			var data = values[0]["data"]
-			for (var nodeId in data) {
-				if (data.hasOwnProperty(nodeId)) {
-					var tr = $("<tr>").attr("id", nodeId + "_cl_row").addClass("nonHeading").append($("<td>").text(data[nodeId]["Org"]).attr('id', nodeId + "_origVal")) //add text and id to the td
-						.append($("<td>").addClass("noBorder"));
-					//add td to seperate org and result
-					tr.data("originalVal", (data[nodeId]["Org"]));
-					cleaningTable.append(tr);
-					nodeIds.push(nodeId);
-				}
-			}
-			//cleaning
-			var tab1 = $("table#recmd");
-			$("tr", tab1).remove();
-			var tab2 = $("table#examples");
-			$("tr", tab2).remove();
-
-			populateResult(values[0]);
-		}
-
-		function fetchCleanningRawData() {
-			var info = generateInfoObject(worksheetId, columnId, "FetchTransformingDataCommand");
-			var json = {};
-			var returned = $.ajax({
-				url: "RequestController",
-				type: "POST",
-				async: false,
-				data: info,
-				dataType: "json",
-				complete: function(xhr, textStatus) {
-					json = $.parseJSON(xhr.responseText);
-					json = json["elements"][0]["result"];
-					hideCleanningWaitingSignOnScreen();
-				},
-				error: function(xhr, textStatus) {
-					hideCleanningWaitingSignOnScreen();
-					$.sticky("Error in Fetching Raw Data!");
-				}
-			});
-			return json;
-		}
-
-		function populateResult(rdata) {
-			try {
-				var examples = cleaningExamples;
-				var cleaningTable = $("table#cleaningExamplesTable");
-				transformedResult = new Object();
-
-				// Remove the old results
-				$("td.ruleResultsValue_rest", cleaningTable).remove();
-				$("tr.suggestion", cleaningTable).remove();
-				//$("td.ruleResultsValue_begin", cleaningTable).remove();
-
-				var data = rdata["data"];
-				$.each(data, function(nodeId, xval) {
-					var trTag = $("tr#" + nodeId + "_cl_row");
-					if (trTag != null) {
-						transformedResult[nodeId] = xval;
-						if (xval == $("div#" + nodeId).text()) {
-							$("div#" + nodeId).attr("class", "cleanExampleDiv");
-							//return true;
-						}
-						$("td.ruleResultsValue_begin", trTag).remove();
-						$("#" + nodeId + "_origVal", trTag).html(xval["Orgdis"]).data("CellValue", xval["Org"]);
-						var cleaningRes = xval["Tardis"];
-						if (cleaningRes == "<span class=\"ins\"></span>")
-							cleaningRes = "";
-						trTag.append(
-							$("<td>").addClass("ruleResultsValue_begin").attr("id", nodeId + "_transformed")
-							.append($("<table>")
-								.append($("<tr>")
-									.append($("<td>").addClass("noinnerBorder")
-										.append($("<div>").data("nodeId", nodeId) // set the original value for the example
-											.data("cellValue", xval["Tar"])
-											.addClass("cleanExampleDiv")
-											.html(cleaningRes) //set the result here
-											.attr("id", nodeId)))
-									.append($("<td>").addClass("noBorder")))));
-
-						console.log($("div#" + nodeId).text() + ":" + xval["Tardis"]);
-						$("div#" + nodeId, trTag).editable({
-							type: 'text',
-							success: function(response, value) {
-								console.log("Set new value:" + value);
-								var tmpnodeId = nodeId;
-								$("div", $(this).parent().prev()).html(xval["Tar"]);
-								if (nodeId.indexOf("suggestion") >= 0) {
-									tmpnodeId = nodeId.substring(0, nodeId.indexOf("_suggestion"));
-									$("div#" + tmpnodeId).text(value);
-								}
-								var editDiv = $("div#" + nodeId);
-								examples.push({
-									"nodeId": tmpnodeId,
-									"before": $("tr#" + tmpnodeId + "_cl_row").data("originalVal"),
-									"after": value
-								});
-								$("div#" + nodeId).text(value);
-								xval["Tardis"] = value;
-								updateResult();
-							},
-							showbuttons: 'bottom',
-							mode: 'popup',
-							inputclass: 'worksheetInputEdit'
-						});
-					}
-				});
-
-			} catch (err) {
-				console.log(err.message)
-			}
-		}
-
-		function updateResult() {
-			var data = results;
-			var newdata = [];
-			var examples = cleaningExamples;
-			console.log(examples)
-			showCleanningWaitingSignOnScreen();
-			handleGenerateCleaningRulesButton();
-			/*else//use the trimmed data
-			 {
-			 populateResult(newdata[0]);
-			 var pdata = getVaritions(newdata);
-			 populateVariations(newdata[0]["top"],pdata);
-			 }*/
-		}
-
-		function handleGenerateCleaningRulesButton() {
-			var info = generateInfoObject(worksheetId, columnId, "GenerateCleaningRulesCommand");
-			info["examples"] = JSON.stringify(cleaningExamples);
-			info["cellIDs"] = JSON.stringify(nodeIds);
-
-			var returned = $.ajax({
-				url: "RequestController",
-				type: "POST",
-				data: info,
-				dataType: "json",
-				complete: function(xhr, textStatus) {
-					var json = $.parseJSON(xhr.responseText);
-					hideCleanningWaitingSignOnScreen();
-					parse(json);
-				},
-				error: function(xhr, textStatus) {
-					hideCleanningWaitingSignOnScreen();
-					$.sticky("Error generating new cleaning rules!");
-				}
-			});
-		}
-
-		function showCleanningWaitingSignOnScreen() {
-			var coverDiv = $("<div>").attr("id", "WaitingDiv").addClass('waitingDiv').append($("<div>").html('<b>Please wait</b>').append($('<img>').attr("src", "images/ajax-loader.gif")));
-
-			var spaceToCoverDiv = dialog;
-			spaceToCoverDiv.append(coverDiv.css({
-				"position": "fixed",
-				"height": $(document).height(),
-				"width": $(document).width(),
-				"zIndex": 100,
-				"top": spaceToCoverDiv.position().top,
-				"left": spaceToCoverDiv.position().left
-			}).show());
-		}
-
-		function hideCleanningWaitingSignOnScreen() {
-			$("div#WaitingDiv").hide();
-		}
-
-		function populateInfoPanel() {
-			var nodeId = topKeys[0];
-			//tab1.append(trTag.clone(true,true));
-			var tab2 = $("table#examples");
-			$("tr", tab2).remove();
-			var examples = cleaningExamples;
-			$.each(examples, function(index, value) {
-				var nodeID = value["nodeId"];
-				var trTag1 = $("tr#" + nodeID + "_suggestion_cl_row", tab2);
-
-				if (trTag1.length == 0) {
-					trTag1 = $("<tr>").attr("id", nodeID + "_suggestion_cl_row").append($("<td>").addClass('info').text($("tr#" + nodeID + "_cl_row").data("originalVal")));
-				}
-
-				var closeButton = $("<button>");
-				closeButton.attr("id", nodeID);
-				closeButton.addClass("ui-icon").addClass("ui-icon-close").addClass("closeButton");
-				closeButton.button({
-					icons: {
-						//primary : "ui-icon-close"
-					},
-					text: false
-				});
-				closeButton.click(function(event) {
-					trTag1.hide();
-					var delInd = -1;
-					var curId = $(this).attr("id");
-					// update examples and rerun the program
-					$.each(examples, function(index2, example) {
-						if (example["nodeId"] == curId)
-							delInd = index2;
-					});
-					if (delInd != -1) {
-						examples.splice(delInd, 1);
-						updateResult();
-					}
-
-				});
-				var tdButton = $("<td>").attr("class", "infobutton").append(closeButton);
-
-				trTag1.append($("<td>").addClass('noBorder'))
-				trTag1.append($("<td>").addClass("info").append($("<table>").append($("<tr>").append($("<td>").attr("class", "contentNoBorder").append($("<div>").data("nodeId", nodeID).data("cellValue", value["after"]).addClass("cleanExampleDiv").html(value["after"]))).append(tdButton))));
-
-				//$(">td",trTag1).addClass("info");
-				tab2.append(trTag1);
-			});
-			// recommanded examples
-			if (nodeId == undefined || nodeId == "-2") {
-				return;
-			}
-			var datadict = results[0]["data"];
-			var tab1 = $("table#recmd");
-			var trTag = $("tr#" + nodeId + "_suggestion_cl_row", tab1);
-			$("tr", tab1).remove();
-			// empty an array in JS
-			if (trTag.length == 0) {
-				trTag = $("<tr>").attr("id", nodeId + "_suggestion_cl_row").append($("<td>").addClass('info').html(datadict[nodeId]["Orgdis"])).append($("<td>").addClass("noBorder"));
-			} else {
-				trTag = trTag[0];
-			}
-			tab1.append(trTag);
-		}
-
-		function preprocessData(data, nodeIds) {
-			data = data["data"];
-			$.each(nodeIds, function(index, value) {
-				var x = data[value];
-				data[value + "_suggestion"] = x;
-			});
-		}
-
-		function handleCleaningResultUpdate(cleaningResults) {
-			console.log("handleCleaningResultUpdate: " + cleaningResults);
-			var topCol = cleaningResults[0];
-			results = cleaningResults;
-			topKeys = topCol["top"];
-
-			//var sndCol = element["result"][1];
-			preprocessData(topCol, topCol["top"]);
-			populateInfoPanel();
-			populateResult(topCol);
-			//var pdata = getVaritions(element["result"]);
-			//populateVariations(topCol["top"], sndCol["data"]);
-		}
-
-		function hide() {
-			dialog.modal('hide');
-		}
-
-		function show(wsId, colId) {
-			worksheetId = wsId;
-			columnId = colId;
-			dialog.modal({
-				keyboard: true,
-				show: true,
-				backdrop: 'static'
-			});
-		};
-
-		return { //Return back the public methods
-			show: show,
-			init: init,
-			handleCleaningResultUpdate: handleCleaningResultUpdate
-		};
-	};
-
-	function getInstance() {
-		if (!instance) {
-			instance = new PrivateConstructor();
-			instance.init();
-		}
-		return instance;
-	}
-
-	return {
-		getInstance: getInstance
-	};
-
-})();
\ No newline at end of file
diff --git a/karma-web/src/main/webapp/js/tableColumnOptions.js b/karma-web/src/main/webapp/js/tableColumnOptions.js
index 0b63dc5af..be14f25df 100755
--- a/karma-web/src/main/webapp/js/tableColumnOptions.js
+++ b/karma-web/src/main/webapp/js/tableColumnOptions.js
@@ -52,11 +52,6 @@ function TableColumnOptions(wsId, wsColumnId, wsColumnTitle, isLeafNode, isOutof
 			func: aggregation,
 			leafOnly: true,
 			leafExcluded: false
-		}, {
-			name: "Transform",
-			func: transform,
-			leafOnly: true,
-			leafExcluded: false
 		},
 		//{name:"Generate Cluster Values", func:clusterValues, leafOnly:true, leafExcluded: false},
 		//{name:"Merge Cluster Values", func:mergeValues, leafOnly:true, leafExcluded: false},
@@ -297,12 +292,6 @@ function TableColumnOptions(wsId, wsColumnId, wsColumnTitle, isLeafNode, isOutof
 		return false;
 	}
 
-	function transform() {
-		hideDropdown();
-		TransformColumnDialog.getInstance().show(worksheetId, columnId);
-		return false;
-	}
-
 	function showChart() {
 		showChartForColumn(worksheetId, columnId);
 	}
diff --git a/karma-web/src/main/webapp/version.jsp b/karma-web/src/main/webapp/version.jsp
index b40cf858e..b99e74a86 100644
--- a/karma-web/src/main/webapp/version.jsp
+++ b/karma-web/src/main/webapp/version.jsp
@@ -1 +1 @@
-v2.043
+v2.044
diff --git a/pom.xml b/pom.xml
index d7505d79c..b39c92b03 100644
--- a/pom.xml
+++ b/pom.xml
@@ -14,7 +14,6 @@
 		<module>karma-offline</module>
 		<module>karma-jdbc</module>
 		<module>karma-util</module>
-		<module>karma-cleaning</module>
 		<module>karma-commands</module>
 		<module>karma-mr</module>
 		<module>karma-storm</module>