Merge pull request #14 from bjoelle/offsets

Offsets
CompEvol · Apr 9, 2019 · 279b455 · 279b455
2 parents 3eeb5ab + ea3760c
commit 279b455
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Showing 48 changed files with 755 additions and 3,571 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,13 @@
 # Build output
 /out
+/bin
 
 # IntelliJ cruft
 /.idea
 /sampled-ancestors.iml
+
+# Eclipse files
+.classpath
+.project
+/build
+/build-lib
diff --git a/dist/SA.v2.0.1.zip b/dist/SA.v2.0.1.zip
diff --git a/examples/brachiopods.xml b/examples/brachiopods.xml
diff --git a/src/beast/app/simulators/SABDSimulator.java b/src/beast/app/simulators/SABDSimulator.java
@@ -5,7 +5,6 @@
 
 import java.io.*;
 import java.util.*;
-import java.util.concurrent.ExecutionException;
 
 /**
  *

diff --git a/src/beast/app/simulators/SABDSkylineTreeSimulator.java b/src/beast/app/simulators/SABDSkylineTreeSimulator.java
@@ -2,7 +2,6 @@
 
 import beast.core.Description;
 import beast.evolution.tree.Node;
-import beast.evolution.tree.ZeroBranchSANode;
 import beast.util.Randomizer;
 
 import java.io.File;
@@ -60,7 +59,7 @@ public SABDSkylineTreeSimulator(double newLambda, double newMu, double newPsi, d
     public int simulate(PrintStream writer) {
 
         //create an initial node (origin of tree)
-        Node initial = new ZeroBranchSANode();
+        Node initial = new Node();
         initial.setNr(-1);
         initial.setHeight(0.0);
         ArrayList<Node> tipNodes = new ArrayList<Node>();    // an array of temporary tip nodes sorted by their heights
@@ -160,7 +159,7 @@ public int simulate(PrintStream writer) {
         }
 
         //the unique node remains in the array is the root of the sampled tree
-        Node root = new ZeroBranchSANode();
+        Node root = new Node();
         for (Node node:children) {
             root=node;
         }
@@ -214,9 +213,9 @@ private ArrayList<Node> getNewNodes(Node node, int typeOfEvent, double timeInter
 
         switch (typeOfEvent) {
             case BIRTH: {
-                Node left = new ZeroBranchSANode();
+                Node left = new Node();
                 left.setNr(-1);
-                Node right = new ZeroBranchSANode();
+                Node right = new Node();
                 right.setNr(-1);
                 left.setHeight(height);
                 right.setHeight(height);
@@ -238,9 +237,9 @@ private ArrayList<Node> getNewNodes(Node node, int typeOfEvent, double timeInter
 
                 double remain = Randomizer.nextDouble();
                 if (r < remain) {
-                    Node left = new ZeroBranchSANode();
+                    Node left = new Node();
                     left.setNr(-1);
-                    Node right = new ZeroBranchSANode();
+                    Node right = new Node();
                     right.setNr(sampleCount);
                     left.setHeight(height);
                     right.setHeight(height);
@@ -434,7 +433,7 @@ private int countSA(Node node){
         if (!node.isLeaf()) {
             return countSA(node.getLeft()) + countSA(node.getRight());
         } else {
-            if (((ZeroBranchSANode)node).isDirectAncestor()) {
+            if (node.isDirectAncestor()) {
                 return 1;
             } else return 0;
         }

diff --git a/src/beast/app/simulators/SABDSkylineTreeSimulatorArbitraryRateChanges.java b/src/beast/app/simulators/SABDSkylineTreeSimulatorArbitraryRateChanges.java
@@ -2,7 +2,6 @@
 
 import beast.core.Description;
 import beast.evolution.tree.Node;
-import beast.evolution.tree.ZeroBranchSANode;
 import beast.util.Randomizer;
 
 import java.util.*;
@@ -65,7 +64,7 @@ public SABDSkylineTreeSimulatorArbitraryRateChanges(double[] newLambda, double[]
     public int simulate() {
 
         //create an initial node (origin of tree)
-        Node initial = new ZeroBranchSANode();
+        Node initial = new Node();
         initial.setNr(-1);
         initial.setHeight(0.0);
         ArrayList<Node> tipNodes = new ArrayList<Node>();    // an array of nodes at the previous stage of simulation
@@ -171,7 +170,7 @@ public int simulate() {
         }
 
         //the unique node remained in the array is the root of the sampled tree
-        Node root = new ZeroBranchSANode();
+        Node root = new Node();
         for (Node node:children) {
             root=node;
         }
@@ -266,9 +265,9 @@ private ArrayList<Node> getNewNodes(Node node, int typeOfEvent, double timeInter
         node.setHeight(height);
         switch (typeOfEvent) {
             case BIRTH: {
-                Node left = new ZeroBranchSANode();
+                Node left = new Node();
                 left.setNr(-1);
-                Node right = new ZeroBranchSANode();
+                Node right = new Node();
                 right.setNr(-1);
                 left.setHeight(height);
                 right.setHeight(height);
@@ -284,9 +283,9 @@ private ArrayList<Node> getNewNodes(Node node, int typeOfEvent, double timeInter
             case SAMPLING: {
                 double remain = Randomizer.nextDouble();
                 if (r[currentInterval] < remain) {
-                    Node left = new ZeroBranchSANode();
+                    Node left = new Node();
                     left.setNr(-1);
-                    Node right = new ZeroBranchSANode();
+                    Node right = new Node();
                     right.setNr(sampleCount);
                     left.setHeight(height);
                     right.setHeight(height);

diff --git a/src/beast/app/simulators/SABDTreeSimulator.java b/src/beast/app/simulators/SABDTreeSimulator.java
@@ -1,7 +1,6 @@
 package beast.app.simulators;
 
 import beast.evolution.tree.Node;
-import beast.evolution.tree.ZeroBranchSANode;
 import beast.math.distributions.LogNormalDistributionModel;
 import beast.util.Randomizer;
 
@@ -77,7 +76,7 @@ public SABDTreeSimulator(double newLambda, double newMu, double newPsi, double n
      */
     public int simulate(PrintStream writer) {
         //create an initial node (origin of tree)
-        Node initial = new ZeroBranchSANode();
+        Node initial = new Node();
         initial.setNr(-1);
         initial.setHeight(0.0);
         ArrayList<Node> tipNodes = new ArrayList<Node>();    // an array of nodes at the previous stage of simulation
@@ -145,7 +144,7 @@ public int simulate(PrintStream writer) {
         }
 
         //the unique node remained in the array is the root of the sampled tree
-        Node root = new ZeroBranchSANode();
+        Node root = new Node();
         for (Node node:children) {
             root=node;
         }
@@ -170,7 +169,7 @@ public int simulate(PrintStream writer) {
     }
 
     public int simulateWithRho(PrintStream writer, double[] rootHeight) {
-        Node initial = new ZeroBranchSANode();
+        Node initial = new Node();
         initial.setNr(-1);
         initial.setHeight(0.0);
         ArrayList<Node> tipNodes = new ArrayList<Node>();    // an array of nodes at the previous stage of simulation
@@ -261,7 +260,7 @@ public int simulateWithRho(PrintStream writer, double[] rootHeight) {
         }
 
         //the unique node remained in the array is the root of the sampled tree
-        Node root = new ZeroBranchSANode();
+        Node root = new Node();
         for (Node node:children) {
             root=node;
         }
@@ -295,7 +294,7 @@ public int simulateWithRho(PrintStream writer, double[] rootHeight) {
      */
     public int simulateWithRhoSamplingTime(PrintStream treeWriter, PrintStream writer, int[] leafCount) {
         //create an initial node (origin of tree)
-        Node initial = new ZeroBranchSANode();
+        Node initial = new Node();
         initial.setNr(-1);
         initial.setHeight(0.0);
         ArrayList<Node> tipNodes = new ArrayList<Node>();    // an array of nodes at the previous stage of simulation
@@ -345,7 +344,7 @@ public int simulateWithRhoSamplingTime(PrintStream treeWriter, PrintStream write
         }
 
         //the unique node remained in the array is the root of the sampled tree
-        Node root = new ZeroBranchSANode();
+        Node root = new Node();
         for (Node node:children) {
             root=node;
         }
@@ -426,9 +425,9 @@ private ArrayList<Node> getNewNodes(Node node, int typeOfEvent, double timeInter
         node.setHeight(height);
         switch (typeOfEvent) {
             case BIRTH: {
-                Node left = new ZeroBranchSANode();
+                Node left = new Node();
                 left.setNr(-1);
-                Node right = new ZeroBranchSANode();
+                Node right = new Node();
                 right.setNr(-1);
                 left.setHeight(height);
                 right.setHeight(height);
@@ -444,9 +443,9 @@ private ArrayList<Node> getNewNodes(Node node, int typeOfEvent, double timeInter
             case SAMPLING: {
                 double remain = Randomizer.nextDouble();
                 if (r < remain) {
-                    Node left = new ZeroBranchSANode();
+                    Node left = new Node();
                     left.setNr(-1);
-                    Node right = new ZeroBranchSANode();
+                    Node right = new Node();
                     right.setNr(sampleCount);
                     left.setHeight(height);
                     right.setHeight(height);
@@ -723,7 +722,7 @@ private int countSA(Node node){
         if (!node.isLeaf()) {
             return countSA(node.getLeft()) + countSA(node.getRight());
         } else {
-            if (((ZeroBranchSANode)node).isDirectAncestor()) {
+            if (node.isDirectAncestor()) {
                 return 1;
             } else return 0;
         }
@@ -749,7 +748,7 @@ private void printTraitsWithRhoSamplingTime(Node node, PrintStream writer){
 
     private double printSAWithRhoSamplingTime(Node node, PrintStream writer){
         if (node.isLeaf()){
-            if (((ZeroBranchSANode)node).isDirectAncestor()) {
+            if (node.isDirectAncestor()) {
                 writer.println(node.getNr() + "=1");
             }   else {
                 writer.println(node.getNr() + "=0");

diff --git a/src/beast/app/tools/FullToExtantTreeConverter.java b/src/beast/app/tools/FullToExtantTreeConverter.java
@@ -64,15 +64,15 @@ private void printConvertedTrees(List<Tree> trees, String outputFile) throws Exc
 
         tree.init(out);
         out.println();
-        tree.log(0, out);
+        tree.log((long) 0, out);
         out.println();
 
         for (int i=1; i< trees.size(); i++) {
             oldTree = trees.get(i);
             removeFossils(oldTree.getRoot(), oldTree, new ArrayList<>());
             numberNodes(oldTree.getRoot(), new int[] {extantTaxa.size()});
             tree = new Tree(oldTree.getRoot());
-            tree.log(i, out);
+            tree.log((long) i, out);
             out.println();
         }
         out.println("End;");
@@ -144,7 +144,7 @@ public void initAndValidate() {
 
 	@Override
 	public void run() throws Exception {
-	       java.io.File file, file_out;
+	       java.io.File file;
 	        String outputFile = "";
 	        double customThreshold = -1.;
 //	        ArrayList<String> taxa = null;

diff --git a/src/beast/app/tools/NexusImporter.java b/src/beast/app/tools/NexusImporter.java
@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.io.Reader;
 import java.util.ArrayList;
-import java.util.Map;
 
 /**
  * @author Alexandra Gavryushkina

diff --git a/src/beast/app/tools/SATreeComparingAnalysis.java b/src/beast/app/tools/SATreeComparingAnalysis.java
@@ -2,8 +2,6 @@
 
 import beast.evolution.tree.Node;
 import beast.evolution.tree.Tree;
-import beast.evolution.tree.ZeroBranchSANode;
-import beast.evolution.tree.ZeroBranchSATree;
 import beast.util.NexusParser;
 
 import java.util.ArrayList;
@@ -50,7 +48,7 @@ private SATreeComparingAnalysis.TreeSummary[] makeTreeSummaryForAllTrees(List<Tr
             Tree tree = trees.get(treeIndex);
             ArrayList<Integer> dAPattern = new ArrayList<Integer>();
             for (int i=tree.getLeafNodeCount(); i< tree.getNodeCount(); i++){
-                if (((ZeroBranchSANode)tree.getNode(i)).isFake()) {
+                if (tree.getNode(i).isFake()) {
                     int descendantsCount = tree.getNode(i).getLeafNodeCount() - 1;
                     if (descendantsCount > 0) {
                         for(int j=dAPattern.size(); j<descendantsCount; j++){
@@ -62,7 +60,7 @@ private SATreeComparingAnalysis.TreeSummary[] makeTreeSummaryForAllTrees(List<Tr
                     }
                 }
             }
-            treeSummary[treeIndex] = new TreeSummary(tree.getRoot().getHeight(), tree.getLeafNodeCount() - ((ZeroBranchSATree)tree).getDirectAncestorNodeCount(), dAPattern);
+            treeSummary[treeIndex] = new TreeSummary(tree.getRoot().getHeight(), tree.getLeafNodeCount() - tree.getDirectAncestorNodeCount(), dAPattern);
         }
         return treeSummary;
     }
@@ -115,7 +113,7 @@ public static void main (String[] arg) throws Exception{
         //process tree. consider Fake SA trees
         ArrayList<Integer> dAPattern = new ArrayList<Integer>();
         for (int i=tree.getLeafNodeCount(); i< tree.getNodeCount(); i++){
-            if (((ZeroBranchSANode)tree.getNode(i)).isFake()) {
+            if (tree.getNode(i).isFake()) {
                 int descendantsCount = tree.getNode(i).getLeafNodeCount() - 1;
                 if (descendantsCount > 0) {
                     for(int j=dAPattern.size(); j<descendantsCount; j++){
@@ -128,7 +126,7 @@ public static void main (String[] arg) throws Exception{
             }
         }
 
-        SATreeComparingAnalysis.TreeSummary treeSummary = analysis.new TreeSummary(tree.getRoot().getHeight(), tree.getLeafNodeCount() - ((ZeroBranchSATree)tree).getDirectAncestorNodeCount(), dAPattern);
+        SATreeComparingAnalysis.TreeSummary treeSummary = analysis.new TreeSummary(tree.getRoot().getHeight(), tree.getLeafNodeCount() - tree.getDirectAncestorNodeCount(), dAPattern);
 
         System.out.println(treeSummary.dAPattern.toString());
         ArrayList<Integer> a = new ArrayList<Integer> (Arrays.asList(new Integer[]{1, 1}));

diff --git a/src/beast/app/tools/SATreeToBinaryTreeConverter.java b/src/beast/app/tools/SATreeToBinaryTreeConverter.java
@@ -1,6 +1,5 @@
 package beast.app.tools;
 
-import beast.evolution.tree.ZeroBranchSANode;
 import beast.util.SANexusParser;
 
 import java.io.BufferedOutputStream;
@@ -19,14 +18,14 @@
  * **/
 public class SATreeToBinaryTreeConverter {
 
-    public static void perform(SampledAncestorTreeTrace trace, boolean useNumbers, String outputFile) throws Exception {
+    public static void perform(SANexusParser trace, boolean useNumbers, String outputFile) throws Exception {
     	PrintStream out = new PrintStream(new BufferedOutputStream(new FileOutputStream(outputFile)));
 
-    	trace.beastTrees.get(0).init(out);
+    	trace.trees.get(0).init(out);
     	out.println();
-    	for (int i=0; i< trace.beastTrees.size(); i++) {
+    	for (int i=0; i< trace.trees.size(); i++) {
     		out.print("tree STATE_" + i + " = ");
-    	    out.print(((ZeroBranchSANode)trace.beastTrees.get(i).getRoot()).toSortedNewickWithZeroBranches(new int[]{0}));
+    	    out.print(trace.trees.get(i).getRoot().toSortedNewick(new int[]{0}, false));
     	    out.println(";");
     	}
     	out.println("End;");
@@ -66,8 +65,7 @@ public static void main(String[] args) throws IOException, Exception {
             reader = new FileReader(file);
             SANexusParser parser = new SANexusParser();
             parser.parseFile(file);
-            SampledAncestorTreeTrace trace = new SampledAncestorTreeTrace(parser);
-            perform(trace, useNumbers, outputFile);
+            perform(parser, useNumbers, outputFile);
         }
         catch (IOException e) {
             //
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,7 +5,6 @@ @@
     import java.io.*;
     import java.util.*;
-    import java.util.concurrent.ExecutionException;
     /**
      *
@@ Expand Down @@