Remove un-necesary class for threads

src/lucxor/Globals.java

@@ -425,7 +425,6 @@ static String[] parseNLLine(String line) {
 	public static void calcFLR() throws InterruptedException, ExecutionException {
 		double maxDeltaScore = -1.0;
 		FLR flr = new FLR();
-		ArrayList<FLR> flrAry = new ArrayList<>();
 
 		log.info("\nComputing False Localization Rate (FLR)");
 

src/lucxor/LucXor.java

@@ -529,12 +529,12 @@ private static void runHCDcode() throws IOException,
                 m.printStats();
 
                 // Compute intensity parameters
-                m.estimateNP_intensity('b');
-                m.estimateNP_intensity('y');
-                m.estimateNP_intensity('n');
+                m.estimateNPIntensity('b');
+                m.estimateNPIntensity('y');
+                m.estimateNPIntensity('n');
 
                 // Compute distance parameters
-                m.estimateNP_posDist();
+                m.estimateNPPosDist();
                 log.info("\n");  // makes for prettier output
 
                 Globals.modelingMapHCD.put(z, m);

src/lucxor/MathFunctions.java

@@ -59,10 +59,14 @@ public static double factorial(double x) {
 	}
 
 
-
+	/**
+	 * Get all combinations for all PTMs
+	 * @param candModSites Candidate Modification sites
+	 * @param k Number of combinations
+	 * @return
+	 */
 	static List<TIntList> getAllCombinations(TIntList candModSites, int k) {
 		List<TIntList> ret = new ArrayList<>();
-		int L = candModSites.size(); // total number of values
 
 		// http://code.google.com/p/combinatoricslib/#3._Simple_combinations
 
@@ -75,7 +79,8 @@ static List<TIntList> getAllCombinations(TIntList candModSites, int k) {
 
 		for(ICombinatoricsVector<Integer> combination : gen) {
 			TIntArrayList curList = new TIntArrayList();
-			for(int i : combination) curList.add(i);
+			for(int i : combination)
+				curList.add(i);
 
 			ret.add(curList);
 			curList = null;

src/lucxor/ModelDataHCD.java

@@ -25,17 +25,15 @@ public class ModelDataHCD {
 	static final int ntick = 2000;
 
 	double bIntBW, yIntBW;  // positive peak intensity bandwidth
-	double negIntBW;  // negative peak intensity bandwidth
 	double posDistBW; // positive peak distance bandwidth
 
 	double bIntMean, bIntVar, yIntMean, yIntVar;
 	double negIntMean, negIntVar;
 	double posDistMean, posDistVar;
-	double negDistMean, negDistVar;
-
-
+
+
 	double[] bTickMarksInt, yTickMarksInt, negTickMarksInt;
-	double[] posTickMarksDist, negTickMarksDist;
+	double[] posTickMarksDist;
 	double[] f_int_b, f_int_y, f_int_neg;
 	double[] f_dist;
 
@@ -165,7 +163,6 @@ public void percentileTrim(char ionType, int dataType, double percentTrim) {
 	// Compute the mean for pos and neg data. This function must be called
 	// *before* the calcVar function
 	public void calcMean() {
-		double mean = 0;
 		double N = 0;
 		double sum = 0;
 
@@ -197,7 +194,6 @@ public void calcMean() {
 		// For the negative distribution we assume a uniform distribution over a
 		// 1 Dalton window. As such, the log of a uniform distribution between 
 		// -1 to 1 is zero
-		negDistMean = 0;
 	}
 
 
@@ -247,12 +243,16 @@ public void calcVar() {
 		negIntVar = (v / N);
 
 	}
-
-
-
-	// Function computes the estimated parameters for the non-parametric model
-	// for the intensity of the peaks assigned to this ModelData object
-	void estimateNP_intensity(char ionType) throws InterruptedException, ExecutionException {
+
+
+	/**
+	 * Function computes the estimated parameters for the non-parametric model
+	 * for the intensity of the peaks assigned to this ModelData object
+	 * @param ionType ionType
+	 * @throws InterruptedException
+	 * @throws ExecutionException
+	 */
+	void estimateNPIntensity(char ionType) throws InterruptedException, ExecutionException {
 		int N = 0;
 		double[] norm_ints = null;
 		double[] tickMarksInt = null;
@@ -369,15 +369,14 @@ else if(ionType == 'y') {
 		else {
 			negTickMarksInt = tickMarksInt;
 			f_int_neg = f_int;
-			negIntBW = bw;
 		}
 
 	}
 
 
 	// Function computes the estimated parameters for the non-parametric model
 	// for the m/z distances for the positive peaks in this model object
-	void estimateNP_posDist() throws InterruptedException, ExecutionException {
+	void estimateNPPosDist() throws InterruptedException, ExecutionException {
 
 		int N = 0;
 		double min_dist = 0, max_dist = 0;

src/lucxor/PSM.java

@@ -96,7 +96,6 @@ void process() {
 		if(isKeeper) {
 			// We will reconstruct the specId here to remove left-padded zeros
 			String suffix = "";
-			String scanStr = Integer.toString(scanNum);
 
 			if(Globals.inputType == Constants.PEPXML) {
 				if(Globals.spectrumSuffix.equalsIgnoreCase(Constants.MZXML_TYPE))
@@ -770,13 +769,13 @@ void debugWriteScoredPeaks() throws IOException {
 		for(Peak pk : mPK) {
 			if(!pk.isMatched()) continue;
 
-			String mz = df.format(MathFunctions.roundDouble(pk.getMz(), 4));
-			String relI = df.format(MathFunctions.roundDouble(pk.getRelIntensity(), 4));
-			String normI = df.format(MathFunctions.roundDouble(pk.getNormIntensity(), 4));
-			String Iscore = df.format(MathFunctions.roundDouble(pk.getIntensityScore(), 4));
-			String Dscore = df.format(MathFunctions.roundDouble(pk.getDistScore(), 4));
-			String score = df.format(MathFunctions.roundDouble(pk.getScore(), 4));
-			String dist = df.format(MathFunctions.roundDouble(pk.getDist(), 4));
+			String mz = df.format(MathFunctions.roundDouble(pk.getMz(), numDecimals));
+			String relI = df.format(MathFunctions.roundDouble(pk.getRelIntensity(), numDecimals));
+			String normI = df.format(MathFunctions.roundDouble(pk.getNormIntensity(), numDecimals));
+			String Iscore = df.format(MathFunctions.roundDouble(pk.getIntensityScore(), numDecimals));
+			String Dscore = df.format(MathFunctions.roundDouble(pk.getDistScore(), numDecimals));
+			String score = df.format(MathFunctions.roundDouble(pk.getScore(), numDecimals));
+			String dist = df.format(MathFunctions.roundDouble(pk.getDist(), numDecimals));
 
 			bw.write("0\t" + score1pep.getModPeptide() + "\t" + pk.getMatchedIonStr() + "\t" + mz + "\t" + dist + "\t" +
 					 relI + "\t" + normI + "\t" + Dscore + "\t" + Iscore + "\t" +
@@ -796,13 +795,13 @@ void debugWriteScoredPeaks() throws IOException {
 		for(Peak pk : mPK) {
 			if(!pk.isMatched()) continue;
 
-			String mz = df.format(MathFunctions.roundDouble(pk.getMz(), 4));
-			String relI = df.format(MathFunctions.roundDouble(pk.getRelIntensity(), 4));
-			String normI = df.format(MathFunctions.roundDouble(pk.getNormIntensity(), 4));
-			String Iscore = df.format(MathFunctions.roundDouble(pk.getIntensityScore(), 4));
-			String Dscore = df.format(MathFunctions.roundDouble(pk.getDistScore(), 4));
-			String score = df.format(MathFunctions.roundDouble(pk.getScore(), 4));
-			String dist = df.format(MathFunctions.roundDouble(pk.getDist(), 4));
+			String mz = df.format(MathFunctions.roundDouble(pk.getMz(), numDecimals));
+			String relI = df.format(MathFunctions.roundDouble(pk.getRelIntensity(), numDecimals));
+			String normI = df.format(MathFunctions.roundDouble(pk.getNormIntensity(), numDecimals));
+			String Iscore = df.format(MathFunctions.roundDouble(pk.getIntensityScore(), numDecimals));
+			String Dscore = df.format(MathFunctions.roundDouble(pk.getDistScore(), numDecimals));
+			String score = df.format(MathFunctions.roundDouble(pk.getScore(), numDecimals));
+			String dist = df.format(MathFunctions.roundDouble(pk.getDist(), numDecimals));
 
 			bw.write("1\t" + score2pep.getModPeptide() + "\t" + pk.getMatchedIonStr() + "\t" + mz + "\t" + dist + "\t" +
 					 relI + "\t" + normI + "\t" + Dscore + "\t" + Iscore + "\t" +
@@ -864,11 +863,11 @@ String writeMatchedPks() {
         for(Peak pk : mPK) {
             if(!pk.isMatched()) continue;
 
-            String mz = df.format(MathFunctions.roundDouble(pk.getMz(), 4));
-            String relI = df.format(MathFunctions.roundDouble(pk.getRelIntensity(), 4));
-            String Iscore = df.format(MathFunctions.roundDouble(pk.getIntensityScore(), 4));
-            String Dscore = df.format(MathFunctions.roundDouble(pk.getDistScore(), 4));
-            String score = df.format(MathFunctions.roundDouble(pk.getScore(), 4));
+            String mz = df.format(MathFunctions.roundDouble(pk.getMz(), numDecimals));
+            String relI = df.format(MathFunctions.roundDouble(pk.getRelIntensity(), numDecimals));
+            String Iscore = df.format(MathFunctions.roundDouble(pk.getIntensityScore(), numDecimals));
+            String Dscore = df.format(MathFunctions.roundDouble(pk.getDistScore(), numDecimals));
+            String score = df.format(MathFunctions.roundDouble(pk.getScore(), numDecimals));
 
             ret.append(specId).append("\t2\t").append(score2pep.getModPeptide()).append("\t").append(pk.getMatchedIonStr()).append("\t").append(mz).append("\t").append(relI).append("\t").append(Dscore).append("\t").append(Iscore).append("\t").append(score).append("\n");
         }
@@ -908,10 +907,6 @@ public int getCharge() {
 		return charge;
 	}
 
-	public double getPSMscore() {
-		return PSMscore;
-	}
-
 	public double getDeltaScore() {
 		return deltaScore;
 	}
@@ -944,22 +939,10 @@ public boolean isDecoy() {
 		return isDecoy;
 	}
 
-	public boolean isUnambiguous() {
-		return isUnambiguous;
-	}
-
 	public TIntDoubleHashMap getModCoordMap() {
 		return modCoordMap;
 	}
 
-	public TMap<String, Double> getPosPermutationScoreMap() {
-		return posPermutationScoreMap;
-	}
-
-	public TMap<String, Double> getNegPermutationScoreMap() {
-		return negPermutationScoreMap;
-	}
-
 	public List<Peak> getPosPeaks() {
 		return posPeaks;
 	}
@@ -968,10 +951,6 @@ public List<Peak> getNegPeaks() {
 		return negPeaks;
 	}
 
-	public Spectrum getPeakList() {
-		return PeakList;
-	}
-
 	public Peptide getOrigPep() {
 		return origPep;
 	}
@@ -980,14 +959,6 @@ public String getPeptideSequence(){
 		return origPep.getPeptide();
 	}
 
-	public Peptide getScore1pep() {
-		return score1pep;
-	}
-
-	public Peptide getScore2pep() {
-		return score2pep;
-	}
-
 	public void setSpecId(String specId) {
 		this.specId = specId;
 	}
@@ -1008,43 +979,8 @@ public void setPSMscore(double PSMscore) {
 		this.PSMscore = PSMscore;
 	}
 
-	public void setDeltaScore(double deltaScore) {
-		this.deltaScore = deltaScore;
-	}
-
-	public void setKeeper(boolean keeper) {
-		isKeeper = keeper;
-	}
-
-	public void setUseForModel(boolean useForModel) {
-		this.useForModel = useForModel;
-	}
-
-	public void setDecoy(boolean decoy) {
-		isDecoy = decoy;
-	}
-
-	public void setUnambiguous(boolean unambiguous) {
-		isUnambiguous = unambiguous;
-	}
-
-	public void setPeakList(Spectrum peakList) {
-		PeakList = peakList;
-	}
-
-	public void setOrigPep(Peptide origPep) {
-		this.origPep = origPep;
-	}
-
 	public void setPeptideSequence(String sequence){
 		this.origPep.setPeptide(sequence);
 	}
 
-	public void setScore1pep(Peptide score1pep) {
-		this.score1pep = score1pep;
-	}
-
-	public void setScore2pep(Peptide score2pep) {
-		this.score2pep = score2pep;
-	}
 }

src/lucxor/PSMList.java

@@ -53,7 +53,7 @@ public Object[] toArray() {
   }
 
   @Override
-  public <T> T[] toArray(T[] a) {
+  public <PSM> PSM[] toArray(PSM[] a) {
     return psmList.toArray(a);
   }
 

src/lucxor/Peak.java

@@ -46,9 +46,6 @@ public class Peak {
   // Comparator to sort Peak objects based upon mz dist values from low to high
   public static Comparator comparator_mz_abs_dist = Comparator.comparingDouble(o -> Math.abs(((Peak)o).dist));
 
-  // default constructor
-  Peak(double x, double y) { mz = x; rawIntensity = y; }
-
   public Peak() {
     mz = 0;
     relIntensity = 0;
@@ -109,10 +106,6 @@ public void setMz(double mz) {
     this.mz = mz;
   }
 
-  public double getRawIntensity() {
-    return rawIntensity;
-  }
-
   public void setRawIntensity(double rawIntensity) {
     this.rawIntensity = rawIntensity;
   }
@@ -181,10 +174,6 @@ public void setMatchedIonStr(String matchedIonStr) {
     this.matchedIonStr = matchedIonStr;
   }
 
-  public double getMatchedIonMZ() {
-    return matchedIonMZ;
-  }
-
   public void setMatchedIonMZ(double matchedIonMZ) {
     this.matchedIonMZ = matchedIonMZ;
   }

src/lucxor/Peptide.java

@@ -371,9 +371,11 @@ else if( nonTargetMods.containsKey(i) ) {
 				String AA = Character.toString( peptide.charAt(i) );
 				String aa = AA.toLowerCase();
 				int score = 0;
-				if( !Globals.TargetModMap.containsKey(AA) ) score++;
+				if( !Globals.TargetModMap.containsKey(AA))
+					score++;
 
-				if( !this.nonTargetMods.containsKey(aa) ) score++;
+				if( !this.nonTargetMods.containsKey(aa) )
+					score++;
 
 				if(score == 2) candModSites.add(i);
 			}