squid:S2131 - Primitives should not be boxed just for String conversion

Mohamed Ezzat · Mohamed Ezzat · commit fa52fd836e80 · 2016-06-05T15:57:25.000+02:00
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
@@ -460,7 +460,7 @@ public static final double getEnrichment(String sequence, SingleLetterAACode ami
 	 * @return the composition of specified amino acid in the sequence
 	 */
 	public static final double getEnrichment(String sequence, char aminoAcidCode){
-		return getEnrichment(sequence, aminoAcidCode + "");
+		return getEnrichment(sequence, aminoAcidCode);
 	}
 
 	/**
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
@@ -75,7 +75,7 @@ public double getMolecularWeight(ProteinSequence sequence) {
 		AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
 		char[] seq = getSequence(sequence.toString(), true);//ignore case
 		for(char aa:seq){
-			AminoAcidCompound c = aaSet.getCompoundForString(aa + "");
+			AminoAcidCompound c = aaSet.getCompoundForString(String.valueOf(aa));
 			if(Constraints.aa2MolecularWeight.containsKey(c)){
 				value += Constraints.aa2MolecularWeight.get(c);
 			}
@@ -263,7 +263,7 @@ public double getAvgHydropathy(ProteinSequence sequence) {
 		AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
 		char[] seq = this.getSequence(sequence.toString(), true);
 		for(char aa:seq){
-			AminoAcidCompound c = aaSet.getCompoundForString(aa + "");
+			AminoAcidCompound c = aaSet.getCompoundForString(String.valueOf(aa));
 			if(Constraints.aa2Hydrophathicity.containsKey(c)){
 				total += Constraints.aa2Hydrophathicity.get(c);
 				validLength++;
@@ -477,13 +477,13 @@ private double getNetChargeInnovagen(Map<AminoAcidCompound, Integer> chargedAA2C
 		AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
 
 		double nTerminalCharge = 0.0;
-		AminoAcidCompound nTermCompound = aaSet.getCompoundForString(nTerminalChar + "");
+		AminoAcidCompound nTermCompound = aaSet.getCompoundForString(String.valueOf(nTerminalChar));
 		if(Constraints.aa2NTerminalPka.containsKey(nTermCompound)){
 			nTerminalCharge = this.getPosCharge(Constraints.aa2NTerminalPka.get(nTermCompound), ph);
 		}
 
 		double cTerminalCharge = 0.0;
-		AminoAcidCompound cTermCompound = aaSet.getCompoundForString(cTerminalChar + "");
+		AminoAcidCompound cTermCompound = aaSet.getCompoundForString(String.valueOf(cTerminalChar));
 		if(Constraints.aa2CTerminalPka.containsKey(cTermCompound)){
 			cTerminalCharge = this.getNegCharge(Constraints.aa2CTerminalPka.get(cTermCompound), ph);
 		}
@@ -548,7 +548,7 @@ public double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAci
 		double counter = 0.0;
 		char[] seq = this.getSequence(sequence.getSequenceAsString(), true);
 		for(char aa:seq){
-			if(aminoAcidCode.getShortName().equals(aa + "")){
+			if(aminoAcidCode.getShortName().equals(String.valueOf(aa))){
 				counter++;
 			}
 		}
@@ -566,7 +566,7 @@ public Map<AminoAcidCompound, Double> getAAComposition(ProteinSequence sequence)
 		char[] seq = this.getSequence(sequence.toString(), true);
 		for(char aa:seq){
 			if(PeptideProperties.standardAASet.contains(aa)){
-				AminoAcidCompound compound = aaSet.getCompoundForString(aa + "");
+				AminoAcidCompound compound = aaSet.getCompoundForString(String.valueOf(aa));
 				aa2Composition.put(compound, aa2Composition.get(compound) + 1.0);
 				validLength++;
 			}
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
@@ -81,7 +81,7 @@ public String convert(ProteinSequence sequence){
 		String convertedSequence = "";
 		String uppercaseSequence = sequence.getSequenceAsString().toUpperCase();
 		for(int x = 0; x < uppercaseSequence.length(); x++){
-			convertedSequence += convert(uppercaseSequence.charAt(x));
+			convertedSequence += String.valueOf(convert(uppercaseSequence.charAt(x)));
 		}
 		return convertedSequence;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
@@ -567,8 +567,8 @@ private void printConservation(StringBuilder s, String idFormat, int seqIndexPad
 	private boolean isSimilar(char c1, char c2) {
 		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
 
-		AminoAcidCompound aa1 = set.getCompoundForString(""+c1);
-		AminoAcidCompound aa2 = set.getCompoundForString(""+c2);
+		AminoAcidCompound aa1 = set.getCompoundForString(String.valueOf(c1));
+		AminoAcidCompound aa2 = set.getCompoundForString(String.valueOf(c2));
 
 		short val = matrix.getValue(aa1,aa2);
 		return val > 0;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.java
@@ -185,14 +185,14 @@ private void initMatrix(String line) {
 		AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
 		for ( int i = 0 ; i < currentRows.length() ; i ++){
 			char c = currentRows.charAt(i);
-			AminoAcidCompound aa = compoundSet.getCompoundForString(c+"");
+			AminoAcidCompound aa = compoundSet.getCompoundForString(String.valueOf(c));
 
 			rows.add(aa);
 		}
 
 		for ( int i = 0 ; i < currentCols.length() ; i ++){
 			char c = currentRows.charAt(i);
-			AminoAcidCompound aa = compoundSet.getCompoundForString(c+"");
+			AminoAcidCompound aa = compoundSet.getCompoundForString(String.valueOf(c));
 
 			cols.add(aa);
 		}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
@@ -94,7 +94,7 @@ public String getCodingSequence() {
 			StringBuilder b = new StringBuilder(getLength());
 			CompoundSet<NucleotideCompound> compoundSet = this.getCompoundSet();
 			for (int i = 0; i < sequence.length(); i++) {
-				String nucleotide = sequence.charAt(i) + "";
+				String nucleotide = String.valueOf(sequence.charAt(i));
 				NucleotideCompound nucleotideCompound = compoundSet.getCompoundForString(nucleotide);
 				b.append(nucleotideCompound.getComplement().getShortName());
 			}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
@@ -298,7 +298,7 @@ public DNASequence getSequence5PrimeTo3Prime() {
 			StringBuilder b = new StringBuilder(getLength());
 			CompoundSet<NucleotideCompound> compoundSet = this.getCompoundSet();
 			for (int i = 0; i < sequence.length(); i++) {
-				String nucleotide = sequence.charAt(i) + "";
+				String nucleotide = String.valueOf(sequence.charAt(i));
 				NucleotideCompound nucleotideCompound = compoundSet.getCompoundForString(nucleotide);
 				b.append(nucleotideCompound.getComplement().getShortName());
 			}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
@@ -110,7 +110,7 @@ public void process() throws Exception {
 						for (int i = featureBioBegin; i <= featureBioEnd; i++) {
 							char ch = sb.charAt(i);
 							//probably not the fastest but the safest way if language is not standard ASCII
-							String temp = ch + "";
+							String temp = String.valueOf(ch);
 							ch = temp.toUpperCase().charAt(0);
 							sb.setCharAt(i, ch);
 						}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
@@ -276,7 +276,7 @@ public static <S extends Sequence<C>, C extends Compound> String getIDFormat(Lis
 	 * @return formatted String
 	 */
 	public static String getPDBCharacter(boolean web, char c1, char c2, boolean similar, char c) {
-		String s = c + "";
+		String s = String.valueOf(c);
 		return getPDBString(web, c1, c2, similar, s, s, s, s);
 	}
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
@@ -212,7 +212,7 @@ private void initAttributeHashMap(){
 		   String[] data = attribute.split(splitData);
 		   String value = "";
 		   if(data.length >= 2 && data[1].indexOf('"') != -1){ // an attibute field could be empty
-			   value = data[1].replaceAll('"' + "","").trim();
+			   value = data[1].replaceAll("\"","").trim();
 		   }else if(data.length >= 2){
 			   value = data[1].trim();
 		   }
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
@@ -74,13 +74,13 @@ public static String toXML(ModifiedCompound mc) throws IOException{
 			for ( StructureAtomLinkage link: linkages){
 				pos ++;
 				xml.openTag("linkage");
-				xml.attribute("pos", pos+"");
-				xml.attribute("total", linkages.size()+"");
+				xml.attribute("pos", String.valueOf(pos));
+				xml.attribute("total", String.valueOf(linkages.size()));
 				StructureAtom atom1 = link.getAtom1();
 				StructureAtom atom2 = link.getAtom2();
 				double distance = link.getDistance();
 
-				xml.attribute("distance", distance+"");
+				xml.attribute("distance", String.valueOf(distance));
 				xml.openTag("atom1");
 				StructureAtomXMLConverter.toXML(atom1,xml);
 				xml.closeTag("atom1");
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java
@@ -122,7 +122,7 @@ public void alignmentEnded() {
 		int v = progressBar.getValue();
 
 		progressBar.setValue(v+1);
-		progressBar.setString(v+"");
+		progressBar.setString(String.valueOf(v));
 		synchronized(this){notifyAll();}
 
 	}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.java
@@ -282,7 +282,7 @@ public void paintComponent(Graphics g){
 							int block = 0;
 							char s = symb[i];
 							try {
-								block = Integer.parseInt(s+"") - 1;
+								block = Integer.parseInt(String.valueOf(s)) - 1;
 								bg  = ColorUtils.getIntermediate(ColorUtils.orange, end1, blockNum, block);
 								bg2   = ColorUtils.getIntermediate(ColorUtils.cyan, end2, blockNum, block);
 								//bg = ColorUtils.rotateHue(ColorUtils.orange,  (1.0f  / 24.0f) * block  );
@@ -347,8 +347,8 @@ public void paintComponent(Graphics g){
 
 			// draw the AA sequence
 			g2D.setColor(Color.black);
-			g2D.drawString(c1+"",xpos1,ypos1);
-			g2D.drawString(c2+"" ,xpos2,ypos2);
+			g2D.drawString(String.valueOf(c1), xpos1, ypos1);
+			g2D.drawString(String.valueOf(c2), xpos2, ypos2);
 
 
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
@@ -286,7 +286,7 @@ else if (colorByAlignmentBlock){
 
 				// draw the AA sequence
 				g2D.setColor(Color.black);
-				g2D.drawString(c+"",points.get(str).x,points.get(str).y);
+				g2D.drawString(String.valueOf(c), points.get(str).x, points.get(str).y);
 			}
 		}
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
@@ -317,7 +317,7 @@ protected int drawScale(Graphics2D g2D, int y){
 					g2D.fillRect(xpos, y+2, aminosize, y+lineH);
 					g2D.setColor(SCALE_COLOR);
 					if ( scale < SEQUENCE_SHOW)
-						g2D.drawString(""+(i+1),xpos,y+DEFAULT_Y_STEP);
+						g2D.drawString(String.valueOf(i+1), xpos, y+DEFAULT_Y_STEP);
 				}
 
 			}else if  ( ((i+1)%50) == 0 ) {
@@ -326,7 +326,7 @@ protected int drawScale(Graphics2D g2D, int y){
 					g2D.fillRect(xpos,y+2, aminosize, y+lineH);
 					g2D.setColor(SCALE_COLOR);
 					if ( scale < SEQUENCE_SHOW)
-						g2D.drawString(""+(i+1),xpos,y+DEFAULT_Y_STEP);
+						g2D.drawString(String.valueOf(i+1), xpos, y+DEFAULT_Y_STEP);
 
 				}
 
@@ -336,7 +336,7 @@ protected int drawScale(Graphics2D g2D, int y){
 					g2D.fillRect(xpos, y+2, aminosize, y+lineH);
 					g2D.setColor(SCALE_COLOR);
 					if ( scale < SEQUENCE_SHOW)
-						g2D.drawString(""+(i+1),xpos,y+DEFAULT_Y_STEP);
+						g2D.drawString(String.valueOf(i+1), xpos, y+DEFAULT_Y_STEP);
 
 				}
 			}
@@ -347,7 +347,7 @@ protected int drawScale(Graphics2D g2D, int y){
 		if ( endpos >= length-1) {
 
 			int endPanel = coordManager.getPanelPos(endpos);
-			g2D.drawString(""+length,endPanel+10,y+DEFAULT_Y_STEP);
+			g2D.drawString(String.valueOf(length), endPanel+10,y+DEFAULT_Y_STEP);
 		}
 
 		return y ;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -1928,7 +1928,7 @@ public static boolean hasDeuteratedEquiv(Atom atom, Group currentGroup) {
 
 	private static String replaceFirstChar(String name, char c, char d) {
 		if(name.charAt(0)==c){
-			return name.replaceFirst(""+c, ""+d);
+			return name.replaceFirst(String.valueOf(c), String.valueOf(d));
 		}
 		return name;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/BioJavaStructureAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/BioJavaStructureAlignment.java
@@ -74,7 +74,7 @@ public void setParameters(ConfigStrucAligParams o){
 
 	@Override
 	public String getVersion() {
-		return versionNr+"";
+		return String.valueOf(versionNr);
 	}
 
 	public String printHelp() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AfpChainWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AfpChainWriter.java
@@ -285,7 +285,7 @@ public static String toFatCatCore(
 					int block = -1 ;
 					if ( cl != ' ') {
 						try {
-							block = Integer.parseInt(cl+"");
+							block = Integer.parseInt(String.valueOf(cl));
 						} catch (Exception e){
 							//
 						}
@@ -1117,7 +1117,7 @@ public static String toRotMat(AFPChain afpChain)
 
 			String origString = "orig";
 			if ( blockNr > 0)
-				origString = (blockNr)+"";
+				origString = String.valueOf(blockNr);
 
 
 			txt.append(String.format("     X"+(blockNr+1)+" = (%9.6f)*X"+ origString +" + (%9.6f)*Y"+ origString +" + (%9.6f)*Z"+ origString +" + (%12.6f)",m.get(0,0),m.get(1,0), m.get(2,0), shift.getX()));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -843,7 +843,7 @@ private void saveHistory(String filePath) throws IOException {
 		writer.append("Step,Length,RMSD,Score\n");
 
 		for (int i = 0; i < lengthHistory.size(); i++) {
-			writer.append("" + (i * 100));
+			writer.append(String.valueOf(i * 100));
 			writer.append("," + lengthHistory.get(i));
 			writer.append("," + rmsdHistory.get(i));
 			writer.append("," + scoreHistory.get(i) + "\n");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -212,9 +212,8 @@ public static List<String> getSequenceAlignment(
 										.set(str,
 												alnSequences
 														.get(str)
-														.concat(""
-																+ Character
-																		.toLowerCase(aa)));
+														.concat(String.valueOf(Character
+																		.toLowerCase(aa))) );
 								previousPos[str]++;
 							} else {
 								// Insert a gap otherwise
@@ -229,7 +228,7 @@ public static List<String> getSequenceAlignment(
 							alnSequences.set(
 									str,
 									alnSequences.get(str).concat(
-											"" + provisionalChar[str]));
+											String.valueOf(provisionalChar[str])));
 
 							if (provisionalChar[str] != '-') {
 								if (alignment.getBlocks().get(b).getAlignRes()
@@ -281,7 +280,7 @@ public static List<String> getSequenceAlignment(
 						alnSequences.set(
 								str,
 								alnSequences.get(str).concat(
-										"" + provisionalChar[str]));
+										String.valueOf(provisionalChar[str])) );
 					}
 					mapSeqToStruct.add(-1); // unaligned position
 				}
@@ -413,7 +412,7 @@ else if (previousPos[str] + 1 == residue) {
 										alnSequences.set(
 												s2,
 												alnSequences.get(s2).concat(
-														"" + aa));
+														String.valueOf(aa)) );
 									} else {
 										alnSequences.set(s2,
 												alnSequences.get(s2)
@@ -429,7 +428,7 @@ else if (previousPos[str] + 1 == residue) {
 							alnSequences.set(
 									str,
 									alnSequences.get(str).concat(
-											"" + provisionalChar[str]));
+											String.valueOf(provisionalChar[str])) );
 							if (provisionalChar[str] != '-') {
 								previousPos[str] = alignment.getBlocks().get(b)
 										.getAlignRes().get(str).get(pos);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
@@ -103,7 +103,7 @@ public static String toFatCat(MultipleAlignment alignment) {
 			int blockNr = MultipleAlignmentTools.getBlockForSequencePosition(
 					alignment, mapSeqToStruct, pos);
 			if (blockNr != -1) {
-				blockNumbers = blockNumbers.concat("" + (blockNr + 1));
+				blockNumbers = blockNumbers.concat(String.valueOf(blockNr + 1));
 			} else
 				blockNumbers = blockNumbers.concat(" ");
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java
@@ -130,7 +130,7 @@ private static void printXMLEQRKnownPositions(PrettyXMLWriter xml,
 			String pdbres2 = spl2[1];
 
 			xml.openTag("eqr");
-			xml.attribute("eqrNr",eqrNr+"");
+			xml.attribute("eqrNr", String.valueOf(eqrNr));
 			xml.attribute("pdbres1",pdbres1);
 			xml.attribute("chain1", chain1);
 			xml.attribute("pdbres2",pdbres2);
@@ -155,7 +155,7 @@ public static void printXMLEQRInferPositions(PrettyXMLWriter xml,
 			int pos1 = optAln[bk][0][pos];
 			int pos2 = optAln[bk][1][pos];
 			xml.openTag("eqr");
-			xml.attribute("eqrNr",pos+"");
+			xml.attribute("eqrNr", String.valueOf(pos));
 			xml.attribute("pdbres1",ca1[pos1].getGroup().getResidueNumber().toString());
 			xml.attribute("chain1", ca1[pos1].getGroup().getChain().getName());
 			xml.attribute("pdbres2",ca2[pos2].getGroup().getResidueNumber().toString());
@@ -185,11 +185,11 @@ private static void printXMLBlockHeader(PrettyXMLWriter xml,
 		double[]blockScore = afpChain.getBlockScore();
 		double[] blockRmsd = afpChain.getBlockRmsd();
 
-		xml.attribute("blockNr",bk+"");
-		xml.attribute("blockSize", blockSize[bk]+"");
+		xml.attribute("blockNr", String.valueOf(bk));
+		xml.attribute("blockSize", String.valueOf(blockSize[bk]));
 		xml.attribute("blockScore", String.format("%5.2f",blockScore[bk]).trim());
 		xml.attribute("blockRmsd", String.format("%5.2f",blockRmsd[bk]).trim());
-		xml.attribute("blockGap", blockGap[bk]+"");
+		xml.attribute("blockGap", String.valueOf(blockGap[bk]));
 
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/HasResultXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/HasResultXMLConverter.java
@@ -58,7 +58,7 @@ public String toXML(boolean hasResult) throws IOException{
 		PrettyXMLWriter xml = new PrettyXMLWriter(writer);
 
 		xml.openTag("alignment");
-		xml.attribute("hasResult", hasResult+"");
+		xml.attribute("hasResult", String.valueOf(hasResult));
 		xml.closeTag("alignment");
 		xml.close();
 		return swriter.toString();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PositionInQueueXMLConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/PositionInQueueXMLConverter.java
@@ -50,7 +50,7 @@ public String toXML(int position) throws IOException{
 		PrettyXMLWriter xml = new PrettyXMLWriter(writer);
 
 		xml.openTag("queue");
-		xml.attribute("position", position+"");
+		xml.attribute("position", String.valueOf(position));
 		xml.closeTag("queue");
 		xml.close();
 		return swriter.toString();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/ResidueIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/ResidueIdentifier.java
@@ -91,7 +91,7 @@ public boolean equals(Object obj) {
 
 	@Override
 	public String toString() {
-		return ""+ seqResIndex;
+		return String.valueOf(seqResIndex);
 	}
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java

Original file line number	Diff line number	Diff line change
`@@ -460,7 +460,7 @@ public static final double getEnrichment(String sequence, SingleLetterAACode ami`
`460`	`460`	`* @return the composition of specified amino acid in the sequence`
`461`	`461`	`*/`
`462`	`462`	`public static final double getEnrichment(String sequence, char aminoAcidCode){`
`463`		`- return getEnrichment(sequence, aminoAcidCode + "");`
	`463`	`+ return getEnrichment(sequence, aminoAcidCode);`
`464`	`464`	`}`
`465`	`465`
`466`	`466`	`/**`
Original file line number	Diff line number	Diff line change
`@@ -81,7 +81,7 @@ public String convert(ProteinSequence sequence){`
`81`	`81`	`String convertedSequence = "";`
`82`	`82`	`String uppercaseSequence = sequence.getSequenceAsString().toUpperCase();`
`83`	`83`	`for(int x = 0; x < uppercaseSequence.length(); x++){`
`84`		`- convertedSequence += convert(uppercaseSequence.charAt(x));`
	`84`	`+ convertedSequence += String.valueOf(convert(uppercaseSequence.charAt(x)));`
`85`	`85`	`}`
`86`	`86`	`return convertedSequence;`
`87`	`87`	`}`
Original file line number	Diff line number	Diff line change
`@@ -185,14 +185,14 @@ private void initMatrix(String line) {`
`185`	`185`	`AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();`
`186`	`186`	`for ( int i = 0 ; i < currentRows.length() ; i ++){`
`187`	`187`	`char c = currentRows.charAt(i);`
`188`		`- AminoAcidCompound aa = compoundSet.getCompoundForString(c+"");`
	`188`	`+ AminoAcidCompound aa = compoundSet.getCompoundForString(String.valueOf(c));`
`189`	`189`
`190`	`190`	`rows.add(aa);`
`191`	`191`	`}`
`192`	`192`
`193`	`193`	`for ( int i = 0 ; i < currentCols.length() ; i ++){`
`194`	`194`	`char c = currentRows.charAt(i);`
`195`		`- AminoAcidCompound aa = compoundSet.getCompoundForString(c+"");`
	`195`	`+ AminoAcidCompound aa = compoundSet.getCompoundForString(String.valueOf(c));`
`196`	`196`
`197`	`197`	`cols.add(aa);`
`198`	`198`	`}`
Original file line number	Diff line number	Diff line change
`@@ -94,7 +94,7 @@ public String getCodingSequence() {`
`94`	`94`	`StringBuilder b = new StringBuilder(getLength());`
`95`	`95`	`CompoundSet<NucleotideCompound> compoundSet = this.getCompoundSet();`
`96`	`96`	`for (int i = 0; i < sequence.length(); i++) {`
`97`		`- String nucleotide = sequence.charAt(i) + "";`
	`97`	`+ String nucleotide = String.valueOf(sequence.charAt(i));`
`98`	`98`	`NucleotideCompound nucleotideCompound = compoundSet.getCompoundForString(nucleotide);`
`99`	`99`	`b.append(nucleotideCompound.getComplement().getShortName());`
`100`	`100`	`}`
Original file line number	Diff line number	Diff line change
`@@ -298,7 +298,7 @@ public DNASequence getSequence5PrimeTo3Prime() {`
`298`	`298`	`StringBuilder b = new StringBuilder(getLength());`
`299`	`299`	`CompoundSet<NucleotideCompound> compoundSet = this.getCompoundSet();`
`300`	`300`	`for (int i = 0; i < sequence.length(); i++) {`
`301`		`- String nucleotide = sequence.charAt(i) + "";`
	`301`	`+ String nucleotide = String.valueOf(sequence.charAt(i));`
`302`	`302`	`NucleotideCompound nucleotideCompound = compoundSet.getCompoundForString(nucleotide);`
`303`	`303`	`b.append(nucleotideCompound.getComplement().getShortName());`
`304`	`304`	`}`
Original file line number	Diff line number	Diff line change
`@@ -110,7 +110,7 @@ public void process() throws Exception {`
`110`	`110`	`for (int i = featureBioBegin; i <= featureBioEnd; i++) {`
`111`	`111`	`char ch = sb.charAt(i);`
`112`	`112`	`//probably not the fastest but the safest way if language is not standard ASCII`
`113`		`- String temp = ch + "";`
	`113`	`+ String temp = String.valueOf(ch);`
`114`	`114`	`ch = temp.toUpperCase().charAt(0);`
`115`	`115`	`sb.setCharAt(i, ch);`
`116`	`116`	`}`
Original file line number	Diff line number	Diff line change
`@@ -276,7 +276,7 @@ public static <S extends Sequence<C>, C extends Compound> String getIDFormat(Lis`
`276`	`276`	`* @return formatted String`
`277`	`277`	`*/`
`278`	`278`	`public static String getPDBCharacter(boolean web, char c1, char c2, boolean similar, char c) {`
`279`		`- String s = c + "";`
	`279`	`+ String s = String.valueOf(c);`
`280`	`280`	`return getPDBString(web, c1, c2, similar, s, s, s, s);`
`281`	`281`	`}`
`282`	`282`
Original file line number	Diff line number	Diff line change
`@@ -212,7 +212,7 @@ private void initAttributeHashMap(){`
`212`	`212`	`String[] data = attribute.split(splitData);`
`213`	`213`	`String value = "";`
`214`	`214`	`if(data.length >= 2 && data[1].indexOf('"') != -1){ // an attibute field could be empty`
`215`		`- value = data[1].replaceAll('"' + "","").trim();`
	`215`	`+ value = data[1].replaceAll("\"","").trim();`
`216`	`216`	`}else if(data.length >= 2){`
`217`	`217`	`value = data[1].trim();`
`218`	`218`	`}`