Merge pull request biojava#519 from DevFactory/release--inefficient-string-buffering-fix-1

josemduarte · web-flow · commit 35deefe1d965 · 2016-07-04T11:38:32.000-07:00
pmd:InefficientStringBuffering - Inefficient String Buffering
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java
@@ -144,7 +144,7 @@ public String toString() {
 		}
 
 		if ( scale != 1)
-			s.append("# Matrix scaled by a factor of " + scale + newline );
+			s.append("# Matrix scaled by a factor of ").append(scale).append(newline);
 		s.append(getMatrixAsString());
 		return s.toString();
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
@@ -368,9 +368,9 @@ private boolean isWithinCutoff(int i, double cutoff) {
 	private String clustersToString(Map<Integer,Set<Integer>> finalClusters) {
 		StringBuilder sb = new StringBuilder();
 		for (int cId:finalClusters.keySet()) {
-			sb.append(cId+": ");
+			sb.append(cId).append(": ");
 			for (int member:finalClusters.get(cId)) {
-				sb.append(member+" ");
+				sb.append(member).append(" ");
 			}
 			sb.append("\n");
 		}
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
@@ -422,7 +422,7 @@ public static String escape(String str, boolean escapespaces) {
 				out.append(c);
 			else {
 				if (escapespaces || (!escapespaces && c != ' ' && c != '\t')) {
-					out.append("\\" + o);
+					out.append("\\").append(o);
 				} else
 					out.append(c);
 			}
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java
@@ -140,11 +140,11 @@ public String toString() {
 		Iterator i = prop.keySet().iterator();
 		if(i.hasNext()) {
 			Object key = i.next();
-			sb.append(key + "=" + prop.get(key));
+			sb.append(key).append("=").append(prop.get(key));
 		}
 		while(i.hasNext()) {
 			Object key = i.next();
-			sb.append("," + key + "=" + prop.get(key));
+			sb.append(",").append(key).append("=").append(prop.get(key));
 		}
 		sb.append("}");
 		return sb.substring(0);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
@@ -633,7 +633,7 @@ private String drawFooter(String text, String color) {
 		s.append(color);
 		s.append(";");
 		s.append("font echo 24 sanserif;");
-		s.append("echo "+ text);
+		s.append("echo ").append(text);
 		s.append(";");
 		return s.toString();
 	}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
@@ -995,7 +995,7 @@ private String drawFooter(String text, String color) {
 		s.append(color);
 		s.append(";");
 		s.append("font echo 24 sanserif;");
-		s.append("echo "+ text);
+		s.append("echo ").append(text);
 		//s.append("echo Point group ");
 		//s.append(rotationGroup.getPointGroup());
 		s.append(";");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
@@ -741,7 +741,7 @@ public String printHelp() {
 		buf.append("-------------------").append(newline);
 		buf.append(newline);
 
-		buf.append(alg.getAlgorithmName() + " accepts the following parameters:" + newline);
+		buf.append(alg.getAlgorithmName()).append(" accepts the following parameters:").append(newline);
 		buf.append(newline);
 
 		buf.append("--- pairwise alignments ---").append(newline);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
@@ -676,7 +676,7 @@ public static ScopDomain guessScopDomain(String name, ScopDatabase scopDB) {
 				if (match.hasNext()) {
 					warnMsg.append(" Other possibilities: ");
 					while (match.hasNext()) {
-						warnMsg.append(match.next().getScopId() + " ");
+						warnMsg.append(match.next().getScopId()).append(" ");
 					}
 				}
 				warnMsg.append(System.getProperty("line.separator"));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
@@ -755,7 +755,7 @@ public String toMMCIF() {
 			molecId2 = molecId2 + "_" +getTransforms().getSecond().getTransformId();
 		}
 
-		sb.append(SimpleMMcifParser.MMCIF_TOP_HEADER+"BioJava_interface_"+getId()+System.getProperty("line.separator"));
+		sb.append(SimpleMMcifParser.MMCIF_TOP_HEADER).append("BioJava_interface_").append(getId()).append(System.getProperty("line.separator"));
 
 		sb.append(FileConvert.getAtomSiteHeader());
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
@@ -73,15 +73,15 @@ private String getCtab(Group thisGroup){
 				String spaceIndOne = getSpace(3, index);
 				String spaceIndTwo = getSpace(3, indexOther);
 				String spaceOrder = getSpace(3, order);
-				bondOrders.append(spaceIndOne+index+spaceIndTwo+indexOther+spaceOrder+order+"  0\n");
+				bondOrders.append(spaceIndOne).append(index).append(spaceIndTwo).append(indexOther).append(spaceOrder).append(order).append("  0\n");
 			}
 		}
 		StringBuilder outString = new  StringBuilder();
 		// Add the first line now
 		String spaceNumAtoms = getSpace(3, Integer.toString(thisGroup.getAtoms().size()));
 		String spaceNumBonds = getSpace(3, Integer.toString(numBonds));
 		header.append("\n");
-		header.append(spaceNumAtoms+thisGroup.getAtoms().size()+spaceNumBonds+numBonds+"  0  0  0  0  0  0  0  0999 V2000\n");
+		header.append(spaceNumAtoms).append(thisGroup.getAtoms().size()).append(spaceNumBonds).append(numBonds).append("  0  0  0  0  0  0  0  0999 V2000\n");
 		// Now add the header, atom, bond and charge information togeyher
 		outString.append(header.toString());
 		outString.append(atomList.toString());
@@ -150,7 +150,7 @@ private String getSpace(int inputNum, String format) {
 	private String getHeader(Group thisGroup) {
 		// Make the header info for the start of the block
 		StringBuilder sb = new StringBuilder();
-		sb.append(thisGroup.getPDBName()+"\n");
+		sb.append(thisGroup.getPDBName()).append("\n");
 		sb.append("Made by BioJava");
 		sb.append("\n");
 		return sb.toString();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
@@ -122,7 +122,7 @@ public static String toMMCIF(String categoryName, Object o) {
 			Field f = fields[i];
 			String name = names[i];
 
-			sb.append(categoryName+"."+name);
+			sb.append(categoryName).append(".").append(name);
 
 			int spacing = maxFieldNameLength - name.length() + 3;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
@@ -257,7 +257,7 @@ else if (resnum < 100)
 
 		// AA
 		char aaLetter = StructureTools.get1LetterCode(parent.getPDBName());
-		buf.append(aaLetter + "  ");
+		buf.append(aaLetter).append("  ");
 
 		// STRUCTURE
 		buf.append(type).append(" ");
@@ -284,11 +284,11 @@ else if (resnum < 100)
 		}
 		// TODO a clever way to do this?
 		if (bp1 < 10)
-			buf.append("   " + bp1);
+			buf.append("   ").append(bp1);
 		else if (bp1 < 100)
-			buf.append("  " + bp1);
+			buf.append("  ").append(bp1);
 		else if (bp1 < 1000)
-			buf.append(" " + bp1);
+			buf.append(" ").append(bp1);
 		else
 			buf.append(bp1);
 
@@ -300,11 +300,11 @@ else if (bp1 < 1000)
 				bp2 = bridge2.partner2 + 1;
 		}
 		if (bp2 < 10)
-			buf.append("   " + bp2);
+			buf.append("   ").append(bp2);
 		else if (bp2 < 100)
-			buf.append("  " + bp2);
+			buf.append("  ").append(bp2);
 		else if (bp2 < 1000)
-			buf.append(" " + bp2);
+			buf.append(" ").append(bp2);
 		else
 			buf.append(bp2);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java
@@ -208,9 +208,9 @@ public void clear() {
 	@Override
 	public String toString() {
 		StringBuilder sb = new StringBuilder();
-		sb.append("Helices: " + size() + "\n");
+		sb.append("Helices: ").append(size()).append("\n");
 		for (Helix s: helices) {
-			sb.append(s.toString() + "\n");
+			sb.append(s.toString()).append("\n");
 		}
 		return sb.toString();
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -193,7 +193,7 @@ public String toString() {
 		StringBuilder sb = new StringBuilder();
 		sb.append("Rotations: " + rotations.size() + "\n");
 		for (Rotation s: rotations) {
-			sb.append(s.toString() + "\n");
+			sb.append(s.toString()).append("\n");
 		}
 		return sb.toString();
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java
@@ -287,7 +287,7 @@ private void calcInterfacesCrystal(StructureInterfaceList set, double cutoff) {
 						}
 
 						StringBuilder builder = null;
-						if (verbose) builder = new StringBuilder(tt+" ");
+						if (verbose) builder = new StringBuilder(String.valueOf(tt)).append(" ");
 
 						// Now that we know that boxes overlap and operator is not redundant, we have to go to the details
 						int contactsFound = 0;

Original file line number	Diff line number	Diff line change
`@@ -144,7 +144,7 @@ public String toString() {`
`144`	`144`	`}`
`145`	`145`
`146`	`146`	`if ( scale != 1)`
`147`		`- s.append("# Matrix scaled by a factor of " + scale + newline );`
	`147`	`+ s.append("# Matrix scaled by a factor of ").append(scale).append(newline);`
`148`	`148`	`s.append(getMatrixAsString());`
`149`	`149`	`return s.toString();`
`150`	`150`	`}`
Original file line number	Diff line number	Diff line change
`@@ -368,9 +368,9 @@ private boolean isWithinCutoff(int i, double cutoff) {`
`368`	`368`	`private String clustersToString(Map<Integer,Set<Integer>> finalClusters) {`
`369`	`369`	`StringBuilder sb = new StringBuilder();`
`370`	`370`	`for (int cId:finalClusters.keySet()) {`
`371`		`- sb.append(cId+": ");`
	`371`	`+ sb.append(cId).append(": ");`
`372`	`372`	`for (int member:finalClusters.get(cId)) {`
`373`		`- sb.append(member+" ");`
	`373`	`+ sb.append(member).append(" ");`
`374`	`374`	`}`
`375`	`375`	`sb.append("\n");`
`376`	`376`	`}`
Original file line number	Diff line number	Diff line change
`@@ -422,7 +422,7 @@ public static String escape(String str, boolean escapespaces) {`
`422`	`422`	`out.append(c);`
`423`	`423`	`else {`
`424`	`424`	`if (escapespaces \|\| (!escapespaces && c != ' ' && c != '\t')) {`
`425`		`- out.append("\\" + o);`
	`425`	`+ out.append("\\").append(o);`
`426`	`426`	`} else`
`427`	`427`	`out.append(c);`
`428`	`428`	`}`
Original file line number	Diff line number	Diff line change
`@@ -140,11 +140,11 @@ public String toString() {`
`140`	`140`	`Iterator i = prop.keySet().iterator();`
`141`	`141`	`if(i.hasNext()) {`
`142`	`142`	`Object key = i.next();`
`143`		`- sb.append(key + "=" + prop.get(key));`
	`143`	`+ sb.append(key).append("=").append(prop.get(key));`
`144`	`144`	`}`
`145`	`145`	`while(i.hasNext()) {`
`146`	`146`	`Object key = i.next();`
`147`		`- sb.append("," + key + "=" + prop.get(key));`
	`147`	`+ sb.append(",").append(key).append("=").append(prop.get(key));`
`148`	`148`	`}`
`149`	`149`	`sb.append("}");`
`150`	`150`	`return sb.substring(0);`
Original file line number	Diff line number	Diff line change
`@@ -633,7 +633,7 @@ private String drawFooter(String text, String color) {`
`633`	`633`	`s.append(color);`
`634`	`634`	`s.append(";");`
`635`	`635`	`s.append("font echo 24 sanserif;");`
`636`		`- s.append("echo "+ text);`
	`636`	`+ s.append("echo ").append(text);`
`637`	`637`	`s.append(";");`
`638`	`638`	`return s.toString();`
`639`	`639`	`}`
Original file line number	Diff line number	Diff line change
`@@ -676,7 +676,7 @@ public static ScopDomain guessScopDomain(String name, ScopDatabase scopDB) {`
`676`	`676`	`if (match.hasNext()) {`
`677`	`677`	`warnMsg.append(" Other possibilities: ");`
`678`	`678`	`while (match.hasNext()) {`
`679`		`- warnMsg.append(match.next().getScopId() + " ");`
	`679`	`+ warnMsg.append(match.next().getScopId()).append(" ");`
`680`	`680`	`}`
`681`	`681`	`}`
`682`	`682`	`warnMsg.append(System.getProperty("line.separator"));`
Original file line number	Diff line number	Diff line change
`@@ -755,7 +755,7 @@ public String toMMCIF() {`
`755`	`755`	`molecId2 = molecId2 + "_" +getTransforms().getSecond().getTransformId();`
`756`	`756`	`}`
`757`	`757`
`758`		`- sb.append(SimpleMMcifParser.MMCIF_TOP_HEADER+"BioJava_interface_"+getId()+System.getProperty("line.separator"));`
	`758`	`+ sb.append(SimpleMMcifParser.MMCIF_TOP_HEADER).append("BioJava_interface_").append(getId()).append(System.getProperty("line.separator"));`
`759`	`759`
`760`	`760`	`sb.append(FileConvert.getAtomSiteHeader());`
`761`	`761`