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pmd:InefficientStringBuffering - Inefficient String Buffering #519

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Merged
josemduarte merged 1 commit into from
Jul 4, 2016
Merged

pmd:InefficientStringBuffering - Inefficient String Buffering #519

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2 changes: 1 addition & 1 deletion ...core/src/main/java/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.java
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Expand Up @@ -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();
}
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4 changes: 2 additions & 2 deletions biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java
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Expand Up @@ -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");
}
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2 changes: 1 addition & 1 deletion biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
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Expand Up @@ -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);
}
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4 changes: 2 additions & 2 deletions biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/AbstractAnnotation.java
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Expand Up @@ -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);
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2 changes: 1 addition & 1 deletion ...ain/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
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Expand Up @@ -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();
}
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2 changes: 1 addition & 1 deletion ...org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
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Expand Up @@ -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(";");
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2 changes: 1 addition & 1 deletion ...ture/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
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Expand Up @@ -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);
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
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Expand Up @@ -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"));
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
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Expand Up @@ -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());

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6 changes: 3 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/GroupToSDF.java
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Expand Up @@ -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());
Expand Down Expand Up @@ -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();
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
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Expand Up @@ -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;

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14 changes: 7 additions & 7 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
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Expand Up @@ -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(" ");
Expand All @@ -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);

Expand All @@ -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);

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4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixLayers.java
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Expand Up @@ -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();
}
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
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Expand Up @@ -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();
}
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.java
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Expand Up @@ -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;
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