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 index e1017352f2..ee26384bfa 100644 --- 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 index 30a4127ddb..ca58257f48 100644 --- 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> 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 index 4675d469cf..76b7d673c2 100644 --- 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 index b93646245a..d6f9374328 100644 --- 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 index 21e7e93c98..609ff0eeee 100644 --- 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 index ffd2b7b1b2..3b04a5c16d 100644 --- 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 index 20141f49a4..89504263d0 100644 --- 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 index b52a783af5..fd59e52e64 100644 --- 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 index fe75469f72..ac319fd95f 100644 --- 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 index 74689578fe..bbc277b89f 100644 --- 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 @@ -73,7 +73,7 @@ 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(); @@ -81,7 +81,7 @@ private String getCtab(Group thisGroup){ 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 index 7075c9fe43..c79ff65ea7 100644 --- 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 index 1b35a3578d..7611b49adc 100644 --- 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 index a69efc3e98..a42958d062 100644 --- 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 index ead65b5b20..f11f03758d 100644 --- 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 index 87d1c5d256..f00c68757d 100644 --- 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;