From 515c623529daf9c7fb643a94fa6e55a374ed7ad4 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Wed, 12 Nov 2025 16:56:00 -0800 Subject: [PATCH 01/17] [maven-release-plugin] prepare for next development iteration --- biojava-aa-prop/pom.xml | 6 +++--- biojava-alignment/pom.xml | 4 ++-- biojava-core/pom.xml | 2 +- biojava-genome/pom.xml | 6 +++--- biojava-integrationtest/pom.xml | 4 ++-- biojava-modfinder/pom.xml | 4 ++-- biojava-ontology/pom.xml | 2 +- biojava-protein-comparison-tool/pom.xml | 10 +++++----- biojava-protein-disorder/pom.xml | 4 ++-- biojava-structure-gui/pom.xml | 6 +++--- biojava-structure/pom.xml | 6 +++--- biojava-survival/pom.xml | 2 +- biojava-ws/pom.xml | 4 ++-- pom.xml | 4 ++-- 14 files changed, 32 insertions(+), 32 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 0c1016c3b6..fd7bfcd086 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.2.3 + 7.2.4-SNAPSHOT org.biojava biojava-structure - 7.2.3 + 7.2.4-SNAPSHOT diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 7bb6e3b2ee..3886b68bd1 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.3 + 7.2.4-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 890ce360bc..6b3eb9d8ae 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 79608afaf4..29479bcfdf 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.3 + 7.2.4-SNAPSHOT compile org.biojava biojava-alignment - 7.2.3 + 7.2.4-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 41d9be230c..4646e96277 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.3 + 7.2.4-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 876203f207..953feeed09 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.3 + 7.2.4-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 02e4a894d2..a6475ce2d7 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.3 + 7.2.4-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index b4de1b1e8a..9b06a29f3b 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.3 + 7.2.4-SNAPSHOT org.biojava biojava-core - 7.2.3 + 7.2.4-SNAPSHOT org.biojava biojava-structure - 7.2.3 + 7.2.4-SNAPSHOT org.biojava biojava-structure-gui - 7.2.3 + 7.2.4-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index d5e216b60d..eba96d6f87 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.3 + 7.2.4-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 62db686d60..caa5e31782 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.3 + 7.2.4-SNAPSHOT compile org.biojava biojava-core - 7.2.3 + 7.2.4-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index aeff7465c0..3cc048a81a 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.3 + 7.2.4-SNAPSHOT compile org.biojava biojava-core - 7.2.3 + 7.2.4-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index a1facab532..e2ca04fe41 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.3 + 7.2.4-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 23866ccbb1..532034b29f 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.3 + 7.2.4-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.3 + 7.2.4-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index c4dfdd3b74..faa29d48ad 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.3 + 7.2.4-SNAPSHOT biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the @@ -51,7 +51,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-7.2.3 + HEAD From 0af196ffd522f98aa093dd569659438f1ab81ebf Mon Sep 17 00:00:00 2001 From: JasonKamsu Date: Fri, 21 Nov 2025 08:24:39 +0100 Subject: [PATCH 03/17] Fix RSPEC-1940 boolean checks --- .../nbio/core/sequence/location/InsdcParser.java | 4 +++- .../java/org/biojava/nbio/core/util/Equals.java | 16 ++++++++++++++-- .../nbio/genome/parsers/gff/Location.java | 4 ++-- .../java/org/biojava/nbio/structure/Author.java | 2 +- .../java/org/biojava/nbio/structure/Element.java | 2 +- .../nbio/structure/align/ce/CECalculator.java | 2 +- .../structure/align/ce/CeCalculatorEnhanced.java | 2 +- .../structure/quaternary/BioAssemblyTools.java | 2 +- .../nbio/structure/secstruc/SecStrucTools.java | 2 +- 9 files changed, 25 insertions(+), 11 deletions(-) diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java index e49bd22216..2d43a481bf 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java @@ -260,7 +260,9 @@ private List parseLocationString(String string, int versus) { l.setPartialOn3prime(true); } - if (!(accession == null || "".equals(accession))) l.setAccession(new AccessionID(accession)); + if (accession != null && !"".equals(accession)) { + l.setAccession(new AccessionID(accession)); + } boundedLocationsCollection.add(l); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java index e8f78243ed..7e2c7128c9 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java @@ -49,7 +49,13 @@ public static boolean equal(boolean one, boolean two) { * @see #classEqual(Object, Object) */ public static boolean equal(Object one, Object two) { - return one == null && two == null || !(one == null || two == null) && (one == two || one.equals(two)); + if (one == two) { + return true; + } + if (one == null || two == null) { + return false; + } + return one.equals(two); } /** @@ -84,6 +90,12 @@ public static boolean equal(Object one, Object two) { * equal at the class level */ public static boolean classEqual(Object one, Object two) { - return one == two || !(one == null || two == null) && one.getClass() == two.getClass(); + if (one == two) { + return true; + } + if (one == null || two == null) { + return false; + } + return one.getClass() == two.getClass(); } } diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java index 4163be2b56..a28f1019fb 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java @@ -135,7 +135,7 @@ public static Location fromBio( int start, int end, char strand ) int s= start - 1; int e= end; - if( !( strand == '-' || strand == '+' || strand == '.' )) + if( strand != '-' && strand != '+' && strand != '.' ) { throw new IllegalArgumentException( "Strand must be '+', '-', or '.'" ); } @@ -166,7 +166,7 @@ public static Location fromBioExt( int start, int length, char strand, int total int s= start; int e= s + length; - if( !( strand == '-' || strand == '+' || strand == '.' )) + if( strand != '-' && strand != '+' && strand != '.' ) { throw new IllegalArgumentException( "Strand must be '+', '-', or '.'" ); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java index b0d7253507..bd5a01b885 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java @@ -62,7 +62,7 @@ public boolean equals(Object obj) { if ((this.surname == null) ? (other.surname != null) : !this.surname.equals(other.surname)) { return false; } - return !((this.initials == null) ? (other.initials != null) : !this.initials.equals(other.initials)); + return (this.initials == null) ? other.initials == null : this.initials.equals(other.initials); } @Override diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java index 2f534b2828..4e2d3e340a 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java @@ -424,7 +424,7 @@ public boolean isHeavyAtom() { * @return true if Element is not Hydrogen and not Carbon. */ public boolean isHeteroAtom() { - return !(this == C || this == H); + return this != C && this != H; } /** diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java index 6c045ba48e..83f16b7982 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java @@ -1450,7 +1450,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str //afpChain.setTotalRmsdOpt(rmsd); //System.out.println("rmsd: " + rmsd); - if(!(nAtom= strLen * 0.95 && !isRmsdLenAssigned) { rmsdLen=rmsd; isRmsdLenAssigned=true; } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java index 4f57161268..cab98b0113 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java @@ -1455,7 +1455,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str //afpChain.setTotalRmsdOpt(rmsd); //System.out.println("rmsd: " + rmsd); - if(!(nAtom= strLen * 0.95 && !isRmsdLenAssigned) { rmsdLen=rmsd; isRmsdLenAssigned=true; } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java index 7c359121de..f65f4617fe 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java @@ -55,7 +55,7 @@ public static boolean isUnaryExpression(String expression) { if (first < 0 || last < 0) { return true; } - return ! (first == 0 && last > first); + return first != 0 || last <= first; } public static List parseUnaryOperatorExpression(String operatorExpression) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java index 7732c04b80..42191d682d 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java @@ -57,7 +57,7 @@ public static List getSecStrucInfo(Structure s) { Group g = iter.next(); if (g.hasAminoAtoms()) { Object p = g.getProperty(Group.SEC_STRUC); - if (!(p == null)) { + if (p != null) { SecStrucInfo ss = (SecStrucInfo) p; listSSI.add(ss); } From 3f039fd3f5128e3f97981873f9855f45949848a0 Mon Sep 17 00:00:00 2001 From: Pasjonat90D <20847880+Pasjonat90D@users.noreply.github.com> Date: Sun, 30 Nov 2025 20:44:39 +0100 Subject: [PATCH 04/17] Fix #1079: Use isEmpty() instead of size() == 0 --- .../nbio/core/alignment/SimpleAlignedSequence.java | 2 +- .../org/biojava/nbio/core/sequence/GeneSequence.java | 2 +- .../sequence/storage/SequenceAsStringHelper.java | 2 +- .../org/biojava/nbio/core/util/PrettyXMLWriter.java | 2 +- .../nbio/structure/gui/util/SequenceScalePanel.java | 2 +- .../nbio/structure/align/ClusterAltAligs.java | 2 +- .../nbio/structure/align/multiple/BlockImpl.java | 2 +- .../nbio/structure/align/multiple/BlockSetImpl.java | 6 +++--- .../align/multiple/MultipleAlignmentImpl.java | 4 ++-- .../align/multiple/mc/MultipleMcOptimizer.java | 2 +- .../structure/align/quaternary/QsAlignResult.java | 2 +- .../biojava/nbio/structure/align/util/AtomCache.java | 12 ++++++------ .../nbio/structure/chem/ZipChemCompProvider.java | 2 +- .../nbio/structure/cluster/SubunitCluster.java | 2 +- .../nbio/structure/cluster/SubunitClusterer.java | 2 +- .../nbio/structure/geometry/MomentsOfInertia.java | 2 +- .../org/biojava/nbio/structure/io/PDBFileParser.java | 4 ++-- .../nbio/structure/io/mmtf/MmtfStructureReader.java | 2 +- .../nbio/structure/quaternary/BioAssemblyTools.java | 2 +- .../quaternary/BiologicalAssemblyBuilder.java | 2 +- .../structure/symmetry/core/HelicalRepeatUnit.java | 2 +- .../nbio/structure/symmetry/core/RotationGroup.java | 2 +- .../nbio/structure/symmetry/core/RotationSolver.java | 2 +- .../structure/symmetry/core/SystematicSolver.java | 2 +- .../structure/symmetry/geometry/DistanceBox.java | 2 +- .../org/biojava/nbio/structure/xtal/SpaceGroup.java | 4 ++-- .../kaplanmeier/figure/NumbersAtRiskPanel.java | 2 +- .../java/org/biojava/nbio/ws/hmmer/HmmerResult.java | 2 +- 28 files changed, 38 insertions(+), 38 deletions(-) diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java index 331480bbef..99b70c036d 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java @@ -411,7 +411,7 @@ private void setLocation(List steps) { } // combine sublocations into 1 Location - if (sublocations.size() == 0) { + if (sublocations.isEmpty()) { location = null; } else if (sublocations.size() == 1) { location = sublocations.get(0); 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 index f0f2662fea..638e4e68d9 100644 --- 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 @@ -119,7 +119,7 @@ public void addIntronsUsingExons() throws Exception { if (intronAdded) { //going to assume introns are correct return; } - if (exonSequenceList.size() == 0) { + if (exonSequenceList.isEmpty()) { return; } ExonComparator exonComparator = new ExonComparator(); diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java index c2b02debee..4acd8969f1 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java @@ -44,7 +44,7 @@ public class SequenceAsStringHelper { */ public String getSequenceAsString(List parsedCompounds, CompoundSet compoundSet, Integer bioBegin, Integer bioEnd, Strand strand) { // TODO Optimise/cache. - if(parsedCompounds.size() == 0) + if(parsedCompounds.isEmpty()) return ""; StringBuilder builder = new StringBuilder(); if (strand.equals(Strand.NEGATIVE)) { diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java index 437085866f..6e4a7db77c 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java @@ -72,7 +72,7 @@ public void declareNamespace(String nsURI, String prefixHint) private void handleDeclaredNamespaces() throws IOException { - if (namespacesDeclared.size() == 0) { + if (namespacesDeclared.isEmpty()) { for (Iterator nsi = namespacesDeclared.iterator(); nsi.hasNext(); ) { String nsURI = nsi.next(); if (!namespacePrefixes.containsKey(nsURI)) { 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 index 06542e5271..75da6c8e28 100644 --- 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 @@ -126,7 +126,7 @@ private void setPrefSize() { public void setAligMap(List apos){ this.apos = apos; - if ( apos.size() == 0) + if (apos.isEmpty()) return; AlignedPosition last = apos.get(apos.size()-1); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java index 373bcf1611..0933198d7b 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java @@ -102,7 +102,7 @@ public static void cluster(AlternativeAlignment[] aligs, int cutoff){ } clusters.add(currentCluster); - if ( remainList.size() == 0) { + if ( remainList.isEmpty()) { break; } } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java index e0423b6f8f..43da1d7c06 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java @@ -127,7 +127,7 @@ public void setAlignRes(List> alignRes) { public int length() { if (alignRes == null) return 0; - if (alignRes.size() == 0) + if (alignRes.isEmpty()) return 0; return alignRes.get(0).size(); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java index cbbb3ae895..344ee3c239 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java @@ -179,7 +179,7 @@ public int size() { // Get the size from the variables that can contain the information if (parent != null) return parent.size(); - else if (getBlocks().size() == 0) { + else if (getBlocks().isEmpty()) { throw new IndexOutOfBoundsException( "Empty BlockSet: number of Blocks == 0."); } else @@ -194,7 +194,7 @@ public int getCoreLength() { } protected void updateLength() { - if (getBlocks().size() == 0) { + if (getBlocks().isEmpty()) { throw new IndexOutOfBoundsException( "Empty BlockSet: number of Blocks == 0."); } @@ -207,7 +207,7 @@ protected void updateLength() { } protected void updateCoreLength() { - if (getBlocks().size() == 0) { + if (getBlocks().isEmpty()) { throw new IndexOutOfBoundsException( "Empty BlockSet: number of Blocks == 0."); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java index 738eee30c5..06c93a4403 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java @@ -207,7 +207,7 @@ public int getCoreLength() { * lengths. */ protected void updateLength() { - if (getBlockSets().size() == 0) { + if (getBlockSets().isEmpty()) { throw new IndexOutOfBoundsException( "Empty MultipleAlignment: blockSets size == 0."); } // Otherwise try to calculate it from the BlockSet information @@ -223,7 +223,7 @@ protected void updateLength() { * BlockSet core lengths. */ protected void updateCoreLength() { - if (getBlockSets().size() == 0) { + if (getBlockSets().isEmpty()) { throw new IndexOutOfBoundsException( "Empty MultipleAlignment: blockSets size == 0."); } // Otherwise try to calculate it from the BlockSet information 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 index 052f147fc6..29c7012801 100644 --- 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 @@ -153,7 +153,7 @@ public MultipleMcOptimizer(MultipleAlignment seedAln, for (Block b : toDelete) { for (BlockSet bs : msa.getBlockSets()) { bs.getBlocks().remove(b); - if (bs.getBlocks().size() == 0) + if (bs.getBlocks().isEmpty()) emptyBs.add(bs); } } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java index 7ac77a602e..fe1c9c411b 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java @@ -117,7 +117,7 @@ public void setSubunitMap(Map subunitMap) { "Subunit Map index higher than Subunit List size."); // Update the relation enum - if (subunitMap.size() == 0) { + if (subunitMap.isEmpty()) { relation = QsRelation.DIFFERENT; } else if (subunitMap.keySet().size() == subunits1.size()) { if (subunitMap.values().size() == subunits2.size()) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java index 1435191c2c..71b8a3da22 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java @@ -228,7 +228,7 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean throws StructureException, IOException { return getBiologicalAssembly(new PdbId(pdbId), bioAssemblyId, multiModel); } - + /** * Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the * assembly from the biounit annotations found in {@link Structure#getPDBHeader()} @@ -284,7 +284,7 @@ public Structure getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean m asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms(); - if (transformations == null || transformations.size() == 0) { + if (transformations == null || transformations.isEmpty()) { throw new StructureException("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId); } @@ -339,7 +339,7 @@ public Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms(); - if (transformations == null || transformations.size() == 0) { + if (transformations == null || transformations.isEmpty()) { throw new StructureException("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId); } @@ -385,7 +385,7 @@ public List getBiologicalAssemblies(String pdbId, boolean multiModel) List transformations = asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms(); - if (transformations == null || transformations.size() == 0) { + if (transformations == null || transformations.isEmpty()) { logger.info("Could not load transformations to recreate biological assembly id {} of {}. Assembly " + "id will be missing in biological assemblies.", bioAssemblyId, pdbId); continue; @@ -807,7 +807,7 @@ public Structure getStructureForPdbId(String id) throws IOException, StructureEx public Structure getStructureForPdbId(PdbId pdbId) throws IOException { if (pdbId == null) return null; - + while (checkLoading(pdbId)) { // waiting for loading to be finished... try { @@ -833,7 +833,7 @@ public Structure getStructureForPdbId(PdbId pdbId) throws IOException { protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException { return loadStructureFromCifByPdbId(new PdbId(pdbId)); } - + protected Structure loadStructureFromCifByPdbId(PdbId pdbId) throws IOException { logger.debug("Loading structure {} from mmCIF file {}.", pdbId, path); Structure s; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java index 4fe19aca58..a68019efb7 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java @@ -120,7 +120,7 @@ public ChemComp getChemComp(String recordName) { } // If a null record or an empty chemcomp, return a default ChemComp and blacklist. - if (cc == null || (null == cc.getName() && cc.getAtoms().size() == 0)) { + if (cc == null || (null == cc.getName() && cc.getAtoms().isEmpty())) { s_logger.info("Unable to find or download {} - excluding from future searches.", recordName); unavailable.add(recordName); return getEmptyChemComp(recordName); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java index 9a87e92f88..b8ef74c8f1 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java @@ -331,7 +331,7 @@ public boolean mergeIdenticalByEntityId(SubunitCluster other) { } } - if (thisAligned.size() == 0 && otherAligned.size() == 0) { + if (thisAligned.isEmpty() && otherAligned.isEmpty()) { logger.warn("No equivalent aligned atoms found between SubunitClusters {}-{} via entity SEQRES alignment. Is FileParsingParameters.setAlignSeqRes() set?", thisName, otherName); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java index 6295f8fdf0..964a0aaba3 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java @@ -58,7 +58,7 @@ public static Stoichiometry cluster(Structure structure, public static Stoichiometry cluster(List subunits, SubunitClustererParameters params) { List clusters = new ArrayList<>(); - if (subunits.size() == 0) + if (subunits.isEmpty()) return new Stoichiometry(clusters); // First generate a new cluster for each Subunit diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java index 8cfd032daa..5a6e69c4cf 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java @@ -72,7 +72,7 @@ public void addPoint(Point3d point, double mass) { public Point3d getCenterOfMass() { - if (points.size() == 0) { + if (points.isEmpty()) { throw new IllegalStateException( "MomentsOfInertia: no points defined"); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java index 176459bbf2..58e4ee6625 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java @@ -1970,7 +1970,7 @@ private Group getCorrectAltLocGroup( Character altLoc, // build it up. if ( groupCode3.equals(currentGroup.getPDBName())) { - if ( currentGroup.getAtoms().size() == 0) { + if ( currentGroup.getAtoms().isEmpty()) { //System.out.println("current group is empty " + current_group + " " + altLoc); return currentGroup; } @@ -2762,7 +2762,7 @@ private void makeCompounds(List compoundList, } // System.out.println("[makeCompounds] adding sources to compounds from sourceLines"); // since we're starting again from the first compound, reset it here - if ( entities.size() == 0){ + if ( entities.isEmpty()){ current_compound = new EntityInfo(); } else { current_compound = entities.get(0); 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 index c2830c1685..21ef8bb64c 100644 --- 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 @@ -396,7 +396,7 @@ private Group getCorrectAltLocGroup(Character altLoc) { } // no matching altLoc group found. // build it up. - if (group.getAtoms().size() == 0) { + if (group.getAtoms().isEmpty()) { return group; } Group altLocG = (Group) group.clone(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java index 7c359121de..786ce7646f 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java @@ -279,7 +279,7 @@ public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit, return centroid; } - if ( transformations.size() == 0) { + if ( transformations.isEmpty()) { return Calc.getCentroid(atoms).getCoords(); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java index c6ec6bc8ff..9edb8f404c 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java @@ -205,7 +205,7 @@ private void addChainMultiModel(Structure s, Chain newChain, String transformId) // multi-model bioassembly - if ( modelIndex.size() == 0) + if (modelIndex.isEmpty()) modelIndex.add("PLACEHOLDER FOR ASYM UNIT"); int modelCount = modelIndex.indexOf(transformId); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java index ff9c77cf13..cd16aa5f87 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java @@ -64,7 +64,7 @@ public Map getInteractingRepeatUnits() { private void run() { this.repeatUnitCenters = calcRepeatUnitCenters(); - if (this.repeatUnitCenters.size() == 0) { + if (this.repeatUnitCenters.isEmpty()) { return; } this.repeatUnits = calcRepeatUnits(); 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 70b69afe14..1490d27036 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 @@ -98,7 +98,7 @@ public void complete() { public String getPointGroup() { if (modified) { - if (rotations.size() == 0) { + if (rotations.isEmpty()) { return "C1"; } complete(); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java index 37a44be7ac..b1566a6d2f 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java @@ -305,7 +305,7 @@ private boolean isSpherical() { * @return null if invalid, or a rotation if valid */ private Rotation isValidPermutation(List permutation) { - if (permutation.size() == 0) { + if (permutation.isEmpty()) { return null; } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java index d13fa4db16..a449771b58 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java @@ -145,7 +145,7 @@ private void completeRotationGroup() { } private boolean isValidPermutation(List permutation) { - if (permutation.size() == 0) { + if (permutation.isEmpty()) { return false; } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java index 2d9b1d6dca..25d37693fb 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java @@ -166,7 +166,7 @@ private List getBoxTwo(long location) { } // ensure that boxTwo has no empty element by copying from tempBox of defined size List boxTwo = null; - if (tempBox.size() == 0) { + if (tempBox.isEmpty()) { boxTwo = Collections.emptyList(); } else if (tempBox.size() == 1) { boxTwo = Collections.singletonList(tempBox.get(0)); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java index cff84c70f8..852d213bb9 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java @@ -645,10 +645,10 @@ public List getTransfAlgebraic() { public void setTransfAlgebraic(List transfAlgebraic) { //System.out.println("setting transfAlgebraic " + transfAlgebraic); - if ( transformations == null || transformations.size() == 0) + if ( transformations == null || transformations.isEmpty()) transformations = new ArrayList(transfAlgebraic.size()); - if ( this.transfAlgebraic == null || this.transfAlgebraic.size() == 0) + if ( this.transfAlgebraic == null || this.transfAlgebraic.isEmpty()) this.transfAlgebraic = new ArrayList<>(transfAlgebraic.size()); for ( String transf : transfAlgebraic){ 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 index c4578f1c8b..144942a809 100644 --- 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 @@ -76,7 +76,7 @@ private void paintTable(Graphics g) { sfiHashMap = sfi.getStrataInfoHashMap(); } - if(sfiHashMap.size() == 0) + if(sfiHashMap.isEmpty()) return; //int height = this.getHeight(); diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java index 3304e78d4f..373b78cd0a 100644 --- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java +++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java @@ -140,7 +140,7 @@ public int compareTo(HmmerResult o) { return(me.getSqFrom().compareTo(other.getSqFrom())); } private boolean emptyDomains(HmmerResult o) { - if ( o.getDomains() == null || o.getDomains().size() == 0) + if ( o.getDomains() == null || o.getDomains().isEmpty()) return true; return false; } From 423cd86fbc2355f9943a3bbd81597c3d0c231627 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Mon, 8 Dec 2025 15:22:01 -0800 Subject: [PATCH 05/17] Bugfix: edge-case with no equiv residues in alignment wasn't dealt with and led to IllegalArgumentException. Also: improved logging --- .../structure/cluster/SubunitCluster.java | 43 ++++++++----------- .../structure/cluster/SubunitClusterer.java | 11 ++--- 2 files changed, 23 insertions(+), 31 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java index 9a87e92f88..2bbad10f1f 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java @@ -507,27 +507,24 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p } } - AFPChain afp = aligner.align(this.subunits.get(this.representative) - .getRepresentativeAtoms(), - other.subunits.get(other.representative) - .getRepresentativeAtoms()); + AFPChain afp = aligner.align(this.subunits.get(this.representative).getRepresentativeAtoms(), + other.subunits.get(other.representative).getRepresentativeAtoms()); + String pairName = this.subunits.get(this.representative).getName() + "-" + other.subunits.get(other.representative).getName(); if (afp.getOptLength() < 1) { // alignment failed (eg if chains were too short) throw new StructureException( - String.format("Subunits failed to align using %s", params.getSuperpositionAlgorithm())); + String.format("Subunits %s failed to align using %s", pairName, params.getSuperpositionAlgorithm())); } // Convert AFPChain to MultipleAlignment for convenience MultipleAlignment msa = new MultipleAlignmentEnsembleImpl( afp, this.subunits.get(this.representative).getRepresentativeAtoms(), - other.subunits.get(other.representative) - .getRepresentativeAtoms(), false) - .getMultipleAlignment(0); + other.subunits.get(other.representative).getRepresentativeAtoms(), + false).getMultipleAlignment(0); - double structureCoverage = Math.min(msa.getCoverages().get(0), msa - .getCoverages().get(1)); + double structureCoverage = Math.min(msa.getCoverages().get(0), msa.getCoverages().get(1)); if(params.isUseStructureCoverage() && structureCoverage < params.getStructureCoverageThreshold()) { return false; @@ -543,8 +540,7 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p return false; } - logger.info(String.format("SubunitClusters are structurally similar with " - + "%.2f RMSD %.2f coverage", rmsd, structureCoverage)); + logger.info("SubunitClusters {} are structurally similar with [ {} ] RMSD and [ {} ] coverage", pairName, String.format("%.2f", rmsd), String.format("%.2f", structureCoverage)); // Merge clusters List> alignedRes = msa.getBlock(0).getAlignRes(); @@ -565,13 +561,18 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p // Only consider residues that are part of the SubunitCluster if (this.subunitEQR.get(this.representative).contains(thisIndex) - && other.subunitEQR.get(other.representative).contains( - otherIndex)) { + && other.subunitEQR.get(other.representative).contains(otherIndex)) { thisAligned.add(thisIndex); otherAligned.add(otherIndex); } } + // this can happen in very rare cases, e.g. 9y9z when merging E_1 into the cluster D_1, OM_1, Y_1 + if (thisAligned.isEmpty() && otherAligned.isEmpty()) { + logger.warn("No equivalent aligned atoms found between SubunitClusters {} via structure alignment. Will not merge the second one into the first.", pairName); + return false; + } + updateEquivResidues(other, thisAligned, otherAligned); this.method = SubunitClustererMethod.STRUCTURE; @@ -602,18 +603,12 @@ private void updateEquivResidues(SubunitCluster other, List thisAligned Collections.sort(otherRemove); Collections.reverse(otherRemove); - for (int t = 0; t < thisRemove.size(); t++) { - for (List eqr : this.subunitEQR) { - int column = thisRemove.get(t); - eqr.remove(column); - } + for (int column : thisRemove) { + this.subunitEQR.forEach(eqr -> eqr.remove(column)); } - for (int t = 0; t < otherRemove.size(); t++) { - for (List eqr : other.subunitEQR) { - int column = otherRemove.get(t); - eqr.remove(column); - } + for (int column : otherRemove) { + other.subunitEQR.forEach(eqr -> eqr.remove(column)); } // The representative is the longest sequence diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java index 6295f8fdf0..70da0b56db 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java @@ -83,8 +83,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara } } catch (CompoundNotFoundException e) { - logger.warn("Could not merge by Sequence. {}", - e.getMessage()); + logger.info("Could not merge by Sequence. {}", e.getMessage()); } } } @@ -100,7 +99,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara clusters.remove(c2); } } catch (StructureException e) { - logger.warn("Could not merge by Structure. {}", e.getMessage()); + logger.info("Could not merge by Structure. {}", e.getMessage()); } } } @@ -112,8 +111,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara try { clusters.get(c).divideInternally(params); } catch (StructureException e) { - logger.warn("Error analyzing internal symmetry. {}", - e.getMessage()); + logger.info("Error analyzing internal symmetry. {}", e.getMessage()); } } @@ -125,8 +123,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara if (clusters.get(c1).mergeStructure(clusters.get(c2), params)) clusters.remove(c2); } catch (StructureException e) { - logger.warn("Could not merge by Structure. {}", - e.getMessage()); + logger.info("Could not merge by Structure. {}", e.getMessage()); } } } From f55940c0612a61e4f347d8cec502797f34cf8c1f Mon Sep 17 00:00:00 2001 From: josemduarte Date: Wed, 10 Dec 2025 13:55:30 -0800 Subject: [PATCH 06/17] [maven-release-plugin] prepare release biojava-7.2.4 --- biojava-aa-prop/pom.xml | 6 +++--- biojava-alignment/pom.xml | 4 ++-- biojava-core/pom.xml | 2 +- biojava-genome/pom.xml | 6 +++--- biojava-integrationtest/pom.xml | 4 ++-- biojava-modfinder/pom.xml | 4 ++-- biojava-ontology/pom.xml | 2 +- biojava-protein-comparison-tool/pom.xml | 10 +++++----- biojava-protein-disorder/pom.xml | 4 ++-- biojava-structure-gui/pom.xml | 6 +++--- biojava-structure/pom.xml | 6 +++--- biojava-survival/pom.xml | 2 +- biojava-ws/pom.xml | 4 ++-- pom.xml | 4 ++-- 14 files changed, 32 insertions(+), 32 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index fd7bfcd086..b1efc6c661 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.2.4-SNAPSHOT + 7.2.4 org.biojava biojava-structure - 7.2.4-SNAPSHOT + 7.2.4 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 3886b68bd1..a03519aeca 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.4-SNAPSHOT + 7.2.4 compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 6b3eb9d8ae..e7f36a646d 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 29479bcfdf..b4e2a0e791 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.4-SNAPSHOT + 7.2.4 compile org.biojava biojava-alignment - 7.2.4-SNAPSHOT + 7.2.4 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 4646e96277..a5b307c637 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.4-SNAPSHOT + 7.2.4 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 953feeed09..4545d15f2f 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.4-SNAPSHOT + 7.2.4 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index a6475ce2d7..82ccc0ed59 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.4-SNAPSHOT + 7.2.4 biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 9b06a29f3b..3425644447 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.4-SNAPSHOT + 7.2.4 org.biojava biojava-core - 7.2.4-SNAPSHOT + 7.2.4 org.biojava biojava-structure - 7.2.4-SNAPSHOT + 7.2.4 org.biojava biojava-structure-gui - 7.2.4-SNAPSHOT + 7.2.4 net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index eba96d6f87..30c263b398 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.4-SNAPSHOT + 7.2.4 diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index caa5e31782..133f64781c 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.4-SNAPSHOT + 7.2.4 compile org.biojava biojava-core - 7.2.4-SNAPSHOT + 7.2.4 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 3cc048a81a..b58fda9a96 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.4-SNAPSHOT + 7.2.4 compile org.biojava biojava-core - 7.2.4-SNAPSHOT + 7.2.4 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index e2ca04fe41..993b9aa1fe 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.4-SNAPSHOT + 7.2.4 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 532034b29f..32a8af0fb4 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.4-SNAPSHOT + 7.2.4 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.4-SNAPSHOT + 7.2.4 compile diff --git a/pom.xml b/pom.xml index faa29d48ad..0cd4634a92 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.4-SNAPSHOT + 7.2.4 biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the @@ -51,7 +51,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - HEAD + biojava-7.2.4 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index a03519aeca..b1d0bd9097 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.4 + 7.2.5-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.4 + 7.2.5-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index e7f36a646d..909f46f088 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.4 + 7.2.5-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index b4e2a0e791..68575bbb9b 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.4 + 7.2.5-SNAPSHOT 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.4 + 7.2.5-SNAPSHOT compile org.biojava biojava-alignment - 7.2.4 + 7.2.5-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index a5b307c637..1c21373bd1 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.4 + 7.2.5-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.4 + 7.2.5-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 4545d15f2f..e8de9e38d9 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.4 + 7.2.5-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.4 + 7.2.5-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 82ccc0ed59..6a3fd5cbc4 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.4 + 7.2.5-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 3425644447..cf8cd570a7 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.4 + 7.2.5-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.4 + 7.2.5-SNAPSHOT org.biojava biojava-core - 7.2.4 + 7.2.5-SNAPSHOT org.biojava biojava-structure - 7.2.4 + 7.2.5-SNAPSHOT org.biojava biojava-structure-gui - 7.2.4 + 7.2.5-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 30c263b398..7273bbff8f 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.4 + 7.2.5-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.4 + 7.2.5-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 133f64781c..581b8a53cc 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.4 + 7.2.5-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.4 + 7.2.5-SNAPSHOT compile org.biojava biojava-core - 7.2.4 + 7.2.5-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index b58fda9a96..7fbc64a3c1 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.4 + 7.2.5-SNAPSHOT biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.4 + 7.2.5-SNAPSHOT compile org.biojava biojava-core - 7.2.4 + 7.2.5-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 993b9aa1fe..88f901cdea 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.4 + 7.2.5-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 32a8af0fb4..7e960b4445 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.4 + 7.2.5-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.4 + 7.2.5-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 0cd4634a92..e9f246202b 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.4 + 7.2.5-SNAPSHOT biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the @@ -51,7 +51,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-7.2.4 + HEAD From c0240dd9d192d2ed3df5bab95830016bc9215133 Mon Sep 17 00:00:00 2001 From: Pasjonat90D <20847880+Pasjonat90D@users.noreply.github.com> Date: Sun, 14 Dec 2025 22:33:43 +0100 Subject: [PATCH 09/17] Refactor: fix SonarQube S1155 issues (#1079) --- .../loader/GenbankProxySequenceReaderTest.java | 2 +- .../org/biojava/nbio/genome/GeneFeatureHelper.java | 14 +++++++------- .../genome/homology/GFF3FromUniprotBlastHits.java | 14 +++++++------- .../nbio/genome/parsers/gff/GFF3Writer.java | 4 ++-- .../nbio/structure/test/io/TestSeqResParsing.java | 2 +- .../protmod/io/ModifiedCompoundXMLConverter.java | 2 +- .../structure/ProteinModificationIdentifier.java | 2 +- .../nbio/protmod/phosphosite/TestAcetylation.java | 7 ++++--- .../nbio/ontology/utils/WeakValueHashMap.java | 4 ++-- .../align/gui/autosuggest/JAutoSuggest.java | 4 ++-- .../gui/autosuggest/SCOPAutoSuggestProvider.java | 6 +++--- .../align/gui/jmol/RasmolCommandListener.java | 2 +- .../main/java/org/biojava/nbio/structure/Site.java | 2 +- .../multiple/util/MultipleAlignmentWriter.java | 2 +- .../nbio/structure/align/util/AlignmentTools.java | 2 +- .../align/xml/MultipleAlignmentXMLParser.java | 2 +- .../nbio/structure/contact/GroupContact.java | 2 +- .../structure/contact/StructureInterfaceList.java | 2 +- .../org/biojava/nbio/structure/io/BondMaker.java | 2 +- .../biojava/nbio/structure/io/PDBFileParser.java | 6 +++--- .../nbio/structure/io/SeqRes2AtomAligner.java | 4 ++-- .../structure/io/cif/CifStructureConsumerImpl.java | 6 +++--- .../structure/io/mmtf/MmtfStructureReader.java | 2 +- .../BiologicalAssemblyTransformation.java | 2 +- .../nbio/structure/scop/ScopInstallation.java | 8 ++++---- .../structure/symmetry/core/PermutationGroup.java | 2 +- .../symmetry/core/QuatSymmetrySubunits.java | 2 +- .../structure/symmetry/core/RotationGroup.java | 4 ++-- .../symmetry/internal/SequenceFunctionRefiner.java | 2 +- .../structure/symmetry/internal/SymmOptimizer.java | 5 +---- .../structure/symmetry/utils/BlastClustReader.java | 2 +- .../nbio/structure/align/util/AtomCacheTest.java | 5 +++-- .../biojava/nbio/structure/io/TestHeaderOnly.java | 3 +-- .../structure/io/TestMMcifOrganismParsing.java | 4 ++-- .../nbio/structure/io/TestSiftsParsing.java | 12 ++++++------ .../structure/io/cif/CifFileConsumerImplTest.java | 4 ++-- .../org/biojava/nbio/survival/cox/CoxInfo.java | 4 ++-- .../biojava/nbio/survival/cox/ResidualsCoxph.java | 4 ++-- .../org/biojava/nbio/survival/data/WorkSheet.java | 4 ++-- 39 files changed, 80 insertions(+), 82 deletions(-) diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java index 6883637a49..0e8f7f41f5 100644 --- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java +++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java @@ -162,7 +162,7 @@ so it should be done here (manualy). logger.info("taxonomy name '{}'", taxonName); Assert.assertNotNull(taxonName); - if (seq.getFeaturesByType("CDS").size() > 0) { + if (!seq.getFeaturesByType("CDS").isEmpty()) { FeatureInterface, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0); logger.info("CDS: {}", CDS); String codedBy = CDS.getQualifiers().get("coded_by").get(0).getValue(); diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java index c9786b3ad0..b417c4608d 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java @@ -36,7 +36,7 @@ /** * - * @author Scooter Willis + * @author Scooter Willis */ public class GeneFeatureHelper { @@ -418,7 +418,7 @@ static public void addGmodGFF3GeneFeatures(Map chrom String startCodonName = ""; String stopCodonName = ""; FeatureList startCodonList = mRNAChildren.selectByType("five_prime_UTR"); - if (startCodonList != null && startCodonList.size() > 0) { + if (startCodonList != null && !startCodonList.isEmpty()) { startCodon = startCodonList.get(0); if (strand == Strand.NEGATIVE) { startCodonBegin = startCodon.location().bioEnd(); @@ -430,7 +430,7 @@ static public void addGmodGFF3GeneFeatures(Map chrom FeatureList stopCodonList = mRNAChildren.selectByType("three_prime_UTR"); - if (stopCodonList != null && stopCodonList.size() > 0) { + if (stopCodonList != null && !stopCodonList.isEmpty()) { stopCodon = stopCodonList.get(0); if (strand == Strand.NEGATIVE) { stopCodonEnd = stopCodon.location().bioStart(); @@ -577,7 +577,7 @@ static public void addGlimmerGFF3GeneFeatures(Map ch String startCodonName = ""; String stopCodonName = ""; FeatureList startCodonList = gene.selectByAttribute("Note", "initial-exon"); - if (startCodonList != null && startCodonList.size() > 0) { + if (startCodonList != null && !startCodonList.isEmpty()) { startCodon = startCodonList.get(0); if (strand == Strand.NEGATIVE) { startCodonBegin = startCodon.location().bioEnd(); @@ -589,7 +589,7 @@ static public void addGlimmerGFF3GeneFeatures(Map ch FeatureList stopCodonList = gene.selectByAttribute("Note", "final-exon"); - if (stopCodonList != null && stopCodonList.size() > 0) { + if (stopCodonList != null && !stopCodonList.isEmpty()) { stopCodon = stopCodonList.get(0); if (strand == Strand.NEGATIVE) { stopCodonEnd = stopCodon.location().bioStart(); @@ -723,7 +723,7 @@ static public void addGeneMarkGTFGeneFeatures(Map ch String startCodonName = ""; String stopCodonName = ""; FeatureList startCodonList = transcriptFeature.selectByType("start_codon"); - if (startCodonList != null && startCodonList.size() > 0) { + if (startCodonList != null && !startCodonList.isEmpty()) { startCodon = startCodonList.get(0); if (strand == Strand.POSITIVE) { startCodonBegin = startCodon.location().bioStart(); @@ -735,7 +735,7 @@ static public void addGeneMarkGTFGeneFeatures(Map ch FeatureList stopCodonList = transcriptFeature.selectByType("stop_codon"); - if (stopCodonList != null && stopCodonList.size() > 0) { + if (stopCodonList != null && !stopCodonList.isEmpty()) { stopCodon = stopCodonList.get(0); if (strand == Strand.POSITIVE) { stopCodonEnd = stopCodon.location().bioEnd(); diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java index 67e22bd992..1547aba2d9 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java @@ -46,7 +46,7 @@ /** * - * @author Scooter Willis + * @author Scooter Willis * @author Mark Chapman */ public class GFF3FromUniprotBlastHits { @@ -163,7 +163,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), String notes = ""; if (featureKeyWords != null) { List keyWords = featureKeyWords.getKeyWords(); - if (keyWords.size() > 0) { + if (!keyWords.isEmpty()) { notes = ";Note="; for (String note : keyWords) { if ("Complete proteome".equals(note)) { @@ -187,7 +187,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), List cazyList = databaseReferenceHashMap.get("CAZy"); List goList = databaseReferenceHashMap.get("GO"); List eccList = databaseReferenceHashMap.get("BRENDA"); - if (pfamList != null && pfamList.size() > 0) { + if (pfamList != null && !pfamList.isEmpty()) { if (notes.length() == 0) { notes = ";Note="; } @@ -197,7 +197,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), } } - if (cazyList != null && cazyList.size() > 0) { + if (cazyList != null && !cazyList.isEmpty()) { if (notes.length() == 0) { notes = ";Note="; } @@ -208,7 +208,7 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), } } - if (eccList != null && eccList.size() > 0) { + if (eccList != null && !eccList.isEmpty()) { if (notes.length() == 0) { notes = ";Note="; } @@ -221,8 +221,8 @@ PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), } } - if (goList != null && goList.size() > 0) { - if (notes.length() == 0) { + if (goList != null && !goList.isEmpty()) { + if (notes.isEmpty()) { notes = ";Note="; } for (DBReferenceInfo note : goList) { diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java index 88af970928..0f8bd97884 100644 --- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java +++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java @@ -31,7 +31,7 @@ /** * - * @author Scooter Willis + * @author Scooter Willis */ public class GFF3Writer { @@ -122,7 +122,7 @@ public void write(OutputStream outputStream, Map chr private String getGFF3Note(List notesList) { String notes = ""; - if (notesList.size() > 0) { + if (!notesList.isEmpty()) { notes = ";Note="; int noteindex = 1; for (String note : notesList) { diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java index de6c072719..6ea23aef8a 100644 --- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java +++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java @@ -53,7 +53,7 @@ public void test11GS() throws IOException, StructureException{ s = StructureIO.getStructure(pdbID); assertNotNull(s); - assertTrue(s.getChains().size() > 0); + assertFalse(s.getChains().isEmpty()); Chain c = s.getChainByIndex(0); assertTrue(c.getSeqResGroups().size() > 2); 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 index 187e113924..e038f57cd3 100644 --- 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 @@ -69,7 +69,7 @@ public static String toXML(ModifiedCompound mc) throws IOException{ Set linkages = mc.getAtomLinkages(); - if ( linkages.size() > 0 ) { + if (!linkages.isEmpty()) { int pos = -1; for ( StructureAtomLinkage link: linkages){ pos ++; diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java index c9575a5444..0d94d36e6e 100644 --- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java +++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java @@ -285,7 +285,7 @@ public void identify(final List chains, if (residues.isEmpty()) { String pdbId = "?"; - if ( chains.size() > 0) { + if (!chains.isEmpty()) { Structure struc = chains.get(0).getStructure(); if ( struc != null) pdbId = struc.getPDBCode(); diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java index 34376307a0..ba8e6d2a3d 100644 --- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java +++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java @@ -32,7 +32,8 @@ import java.net.URL; import java.util.List; -import static org.junit.Assert.assertTrue; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertNotNull; import static org.junit.Assert.fail; @@ -100,11 +101,11 @@ public void testAcetylation() throws IOException { List sites = Site.parseSites(localFile); - assertTrue(sites.size() > 0); + assertFalse(sites.isEmpty()); for (Site s : sites) { - assertTrue(s.getResidue() != null); + assertNotNull(s.getResidue()); } diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java index 7762642c76..c508cdc206 100644 --- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java +++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java @@ -58,12 +58,12 @@ public WeakValueHashMap() { private void diddleReferenceQueue() { // Avoid making behind-the-scenes modifications while iterators exist. - if (iteratorRefs.size() > 0) { + if (!iteratorRefs.isEmpty()) { Reference ref; while ((ref = iteratorRefQueue.poll()) != null) { iteratorRefs.remove(ref); } - if (iteratorRefs.size() > 0) { + if (!iteratorRefs.isEmpty()) { return; } } diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java index 9e3c825910..c5542b4edc 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java @@ -229,7 +229,7 @@ public void keyReleased(KeyEvent e) { list.ensureIndexIsVisible(list.getSelectedIndex() - 1); return; } else if (e.getKeyCode() == KeyEvent.VK_ENTER - && list.getSelectedIndex() != -1 && suggestions.size() > 0) { + && list.getSelectedIndex() != -1 && !suggestions.isEmpty()) { setText((String) list.getSelectedValue()); @@ -365,7 +365,7 @@ public String doInBackground() { setFont(regular); - if (suggestions.size() > 0) { + if (!suggestions.isEmpty()) { list.setListData(suggestions); list.setSelectedIndex(0); list.ensureIndexIsVisible(0); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java index 136f184584..8e1a975205 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java @@ -111,7 +111,7 @@ private List getPossibleScopDomains(String userInput) { if ( stop.get()) return domains; - if ( domains == null || domains.size() < 1){ + if ( domains == null || domains.isEmpty()){ if ( userInput.length() > 5){ // e.g. d4hhba @@ -127,11 +127,11 @@ private List getPossibleScopDomains(String userInput) { if (DEBUG) System.out.println("domains: " + domains); - if ( domains == null || domains.size() < 1) { + if ( domains == null || domains.isEmpty()) { if ( userInput.length() > 0 ){ List descs = scop.filterByClassificationId(userInput); - if ( descs == null || descs.size() < 1){ + if ( descs == null || descs.isEmpty()){ descs = scop.filterByDescription(userInput); } diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java index d1ce5c0e30..feec8b0366 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java @@ -74,7 +74,7 @@ public void actionPerformed(ActionEvent event) { // check last command in history // if equivalent, don't add, // otherwise add - if (history.size()>0){ + if (!history.isEmpty()){ String txt=history.get(history.size()-1); if (! txt.equals(cmd)) { history.add(cmd); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java index 9158906d23..341483f31b 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java @@ -83,7 +83,7 @@ public String toPDB() { @Override public void toPDB(StringBuffer buf) { - if (groups == null || groups.size() < 1) { + if (groups == null || groups.isEmpty()) { return; } 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 index 771b8b5f68..5033576df0 100644 --- 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 @@ -205,7 +205,7 @@ public static String toTransformMatrices(MultipleAlignment alignment) { List btransforms = alignment.getBlockSet(bs) .getTransformations(); - if (btransforms == null || btransforms.size() < 1) + if (btransforms == null || btransforms.isEmpty()) continue; if (alignment.getBlockSets().size() > 1) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java index c6791f4ed2..e535a87508 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java @@ -1313,7 +1313,7 @@ public static Group[] prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Ato if ( afpChain.getBlockNum() > 0){ // Superimpose ligands relative to the first block - if( hetatms2.size() > 0 ) { + if(!hetatms2.isEmpty()) { if ( afpChain.getBlockRotationMatrix().length > 0 ) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java index 759ee61931..e8d5434578 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java @@ -169,7 +169,7 @@ else if ("ScoresCache".equals(child.getNodeName())){ } } //Because if it is 0 means that there were no transformations - if (transforms.size() != 0){ + if (!transforms.isEmpty()){ bs.setTransformations(transforms); } return bs; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java index 07b163730d..245d4481f6 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java @@ -57,7 +57,7 @@ public void setPair(Pair pair) { } public double getMinDistance() { - if (atomContacts.size()==0) return 0; + if (atomContacts.isEmpty()) return 0; double minDistance = Double.MAX_VALUE; for (AtomContact atomContact:atomContacts) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java index 60f7c3a91b..00cf7ef65c 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java @@ -380,7 +380,7 @@ public List getClusters(double contactOverlapScoreClu clusters = new ArrayList<>(); // nothing to do if we have no interfaces - if (list.size()==0) return clusters; + if (list.isEmpty()) return clusters; logger.debug("Calculating all-vs-all Jaccard scores for {} interfaces", list.size()); double[][] matrix = new double[list.size()][list.size()]; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java index e6b8548025..e81f7fb867 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java @@ -273,7 +273,7 @@ private void trimBondLists() { for (Chain chain : structure.getChains(modelInd)) { for (Group group : chain.getAtomGroups()) { for (Atom atom : group.getAtoms()) { - if (atom.getBonds()!=null && atom.getBonds().size() > 0) { + if (atom.getBonds()!=null && !atom.getBonds().isEmpty()) { ((ArrayList) atom.getBonds()).trimToSize(); } } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java index 58e4ee6625..f5cc851fec 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java @@ -1943,7 +1943,7 @@ private Group getCorrectAltLocGroup( Character altLoc, // see if we know this altLoc already; List atoms = currentGroup.getAtoms(); - if ( atoms.size() > 0) { + if (!atoms.isEmpty()) { Atom a1 = atoms.get(0); // we are just adding atoms to the current group // probably there is a second group following later... @@ -1956,7 +1956,7 @@ private Group getCorrectAltLocGroup( Character altLoc, List altLocs = currentGroup.getAltLocs(); for ( Group altLocG : altLocs ){ atoms = altLocG.getAtoms(); - if ( atoms.size() > 0) { + if (!atoms.isEmpty()) { for ( Atom a1 : atoms) { if (a1.getAltLoc().equals( altLoc)) { @@ -2921,7 +2921,7 @@ private void triggerEndFileChecks(){ pdbHeader.setBioAssemblies(bioAssemblyParser.getTransformationMap()); } - if (ncsOperators !=null && ncsOperators.size()>0) { + if (ncsOperators !=null && !ncsOperators.isEmpty()) { crystallographicInfo.setNcsOperators( ncsOperators.toArray(new Matrix4d[ncsOperators.size()])); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java index 7ee21de4b4..0652ad1809 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java @@ -198,7 +198,7 @@ public void mapSeqresRecords(Chain atomRes, Chain seqRes) { } } - if ( atomRes.getAtomGroups(GroupType.AMINOACID).size() < 1) { + if (atomRes.getAtomGroups(GroupType.AMINOACID).isEmpty()) { logger.debug("ATOM chain {} does not contain amino acids, ignoring...", atomRes.getId()); return; } @@ -215,7 +215,7 @@ public void mapSeqresRecords(Chain atomRes, Chain seqRes) { private void alignNucleotideChains(Chain seqRes, Chain atomRes) { - if ( atomRes.getAtomGroups(GroupType.NUCLEOTIDE).size() < 1) { + if (atomRes.getAtomGroups(GroupType.NUCLEOTIDE).isEmpty()) { logger.debug("ATOM chain {} does not contain nucleotides, ignoring...", atomRes.getId()); return; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java index 67514edd84..03ebd027c6 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java @@ -372,7 +372,7 @@ public void consumeAtomSite(AtomSite atomSite) { private Group getAltLocGroup(String recordName, Character altLoc, Character oneLetterCode, String threeLetterCode, long seqId) { List atoms = currentGroup.getAtoms(); - if (atoms.size() > 0) { + if (!atoms.isEmpty()) { if (atoms.get(0).getAltLoc().equals(altLoc)) { return currentGroup; } @@ -381,7 +381,7 @@ private Group getAltLocGroup(String recordName, Character altLoc, Character oneL List altLocs = currentGroup.getAltLocs(); for (Group altLocGroup : altLocs) { atoms = altLocGroup.getAtoms(); - if (atoms.size() > 0) { + if (!atoms.isEmpty()) { for (Atom a1 : atoms) { if (a1.getAltLoc().equals(altLoc)) { return altLocGroup; @@ -1478,7 +1478,7 @@ private void setStructNcsOps() { } } - if (ncsOperators.size() > 0) { + if (!ncsOperators.isEmpty()) { structure.getCrystallographicInfo() .setNcsOperators(ncsOperators.toArray(new Matrix4d[0])); } 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 index 21ef8bb64c..865c9e0da4 100644 --- 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 @@ -372,7 +372,7 @@ public void setInterGroupBond(int indOne, int indTwo, int bondOrder) { private Group getCorrectAltLocGroup(Character altLoc) { // see if we know this altLoc already; List atoms = group.getAtoms(); - if (atoms.size() > 0) { + if (!atoms.isEmpty()) { Atom a1 = atoms.get(0); // we are just adding atoms to the current group // probably there is a second group following later... diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java index 36bccd7b39..ff1efd6e32 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java @@ -226,7 +226,7 @@ public static BiologicalAssemblyTransformation fromXML(String xml) List transformations = fromMultiXML(xml); - if ( transformations.size() > 0) + if (!transformations.isEmpty()) return transformations.get(0); else diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java index d092d5485e..4ac55cfa08 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java @@ -655,7 +655,7 @@ private List extractRanges(String range) { } protected void downloadClaFile() throws IOException{ - if(mirrors.size()<1) { + if(mirrors.isEmpty()) { initScopURLs(); } IOException exception = null; @@ -676,7 +676,7 @@ protected void downloadClaFile() throws IOException{ } protected void downloadDesFile() throws IOException{ - if(mirrors.size()<1) { + if(mirrors.isEmpty()) { initScopURLs(); } IOException exception = null; @@ -697,7 +697,7 @@ protected void downloadDesFile() throws IOException{ } protected void downloadHieFile() throws IOException{ - if(mirrors.size()<1) { + if(mirrors.isEmpty()) { initScopURLs(); } IOException exception = null; @@ -719,7 +719,7 @@ protected void downloadHieFile() throws IOException{ } protected void downloadComFile() throws IOException{ - if(mirrors.size()<1) { + if(mirrors.isEmpty()) { initScopURLs(); } IOException exception = null; diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java index e1f4792410..b3ac53f385 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java @@ -65,7 +65,7 @@ public void completeGroup() { Set> known = new HashSet<>(permutations); //breadth-first search through the map of all members List> currentLevel = new ArrayList<>(permutations); - while( currentLevel.size() > 0) { + while(!currentLevel.isEmpty()) { List> nextLevel = new ArrayList<>(); for( List p : currentLevel) { for(List gen : gens) { diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java index b0bef7f1e6..7f434cabaf 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java @@ -211,7 +211,7 @@ public MomentsOfInertia getMomentsOfInertia() { } private void run() { - if (centers.size() > 0) { + if (!centers.isEmpty()) { return; } calcOriginalCenters(); 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 1490d27036..002d046e52 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 @@ -83,7 +83,7 @@ public void removeRotation(int index) { public void complete() { if (modified) { - if (rotations.size() > 0) { + if (!rotations.isEmpty()) { findHighestOrderAxis(); setEAxis(); calcAxesDirections(); @@ -344,7 +344,7 @@ private void calcPointGroup() { // when a structure is symmetric, some subunits are below the rmsd threshold, // and some are just above the rmsd threshold int n = 0; - if (rotations.size() > 0) { + if (!rotations.isEmpty()) { n = rotations.get(0).getPermutation().size(); rotations.clear(); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java index a6ad226698..0d52e92fef 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java @@ -79,7 +79,7 @@ public static AFPChain refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2, // Refine the alignment Map Map refined = refineSymmetry(alignment, k); - if (refined.size() < 1) + if (refined.isEmpty()) throw new RefinerFailedException("Refiner returned empty alignment"); //Substitute and partition the alignment diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java index d03e90080f..627908ac8b 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java @@ -392,10 +392,7 @@ private boolean checkGaps() { length--; } - if (shrinkColumns.size() != 0) - return true; - else - return false; + return !shrinkColumns.isEmpty(); } /** diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java index b2b3298157..5d1faa8754 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java @@ -140,7 +140,7 @@ public List> getChainIdsInEntry(String pdbId) { private void loadClusters(int sequenceIdentity) { // load clusters only once - if (clusters.size() > 0) { + if (!clusters.isEmpty()) { return; } diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java index 073a679dbb..f2f06ed2f5 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java @@ -24,6 +24,7 @@ import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertNull; import static org.junit.Assert.assertTrue; +import static org.junit.Assert.assertFalse; import static org.junit.Assert.fail; import java.io.File; @@ -408,7 +409,7 @@ public void testEmptyChemComp() throws IOException, StructureException { // should be unknown ChemComp chem = g.getChemComp(); assertNotNull(chem); - assertTrue(chem.getAtoms().size() > 0); + assertFalse(chem.getAtoms().isEmpty()); assertEquals("NON-POLYMER", chem.getType()); } finally { FileDownloadUtils.deleteDirectory(tmpCache); @@ -471,7 +472,7 @@ public void testEmptyGZChemComp() throws IOException, StructureException { // should be unknown ChemComp chem = g.getChemComp(); assertNotNull(chem); - assertTrue(chem.getAtoms().size() > 0); + assertFalse(chem.getAtoms().isEmpty()); assertEquals("NON-POLYMER", chem.getType()); } finally { FileDownloadUtils.deleteDirectory(tmpCache); diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java index d3c9568240..f579752d4c 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java @@ -205,8 +205,7 @@ public boolean doSeqResHaveAtoms(Structure s) { * @return true if has any Atom(s) */ public boolean hasAtoms(Group g) { - if (g.getAtoms().size() > 0) return true; - return false; + return !g.getAtoms().isEmpty(); } /** diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java index 8d018f6c0a..2cbdbca679 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java @@ -37,7 +37,7 @@ import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; +import static org.junit.Assert.assertFalse; public class TestMMcifOrganismParsing { @@ -90,7 +90,7 @@ private void checkPDB(String pdbId, String organismTaxId) throws IOException, St Structure s = StructureIO.getStructure(pdbId); assertNotNull(s.getEntityInfos()); - assertTrue(s.getEntityInfos().size() > 0); + assertFalse(s.getEntityInfos().isEmpty()); for ( EntityInfo c : s.getEntityInfos()) { if(EntityType.POLYMER.equals(c.getType())) { diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java index 6a9f6ae93c..2b99d660d8 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java @@ -47,9 +47,9 @@ public void test4DIA() throws Exception { for (SiftsEntity e : entities) { //System.out.println(e.getEntityId() + " " +e.getType()); - Assert.assertTrue(e.getSegments().size() > 0); + Assert.assertFalse(e.getSegments().isEmpty()); for (SiftsSegment seg : e.getSegments()) { - Assert.assertTrue(seg.getResidues().size() > 0); + Assert.assertFalse(seg.getResidues().isEmpty()); for (SiftsResidue res : seg.getResidues()) { @@ -78,9 +78,9 @@ public void test4jn3() throws Exception { for (SiftsEntity e : entities) { //System.out.println(e.getEntityId() + " " +e.getType()); - Assert.assertTrue(e.getSegments().size() > 0); + Assert.assertFalse(e.getSegments().isEmpty()); for (SiftsSegment seg : e.getSegments()) { - Assert.assertTrue(seg.getResidues().size() > 0); + Assert.assertFalse(seg.getResidues().isEmpty()); //System.out.println(seg.getResidues().size()); //System.out.println(" Segment: " + seg.getSegId() + " " + seg.getStart() + " " + seg.getEnd()) ; @@ -125,7 +125,7 @@ public void test4DOU() throws Exception { //assertTrue(seg1.getResidues().size() == 17); for (SiftsSegment seg : e.getSegments()) { - Assert.assertTrue(seg.getResidues().size() > 0); + Assert.assertFalse(seg.getResidues().isEmpty()); //System.out.println(" Segment: " + seg.getSegId() + " " + seg.getStart() + " " + seg.getEnd() + " res. size: " + seg.getResidues().size()) ; @@ -175,7 +175,7 @@ public void test4O6W() throws Exception { //System.out.println(" Segment: " + seg1.getSegId() + " " + seg1.getStart() + " " + seg1.getEnd() + " res. size: " + seg1.getResidues().size()); //assertTrue(seg1.getResidues().size() == 17); - Assert.assertTrue(seg.getResidues().size() > 0); + Assert.assertFalse(seg.getResidues().isEmpty()); for (SiftsResidue res : seg.getResidues()) { diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java index a8925afa88..8fbd1060b0 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java @@ -147,7 +147,7 @@ public void testWaterOnlyChainCif() throws IOException { Chain c = s2.getWaterChainByPDB("F"); assertNotNull("Got null when looking for water-only chain with author id F", c); - assertTrue(c.getAtomGroups().size() > 0); + assertFalse(c.getAtomGroups().isEmpty()); // checking that compounds are linked assertNotNull(c.getEntityInfo()); @@ -157,7 +157,7 @@ public void testWaterOnlyChainCif() throws IOException { Chain cAsymId = s2.getWaterChain("E"); assertNotNull("Got null when looking for water-only chain with asym id E", cAsymId); - assertTrue(cAsymId.getAtomGroups().size() > 0); + assertFalse(cAsymId.getAtomGroups().isEmpty()); assertSame(c, cAsymId); } diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java index c9f4f18056..eebdaf86ba 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java @@ -32,7 +32,7 @@ /** * Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R - * @author Scooter Willis + * @author Scooter Willis */ public class CoxInfo { @@ -505,7 +505,7 @@ public String toString(String beginLine, String del, String endLine) { o = o + beginLine + endLine; - if (baselineSurvivorFunction.size() > 0) { + if (!baselineSurvivorFunction.isEmpty()) { o = o + beginLine + "Baseline Survivor Function (at predictor means)" + endLine; for (Double time : baselineSurvivorFunction.keySet()) { Double mean = baselineSurvivorFunction.get(time); diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java index 42b34905cc..955a7c1f6d 100644 --- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java +++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java @@ -29,7 +29,7 @@ /** * - * @author Scooter Willis + * @author Scooter Willis */ public class ResidualsCoxph { @@ -108,7 +108,7 @@ public static double[][] process(CoxInfo ci, Type type, boolean useWeighted, Arr double[] weighted = ci.getWeighted(); rr = Matrix.scale(rr, weighted); } - if (cluster != null && cluster.size() > 0) { + if (cluster != null && !cluster.isEmpty()) { rr = rowsum(rr, cluster); } 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 index 542085942e..17ed18419a 100644 --- 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 @@ -27,7 +27,7 @@ * Need to handle very large spreadsheets of expression data so keep memory * footprint low * - * @author Scooter Willis + * @author Scooter Willis */ public class WorkSheet { @@ -1391,7 +1391,7 @@ static public WorkSheet unionWorkSheetsRowJoin(WorkSheet w1, WorkSheet w2, boole ArrayList joinedColumns = new ArrayList<>(); joinedColumns.addAll(w1DataColumns); joinedColumns.addAll(w2DataColumns); - if (!joinedColumns.contains("META_DATA") && (w1MetaDataColumns.size() > 0 || w2MetaDataColumns.size() > 0)) { + if (!joinedColumns.contains("META_DATA") && (!w1MetaDataColumns.isEmpty() || !w2MetaDataColumns.isEmpty())) { joinedColumns.add("META_DATA"); } for (String column : w1MetaDataColumns) { From ffff7687258311068742a61a57fcd9709204b538 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 19 Dec 2025 23:45:13 +0000 Subject: [PATCH 10/17] Bump org.apache.logging.log4j:log4j-core from 2.23.1 to 2.25.3 Bumps org.apache.logging.log4j:log4j-core from 2.23.1 to 2.25.3. --- updated-dependencies: - dependency-name: org.apache.logging.log4j:log4j-core dependency-version: 2.25.3 dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index e9f246202b..76397ae657 100644 --- a/pom.xml +++ b/pom.xml @@ -41,7 +41,7 @@ 512M 1.0.11 2.0.12 - 2.23.1 + 2.25.3 5.10.1 ciftools-java 7.0.1 From 01669f8a1402249451550c9b30608b592cadfb21 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Mon, 27 Apr 2026 05:44:25 -0500 Subject: [PATCH 11/17] Update guava dependency version to 33.6.0-jre --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index e9f246202b..998512c549 100644 --- a/pom.xml +++ b/pom.xml @@ -486,7 +486,7 @@ com.google.guava guava - 33.4.0-jre + 33.6.0-jre From 97db9acd64e4d2f0861ea28c4ac0fab2c021507c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 5 May 2026 21:44:09 +0000 Subject: [PATCH 12/17] Bump org.apache.logging.log4j:log4j-core from 2.25.3 to 2.25.4 Bumps org.apache.logging.log4j:log4j-core from 2.25.3 to 2.25.4. --- updated-dependencies: - dependency-name: org.apache.logging.log4j:log4j-core dependency-version: 2.25.4 dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 76397ae657..626206a48f 100644 --- a/pom.xml +++ b/pom.xml @@ -41,7 +41,7 @@ 512M 1.0.11 2.0.12 - 2.25.3 + 2.25.4 5.10.1 ciftools-java 7.0.1 From 96de89a50dd14011596ccaf5ee1a39c0a48a3503 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Tue, 5 May 2026 14:58:47 -0700 Subject: [PATCH 13/17] Duplicate plugin --- pom.xml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/pom.xml b/pom.xml index 76397ae657..dea60d1110 100644 --- a/pom.xml +++ b/pom.xml @@ -325,12 +325,6 @@ 3.1.3 - - org.apache.maven.plugins - maven-javadoc-plugin - 3.11.2 - - org.apache.maven.plugins maven-site-plugin From 7c3909fcff05b76440632518d6350474ca4365da Mon Sep 17 00:00:00 2001 From: josemduarte Date: Tue, 5 May 2026 15:04:44 -0700 Subject: [PATCH 14/17] Adding safeguard, bug introduced in #1116 and reported in Biojava-l --- .../biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java index 7e9d8ad7ac..6bf8af90ef 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java @@ -309,7 +309,8 @@ public void accept(WrappedAtom wrappedAtom) { } labelEntityId.add(entityId); // see https://github.com/biojava/biojava/issues/1116 - if (chain.getEntityInfo().getType() == EntityType.POLYMER) { + // note the first condition is to safeguard and to have a default that writes labelSeqId if there's no knowledge about what's the entity type + if (chain.getEntityInfo()==null || chain.getEntityInfo().getType() == EntityType.POLYMER) { labelSeqId.add(seqId); } else { labelSeqId.markNextNotPresent(); From 5d047ab428b176a437131d31171c7f779caa239e Mon Sep 17 00:00:00 2001 From: josemduarte Date: Tue, 5 May 2026 15:22:40 -0700 Subject: [PATCH 15/17] [maven-release-plugin] prepare release biojava-7.2.5 --- biojava-aa-prop/pom.xml | 6 +++--- biojava-alignment/pom.xml | 4 ++-- biojava-core/pom.xml | 2 +- biojava-genome/pom.xml | 6 +++--- biojava-integrationtest/pom.xml | 4 ++-- biojava-modfinder/pom.xml | 4 ++-- biojava-ontology/pom.xml | 2 +- biojava-protein-comparison-tool/pom.xml | 10 +++++----- biojava-protein-disorder/pom.xml | 4 ++-- biojava-structure-gui/pom.xml | 6 +++--- biojava-structure/pom.xml | 6 +++--- biojava-survival/pom.xml | 2 +- biojava-ws/pom.xml | 4 ++-- pom.xml | 4 ++-- 14 files changed, 32 insertions(+), 32 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index cbc82fff7b..ca38a3aacc 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.2.5-SNAPSHOT + 7.2.5 org.biojava biojava-structure - 7.2.5-SNAPSHOT + 7.2.5 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index b1d0bd9097..f73fa949c0 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.5-SNAPSHOT + 7.2.5 compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 909f46f088..cb7f3b5208 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 68575bbb9b..aca993304f 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.5-SNAPSHOT + 7.2.5 compile org.biojava biojava-alignment - 7.2.5-SNAPSHOT + 7.2.5 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 1c21373bd1..e3d4122962 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.5-SNAPSHOT + 7.2.5 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index e8de9e38d9..fbc0c89ad6 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.5-SNAPSHOT + 7.2.5 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 6a3fd5cbc4..f99f80e60c 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.5-SNAPSHOT + 7.2.5 biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index cf8cd570a7..cf5b3181fc 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.5-SNAPSHOT + 7.2.5 org.biojava biojava-core - 7.2.5-SNAPSHOT + 7.2.5 org.biojava biojava-structure - 7.2.5-SNAPSHOT + 7.2.5 org.biojava biojava-structure-gui - 7.2.5-SNAPSHOT + 7.2.5 net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 7273bbff8f..5fe23d98ea 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.5-SNAPSHOT + 7.2.5 diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 581b8a53cc..36d676b671 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.5-SNAPSHOT + 7.2.5 compile org.biojava biojava-core - 7.2.5-SNAPSHOT + 7.2.5 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 7fbc64a3c1..6c70ab9c58 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.5-SNAPSHOT + 7.2.5 compile org.biojava biojava-core - 7.2.5-SNAPSHOT + 7.2.5 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 88f901cdea..e4ae967a4e 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.5-SNAPSHOT + 7.2.5 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 7e960b4445..920c77414d 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5-SNAPSHOT + 7.2.5 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.5-SNAPSHOT + 7.2.5 compile diff --git a/pom.xml b/pom.xml index 581c5423be..94ef570778 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.5-SNAPSHOT + 7.2.5 biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the @@ -51,7 +51,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - HEAD + biojava-7.2.5 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index f73fa949c0..6f57e23426 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index cb7f3b5208..3ad7189c9e 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index aca993304f..698fa280c7 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT compile org.biojava biojava-alignment - 7.2.5 + 7.2.6-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index e3d4122962..349393cfa6 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.5 + 7.2.6-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index fbc0c89ad6..cec4445407 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.5 + 7.2.6-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index f99f80e60c..dff3450bc9 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index cf5b3181fc..3b43bc492d 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.5 + 7.2.6-SNAPSHOT org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT org.biojava biojava-structure - 7.2.5 + 7.2.6-SNAPSHOT org.biojava biojava-structure-gui - 7.2.5 + 7.2.6-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 5fe23d98ea..d0267a7519 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 36d676b671..314c32bf16 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.5 + 7.2.6-SNAPSHOT compile org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 6c70ab9c58..c80a8490bd 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.5 + 7.2.6-SNAPSHOT compile org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index e4ae967a4e..a8c8616fa1 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 920c77414d..eafd87dff8 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.5 + 7.2.6-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.5 + 7.2.6-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 94ef570778..9fae069ae0 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.5 + 7.2.6-SNAPSHOT biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the @@ -51,7 +51,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-7.2.5 + HEAD