From 515c623529daf9c7fb643a94fa6e55a374ed7ad4 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Wed, 12 Nov 2025 16:56:00 -0800 Subject: [PATCH 1/8] [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 3/8] 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 4/8] 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 5/8] 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 6/8] [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