From 6da7fd904f77d3c84bbb326671ea43d9c2a305d3 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Thu, 27 Feb 2025 10:18:20 -0800 Subject: [PATCH 01/32] [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 6b06141174..b417f96f4d 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.2.0 + 7.2.1-SNAPSHOT org.biojava biojava-structure - 7.2.0 + 7.2.1-SNAPSHOT diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 1d860b9ea0..4d6be17cc5 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.0 + 7.2.1-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 776112a6ed..60334dd098 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 8d8ee15617..ef5598c959 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.0 + 7.2.1-SNAPSHOT compile org.biojava biojava-alignment - 7.2.0 + 7.2.1-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 01d398e4e3..e492366488 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.0 + 7.2.1-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index e8a940627a..1f7def0959 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.0 + 7.2.1-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index ee76a29c39..013d82a5a6 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.0 + 7.2.1-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 2ab628e46f..068801a027 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.0 + 7.2.1-SNAPSHOT org.biojava biojava-core - 7.2.0 + 7.2.1-SNAPSHOT org.biojava biojava-structure - 7.2.0 + 7.2.1-SNAPSHOT org.biojava biojava-structure-gui - 7.2.0 + 7.2.1-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 90719b4aca..e643485899 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.0 + 7.2.1-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 35763e930c..589fc60734 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.0 + 7.2.1-SNAPSHOT compile org.biojava biojava-core - 7.2.0 + 7.2.1-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index de8df79dd8..5492c03468 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.0 + 7.2.1-SNAPSHOT compile org.biojava biojava-core - 7.2.0 + 7.2.1-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 8eee2ee49d..9f103b485a 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.0 + 7.2.1-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index a242020712..656570d8a4 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.0 + 7.2.1-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.0 + 7.2.1-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 84774f7281..064503177e 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.0 + 7.2.1-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-7.2.0 + HEAD From a6723d42a22166de949bed6a6c4f4f1f29a87ee7 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Fri, 28 Feb 2025 11:12:52 -0800 Subject: [PATCH 03/32] Deal with some missing fields in IHM --- .../structure/io/cif/CifStructureConsumerImpl.java | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) 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 c610c05f2b..c9ab103037 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 @@ -1297,15 +1297,18 @@ public void finish() { SeqMisMatch seqMisMatch = new SeqMisMatchImpl(); seqMisMatch.setDetails(structRefSeqDif.getDetails().get(rowIndex)); - String insCode = structRefSeqDif.getPdbxPdbInsCode().get(rowIndex); + String insCode = null; + if (structRefSeqDif.getPdbxPdbInsCode().isDefined()) { + insCode = structRefSeqDif.getPdbxPdbInsCode().get(rowIndex); if ("?".equals(insCode)) { - insCode = null; + insCode = null; + } } seqMisMatch.setInsCode(insCode); seqMisMatch.setOrigGroup(structRefSeqDif.getDbMonId().get(rowIndex)); seqMisMatch.setPdbGroup(structRefSeqDif.getMonId().get(rowIndex)); - seqMisMatch.setPdbResNum(structRefSeqDif.getPdbxAuthSeqNum().get(rowIndex)); - seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex)); + seqMisMatch.setPdbResNum(structRefSeqDif.getPdbxAuthSeqNum().isDefined()? structRefSeqDif.getPdbxAuthSeqNum().get(rowIndex):null); + seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null); seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex)); String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex); From 8286260589643583c6d631a989b708b4d8c7b956 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Fri, 28 Feb 2025 11:15:03 -0800 Subject: [PATCH 04/32] Dealing with struct_ref_seq_dif strand_id by referencing through struct_ref_seq and struct_ref --- .../io/cif/CifStructureConsumerImpl.java | 81 ++++++++++++++----- 1 file changed, 63 insertions(+), 18 deletions(-) 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 c9ab103037..23ab32f3bf 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 @@ -144,6 +144,7 @@ public class CifStructureConsumerImpl implements CifStructureConsumer { private StructNcsOper structNcsOper; private PdbxStructOperList structOpers; private StructRef structRef; + private StructRefSeq structRefSeq; private StructRefSeqDif structRefSeqDif; private StructSiteGen structSiteGen; @@ -689,7 +690,7 @@ public void consumeEntitySrcSyn(PdbxEntitySrcSyn entitySrcSyn) { @Override public void consumeEntityPolySeq(EntityPolySeq entityPolySeq) { for (int rowIndex = 0; rowIndex < entityPolySeq.getRowCount(); rowIndex++) { - Chain entityChain = getEntityChain(entityPolySeq.getEntityId().get(rowIndex)); + Chain entityChain = getEntityChain(entityPolySeq.getEntityId().get(rowIndex), true); // first we check through the chemcomp provider, if it fails we do some heuristics to guess the type of group // TODO some of this code is analogous to getNewGroup() and we should try to unify them - JD 2016-03-08 @@ -728,19 +729,27 @@ public void consumeEntityPolySeq(EntityPolySeq entityPolySeq) { } } - private Chain getEntityChain(String entityId) { + /** + * Get a chain from the temporary list holding them. If createNewChains is true, a new chain + * will be added is none are found with the given entityId + * @param entityId the entity id + * @param createNewChains whether to add new chains if not found or not. If false, null will be returned if chain not found + * @return the chain + */ + private Chain getEntityChain(String entityId, boolean createNewChains) { for (Chain chain : entityChains) { if (chain.getId().equals(entityId)) { return chain; } } - - // does not exist yet, so create... - Chain chain = new ChainImpl(); - chain.setId(entityId); - entityChains.add(chain); - - return chain; + if (createNewChains) { + // does not exist yet, so create... + Chain chain = new ChainImpl(); + chain.setId(entityId); + entityChains.add(chain); + return chain; + } + return null; } @Override @@ -967,6 +976,7 @@ public void consumeStructRef(StructRef structRef) { @Override public void consumeStructRefSeq(StructRefSeq structRefSeq) { + this.structRefSeq = structRefSeq; for (int rowIndex = 0; rowIndex < structRefSeq.getRowCount(); rowIndex++) { String refId = structRefSeq.getRefId().get(rowIndex); @@ -1173,7 +1183,7 @@ public void finish() { String entityId = structAsym.getEntityId().get(rowIndex); logger.debug("Entity {} matches asym_id: {}", entityId, id); - Chain chain = getEntityChain(entityId); + Chain chain = getEntityChain(entityId, true); Chain seqRes = (Chain) chain.clone(); // to solve issue #160 (e.g. 3u7t) seqRes = removeSeqResHeterogeneity(seqRes); @@ -1292,7 +1302,8 @@ public void finish() { setStructNcsOps(); setCrystallographicInfoMetadata(); - Map> misMatchMap = new HashMap<>(); + // entity id to list of SeqMisMatch + Map> misMatchMap = new HashMap<>(); for (int rowIndex = 0; rowIndex < structRefSeqDif.getRowCount(); rowIndex++) { SeqMisMatch seqMisMatch = new SeqMisMatchImpl(); seqMisMatch.setDetails(structRefSeqDif.getDetails().get(rowIndex)); @@ -1311,20 +1322,54 @@ public void finish() { seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null); seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex)); - String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex); - List seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>()); - seqMisMatches.add(seqMisMatch); + // try to trace the reference entity_id to struct_ref_seq -> struct_ref + String alignId = findRefIdInStructRefSeq(structRefSeqDif.getAlignId().get(rowIndex)); + if (alignId!=null) { + int entityId = findEntityIdInStructRef(alignId); + if (entityId > 0) { + List seqMisMatches = misMatchMap.computeIfAbsent(entityId, k -> new ArrayList<>()); + seqMisMatches.add(seqMisMatch); + } + } } - for (String chainId : misMatchMap.keySet()){ - Chain chain = structure.getPolyChainByPDB(chainId); + for (int entityId : misMatchMap.keySet()){ + Chain chain = getEntityChain(String.valueOf(entityId), false); if (chain == null) { - logger.warn("Could not set mismatches for chain with author id {}", chainId); + logger.warn("Could not set mismatches for chain with entity id {}", entityId); continue; } + chain.setSeqMisMatches(misMatchMap.get(entityId)); + } + } - chain.setSeqMisMatches(misMatchMap.get(chainId)); + private String findRefIdInStructRefSeq(String alignId) { + for (int rowIndex = 0; rowIndex < structRefSeq.getRowCount(); rowIndex++) { + String currentAlignId = structRefSeq.getAlignId().get(rowIndex); + if (alignId.equals(currentAlignId)) { + return structRefSeq.getRefId().isDefined()? structRefSeq.getRefId().get(rowIndex) : null; + } + } + return null; + } + + private int findEntityIdInStructRef(String refId) { + String entityIdStr = null; + for (int rowIndex = 0; rowIndex < structRef.getRowCount(); rowIndex++) { + String currentId = structRef.getId().get(rowIndex); + if (refId.equals(currentId)) { + entityIdStr = structRef.getEntityId().isDefined()? structRef.getEntityId().get(rowIndex) : null; + } + } + int entityId = -1; + if (entityIdStr != null) { + try { + entityId = Integer.parseInt(entityIdStr); + } catch (NumberFormatException e) { + logger.warn("Could not parse entity id from '{}'", entityIdStr); + } } + return entityId; } private String getEntityType(String entityId) { From 58136fe36f4c0c25d3227580e9e3d0b7f869dc7d Mon Sep 17 00:00:00 2001 From: josemduarte Date: Fri, 28 Feb 2025 13:13:47 -0800 Subject: [PATCH 05/32] Logging --- .../biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 23ab32f3bf..1de00f7e4c 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 @@ -1171,7 +1171,7 @@ public void finish() { currentModel.add(currentChain); } } else if (!params.isHeaderOnly()) { - logger.warn("current chain is null at end of document."); + logger.warn("No chains were instantiated after parsing the whole CIF document. This could be due to the atom_site category being absent"); } allModels.add(currentModel); From fdf98644c046416531cb53da0f67e8b7fc6a44cf Mon Sep 17 00:00:00 2001 From: josemduarte Date: Fri, 28 Feb 2025 13:22:51 -0800 Subject: [PATCH 06/32] Revert "Dealing with struct_ref_seq_dif strand_id by referencing through struct_ref_seq and struct_ref" This reverts commit 8286260589643583c6d631a989b708b4d8c7b956. --- .../io/cif/CifStructureConsumerImpl.java | 81 +++++-------------- 1 file changed, 18 insertions(+), 63 deletions(-) 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 1de00f7e4c..b90b085609 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 @@ -144,7 +144,6 @@ public class CifStructureConsumerImpl implements CifStructureConsumer { private StructNcsOper structNcsOper; private PdbxStructOperList structOpers; private StructRef structRef; - private StructRefSeq structRefSeq; private StructRefSeqDif structRefSeqDif; private StructSiteGen structSiteGen; @@ -690,7 +689,7 @@ public void consumeEntitySrcSyn(PdbxEntitySrcSyn entitySrcSyn) { @Override public void consumeEntityPolySeq(EntityPolySeq entityPolySeq) { for (int rowIndex = 0; rowIndex < entityPolySeq.getRowCount(); rowIndex++) { - Chain entityChain = getEntityChain(entityPolySeq.getEntityId().get(rowIndex), true); + Chain entityChain = getEntityChain(entityPolySeq.getEntityId().get(rowIndex)); // first we check through the chemcomp provider, if it fails we do some heuristics to guess the type of group // TODO some of this code is analogous to getNewGroup() and we should try to unify them - JD 2016-03-08 @@ -729,27 +728,19 @@ public void consumeEntityPolySeq(EntityPolySeq entityPolySeq) { } } - /** - * Get a chain from the temporary list holding them. If createNewChains is true, a new chain - * will be added is none are found with the given entityId - * @param entityId the entity id - * @param createNewChains whether to add new chains if not found or not. If false, null will be returned if chain not found - * @return the chain - */ - private Chain getEntityChain(String entityId, boolean createNewChains) { + private Chain getEntityChain(String entityId) { for (Chain chain : entityChains) { if (chain.getId().equals(entityId)) { return chain; } } - if (createNewChains) { - // does not exist yet, so create... - Chain chain = new ChainImpl(); - chain.setId(entityId); - entityChains.add(chain); - return chain; - } - return null; + + // does not exist yet, so create... + Chain chain = new ChainImpl(); + chain.setId(entityId); + entityChains.add(chain); + + return chain; } @Override @@ -976,7 +967,6 @@ public void consumeStructRef(StructRef structRef) { @Override public void consumeStructRefSeq(StructRefSeq structRefSeq) { - this.structRefSeq = structRefSeq; for (int rowIndex = 0; rowIndex < structRefSeq.getRowCount(); rowIndex++) { String refId = structRefSeq.getRefId().get(rowIndex); @@ -1183,7 +1173,7 @@ public void finish() { String entityId = structAsym.getEntityId().get(rowIndex); logger.debug("Entity {} matches asym_id: {}", entityId, id); - Chain chain = getEntityChain(entityId, true); + Chain chain = getEntityChain(entityId); Chain seqRes = (Chain) chain.clone(); // to solve issue #160 (e.g. 3u7t) seqRes = removeSeqResHeterogeneity(seqRes); @@ -1302,8 +1292,7 @@ public void finish() { setStructNcsOps(); setCrystallographicInfoMetadata(); - // entity id to list of SeqMisMatch - Map> misMatchMap = new HashMap<>(); + Map> misMatchMap = new HashMap<>(); for (int rowIndex = 0; rowIndex < structRefSeqDif.getRowCount(); rowIndex++) { SeqMisMatch seqMisMatch = new SeqMisMatchImpl(); seqMisMatch.setDetails(structRefSeqDif.getDetails().get(rowIndex)); @@ -1322,54 +1311,20 @@ public void finish() { seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null); seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex)); - // try to trace the reference entity_id to struct_ref_seq -> struct_ref - String alignId = findRefIdInStructRefSeq(structRefSeqDif.getAlignId().get(rowIndex)); - if (alignId!=null) { - int entityId = findEntityIdInStructRef(alignId); - if (entityId > 0) { - List seqMisMatches = misMatchMap.computeIfAbsent(entityId, k -> new ArrayList<>()); - seqMisMatches.add(seqMisMatch); - } - } + String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex); + List seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>()); + seqMisMatches.add(seqMisMatch); } - for (int entityId : misMatchMap.keySet()){ - Chain chain = getEntityChain(String.valueOf(entityId), false); + for (String chainId : misMatchMap.keySet()){ + Chain chain = structure.getPolyChainByPDB(chainId); if (chain == null) { - logger.warn("Could not set mismatches for chain with entity id {}", entityId); + logger.warn("Could not set mismatches for chain with author id {}", chainId); continue; } - chain.setSeqMisMatches(misMatchMap.get(entityId)); - } - } - private String findRefIdInStructRefSeq(String alignId) { - for (int rowIndex = 0; rowIndex < structRefSeq.getRowCount(); rowIndex++) { - String currentAlignId = structRefSeq.getAlignId().get(rowIndex); - if (alignId.equals(currentAlignId)) { - return structRefSeq.getRefId().isDefined()? structRefSeq.getRefId().get(rowIndex) : null; - } - } - return null; - } - - private int findEntityIdInStructRef(String refId) { - String entityIdStr = null; - for (int rowIndex = 0; rowIndex < structRef.getRowCount(); rowIndex++) { - String currentId = structRef.getId().get(rowIndex); - if (refId.equals(currentId)) { - entityIdStr = structRef.getEntityId().isDefined()? structRef.getEntityId().get(rowIndex) : null; - } - } - int entityId = -1; - if (entityIdStr != null) { - try { - entityId = Integer.parseInt(entityIdStr); - } catch (NumberFormatException e) { - logger.warn("Could not parse entity id from '{}'", entityIdStr); - } + chain.setSeqMisMatches(misMatchMap.get(chainId)); } - return entityId; } private String getEntityType(String entityId) { From 2841770e794679818e8eab458b387d157b97f9ec Mon Sep 17 00:00:00 2001 From: josemduarte Date: Fri, 28 Feb 2025 13:24:40 -0800 Subject: [PATCH 07/32] Deal with missing strand_id --- .../nbio/structure/io/cif/CifStructureConsumerImpl.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 b90b085609..8451d7b8fb 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 @@ -1311,7 +1311,8 @@ public void finish() { seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null); seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex)); - String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex); + String strandId = structRefSeqDif.getPdbxPdbStrandId().isDefined()? structRefSeqDif.getPdbxPdbStrandId().get(rowIndex) : null; + if (strandId == null) continue; List seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>()); seqMisMatches.add(seqMisMatch); } From 48cb462e137a17d5161f390bbf265a11bc4f48ee Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Tue, 4 Mar 2025 13:52:57 -0800 Subject: [PATCH 08/32] Update biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java Co-authored-by: Sebastian Bittrich --- .../nbio/structure/io/cif/CifStructureConsumerImpl.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 8451d7b8fb..67514edd84 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 @@ -1311,8 +1311,8 @@ public void finish() { seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null); seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex)); - String strandId = structRefSeqDif.getPdbxPdbStrandId().isDefined()? structRefSeqDif.getPdbxPdbStrandId().get(rowIndex) : null; - if (strandId == null) continue; + if (!structRefSeqDif.getPdbxPdbStrandId().isDefined()) continue; + String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex); List seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>()); seqMisMatches.add(seqMisMatch); } From 5589e1eed3c92170c71fa5da80a3f528b37413a3 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Wed, 5 Mar 2025 11:58:40 -0800 Subject: [PATCH 09/32] [maven-release-plugin] prepare release biojava-7.2.1 --- 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 b417f96f4d..4642728024 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.2.1-SNAPSHOT + 7.2.1 org.biojava biojava-structure - 7.2.1-SNAPSHOT + 7.2.1 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 4d6be17cc5..ad562e3ef9 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.1-SNAPSHOT + 7.2.1 compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 60334dd098..8a26fa5fef 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index ef5598c959..1875291310 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.1-SNAPSHOT + 7.2.1 compile org.biojava biojava-alignment - 7.2.1-SNAPSHOT + 7.2.1 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index e492366488..2b169e7212 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.1-SNAPSHOT + 7.2.1 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 1f7def0959..e99c843aa9 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.1-SNAPSHOT + 7.2.1 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 013d82a5a6..befd1e208e 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.1-SNAPSHOT + 7.2.1 biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 068801a027..82f5c7507d 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.1-SNAPSHOT + 7.2.1 org.biojava biojava-core - 7.2.1-SNAPSHOT + 7.2.1 org.biojava biojava-structure - 7.2.1-SNAPSHOT + 7.2.1 org.biojava biojava-structure-gui - 7.2.1-SNAPSHOT + 7.2.1 net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index e643485899..72705a2ec5 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.1-SNAPSHOT + 7.2.1 diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 589fc60734..27061b3c5c 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.1-SNAPSHOT + 7.2.1 compile org.biojava biojava-core - 7.2.1-SNAPSHOT + 7.2.1 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 5492c03468..72b76cbed9 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.1-SNAPSHOT + 7.2.1 compile org.biojava biojava-core - 7.2.1-SNAPSHOT + 7.2.1 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 9f103b485a..6f73371344 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.1-SNAPSHOT + 7.2.1 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 656570d8a4..e68c318de9 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.1-SNAPSHOT + 7.2.1 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.1-SNAPSHOT + 7.2.1 compile diff --git a/pom.xml b/pom.xml index 064503177e..7ae8b07016 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.1-SNAPSHOT + 7.2.1 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-7.2.1 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index ad562e3ef9..2c6b2b1ce6 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.1 + 7.2.2-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.1 + 7.2.2-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 8a26fa5fef..e3b7b4cc95 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.1 + 7.2.2-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 1875291310..4d8696959a 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.1 + 7.2.2-SNAPSHOT 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.1 + 7.2.2-SNAPSHOT compile org.biojava biojava-alignment - 7.2.1 + 7.2.2-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 2b169e7212..d20cf89df6 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.1 + 7.2.2-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.1 + 7.2.2-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index e99c843aa9..981c499e0a 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.1 + 7.2.2-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.1 + 7.2.2-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index befd1e208e..9044de341f 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.1 + 7.2.2-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 82f5c7507d..29be159250 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.1 + 7.2.2-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.1 + 7.2.2-SNAPSHOT org.biojava biojava-core - 7.2.1 + 7.2.2-SNAPSHOT org.biojava biojava-structure - 7.2.1 + 7.2.2-SNAPSHOT org.biojava biojava-structure-gui - 7.2.1 + 7.2.2-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 72705a2ec5..3c70be5d34 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.1 + 7.2.2-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.1 + 7.2.2-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 27061b3c5c..3b8112acfa 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.1 + 7.2.2-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.1 + 7.2.2-SNAPSHOT compile org.biojava biojava-core - 7.2.1 + 7.2.2-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 72b76cbed9..39baa731dd 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.1 + 7.2.2-SNAPSHOT biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.1 + 7.2.2-SNAPSHOT compile org.biojava biojava-core - 7.2.1 + 7.2.2-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 6f73371344..d5ac6b03ab 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.1 + 7.2.2-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index e68c318de9..e28c7823a3 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.1 + 7.2.2-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.1 + 7.2.2-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 7ae8b07016..899abc3d64 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.1 + 7.2.2-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-7.2.1 + HEAD From 501a09e2590965318d0a85c52d1759291060f450 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Mon, 17 Mar 2025 15:08:43 -0700 Subject: [PATCH 12/32] Make entity type case insensitive. Also improved docs --- .../biojava/nbio/structure/EntityType.java | 23 +++++++------------ 1 file changed, 8 insertions(+), 15 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java index de8b5ca4d1..f41930681a 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java @@ -21,8 +21,7 @@ package org.biojava.nbio.structure; /** - * - * The type of entity (polymer, non-polymer, water, macrolide) + * The type of entity (polymer, non-polymer, water, macrolide, branched) * as defined in the mmCIF dictionary: *

* Entities are of four types: polymer, non-polymer, macrolide and water. @@ -76,10 +75,8 @@ public enum EntityType { /** * @param entType the type of the Entity */ - private EntityType(String entType) { - + EntityType(String entType) { this.setEntityType(entType); - } /** @@ -101,19 +98,15 @@ private void setEntityType(String entityType) { * Returns null if entityType is null or not one of the supported * standard types. * - * @param entityType String value , should be one of "polymer","non-polymer","water","macrolide" - * @return an EntityType object + * @param entityType should be one of "polymer", "non-polymer", "water", "macrolide", "branched" (case insensitive) + * @return an EntityType object or null if the input string doesn't correspond to a known entity */ - public static EntityType entityTypeFromString(String entityType) - { - - if ( entityType == null) + public static EntityType entityTypeFromString(String entityType) { + if (entityType == null) return null; - for(EntityType et : EntityType.values()) - { - if(entityType.equals(et.entityType)) - { + for(EntityType et : EntityType.values()) { + if (entityType.toLowerCase().equals(et.entityType)) { return et; } } From aa0d5767badb81bc672127343ae8a1ce3ea84ad9 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Tue, 18 Mar 2025 10:59:54 -0700 Subject: [PATCH 13/32] Update biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java Co-authored-by: Sebastian Bittrich --- .../src/main/java/org/biojava/nbio/structure/EntityType.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java index f41930681a..b4978fc582 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java @@ -106,7 +106,7 @@ public static EntityType entityTypeFromString(String entityType) { return null; for(EntityType et : EntityType.values()) { - if (entityType.toLowerCase().equals(et.entityType)) { + if (entityType.equalsIgnoreCase(et.entityType)) { return et; } } From a24b6f601b4bae2c58b96bc5cf760724e06a1801 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Tue, 18 Mar 2025 13:24:36 -0700 Subject: [PATCH 14/32] Latest ciftools: should fix performance for some bcif edgecases --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 899abc3d64..10b10b029c 100644 --- a/pom.xml +++ b/pom.xml @@ -44,7 +44,7 @@ 2.23.1 5.10.1 ciftools-java - 5.0.1 + 7.0.1 scm:git:git://github.com/biojava/biojava.git From 381fedd40e6b105fa1b806b1d28b02533fb48436 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Wed, 19 Mar 2025 10:44:51 -0700 Subject: [PATCH 15/32] Formatting and docs cleanup --- .../org/biojava/nbio/structure/Structure.java | 24 ++-- .../biojava/nbio/structure/StructureImpl.java | 115 +++++------------- 2 files changed, 42 insertions(+), 97 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java index 51d69234c7..605a717577 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java @@ -232,10 +232,10 @@ public interface Structure extends Cloneable, Serializable { * Retrieve all Chains belonging to a model . * @see #getChains(int modelnr) * - * @param modelnr an int + * @param modelIdx the model index * @return a List object containing the Chains of Model nr. modelnr */ - List getModel(int modelnr); + List getModel(int modelIdx); /** * Retrieve all chains for the first model. @@ -261,17 +261,17 @@ public interface Structure extends Cloneable, Serializable { * Retrieve all chains of a model. * @see #getModel * - * @param modelnr an int + * @param modelIdx the model index * @return a List object containing the Chains of Model nr. modelnr */ - List getChains(int modelnr); + List getChains(int modelIdx); /** * Set the chains for a model * @param chains the chains for a model * @param modelnr the number of the model */ - void setChains( int modelnr, List chains); + void setChains(int modelnr, List chains); /** * Return all polymeric chains for the first model @@ -315,7 +315,7 @@ public interface Structure extends Cloneable, Serializable { /** * Return all water chains for the given model index - * @param modelIdx + * @param modelIdx the model index * @return * @since 5.0 */ @@ -332,9 +332,9 @@ public interface Structure extends Cloneable, Serializable { * Add a new chain to the model specified by the given index * * @param chain a Chain object - * @param modelnr an int specifying to which model the Chain should be added + * @param modelIdx an int specifying to which model the Chain should be added */ - void addChain(Chain chain, int modelnr); + void addChain(Chain chain, int modelIdx); /** * Retrieve a chain by its index within the Structure . @@ -348,10 +348,10 @@ public interface Structure extends Cloneable, Serializable { * Retrieve a chain by its indices within the Structure and model. * * @param chainIndex the index of the desired chain in the structure - * @param modelnr the model the desired chain is in + * @param modelIdx the model index * @return a Chain object */ - Chain getChainByIndex(int modelnr, int chainIndex); + Chain getChainByIndex(int modelIdx, int chainIndex); /** * Check if a chain with the chainId aymId is contained in this structure. @@ -394,11 +394,11 @@ public interface Structure extends Cloneable, Serializable { * considers only model nr X. count starts with 0. * @param authId the chain name of the chain to use * @param pdbResnum the PDB residue number of the requested group - * @param modelnr the number of the model to use + * @param modelIdx the model index * @return Group the requested Group * @throws StructureException */ - Group findGroup(String authId, String pdbResnum, int modelnr) throws StructureException; + Group findGroup(String authId, String pdbResnum, int modelIdx) throws StructureException; /** * Retrieve a Chain (polymeric, non-polymeric or water) based on diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java index ae00c8f7f3..1f5e371e56 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java @@ -123,20 +123,15 @@ public Structure clone() { n.setDBRefs(this.getDBRefs()); n.setSites(getSites()); - // go through each chain and clone chain for (int i=0;i cloned_model = new ArrayList<>(); for (int j=0;j models.size()) - throw new StructureException(" no model nr " + modelnr + + if ( modelIdx > models.size()) + throw new StructureException(" no model nr " + modelIdx + " in this structure. (contains "+models.size()+")"); - // first we need to gather all groups with the author id chainName: polymers, non-polymers and waters - Chain polyChain = getPolyChainByPDB(chainName, modelnr); + Chain polyChain = getPolyChainByPDB(chainName, modelIdx); if(polyChain != null) { - List groups = new ArrayList<>(); - - groups.addAll(polyChain.getAtomGroups()); + List groups = new ArrayList<>(polyChain.getAtomGroups()); // there can be more than one non-poly chain for a given author id - for (Chain chain: getNonPolyChainsByPDB(chainName, modelnr)) { + for (Chain chain: getNonPolyChainsByPDB(chainName, modelIdx)) { groups.addAll(chain.getAtomGroups()); } - Chain water = getWaterChainByPDB(chainName, modelnr); + Chain water = getWaterChainByPDB(chainName, modelIdx); if (water!=null) groups.addAll(water.getAtomGroups()); - - // now iterate over all groups // in order to find the amino acid that has this pdbRenum. @@ -260,7 +249,7 @@ public void addChain(Chain chain) { /** {@inheritDoc} */ @Override - public void addChain(Chain chain, int modelnr) { + public void addChain(Chain chain, int modelIdx) { // if model has not been initialized, init it! chain.setStructure(this); if (models.isEmpty()) { @@ -271,16 +260,11 @@ public void addChain(Chain chain, int modelnr) { models.add(model); } else { - Model model = models.get(modelnr); + Model model = models.get(modelIdx); model.addChain(chain); } - - - } - - /** {@inheritDoc} */ @Override public Chain getChainByIndex(int number) { @@ -293,9 +277,9 @@ public Chain getChainByIndex(int number) { /** {@inheritDoc} */ @Override - public Chain getChainByIndex(int modelnr,int number) { + public Chain getChainByIndex(int modelIdx, int number) { - Model model = models.get(modelnr); + Model model = models.get(modelIdx); return model.getChains().get(number); } @@ -333,8 +317,6 @@ public void setModel(int position, List modelChains){ c.setStructure(this); //System.out.println("model size:" + models.size()); - - Model model = new Model(); model.setChains(modelChains); @@ -350,7 +332,7 @@ public void setModel(int position, List modelChains){ */ @Override public String toString(){ - String newline = System.getProperty("line.separator"); + String newline = System.lineSeparator(); StringBuilder str = new StringBuilder(); str.append("structure "); str.append(name); @@ -384,16 +366,12 @@ public String toString(){ List hgr = cha.getAtomGroups(GroupType.HETATM); List ngr = cha.getAtomGroups(GroupType.NUCLEOTIDE); - - - str.append("chain ") .append(j).append(": asymId:") .append(cha.getId()) .append(" authId:") .append(cha.getName()).append(" "); - if ( cha.getEntityInfo() != null){ EntityInfo comp = cha.getEntityInfo(); String molName = comp.getDescription(); @@ -406,7 +384,6 @@ public String toString(){ .append(")"); } - str.append(newline); str.append(" length SEQRES: ").append(cha.getSeqResLength()); str.append(" length ATOM: ").append(cha.getAtomLength()); @@ -425,7 +402,6 @@ public String toString(){ str.append(mol).append(newline); } - return str.toString() ; } @@ -566,8 +542,6 @@ public List getWaterChains(int modelIdx) { return models.get(modelIdx).getWaterChains(); } - - /** {@inheritDoc} */ @Override public void setChains(int modelnr, List chains){ @@ -584,37 +558,32 @@ public void setChains(int modelnr, List chains){ } - /** Retrieve all Chains belonging to a model . - * - * @param modelnr an int - * @return a List object + /** + * {@inheritDoc} */ @Override - public List getModel(int modelnr) { + public List getModel(int modelIdx) { - return models.get(modelnr).getChains(); + return models.get(modelIdx).getChains(); } /** {@inheritDoc} */ @Override - public Chain getChain(String asymId, int modelnr) { + public Chain getChain(String asymId, int modelIdx) { - List chains = getChains(modelnr); + List chains = getChains(modelIdx); for (Chain c : chains) { if (c.getId().equals(asymId)) { return c; } } return null; - } /** {@inheritDoc} */ @Override public Chain getChain(String asymId) { - return getChain(asymId,0); - } @Override @@ -693,7 +662,6 @@ public List getNonPolyChainsByPDB(String authId, int modelIdx) { return chains; } - List nonpolyChains = model.getNonPolyChains(); for (Chain c : nonpolyChains){ if (c.getName().equals(authId)) @@ -745,8 +713,6 @@ public Chain getWaterChainByPDB(String authId, int modelIdx) { return null; } - - /** {@inheritDoc} */ @Override public String toPDB() { @@ -835,7 +801,6 @@ public EntityInfo getEntityById(int entityId) { return null; } - /** {@inheritDoc} */ @Override public List getDBRefs() { @@ -872,7 +837,6 @@ public void setPDBHeader(PDBHeader pdbHeader){ @Override public List getSSBonds(){ return ssbonds; - } /** {@inheritDoc} */ @@ -882,9 +846,7 @@ public void setSSBonds(List ssbonds){ } /** - * Adds a single disulfide Bond to this structure - * - * @param ssbond the SSBond. + * {@inheritDoc} */ @Override public void addSSBond(Bond ssbond){ @@ -892,10 +854,7 @@ public void addSSBond(Bond ssbond){ } /** - * Return whether or not the entry has an associated journal article - * or publication. The JRNL section is not mandatory and thus may not be - * present. - * @return flag if a JournalArticle could be found. + * R{@inheritDoc} */ @Override public boolean hasJournalArticle() { @@ -903,9 +862,7 @@ public boolean hasJournalArticle() { } /** - * get the associated publication as defined by the JRNL records in a PDB - * file. - * @return a JournalArticle + * {@inheritDoc} */ @Override public JournalArticle getJournalArticle() { @@ -913,9 +870,7 @@ public JournalArticle getJournalArticle() { } /** - * set the associated publication as defined by the JRNL records in a PDB - * file. - * @param journalArticle the article + * {@inheritDoc} */ @Override public void setJournalArticle(JournalArticle journalArticle) { @@ -923,29 +878,21 @@ public void setJournalArticle(JournalArticle journalArticle) { } /** - * @return the sites contained in this structure + * {@inheritDoc} */ - @Override public List getSites() { return sites; } /** - * @param sites the sites to set in the structure + * {@inheritDoc} */ - @Override public void setSites(List sites) { this.sites = sites; } - /** Caution: we should probably remove this to avoid confusion. Currently this is always an empty list! - * - * @return a list of Groups listed in the HET records - this will not - * include any waters. - */ - /** * Sets a flag to indicate if this structure is a biological assembly * @param biologicalAssembly true if biological assembly, otherwise false @@ -1026,19 +973,17 @@ public void setPDBCode(String pdb_id){ pdbId = new PdbId(pdb_id); } } - - - /** {@inheritDoc} - * @since 6.0.0 - * */ + /** + * {@inheritDoc} + **/ public PdbId getPdbId() { return this.pdbId; } - /** {@inheritDoc} - * @since 6.0.0 - * */ + /** + * {@inheritDoc} + **/ public void setPdbId(PdbId pdbId) { this.pdbId = pdbId; } From 743a9fdc23eaadd4f60a93e57618a33bb2857c49 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Wed, 19 Mar 2025 10:53:06 -0700 Subject: [PATCH 16/32] More cleanup --- .../org/biojava/nbio/structure/Structure.java | 8 ++-- .../biojava/nbio/structure/StructureImpl.java | 45 +++++-------------- 2 files changed, 14 insertions(+), 39 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java index 605a717577..05bd0ba859 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java @@ -178,10 +178,10 @@ public interface Structure extends Cloneable, Serializable { /** * Return number of chains of model. * - * @param modelnr an int specifying the number of the Model that should be used + * @param modelIdx an int specifying the index of the Model that should be used * @return an int representing the number of Chains in this Model */ - int size(int modelnr); + int size(int modelIdx); /** * Return the number of models . @@ -269,9 +269,9 @@ public interface Structure extends Cloneable, Serializable { /** * Set the chains for a model * @param chains the chains for a model - * @param modelnr the number of the model + * @param modelIdx the model index */ - void setChains(int modelnr, List chains); + void setChains(int modelIdx, List chains); /** * Return all polymeric chains for the first model diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java index 1f5e371e56..f91f8aff23 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java @@ -268,24 +268,17 @@ public void addChain(Chain chain, int modelIdx) { /** {@inheritDoc} */ @Override public Chain getChainByIndex(int number) { - - int modelnr = 0 ; - - return getChainByIndex(modelnr,number); + return getChainByIndex(0, number); } /** {@inheritDoc} */ @Override public Chain getChainByIndex(int modelIdx, int number) { - Model model = models.get(modelIdx); - return model.getChains().get(number); } - - /** {@inheritDoc} */ @Override public void addModel(List modelChains){ @@ -297,7 +290,6 @@ public void addModel(List modelChains){ models.add(model); } - /** {@inheritDoc} */ @Override public void setChains(List chains){ @@ -305,8 +297,6 @@ public void setChains(List chains){ setModel(0,chains); } - - /** {@inheritDoc} */ @Override public void setModel(int position, List modelChains){ @@ -327,9 +317,6 @@ public void setModel(int position, List modelChains){ } } - /** String representation. - * - */ @Override public String toString(){ String newline = System.lineSeparator(); @@ -418,15 +405,11 @@ public int size() { } - /** return number of chains of model. - * - */ @Override - public int size(int modelnr) { return models.get(modelnr).size(); } + public int size(int modelIdx) { return models.get(modelIdx).size(); } // some NMR stuff : - /** return number of models. */ @Override public int nrModels() { return models.size() ; @@ -496,16 +479,15 @@ public List getChains(int modelIdx){ /** {@inheritDoc} */ @Override public List getChains(){ - if (models.size()==0) { + if (models.isEmpty()) { return new ArrayList<>(0); } return getChains(0); - } @Override public List getPolyChains() { - if (models.size()==0) { + if (models.isEmpty()) { return new ArrayList<>(0); } return getPolyChains(0); @@ -518,7 +500,7 @@ public List getPolyChains(int modelIdx) { @Override public List getNonPolyChains() { - if (models.size()==0) { + if (models.isEmpty()) { return new ArrayList<>(0); } return getNonPolyChains(0); @@ -531,7 +513,7 @@ public List getNonPolyChains(int modelIdx) { @Override public List getWaterChains() { - if (models.size()==0) { + if (models.isEmpty()) { return new ArrayList<>(0); } return getWaterChains(0); @@ -544,18 +526,17 @@ public List getWaterChains(int modelIdx) { /** {@inheritDoc} */ @Override - public void setChains(int modelnr, List chains){ + public void setChains(int modelIdx, List chains){ for (Chain c: chains){ c.setStructure(this); } - if (models.size()>modelnr) { - models.remove(modelnr); + if (models.size()> modelIdx) { + models.remove(modelIdx); } Model model = new Model(); model.setChains(chains); - models.add(modelnr, model); - + models.add(modelIdx, model); } /** @@ -563,7 +544,6 @@ public void setChains(int modelnr, List chains){ */ @Override public List getModel(int modelIdx) { - return models.get(modelIdx).getChains(); } @@ -606,7 +586,6 @@ public Chain getPolyChain(String asymId, int modelIdx) { return null; } - @Override public Chain getNonPolyChain(String asymId) { return getNonPolyChain(asymId, 0); @@ -624,7 +603,6 @@ public Chain getNonPolyChain(String asymId, int modelIdx) { if (c.getId().equals(asymId)) return c; } - return null; } @@ -676,7 +654,6 @@ public Chain getWaterChain(String asymId) { return getWaterChain(asymId, 0); } - @Override public Chain getWaterChain(String asymId, int modelIdx) { Model model = models.get(modelIdx); @@ -697,7 +674,6 @@ public Chain getWaterChainByPDB(String authId) { return getWaterChainByPDB(authId, 0); } - @Override public Chain getWaterChainByPDB(String authId, int modelIdx) { Model model = models.get(modelIdx); @@ -820,7 +796,6 @@ public void setDBRefs(List dbrefs) { this.dbrefs = dbrefs; } - /** {@inheritDoc} */ @Override public PDBHeader getPDBHeader() { From c33627f85311f35b5efc947c94cd7439b0db82c5 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Wed, 19 Mar 2025 11:03:04 -0700 Subject: [PATCH 17/32] More cleanup --- .../biojava/nbio/structure/StructureImpl.java | 18 +++++------------- 1 file changed, 5 insertions(+), 13 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java index f91f8aff23..b0165ec3a7 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java @@ -243,8 +243,7 @@ public void setStructureIdentifier(StructureIdentifier structureIdentifier) { /** {@inheritDoc} */ @Override public void addChain(Chain chain) { - int modelnr = 0 ; - addChain(chain,modelnr); + addChain(chain, 0); } /** {@inheritDoc} */ @@ -293,8 +292,7 @@ public void addModel(List modelChains){ /** {@inheritDoc} */ @Override public void setChains(List chains){ - - setModel(0,chains); + setModel(0, chains); } /** {@inheritDoc} */ @@ -359,7 +357,7 @@ public String toString(){ .append(" authId:") .append(cha.getName()).append(" "); - if ( cha.getEntityInfo() != null){ + if (cha.getEntityInfo() != null){ EntityInfo comp = cha.getEntityInfo(); String molName = comp.getDescription(); if ( molName != null){ @@ -394,22 +392,16 @@ public String toString(){ @Override public int size() { - int modelnr = 0 ; - if (!models.isEmpty()) { - return models.get(modelnr).getPolyChains().size(); - } - else { + return models.get(0).getPolyChains().size(); + } else { return 0 ; } - } @Override public int size(int modelIdx) { return models.get(modelIdx).size(); } - // some NMR stuff : - @Override public int nrModels() { return models.size() ; From 7217ee82acf8098206d67b67feb54c0ed5170b6a Mon Sep 17 00:00:00 2001 From: josemduarte Date: Wed, 19 Mar 2025 12:58:42 -0700 Subject: [PATCH 18/32] Safeguards --- .../main/java/org/biojava/nbio/structure/StructureImpl.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java index b0165ec3a7..0a697e2d7b 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java @@ -536,13 +536,13 @@ public void setChains(int modelIdx, List chains){ */ @Override public List getModel(int modelIdx) { + if (models.isEmpty()) return new ArrayList<>(); return models.get(modelIdx).getChains(); } /** {@inheritDoc} */ @Override public Chain getChain(String asymId, int modelIdx) { - List chains = getChains(modelIdx); for (Chain c : chains) { if (c.getId().equals(asymId)) { @@ -566,6 +566,8 @@ public Chain getPolyChain(String asymId) { @Override public Chain getPolyChain(String asymId, int modelIdx) { + if (models.isEmpty()) return null; + Model model = models.get(modelIdx); if (model==null) { return null; From 6e7891b630262ff75f70430ac27629932e6740c5 Mon Sep 17 00:00:00 2001 From: josemduarte Date: Thu, 20 Mar 2025 12:19:40 -0700 Subject: [PATCH 19/32] [maven-release-plugin] prepare release biojava-7.2.2 --- 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 4de0856cdb..e53c796e3d 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.2.2-SNAPSHOT + 7.2.2 org.biojava biojava-structure - 7.2.2-SNAPSHOT + 7.2.2 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 2c6b2b1ce6..4d64a820ce 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.2-SNAPSHOT + 7.2.2 compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index e3b7b4cc95..7662ec2488 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 4d8696959a..4ce37b1110 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.2-SNAPSHOT + 7.2.2 compile org.biojava biojava-alignment - 7.2.2-SNAPSHOT + 7.2.2 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index d20cf89df6..12bb171142 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.2-SNAPSHOT + 7.2.2 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 981c499e0a..baf5f746ce 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.2-SNAPSHOT + 7.2.2 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 9044de341f..4fa75588f4 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.2-SNAPSHOT + 7.2.2 biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 29be159250..e8c0c8da22 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.2-SNAPSHOT + 7.2.2 org.biojava biojava-core - 7.2.2-SNAPSHOT + 7.2.2 org.biojava biojava-structure - 7.2.2-SNAPSHOT + 7.2.2 org.biojava biojava-structure-gui - 7.2.2-SNAPSHOT + 7.2.2 net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 3c70be5d34..bb8885d2d8 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.2-SNAPSHOT + 7.2.2 diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 3b8112acfa..569a2b4d43 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.2-SNAPSHOT + 7.2.2 compile org.biojava biojava-core - 7.2.2-SNAPSHOT + 7.2.2 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 39baa731dd..7a9e8da139 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.2-SNAPSHOT + 7.2.2 compile org.biojava biojava-core - 7.2.2-SNAPSHOT + 7.2.2 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index d5ac6b03ab..8deffb1d69 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.2-SNAPSHOT + 7.2.2 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index e28c7823a3..2a649166a1 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.2-SNAPSHOT + 7.2.2 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.2-SNAPSHOT + 7.2.2 compile diff --git a/pom.xml b/pom.xml index 10b10b029c..a7ba4e4e52 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.2-SNAPSHOT + 7.2.2 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-7.2.2 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 4d64a820ce..fe75c181c7 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.2 + 7.2.3-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.2 + 7.2.3-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 7662ec2488..0836ffe54c 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.2 + 7.2.3-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 4ce37b1110..7729a6e9e3 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.2 + 7.2.3-SNAPSHOT 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.2 + 7.2.3-SNAPSHOT compile org.biojava biojava-alignment - 7.2.2 + 7.2.3-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 12bb171142..2c44988004 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.2 + 7.2.3-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.2 + 7.2.3-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index baf5f746ce..0b8cb53791 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.2 + 7.2.3-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.2 + 7.2.3-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 4fa75588f4..001e3e52f1 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.2 + 7.2.3-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index e8c0c8da22..12e4941d55 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.2 + 7.2.3-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.2 + 7.2.3-SNAPSHOT org.biojava biojava-core - 7.2.2 + 7.2.3-SNAPSHOT org.biojava biojava-structure - 7.2.2 + 7.2.3-SNAPSHOT org.biojava biojava-structure-gui - 7.2.2 + 7.2.3-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index bb8885d2d8..82107e8058 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.2 + 7.2.3-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.2 + 7.2.3-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 569a2b4d43..24644c8ffe 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.2 + 7.2.3-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.2 + 7.2.3-SNAPSHOT compile org.biojava biojava-core - 7.2.2 + 7.2.3-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 7a9e8da139..5392798310 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.2 + 7.2.3-SNAPSHOT biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.2 + 7.2.3-SNAPSHOT compile org.biojava biojava-core - 7.2.2 + 7.2.3-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 8deffb1d69..4f3e00f56b 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.2 + 7.2.3-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 2a649166a1..7a4fa63589 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.2 + 7.2.3-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.2 + 7.2.3-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index a7ba4e4e52..f17d3c2d67 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.2 + 7.2.3-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-7.2.2 + HEAD From 7b82b27b15c76899a9042386ea955882feaa070e Mon Sep 17 00:00:00 2001 From: Jose Duarte Date: Fri, 18 Jul 2025 08:18:34 -0700 Subject: [PATCH 22/32] Using new mvn central plugin --- pom.xml | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/pom.xml b/pom.xml index f17d3c2d67..c2a70eb02e 100644 --- a/pom.xml +++ b/pom.xml @@ -580,17 +580,20 @@ release - - + - org.sonatype.plugins - nexus-staging-maven-plugin - 1.6.13 + org.sonatype.central + central-publishing-maven-plugin + 0.8.0 true - ossrh - https://oss.sonatype.org/ - true + + central + + + true + + published From 274a36abf39908eb0eb27c3da6d8e47ae875a83d Mon Sep 17 00:00:00 2001 From: Jose Duarte Date: Fri, 7 Nov 2025 21:53:06 -0800 Subject: [PATCH 23/32] Fix for #1116 --- CHANGELOG.md | 5 +++++ .../nbio/structure/io/cif/AbstractCifFileSupplier.java | 7 ++++++- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 74b52303b0..07be3a5172 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,11 @@ BioJava Changelog ----------------- +BioJava 7.2.3 - future release +============================== +### Fixed +* Don't use label_seq_id in mmCIF output for non-polymers #1116 + BioJava 7.2.2 ============================== ### Fixed 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 826d9588ef..7e9d8ad7ac 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 @@ -308,7 +308,12 @@ public void accept(WrappedAtom wrappedAtom) { } } labelEntityId.add(entityId); - labelSeqId.add(seqId); + // see https://github.com/biojava/biojava/issues/1116 + if (chain.getEntityInfo().getType() == EntityType.POLYMER) { + labelSeqId.add(seqId); + } else { + labelSeqId.markNextNotPresent(); + } String insCode = ""; if (group.getResidueNumber().getInsCode() != null) { insCode = Character.toString(group.getResidueNumber().getInsCode()); From 611fcadeaa9f7dee203de34ae5d8d448df03ea8c Mon Sep 17 00:00:00 2001 From: josemduarte Date: Wed, 12 Nov 2025 16:55:57 -0800 Subject: [PATCH 24/32] [maven-release-plugin] prepare release biojava-7.2.3 --- 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 b2b642b661..0c1016c3b6 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.2.3-SNAPSHOT + 7.2.3 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.2.3-SNAPSHOT + 7.2.3 org.biojava biojava-structure - 7.2.3-SNAPSHOT + 7.2.3 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index fe75c181c7..7bb6e3b2ee 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.3-SNAPSHOT + 7.2.3 biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.2.3-SNAPSHOT + 7.2.3 compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 0836ffe54c..890ce360bc 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.3-SNAPSHOT + 7.2.3 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 7729a6e9e3..79608afaf4 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.3-SNAPSHOT + 7.2.3 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.2.3-SNAPSHOT + 7.2.3 compile org.biojava biojava-alignment - 7.2.3-SNAPSHOT + 7.2.3 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 2c44988004..41d9be230c 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.3-SNAPSHOT + 7.2.3 biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.2.3-SNAPSHOT + 7.2.3 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 0b8cb53791..876203f207 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.3-SNAPSHOT + 7.2.3 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.2.3-SNAPSHOT + 7.2.3 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 001e3e52f1..02e4a894d2 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.3-SNAPSHOT + 7.2.3 biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 12e4941d55..b4de1b1e8a 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-SNAPSHOT + 7.2.3 biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.2.3-SNAPSHOT + 7.2.3 org.biojava biojava-core - 7.2.3-SNAPSHOT + 7.2.3 org.biojava biojava-structure - 7.2.3-SNAPSHOT + 7.2.3 org.biojava biojava-structure-gui - 7.2.3-SNAPSHOT + 7.2.3 net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 82107e8058..d5e216b60d 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.3-SNAPSHOT + 7.2.3 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.2.3-SNAPSHOT + 7.2.3 diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 24644c8ffe..62db686d60 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.3-SNAPSHOT + 7.2.3 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.2.3-SNAPSHOT + 7.2.3 compile org.biojava biojava-core - 7.2.3-SNAPSHOT + 7.2.3 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 5392798310..aeff7465c0 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.2.3-SNAPSHOT + 7.2.3 biojava-structure biojava-structure @@ -51,13 +51,13 @@ org.biojava biojava-alignment - 7.2.3-SNAPSHOT + 7.2.3 compile org.biojava biojava-core - 7.2.3-SNAPSHOT + 7.2.3 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 4f3e00f56b..a1facab532 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.2.3-SNAPSHOT + 7.2.3 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 7a4fa63589..23866ccbb1 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.2.3-SNAPSHOT + 7.2.3 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.2.3-SNAPSHOT + 7.2.3 compile diff --git a/pom.xml b/pom.xml index c2a70eb02e..c4dfdd3b74 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.2.3-SNAPSHOT + 7.2.3 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-7.2.3 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 27/32] 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 28/32] 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 29/32] 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 30/32] [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