From 9db10aab4d3018cfb4dcc28245e7ea61969768c2 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Wed, 29 Aug 2018 16:37:16 -0700 Subject: [PATCH 01/18] [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-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 ++-- 13 files changed, 27 insertions(+), 27 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index fe4b22fc76..8f0647227f 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 5.1.0 + 5.1.1-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 5.1.0 + 5.1.1-SNAPSHOT org.biojava biojava-structure - 5.1.0 + 5.1.1-SNAPSHOT diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index edef4a4126..447ff8d99d 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 5.1.0 + 5.1.1-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 5.1.0 + 5.1.1-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 1af462e7f2..173aa0c21b 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 5.1.0 + 5.1.1-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 8c290fb3ce..c0322a8298 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 5.1.0 + 5.1.1-SNAPSHOT 4.0.0 biojava-genome @@ -85,13 +85,13 @@ org.biojava biojava-core - 5.1.0 + 5.1.1-SNAPSHOT compile org.biojava biojava-alignment - 5.1.0 + 5.1.1-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index cd9ce7282e..942ec5f494 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 5.1.0 + 5.1.1-SNAPSHOT biojava-integrationtest jar @@ -28,7 +28,7 @@ org.biojava biojava-structure - 5.1.0 + 5.1.1-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index b726e28519..6e4bb240c2 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 5.1.0 + 5.1.1-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 5.1.0 + 5.1.1-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 41cfe229df..cf670de666 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 5.1.0 + 5.1.1-SNAPSHOT biojava-ontology diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index ca7c3130a5..0981772719 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 5.1.0 + 5.1.1-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 5.1.0 + 5.1.1-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 7f0e8d9eac..eb3be1bda1 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 5.1.0 + 5.1.1-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 5.1.0 + 5.1.1-SNAPSHOT compile org.biojava biojava-core - 5.1.0 + 5.1.1-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 88ee84457e..41d65cf3ab 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 5.1.0 + 5.1.1-SNAPSHOT biojava-structure biojava-structure @@ -40,13 +40,13 @@ org.biojava biojava-alignment - 5.1.0 + 5.1.1-SNAPSHOT compile org.biojava biojava-core - 5.1.0 + 5.1.1-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index a90e42d981..0b682a90ae 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 5.1.0 + 5.1.1-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index e7282143aa..e500b9ee8a 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 5.1.0 + 5.1.1-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 5.1.0 + 5.1.1-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index a71b8756e6..1cfcaedd38 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 5.1.0 + 5.1.1-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 @@ -48,7 +48,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-5.1.0 + HEAD From edd7554501323e81cc1dafd167514c06ad2e2c2a Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Wed, 29 Aug 2018 17:11:45 -0700 Subject: [PATCH 03/18] Updating readme --- readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/readme.md b/readme.md index 7a8bd283ad..dd26f0e8e1 100644 --- a/readme.md +++ b/readme.md @@ -1,6 +1,6 @@ # Welcome to -[![Build Status](https://travis-ci.org/biojava/biojava.svg?branch=master)](https://travis-ci.org/biojava/biojava) [![Version](http://img.shields.io/badge/version-5.0.2-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-5.0.2) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) +[![Build Status](https://travis-ci.org/biojava/biojava.svg?branch=master)](https://travis-ci.org/biojava/biojava) [![Version](http://img.shields.io/badge/version-5.1.0-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-5.1.0) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) 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, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. From ee92195c44c552242588893aeedbc9ecb1253bd5 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Mon, 3 Sep 2018 14:20:47 -0700 Subject: [PATCH 04/18] More explicit operator ids for assembly cases with cartesian product. Added test --- .../structure/test/io/TestBioassemblies.java | 35 ++++++ .../io/mmcif/model/PdbxStructOperList.java | 90 ++++++--------- .../io/mmtf/MmtfStructureReader.java | 2 +- .../quaternary/BiologicalAssemblyBuilder.java | 103 +++++++++++------- .../quaternary/OperatorResolver.java | 3 +- 5 files changed, 133 insertions(+), 100 deletions(-) diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java index a18d453d7d..f98dbfb2d3 100644 --- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java +++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestBioassemblies.java @@ -104,6 +104,41 @@ public void test4TTX() throws IOException, StructureException { assertEquals(2, multiModelBioAssemblies.get(2).getPolyChains().size()); assertEquals(2, flattenedBioAssemblies.get(2).getPolyChains().size()); + // all 3 flattened bioassemblies have operator id 1 in their new chain ids + assertEquals("1", flattenedBioAssemblies.get(0).getPolyChains().get(0).getId().split("_")[1]); + assertEquals("1", flattenedBioAssemblies.get(1).getPolyChains().get(0).getId().split("_")[1]); + assertEquals("1", flattenedBioAssemblies.get(2).getPolyChains().get(0).getId().split("_")[1]); + + StructureIO.setAtomCache(prevAtomCache); + + } + + + /** + * A test for an entry with cartesian product in assembly operators + * @throws StructureException + * @throws IOException + */ + @Test + public void test1M4X() throws IOException, StructureException { + + AtomCache prevAtomCache = StructureIO.getAtomCache(); + AtomCache cache = new AtomCache(); + cache.setUseMmCif(true); + StructureIO.setAtomCache(cache); + + Structure flattenedBioAssembly5 = StructureIO.getBiologicalAssembly("1M4X" , 5); + + // checking that we have 1 model only + assertEquals(1, flattenedBioAssembly5.nrModels()); + + // bioassembly 5 expands to 90 chains (3 chains x 5 operators x 6 operators), the expression is '(1-5)(61-88)' + assertEquals(90, flattenedBioAssembly5.getPolyChains().size()); + + // the operator ids are composed for this case, e.g. A_5x61 + assertTrue(flattenedBioAssembly5.getPolyChains().get(0).getId().contains("x")); + assertEquals(2, flattenedBioAssembly5.getPolyChains().get(0).getId().split("_").length); + StructureIO.setAtomCache(prevAtomCache); } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java index 34effb0657..3a0819f4f4 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java @@ -20,15 +20,11 @@ */ package org.biojava.nbio.structure.io.mmcif.model; - -import org.biojava.nbio.structure.jama.Matrix; - import javax.xml.bind.annotation.XmlAccessType; import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import java.io.Serializable; -import java.util.Arrays; /** * The bean for pdbx_struct_oper_list category @@ -59,8 +55,7 @@ public class PdbxStructOperList implements Serializable{ @Override public String toString() { - return "PdbxStructOperList [id=" + id + ", type=" + type + ", matrix=" - + matrix + ", vector=" + Arrays.toString(vector) + "]"; + return "PdbxStructOperList [id=" + id + ", type=" + type + "]"; } @@ -104,18 +99,12 @@ public String toString() { // from here fields that are not in the cif category - - @IgnoreField - private Matrix matrix; - @IgnoreField - private double[] vector; public PdbxStructOperList(){ - matrix = Matrix.identity(3,3); - vector = new double[3]; } + @XmlAttribute public String getType() { return type; @@ -125,21 +114,6 @@ public void setType(String type) { this.type = type; } - public Matrix getMatrix() { - return matrix; - } - - public void setMatrix(Matrix matrix) { - this.matrix = matrix; - } - @XmlAttribute - public double[] getVector() { - return vector; - } - - public void setVector(double[] vector) { - this.vector = vector; - } @XmlAttribute public String getId() { return id; @@ -150,32 +124,32 @@ public void setId(String id) { } public void setMatrix11(String val){ - matrix.set(0,0,Double.parseDouble(val)); + this.matrix11 = val; } public void setMatrix21(String val){ - matrix.set(1,0,Double.parseDouble(val)); + this.matrix21 = val; } public void setMatrix31(String val){ - matrix.set(2,0,Double.parseDouble(val)); + this.matrix31 = val; } public void setMatrix12(String val){ - matrix.set(0,1,Double.parseDouble(val)); + this.matrix12 = val; } public void setMatrix22(String val){ - matrix.set(1,1,Double.parseDouble(val)); + this.matrix22 = val; } public void setMatrix32(String val){ - matrix.set(2,1,Double.parseDouble(val)); + this.matrix32 = val; } public void setMatrix13(String val){ - matrix.set(0,2,Double.parseDouble(val)); + this.matrix13 = val; } public void setMatrix23(String val){ - matrix.set(1,2,Double.parseDouble(val)); + this.matrix23 = val; } public void setMatrix33(String val){ - matrix.set(2,2,Double.parseDouble(val)); + this.matrix33 =val; } public void setName(String name) { @@ -186,19 +160,19 @@ public String getVector1() { return vector1; } public void setVector1(String vector1) { - vector[0] = Double.parseDouble(vector1); + this.vector1 = vector1; } public String getVector2() { return vector2; } public void setVector2(String vector2) { - vector[1] = Double.parseDouble(vector2); + this.vector2 = vector2; } public String getVector3() { return vector3; } public void setVector3(String vector3) { - vector[2] = Double.parseDouble(vector3); + this.vector3 = vector3; } public String getName() { return name; @@ -210,39 +184,39 @@ public void setSymmetry_operation(String symmetry_operation) { this.symmetry_operation = symmetry_operation; } @XmlElement - public double getMatrix11(){ - return matrix.get(0,0); + public String getMatrix11(){ + return matrix11; } @XmlElement - public double getMatrix21(){ - return matrix.get(1,0); + public String getMatrix21(){ + return matrix21; } @XmlElement - public double getMatrix31(){ - return matrix.get(2,0); + public String getMatrix31(){ + return matrix31; } @XmlElement - public double getMatrix12(){ - return matrix.get(0,1); + public String getMatrix12(){ + return matrix12; } @XmlElement - public double getMatrix22(){ - return matrix.get(1,1); + public String getMatrix22(){ + return matrix22; } @XmlElement - public double getMatrix32(){ - return matrix.get(2,1); + public String getMatrix32(){ + return matrix32; } @XmlElement - public double getMatrix13(){ - return matrix.get(0,2); + public String getMatrix13(){ + return matrix13; } @XmlElement - public double getMatrix23(){ - return matrix.get(1,2); + public String getMatrix23(){ + return matrix23; } @XmlElement - public double getMatrix33(){ - return matrix.get(2,2); + public String getMatrix33(){ + return matrix33; } } 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 bf3b28d0f0..2e84b42ac2 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 @@ -423,7 +423,7 @@ public void setXtalInfo(String spaceGroupString, float[] unitCell, double[][] nc /** * Get the type of group (0,1 or 2) depending on whether it is an amino aicd (1), nucleic acid (2) or ligand (0) - * @param currentGroup + * @param polymerType * @return The type of group. (0,1 or 2) depending on whether it is an amino aicd (1), nucleic acid (2) or ligand (0) */ private int getGroupTypIndicator(PolymerType polymerType) { 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 8c1832cf00..321dd08d28 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 @@ -30,6 +30,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import javax.vecmath.Matrix4d; import java.util.*; /** @@ -45,9 +46,13 @@ public class BiologicalAssemblyBuilder { private static final Logger logger = LoggerFactory.getLogger(BiologicalAssemblyBuilder.class); private OperatorResolver operatorResolver; - private List psags; - private List modelTransformations; + + /** + * All matrix operators present in _pdbx_struct_oper_list. + * Identifiers (_pdbx_struct_oper_list.id) to matrix operators. + */ + private Map allTransformations; private List modelIndex = new ArrayList(); @@ -216,34 +221,55 @@ private void addChainFlattened(Structure s, Chain newChain, String transformId) * Returns a list of transformation matrices for the generation of a macromolecular * assembly for the specified assembly Id. * - * @param assemblyId Id of the macromolecular assembly to be generated + * @param psa + * @param psags + * @param operators * @return list of transformation matrices to generate macromolecular assembly */ public ArrayList getBioUnitTransformationList(PdbxStructAssembly psa, List psags, List operators) { - //System.out.println("Rebuilding " + psa.getDetails() + " | " + psa.getOligomeric_details() + " | " + psa.getOligomeric_count()); - //System.out.println(psag); init(); - this.psags = psags; - - //psa.getId(); + // first we populate the list of all operators from pdbx_struct_oper_list so that we can then + // get them from getBioUnitTransformationsListUnaryOperators() and getBioUnitTransformationsListBinaryOperators() for (PdbxStructOperList oper: operators){ - BiologicalAssemblyTransformation transform = new BiologicalAssemblyTransformation(); - transform.setId(oper.getId()); - transform.setRotationMatrix(oper.getMatrix().getArray()); - transform.setTranslation(oper.getVector()); -// transform.setTransformationMatrix(oper.getMatrix(), oper.getVector()); - modelTransformations.add(transform); + try { + Matrix4d m = new Matrix4d(); + m.m00 = Double.parseDouble(oper.getMatrix11()); + m.m01 = Double.parseDouble(oper.getMatrix12()); + m.m02 = Double.parseDouble(oper.getMatrix13()); + + m.m10 = Double.parseDouble(oper.getMatrix21()); + m.m11 = Double.parseDouble(oper.getMatrix22()); + m.m12 = Double.parseDouble(oper.getMatrix23()); + + m.m20 = Double.parseDouble(oper.getMatrix31()); + m.m21 = Double.parseDouble(oper.getMatrix32()); + m.m22 = Double.parseDouble(oper.getMatrix33()); + + m.m03 = Double.parseDouble(oper.getVector1()); + m.m13 = Double.parseDouble(oper.getVector2()); + m.m23 = Double.parseDouble(oper.getVector3()); + + m.m30 = 0; + m.m31 = 0; + m.m32 = 0; + m.m33 = 1; + + allTransformations.put(oper.getId(), m); + + } catch (NumberFormatException e) { + logger.warn("Could not parse a matrix value from pdbx_struct_oper_list for id {}. The operator id will be ignored. Error: {}", oper.getId(), e.getMessage()); + } } - ArrayList transformations = getBioUnitTransformationsListUnaryOperators(psa.getId()); - transformations.addAll(getBioUnitTransformationsListBinaryOperators(psa.getId())); + ArrayList transformations = getBioUnitTransformationsListUnaryOperators(psa.getId(), psags); + transformations.addAll(getBioUnitTransformationsListBinaryOperators(psa.getId(), psags)); transformations.trimToSize(); return transformations; } - private ArrayList getBioUnitTransformationsListBinaryOperators(String assemblyId) { + private ArrayList getBioUnitTransformationsListBinaryOperators(String assemblyId, List psags) { ArrayList transformations = new ArrayList(); @@ -261,17 +287,20 @@ private ArrayList getBioUnitTransformationsLis // Example 1M4X: generates all products of transformation matrices (1-60)(61-88) for (String chainId : asymIds) { - int modelNumber = 1; for (OrderedPair operator : operators) { - BiologicalAssemblyTransformation original1 = getModelTransformationMatrix(operator.getElement1()); - BiologicalAssemblyTransformation original2 = getModelTransformationMatrix(operator.getElement2()); - // ModelTransformationMatrix transform = ModelTransformationMatrix.multiply4square_x_4square2(original1, original2); - BiologicalAssemblyTransformation transform = BiologicalAssemblyTransformation.combine(original1, original2); + Matrix4d original1 = allTransformations.get(operator.getElement1()); + Matrix4d original2 = allTransformations.get(operator.getElement2()); + if (original1 == null || original2 == null) { + logger.warn("Could not find matrix operator for operator id {} or {}. Assembly id {} will not contain the composed operator.", operator.getElement1(), operator.getElement2(), assemblyId); + continue; + } + Matrix4d composed = new Matrix4d(original1); + composed.mul(original2); + BiologicalAssemblyTransformation transform = new BiologicalAssemblyTransformation(); transform.setChainId(chainId); - // transform.setId(original1.getId() + "x" + original2.getId()); - transform.setId(String.valueOf(modelNumber)); + transform.setId(operator.getElement1() + "x" + operator.getElement2()); + transform.setTransformationMatrix(composed); transformations.add(transform); - modelNumber++; } } } @@ -281,17 +310,7 @@ private ArrayList getBioUnitTransformationsLis return transformations; } - private BiologicalAssemblyTransformation getModelTransformationMatrix(String operator) { - for (BiologicalAssemblyTransformation transform: modelTransformations) { - if (transform.getId().equals(operator)) { - return transform; - } - } - logger.error("Could not find modelTransformationmatrix for " + operator); - return new BiologicalAssemblyTransformation(); - } - - private ArrayList getBioUnitTransformationsListUnaryOperators(String assemblyId) { + private ArrayList getBioUnitTransformationsListUnaryOperators(String assemblyId, List psags) { ArrayList transformations = new ArrayList(); @@ -306,11 +325,15 @@ private ArrayList getBioUnitTransformationsLis // apply unary operators to the specified chains for (String chainId : asymIds) { for (String operator : operators) { - - BiologicalAssemblyTransformation original = getModelTransformationMatrix(operator); - BiologicalAssemblyTransformation transform = new BiologicalAssemblyTransformation(original); + Matrix4d original = allTransformations.get(operator); + if (original == null) { + logger.warn("Could not find matrix operator for operator id {}. Assembly id {} will not contain the operator.", operator, assemblyId); + continue; + } + BiologicalAssemblyTransformation transform = new BiologicalAssemblyTransformation(); transform.setChainId(chainId); transform.setId(operator); + transform.setTransformationMatrix(original); transformations.add(transform); } } @@ -322,6 +345,6 @@ private ArrayList getBioUnitTransformationsLis private void init(){ operatorResolver= new OperatorResolver(); - modelTransformations = new ArrayList(1); + allTransformations = new HashMap<>(); } } diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/OperatorResolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/OperatorResolver.java index 08ad5224b2..b9b11a2f61 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/OperatorResolver.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/OperatorResolver.java @@ -24,7 +24,8 @@ import java.util.List; -/** A class to resolve the operators for transformations +/** + * A class to resolve the operators for transformations * * @author Peter Rose * From 8e98df4c5aa3a61d4087438f2dfc198713990c9a Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Mon, 3 Sep 2018 14:43:21 -0700 Subject: [PATCH 05/18] Using asym ids for Subunit names --- .../org/biojava/nbio/structure/cluster/SubunitExtractor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java index e18b0def24..1ae0b818ee 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java @@ -75,7 +75,7 @@ public static List extractSubunits(Structure structure, logger.debug("Chain " + c.getId() + "; CA Atoms: " + ca.length + "; SEQRES: " + c.getSeqResSequence()); if (ca.length==0) continue; - subunits.add(new Subunit(ca, c.getName(), null, structure)); + subunits.add(new Subunit(ca, c.getId(), null, structure)); } } From 2b1775fac167dcdbb2f1bfefb4b503fe0b480f04 Mon Sep 17 00:00:00 2001 From: Aleix Lafita Date: Wed, 5 Sep 2018 13:41:34 +0100 Subject: [PATCH 06/18] Change download chemcomp log to WARN --- .../nbio/structure/io/mmcif/DownloadChemCompProvider.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java index 06d7534091..d1dcbb08f7 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java @@ -284,8 +284,9 @@ public ChemComp getChemComp(String recordName) { } catch (IOException e) { - logger.error("Could not parse chemical component file {}. Error: {}. " - + "There will be no chemical component info available for {}", filename, e.getMessage(), recordName); + logger.warn( + "Could not download chemical component file {} for {}. Error: {}. Now trying to use the local chemical component definitions.", + filename, recordName, e.getMessage()); } finally{ From 446267e048f2a72a69c108bcdc55e93786ff2331 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Wed, 5 Sep 2018 17:02:34 -0700 Subject: [PATCH 07/18] Using raw arrays for neighbor indices --- .../nbio/structure/asa/AsaCalculator.java | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java index cc47ff079c..0626b37804 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java @@ -112,7 +112,7 @@ public void run() { * @param nThreads * @param hetAtoms if true HET residues are considered, if false they aren't, equivalent to * NACCESS' -h option - * @see StructureTools.getAllNonHAtomArray + * @see StructureTools#getAllNonHAtomArray */ public AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms) { this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms); @@ -320,7 +320,7 @@ private Point3d[] generateSpherePoints(int nSpherePoints) { * Returns list of indices of atoms within probe distance to atom k. * @param k index of atom for which we want neighbor indices */ - private ArrayList findNeighborIndices(int k) { + private Integer[] findNeighborIndices(int k) { // looking at a typical protein case, number of neighbours are from ~10 to ~50, with an average of ~30 // Thus 40 seems to be a good compromise for the starting capacity ArrayList neighbor_indices = new ArrayList(40); @@ -340,13 +340,15 @@ private ArrayList findNeighborIndices(int k) { } - return neighbor_indices; + Integer[] indicesArray = new Integer[neighbor_indices.size()]; + indicesArray = neighbor_indices.toArray(indicesArray); + return indicesArray; } private double calcSingleAsa(int i) { Point3d atom_i = atomCoords[i]; - ArrayList neighbor_indices = findNeighborIndices(i); - int n_neighbor = neighbor_indices.size(); + Integer[] neighbor_indices = findNeighborIndices(i); + int n_neighbor = neighbor_indices.length; int j_closest_neighbor = 0; double radius = probe + radii[i]; @@ -370,8 +372,8 @@ private double calcSingleAsa(int i) { } for (int j: cycled_indices) { - Point3d atom_j = atomCoords[neighbor_indices.get(j)]; - double r = radii[neighbor_indices.get(j)] + probe; + Point3d atom_j = atomCoords[neighbor_indices[j]]; + double r = radii[neighbor_indices[j]] + probe; double diff_sq = test_point.distanceSquared(atom_j); if (diff_sq < r*r) { j_closest_neighbor = j; @@ -388,7 +390,7 @@ private double calcSingleAsa(int i) { /** * Gets the radius for given amino acid and atom - * @param aa + * @param amino * @param atom * @return */ From 5b6992b6859ddac7549cfbd8935d36ec507d9966 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Fri, 7 Sep 2018 09:40:02 -0700 Subject: [PATCH 08/18] Cleanup --- .../java/org/biojava/nbio/structure/asa/AsaCalculator.java | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java index 0626b37804..dc34ff8782 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java @@ -323,16 +323,14 @@ private Point3d[] generateSpherePoints(int nSpherePoints) { private Integer[] findNeighborIndices(int k) { // looking at a typical protein case, number of neighbours are from ~10 to ~50, with an average of ~30 // Thus 40 seems to be a good compromise for the starting capacity - ArrayList neighbor_indices = new ArrayList(40); + ArrayList neighbor_indices = new ArrayList<>(40); double radius = radii[k] + probe + probe; for (int i=0;i Date: Mon, 18 Jun 2018 15:23:34 +0200 Subject: [PATCH 09/18] Make BioJava compile under java9 --- .../biojava/nbio/core/sequence/io/embl/EmblId.java | 3 --- biojava-protein-disorder/pom.xml | 4 ++++ biojava-structure/pom.xml | 5 +++++ pom.xml | 11 ++++++++--- 4 files changed, 17 insertions(+), 6 deletions(-) diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblId.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblId.java index 4c93427767..f89c79762c 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblId.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblId.java @@ -20,8 +20,6 @@ */ package org.biojava.nbio.core.sequence.io.embl; -import jdk.nashorn.internal.ir.annotations.Immutable; - /** * This class contains the processed data of embl file * Primary accession number @@ -35,7 +33,6 @@ * @author Noor Aldeen Al Mbaidin * @since 5.0.0 */ -@Immutable public class EmblId { diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 0981772719..b04aaceee8 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -84,6 +84,10 @@ org.apache.logging.log4j log4j-core + + javax.xml.bind + jaxb-api + diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 41d65cf3ab..3d5adc40df 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -62,6 +62,11 @@ 1.1.0 + + javax.xml.bind + jaxb-api + + diff --git a/pom.xml b/pom.xml index 1cfcaedd38..48c57cf1a3 100644 --- a/pom.xml +++ b/pom.xml @@ -32,8 +32,8 @@ - 1.8 - 1.8 + 9 + 9 UTF-8 UTF-8 @@ -507,6 +507,11 @@ forester 1.038 + + javax.xml.bind + jaxb-api + 2.3.0 + @@ -518,7 +523,7 @@ true true true - 1.8 + ${jdk.version} false true From 80316d71446829888139af4a38655568a34c3df7 Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Wed, 20 Jun 2018 11:00:48 +0200 Subject: [PATCH 10/18] Update travis JDK --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 6be4786ae3..f9a66a457b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,6 +1,6 @@ language: java jdk: - - oraclejdk8 + - oraclejdk9 sudo: required cache: directories: From 84df99b412d269d3aea2eb8a934dc55f56d68b82 Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Wed, 20 Jun 2018 11:01:03 +0200 Subject: [PATCH 11/18] Update maven plugin versions. --- pom.xml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/pom.xml b/pom.xml index 48c57cf1a3..4a59004073 100644 --- a/pom.xml +++ b/pom.xml @@ -171,7 +171,7 @@ maven-dependency-plugin - 3.0.2 + 3.1.1 maven-jar-plugin @@ -179,11 +179,11 @@ there are some config changes required. see https://github.com/biojava/biojava/issues/531 --> - 3.0.2 + 3.1.0 maven-scm-plugin - 1.9.5 + 1.10.0 maven-source-plugin @@ -191,7 +191,7 @@ maven-failsafe-plugin - 2.21.0 + 2.22.0 net.sf @@ -201,7 +201,7 @@ org.jvnet.jaxb2.maven2 maven-jaxb2-plugin - 0.13.1 + 0.14.0 org.apache.maven.plugins @@ -224,7 +224,7 @@ org.apache.maven.plugins maven-javadoc-plugin - 3.0.0 + 3.0.1 -Xdoclint:none @@ -242,7 +242,7 @@ org.apache.maven.plugins maven-shade-plugin - 3.1.0 + 3.1.1 maven-assembly-plugin @@ -280,18 +280,18 @@ org.apache.maven.plugins maven-checkstyle-plugin - 2.17 + 3.0.0 org.apache.maven.plugins maven-resources-plugin - 3.0.2 + 3.1.0 maven-enforcer-plugin - 3.0.0-M1 + 3.0.0-M2 enforce-java @@ -316,12 +316,12 @@ org.apache.maven.plugins maven-surefire-plugin - 2.21.0 + 2.22.0 org.apache.maven.plugins maven-site-plugin - 3.7 + 3.7.1 From ac45053b9a0f53f09294d170cc2ec4a984529cdb Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Fri, 7 Sep 2018 13:57:48 -0700 Subject: [PATCH 12/18] Explicit jaxb dependencies so that biojava can compile/run in all jdks up to 11 --- biojava-structure/pom.xml | 14 ++++++++++++++ pom.xml | 15 +++++++++++++++ 2 files changed, 29 insertions(+) diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 3d5adc40df..6db447ae6f 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -62,10 +62,24 @@ 1.1.0 + javax.xml.bind jaxb-api + + com.sun.xml.bind + jaxb-core + + + com.sun.xml.bind + jaxb-impl + + + javax.activation + activation + diff --git a/pom.xml b/pom.xml index 4a59004073..3d9e561ebc 100644 --- a/pom.xml +++ b/pom.xml @@ -512,6 +512,21 @@ jaxb-api 2.3.0 + + com.sun.xml.bind + jaxb-core + 2.3.0 + + + com.sun.xml.bind + jaxb-impl + 2.3.0 + + + javax.activation + activation + 1.1.1 + From 941b074bb3125cca2ee7acbca41182dfd63fc27b Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Fri, 7 Sep 2018 14:32:05 -0700 Subject: [PATCH 13/18] Keeping the java 8 compliance level (compiled byte code is 8). Still it works under 9, 10, 11 JREs --- pom.xml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 3d9e561ebc..83082896ee 100644 --- a/pom.xml +++ b/pom.xml @@ -32,8 +32,9 @@ - 9 - 9 + + 1.8 + 1.8 UTF-8 UTF-8 From 5255bc35480b3c788980c0a8d09af39d57f6265f Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Tue, 11 Sep 2018 11:14:16 -0700 Subject: [PATCH 14/18] Reverting travis jre version to 8 --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index f9a66a457b..6be4786ae3 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,6 +1,6 @@ language: java jdk: - - oraclejdk9 + - oraclejdk8 sudo: required cache: directories: From 27c5fbb8f26101b9aa8edb3f896233d31318b1e7 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Tue, 11 Sep 2018 12:06:29 -0700 Subject: [PATCH 15/18] Removing comment that doesn't apply anymore --- pom.xml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/pom.xml b/pom.xml index 83082896ee..778b022ec6 100644 --- a/pom.xml +++ b/pom.xml @@ -176,10 +176,6 @@ maven-jar-plugin - 3.1.0 From 59687042050e7df2013c1294c859ba26e517fdce Mon Sep 17 00:00:00 2001 From: Aleix Lafita Date: Wed, 12 Sep 2018 21:16:54 +0100 Subject: [PATCH 16/18] Fix website URL --- readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/readme.md b/readme.md index dd26f0e8e1..e7689982f5 100644 --- a/readme.md +++ b/readme.md @@ -5,7 +5,7 @@ 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, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. -Please visit our [homepage](http://www.biojava.org/). +Please visit our [homepage](http://biojava.org/). ### Documentation From 5377a9872ced428d3b2483c832088d4d7fa8680e Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Mon, 24 Sep 2018 11:00:32 -0700 Subject: [PATCH 17/18] Docs --- .../org/biojava/nbio/structure/cluster/SubunitExtractor.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java index 1ae0b818ee..b418884ce0 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java @@ -48,8 +48,8 @@ private SubunitExtractor() { /** * Extract the information of each protein Chain in a Structure and converts - * them into a List of Subunit. The name of the Subunits is set to the - * {@link Chain#getName()}. + * them into a List of Subunit. The name of the Subunits is set to + * {@link Chain#getId()}. * * * @param structure From 10c1c6c234e2ee1d2adf6488ee6f32855181360a Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Fri, 28 Sep 2018 15:53:40 -0700 Subject: [PATCH 18/18] [maven-release-plugin] prepare release biojava-5.1.1 --- 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-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 ++-- 13 files changed, 27 insertions(+), 27 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 8f0647227f..157632d1e5 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 5.1.1-SNAPSHOT + 5.1.1 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 5.1.1-SNAPSHOT + 5.1.1 org.biojava biojava-structure - 5.1.1-SNAPSHOT + 5.1.1 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 447ff8d99d..ac55ba88ee 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 5.1.1-SNAPSHOT + 5.1.1 biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 5.1.1-SNAPSHOT + 5.1.1 compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 173aa0c21b..ab8fc3c17f 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 5.1.1-SNAPSHOT + 5.1.1 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index c0322a8298..b6b630f93c 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 5.1.1-SNAPSHOT + 5.1.1 4.0.0 biojava-genome @@ -85,13 +85,13 @@ org.biojava biojava-core - 5.1.1-SNAPSHOT + 5.1.1 compile org.biojava biojava-alignment - 5.1.1-SNAPSHOT + 5.1.1 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 942ec5f494..699780916d 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 5.1.1-SNAPSHOT + 5.1.1 biojava-integrationtest jar @@ -28,7 +28,7 @@ org.biojava biojava-structure - 5.1.1-SNAPSHOT + 5.1.1 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 6e4bb240c2..1697958d07 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 5.1.1-SNAPSHOT + 5.1.1 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 5.1.1-SNAPSHOT + 5.1.1 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index cf670de666..685477fa67 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 5.1.1-SNAPSHOT + 5.1.1 biojava-ontology diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index b04aaceee8..d63fe7281f 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 5.1.1-SNAPSHOT + 5.1.1 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 5.1.1-SNAPSHOT + 5.1.1 diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index eb3be1bda1..5045b8b44b 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 5.1.1-SNAPSHOT + 5.1.1 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 5.1.1-SNAPSHOT + 5.1.1 compile org.biojava biojava-core - 5.1.1-SNAPSHOT + 5.1.1 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 6db447ae6f..9f23bf431f 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 5.1.1-SNAPSHOT + 5.1.1 biojava-structure biojava-structure @@ -40,13 +40,13 @@ org.biojava biojava-alignment - 5.1.1-SNAPSHOT + 5.1.1 compile org.biojava biojava-core - 5.1.1-SNAPSHOT + 5.1.1 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 0b682a90ae..ce0c57f6d0 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 5.1.1-SNAPSHOT + 5.1.1 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index e500b9ee8a..c57afd2cd7 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 5.1.1-SNAPSHOT + 5.1.1 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 5.1.1-SNAPSHOT + 5.1.1 compile diff --git a/pom.xml b/pom.xml index 778b022ec6..ee32f576f7 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 5.1.1-SNAPSHOT + 5.1.1 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 @@ -49,7 +49,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - HEAD + biojava-5.1.1