From 50c34d356c621873482fdcad167c161a93a896d1 Mon Sep 17 00:00:00 2001 From: Matt Larson Date: Wed, 30 Nov 2016 14:39:58 -0600 Subject: [PATCH 001/954] Added exception handler for out-of-bounds errors when parsing lines, usually indicative of misformated lines. Added line length checks within the LINK and CONECT parsing blocks to allow for short lines to be parsed. --- .../nbio/structure/io/PDBFileParser.java | 115 ++++++++++-------- .../nbio/structure/io/TestShortLines.java | 74 +++++++++++ 2 files changed, 138 insertions(+), 51 deletions(-) create mode 100644 biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestShortLines.java 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 10cade8e16..c6dcf34f24 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 @@ -2017,6 +2017,8 @@ private void switchCAOnly(){ /** safes repeating a few lines ... */ private Integer conect_helper (String line,int start,int end) { + if (line.length() < end) return null; + String sbond = line.substring(start,end).trim(); int bond = -1 ; Integer b = null ; @@ -2343,7 +2345,15 @@ private void pdb_SSBOND_Handler(String line){ private void pdb_LINK_Handler(String line) { if (params.isHeaderOnly()) return; + + // Check for the minimal set of fields. + if (line.length()<56) { + logger.info("LINK line has length under 56. Ignoring it."); + return; + } + int len = line.length(); + String name1 = line.substring(12, 16).trim(); String altLoc1 = line.substring(16, 17).trim(); String resName1 = line.substring(17, 20).trim(); @@ -2356,10 +2366,13 @@ private void pdb_LINK_Handler(String line) { String resName2 = line.substring(47, 50).trim(); String chainID2 = line.substring(51, 52).trim(); String resSeq2 = line.substring(52, 56).trim(); - String iCode2 = line.substring(56, 57).trim(); + String iCode2 = null; // Might get trimmed if blank. + if (len > 56) iCode2 = line.substring(56, 57).trim(); - String sym1 = line.substring(59, 65).trim(); - String sym2 = line.substring(66, 72).trim(); + String sym1 = null; + if (len > 64) sym1 = line.substring(59, 65).trim(); + String sym2 = null; + if (len > 71) sym2 = line.substring(66, 72).trim(); // System.err.println("LINK"); // System.err.println("\tName: " + name1); @@ -2690,54 +2703,54 @@ public Structure parsePDBFile(BufferedReader buf) String recordName = line.substring (0, 6).trim (); - if (recordName.equals("ATOM")) - pdb_ATOM_Handler(line); - else if (recordName.equals("SEQRES")) - pdb_SEQRES_Handler(line); - else if (recordName.equals("HETATM")) - pdb_ATOM_Handler(line); - else if (recordName.equals("MODEL")) - pdb_MODEL_Handler(line); - else if (recordName.equals("HEADER")) - pdb_HEADER_Handler(line); - else if (recordName.equals("AUTHOR")) - pdb_AUTHOR_Handler(line); - else if (recordName.equals("TITLE")) - pdb_TITLE_Handler(line); - else if (recordName.equals("SOURCE")) - sourceLines.add(line); //pdb_SOURCE_Handler - else if (recordName.equals("COMPND")) - compndLines.add(line); //pdb_COMPND_Handler - else if (recordName.equals("JRNL")) - pdb_JRNL_Handler(line); - else if (recordName.equals("EXPDTA")) - pdb_EXPDTA_Handler(line); - else if (recordName.equals("CRYST1")) - pdb_CRYST1_Handler(line); - else if (recordName.startsWith("MTRIX")) - pdb_MTRIXn_Handler(line); - else if (recordName.equals("REMARK")) - pdb_REMARK_Handler(line); - else if (recordName.equals("CONECT")) - pdb_CONECT_Handler(line); - else if (recordName.equals("REVDAT")) - pdb_REVDAT_Handler(line); - else if (recordName.equals("DBREF")) - pdb_DBREF_Handler(line); - else if (recordName.equals("SITE")) - pdb_SITE_Handler(line); - else if (recordName.equals("SSBOND")) - pdb_SSBOND_Handler(line); - else if (recordName.equals("LINK")) - pdb_LINK_Handler(line); - else if ( params.isParseSecStruc()) { - if ( recordName.equals("HELIX") ) pdb_HELIX_Handler ( line ) ; - else if (recordName.equals("SHEET")) pdb_SHEET_Handler(line ) ; - else if (recordName.equals("TURN")) pdb_TURN_Handler( line ) ; - } - else { - // this line type is not supported, yet. - // we ignore it + try { + if (recordName.equals("ATOM")) + pdb_ATOM_Handler(line); + else if (recordName.equals("SEQRES")) + pdb_SEQRES_Handler(line); + else if (recordName.equals("HETATM")) + pdb_ATOM_Handler(line); + else if (recordName.equals("MODEL")) + pdb_MODEL_Handler(line); + else if (recordName.equals("HEADER")) + pdb_HEADER_Handler(line); + else if (recordName.equals("AUTHOR")) + pdb_AUTHOR_Handler(line); + else if (recordName.equals("TITLE")) + pdb_TITLE_Handler(line); + else if (recordName.equals("SOURCE")) + sourceLines.add(line); //pdb_SOURCE_Handler + else if (recordName.equals("COMPND")) + compndLines.add(line); //pdb_COMPND_Handler + else if (recordName.equals("JRNL")) + pdb_JRNL_Handler(line); + else if (recordName.equals("EXPDTA")) + pdb_EXPDTA_Handler(line); + else if (recordName.equals("CRYST1")) + pdb_CRYST1_Handler(line); + else if (recordName.startsWith("MTRIX")) + pdb_MTRIXn_Handler(line); + else if (recordName.equals("REMARK")) + pdb_REMARK_Handler(line); + else if (recordName.equals("CONECT")) + pdb_CONECT_Handler(line); + else if (recordName.equals("REVDAT")) + pdb_REVDAT_Handler(line); + else if (recordName.equals("DBREF")) + pdb_DBREF_Handler(line); + else if (recordName.equals("SITE")) + pdb_SITE_Handler(line); + else if (recordName.equals("SSBOND")) + pdb_SSBOND_Handler(line); + else if (recordName.equals("LINK")) + pdb_LINK_Handler(line); + else if ( params.isParseSecStruc()) { + if ( recordName.equals("HELIX") ) pdb_HELIX_Handler ( line ) ; + else if (recordName.equals("SHEET")) pdb_SHEET_Handler(line ) ; + else if (recordName.equals("TURN")) pdb_TURN_Handler( line ) ; + } + } catch (StringIndexOutOfBoundsException ex) { + logger.info("Unable to parse [" + line + "]"); } diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestShortLines.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestShortLines.java new file mode 100644 index 0000000000..70a35b542d --- /dev/null +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestShortLines.java @@ -0,0 +1,74 @@ +package org.biojava.nbio.structure.io; + +import static org.junit.Assert.assertEquals; + +import java.io.ByteArrayInputStream; +import java.io.IOException; +import java.io.InputStream; + +import org.biojava.nbio.structure.Atom; +import org.biojava.nbio.structure.Chain; +import org.biojava.nbio.structure.Group; +import org.biojava.nbio.structure.Structure; +import org.junit.Test; + +/** + * This class will test parsing short CONECT lines. + *

(c) 2016 DNASTAR, Inc.

+ * @since Nov 30, 2016 + * @author larsonm + */ +public class TestShortLines { + + @Test + public void testConect() throws IOException { + PDBFileParser pdbPars = new PDBFileParser(); + FileParsingParameters params = pdbPars.getFileParsingParameters(); + params.setCreateAtomBonds(true); + + // CONECTS will be deprecated, but will we create bonds? + // Like the LINK records, should BioJava create BondImpl when params.setCreateAtomBonds(true)? + + StringBuilder sb = new StringBuilder(); + sb.append("HETATM 2398 P FAD A 500 8.398 46.448 73.490 1.00 13.51 P \n"); + sb.append("HETATM 2399 PA FAD A 500 6.089 45.580 75.235 1.00 15.88 P \n"); + sb.append("HETATM 2400 O1P FAD A 500 7.908 47.684 72.869 1.00 4.19 O \n"); + sb.append("CONECT 2400 2398\n"); + String shortLine = sb.toString(); + Structure s; + // Parse short + try(InputStream is = new ByteArrayInputStream(shortLine.getBytes())) { + s = pdbPars.parsePDBFile(is); + } + + // After 4.2, CONECTS are deprecated, but there is not yet an implementation + // describing how CONECTS will be replaced - will Bonds be created? + assertEquals(1, s.getConnections().size()); + } + + @Test + public void testLINK() throws IOException { + Structure s; + PDBFileParser pdbPars = new PDBFileParser(); + FileParsingParameters params = pdbPars.getFileParsingParameters(); + params.setCreateAtomBonds(true); + + StringBuilder sb = new StringBuilder(); + sb.append("ATOM 2412 C21 2EG A 7 0.888 44.973 72.238 1.00 29.17 C \n"); + sb.append("ATOM 2413 C22 2EG B 19 0.888 44.973 72.238 1.00 29.17 C \n"); + //sb.append("LINK C21 2EG A 7 C22 2EG B 19 1555 1555 1.56 "); + sb.append("LINK C21 2EG A 7 C22 2EG B 19\n"); + String shortLine = sb.toString(); + + // Parse short + try(InputStream is = new ByteArrayInputStream(shortLine.getBytes())) { + s = pdbPars.parsePDBFile(is); + } + + // Should be a bond present in the Atoms. + Chain c = s.getChain(0, 0); + Group g = c.getAtomGroups().get(0); + Atom a = g.getAtom(0); + assertEquals(1, a.getBonds().size()); + } +} From 0f322ee84f9ec3e2e86d710fe91ad47016c15032 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Fri, 17 Feb 2017 17:54:30 -0800 Subject: [PATCH 002/954] Catching empty coordinates earlier in quat sym detection --- .../org/biojava/nbio/structure/symmetry/core/Subunits.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Subunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Subunits.java index 6e980be703..c639cae3bc 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Subunits.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Subunits.java @@ -65,6 +65,12 @@ public class Subunits { * @param modelNumbers Model number for the subunit */ public Subunits(List caCoords, List sequenceClusterIds, List pseudoStoichiometry, List minSequenceIdentity, List maxSequenceIdentity, List folds, List chainIds, List modelNumbers) { + + for (int i=0; i Date: Fri, 17 Feb 2017 18:36:46 -0800 Subject: [PATCH 003/954] [maven-release-plugin]prepare release biojava-4.2.6 --- biojava-aa-prop/pom.xml | 6 +++--- biojava-alignment/pom.xml | 6 +++--- 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-phylo/pom.xml | 4 ++-- biojava-protein-disorder/pom.xml | 4 ++-- biojava-sequencing/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 ++-- 15 files changed, 32 insertions(+), 32 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index cf0a6a47bb..89ef2154ef 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 4.2.6-SNAPSHOT + 4.2.6 org.biojava biojava-structure - 4.2.6-SNAPSHOT + 4.2.6 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 21dbb40126..41389cdd4e 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.6-SNAPSHOT + 4.2.6 compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.6-SNAPSHOT + 4.2.6 diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 012c2b83b7..e3b0e9a7a1 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 435a45fa52..b382489846 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 4.0.0 biojava-genome @@ -85,13 +85,13 @@ org.biojava biojava-core - 4.2.6-SNAPSHOT + 4.2.6 compile org.biojava biojava-alignment - 4.2.6-SNAPSHOT + 4.2.6 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 30d11aeb0f..dca85357b3 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.6-SNAPSHOT + 4.2.6 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 7389115bd0..e969b11f09 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.6-SNAPSHOT + 4.2.6 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 96f142698c..305039b548 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.6-SNAPSHOT + 4.2.6 biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index 915e7612b6..bc55ac6307 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.6-SNAPSHOT + 4.2.6 compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 75ef22d9f6..b95632bc2c 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.6-SNAPSHOT + 4.2.6 diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index 603ffd6607..0990a8e9b2 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.6-SNAPSHOT + 4.2.6 compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 84d2e8fb68..f96aad2a97 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.6-SNAPSHOT + 4.2.6 compile org.biojava biojava-core - 4.2.6-SNAPSHOT + 4.2.6 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 8ae2b94af1..ac6de4757a 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.6-SNAPSHOT + 4.2.6 compile org.biojava biojava-core - 4.2.6-SNAPSHOT + 4.2.6 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index feec28d8c8..1f03bad9be 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.6-SNAPSHOT + 4.2.6 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 5aee2ec148..646bd14a0b 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6-SNAPSHOT + 4.2.6 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.6-SNAPSHOT + 4.2.6 compile diff --git a/pom.xml b/pom.xml index 1d648a11be..3993929e35 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.6-SNAPSHOT + 4.2.6 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 @@ -44,7 +44,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-4.2.1 + biojava-4.2.6 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 41389cdd4e..1d4051dec0 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.6 + 4.2.7-SNAPSHOT compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.6 + 4.2.7-SNAPSHOT diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index e3b0e9a7a1..358cae9ab3 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index b382489846..b53bd2df99 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT 4.0.0 biojava-genome @@ -85,13 +85,13 @@ org.biojava biojava-core - 4.2.6 + 4.2.7-SNAPSHOT compile org.biojava biojava-alignment - 4.2.6 + 4.2.7-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index dca85357b3..930ed7a555 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.6 + 4.2.7-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index e969b11f09..03ac151f18 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.6 + 4.2.7-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 305039b548..79e2415534 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.6 + 4.2.7-SNAPSHOT biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index bc55ac6307..7ef7750049 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.6 + 4.2.7-SNAPSHOT compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index b95632bc2c..3b1b7789b1 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.6 + 4.2.7-SNAPSHOT diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index 0990a8e9b2..fa0030a998 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.6 + 4.2.7-SNAPSHOT compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index f96aad2a97..8110e5ff82 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.6 + 4.2.7-SNAPSHOT compile org.biojava biojava-core - 4.2.6 + 4.2.7-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index ac6de4757a..916f1acb74 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.6 + 4.2.7-SNAPSHOT compile org.biojava biojava-core - 4.2.6 + 4.2.7-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 1f03bad9be..5787cb90f4 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.6 + 4.2.7-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 646bd14a0b..d0dba4c0d6 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.6 + 4.2.7-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.6 + 4.2.7-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 3993929e35..4bad7b322d 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.6 + 4.2.7-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 @@ -44,7 +44,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-4.2.6 + biojava-4.2.1 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 1d4051dec0..7dfe24c010 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.7-SNAPSHOT + 4.2.7 compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.7-SNAPSHOT + 4.2.7 diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 358cae9ab3..90e465d2dc 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index b53bd2df99..c82fade42d 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 4.0.0 biojava-genome @@ -85,13 +85,13 @@ org.biojava biojava-core - 4.2.7-SNAPSHOT + 4.2.7 compile org.biojava biojava-alignment - 4.2.7-SNAPSHOT + 4.2.7 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 930ed7a555..c52783d2a1 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.7-SNAPSHOT + 4.2.7 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 03ac151f18..0ca1247f39 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.7-SNAPSHOT + 4.2.7 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 79e2415534..03b1c00b76 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.7-SNAPSHOT + 4.2.7 biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index 7ef7750049..d374a993fd 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.7-SNAPSHOT + 4.2.7 compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 3b1b7789b1..73c642d3e1 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.7-SNAPSHOT + 4.2.7 diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index fa0030a998..0b4d66e069 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.7-SNAPSHOT + 4.2.7 compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 8110e5ff82..cfd684d103 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.7-SNAPSHOT + 4.2.7 compile org.biojava biojava-core - 4.2.7-SNAPSHOT + 4.2.7 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 916f1acb74..db1c41a4f1 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.7-SNAPSHOT + 4.2.7 compile org.biojava biojava-core - 4.2.7-SNAPSHOT + 4.2.7 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 5787cb90f4..e6c0294b34 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.7-SNAPSHOT + 4.2.7 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index d0dba4c0d6..0f2e83e414 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7-SNAPSHOT + 4.2.7 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.7-SNAPSHOT + 4.2.7 compile diff --git a/pom.xml b/pom.xml index 4bad7b322d..6513c4cb61 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.7-SNAPSHOT + 4.2.7 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 @@ -44,7 +44,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-4.2.1 + biojava-4.2.7 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 7dfe24c010..6faea5b5c2 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.7 + 4.2.8-SNAPSHOT compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.7 + 4.2.8-SNAPSHOT diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 90e465d2dc..3530fbb568 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index c82fade42d..98d334f9de 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT 4.0.0 biojava-genome @@ -85,13 +85,13 @@ org.biojava biojava-core - 4.2.7 + 4.2.8-SNAPSHOT compile org.biojava biojava-alignment - 4.2.7 + 4.2.8-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index c52783d2a1..eef43d9c3a 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.7 + 4.2.8-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 0ca1247f39..296a38bd63 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.7 + 4.2.8-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 03b1c00b76..cbfec2ba46 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.7 + 4.2.8-SNAPSHOT biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index d374a993fd..59f4080f6a 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.7 + 4.2.8-SNAPSHOT compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 73c642d3e1..67415f4fe4 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.7 + 4.2.8-SNAPSHOT diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index 0b4d66e069..cc6fd99460 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.7 + 4.2.8-SNAPSHOT compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index cfd684d103..5ba8f8353c 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.7 + 4.2.8-SNAPSHOT compile org.biojava biojava-core - 4.2.7 + 4.2.8-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index db1c41a4f1..64316bf8e6 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.7 + 4.2.8-SNAPSHOT compile org.biojava biojava-core - 4.2.7 + 4.2.8-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index e6c0294b34..09925ab0df 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.7 + 4.2.8-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 0f2e83e414..b5990c0ea7 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.7 + 4.2.8-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.7 + 4.2.8-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 6513c4cb61..e594cba972 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.7 + 4.2.8-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 @@ -44,7 +44,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-4.2.7 + biojava-4.2.1 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 6faea5b5c2..d1ebe860f9 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.8-SNAPSHOT + 4.2.8 compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.8-SNAPSHOT + 4.2.8 diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 3530fbb568..20b75fcb33 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 98d334f9de..452b909abd 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 4.0.0 biojava-genome @@ -85,13 +85,13 @@ org.biojava biojava-core - 4.2.8-SNAPSHOT + 4.2.8 compile org.biojava biojava-alignment - 4.2.8-SNAPSHOT + 4.2.8 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index eef43d9c3a..7fbc1deff2 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.8-SNAPSHOT + 4.2.8 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 296a38bd63..fded08c306 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.8-SNAPSHOT + 4.2.8 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index cbfec2ba46..cf6af99b55 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.8-SNAPSHOT + 4.2.8 biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index 59f4080f6a..8f4fae1576 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.8-SNAPSHOT + 4.2.8 compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 67415f4fe4..cdbd04df3b 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.8-SNAPSHOT + 4.2.8 diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index cc6fd99460..2e5f4af250 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.8-SNAPSHOT + 4.2.8 compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 5ba8f8353c..d9ea4db9f5 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.8-SNAPSHOT + 4.2.8 compile org.biojava biojava-core - 4.2.8-SNAPSHOT + 4.2.8 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 64316bf8e6..0577749f78 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.8-SNAPSHOT + 4.2.8 compile org.biojava biojava-core - 4.2.8-SNAPSHOT + 4.2.8 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 09925ab0df..784fe909ab 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.8-SNAPSHOT + 4.2.8 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index b5990c0ea7..fa83379487 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8-SNAPSHOT + 4.2.8 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.8-SNAPSHOT + 4.2.8 compile diff --git a/pom.xml b/pom.xml index e594cba972..6b4be3f56d 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.8-SNAPSHOT + 4.2.8 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 @@ -44,7 +44,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-4.2.1 + biojava-4.2.8 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index d1ebe860f9..a0303b0dae 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.8 + 4.2.9-SNAPSHOT compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.8 + 4.2.9-SNAPSHOT diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 20b75fcb33..0f629b0f23 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 452b909abd..d0d9df8990 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT 4.0.0 biojava-genome @@ -85,13 +85,13 @@ org.biojava biojava-core - 4.2.8 + 4.2.9-SNAPSHOT compile org.biojava biojava-alignment - 4.2.8 + 4.2.9-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 7fbc1deff2..b65c612ea0 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.8 + 4.2.9-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index fded08c306..8ded38b053 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.8 + 4.2.9-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index cf6af99b55..3cbfe076b7 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.8 + 4.2.9-SNAPSHOT biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index 8f4fae1576..6f4e0477e5 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.8 + 4.2.9-SNAPSHOT compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index cdbd04df3b..6d2dc6ff41 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.8 + 4.2.9-SNAPSHOT diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index 2e5f4af250..2cc15beadd 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.8 + 4.2.9-SNAPSHOT compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index d9ea4db9f5..dcc92b9372 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.8 + 4.2.9-SNAPSHOT compile org.biojava biojava-core - 4.2.8 + 4.2.9-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 0577749f78..85feaccc3b 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.8 + 4.2.9-SNAPSHOT compile org.biojava biojava-core - 4.2.8 + 4.2.9-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 784fe909ab..75854051ee 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.8 + 4.2.9-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index fa83379487..97f9d915b9 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.8 + 4.2.9-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.8 + 4.2.9-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 6b4be3f56d..ed284f9e1c 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.8 + 4.2.9-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 @@ -44,7 +44,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-4.2.8 + biojava-4.2.1 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index a0303b0dae..6faea5b5c2 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 0f629b0f23..3530fbb568 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index d0d9df8990..98d334f9de 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT 4.0.0 biojava-genome @@ -85,13 +85,13 @@ org.biojava biojava-core - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT compile org.biojava biojava-alignment - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index b65c612ea0..eef43d9c3a 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 8ded38b053..296a38bd63 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 3cbfe076b7..cbfec2ba46 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index 6f4e0477e5..59f4080f6a 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 6d2dc6ff41..67415f4fe4 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index 2cc15beadd..cc6fd99460 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index dcc92b9372..5ba8f8353c 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT compile org.biojava biojava-core - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 85feaccc3b..64316bf8e6 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT compile org.biojava biojava-core - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 75854051ee..09925ab0df 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 97f9d915b9..b5990c0ea7 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.9-SNAPSHOT + 4.2.8-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index ed284f9e1c..e594cba972 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.9-SNAPSHOT + 4.2.8-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 From d7d7a28d29cbe5bc6dcaaeaf5899862207408c48 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Thu, 6 Jul 2017 14:34:01 -0700 Subject: [PATCH 025/954] Fix for pom needed for release to be performed --- pom.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pom.xml b/pom.xml index e594cba972..09e6e0a4dd 100644 --- a/pom.xml +++ b/pom.xml @@ -211,6 +211,8 @@ maven-javadoc-plugin 2.10.3 + + --allow-script-in-comments 256m