From 196e14fbe1a4a32b2be33600a8bfc5d42abb1d7b Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Mon, 14 Mar 2016 16:02:09 -0700 Subject: [PATCH 01/30] Setting 4.2.1-SNAPSHOT in pom --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 69aa2f705d..bcc44c3e25 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.0 + 4.2.1-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 From 98f0f97ac354004c3b200f9d52b586a78146a03d Mon Sep 17 00:00:00 2001 From: Anthony Bradley Date: Fri, 11 Mar 2016 16:35:03 -0800 Subject: [PATCH 02/30] Fixed a bug where nucleotide bonds were not being generated. Added a test to ensure nucleotide bonds are being generated. --- .../biojava/nbio/structure/io/BondMaker.java | 6 ++-- .../org/biojava/nbio/structure/TestBond.java | 35 ++++++++++++++++++- 2 files changed, 37 insertions(+), 4 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java index fa43a31e20..af34edc0d6 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java @@ -148,7 +148,7 @@ private void formPeptideBonds() { } private void formNucleotideBonds() { - for (Chain chain : structure.getChains()) { + for (Chain chain : structure.getChains()) { List groups = chain.getSeqResGroups(); for (int i = 0; i < groups.size() - 1; i++) { @@ -165,8 +165,8 @@ private void formNucleotideBonds() { continue; } - Atom phosphorous = tail.getP(); - Atom oThreePrime = head.getO3Prime(); + Atom phosphorous = head.getP(); + Atom oThreePrime = tail.getO3Prime(); if (phosphorous == null || oThreePrime == null) { continue; diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java index 7e73a2b3e8..c0da9c4a41 100644 --- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java +++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java @@ -21,6 +21,8 @@ package org.biojava.nbio.structure; import java.io.IOException; +import java.util.ArrayList; +import java.util.List; import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.io.FileParsingParameters; @@ -45,7 +47,6 @@ public static void setUp() throws IOException, StructureException { params.setAlignSeqRes(true); params.setCreateAtomBonds(true); - StructureIO.setAtomCache(cache); @@ -138,6 +139,38 @@ public void testLigandBonds() throws StructureException, IOException { assertTrue(areBonded(phosphateP, phosphateO)); } + + /** + * Test whether nucleotide bonds are being generated + * @throws IOException + * @throws StructureException + */ + @Test + public void testNucleotideBonds() throws IOException, StructureException { + Structure bio = StructureIO.getStructure("4y60"); + for( Chain c : bio.getChains()) { + int groupCounter = 0; + List currentGroups = c.getAtomGroups(); + for ( Group g : currentGroups) { + if(groupCounter!=0 && groupCounter atoms = g.getAtoms(); + for ( Atom a : atoms) { + if ( a.getName().equals("P")){ + // Check to see if one of the phosphate atoms has bonding to something + // outside of the group. + List indexList = new ArrayList<>(); + for (Bond b : a.getBonds()){ + indexList.add(atoms.indexOf(b.getOther(a))); + } + assertTrue(indexList.contains(-1)); + } + } + } + groupCounter++; + } + + } + } private boolean areBonded(Atom a, Atom b) { for (Bond bond : a.getBonds()) { if (bond.getOther(a) == b) { From 5ea01f4c02e4f934c8121240497eb6138359e8dd Mon Sep 17 00:00:00 2001 From: lafita Date: Tue, 22 Mar 2016 14:36:44 +0100 Subject: [PATCH 03/30] Fix small jmol display bug for internal symmetry --- .../org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java | 1 - 1 file changed, 1 deletion(-) diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java index 0ac39ed25e..373b8ad3d2 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java @@ -123,7 +123,6 @@ public static AbstractAlignmentJmol display(CeSymmResult symmResult) cloned); RotationAxis axis = new RotationAxis(symmResult.getSelfAlignment()); jmol.evalString(axis.getJmolScript(symmResult.getAtoms())); - jmol.setTitle(getSymmTitle(symmResult)); return jmol; } } From 4669ea2d959af13c0ae57b605297476e5b2c5c92 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 18 Mar 2016 15:23:27 -0500 Subject: [PATCH 04/30] Fixes for jdk8 javadoc errors --- .../nbio/sequencing/io/fastq/package-info.java | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/package-info.java b/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/package-info.java index 42650e5389..5a32784d47 100755 --- a/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/package-info.java +++ b/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/package-info.java @@ -22,7 +22,7 @@ /** * FASTQ and variants sequence format I/O. * - *

+ *

* To read from an Illumina variant FASTQ sequence file: * 

  * FastqReader reader = new IlluminaFastqReader();
@@ -31,30 +31,24 @@
  *   // ...
  * }
  *
- *

* - *

* To write to an Sanger variant FASTQ sequence file: * 

  * Collection<Fastq> fastq = ...;
  * SangerFastqWriter writer = new SangerFastqWriter();
  * writer.write(new File("sanger.fastq"), fastq);
  *
- *

* - *

* For further documentation on the FASTQ sequence format, * its variants, and how they are handled in O|B|F projects, * see: - *

* - *

+ *

* The Sanger FASTQ file format for sequences - * with quality scores, and the Solexa/Illumina FASTQ variants
+ * with quality scores, and the Solexa/Illumina FASTQ variants
* Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto (BioRuby), - * Michael L. Heuer (BioJava) and Peter M. Rice (EMBOSS).
+ * Michael L. Heuer (BioJava) and Peter M. Rice (EMBOSS).
* Nucleic Acids Research, doi:10.1093/nar/gkp1137 - *

* * @since 3.0.3 */ From 2283913f46529e35bed8f888c9e2324d6fca971b Mon Sep 17 00:00:00 2001 From: Christiam Camacho Date: Wed, 16 Mar 2016 16:21:30 -0400 Subject: [PATCH 05/30] Add parameterized constructor to NCBIQBlastService to support BLAST on the cloud service providers --- .../main/java/demo/NCBIQBlastServiceDemo.java | 7 ++++- .../alignment/qblast/NCBIQBlastService.java | 31 ++++++++++++++++--- 2 files changed, 33 insertions(+), 5 deletions(-) diff --git a/biojava-ws/src/main/java/demo/NCBIQBlastServiceDemo.java b/biojava-ws/src/main/java/demo/NCBIQBlastServiceDemo.java index f51d2f03e4..f171c39bfb 100644 --- a/biojava-ws/src/main/java/demo/NCBIQBlastServiceDemo.java +++ b/biojava-ws/src/main/java/demo/NCBIQBlastServiceDemo.java @@ -41,7 +41,12 @@ public class NCBIQBlastServiceDemo { private static final String SEQUENCE = "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKS"; public static void main(String[] args) { - NCBIQBlastService service = new NCBIQBlastService(); + NCBIQBlastService service = null; + if (args.length == 1) { + service = new NCBIQBlastService(args[0]); + } else { + service = new NCBIQBlastService(); + } // set alignment options NCBIQBlastAlignmentProperties props = new NCBIQBlastAlignmentProperties(); diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java index 81b31a3600..12538465bf 100644 --- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java +++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java @@ -74,13 +74,36 @@ public class NCBIQBlastService implements RemotePairwiseAlignmentService { private Map jobs = new HashMap(); + /** Constructs a service object that targets the public NCBI BLAST network + * service. + */ public NCBIQBlastService() { + init(SERVICE_URL); + } + + /** Constructs a service object which targets a custom NCBI BLAST network + * service (e.g.: an instance of BLAST in the cloud). + * + * @param svcUrl : a {@code String} containing the base URL to send requests to, + * e.g.: http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi + * + * @see BLAST on the cloud documentation + */ + public NCBIQBlastService(String svcUrl) { + init(svcUrl); + } + + /** Initialize the serviceUrl data member + * @throws MalformedURLException on invalid URL + */ + private void init(String svcUrl) { try { - serviceUrl = new URL(SERVICE_URL); + serviceUrl = new URL(svcUrl); } catch (MalformedURLException e) { - throw new RuntimeException("It looks like the URL for NCBI QBlast service is wrong. Cause: " + e.getMessage(), e); + throw new RuntimeException("It looks like the URL for remote NCBI BLAST service (" + + svcUrl + ") is wrong. Cause: " + e.getMessage(), e); } - } + } /** * A simple method to check the availability of the QBlast service. Sends {@code Info} command to QBlast @@ -252,7 +275,7 @@ public boolean isReady(String id, long present) throws Exception { OutputStreamWriter writer = null; BufferedReader reader = null; try { - String checkRequest = "CMD=Get&RID=" + job.getId(); + String checkRequest = "CMD=Get&RID=" + job.getId() + "&FORMAT_OBJECT=SearchInfo"; URLConnection serviceConnection = setQBlastServiceProperties(serviceUrl.openConnection()); writer = new OutputStreamWriter(serviceConnection.getOutputStream()); writer.write(checkRequest); From ea78f97c2fff816ccec5f039d19df2c941b75514 Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Fri, 25 Mar 2016 10:49:57 +0100 Subject: [PATCH 06/30] Fix major bug with BIO: identifiers --- .../org/biojava/nbio/structure/align/client/StructureName.java | 1 + 1 file changed, 1 insertion(+) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java index 3ad51ab9ef..401b131ac5 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java @@ -522,6 +522,7 @@ public StructureIdentifier getBaseIdentifier() throws StructureException { break; case BIO: base = new BioAssemblyIdentifier(name); + break; case PDB: base = new SubstructureIdentifier(getIdentifier()); break; From 402c1773208c7c26b8cbdc909b41fdbd436a5766 Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Fri, 25 Mar 2016 10:54:15 +0100 Subject: [PATCH 07/30] Logging and documentation --- .../structure/align/gui/jmol/AbstractAlignmentJmol.java | 9 ++++++--- .../structure/symmetry/internal/CESymmParameters.java | 6 ++++-- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java index 83e546de8d..ec2c660deb 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java @@ -41,6 +41,8 @@ import org.biojava.nbio.structure.jama.Matrix; import org.jcolorbrewer.ColorBrewer; import org.jmol.api.JmolViewer; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; /** * An Abstract Class to generalize the visualization of AFP and @@ -52,6 +54,7 @@ public abstract class AbstractAlignmentJmol implements MouseMotionListener, MouseListener, WindowListener, ActionListener { + private static final Logger logger = LoggerFactory.getLogger(AbstractAlignmentJmol.class); protected Structure structure; protected ColorBrewer colorPalette = ColorBrewer.Spectral; @@ -81,7 +84,7 @@ public abstract class AbstractAlignmentJmol * Set all the member variables to null. */ public void destroy(){ - System.err.println("cleaning up AlignmentJmol window"); + logger.debug("cleaning up AlignmentJmol window"); jmolPanel.removeMouseListener(this); jmolPanel.removeMouseMotionListener(this); jmolPanel.destroy(); @@ -135,7 +138,7 @@ public void setJmolPanel(JmolPanel jmolPanel) { */ public void evalString(String rasmolScript){ if ( jmolPanel == null ){ - System.err.println("please install Jmol first"); + logger.error("please install Jmol first"); return; } jmolPanel.evalString(rasmolScript); @@ -148,7 +151,7 @@ public void evalString(String rasmolScript){ public void setStructure(Structure s) { if (jmolPanel == null){ - System.err.println("please install Jmol first"); + logger.error("please install Jmol first"); return; } setTitle(s.getPDBCode()); diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java index 0423c69044..a8a9677f5a 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java @@ -222,7 +222,9 @@ public List getUserConfigHelp() { + "between two aligned residues."); // gaps - params.add("MStA Gaps: allow gaps in the multiple alignment if true."); + params.add("Internal Gaps: allow up to 50% of repeats to have gaps in " + + "the multiple alignment if true, " + + "otherwise all repeats must be aligned at each position."); // optimization steps params.add("Optimization Steps: maximum number of optimization steps:" @@ -266,7 +268,7 @@ public List getUserConfigParameterNames() { params.add("SSE Threshold"); params.add("Minimum Core Length"); params.add("Distance Cutoff"); - params.add("MStA Gaps"); + params.add("Internal Gaps"); params.add("Optimization Steps"); return params; } From de603088aa961643a82f4e4abfc824d2ed41678c Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Fri, 25 Mar 2016 11:08:57 +0100 Subject: [PATCH 08/30] Setting 4.2.1-SNAPSHOT in all other poms Note that the biojava-protein-comparison-tool 4.2.0 wasn't even released, since the parent version wasn't updated properly --- 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-comparison-tool/pom.xml | 2 +- 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 | 2 +- 16 files changed, 32 insertions(+), 32 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 3909e67ed0..2abf1a64ce 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 4.2.0 + 4.2.1-SNAPSHOT org.biojava biojava-structure - 4.2.0 + 4.2.1-SNAPSHOT diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 7a815ebc3c..128baf980a 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.0 + 4.2.1-SNAPSHOT compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.0 + 4.2.1-SNAPSHOT diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index e1f805029d..e251cb1bac 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 5543090077..df5e7d5e98 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT 4.0.0 biojava-genome @@ -79,13 +79,13 @@ org.biojava biojava-core - 4.2.0 + 4.2.1-SNAPSHOT compile org.biojava biojava-alignment - 4.2.0 + 4.2.1-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index e488be4e14..afb90af6cc 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.0 + 4.2.1-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 49dbd60c73..9e5c3c47fc 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.0 + 4.2.1-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 973e53f4a9..e14307a9a0 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.0 + 4.2.1-SNAPSHOT biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index 9ed7013816..cc85f2809f 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.0 + 4.2.1-SNAPSHOT compile diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 9fef34af1c..01573d4b18 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -5,7 +5,7 @@ biojava org.biojava - 4.1.1-SNAPSHOT + 4.2.1-SNAPSHOT biojava-protein-comparison-tool diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index d55af261df..5c32781aa9 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.0 + 4.2.1-SNAPSHOT diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index 0d788a057f..eb332ae145 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.0 + 4.2.1-SNAPSHOT compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 580dcbb412..9090b0a75f 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT 4.0.0 biojava-structure-gui @@ -45,13 +45,13 @@ org.biojava biojava-structure - 4.2.0 + 4.2.1-SNAPSHOT compile org.biojava biojava-core - 4.2.0 + 4.2.1-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index d6efe31b01..ecbf5df677 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.0 + 4.2.1-SNAPSHOT compile org.biojava biojava-core - 4.2.0 + 4.2.1-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index d030f2b945..6a686e0e3d 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.0 + 4.2.1-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 776f3a1926..d124d0ce5a 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.0 + 4.2.1-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.0 + 4.2.1-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index bcc44c3e25..dd5a3de4b6 100644 --- a/pom.xml +++ b/pom.xml @@ -44,7 +44,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-4.2.0 + biojava-4.2.1 - - biojava-maven-repo - BioJava repository - http://www.biojava.org/download/maven/ - - true - - - true - always - - - junit junit test - - javaws - javaws - 1.0 - org.biojava biojava-structure @@ -94,7 +74,7 @@ - + org.apache.maven.plugins maven-jar-plugin @@ -108,4 +88,5 @@ + diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java index 356a644cb1..237dbc0fc3 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java @@ -62,14 +62,7 @@ public void actionPerformed(ActionEvent evt) { if ( txt != null){ chooser.setCurrentDirectory(new java.io.File(txt)); config.setPdbFilePath(txt); - try { - PersistentConfig webstartConfig = new PersistentConfig(); - webstartConfig.save(config); - - } catch (Exception e){ - e.printStackTrace(); - } } chooser.setDialogTitle("Choose directory that contains your PDB files"); chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/PersistentConfig.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/PersistentConfig.java deleted file mode 100644 index b984da8207..0000000000 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/PersistentConfig.java +++ /dev/null @@ -1,212 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on 20.09.2004 - * @author Andreas Prlic - * - */ - -package org.biojava.nbio.structure.align.webstart; - -import org.biojava.nbio.structure.align.util.UserConfiguration; -import org.biojava.nbio.core.util.XMLWriter; -import org.xml.sax.InputSource; -import org.xml.sax.XMLReader; - -import javax.jnlp.*; -import javax.xml.parsers.ParserConfigurationException; -import javax.xml.parsers.SAXParser; -import javax.xml.parsers.SAXParserFactory; -import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; -import java.io.PrintWriter; -import java.net.URL; - - -/** a class to store the config using the Java Web Start - * PersistenService. - * @author Andreas Prlic - */ -public class PersistentConfig -{ - - PersistenceService ps; - BasicService bs ; - - public PersistentConfig() - throws UnavailableServiceException - { - try { - ps = (PersistenceService)ServiceManager.lookup("javax.jnlp.PersistenceService"); - bs = (BasicService)ServiceManager.lookup("javax.jnlp.BasicService"); - } catch (Exception e){ - System.err.println("Can't init webstart - persistent configuration. " + e.getMessage() ); - } - } - - /** writes the configuration - * - * @param config - */ - public void save(UserConfiguration config ) { - if (ps != null && bs != null) { - // Persistent Service is available, running as javaws - saveWebStart(config) ; - } else { - System.err.println("can not save using persistentservice!"); - } - } - - private void saveWebStart(UserConfiguration config ){ - //System.out.println("saving webstart"); - - - try { - - // find all the muffins for our URL - URL codebase = bs.getCodeBase(); - - FileContents fc = null ; - - - try { - // test if persistent storage already created - - fc = ps.get(codebase); - - ps.delete(codebase); - - } catch (IOException e){ - } - - // seems not, create it first - ps.create(codebase,3000000); - fc = ps.get(codebase); - - - OutputStream os = fc.getOutputStream(true); - - //StringWriter sw = new StringWriter(); - //StringWriter stw = new StringWriter(os) ; - PrintWriter pw = new PrintWriter(os,true); - XMLWriter xw = config.toXML(pw); - - - pw.flush(); - os.flush(); - - xw.close(); - pw.close(); - os.close(); - - - } catch (Exception e) { - System.err.println(e.getMessage()); - } - } - - - /** loads Config from PersistenceService - * returns null if no PErsistenceService has been created ... - * - * @return WebStartConfiguration - */ - public UserConfiguration load() { - if (ps != null && bs != null) { - // Persistent Service is available, running as javaws - return loadWebStart() ; - } else { - System.err.println("can not load from persistentservice!"); - } - return null ; - } - - - /** loads Config from PersistenceService - * returns null if no PErsistenceService has been created ... - */ - private UserConfiguration loadWebStart() { - UserConfiguration config = null; - try { - URL codebase = bs.getCodeBase(); - - FileContents fc = null ; - - try { - - fc = ps.get(codebase); - } catch (IOException e){ - // has not been created, so nothing can be loaded ... - e.printStackTrace(); - return null ; - } - - - // parse the XML file ... - InputStream stream = fc.getInputStream(); - config = parseConfigFile(stream); - - } catch (Exception e) { - System.err.println(e.getMessage()); - } - - return config ; - - } - - - private UserConfiguration parseConfigFile(InputStream inStream) { - - try { - SAXParserFactory spfactory = - SAXParserFactory.newInstance(); - - SAXParser saxParser = null ; - - try{ - saxParser = - spfactory.newSAXParser(); - } catch (ParserConfigurationException e) { - e.printStackTrace(); - } - - XMLReader xmlreader = saxParser.getXMLReader(); - - ConfigXMLHandler cont_handle = new ConfigXMLHandler(); - xmlreader.setContentHandler(cont_handle); - xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler()); - - InputSource insource = new InputSource() ; - insource.setByteStream(inStream); - - // the actual parsing starts now ... - xmlreader.parse(insource); - - - UserConfiguration config = cont_handle.getConfig(); - return config ; - - } catch (Exception e){ - e.printStackTrace(); - return null; - } - - } -} diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java index febf4e65df..ba34cc4e18 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java @@ -229,29 +229,10 @@ private static JProgressBar showProgressBar(JFrame frame, String title, String d public static UserConfiguration getWebStartConfig(){ - if ( userConfig == null) { - try { - PersistentConfig webstartConfig = new PersistentConfig(); - - userConfig = webstartConfig.load(); - - } catch (Exception e){ - System.err.println(e.getMessage()); - } - } - // check if we could load it (i.e. we are running in web start mode) if ( userConfig == null ) { userConfig = WebStartMain.getDefaultConfig(); - try { - PersistentConfig webstartConfig = new PersistentConfig(); - - webstartConfig.save(userConfig); - - } catch (UnavailableServiceException e){ - System.err.println(e.getMessage()); - } } return userConfig; @@ -270,18 +251,6 @@ public static UserConfiguration getDefaultConfig(){ return userConfig; } - public static void persistConfig(UserConfiguration config){ - - try { - PersistentConfig webstartConfig = new PersistentConfig(); - - webstartConfig.save(config); - - } catch (UnavailableServiceException e){ - e.printStackTrace(); - } - - } public static UserConfiguration requestUserConfig(){ From db37b87096a4b2d11cdb3790747f33a4c0b303b4 Mon Sep 17 00:00:00 2001 From: Andreas Prlic Date: Fri, 29 Apr 2016 13:40:01 -0700 Subject: [PATCH 26/30] #459 removing javaws dependency part 2 --- .../org/biojava/nbio/structure/align/gui/ChooseDirAction.java | 1 - .../nbio/structure/align/gui/ConfigPDBInstallPanel.java | 3 +-- .../biojava/nbio/structure/align/webstart/WebStartMain.java | 1 - 3 files changed, 1 insertion(+), 4 deletions(-) diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java index 237dbc0fc3..c603392c08 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ChooseDirAction.java @@ -25,7 +25,6 @@ package org.biojava.nbio.structure.align.gui; import org.biojava.nbio.structure.align.util.UserConfiguration; -import org.biojava.nbio.structure.align.webstart.PersistentConfig; import org.biojava.nbio.structure.align.webstart.WebStartMain; import javax.swing.*; diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java index 731da66b2a..6c4949dc2c 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java @@ -181,8 +181,7 @@ protected void applyValues() String fileFormat = (String)fileType.getSelectedItem(); config.setFileFormat(fileFormat); - // and now persist.. - WebStartMain.persistConfig(config); + } diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java index ba34cc4e18..27c0ceb322 100644 --- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java +++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java @@ -40,7 +40,6 @@ import org.biojava.nbio.structure.align.util.AtomCache; import org.biojava.nbio.structure.align.util.UserConfiguration; -import javax.jnlp.UnavailableServiceException; import javax.swing.*; import java.io.File; From 9f48f1700604fdb1e07d78d9172cedb44a1313af Mon Sep 17 00:00:00 2001 From: Anthony Bradley Date: Tue, 3 May 2016 09:10:04 -0700 Subject: [PATCH 27/30] Updated MMCif Parser to handle non-numeric data in the NCS operator field. --- .../structure/io/mmcif/SimpleMMcifParser.java | 38 +++++++++++-------- 1 file changed, 23 insertions(+), 15 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java index 708feb91c8..3878890eb2 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java @@ -524,9 +524,9 @@ private List processSingleLine(String line){ * @return */ private List processLine(String line, - BufferedReader buf, - int fieldLength) - throws IOException{ + BufferedReader buf, + int fieldLength) + throws IOException{ //System.out.println("XX processLine " + fieldLength + " " + line); // go through the line and process each character @@ -594,9 +594,9 @@ private List processLine(String line, private void endLineChecks(String category,List loopFields, List lineData, Set loopWarnings ) throws IOException{ logger.debug("Processing category {}, with fields: {}",category,loopFields.toString()); -// System.out.println("parsed the following data: " +category + " fields: "+ -// loopFields + " DATA: " + -// lineData); + // System.out.println("parsed the following data: " +category + " fields: "+ + // loopFields + " DATA: " + + // lineData); if ( loopFields.size() != lineData.size()){ logger.warn("looks like we got a problem with nested string quote characters:"); @@ -671,8 +671,16 @@ private void endLineChecks(String category,List loopFields, List } else if ( category.equals("_struct_ncs_oper")) { // this guy is special because of the [] in the field names - StructNcsOper sNcsOper = getStructNcsOper(loopFields,lineData); - triggerNewStructNcsOper(sNcsOper); + StructNcsOper sNcsOper = null; + try{ + sNcsOper = getStructNcsOper(loopFields,lineData); + } + catch(NumberFormatException e){ + logger.warn("Error parsing doubles in NCS operator list"); + } + if(sNcsOper!=null){ + triggerNewStructNcsOper(sNcsOper); + } } else if ( category.equals("_struct_ref")){ StructRef sref = (StructRef) buildObject( @@ -750,25 +758,25 @@ private void endLineChecks(String category,List loopFields, List PdbxEntityNonPoly pen = (PdbxEntityNonPoly) buildObject( PdbxEntityNonPoly.class.getName(), loopFields,lineData, loopWarnings - ); + ); triggerNewPdbxEntityNonPoly(pen); } else if ( category.equals("_struct_keywords")){ StructKeywords kw = (StructKeywords)buildObject( StructKeywords.class.getName(), loopFields,lineData, loopWarnings - ); + ); triggerNewStructKeywords(kw); } else if (category.equals("_refine")){ Refine r = (Refine)buildObject( Refine.class.getName(), loopFields,lineData, loopWarnings - ); + ); triggerNewRefine(r); } else if (category.equals("_chem_comp")){ ChemComp c = (ChemComp)buildObject( ChemComp.class.getName(), loopFields, lineData, loopWarnings - ); + ); triggerNewChemComp(c); } else if (category.equals("_audit_author")) { AuditAuthor aa = (AuditAuthor)buildObject( @@ -839,7 +847,7 @@ private void endLineChecks(String category,List loopFields, List private PdbxStructOperList getPdbxStructOperList(List loopFields, - List lineData) { + List lineData) { PdbxStructOperList so = new PdbxStructOperList(); //System.out.println(loopFields); @@ -856,7 +864,7 @@ private PdbxStructOperList getPdbxStructOperList(List loopFields, String val = lineData.get(loopFields.indexOf(max)); Double d = Double.parseDouble(val); matrix.set(j-1,i-1,d); -// matrix.set(i-1,j-1,d); + // matrix.set(i-1,j-1,d); } } @@ -900,10 +908,10 @@ private StructNcsOper getStructNcsOper(List loopFields, List lin op.setElement(3, 2, 0.0); op.setElement(3, 3, 1.0); + for (int i = 1 ; i <=3 ; i++){ for (int j =1 ; j <= 3 ; j++){ String max = String.format("matrix[%d][%d]",i,j); - String val = lineData.get(loopFields.indexOf(max)); Double d = Double.parseDouble(val); op.setElement(i-1,j-1,d); From 337ea1a9a536af12d68feb45dca83ea0ce8b8c47 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Tue, 3 May 2016 15:06:13 -0700 Subject: [PATCH 28/30] [maven-release-plugin] prepare release biojava-4.2.1 --- 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 | 2 +- 15 files changed, 31 insertions(+), 31 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 2abf1a64ce..56992a067a 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 org.biojava biojava-structure - 4.2.1-SNAPSHOT + 4.2.1 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 128baf980a..99133e7a97 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.1-SNAPSHOT + 4.2.1 diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index e251cb1bac..d5f45ef45b 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index df5e7d5e98..5ca7be55b6 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-genome @@ -79,13 +79,13 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile org.biojava biojava-alignment - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index afb90af6cc..c269db8521 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.1-SNAPSHOT + 4.2.1 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 9e5c3c47fc..eda4cc2aae 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.1-SNAPSHOT + 4.2.1 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index e14307a9a0..d6558f3875 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index cc85f2809f..650a14d4f6 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 5c32781aa9..5a1283acba 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index eb332ae145..16f7b04040 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 4342858fed..cb01913352 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.1-SNAPSHOT + 4.2.1 compile org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index ecbf5df677..31c3cddc03 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.1-SNAPSHOT + 4.2.1 compile org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 6a686e0e3d..5bffa2139e 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index d124d0ce5a..9d643a2368 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/pom.xml b/pom.xml index dd5a3de4b6..330c0798a3 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.1-SNAPSHOT + 4.2.1 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 From 9c4091ae5177b0753197ce8e56114b3eea84c7b2 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Tue, 3 May 2016 15:21:15 -0700 Subject: [PATCH 29/30] [maven-release-plugin] rollback the release of biojava-4.2.1 --- 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 | 2 +- 15 files changed, 31 insertions(+), 31 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 56992a067a..2abf1a64ce 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 4.2.1 + 4.2.1-SNAPSHOT org.biojava biojava-structure - 4.2.1 + 4.2.1-SNAPSHOT diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 99133e7a97..128baf980a 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.1 + 4.2.1-SNAPSHOT compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.1 + 4.2.1-SNAPSHOT diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index d5f45ef45b..e251cb1bac 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 5ca7be55b6..df5e7d5e98 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT 4.0.0 biojava-genome @@ -79,13 +79,13 @@ org.biojava biojava-core - 4.2.1 + 4.2.1-SNAPSHOT compile org.biojava biojava-alignment - 4.2.1 + 4.2.1-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index c269db8521..afb90af6cc 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.1 + 4.2.1-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index eda4cc2aae..9e5c3c47fc 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.1 + 4.2.1-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index d6558f3875..e14307a9a0 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.1 + 4.2.1-SNAPSHOT biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index 650a14d4f6..cc85f2809f 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.1 + 4.2.1-SNAPSHOT compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 5a1283acba..5c32781aa9 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.1 + 4.2.1-SNAPSHOT diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index 16f7b04040..eb332ae145 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.1 + 4.2.1-SNAPSHOT compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index cb01913352..4342858fed 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.1 + 4.2.1-SNAPSHOT compile org.biojava biojava-core - 4.2.1 + 4.2.1-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 31c3cddc03..ecbf5df677 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.1 + 4.2.1-SNAPSHOT compile org.biojava biojava-core - 4.2.1 + 4.2.1-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 5bffa2139e..6a686e0e3d 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.1 + 4.2.1-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 9d643a2368..d124d0ce5a 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1 + 4.2.1-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.1 + 4.2.1-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 330c0798a3..dd5a3de4b6 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.1 + 4.2.1-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 From 8504664c989dad5adeb4a0832e4d224f4d8e02bf Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Tue, 3 May 2016 15:29:16 -0700 Subject: [PATCH 30/30] [maven-release-plugin] prepare release biojava-4.2.1 --- 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 | 2 +- 15 files changed, 31 insertions(+), 31 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 2abf1a64ce..56992a067a 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 org.biojava biojava-structure - 4.2.1-SNAPSHOT + 4.2.1 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 128baf980a..99133e7a97 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.1-SNAPSHOT + 4.2.1 diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index e251cb1bac..d5f45ef45b 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index df5e7d5e98..5ca7be55b6 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-genome @@ -79,13 +79,13 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile org.biojava biojava-alignment - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index afb90af6cc..c269db8521 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.1-SNAPSHOT + 4.2.1 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 9e5c3c47fc..eda4cc2aae 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.1-SNAPSHOT + 4.2.1 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index e14307a9a0..d6558f3875 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index cc85f2809f..650a14d4f6 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 5c32781aa9..5a1283acba 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index eb332ae145..16f7b04040 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 4342858fed..cb01913352 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.1-SNAPSHOT + 4.2.1 compile org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index ecbf5df677..31c3cddc03 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.1-SNAPSHOT + 4.2.1 compile org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 6a686e0e3d..5bffa2139e 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index d124d0ce5a..9d643a2368 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.1-SNAPSHOT + 4.2.1 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.1-SNAPSHOT + 4.2.1 compile diff --git a/pom.xml b/pom.xml index dd5a3de4b6..330c0798a3 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.1-SNAPSHOT + 4.2.1 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