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raw | compact (merge: bc03616 be719c4)
Merge branch 'develop' into LibrAlign
authorPatrick Plitzner <p.plitzner@bgbm.org>
Mon, 24 Oct 2016 07:20:39 +0000 (09:20 +0200)
committerPatrick Plitzner <p.plitzner@bgbm.org>
Mon, 24 Oct 2016 07:27:25 +0000 (09:27 +0200)
# Conflicts:
# eu.etaxonomy.taxeditor.molecular.lib/.classpath

1  2 
eu.etaxonomy.taxeditor.molecular.lib/.classpath patch | diff1 | diff2 | blob | history
eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF patch | diff1 | diff2 | blob | history
eu.etaxonomy.taxeditor.molecular.lib/pom.xml patch | diff1 | diff2 | blob | history
eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF patch | diff1 | diff2 | blob | history

diff --combined eu.etaxonomy.taxeditor.molecular.lib/.classpath
index a7281ddfe9e6f1874f47193f245ecc33d2df4710,5918c4c4dbec2d926510c448e8396a5d3dcba42c..cedc1756f6cc8969124d508a1b2eb0f093a088a5
--- 1/eu.etaxonomy.taxeditor.molecular.lib/.classpath
--- 2/eu.etaxonomy.taxeditor.molecular.lib/.classpath
+++ b/eu.etaxonomy.taxeditor.molecular.lib/.classpath
@@@ -1,20 -1,17 +1,20 @@@
  <?xml version="1.0" encoding="UTF-8"?>
  <classpath>
-       <classpathentry exported="true" kind="lib" path="lib/commons-collections4-4.1.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/core-1.9.2.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/sequencing-1.9.2.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
        <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 -      <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-bio-2.0.0-preview-1.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-core-2.0.0-preview-1.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swing-2.0.0-preview-1.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swt-2.0.0-preview-1.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/core-1.9.2-SNAPSHOT.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/libralign-biojava1-0.4.0-preview-1.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/libralign-core-0.4.0-preview-1.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/libralign-swt-0.4.0-preview-1.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/sequencing-1.9.2-SNAPSHOT.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/tic-core-2.0.0-preview-1.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/tic-swt-2.0.0-preview-1.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/owlapi-xmlutils-4.1.4.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-bio-2-SNAPSHOT.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-core-2-SNAPSHOT.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swing-2-SNAPSHOT.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swt-2-SNAPSHOT.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/jphyloio-core-0-SNAPSHOT.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/libralign-biojava1-0-SNAPSHOT.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/libralign-core-0-SNAPSHOT.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/libralign-swt-0-SNAPSHOT.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/tic-core-2-SNAPSHOT.jar"/>
 +      <classpathentry exported="true" kind="lib" path="lib/tic-swt-2-SNAPSHOT.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/commons-collections4-4.1.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/core-1.9.2.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/sequencing-1.9.2.jar"/>
        <classpathentry kind="output" path="target/classes"/>
  </classpath>
diff --combined eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
index 454039ef978762fa7abec217417816242a874307,94b1e70f49b2680da187380b271b93bb632b4e14..414a0e99f88290cebddbaf2a9ab123675414fe5a
--- 1/eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
--- 2/eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
@@@ -2,22 -2,19 +2,22 @@@ Manifest-Version: 1.
  Bundle-ManifestVersion: 2
  Bundle-Name: eu.etaxonomy.taxeditor.molecular.lib
  Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular.lib;singleton:=true
- Bundle-Version: 4.2.0.qualifier
+ Bundle-Version: 4.4.0.qualifier
  Bundle-ClassPath: .,
 - lib/bioinfweb-commons-bio-2.0.0-preview-1.jar,
 - lib/bioinfweb-commons-core-2.0.0-preview-1.jar,
 - lib/bioinfweb-commons-swing-2.0.0-preview-1.jar,
 - lib/bioinfweb-commons-swt-2.0.0-preview-1.jar,
 - lib/core-1.9.2-SNAPSHOT.jar,
 - lib/libralign-biojava1-0.4.0-preview-1.jar,
 - lib/libralign-core-0.4.0-preview-1.jar,
 - lib/libralign-swt-0.4.0-preview-1.jar,
 - lib/sequencing-1.9.2-SNAPSHOT.jar,
 - lib/tic-core-2.0.0-preview-1.jar,
 - lib/tic-swt-2.0.0-preview-1.jar
 + lib/owlapi-xmlutils-4.1.4.jar,
 + lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,
 + lib/bioinfweb-commons-core-2-SNAPSHOT.jar,
 + lib/bioinfweb-commons-swing-2-SNAPSHOT.jar,
 + lib/bioinfweb-commons-swt-2-SNAPSHOT.jar,
 + lib/jphyloio-core-0-SNAPSHOT.jar,
 + lib/libralign-biojava1-0-SNAPSHOT.jar,
 + lib/libralign-core-0-SNAPSHOT.jar,
 + lib/libralign-swt-0-SNAPSHOT.jar,
 + lib/tic-core-2-SNAPSHOT.jar,
 + lib/tic-swt-2-SNAPSHOT.jar,
 + lib/commons-collections4-4.1.jar,
 + lib/core-1.9.2.jar,
 + lib/sequencing-1.9.2.jar
  Export-Package: info.bioinfweb.commons,
   info.bioinfweb.commons.appversion,
   info.bioinfweb.commons.beans,
@@@ -33,37 -30,6 +33,37 @@@
   info.bioinfweb.commons.swing.scrollpaneselector,
   info.bioinfweb.commons.swt,
   info.bioinfweb.commons.text,
 + info.bioinfweb.jphyloio,
 + info.bioinfweb.jphyloio.dataadapters,
 + info.bioinfweb.jphyloio.dataadapters.implementations,
 + info.bioinfweb.jphyloio.dataadapters.implementations.readtowriteadapter,
 + info.bioinfweb.jphyloio.dataadapters.implementations.receivers,
 + info.bioinfweb.jphyloio.events,
 + info.bioinfweb.jphyloio.events.meta,
 + info.bioinfweb.jphyloio.events.type,
 + info.bioinfweb.jphyloio.exception,
 + info.bioinfweb.jphyloio.factory,
 + info.bioinfweb.jphyloio.formats,
 + info.bioinfweb.jphyloio.formats.fasta,
 + info.bioinfweb.jphyloio.formats.mega,
 + info.bioinfweb.jphyloio.formats.newick,
 + info.bioinfweb.jphyloio.formats.nexml,
 + info.bioinfweb.jphyloio.formats.nexml.nexmlreceivers,
 + info.bioinfweb.jphyloio.formats.nexus,
 + info.bioinfweb.jphyloio.formats.nexus.blockhandlers,
 + info.bioinfweb.jphyloio.formats.nexus.commandreaders,
 + info.bioinfweb.jphyloio.formats.nexus.commandreaders.all,
 + info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters,
 + info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets,
 + info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa,
 + info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees,
 + info.bioinfweb.jphyloio.formats.pde,
 + info.bioinfweb.jphyloio.formats.phylip,
 + info.bioinfweb.jphyloio.formats.phyloxml,
 + info.bioinfweb.jphyloio.formats.text,
 + info.bioinfweb.jphyloio.formats.xml,
 + info.bioinfweb.jphyloio.formats.xtg,
 + info.bioinfweb.jphyloio.tools,
   info.bioinfweb.libralign,
   info.bioinfweb.libralign.actions,
   info.bioinfweb.libralign.alignmentarea,
@@@ -108,24 -74,6 +108,24 @@@
   info.bioinfweb.tic.input,
   info.bioinfweb.tic.toolkit,
   info.bioinfweb.tic.toolkit.layoutdata,
 + org.apache.commons.collections4,
 + org.apache.commons.collections4.bag,
 + org.apache.commons.collections4.bidimap,
 + org.apache.commons.collections4.collection,
 + org.apache.commons.collections4.comparators,
 + org.apache.commons.collections4.functors,
 + org.apache.commons.collections4.iterators,
 + org.apache.commons.collections4.keyvalue,
 + org.apache.commons.collections4.list,
 + org.apache.commons.collections4.map,
 + org.apache.commons.collections4.multimap,
 + org.apache.commons.collections4.multiset,
 + org.apache.commons.collections4.queue,
 + org.apache.commons.collections4.sequence,
 + org.apache.commons.collections4.set,
 + org.apache.commons.collections4.splitmap,
 + org.apache.commons.collections4.trie,
 + org.apache.commons.collections4.trie.analyzer,
   org.biojava.bibliography,
   org.biojava.bio,
   org.biojava.bio.alignment,
@@@ -212,8 -160,7 +212,8 @@@
   org.biojavax.ga.util,
   org.biojavax.ontology,
   org.biojavax.utils,
 - org.jdesktop.swingx.scrollpaneselector
 + org.jdesktop.swingx.scrollpaneselector,
 + org.semanticweb.owlapi.io
  Bundle-ActivationPolicy: lazy
  Import-Package: javax.swing
  Require-Bundle: org.eclipse.swt
diff --combined eu.etaxonomy.taxeditor.molecular.lib/pom.xml
index d98ea1c36884670c9633a00192b164032248dd38,39427a3d428ab8647c01bea362060ff8682d845e..3458f1c6faaa184684c8d01b9ce14a3587085b3e
--- 1/eu.etaxonomy.taxeditor.molecular.lib/pom.xml
--- 2/eu.etaxonomy.taxeditor.molecular.lib/pom.xml
+++ b/eu.etaxonomy.taxeditor.molecular.lib/pom.xml
@@@ -7,7 -7,7 +7,7 @@@
    <parent>
      <groupId>eu.etaxonomy</groupId>
      <artifactId>taxeditor-parent</artifactId>
-     <version>4.2.0-SNAPSHOT</version>
+     <version>4.4.0-SNAPSHOT</version>
    </parent>
  
    <build>
@@@ -27,8 -27,7 +27,8 @@@
                <includeArtifactIds>libralign-swt, libralign-core,
                  bioinfweb-commons-swt, bioinfweb-commons-core,
                  bioinfweb-commons-bio, bioinfweb-commons-swing,
 -                tic-core, libralign-biojava1, core, sequencing, tic-swt</includeArtifactIds>
 +                tic-core, libralign-biojava1, core, sequencing, 
 +                tic-swt, jphyloio-core, owlapi-xmlutils, commons-collections4</includeArtifactIds>
                <outputDirectory>lib</outputDirectory>
                <overWriteReleases>true</overWriteReleases>
                <overWriteSnapshots>true</overWriteSnapshots>
@@@ -97,7 -96,11 +97,7 @@@
                  </move>
                  <move todir="./lib">
                    <fileset dir="./lib" />
 -                  <mapper type="regexp" from="(^core\-[0-9]\.[0-9]\.[0-9])(\.jar)" to="\1-SNAPSHOT\2" />
 -                </move>
 -                <move todir="./lib">
 -                  <fileset dir="./lib" />
 -                  <mapper type="regexp" from="(^sequencing\-[0-9]\.[0-9]\.[0-9])(\.jar)" to="\1-SNAPSHOT\2" />
 +                  <mapper type="regexp" from="(^jphyloio\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
                  </move>
                </target>
              </configuration>
@@@ -108,66 -111,55 +108,66 @@@
    </build>
  
    <dependencies>
 -    <!-- LibrAling -->
 +    <!-- JPhyloIO -->
 +    <dependency>
 +      <groupId>info.bioinfweb.jphyloio</groupId>
 +      <artifactId>jphyloio-core</artifactId>
 +      <version>0-SNAPSHOT</version>
 +    </dependency>
 +    <dependency>
 +      <groupId>info.bioinfweb.thirdparty.owlapi</groupId>
 +      <artifactId>owlapi-xmlutils</artifactId>
 +      <version>4.1.4</version>
 +    </dependency>
 +    <!-- LibrAlign -->
      <dependency>
        <groupId>info.bioinfweb.libralign</groupId>
        <artifactId>libralign-core</artifactId>
 -      <version>0.4.0-preview-1</version>
 +      <version>0-SNAPSHOT</version>
      </dependency>
      <dependency>
        <groupId>info.bioinfweb.libralign</groupId>
        <artifactId>libralign-swt</artifactId>
 -      <version>0.4.0-preview-1</version>
 +      <version>0-SNAPSHOT</version>
      </dependency>
      <dependency>
        <groupId>info.bioinfweb.libralign</groupId>
        <artifactId>libralign-biojava1</artifactId>
 -      <version>0.4.0-preview-1</version>
 +      <version>0-SNAPSHOT</version>
      </dependency>
 -    <!-- commons -->
 +    <!-- bioinfweb.commons -->
      <dependency>
        <groupId>info.bioinfweb.commons.java</groupId>
        <artifactId>bioinfweb-commons-swt</artifactId>
 -      <version>2.0.0-preview-1</version>
 +      <version>2-SNAPSHOT</version>
      </dependency>
      <dependency>
        <groupId>info.bioinfweb.commons.java</groupId>
        <artifactId>bioinfweb-commons-core</artifactId>
 -      <version>2.0.0-preview-1</version>
 +      <version>2-SNAPSHOT</version>
      </dependency>
      <dependency>
        <groupId>info.bioinfweb.commons.java</groupId>
        <artifactId>bioinfweb-commons-bio</artifactId>
 -      <version>2.0.0-preview-1</version>
 +      <version>2-SNAPSHOT</version>
      </dependency>
      <dependency>
        <groupId>info.bioinfweb.commons.java</groupId>
        <artifactId>bioinfweb-commons-swing</artifactId>
 -      <version>2.0.0-preview-1</version>
 +      <version>2-SNAPSHOT</version>
      </dependency>
 -    <!-- tic -->
 +    <!-- TIC -->
      <dependency>
        <groupId>info.bioinfweb.tic</groupId>
        <artifactId>tic-core</artifactId>
 -      <version>2.0.0-preview-1</version>
 +      <version>2-SNAPSHOT</version>
      </dependency>
      <dependency>
        <groupId>info.bioinfweb.tic</groupId>
        <artifactId>tic-swt</artifactId>
 -      <version>2.0.0-preview-1</version>
 +      <version>2-SNAPSHOT</version>
      </dependency>
 -    <!-- biojava -->
 +    <!-- BioJava -->
      <dependency>
        <groupId>org.biojava</groupId>
        <artifactId>core</artifactId>
@@@ -178,12 -170,6 +178,12 @@@
        <artifactId>sequencing</artifactId>
        <version>1.9.2</version>
      </dependency>
 +    <!-- Apache commons -->
 +    <dependency>
 +      <groupId>org.apache.commons</groupId>
 +      <artifactId>commons-collections4</artifactId>
 +      <version>4.1</version>
 +    </dependency>
    </dependencies>
  
    <repositories>
@@@ -192,11 -178,7 +192,11 @@@
        <name>bioinfweb repository</name>
        <url>http://bioinfweb.info/MavenRepository/</url>
      </repository>
 +    <!-- <repository>
 +      <id>central-maven-repo</id>
 +      <name>Maven Central</name>
 +      <url>http://central.maven.org/maven2/</url>
 +    </repository> -->
    </repositories>
 -  
  </project> 
  
diff --combined eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
index 8afdbe3f26faf0d4367374896572f7fee7a4f73f,889e482eef2efa9970e5be9e5a907ef288972951..2ad5bf685c3a39a2dc917a860c723745e2d120fc
--- 1/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
--- 2/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
@@@ -2,7 -2,7 +2,7 @@@ Manifest-Version: 1.
  Bundle-ManifestVersion: 2
  Bundle-Name: Molecular Bundle
  Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular;singleton:=true
- Bundle-Version: 4.2.0.qualifier
+ Bundle-Version: 4.4.0.qualifier
  Bundle-Activator: eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin
  Require-Bundle: org.eclipse.ui,
   org.eclipse.core.runtime,
@@@ -18,5 -18,4 +18,5 @@@ Bundle-ActivationPolicy: laz
  Bundle-Vendor: EDIT
  Export-Package: eu.etaxonomy.taxeditor.molecular,
   eu.etaxonomy.taxeditor.molecular.editor,
 - eu.etaxonomy.taxeditor.molecular.handler
 + eu.etaxonomy.taxeditor.molecular.handler,
 + eu.etaxonomy.taxeditor.molecular.io