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Merge branch 'develop' into LibrAlign
authorPatrick Plitzner <p.plitzner@bgbm.org>
Wed, 4 May 2016 16:00:54 +0000 (18:00 +0200)
committerPatrick Plitzner <p.plitzner@bgbm.org>
Wed, 4 May 2016 16:00:54 +0000 (18:00 +0200)
1  2 
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/META-INF/MANIFEST.MF
index eeb8f126c3d4cf34b1b1eaf6a8f48a18236d4502,3eecefd40f01e24067d59fd830f3d503459bbe6c..0af449c8bf369f5c172c27f2acd0431ca5b4ed44
--- 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
@@@ -2,7 -2,7 +2,7 @@@ Manifest-Version: 1.
  Bundle-ManifestVersion: 2
  Bundle-Name: eu.etaxonomy.taxeditor.molecular.lib
  Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular.lib;singleton:=true
- Bundle-Version: 4.0.0.qualifier
+ Bundle-Version: 4.1.0.qualifier
  Bundle-ClassPath: .,
   lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,
   lib/bioinfweb-commons-core-2-SNAPSHOT.jar,
@@@ -14,9 -14,7 +14,9 @@@
   lib/libralign-swt-0-SNAPSHOT.jar,
   lib/sequencing-1.9.2-SNAPSHOT.jar,
   lib/tic-core-2-SNAPSHOT.jar,
 - lib/tic-swt-2-SNAPSHOT.jar
 + lib/tic-swt-2-SNAPSHOT.jar,
 + lib/jphyloio-core-0-SNAPSHOT.jar,
 + lib/owlapi-xmlutils-4.1.4.jar
  Export-Package: info.bioinfweb.commons,
   info.bioinfweb.commons.appversion,
   info.bioinfweb.commons.beans,
@@@ -32,37 -30,6 +32,37 @@@
   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,
@@@ -193,8 -160,7 +193,8 @@@
   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 52322e9eec0a881d753db94c222e0506fa3b1c4e,d37ef8c9aad036b64819a3d8d14554efcda50c12..80564a28c6b67f4eaed89809b2102518a5b7334c
--- 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>4.0.0-SNAPSHOT</version>
+     <version>4.1.0-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</includeArtifactIds>
                <outputDirectory>lib</outputDirectory>
                <overWriteReleases>true</overWriteReleases>
                <overWriteSnapshots>true</overWriteSnapshots>
@@@ -95,18 -94,6 +95,18 @@@
                    <fileset dir="./lib" />
                    <mapper type="regexp" from="(^tic\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
                  </move>
 +                <move todir="./lib">
 +                  <fileset dir="./lib" />
 +                  <mapper type="regexp" from="(^jphyloio\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
 +                </move>
 +                <move todir="./lib">
 +                  <fileset dir="./lib" />
 +                  <mapper type="regexp" from="(^owlapi\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
 +                </move>
 +                <move todir="./lib">
 +                  <fileset dir="./lib" />
 +                  <mapper type="regexp" from="commons-collections4-4.1.jar" to="commons-collections4-4.1.jar" />
 +                </move>
                  <move todir="./lib">
                    <fileset dir="./lib" />
                    <mapper type="regexp" from="(^core\-[0-9]\.[0-9]\.[0-9])(\.jar)" to="\1-SNAPSHOT\2" />
@@@ -124,23 -111,7 +124,23 @@@
    </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>
 +    <dependency>
 +      <groupId>org.apache.commons</groupId>
 +      <artifactId>commons-collections4</artifactId>
 +      <version>4.1</version>
 +    </dependency>
 +    <!-- LibrAlign -->
      <dependency>
        <groupId>info.bioinfweb.libralign</groupId>
        <artifactId>libralign-core</artifactId>
@@@ -156,7 -127,7 +156,7 @@@
        <artifactId>libralign-biojava1</artifactId>
        <version>0-SNAPSHOT</version>
      </dependency>
 -    <!-- commons -->
 +    <!-- bioinfweb.commons -->
      <dependency>
        <groupId>info.bioinfweb.commons.java</groupId>
        <artifactId>bioinfweb-commons-swt</artifactId>
@@@ -177,7 -148,7 +177,7 @@@
        <artifactId>bioinfweb-commons-swing</artifactId>
        <version>2-SNAPSHOT</version>
      </dependency>
 -    <!-- tic -->
 +    <!-- TIC -->
      <dependency>
        <groupId>info.bioinfweb.tic</groupId>
        <artifactId>tic-core</artifactId>
@@@ -188,7 -159,7 +188,7 @@@
        <artifactId>tic-swt</artifactId>
        <version>2-SNAPSHOT</version>
      </dependency>
 -    <!-- biojava -->
 +    <!-- BioJava -->
      <dependency>
        <groupId>org.biojava</groupId>
        <artifactId>core</artifactId>
@@@ -207,11 -178,7 +207,11 @@@
        <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 cc67becb1e5f5d12ceed7421e049c47275c5e2db,2a4f2dddbbdfbd00792e492d8e690a7d3021cc0c..f5c503763aad606c251abe96dd0f2ae39b1a35ad
--- 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: 4.0.0.qualifier
+ Bundle-Version: 4.1.0.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