Integrate molecular plugins

diff --git a/eu.etaxonomy.taxeditor.feature/feature.xml b/eu.etaxonomy.taxeditor.feature/feature.xml
index f86f25f0501ed9e31f309ad0e30ad1954947dee0..ac7ccae4827e3084e8a9f918a6e32be9eb3baa69 100644 (file)
--- a/eu.etaxonomy.taxeditor.feature/feature.xml
+++ b/eu.etaxonomy.taxeditor.feature/feature.xml
@@ -121,4 +121,11 @@
          version="0.0.0"
          unpack="false"/>
 
          version="0.0.0"
          unpack="false"/>
 

+   <plugin
+         id="eu.etaxonomy.taxeditor.molecular.aggregator"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+

 </feature>
 </feature>

diff --git a/eu.etaxonomy.taxeditor.molecular.aggregator/.classpath b/eu.etaxonomy.taxeditor.molecular.aggregator/.classpath
new file mode 100644 (file)
index 0000000..1d66dd2
--- /dev/null
+++ b/eu.etaxonomy.taxeditor.molecular.aggregator/.classpath
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+       <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+       <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/core-1.9.2-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/sequencing-1.9.2-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 kind="output" path="target/classes"/>
+</classpath>

diff --git a/eu.etaxonomy.taxeditor.molecular.aggregator/.gitignore b/eu.etaxonomy.taxeditor.molecular.aggregator/.gitignore
new file mode 100644 (file)
index 0000000..e6066b2
--- /dev/null
+++ b/eu.etaxonomy.taxeditor.molecular.aggregator/.gitignore
@@ -0,0 +1,2 @@
+/target
+.settings/

diff --git a/eu.etaxonomy.taxeditor.molecular.aggregator/.project b/eu.etaxonomy.taxeditor.molecular.aggregator/.project
index 0daf6c1828eebd68c4ccc966ccf468965cd103dd..a115d4e7fb8d1705b79993ebdfc5792744c956b0 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular.aggregator/.project
+++ b/eu.etaxonomy.taxeditor.molecular.aggregator/.project
@@ -1,11 +1,29 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
        <name>eu.etaxonomy.taxeditor.molecular.aggregator</name>
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
        <name>eu.etaxonomy.taxeditor.molecular.aggregator</name>

-       <comment></comment>
+       <comment>The Taxonomic Editor for EDIT&apos;s platform for
+    cybertaxonomy. NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>

        <projects>
        </projects>
        <buildSpec>
        <projects>
        </projects>
        <buildSpec>

+               <buildCommand>
+                       <name>org.eclipse.pde.ManifestBuilder</name>
+                       <arguments>
+                       </arguments>
+               </buildCommand>
+               <buildCommand>
+                       <name>org.eclipse.pde.SchemaBuilder</name>
+                       <arguments>
+                       </arguments>
+               </buildCommand>
+               <buildCommand>
+                       <name>org.eclipse.jdt.core.javabuilder</name>
+                       <arguments>
+                       </arguments>
+               </buildCommand>

        </buildSpec>
        <natures>
        </buildSpec>
        <natures>

+               <nature>org.eclipse.pde.PluginNature</nature>
+               <nature>org.eclipse.jdt.core.javanature</nature>

        </natures>
 </projectDescription>
        </natures>
 </projectDescription>

diff --git a/eu.etaxonomy.taxeditor.molecular.aggregator/META-INF/MANIFEST.MF b/eu.etaxonomy.taxeditor.molecular.aggregator/META-INF/MANIFEST.MF
new file mode 100644 (file)
index 0000000..60b04e4
--- /dev/null
+++ b/eu.etaxonomy.taxeditor.molecular.aggregator/META-INF/MANIFEST.MF
@@ -0,0 +1,41 @@
+Manifest-Version: 1.0
+Bundle-ManifestVersion: 2
+Bundle-Name: eu.etaxonomy.taxeditor.molecular.aggregator
+Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular.aggregator;singleton:=true
+Bundle-Version: 3.8.0.qualifier
+Bundle-ClassPath: .,
+ 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/core-1.9.2-SNAPSHOT.jar,
+ lib/libralign-biojava1-0-SNAPSHOT.jar,
+ lib/libralign-core-0-SNAPSHOT.jar,
+ 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
+Export-Package: info.bioinfweb.commons.collections,
+ info.bioinfweb.libralign.alignmentarea,
+ info.bioinfweb.libralign.alignmentarea.order,
+ info.bioinfweb.libralign.alignmentarea.paintsettings,
+ info.bioinfweb.libralign.alignmentarea.selection,
+ info.bioinfweb.libralign.alignmentarea.tokenpainter,
+ info.bioinfweb.libralign.dataarea,
+ info.bioinfweb.libralign.dataarea.implementations,
+ info.bioinfweb.libralign.dataarea.implementations.pherogram,
+ info.bioinfweb.libralign.editsettings,
+ info.bioinfweb.libralign.model,
+ info.bioinfweb.libralign.model.adapters,
+ info.bioinfweb.libralign.model.events,
+ info.bioinfweb.libralign.model.implementations,
+ info.bioinfweb.libralign.model.tokenset,
+ info.bioinfweb.libralign.multiplealignments,
+ info.bioinfweb.libralign.pherogram,
+ info.bioinfweb.libralign.pherogram.model,
+ info.bioinfweb.libralign.pherogram.provider,
+ info.bioinfweb.libralign.pherogram.view,
+ info.bioinfweb.tic,
+ info.bioinfweb.tic.input,
+ org.biojava.bio.chromatogram
+Bundle-ActivationPolicy: lazy

diff --git a/eu.etaxonomy.taxeditor.molecular.aggregator/pom.xml b/eu.etaxonomy.taxeditor.molecular.aggregator/pom.xml
index ff20500b7aa3bd149dc480fa99318f4d26190a07..ddc1dd6896288255826b0f19c23167733eb75b79 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular.aggregator/pom.xml
+++ b/eu.etaxonomy.taxeditor.molecular.aggregator/pom.xml
@@ -1,8 +1,8 @@
 <project>
   <modelVersion>4.0.0</modelVersion>
   <groupId>eu.etaxonomy.taxeditor</groupId>
 <project>
   <modelVersion>4.0.0</modelVersion>
   <groupId>eu.etaxonomy.taxeditor</groupId>

-  <artifactId>eu.etaxonomy.taxeditor.aggregator</artifactId>
-  <packaging>pom</packaging>
+  <artifactId>eu.etaxonomy.taxeditor.molecular.aggregator</artifactId>
+  <packaging>eclipse-plugin</packaging>

   
   <parent>
     <groupId>eu.etaxonomy</groupId>
   
   <parent>
     <groupId>eu.etaxonomy</groupId>


@@ -10,13 +10,180 @@
     <version>3.8.0-SNAPSHOT</version>
   </parent>
 
     <version>3.8.0-SNAPSHOT</version>
   </parent>
 

-    <modules>
-    <module>../eu.etaxonomy.taxeditor.cdmlib</module>
-    <module>../eu.etaxonomy.taxeditor.store</module>
-    <module>../eu.etaxonomy.taxeditor.bulkeditor</module>
-    <module>../eu.etaxonomy.taxeditor.editor</module>
-    <module>../eu.etaxonomy.taxeditor.molecular</module>
-  </modules>
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-dependency-plugin</artifactId>
+        <version>2.4</version>
+        <executions>
+          <execution>
+            <id>copy-dependencies</id>
+            <phase>validate</phase>
+            <goals>
+              <goal>copy-dependencies</goal>
+            </goals>
+            <configuration>
+              <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>
+              <outputDirectory>lib</outputDirectory>
+              <overWriteReleases>true</overWriteReleases>
+              <overWriteSnapshots>true</overWriteSnapshots>
+              <excludeTransitive>true</excludeTransitive>
+            </configuration>
+          </execution>
+          <!-- <execution> -->
+          <!-- <id>copy-dependencies-sources</id> -->
+          <!-- <phase>validate</phase> -->
+          <!-- <goals> -->
+          <!-- <goal>copy-dependencies</goal> -->
+          <!-- </goals> -->
+          <!-- <configuration> -->
+          <!-- <classifier>sources</classifier> -->
+          <!-- <includeArtifactIds>cdmlib-commons,cdmlib-model,cdmlib-persistence,cdmlib-remote,cdmlib-print,cdmlib-services,cdmlib-ext,cdmlib-io</includeArtifactIds> -->
+          <!-- <outputDirectory>lib</outputDirectory> -->
+          <!-- <overWriteReleases>true</overWriteReleases> -->
+          <!-- <overWriteSnapshots>true</overWriteSnapshots> -->
+          <!-- <excludeTransitive>true</excludeTransitive> -->
+          <!-- <failOnMissingClassifierArtifact>false</failOnMissingClassifierArtifact> -->
+          <!-- </configuration> -->
+          <!-- </execution> -->
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-antrun-plugin</artifactId>
+        <version>1.7</version>
+        <executions>
+          <execution>
+            <id>remove-existing-jars</id>
+            <phase>clean</phase>
+            <goals>
+              <goal>run</goal>
+            </goals>
+            <configuration>
+              <target>
+                <echo>Remove all jars</echo>
+                <delete>
+                  <fileset dir="./lib" includes="*" />
+                </delete>
+              </target>
+            </configuration>
+          </execution>
+          <execution>
+            <id>update-snapshot-jar-names</id>
+            <phase>validate</phase>
+            <goals>
+              <goal>run</goal>
+            </goals>
+            <configuration>
+              <target>
+                <echo>Update jars to SNAPSHOT when build with
+                  timestamp</echo>
+                <move todir="./lib">
+                  <fileset dir="./lib" />
+                  <mapper type="regexp"
+                    from="(^bioinfweb\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
+                </move>
+                <move todir="./lib">
+                  <fileset dir="./lib" />
+                  <mapper type="regexp"
+                    from="(^libralign\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
+                </move>
+                <move todir="./lib">
+                  <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="(^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" />
+                </move>
+              </target>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+
+  <dependencies>
+    <!-- LibrAling -->
+    <dependency>
+      <groupId>info.bioinfweb.libralign</groupId>
+      <artifactId>libralign-core</artifactId>
+      <version>0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>info.bioinfweb.libralign</groupId>
+      <artifactId>libralign-swt</artifactId>
+      <version>0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>info.bioinfweb.libralign</groupId>
+      <artifactId>libralign-biojava1</artifactId>
+      <version>0-SNAPSHOT</version>
+    </dependency>
+    <!-- commons -->
+    <dependency>
+      <groupId>info.bioinfweb.commons.java</groupId>
+      <artifactId>bioinfweb-commons-swt</artifactId>
+      <version>2-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>info.bioinfweb.commons.java</groupId>
+      <artifactId>bioinfweb-commons-core</artifactId>
+      <version>2-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>info.bioinfweb.commons.java</groupId>
+      <artifactId>bioinfweb-commons-bio</artifactId>
+      <version>2-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>info.bioinfweb.commons.java</groupId>
+      <artifactId>bioinfweb-commons-swing</artifactId>
+      <version>2-SNAPSHOT</version>
+    </dependency>
+    <!-- tic -->
+    <dependency>
+      <groupId>info.bioinfweb.tic</groupId>
+      <artifactId>tic-core</artifactId>
+      <version>2-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>info.bioinfweb.tic</groupId>
+      <artifactId>tic-swt</artifactId>
+      <version>2-SNAPSHOT</version>
+    </dependency>
+    <!-- biojava -->
+    <dependency>
+      <groupId>org.biojava</groupId>
+      <artifactId>core</artifactId>
+      <version>1.9.2</version>
+    </dependency>
+    <dependency>
+      <groupId>org.biojava</groupId>
+      <artifactId>sequencing</artifactId>
+      <version>1.9.2</version>
+    </dependency>
+  </dependencies>
+
+  <repositories>
+    <repository>
+      <id>bioinfweb-maven-repo</id>
+      <name>bioinfweb repository</name>
+      <url>http://bioinfweb.info/MavenRepository/</url>
+    </repository>
+  </repositories>

   
 </project> 
 
   
 </project> 
 

diff --git a/eu.etaxonomy.taxeditor.molecular/.classpath b/eu.etaxonomy.taxeditor.molecular/.classpath
index a4fa48b4ae3024ac43710421f41f8e1d98f86c57..f14ba2c2e26a0591f2789a408011882ac75ed185 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/.classpath
+++ b/eu.etaxonomy.taxeditor.molecular/.classpath
@@ -1,17 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>

-       <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/core-1.9.2-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/sequencing-1.9.2-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 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.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>

        <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
        <classpathentry including="**/*.java" kind="src" path="src/main/java"/>
        <classpathentry kind="output" path="target/classes"/>
        <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
        <classpathentry including="**/*.java" kind="src" path="src/main/java"/>
        <classpathentry kind="output" path="target/classes"/>

diff --git a/eu.etaxonomy.taxeditor.molecular/.gitignore b/eu.etaxonomy.taxeditor.molecular/.gitignore
index b83d22266ac8aa2f8df2edef68082c789727841d..e6066b230568e29e52c4935812bcdf841f8a311b 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/.gitignore
+++ b/eu.etaxonomy.taxeditor.molecular/.gitignore
@@ -1 +1,2 @@
-/target/
+/target
+.settings/

diff --git a/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF b/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
index e70a7ed3a58216aa024795354c94484794b345d8..f3eca7301911f2dc2ef4d5809e1ae43aef0bcdbd 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
@@ -8,26 +8,11 @@ Require-Bundle: org.eclipse.ui,
  org.eclipse.core.runtime,
  org.eclipse.core.expressions,
  org.eclipse.ui.ide,
  org.eclipse.core.runtime,
  org.eclipse.core.expressions,
  org.eclipse.ui.ide,

- eu.etaxonomy.taxeditor.bulkeditor;bundle-version="3.6.1",
- eu.etaxonomy.taxeditor.cdmlib;bundle-version="3.6.1",
- eu.etaxonomy.taxeditor.editor;bundle-version="3.6.1",
- eu.etaxonomy.taxeditor.store;bundle-version="3.6.1"
+ eu.etaxonomy.taxeditor.bulkeditor,
+ eu.etaxonomy.taxeditor.cdmlib,
+ eu.etaxonomy.taxeditor.editor,
+ eu.etaxonomy.taxeditor.store,
+ eu.etaxonomy.taxeditor.molecular.aggregator

 Bundle-RequiredExecutionEnvironment: JavaSE-1.6
 Bundle-ActivationPolicy: lazy
 Bundle-Vendor: EDIT
 Bundle-RequiredExecutionEnvironment: JavaSE-1.6
 Bundle-ActivationPolicy: lazy
 Bundle-Vendor: EDIT

-Bundle-ClassPath: .,
- 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/core-1.9.2-SNAPSHOT.jar,
- lib/libralign-biojava1-0-SNAPSHOT.jar,
- lib/libralign-core-0-SNAPSHOT.jar,
- 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
-Export-Package: eu.etaxonomy.taxeditor.molecular,
- eu.etaxonomy.taxeditor.molecular.editor,
- eu.etaxonomy.taxeditor.molecular.handler,
- info.bioinfweb.commons

diff --git a/eu.etaxonomy.taxeditor.molecular/build.properties b/eu.etaxonomy.taxeditor.molecular/build.properties
index fdb877c3225eda82388af81b0439ffcb5f775a40..e4bf8ac385bd985f3c91555d812a0bdfba38c571 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/build.properties
+++ b/eu.etaxonomy.taxeditor.molecular/build.properties
@@ -1,17 +1,4 @@
-source.. = src/main/java/

 bin.includes = META-INF/,\
 bin.includes = META-INF/,\

-               .,\

                plugin.xml,\
                icons/,\
                plugin.xml,\
                icons/,\

-               OSGI-INF/,\
-               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/core-1.9.2-SNAPSHOT.jar,\
-               lib/libralign-biojava1-0-SNAPSHOT.jar,\
-               lib/libralign-core-0-SNAPSHOT.jar,\
-               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
+               OSGI-INF/

diff --git a/eu.etaxonomy.taxeditor.molecular/pom.xml b/eu.etaxonomy.taxeditor.molecular/pom.xml
index cc17342fce3db44c6f680b2baaea154abaffae77..1e91c23b5485a8efa209b33091ba62c3f86c736f 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/pom.xml
+++ b/eu.etaxonomy.taxeditor.molecular/pom.xml
@@ -14,179 +14,4 @@
   <name>Molecular Bundle</name>
   <description>Provides editors, views and operations for handling molecular data and alignments</description>
 
   <name>Molecular Bundle</name>
   <description>Provides editors, views and operations for handling molecular data and alignments</description>
 

-  <build>
-    <plugins>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-dependency-plugin</artifactId>
-        <version>2.4</version>
-        <executions>
-          <execution>
-            <id>copy-dependencies</id>
-            <phase>validate</phase>
-            <goals>
-              <goal>copy-dependencies</goal>
-            </goals>
-            <configuration>
-              <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>
-              <outputDirectory>lib</outputDirectory>
-              <overWriteReleases>true</overWriteReleases>
-              <overWriteSnapshots>true</overWriteSnapshots>
-              <excludeTransitive>true</excludeTransitive>
-            </configuration>
-          </execution>
-          <!-- <execution> -->
-          <!-- <id>copy-dependencies-sources</id> -->
-          <!-- <phase>validate</phase> -->
-          <!-- <goals> -->
-          <!-- <goal>copy-dependencies</goal> -->
-          <!-- </goals> -->
-          <!-- <configuration> -->
-          <!-- <classifier>sources</classifier> -->
-          <!-- <includeArtifactIds>cdmlib-commons,cdmlib-model,cdmlib-persistence,cdmlib-remote,cdmlib-print,cdmlib-services,cdmlib-ext,cdmlib-io</includeArtifactIds> -->
-          <!-- <outputDirectory>lib</outputDirectory> -->
-          <!-- <overWriteReleases>true</overWriteReleases> -->
-          <!-- <overWriteSnapshots>true</overWriteSnapshots> -->
-          <!-- <excludeTransitive>true</excludeTransitive> -->
-          <!-- <failOnMissingClassifierArtifact>false</failOnMissingClassifierArtifact> -->
-          <!-- </configuration> -->
-          <!-- </execution> -->
-        </executions>
-      </plugin>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-antrun-plugin</artifactId>
-        <version>1.7</version>
-        <executions>
-          <execution>
-            <id>remove-existing-jars</id>
-            <phase>clean</phase>
-            <goals>
-              <goal>run</goal>
-            </goals>
-            <configuration>
-              <target>
-                <echo>Remove all jars</echo>
-                <delete>
-                  <fileset dir="./lib" includes="*" />
-                </delete>
-              </target>
-            </configuration>
-          </execution>
-          <execution>
-            <id>update-snapshot-jar-names</id>
-            <phase>validate</phase>
-            <goals>
-              <goal>run</goal>
-            </goals>
-            <configuration>
-              <target>
-                <echo>Update jars to SNAPSHOT when build with
-                  timestamp</echo>
-                <move todir="./lib">
-                  <fileset dir="./lib" />
-                  <mapper type="regexp"
-                    from="(^bioinfweb\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
-                </move>
-                <move todir="./lib">
-                  <fileset dir="./lib" />
-                  <mapper type="regexp"
-                    from="(^libralign\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
-                </move>
-                <move todir="./lib">
-                  <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="(^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" />
-                </move>
-              </target>
-            </configuration>
-          </execution>
-        </executions>
-      </plugin>
-    </plugins>
-  </build>
-
-  <dependencies>
-    <!-- LibrAling -->
-    <dependency>
-      <groupId>info.bioinfweb.libralign</groupId>
-      <artifactId>libralign-core</artifactId>
-      <version>0-SNAPSHOT</version>
-    </dependency>
-    <dependency>
-      <groupId>info.bioinfweb.libralign</groupId>
-      <artifactId>libralign-swt</artifactId>
-      <version>0-SNAPSHOT</version>
-    </dependency>
-    <dependency>
-      <groupId>info.bioinfweb.libralign</groupId>
-      <artifactId>libralign-biojava1</artifactId>
-      <version>0-SNAPSHOT</version>
-    </dependency>
-    <!-- commons -->
-    <dependency>
-      <groupId>info.bioinfweb.commons.java</groupId>
-      <artifactId>bioinfweb-commons-swt</artifactId>
-      <version>2-SNAPSHOT</version>
-    </dependency>
-    <dependency>
-      <groupId>info.bioinfweb.commons.java</groupId>
-      <artifactId>bioinfweb-commons-core</artifactId>
-      <version>2-SNAPSHOT</version>
-    </dependency>
-    <dependency>
-      <groupId>info.bioinfweb.commons.java</groupId>
-      <artifactId>bioinfweb-commons-bio</artifactId>
-      <version>2-SNAPSHOT</version>
-    </dependency>
-    <dependency>
-      <groupId>info.bioinfweb.commons.java</groupId>
-      <artifactId>bioinfweb-commons-swing</artifactId>
-      <version>2-SNAPSHOT</version>
-    </dependency>
-    <!-- tic -->
-    <dependency>
-      <groupId>info.bioinfweb.tic</groupId>
-      <artifactId>tic-core</artifactId>
-      <version>2-SNAPSHOT</version>
-    </dependency>
-    <dependency>
-      <groupId>info.bioinfweb.tic</groupId>
-      <artifactId>tic-swt</artifactId>
-      <version>2-SNAPSHOT</version>
-    </dependency>
-    <!-- biojava -->
-    <dependency>
-      <groupId>org.biojava</groupId>
-      <artifactId>core</artifactId>
-      <version>1.9.2</version>
-    </dependency>
-    <dependency>
-      <groupId>org.biojava</groupId>
-      <artifactId>sequencing</artifactId>
-      <version>1.9.2</version>
-    </dependency>
-  </dependencies>
-
-  <repositories>
-    <repository>
-      <id>bioinfweb-maven-repo</id>
-      <name>bioinfweb repository</name>
-      <url>http://bioinfweb.info/MavenRepository/</url>
-    </repository>
-  </repositories>
-

 </project>
 </project>

diff --git a/pom.xml b/pom.xml
index fac701883c8eeb755b6f013ecf24c5f111a4ad16..c595378bf3126318d9410721f39e77426a89d7c9 100644 (file)
--- a/pom.xml
+++ b/pom.xml
@@ -34,6 +34,8 @@
     <module>eu.etaxonomy.taxeditor.application</module>
     <module>eu.etaxonomy.taxeditor.feature.platform</module>
     <module>eu.etaxonomy.taxeditor.feature</module>
     <module>eu.etaxonomy.taxeditor.application</module>
     <module>eu.etaxonomy.taxeditor.feature.platform</module>
     <module>eu.etaxonomy.taxeditor.feature</module>

+    <module>eu.etaxonomy.taxeditor.molecular</module>
+    <module>eu.etaxonomy.taxeditor.molecular.aggregator</module>

     <module>eu.etaxonomy.taxeditor</module>
   </modules>
   <scm>
     <module>eu.etaxonomy.taxeditor</module>
   </modules>
   <scm>