Release 2.6.0

Merge from branch '2.5.x'
bioclipse · Jan 29, 2013 · 05b6fa7 · 05b6fa7
2 parents 46d24c3 + bb600b4
commit 05b6fa7
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Showing 24 changed files with 924 additions and 206 deletions.
diff --git a/features/net.bioclipse.balloon_feature/feature.xml b/features/net.bioclipse.balloon_feature/feature.xml
@@ -1,13 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <feature
       id="net.bioclipse.balloon_feature"
-      label="Balloon Feature"
-      version="2.5.0.qualifier"
-      provider-name="The Bioclispe Team"
-      plugin="net.bioclipse.balloon.business">
+      label="Balloon"
+      version="2.6.0.vqualifier"
+      provider-name="bioclipse.net"
+      plugin="net.bioclipse.balloon.business"
+      os="linux,macosx,win32">
 
    <description>
-      Balloon provides Bioclipse with features to generate 3D conformations from chemical structures.
+      3D conformer generation for chemical structures using Balloon (Vainio et al. 2007).
    </description>
 
    <copyright>
@@ -26,12 +27,9 @@ This feature and the accompanying materials are made available under the terms o
 The Eclipse Public License accompanies this distribution, and is available at http://www.eclipse.org/legal/epl-v10.html
    </license>
 
-   <url>
-      <update label="Bioclipse2 update site" url="http://update2.bioclipse.net"/>
-   </url>
-
    <requires>
-      <import feature="net.bioclipse.chemoinformatics_feature" version="2.4.0" match="greaterOrEqual"/>
+      <import feature="net.bioclipse.core_feature" version="2.5" match="greaterOrEqual"/>
+      <import feature="net.bioclipse.chemoinformatics_feature" version="2.5" match="greaterOrEqual"/>
    </requires>
 
    <plugin
@@ -73,7 +71,7 @@ The Eclipse Public License accompanies this distribution, and is available at ht
          unpack="false"/>
 
    <plugin
-         id="net.bioclipse.jnati"
+         id="jnati-proc"
          download-size="0"
          install-size="0"
          version="0.0.0"

diff --git a/features/net.bioclipse.balloon_site/feature.xml b/features/net.bioclipse.balloon_site/feature.xml
@@ -20,4 +20,25 @@
          id="net.bioclipse.balloon_feature"
          version="0.0.0"/>
 
+   <plugin
+         id="net.bioclipse.balloon.linux"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         fragment="true"/>
+
+   <plugin
+         id="net.bioclipse.balloon.macosx"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         fragment="true"/>
+
+   <plugin
+         id="net.bioclipse.balloon.win32"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         fragment="true"/>
+
 </feature>
diff --git a/plugins/net.bioclipse.balloon.business/META-INF/MANIFEST.MF b/plugins/net.bioclipse.balloon.business/META-INF/MANIFEST.MF
@@ -2,25 +2,20 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Balloon
 Bundle-SymbolicName: net.bioclipse.balloon.business;singleton:=true
-Bundle-Version: 2.5.0.qualifier
+Bundle-Version: 2.6.0.vqualifier
 Bundle-Activator: net.bioclipse.balloon.business.Activator
 Bundle-Vendor: The Bioclipse Team
 Require-Bundle: org.eclipse.ui,
  org.eclipse.core.runtime,
  net.bioclipse.core,
  org.eclipse.core.resources,
- net.bioclipse.scripting,
- net.bioclipse.balloon,
- net.bioclipse.chemoinformatics,
  net.bioclipse.ui.business,
  net.bioclipse.cdk.business,
- net.bioclipse.cml,
- net.bioclipse.ui,
- org.eclipse.help,
- net.bioclipse.ioformats,
- org.openscience.cdk.ioformats,
+ org.openscience.cdk.interfaces,
+ org.openscience.cdk.io,
  org.openscience.cdk.core,
- org.openscience.cdk.interfaces;bundle-version="1.3.8"
+ org.eclipse.core.filesystem;bundle-version="1.3.200",
+ org.openscience.cdk.ioformats
 Bundle-RequiredExecutionEnvironment: J2SE-1.5
 Bundle-ActivationPolicy: lazy
 Export-Package: net.bioclipse.balloon.business

diff --git a/plugins/net.bioclipse.balloon.business/plugin.xml b/plugins/net.bioclipse.balloon.business/plugin.xml
@@ -35,16 +35,24 @@
          		<or>
                     <!--test property="org.eclipse.core.resources.contentTypeId" 
             	    	value="net.bioclipse.contenttypes.smi"/-->
+   	      		     <test property="org.eclipse.core.resources.contentTypeId" 
+        	        	value="net.bioclipse.contenttypes.sdf0d"/>
    	      		     <test property="org.eclipse.core.resources.contentTypeId" 
         	        	value="net.bioclipse.contenttypes.sdf2d"/>
    	      		     <test property="org.eclipse.core.resources.contentTypeId" 
         	        	value="net.bioclipse.contenttypes.sdf3d"/>
+   	      		     <test property="org.eclipse.core.resources.contentTypeId" 
+        	        	value="net.bioclipse.contenttypes.mdlMolFile0D"/>
    	      		     <test property="org.eclipse.core.resources.contentTypeId" 
         	        	value="net.bioclipse.contenttypes.mdlMolFile2D"/>
    	      		     <test property="org.eclipse.core.resources.contentTypeId" 
         	        	value="net.bioclipse.contenttypes.mdlMolFile3D"/>
   	      		     <test property="org.eclipse.core.resources.contentTypeId" 
         	        	value="net.bioclipse.contenttypes.cml.singleMolecule2d"/>
+  	      		     <!--test property="org.eclipse.core.resources.contentTypeId" 
+        	        	value="net.bioclipse.contenttypes.cml.singleMolecule0d"/>
+  	      		     <test property="org.eclipse.core.resources.contentTypeId" 
+        	        	value="net.bioclipse.contenttypes.cml.singleMolecule3d"/-->
                	</or>
                </adapt>
 	        </iterate>
@@ -120,5 +128,11 @@
             primary="true">
       </toc>
    </extension>
+   <extension
+         point="org.eclipse.core.runtime.preferences">
+      <initializer
+            class="net.bioclipse.balloon.ui.BalloonPreferenceInitializer">
+      </initializer>
+   </extension>
 
 </plugin>
diff --git a/plugins/net.bioclipse.balloon.business/src/net/bioclipse/balloon/business/Activator.java b/plugins/net.bioclipse.balloon.business/src/net/bioclipse/balloon/business/Activator.java
@@ -65,8 +65,6 @@ public void start(BundleContext context) throws Exception {
                                   null );
         javaFinderTracker.open();
 
-        getPreferenceStore().setDefault(BALLOON_TIMEOUT, DEFAULT_BALLOON_TIMEOUT);
-
     }
 
     /*
@@ -130,13 +128,4 @@ public IBalloonManager getJavaScriptBalloonManager() {
         return manager;
     }
 
-    /** 
-     * Initializes a preference store with default preference values 
-     * for this plug-in.
-     */
-    protected void initializeDefaultPreferences(IPreferenceStore store) {
-        store.setDefault(BALLOON_TIMEOUT, DEFAULT_BALLOON_TIMEOUT);
-        logger.debug( "Default balloon preferences set timeout: " 
-                      + DEFAULT_BALLOON_TIMEOUT );
-    }
 }