Test version of an AlignmentArea added to AlignmentEditor.

Dependencies of LibrAlign added in provisional form.
  During initial development stage you need to check out the following two additional project into your workspace:
  - bioinfweb.commons as "_Lib" from https://secure.bioinfweb.info/Code/svn/commons.java/trunk/main/
  - LibrAlign as "LibrAlign" from https://secure.nefertem.bioinfweb.info/private/svn/LibrAlign/trunk/main/
  (These dependencies will be replaced by JARs after the initial development phase of this branch.)

diff --git a/.gitattributes b/.gitattributes
index d6e15b3a7e7a16e026efdcac72d64679c7f26591..2c5d2340d4d380b39495a818d69388f19e8ee956 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -357,6 +357,10 @@ eu.etaxonomy.taxeditor.editor/icons/edit_16x16.gif -text
 eu.etaxonomy.taxeditor.editor/icons/emblem-photos.png -text
 eu.etaxonomy.taxeditor.editor/icons/leaf_detail.png -text
 eu.etaxonomy.taxeditor.editor/icons/xper64.png -text
 eu.etaxonomy.taxeditor.editor/icons/emblem-photos.png -text
 eu.etaxonomy.taxeditor.editor/icons/leaf_detail.png -text
 eu.etaxonomy.taxeditor.editor/icons/xper64.png -text

+eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar -text
+eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar -text
+eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar -text
+eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar -text

 eu.etaxonomy.taxeditor.editor/p2.inf -text
 eu.etaxonomy.taxeditor.editor/plugin.properties -text
 eu.etaxonomy.taxeditor.editor/plugin.xml -text
 eu.etaxonomy.taxeditor.editor/p2.inf -text
 eu.etaxonomy.taxeditor.editor/plugin.properties -text
 eu.etaxonomy.taxeditor.editor/plugin.xml -text

diff --git a/eu.etaxonomy.taxeditor.editor/.classpath b/eu.etaxonomy.taxeditor.editor/.classpath
index 856e9f909acec2ac78d360355e9cb4be88f8eaa3..1b2ee01870a0f3101361da87643d0fd792e18868 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/.classpath
+++ b/eu.etaxonomy.taxeditor.editor/.classpath
@@ -1,9 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-       <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 including="**/*.java" kind="src" path="src/test/java"/>
-       <classpathentry excluding="**/*.java" kind="src" path="src/main/resources"/>
-       <classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>\r
+<classpath>\r
+       <classpathentry exported="true" kind="lib" path="lib/LibrAlign/"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/bioinfweb.commons/"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/biojava3-core-3.0.7.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/core-1.8.5.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/sequencing-1.8.5.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/biojava3-alignment-3.0.7.jar"/>\r
+       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>\r
+       <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>\r
+       <classpathentry including="**/*.java" kind="src" path="src/main/java"/>\r
+       <classpathentry including="**/*.java" kind="src" path="src/test/java"/>\r
+       <classpathentry excluding="**/*.java" kind="src" path="src/main/resources"/>\r
+       <classpathentry kind="output" path="target/classes"/>\r
+</classpath>\r

diff --git a/eu.etaxonomy.taxeditor.editor/.project b/eu.etaxonomy.taxeditor.editor/.project
index e25293c2fcd8c813e182d2540716f7b232713c7e..ce8935ac2072251cf6f225298b65070a1a8fc91e 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/.project
+++ b/eu.etaxonomy.taxeditor.editor/.project
@@ -1,28 +1,40 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-       <name>eu.etaxonomy.taxeditor.editor</name>
-       <comment>NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>
-       <projects>
-       </projects>
-       <buildSpec>
-               <buildCommand>
-                       <name>org.eclipse.jdt.core.javabuilder</name>
-                       <arguments>
-                       </arguments>
-               </buildCommand>
-               <buildCommand>
-                       <name>org.eclipse.pde.ManifestBuilder</name>
-                       <arguments>
-                       </arguments>
-               </buildCommand>
-               <buildCommand>
-                       <name>org.eclipse.pde.SchemaBuilder</name>
-                       <arguments>
-                       </arguments>
-               </buildCommand>
-       </buildSpec>
-       <natures>
-               <nature>org.eclipse.jdt.core.javanature</nature>
-               <nature>org.eclipse.pde.PluginNature</nature>
-       </natures>
-</projectDescription>
+<?xml version="1.0" encoding="UTF-8"?>\r
+<projectDescription>\r
+       <name>eu.etaxonomy.taxeditor.editor</name>\r
+       <comment>NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>\r
+       <projects>\r
+       </projects>\r
+       <buildSpec>\r
+               <buildCommand>\r
+                       <name>org.eclipse.jdt.core.javabuilder</name>\r
+                       <arguments>\r
+                       </arguments>\r
+               </buildCommand>\r
+               <buildCommand>\r
+                       <name>org.eclipse.pde.ManifestBuilder</name>\r
+                       <arguments>\r
+                       </arguments>\r
+               </buildCommand>\r
+               <buildCommand>\r
+                       <name>org.eclipse.pde.SchemaBuilder</name>\r
+                       <arguments>\r
+                       </arguments>\r
+               </buildCommand>\r
+       </buildSpec>\r
+       <natures>\r
+               <nature>org.eclipse.jdt.core.javanature</nature>\r
+               <nature>org.eclipse.pde.PluginNature</nature>\r
+       </natures>\r
+       <linkedResources>\r
+               <link>\r
+                       <name>lib/LibrAlign</name>\r
+                       <type>2</type>\r
+                       <locationURI>WORKSPACE_LOC/LibrAlign/bin</locationURI>\r
+               </link>\r
+               <link>\r
+                       <name>lib/bioinfweb.commons</name>\r
+                       <type>2</type>\r
+                       <locationURI>WORKSPACE_LOC/_Lib/bin</locationURI>\r
+               </link>\r
+       </linkedResources>\r
+</projectDescription>\r

diff --git a/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF b/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
index 0c7bd01605402d4bb9cf9ac359d02ed48ca9ff1b..6e489f2d0f4334e5ac3233808930a399f218544c 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
@@ -175,4 +175,10 @@ Bundle-ClassPath: .,
  jdimodel.jar,
  pdebuild.jar,
  compatibility.jar,
  jdimodel.jar,
  pdebuild.jar,
  compatibility.jar,

- junit.jar
+ junit.jar,
+ lib/biojava3-alignment-3.0.7.jar,
+ lib/biojava3-core-3.0.7.jar,
+ lib/core-1.8.5.jar,
+ lib/sequencing-1.8.5.jar,
+ lib/bioinfweb.commons/,
+ lib/LibrAlign/

diff --git a/eu.etaxonomy.taxeditor.editor/build.properties b/eu.etaxonomy.taxeditor.editor/build.properties
index 4c434ef68a020b2f38beb7359a71dbe99cf80aa0..506d9dbd52bf5203ba7bd483baaf048d8fc74e78 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/build.properties
+++ b/eu.etaxonomy.taxeditor.editor/build.properties
@@ -5,4 +5,10 @@ bin.includes = META-INF/,\
                plugin.xml,\
                plugin.properties,\
                icons/,\
                plugin.xml,\
                plugin.properties,\
                icons/,\

-               p2.inf
+               p2.inf,\
+               lib/biojava3-alignment-3.0.7.jar,\
+               lib/biojava3-core-3.0.7.jar,\
+               lib/core-1.8.5.jar,\
+               lib/sequencing-1.8.5.jar,\
+               lib/bioinfweb.commons/,\
+               lib/LibrAlign/

diff --git a/eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar b/eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar
new file mode 100644 (file)
index 0000000..e5f1d6b
Binary files /dev/null and b/eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar differ

diff --git a/eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar b/eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar
new file mode 100644 (file)
index 0000000..c9f1f81
Binary files /dev/null and b/eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar differ

diff --git a/eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar b/eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar
new file mode 100644 (file)
index 0000000..c6c7bdc
Binary files /dev/null and b/eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar differ

diff --git a/eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar b/eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar
new file mode 100644 (file)
index 0000000..b987ebe
Binary files /dev/null and b/eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar differ

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
index 8310740095c8c34d6882aa402cce11fef24018df..3d823745613c20b36ea4465a3caf12f7245809fb 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
@@ -9,36 +9,78 @@
 */
 package eu.etaxonomy.taxeditor.editor.molecular;
 
 */
 package eu.etaxonomy.taxeditor.editor.molecular;
 

+
+import info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment;
+import info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment;
+import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet;
+import info.bioinfweb.libralign.AlignmentArea;
+import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
+import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
+import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider;
+import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;
+
+import org.biojava3.core.sequence.DNASequence;
+import org.biojava3.core.sequence.compound.NucleotideCompound;

 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.swt.SWT;
 import org.eclipse.swt.widgets.Composite;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.swt.SWT;
 import org.eclipse.swt.widgets.Composite;

-import org.eclipse.swt.widgets.Label;

 import org.eclipse.ui.IEditorInput;
 import org.eclipse.ui.IEditorSite;
 import org.eclipse.ui.PartInitException;
 import org.eclipse.ui.part.EditorPart;
 
 import org.eclipse.ui.IEditorInput;
 import org.eclipse.ui.IEditorSite;
 import org.eclipse.ui.PartInitException;
 import org.eclipse.ui.part.EditorPart;
 

+
+

 /**
 /**

+ * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
+ * a consensus sequence.
+ * <p>
+ * The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
+ * 

  * @author pplitzner
  * @author pplitzner

+ * @author Ben Stöver

  * @date 04.08.2014
  * @date 04.08.2014

- *

  */
 public class AlignmentEditor extends EditorPart {
  */
 public class AlignmentEditor extends EditorPart {

-

     public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
     public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";

-
-
+    
+    private AlignmentArea alignmentArea;
+
+
+       private AlignmentArea createAlignmentArea() {
+               Alignment<DNASequence, NucleotideCompound> alignment = 
+                               new SimpleAlignment<DNASequence, NucleotideCompound>();
+               alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));
+               alignment.add("Sequence 2", new DNASequence("AT-GTTG"));
+               alignment.add("Sequence 3", new DNASequence("AT-GTAG"));
+               
+               BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider = 
+                               new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
+                                               new BioJavaTokenSet<NucleotideCompound>(
+                                                               AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
+                                               alignment);
+               
+               AlignmentArea result = new AlignmentArea();
+               result.setSequenceProvider(sequenceProvider, false);
+               SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);
+               //sequenceIndexArea.setFirstIndex(5);
+               //sequenceIndexArea.setHeight(25);
+               result.getDataAreas().getTopAreas().add(sequenceIndexArea);
+               result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
+               return result;
+       }
+       
+       

     /* (non-Javadoc)
      * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
      */
     @Override
     public void createPartControl(Composite parent) {
     /* (non-Javadoc)
      * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
      */
     @Override
     public void createPartControl(Composite parent) {

-        Label label = new Label(parent, SWT.NONE);
-        label.setText("AlignmentEditor under construction!");
-
-
+       alignmentArea = createAlignmentArea();
+               Composite alignmentWidget = alignmentArea.createSWTWidget(parent, SWT.NONE);

     }
 
     }
 

+    

     /* (non-Javadoc)
      * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
      */
     /* (non-Javadoc)
      * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
      */


@@ -48,6 +90,7 @@ public class AlignmentEditor extends EditorPart {
 
     }
 
 
     }
 

+    

     /* (non-Javadoc)
      * @see org.eclipse.ui.part.EditorPart#doSaveAs()
      */
     /* (non-Javadoc)
      * @see org.eclipse.ui.part.EditorPart#doSaveAs()
      */


@@ -56,6 +99,7 @@ public class AlignmentEditor extends EditorPart {
         // TODO Auto-generated method stub
 
     }
         // TODO Auto-generated method stub
 
     }

+    

 
     /* (non-Javadoc)
      * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
 
     /* (non-Javadoc)
      * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)


@@ -65,6 +109,7 @@ public class AlignmentEditor extends EditorPart {
         setSite(site);
         setInput(input);
     }
         setSite(site);
         setInput(input);
     }

+    

 
     /* (non-Javadoc)
      * @see org.eclipse.ui.part.EditorPart#isDirty()
 
     /* (non-Javadoc)
      * @see org.eclipse.ui.part.EditorPart#isDirty()


@@ -75,6 +120,7 @@ public class AlignmentEditor extends EditorPart {
         return false;
     }
 
         return false;
     }
 

+    

     /* (non-Javadoc)
      * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
      */
     /* (non-Javadoc)
      * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
      */


@@ -83,6 +129,7 @@ public class AlignmentEditor extends EditorPart {
         // TODO Auto-generated method stub
         return false;
     }
         // TODO Auto-generated method stub
         return false;
     }

+    

 
     /* (non-Javadoc)
      * @see org.eclipse.ui.part.WorkbenchPart#setFocus()
 
     /* (non-Javadoc)
      * @see org.eclipse.ui.part.WorkbenchPart#setFocus()


@@ -92,5 +139,4 @@ public class AlignmentEditor extends EditorPart {
         // TODO Auto-generated method stub
 
     }
         // TODO Auto-generated method stub
 
     }

-

 }
 }

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java
index 31f2a2469021f85f8ca6939848ac921a7cfae258..3ec4ae3d319acc500929240c6759b7b688f082f8 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java
@@ -9,18 +9,21 @@
 */
 package eu.etaxonomy.taxeditor.editor.molecular;
 
 */
 package eu.etaxonomy.taxeditor.editor.molecular;
 

+

 import org.eclipse.jface.resource.ImageDescriptor;
 import org.eclipse.ui.IEditorInput;
 import org.eclipse.ui.IPersistableElement;
 
 import org.eclipse.jface.resource.ImageDescriptor;
 import org.eclipse.ui.IEditorInput;
 import org.eclipse.ui.IPersistableElement;
 

+
+

 /**
  * @author pplitzner
 /**
  * @author pplitzner

+ * @author Ben Stöver

  * @date 04.08.2014
  * @date 04.08.2014

- *

  */
  */

-public class AlignmentEditorInput implements IEditorInput{
-
+public class AlignmentEditorInput implements IEditorInput {

     private static final String name = "AlignmentEditor";
     private static final String name = "AlignmentEditor";

+    

 
     /* (non-Javadoc)
      * @see org.eclipse.core.runtime.IAdaptable#getAdapter(java.lang.Class)
 
     /* (non-Javadoc)
      * @see org.eclipse.core.runtime.IAdaptable#getAdapter(java.lang.Class)


@@ -31,6 +34,7 @@ public class AlignmentEditorInput implements IEditorInput{
         return null;
     }
 
         return null;
     }
 

+    

     /* (non-Javadoc)
      * @see org.eclipse.ui.IEditorInput#exists()
      */
     /* (non-Javadoc)
      * @see org.eclipse.ui.IEditorInput#exists()
      */


@@ -40,6 +44,7 @@ public class AlignmentEditorInput implements IEditorInput{
         return false;
     }
 
         return false;
     }
 

+    

     /* (non-Javadoc)
      * @see org.eclipse.ui.IEditorInput#getImageDescriptor()
      */
     /* (non-Javadoc)
      * @see org.eclipse.ui.IEditorInput#getImageDescriptor()
      */


@@ -48,6 +53,7 @@ public class AlignmentEditorInput implements IEditorInput{
         // TODO Auto-generated method stub
         return null;
     }
         // TODO Auto-generated method stub
         return null;
     }

+    

 
     /* (non-Javadoc)
      * @see org.eclipse.ui.IEditorInput#getName()
 
     /* (non-Javadoc)
      * @see org.eclipse.ui.IEditorInput#getName()


@@ -56,6 +62,7 @@ public class AlignmentEditorInput implements IEditorInput{
     public String getName() {
         return name;
     }
     public String getName() {
         return name;
     }

+    

 
     /* (non-Javadoc)
      * @see org.eclipse.ui.IEditorInput#getPersistable()
 
     /* (non-Javadoc)
      * @see org.eclipse.ui.IEditorInput#getPersistable()


@@ -64,6 +71,7 @@ public class AlignmentEditorInput implements IEditorInput{
     public IPersistableElement getPersistable() {
         return null;
     }
     public IPersistableElement getPersistable() {
         return null;
     }

+    

 
     /* (non-Javadoc)
      * @see org.eclipse.ui.IEditorInput#getToolTipText()
 
     /* (non-Javadoc)
      * @see org.eclipse.ui.IEditorInput#getToolTipText()


@@ -72,5 +80,4 @@ public class AlignmentEditorInput implements IEditorInput{
     public String getToolTipText() {
         return name;
     }
     public String getToolTipText() {
         return name;
     }

-

 }
 }

diff --git a/eu.etaxonomy.taxeditor/.classpath b/eu.etaxonomy.taxeditor/.classpath
index 7c95b583fcd7040a62be4722c8119d5f1ae50409..3446faf90f1926ee4bb2b230c4ec8ee62efaabbc 100644 (file)
--- a/eu.etaxonomy.taxeditor/.classpath
+++ b/eu.etaxonomy.taxeditor/.classpath
@@ -1,12 +1,12 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.application"/>
-       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.bulkeditor"/>
-       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.cdmlib"/>
-       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.editor"/>
-       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.navigation"/>
-       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.printpublisher"/>
-       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.store"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-       <classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>\r
+<classpath>\r
+       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.application"/>\r
+       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.bulkeditor"/>\r
+       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.cdmlib"/>\r
+       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.editor"/>\r
+       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.navigation"/>\r
+       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.printpublisher"/>\r
+       <classpathentry kind="src" path="/eu.etaxonomy.taxeditor.store"/>\r
+       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>\r
+       <classpathentry kind="output" path="target/classes"/>\r
+</classpath>\r