Merge branch 'LibrAlign' of ssh://dev.e-taxonomy.eu/var/git/taxeditor into LibrAlign
authorb.stoever <stoever@bioinfweb.info>
Wed, 26 Oct 2016 15:31:46 +0000 (17:31 +0200)
committerb.stoever <stoever@bioinfweb.info>
Wed, 26 Oct 2016 15:31:46 +0000 (17:31 +0200)
.gitignore
eu.etaxonomy.taxeditor.molecular.lib/.classpath
eu.etaxonomy.taxeditor.molecular.lib/.project
eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
eu.etaxonomy.taxeditor.molecular.lib/build.properties
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AbstractPherogramComponentHandler.java
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AlignmentEditorPasteHandler.java
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java
eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product
eu.etaxonomy.taxeditor/rcp.target

index a8063308514ddeb3f0d453b097680cc729511ff4..05274d7b9b64f63005764ed53e4f513e52fcbd3f 100644 (file)
@@ -31,3 +31,4 @@ eu.etaxonomy.taxeditor.webapp/lib/cdmlib-remote-webapp.war
 /eu.etaxonomy.taxeditor.webapp/.settings/org.eclipse.m2e.core.prefs
 /eu.etaxonomy.taxeditor.webapp/lib/
 
+/.ssh
index cedc1756f6cc8969124d508a1b2eb0f093a088a5..42448a1f344e1becfd1a8fba8eeab2bacbd86b45 100644 (file)
@@ -3,18 +3,19 @@
        <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/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 exported="true" kind="lib" path="lib/info.bioinfweb.commons.bio/bin"/>
+       <classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.commons.core/bin"/>
+       <classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.commons.swing/bin"/>
+       <classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.commons.swt/bin"/>
+       <classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.tic.core/bin"/>
+       <classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.tic.swt/bin"/>
+       <classpathentry exported="true" kind="lib" path="lib/JPhyloIO/bin" sourcepath="lib/JPhyloIO/bin"/>
+       <classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.libralign.core/bin"/>
+       <classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.libralign.io/bin"/>
+       <classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.libralign.swt/bin"/>
+       <classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.libralign.biojava1/bin"/>
        <classpathentry kind="output" path="target/classes"/>
 </classpath>
index 45f118a13f93c5f2b551a880f0e56c7f62ac179c..61fe6212a123c89948fb4c1667db080676fc43db 100644 (file)
                <nature>org.eclipse.pde.PluginNature</nature>
                <nature>org.eclipse.jdt.core.javanature</nature>
        </natures>
+       <linkedResources>
+               <link>
+                       <name>lib/JPhyloIO</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/JPhyloIO</locationURI>
+               </link>
+               <link>
+                       <name>lib/info.bioinfweb.commons.bio</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/info.bioinfweb.commons.bio</locationURI>
+               </link>
+               <link>
+                       <name>lib/info.bioinfweb.commons.core</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/info.bioinfweb.commons.core</locationURI>
+               </link>
+               <link>
+                       <name>lib/info.bioinfweb.commons.swing</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/info.bioinfweb.commons.swing</locationURI>
+               </link>
+               <link>
+                       <name>lib/info.bioinfweb.commons.swt</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/info.bioinfweb.commons.swt</locationURI>
+               </link>
+               <link>
+                       <name>lib/info.bioinfweb.libralign.biojava1</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/info.bioinfweb.libralign.biojava1</locationURI>
+               </link>
+               <link>
+                       <name>lib/info.bioinfweb.libralign.core</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/info.bioinfweb.libralign.core</locationURI>
+               </link>
+               <link>
+                       <name>lib/info.bioinfweb.libralign.io</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/info.bioinfweb.libralign.io</locationURI>
+               </link>
+               <link>
+                       <name>lib/info.bioinfweb.libralign.swt</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/info.bioinfweb.libralign.swt</locationURI>
+               </link>
+               <link>
+                       <name>lib/info.bioinfweb.tic.core</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/info.bioinfweb.tic.core</locationURI>
+               </link>
+               <link>
+                       <name>lib/info.bioinfweb.tic.swt</name>
+                       <type>2</type>
+                       <locationURI>WORKSPACE_LOC/info.bioinfweb.tic.swt</locationURI>
+               </link>
+       </linkedResources>
 </projectDescription>
index 414a0e99f88290cebddbaf2a9ab123675414fe5a..e6f15330ff5c20f82cba6c0e44a237e8a41bf770 100644 (file)
@@ -5,19 +5,20 @@ Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular.lib;singleton:=true
 Bundle-Version: 4.4.0.qualifier
 Bundle-ClassPath: .,
  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
+ lib/sequencing-1.9.2.jar,
+ lib/info.bioinfweb.commons.bio/bin/,
+ lib/info.bioinfweb.commons.core/bin/,
+ lib/info.bioinfweb.commons.swing/bin/,
+ lib/info.bioinfweb.commons.swt/bin/,
+ lib/info.bioinfweb.tic.core/bin/,
+ lib/info.bioinfweb.tic.swt/bin/,
+ lib/JPhyloIO/bin/,
+ lib/info.bioinfweb.libralign.core/bin/,
+ lib/info.bioinfweb.libralign.io/bin/,
+ lib/info.bioinfweb.libralign.swt/bin/,
+ lib/info.bioinfweb.libralign.biojava1/bin/
 Export-Package: info.bioinfweb.commons,
  info.bioinfweb.commons.appversion,
  info.bioinfweb.commons.beans,
@@ -36,7 +37,7 @@ Export-Package: info.bioinfweb.commons,
  info.bioinfweb.jphyloio,
  info.bioinfweb.jphyloio.dataadapters,
  info.bioinfweb.jphyloio.dataadapters.implementations,
- info.bioinfweb.jphyloio.dataadapters.implementations.readtowriteadapter,
+ info.bioinfweb.jphyloio.dataadapters.implementations.store,
  info.bioinfweb.jphyloio.dataadapters.implementations.receivers,
  info.bioinfweb.jphyloio.events,
  info.bioinfweb.jphyloio.events.meta,
@@ -48,7 +49,6 @@ Export-Package: info.bioinfweb.commons,
  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,
@@ -60,10 +60,13 @@ Export-Package: info.bioinfweb.commons,
  info.bioinfweb.jphyloio.formats.pde,
  info.bioinfweb.jphyloio.formats.phylip,
  info.bioinfweb.jphyloio.formats.phyloxml,
+ info.bioinfweb.jphyloio.formats.phyloxml.elementreader,
  info.bioinfweb.jphyloio.formats.text,
  info.bioinfweb.jphyloio.formats.xml,
  info.bioinfweb.jphyloio.formats.xtg,
- info.bioinfweb.jphyloio.tools,
+ info.bioinfweb.jphyloio.utils,
+ info.bioinfweb.jphyloio.objecttranslation,
+ info.bioinfweb.jphyloio.objecttranslation.implementations,
  info.bioinfweb.libralign,
  info.bioinfweb.libralign.actions,
  info.bioinfweb.libralign.alignmentarea,
index 2bcb762d74d1fdf249a3c8845e0bc298b8bd3cee..4cd6b03859e7a2f0f50211f18804318c92b7b87b 100644 (file)
@@ -1,17 +1,18 @@
 bin.includes = META-INF/,\
                lib/tic-swt-2.0.0-preview-1.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
+               lib/sequencing-1.9.2.jar,\
+               lib/info.bioinfweb.commons.bio/bin/,\
+               lib/info.bioinfweb.commons.core/bin/,\
+               lib/info.bioinfweb.commons.swing/bin/,\
+               lib/info.bioinfweb.commons.swt/bin/,\
+               lib/info.bioinfweb.libralign.core/bin/,\
+               lib/info.bioinfweb.libralign.io/bin/,\
+               lib/info.bioinfweb.libralign.swt/bin/,\
+               lib/info.bioinfweb.tic.core/bin/,\
+               lib/info.bioinfweb.tic.swt/bin/,\
+               lib/JPhyloIO/bin/,\
+               lib/info.bioinfweb.libralign.biojava1/bin/
                lib/jphyloio-core-0-SNAPSHOT.jar,\
                lib/owlapi-xmlutils-4.1.4.jar
index 90b98375553efb432e3050ef541784546a5b1426..12b1d8e5a1301ce91b1f558a23c80a490e2e2d83 100644 (file)
@@ -134,7 +134,7 @@ public class AlignmentEditor extends EditorPart {
 
 
     private MultipleAlignmentsContainer alignmentsContainer = null;
-    private final Map<Integer, SingleReadAlignment> cdmMap = new TreeMap<Integer, SingleReadAlignment>();  //TODO Move this to ContigSequenceDataProvider
+    private final Map<String, SingleReadAlignment> cdmMap = new TreeMap<String, SingleReadAlignment>();  //TODO Move this to ContigSequenceDataProvider
     private boolean dirty = false;
 
     public AlignmentEditor()
@@ -275,12 +275,12 @@ public class AlignmentEditor extends EditorPart {
     }
 
 
-    public boolean hasPherogram(int sequenceID) {
+    public boolean hasPherogram(String sequenceID) {
         return getReadsArea().getDataAreas().getSequenceAreas(sequenceID).size() > PHEROGRAM_AREA_INDEX;
     }
 
 
-    public PherogramArea getPherogramArea(int sequenceID) {
+    public PherogramArea getPherogramArea(String sequenceID) {
         if (hasPherogram(sequenceID)) {
             return (PherogramArea)getReadsArea().getDataAreas().getSequenceAreas(sequenceID).get(PHEROGRAM_AREA_INDEX);
         }
@@ -307,7 +307,7 @@ public class AlignmentEditor extends EditorPart {
 
                        // Add test consensus sequence:
                        AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel();
-                       int id = consensusModel.addSequence(CONSENSUS_NAME);
+                       String id = consensusModel.addSequence(CONSENSUS_NAME);
                        Collection<Object> tokens = new ArrayList<Object>();  // First save tokens in a collection to avoid GUI updated for each token.
                        tokens.add(consensusModel.getTokenSet().tokenByRepresentation("A"));
                        tokens.add(consensusModel.getTokenSet().tokenByRepresentation("C"));
@@ -332,7 +332,7 @@ public class AlignmentEditor extends EditorPart {
                                if (pherogramInfo.getPherogram() != null) {
                                    uri = MediaUtils.getFirstMediaRepresentationPart(pherogramInfo.getPherogram()).getUri();
                                }
-                               int id = addRead(DerivateLabelProvider.getDerivateText(pherogramInfo, conversationHolder),
+                               String id = addRead(DerivateLabelProvider.getDerivateText(pherogramInfo, conversationHolder),
                                                uri,
                                                singleReadAlignment.isReverseComplement(),
                                                singleReadAlignment.getEditedSequence(),
@@ -350,7 +350,7 @@ public class AlignmentEditor extends EditorPart {
 
                // Set consensus sequence:
                AlignmentModel consensusProvider = getEditableConsensusArea().getAlignmentModel();
-               int id = consensusProvider.addSequence(CONSENSUS_NAME);
+               String id = consensusProvider.addSequence(CONSENSUS_NAME);
                consensusProvider.insertTokensAt(id, 0, AlignmentModelUtils.charSequenceToTokenList(
                                sequenceNode.getConsensusSequence().getString(), consensusProvider.getTokenSet()));
                //TODO Can the consensus sequence also be null? / Should it be created here, if nothing is in the DB?
@@ -439,9 +439,9 @@ public class AlignmentEditor extends EditorPart {
                // Write single reads:
                stringProvider.setUnderlyingModel(getReadsArea().getAlignmentModel());
                sequenceNode.getSingleReadAlignments().retainAll(cdmMap.values());  // Remove all reads that are not in the alignment anymore.
-               Iterator<Integer> iterator = getReadsArea().getAlignmentModel().sequenceIDIterator();
+               Iterator<String> iterator = getReadsArea().getAlignmentModel().sequenceIDIterator();
                while (iterator.hasNext()) {
-                       int id = iterator.next();
+                       String id = iterator.next();
                        SingleReadAlignment singleRead = cdmMap.get(id);
                        if (singleRead == null) {
                            throw new InternalError("Creating new reads from AlignmentEditor not implemented.");
@@ -587,7 +587,7 @@ public class AlignmentEditor extends EditorPart {
        SelectionModel selection = getReadsArea().getSelection();
        AlignmentModel<?> model = getReadsArea().getAlignmentModel();
        for (int row = selection.getFirstRow(); row < selection.getFirstRow() + selection.getCursorHeight(); row++) {
-                       int sequenceID = getReadsArea().getSequenceOrder().idByIndex(row);
+               String sequenceID = getReadsArea().getSequenceOrder().idByIndex(row);
                        PherogramArea area = getPherogramArea(sequenceID);
                        PherogramAreaModel pherogramAlignmentModel = area.getModel();
                        AlignmentModelUtils.reverseComplement(model, sequenceID,
@@ -608,7 +608,7 @@ public class AlignmentEditor extends EditorPart {
     public <T> void createConsensusSequence() {
         ConsensusSequenceArea area = getConsensusHintDataArea();
         AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
-        int sequenceID = model.sequenceIDIterator().next();  // There is always one sequence contained.
+        String sequenceID = model.sequenceIDIterator().next();  // There is always one sequence contained.
         int length = getReadsArea().getAlignmentModel().getMaxSequenceLength();
 
         Collection<T> tokens = new ArrayList<T>(length);
@@ -630,7 +630,7 @@ public class AlignmentEditor extends EditorPart {
         ConsensusSequenceArea area = getConsensusHintDataArea();
         AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
         TokenSet<T> tokenSet = model.getTokenSet();
-        int sequenceID = model.sequenceIDIterator().next();  // There is always one sequence contained.
+        String sequenceID = model.sequenceIDIterator().next();  // There is always one sequence contained.
         int currentConsensusLength = model.getSequenceLength(sequenceID);
         int overallLength = getReadsArea().getAlignmentModel().getMaxSequenceLength();
 
@@ -670,9 +670,7 @@ public class AlignmentEditor extends EditorPart {
 
        private String newReadName() {
                int index = 1;
-               while (getReadsArea().getAlignmentModel().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index)
-                               != AlignmentModel.NO_SEQUENCE_FOUND) {
-
+               while (getReadsArea().getAlignmentModel().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index) != null) {
                        index++;
                }
                return DEFAULT_READ_NAME_PREFIX + index;
@@ -701,7 +699,7 @@ public class AlignmentEditor extends EditorPart {
      * @throws IOException if an error occurred when trying to read the pherogram file
      * @throws UnsupportedChromatogramFormatException if the format of the pherogram file is not supported
      */
-    public int addRead(String name, URI pherogramURI, boolean reverseComplemented, String editedSequence,
+    public String addRead(String name, URI pherogramURI, boolean reverseComplemented, String editedSequence,
             Integer firstSeqPos, Integer leftCutPos, Integer rightCutPos, SingleReadAlignment.Shift[] shifts)
             throws IOException, UnsupportedChromatogramFormatException {
 
@@ -716,7 +714,7 @@ public class AlignmentEditor extends EditorPart {
 
         // Create sequence:
                provider.addSequence(name);
-               int id = provider.sequenceIDByName(name);
+               String id = provider.sequenceIDByName(name);
 
                // Set edited sequence:
                Collection<Object> tokens = null;  // First save tokens in a collection to avoid GUI updated for each token.
index 55c24e32aab50088dfbd93aa3c363c67a988cc45..b0bf979c5a54c643a632534e6c3b6cf0edb7759a 100644 (file)
@@ -41,7 +41,7 @@ public abstract class AbstractPherogramComponentHandler extends AbstractHandler
 
         if (activePart instanceof AlignmentEditor) {
             AlignmentEditor editor = (AlignmentEditor)activePart;
-            Iterator<Integer> idIterator = editor.getReadsArea().getAlignmentModel().sequenceIDIterator();
+            Iterator<String> idIterator = editor.getReadsArea().getAlignmentModel().sequenceIDIterator();
             while (idIterator.hasNext()) {
                 PherogramArea area = editor.getPherogramArea(idIterator.next());
                 if (area != null) {
index 590aab56cda513d4684b25da531f4949cf16aea3..98205803035aa38a307005ee86efc049a0a21c9d 100644 (file)
@@ -30,10 +30,11 @@ import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
  * @date 26.08.2015\r
  */\r
 public class AlignmentEditorPasteHandler extends AbstractFocusedAlignmentAreaHandler implements IElementUpdater {\r
-       private void pasteString(AlignmentArea area, int sequenceID, String content) {\r
+       private void pasteString(AlignmentArea area, String sequenceID, String content) {\r
                area.getActionProvider().deleteSelection();  // Overwrite selected tokens.\r
                area.getActionProvider().elongateSequence(sequenceID, area.getSelection().getCursorColumn());\r
 \r
+               @SuppressWarnings("unchecked")\r
                AlignmentModel<Object> alignmentModel = (AlignmentModel<Object>)area.getAlignmentModel();\r
                alignmentModel.insertTokensAt(sequenceID, area.getSelection().getCursorColumn(),\r
                                AlignmentModelUtils.charSequenceToTokenList(content, alignmentModel.getTokenSet(),\r
@@ -62,7 +63,7 @@ public class AlignmentEditorPasteHandler extends AbstractFocusedAlignmentAreaHan
 \r
                        if (!lines.isEmpty()) { //TODO Can lines be empty? (Can an empty string "" be copied to the clipboard?)\r
                                if (selection.getCursorHeight() == 1) {  // If the consensus sequence is focused, this is the only possible case.\r
-                                       int sequenceID = focusedArea.getSequenceOrder().idByIndex(selection.getCursorRow());\r
+                                       String sequenceID = focusedArea.getSequenceOrder().idByIndex(selection.getCursorRow());\r
                                        if (lines.size() == 1) {\r
                                                pasteString(focusedArea, sequenceID, lines.get(0));\r
                                        }\r
index 41175772f9233a6bb5ab3567e14d535dc0ebc8a5..7f84fcbcbce67c8d7f08013cb0e202ae8277af66 100644 (file)
@@ -18,7 +18,7 @@ import info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver;
 import info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter;\r
 import info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter;\r
 import info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter;\r
-import info.bioinfweb.jphyloio.dataadapters.implementations.readtowriteadapter.StoreObjectListDataAdapter;\r
+import info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter;\r
 import info.bioinfweb.jphyloio.events.CharacterSetIntervalEvent;\r
 import info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent;\r
 import info.bioinfweb.jphyloio.events.SequenceTokensEvent;\r
index e0c70a98b0cfa8d1ac585568a4dcb0107ac789c7..41c429529c90fe3c5f157820a21fc87e75453a32 100644 (file)
@@ -1,39 +1,58 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?pde version="3.5"?><product application="eu.etaxonomy.taxeditor.application.application" id="eu.etaxonomy.taxeditor.application.eu_etaxonomy_taxeditor_product" includeLaunchers="true" name="EDIT Taxonomic Editor" uid="eu.etaxonomy.taxeditor.product" useFeatures="true" version="4.4.0.qualifier">
-  <aboutInfo>
-    <image path="/eu.etaxonomy.taxeditor.application/icons/256color_48x48.gif"/>
-    <text>
-         %productBlurb
-      </text>
-  </aboutInfo>
-  <configIni use="default"></configIni>
-  <launcherArgs>
-    <programArgs>-data @user.home/.cdmLibrary -Dserver_port=58080
-      </programArgs>
-    <vmArgs>-Xmx512M -XX:MaxPermSize=256M -Dorg.eclipse.update.reconcile=false -Declipse.p2.unsignedPolicy=allow
-      </vmArgs>
-    <vmArgsMac>-XstartOnFirstThread -Dorg.eclipse.swt.internal.carbon.smallFonts
-      </vmArgsMac>
-  </launcherArgs>
-  <windowImages i16="/eu.etaxonomy.taxeditor.application/icons/256color_16x16.gif" i32="/eu.etaxonomy.taxeditor.application/icons/256color_32x32.gif" i48="/eu.etaxonomy.taxeditor.application/icons/256color_48x48.gif"/>
-  <splash location="eu.etaxonomy.taxeditor.application" startupForegroundColor="000000" startupMessageRect="7,432,360,20" startupProgressRect="5,447,366,15"/>
-  <launcher name="TaxonomicEditor">
-    <solaris/>
-    <win useIco="false">
-      <bmp/>
-    </win>
-  </launcher>
-  <vm></vm>
-  <plugins></plugins>
-  <features>
-    <feature id="eu.etaxonomy.taxeditor.feature"/>
-  </features>
-  <configurations>
-    <plugin autoStart="true" id="eu.etaxonomy.taxeditor.application" startLevel="5"/>
-    <plugin autoStart="true" id="org.eclipse.core.runtime" startLevel="4"/>
-    <plugin autoStart="true" id="org.eclipse.equinox.common" startLevel="2"/>
-    <plugin autoStart="true" id="org.eclipse.equinox.ds" startLevel="2"/>
-    <plugin autoStart="true" id="org.eclipse.equinox.p2.transport.ecf" startLevel="4"/>
-    <plugin autoStart="true" id="org.eclipse.equinox.simpleconfigurator" startLevel="1"/>
-  </configurations>
-</product>
+<?xml version="1.0" encoding="UTF-8"?>\r
+<?pde version="3.5"?>\r
+\r
+<product name="EDIT Taxonomic Editor" uid="eu.etaxonomy.taxeditor.product" id="eu.etaxonomy.taxeditor.application.eu_etaxonomy_taxeditor_product" application="eu.etaxonomy.taxeditor.application.application" version="4.4.0.qualifier" useFeatures="true" includeLaunchers="true">\r
+\r
+   <aboutInfo>\r
+      <image path="/eu.etaxonomy.taxeditor.application/icons/256color_48x48.gif"/>\r
+      <text>\r
+         %productBlurb\r
+      </text>\r
+   </aboutInfo>\r
+\r
+   <configIni use="default">\r
+   </configIni>\r
+\r
+   <launcherArgs>\r
+      <programArgs>-data @user.home/.cdmLibrary -Dserver_port=58080\r
+      </programArgs>\r
+      <vmArgs>-Xmx512M -XX:MaxPermSize=256M -Dorg.eclipse.update.reconcile=false -Declipse.p2.unsignedPolicy=allow\r
+      </vmArgs>\r
+      <vmArgsMac>-XstartOnFirstThread -Dorg.eclipse.swt.internal.carbon.smallFonts\r
+      </vmArgsMac>\r
+   </launcherArgs>\r
+\r
+   <windowImages i16="/eu.etaxonomy.taxeditor.application/icons/256color_16x16.gif" i32="/eu.etaxonomy.taxeditor.application/icons/256color_32x32.gif" i48="/eu.etaxonomy.taxeditor.application/icons/256color_48x48.gif"/>\r
+\r
+   <splash\r
+      location="eu.etaxonomy.taxeditor.application"\r
+      startupProgressRect="5,447,366,15"\r
+      startupMessageRect="7,432,360,20"\r
+      startupForegroundColor="000000" />\r
+   <launcher name="TaxonomicEditor">\r
+      <solaris/>\r
+      <win useIco="false">\r
+         <bmp/>\r
+      </win>\r
+   </launcher>\r
+\r
+   <vm>\r
+   </vm>\r
+\r
+   <plugins>\r
+   </plugins>\r
+\r
+   <features>\r
+      <feature id="eu.etaxonomy.taxeditor.feature"/>\r
+   </features>\r
+\r
+   <configurations>\r
+      <plugin id="eu.etaxonomy.taxeditor.application" autoStart="true" startLevel="5" />\r
+      <plugin id="org.eclipse.core.runtime" autoStart="true" startLevel="4" />\r
+      <plugin id="org.eclipse.equinox.common" autoStart="true" startLevel="2" />\r
+      <plugin id="org.eclipse.equinox.ds" autoStart="true" startLevel="2" />\r
+      <plugin id="org.eclipse.equinox.p2.transport.ecf" autoStart="true" startLevel="4" />\r
+      <plugin id="org.eclipse.equinox.simpleconfigurator" autoStart="true" startLevel="1" />\r
+   </configurations>\r
+\r
+</product>\r
index ac61176b388b77193e8559732983acaf9be366a7..870c330f0ba596072af4ed4437fd08ed081b027b 100644 (file)
@@ -1,31 +1,31 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<?pde version="3.8"?><target name="Eclipse Indigo Target" sequenceNumber="7">
-<locations>
-<location includeAllPlatforms="true" includeConfigurePhase="false" includeMode="slicer" includeSource="true" type="InstallableUnit">
-<unit id="org.eclipse.swtbot.eclipse.feature.group" version="2.0.5.20111003_1754-3676ac8-dev-e36"/>
-<unit id="org.eclipse.swtbot.eclipse.gef.feature.group" version="2.0.5.20111003_1754-3676ac8-dev-e36"/>
-<unit id="org.eclipse.swtbot.ide.feature.group" version="2.0.5.20111003_1754-3676ac8-dev-e36"/>
-<unit id="org.eclipse.swtbot.eclipse.test.junit4.feature.group" version="2.0.5.20111003_1754-3676ac8-dev-e36"/>
-<repository location="http://download.eclipse.org/technology/swtbot/helios/dev-build/update-site"/>
-</location>
-<location includeAllPlatforms="true" includeConfigurePhase="false" includeMode="slicer" includeSource="true" type="InstallableUnit">
-<unit id="org.eclipse.jdt.feature.group" version="3.7.2.v20120120-1414-7z8gFcuFMP7BW5XTz0jLTnz0l9B1"/>
-<unit id="org.eclipse.pde.source.feature.group" version="3.7.2.v20120120-1420-7b7rFUOFEx2Xnqafnpz0E--0"/>
-<unit id="org.eclipse.platform.feature.group" version="3.7.2.v20120207-1839-9gF7UHPDFxGjd-PqDr2jX_4yKaumkoHTz04_q-q"/>
-<unit id="org.eclipse.equinox.executable.feature.group" version="3.5.1.v20111216-1653-7P7NFUIFIbaUcU77s0KQWHw5HZTZ"/>
-<unit id="org.eclipse.platform.source.feature.group" version="3.7.2.v20120207-1839-9gF7UHPDFxGjd-PqDr2jX_4yKaumkoHTz04_q-q"/>
-<unit id="org.eclipse.platform.sdk" version="3.7.2.M20120208-0800"/>
-<unit id="org.eclipse.rcp.feature.group" version="3.7.2.v20120120-1424-9DB5FmnFq5JCf1UA38R-kz0S0272"/>
-<unit id="org.eclipse.rcp.source.feature.group" version="3.7.2.v20120120-1424-9DB5FmnFq5JCf1UA38R-kz0S0272"/>
-<unit id="org.eclipse.rcp.sdk.id" version="3.7.2.M20120208-0800"/>
-<unit id="org.eclipse.equinox.sdk.feature.group" version="3.7.1.R37x_v20110907-7M7W8i8eNV4WsRkue-4Vq4J6pCyW"/>
-<unit id="org.eclipse.zest.sdk.feature.group" version="1.3.0.v20110425-2050-67C18COMPIAKSVKGQaRTQTiSN8WP"/>
-<unit id="org.eclipse.pde.feature.group" version="3.7.2.v20120120-1420-7b7rFUOFEx2Xnqafnpz0E--0"/>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>\r
+<?pde version="3.8"?><target name="Eclipse Indigo Target" sequenceNumber="8">\r
+<locations>\r
+<location includeAllPlatforms="true" includeConfigurePhase="false" includeMode="slicer" includeSource="true" type="InstallableUnit">\r
+<unit id="org.eclipse.swtbot.eclipse.feature.group" version="2.0.5.20111003_1754-3676ac8-dev-e36"/>\r
+<unit id="org.eclipse.swtbot.eclipse.gef.feature.group" version="2.0.5.20111003_1754-3676ac8-dev-e36"/>\r
+<unit id="org.eclipse.swtbot.ide.feature.group" version="2.0.5.20111003_1754-3676ac8-dev-e36"/>\r
+<unit id="org.eclipse.swtbot.eclipse.test.junit4.feature.group" version="2.0.5.20111003_1754-3676ac8-dev-e36"/>\r
+<repository location="http://download.eclipse.org/technology/swtbot/helios/dev-build/update-site"/>\r
+</location>\r
+<location includeAllPlatforms="true" includeConfigurePhase="false" includeMode="slicer" includeSource="true" type="InstallableUnit">\r
+<unit id="org.eclipse.jdt.feature.group" version="3.7.2.v20120120-1414-7z8gFcuFMP7BW5XTz0jLTnz0l9B1"/>\r
+<unit id="org.eclipse.pde.source.feature.group" version="3.7.2.v20120120-1420-7b7rFUOFEx2Xnqafnpz0E--0"/>\r
+<unit id="org.eclipse.platform.feature.group" version="3.7.2.v20120207-1839-9gF7UHPDFxGjd-PqDr2jX_4yKaumkoHTz04_q-q"/>\r
+<unit id="org.eclipse.equinox.executable.feature.group" version="3.5.1.v20111216-1653-7P7NFUIFIbaUcU77s0KQWHw5HZTZ"/>\r
+<unit id="org.eclipse.platform.source.feature.group" version="3.7.2.v20120207-1839-9gF7UHPDFxGjd-PqDr2jX_4yKaumkoHTz04_q-q"/>\r
+<unit id="org.eclipse.platform.sdk" version="3.7.2.M20120208-0800"/>\r
+<unit id="org.eclipse.rcp.feature.group" version="3.7.2.v20120120-1424-9DB5FmnFq5JCf1UA38R-kz0S0272"/>\r
+<unit id="org.eclipse.rcp.source.feature.group" version="3.7.2.v20120120-1424-9DB5FmnFq5JCf1UA38R-kz0S0272"/>\r
+<unit id="org.eclipse.rcp.sdk.id" version="3.7.2.M20120208-0800"/>\r
+<unit id="org.eclipse.equinox.sdk.feature.group" version="3.7.1.R37x_v20110907-7M7W8i8eNV4WsRkue-4Vq4J6pCyW"/>\r
+<unit id="org.eclipse.zest.sdk.feature.group" version="1.3.0.v20110425-2050-67C18COMPIAKSVKGQaRTQTiSN8WP"/>\r
+<unit id="org.eclipse.pde.feature.group" version="3.7.2.v20120120-1420-7b7rFUOFEx2Xnqafnpz0E--0"/>\r
 <repository location="http://download.eclipse.org/releases/indigo/"/>
-</location>
-<location includeAllPlatforms="true" includeConfigurePhase="false" includeMode="slicer" includeSource="true" type="InstallableUnit">
-<unit id="org.eclipse.nebula.widgets.compositetable.feature.feature.group" version="1.0.0.201409040043"/>
-<repository location="http://archive.eclipse.org/nebula/Q32014/release/"/>
-</location>
-</locations>
-</target>
+</location>\r
+<location includeAllPlatforms="true" includeConfigurePhase="false" includeMode="slicer" includeSource="true" type="InstallableUnit">\r
+<unit id="org.eclipse.nebula.widgets.compositetable.feature.feature.group" version="1.0.0.201409040043"/>\r
+<repository location="http://archive.eclipse.org/nebula/Q32014/release/"/>\r
+</location>\r
+</locations>\r
+</target>\r