- removed accidentally commited LibrAlign code

diff --git a/eu.etaxonomy.taxeditor.store/.classpath b/eu.etaxonomy.taxeditor.store/.classpath
index 666d5b1fe50f830ec445655a369f9decdea964c1..753a09f69dd49e88d13a9a38663f801af121a6b5 100644 (file)
--- a/eu.etaxonomy.taxeditor.store/.classpath
+++ b/eu.etaxonomy.taxeditor.store/.classpath
@@ -1,15 +1,5 @@
 <?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.swing.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/core-1.8.5.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/sequencing-1.8.5.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/jfreechart-1.0.17/lib/jfreechart-1.0.17-swt.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/bioinfweb.commons.tic.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/LibrAlign.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/biojava3-alignment-3.0.7.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/bioinfweb.commons.experimental.bio.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/biojava3-core-3.0.7.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/bioinfweb.commons.core.jar"/>

        <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 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"/>

diff --git a/eu.etaxonomy.taxeditor.store/META-INF/MANIFEST.MF b/eu.etaxonomy.taxeditor.store/META-INF/MANIFEST.MF
index d2216872f27da235fabe65170d2989bad3c9473e..9344dffeabf5c66c3a341c302adff688881316be 100644 (file)
--- a/eu.etaxonomy.taxeditor.store/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.store/META-INF/MANIFEST.MF
@@ -52,32 +52,7 @@ Export-Package: eu.etaxonomy.cdm,
  eu.etaxonomy.taxeditor.view.derivateSearch,
  eu.etaxonomy.taxeditor.view.detail,
  eu.etaxonomy.taxeditor.view.specimenSearch,
  eu.etaxonomy.taxeditor.view.derivateSearch,
  eu.etaxonomy.taxeditor.view.detail,
  eu.etaxonomy.taxeditor.view.specimenSearch,

- eu.etaxonomy.taxeditor.view.supplementaldata,
- info.bioinfweb.commons,
- info.bioinfweb.commons.appversion,
- info.bioinfweb.commons.bio,
- info.bioinfweb.commons.bio.alignment.pairwise,
- info.bioinfweb.commons.bio.biojava3.alignment,
- info.bioinfweb.commons.bio.biojava3.alignment.io,
- info.bioinfweb.commons.bio.biojava3.alignment.io.fasta,
- info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86,
- info.bioinfweb.commons.bio.biojava3.alignment.io.mega,
- info.bioinfweb.commons.bio.biojava3.alignment.io.nexus,
- info.bioinfweb.commons.bio.biojava3.alignment.io.phylip,
- info.bioinfweb.commons.bio.biojava3.alignment.template,
- info.bioinfweb.commons.bio.biojava3.core.sequence,
- info.bioinfweb.commons.bio.biojava3.core.sequence.compound,
- info.bioinfweb.commons.bio.biojava3.core.sequence.io,
- info.bioinfweb.commons.bio.biojava3.core.sequence.template,
- info.bioinfweb.commons.bio.biojava3.core.sequence.views,
- info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus,
- info.bioinfweb.commons.changemonitor,
- info.bioinfweb.commons.collections,
- info.bioinfweb.commons.graphics,
- info.bioinfweb.commons.io,
- info.bioinfweb.commons.log,
- info.bioinfweb.commons.progress,
- info.bioinfweb.commons.text
+ eu.etaxonomy.taxeditor.view.supplementaldata

 Require-Bundle: org.eclipse.osgi,
  org.eclipse.ui,
  org.eclipse.jface.text,
 Require-Bundle: org.eclipse.osgi,
  org.eclipse.ui,
  org.eclipse.jface.text,


@@ -265,14 +240,4 @@ Bundle-ClassPath: .,
  xpp3-1.1.4c.jar,
  xpp3_min-1.1.4c.jar,
  xstream-1.4.4.jar,
  xpp3-1.1.4c.jar,
  xpp3_min-1.1.4c.jar,
  xstream-1.4.4.jar,

- yjp-controller-api-redist-9.0.8.jar,
- lib/bioinfweb.commons.core.jar,
- lib/biojava3-core-3.0.7.jar,
- lib/bioinfweb.commons.experimental.bio.jar,
- lib/biojava3-alignment-3.0.7.jar,
- lib/LibrAlign.jar,
- lib/bioinfweb.commons.tic.jar,
- lib/jfreechart-1.0.17/lib/jfreechart-1.0.17-swt.jar,
- lib/bioinfweb.commons.swing.jar,
- lib/core-1.8.5.jar,
- lib/sequencing-1.8.5.jar
+ yjp-controller-api-redist-9.0.8.jar

diff --git a/eu.etaxonomy.taxeditor.store/build.properties b/eu.etaxonomy.taxeditor.store/build.properties
index 0ed4bb68791fcaf03afbb3ee025bfbede0921f3a..925934e50ff1d92c868e24dda037b16c48abeb72 100644 (file)
--- a/eu.etaxonomy.taxeditor.store/build.properties
+++ b/eu.etaxonomy.taxeditor.store/build.properties
@@ -6,14 +6,4 @@ bin.includes = META-INF/,\
                .,\
                plugin.xml,\
                icons/,\
                .,\
                plugin.xml,\
                icons/,\

-               p2.inf,\
-               lib/bioinfweb.commons.core.jar,\
-               lib/biojava3-core-3.0.7.jar,\
-               lib/bioinfweb.commons.experimental.bio.jar,\
-               lib/biojava3-alignment-3.0.7.jar,\
-               lib/LibrAlign.jar,\
-               lib/bioinfweb.commons.tic.jar,\
-               lib/jfreechart-1.0.17/lib/jfreechart-1.0.17-swt.jar,\
-               lib/bioinfweb.commons.swing.jar,\
-               lib/core-1.8.5.jar,\
-               lib/sequencing-1.8.5.jar
+               p2.inf

diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/CdmDataSourceViewPart.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/CdmDataSourceViewPart.java
index 34afe6bb9e57404ac6dd27f3337460ebbef0e809..ca1519081b2ca09dd7185af4636b5b7a6c4c059b 100644 (file)
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/CdmDataSourceViewPart.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/CdmDataSourceViewPart.java
@@ -10,50 +10,47 @@
 
 package eu.etaxonomy.taxeditor.view.datasource;
 
 
 package eu.etaxonomy.taxeditor.view.datasource;
 

-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.pherogram.BioJavaPherogramProvider;
-import info.bioinfweb.libralign.pherogram.PherogramFormats.QualityOutputType;
-import info.bioinfweb.libralign.pherogram.PherogramHeadingView;
-import info.bioinfweb.libralign.pherogram.PherogramTraceCurveView;
-import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider;
-import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;
-
-import java.io.File;
-import java.io.IOException;

 import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.log4j.Logger;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.log4j.Logger;

-import org.biojava.bio.chromatogram.ChromatogramFactory;
-import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
-import org.biojava3.core.sequence.DNASequence;
-import org.biojava3.core.sequence.compound.NucleotideCompound;
+import org.eclipse.core.commands.Command;
+import org.eclipse.core.commands.ExecutionException;
+import org.eclipse.core.commands.NotEnabledException;
+import org.eclipse.core.commands.NotHandledException;
+import org.eclipse.core.commands.common.NotDefinedException;

 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.IStatus;
 import org.eclipse.core.runtime.Status;
 import org.eclipse.core.runtime.jobs.Job;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.IStatus;
 import org.eclipse.core.runtime.Status;
 import org.eclipse.core.runtime.jobs.Job;

+import org.eclipse.jface.action.GroupMarker;
+import org.eclipse.jface.action.MenuManager;
+import org.eclipse.jface.viewers.DoubleClickEvent;
+import org.eclipse.jface.viewers.IDoubleClickListener;
+import org.eclipse.jface.viewers.StructuredSelection;

 import org.eclipse.jface.viewers.StructuredViewer;
 import org.eclipse.jface.viewers.TableViewer;
 import org.eclipse.jface.viewers.TableViewerColumn;
 import org.eclipse.swt.SWT;
 import org.eclipse.jface.viewers.StructuredViewer;
 import org.eclipse.jface.viewers.TableViewer;
 import org.eclipse.jface.viewers.TableViewerColumn;
 import org.eclipse.swt.SWT;

-import org.eclipse.swt.custom.ScrolledComposite;

 import org.eclipse.swt.events.SelectionAdapter;
 import org.eclipse.swt.events.SelectionEvent;
 import org.eclipse.swt.layout.FillLayout;
 import org.eclipse.swt.widgets.Composite;
 import org.eclipse.swt.events.SelectionAdapter;
 import org.eclipse.swt.events.SelectionEvent;
 import org.eclipse.swt.layout.FillLayout;
 import org.eclipse.swt.widgets.Composite;

+import org.eclipse.swt.widgets.Control;

 import org.eclipse.swt.widgets.Display;
 import org.eclipse.swt.widgets.Display;

+import org.eclipse.swt.widgets.Menu;

 import org.eclipse.swt.widgets.Table;
 import org.eclipse.swt.widgets.TableColumn;
 import org.eclipse.ui.IMemento;
 import org.eclipse.swt.widgets.Table;
 import org.eclipse.swt.widgets.TableColumn;
 import org.eclipse.ui.IMemento;

+import org.eclipse.ui.IWorkbenchActionConstants;
+import org.eclipse.ui.commands.ICommandService;
+import org.eclipse.ui.handlers.IHandlerService;

 import org.eclipse.ui.part.ViewPart;
 import org.eclipse.ui.progress.IWorkbenchSiteProgressService;
 
 import eu.etaxonomy.cdm.config.ICdmSource;
 import eu.etaxonomy.taxeditor.datasource.CdmDataSourceRepository;
 import org.eclipse.ui.part.ViewPart;
 import org.eclipse.ui.progress.IWorkbenchSiteProgressService;
 
 import eu.etaxonomy.cdm.config.ICdmSource;
 import eu.etaxonomy.taxeditor.datasource.CdmDataSourceRepository;

+import eu.etaxonomy.taxeditor.model.AbstractUtility;

 import eu.etaxonomy.taxeditor.model.ContextListenerAdapter;
 import eu.etaxonomy.taxeditor.model.IContextListener;
 import eu.etaxonomy.taxeditor.store.CdmStore;
 import eu.etaxonomy.taxeditor.model.ContextListenerAdapter;
 import eu.etaxonomy.taxeditor.model.IContextListener;
 import eu.etaxonomy.taxeditor.store.CdmStore;


@@ -189,68 +186,6 @@ public class CdmDataSourceViewPart extends ViewPart{
        public CdmDataSourceViewPart(){
        }
 
        public CdmDataSourceViewPart(){
        }
 

-       private void librAlignInit(Composite parent){
-           ScrolledComposite scrolledComposite = new ScrolledComposite(parent, SWT.BORDER | SWT.H_SCROLL | SWT.V_SCROLL);
-        scrolledComposite.setExpandHorizontal(true);
-        scrolledComposite.setExpandVertical(true);
-
-        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);
-        result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
-
-//        Composite alignmentWidget = result.createSWTWidget(scrolledComposite, SWT.NONE);
-//        scrolledComposite.setContent(alignmentWidget);
-//        scrolledComposite.setMinSize(alignmentWidget.computeSize(SWT.DEFAULT, SWT.DEFAULT));
-
-        //+++ConsensusSequenceArea
-        ConsensusSequenceArea consensusSequenceArea = new ConsensusSequenceArea(result);
-        Composite consensusWidget = consensusSequenceArea.createSWTWidget(scrolledComposite, SWT.NONE);
-        scrolledComposite.setContent(consensusWidget);
-
-
-        //+++PherogramTraceCurveView+++
-        PherogramTraceCurveView pherogramView = new PherogramTraceCurveView();
-        //      pherogramView.setProvider(new BioJavaPherogramProvider(ChromatogramFactory.create(
-        //      new File("data\\pherograms\\Test_pel1PCR_Pel2Wdhg_PCR-7-A_1.ab1"))));
-        try {
-            pherogramView.setProvider(new BioJavaPherogramProvider(ChromatogramFactory.create(
-                    new File("/home/pplitzner/svn/branch/taxeditor-3.4/eu.etaxonomy.taxeditor.store/lib/jfreechart-1.0.17/lib/A10001_GM106-petD_F.scf"))));
-        } catch (UnsupportedChromatogramFormatException e) {
-            // TODO Auto-generated catch block
-            e.printStackTrace();
-        } catch (IOException e) {
-            // TODO Auto-generated catch block
-            e.printStackTrace();
-        }
-        pherogramView.setHorizontalScale(1);
-        pherogramView.setVerticalScale(100);
-        pherogramView.getFormats().setQualityOutputType(QualityOutputType.ALL);
-        pherogramView.getFormats().setShowProbabilityValues(true);
-
-//        Composite pherogramWidget = pherogramView.createSWTWidget(scrolledComposite, SWT.NONE);
-//        scrolledComposite.setContent(pherogramWidget);
-//        scrolledComposite.setMinSize(pherogramWidget.computeSize(SWT.DEFAULT, SWT.DEFAULT));
-
-        //+++Pherogramm Heading View+++
-        PherogramHeadingView pherogramHeadingView = new PherogramHeadingView(pherogramView);
-//        Composite pherogramHeadingWidget = pherogramHeadingView.createSWTWidget(scrolledComposite, SWT.NONE);
-//        scrolledComposite.setContent(pherogramHeadingWidget);
-//        scrolledComposite.setMinSize(pherogramHeadingWidget.computeSize(SWT.DEFAULT, SWT.DEFAULT));
-
-       }
-

        /** {@inheritDoc} */
        @Override
        public void createPartControl(Composite parent) {
        /** {@inheritDoc} */
        @Override
        public void createPartControl(Composite parent) {


@@ -265,67 +200,64 @@ public class CdmDataSourceViewPart extends ViewPart{
                fillLayout.type = SWT.VERTICAL;
                parent.setLayout(fillLayout);
 
                fillLayout.type = SWT.VERTICAL;
                parent.setLayout(fillLayout);
 

-        librAlignInit(parent);
-
-
-//             viewer = new TableViewer(parent, SWT.MULTI | SWT.H_SCROLL
-//                                                                                             | SWT.V_SCROLL | SWT.FULL_SELECTION);
-//             getSite().setSelectionProvider(viewer);
-//
-//             createColumns(viewer);
-//
-//             viewer.setContentProvider(new CdmDataSourceContentProvider());
-//             viewer.setLabelProvider(new CdmDataSourceLabelProvider());
-//             comparator = new CdmDataSourceViewerComparator();
-//             viewer.setComparator(comparator);
-//
-//
-//             // register context menu
-//             MenuManager menuMgr = new MenuManager();
-//             menuMgr.add(new GroupMarker(IWorkbenchActionConstants.MB_ADDITIONS));
-//             getSite().registerContextMenu(menuMgr, viewer);
-//
-//             Control control = viewer.getControl();
-//             Menu menu = menuMgr.createContextMenu(control);
-//             control.setMenu(menu);
-//
-//             // connect on doubleclick
-//             viewer.addDoubleClickListener(new IDoubleClickListener() {
-//
-//                     @Override
-//            public void doubleClick(DoubleClickEvent event) {
-//                             if (event.getSelection() instanceof StructuredSelection) {
-//
-//                                     Object element = ((StructuredSelection) event
-//                                                     .getSelection()).getFirstElement();
-//                                     if (element instanceof CdmMetaDataAwareDataSourceContainer) {
-//                                             String commandId = "eu.etaxonomy.taxeditor.store.datasource.change";
-//
-//                                             ICommandService commandService = (ICommandService)getSite().getService(ICommandService.class);
-//
-//                                             Command command = commandService.getCommand(commandId);
-//                                             if(command.isEnabled()) {
-//
-//                                                     IHandlerService handlerService = (IHandlerService) AbstractUtility.getService(IHandlerService.class);
-//
-//                                                     try {
-//                                                             handlerService.executeCommand(commandId, null);
-//                                                     } catch (ExecutionException e) {
-//                                                             AbstractUtility.error(this.getClass(), e);
-//                                                     } catch (NotDefinedException e) {
-//                                                             AbstractUtility.error(this.getClass(), e);
-//                                                     } catch (NotEnabledException e) {
-//                                                             AbstractUtility.error(this.getClass(), e);
-//                                                     } catch (NotHandledException e) {
-//                                                             AbstractUtility.error(this.getClass(), e);
-//                                                     }
-//                                             }
-//                                     }
-//                             }
-//                     }
-//             });
-//
-//             refresh();
+               viewer = new TableViewer(parent, SWT.MULTI | SWT.H_SCROLL
+                                                                                               | SWT.V_SCROLL | SWT.FULL_SELECTION);
+               getSite().setSelectionProvider(viewer);
+
+               createColumns(viewer);
+
+               viewer.setContentProvider(new CdmDataSourceContentProvider());
+               viewer.setLabelProvider(new CdmDataSourceLabelProvider());
+               comparator = new CdmDataSourceViewerComparator();
+               viewer.setComparator(comparator);
+
+
+               // register context menu
+               MenuManager menuMgr = new MenuManager();
+               menuMgr.add(new GroupMarker(IWorkbenchActionConstants.MB_ADDITIONS));
+               getSite().registerContextMenu(menuMgr, viewer);
+
+               Control control = viewer.getControl();
+               Menu menu = menuMgr.createContextMenu(control);
+               control.setMenu(menu);
+
+               // connect on doubleclick
+               viewer.addDoubleClickListener(new IDoubleClickListener() {
+
+                       @Override
+            public void doubleClick(DoubleClickEvent event) {
+                               if (event.getSelection() instanceof StructuredSelection) {
+
+                                       Object element = ((StructuredSelection) event
+                                                       .getSelection()).getFirstElement();
+                                       if (element instanceof CdmMetaDataAwareDataSourceContainer) {
+                                               String commandId = "eu.etaxonomy.taxeditor.store.datasource.change";
+
+                                               ICommandService commandService = (ICommandService)getSite().getService(ICommandService.class);
+
+                                               Command command = commandService.getCommand(commandId);
+                                               if(command.isEnabled()) {
+
+                                                       IHandlerService handlerService = (IHandlerService) AbstractUtility.getService(IHandlerService.class);
+
+                                                       try {
+                                                               handlerService.executeCommand(commandId, null);
+                                                       } catch (ExecutionException e) {
+                                                               AbstractUtility.error(this.getClass(), e);
+                                                       } catch (NotDefinedException e) {
+                                                               AbstractUtility.error(this.getClass(), e);
+                                                       } catch (NotEnabledException e) {
+                                                               AbstractUtility.error(this.getClass(), e);
+                                                       } catch (NotHandledException e) {
+                                                               AbstractUtility.error(this.getClass(), e);
+                                                       }
+                                               }
+                                       }
+                               }
+                       }
+               });
+
+               refresh();

        }
 
 
        }