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 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.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.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.widgets.Control;
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.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 eu.etaxonomy.taxeditor.model.AbstractUtility;
import eu.etaxonomy.taxeditor.model.ContextListenerAdapter;
import eu.etaxonomy.taxeditor.model.IContextListener;
import eu.etaxonomy.taxeditor.store.CdmStore;
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) {
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();
}
BGBM BDI Projects / taxeditor.git / blobdiff