eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/datasource/CdmDataSourceViewPart.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2007 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10
  11 package eu.etaxonomy.taxeditor.view.datasource;
  12
  13 import info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment;
  14 import info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment;
  15 import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet;
  16 import info.bioinfweb.libralign.AlignmentArea;
  17 import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
  18 import info.bioinfweb.libralign.pherogram.BioJavaPherogramProvider;
  19 import info.bioinfweb.libralign.pherogram.PherogramFormats.QualityOutputType;
  20 import info.bioinfweb.libralign.pherogram.PherogramHeadingView;
  21 import info.bioinfweb.libralign.pherogram.PherogramTraceCurveView;
  22 import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider;
  23 import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;
  24
  25 import java.io.File;
  26 import java.io.IOException;
  27 import java.util.ArrayList;
  28 import java.util.List;
  29
  30 import org.apache.log4j.Logger;
  31 import org.biojava.bio.chromatogram.ChromatogramFactory;
  32 import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
  33 import org.biojava3.core.sequence.DNASequence;
  34 import org.biojava3.core.sequence.compound.NucleotideCompound;
  35 import org.eclipse.core.runtime.IProgressMonitor;
  36 import org.eclipse.core.runtime.IStatus;
  37 import org.eclipse.core.runtime.Status;
  38 import org.eclipse.core.runtime.jobs.Job;
  39 import org.eclipse.jface.viewers.StructuredViewer;
  40 import org.eclipse.jface.viewers.TableViewer;
  41 import org.eclipse.jface.viewers.TableViewerColumn;
  42 import org.eclipse.swt.SWT;
  43 import org.eclipse.swt.custom.ScrolledComposite;
  44 import org.eclipse.swt.events.SelectionAdapter;
  45 import org.eclipse.swt.events.SelectionEvent;
  46 import org.eclipse.swt.layout.FillLayout;
  47 import org.eclipse.swt.widgets.Composite;
  48 import org.eclipse.swt.widgets.Display;
  49 import org.eclipse.swt.widgets.Table;
  50 import org.eclipse.swt.widgets.TableColumn;
  51 import org.eclipse.ui.IMemento;
  52 import org.eclipse.ui.part.ViewPart;
  53 import org.eclipse.ui.progress.IWorkbenchSiteProgressService;
  54
  55 import eu.etaxonomy.cdm.config.ICdmSource;
  56 import eu.etaxonomy.taxeditor.datasource.CdmDataSourceRepository;
  57 import eu.etaxonomy.taxeditor.model.ContextListenerAdapter;
  58 import eu.etaxonomy.taxeditor.model.IContextListener;
  59 import eu.etaxonomy.taxeditor.store.CdmStore;
  60
  61 /**
  62  * <p>CdmDataSourceViewPart class.</p>
  63  *
  64  * @author n.hoffmann
  65  * @created 14.04.2009
  66  * @version 1.0
  67  */
  68 public class CdmDataSourceViewPart extends ViewPart{
  69
  70     private static final Logger logger = Logger.getLogger(CdmDataSourceViewPart.class);
  71
  72         private class ContextListener extends ContextListenerAdapter{
  73                 /* (non-Javadoc)
  74                  * @see eu.etaxonomy.taxeditor.model.IContextListener#contextAboutToStop(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
  75                  */
  76                 @Override
  77                 public void contextAboutToStop(IMemento memento, IProgressMonitor monitor) {
  78                         monitor.subTask("Refreshing Datasource View");
  79                         viewer.refresh();
  80                 }
  81
  82                 /* (non-Javadoc)
  83                  * @see eu.etaxonomy.taxeditor.model.IContextListener#contextStop(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
  84                  */
  85                 @Override
  86                 public void contextStop(IMemento memento, IProgressMonitor monitor) {
  87                         monitor.subTask("Refreshing Datasource View");
  88                         viewer.refresh();
  89                 }
  90
  91                 /* (non-Javadoc)
  92                  * @see eu.etaxonomy.taxeditor.model.IContextListener#contextStart(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
  93                  */
  94                 @Override
  95                 public void contextStart(IMemento memento, IProgressMonitor monitor) {
  96                         monitor.subTask("Refreshing Datasource View");
  97                         viewer.refresh();
  98                 }
  99         }
 100
 101         private class DataSourceJob extends Job{
 102
 103                 private final List<ICdmSource> cdmSources;
 104
 105                 /**
 106                  * @param name
 107                  */
 108                 public DataSourceJob(String title, List<ICdmSource> cdmSources) {
 109                         super(title);
 110                         this.cdmSources = cdmSources;
 111                 }
 112
 113                 /* (non-Javadoc)
 114                  * @see org.eclipse.core.runtime.jobs.Job#run(org.eclipse.core.runtime.IProgressMonitor)
 115                  */
 116                 @Override
 117                 public IStatus run(final IProgressMonitor monitor) {
 118                         try{
 119                                 logger.debug("Begin of eclipse core runtime Job to Retrieve datasources");
 120                                 monitor.beginTask("Retrieving datasources", cdmSources.size() + 1);
 121
 122                                 final List<CdmMetaDataAwareDataSourceContainer> containers = new ArrayList<CdmMetaDataAwareDataSourceContainer>();
 123
 124                                 for(ICdmSource cdmSource : cdmSources){
 125                                         containers.add(new CdmMetaDataAwareDataSourceContainer(cdmSource));
 126                                 }
 127
 128                                 Display.getDefault().asyncExec(new Runnable() {
 129
 130                                         @Override
 131                                         public void run() {
 132                                                 viewer.setInput(containers);
 133                                         }
 134                                 });
 135                                 monitor.worked(1);
 136
 137                                 for(final CdmMetaDataAwareDataSourceContainer container : containers){
 138
 139
 140                                         if(logger.isDebugEnabled()) {
 141                         logger.debug("  #" + container.hashCode() + " : next DataSourceContainer");
 142                     }
 143                                         container.getMetaDataFromDataSource();
 144                                         if(logger.isDebugEnabled()) {
 145                         logger.debug("  #" + container.hashCode() + " : metadata retrieved, creating new runnable ...");
 146                     }
 147                                         Display.getDefault().asyncExec(new Runnable() {
 148
 149                                                 @Override
 150                                                 public void run() {
 151                                                         if(logger.isDebugEnabled()) {
 152                                 logger.debug("  #" + container.hashCode() + " starting sub thread to update ...");
 153                             }
 154                                                         viewer.update(container, null);
 155                                                         if(logger.isDebugEnabled()) {
 156                                 logger.debug("  #" + container.hashCode() + " end of sub thread to update ...");
 157                             }
 158                                                 }
 159                                         });
 160                                         if(logger.isDebugEnabled()) {
 161                         logger.debug("  #" + container.hashCode() + " done");
 162                     }
 163                                         monitor.worked(1);
 164                                 }
 165
 166                         }finally{
 167                                 monitor.done();
 168                         }
 169                         return Status.OK_STATUS;
 170                 }
 171         }
 172
 173         /** Constant <code>ID="eu.etaxonomy.taxeditor.store.datasource"{trunked}</code> */
 174         public static String ID = "eu.etaxonomy.taxeditor.view.datasource";
 175
 176         private TableViewer viewer;
 177
 178         private String partNameCache;
 179
 180         private IWorkbenchSiteProgressService service;
 181
 182         private IContextListener contextListener;
 183
 184         private CdmDataSourceViewerComparator comparator;
 185
 186         /**
 187          * <p>Constructor for CdmDataSourceViewPart.</p>
 188          */
 189         public CdmDataSourceViewPart(){
 190         }
 191
 192         private void librAlignInit(Composite parent){
 193             ScrolledComposite scrolledComposite = new ScrolledComposite(parent, SWT.BORDER | SWT.H_SCROLL | SWT.V_SCROLL);
 194         scrolledComposite.setExpandHorizontal(true);
 195         scrolledComposite.setExpandVertical(true);
 196
 197         Alignment<DNASequence, NucleotideCompound> alignment =
 198                 new SimpleAlignment<DNASequence, NucleotideCompound>();
 199         alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));
 200         alignment.add("Sequence 2", new DNASequence("AT-GTTG"));
 201         alignment.add("Sequence 3", new DNASequence("AT-GTAG"));
 202
 203         BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =
 204                 new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
 205                         new BioJavaTokenSet<NucleotideCompound>(
 206                                 AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
 207                         alignment);
 208
 209         AlignmentArea result = new AlignmentArea();
 210         result.setSequenceProvider(sequenceProvider, false);
 211         result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
 212
 213 //        Composite alignmentWidget = result.createSWTWidget(scrolledComposite, SWT.NONE);
 214 //        scrolledComposite.setContent(alignmentWidget);
 215 //        scrolledComposite.setMinSize(alignmentWidget.computeSize(SWT.DEFAULT, SWT.DEFAULT));
 216
 217         //+++ConsensusSequenceArea
 218         ConsensusSequenceArea consensusSequenceArea = new ConsensusSequenceArea(result);
 219         Composite consensusWidget = consensusSequenceArea.createSWTWidget(scrolledComposite, SWT.NONE);
 220         scrolledComposite.setContent(consensusWidget);
 221
 222
 223         //+++PherogramTraceCurveView+++
 224         PherogramTraceCurveView pherogramView = new PherogramTraceCurveView();
 225         //      pherogramView.setProvider(new BioJavaPherogramProvider(ChromatogramFactory.create(
 226         //      new File("data\\pherograms\\Test_pel1PCR_Pel2Wdhg_PCR-7-A_1.ab1"))));
 227         try {
 228             pherogramView.setProvider(new BioJavaPherogramProvider(ChromatogramFactory.create(
 229                     new File("/home/pplitzner/svn/branch/taxeditor-3.4/eu.etaxonomy.taxeditor.store/lib/jfreechart-1.0.17/lib/A10001_GM106-petD_F.scf"))));
 230         } catch (UnsupportedChromatogramFormatException e) {
 231             // TODO Auto-generated catch block
 232             e.printStackTrace();
 233         } catch (IOException e) {
 234             // TODO Auto-generated catch block
 235             e.printStackTrace();
 236         }
 237         pherogramView.setHorizontalScale(1);
 238         pherogramView.setVerticalScale(100);
 239         pherogramView.getFormats().setQualityOutputType(QualityOutputType.ALL);
 240         pherogramView.getFormats().setShowProbabilityValues(true);
 241
 242 //        Composite pherogramWidget = pherogramView.createSWTWidget(scrolledComposite, SWT.NONE);
 243 //        scrolledComposite.setContent(pherogramWidget);
 244 //        scrolledComposite.setMinSize(pherogramWidget.computeSize(SWT.DEFAULT, SWT.DEFAULT));
 245
 246         //+++Pherogramm Heading View+++
 247         PherogramHeadingView pherogramHeadingView = new PherogramHeadingView(pherogramView);
 248 //        Composite pherogramHeadingWidget = pherogramHeadingView.createSWTWidget(scrolledComposite, SWT.NONE);
 249 //        scrolledComposite.setContent(pherogramHeadingWidget);
 250 //        scrolledComposite.setMinSize(pherogramHeadingWidget.computeSize(SWT.DEFAULT, SWT.DEFAULT));
 251
 252         }
 253
 254         /** {@inheritDoc} */
 255         @Override
 256         public void createPartControl(Composite parent) {
 257                 service = (IWorkbenchSiteProgressService) getSite().getAdapter(IWorkbenchSiteProgressService.class);
 258                 contextListener = new ContextListener();
 259                 CdmStore.getContextManager().addContextListener(contextListener);
 260
 261                 // Create top composite
 262                 FillLayout fillLayout = new FillLayout();
 263                 fillLayout.marginWidth = 0;
 264                 fillLayout.marginHeight = 0;
 265                 fillLayout.type = SWT.VERTICAL;
 266                 parent.setLayout(fillLayout);
 267
 268         librAlignInit(parent);
 269
 270
 271 //              viewer = new TableViewer(parent, SWT.MULTI | SWT.H_SCROLL
 272 //                                                                                              | SWT.V_SCROLL | SWT.FULL_SELECTION);
 273 //              getSite().setSelectionProvider(viewer);
 274 //
 275 //              createColumns(viewer);
 276 //
 277 //              viewer.setContentProvider(new CdmDataSourceContentProvider());
 278 //              viewer.setLabelProvider(new CdmDataSourceLabelProvider());
 279 //              comparator = new CdmDataSourceViewerComparator();
 280 //              viewer.setComparator(comparator);
 281 //
 282 //
 283 //              // register context menu
 284 //              MenuManager menuMgr = new MenuManager();
 285 //              menuMgr.add(new GroupMarker(IWorkbenchActionConstants.MB_ADDITIONS));
 286 //              getSite().registerContextMenu(menuMgr, viewer);
 287 //
 288 //              Control control = viewer.getControl();
 289 //              Menu menu = menuMgr.createContextMenu(control);
 290 //              control.setMenu(menu);
 291 //
 292 //              // connect on doubleclick
 293 //              viewer.addDoubleClickListener(new IDoubleClickListener() {
 294 //
 295 //                      @Override
 296 //            public void doubleClick(DoubleClickEvent event) {
 297 //                              if (event.getSelection() instanceof StructuredSelection) {
 298 //
 299 //                                      Object element = ((StructuredSelection) event
 300 //                                                      .getSelection()).getFirstElement();
 301 //                                      if (element instanceof CdmMetaDataAwareDataSourceContainer) {
 302 //                                              String commandId = "eu.etaxonomy.taxeditor.store.datasource.change";
 303 //
 304 //                                              ICommandService commandService = (ICommandService)getSite().getService(ICommandService.class);
 305 //
 306 //                                              Command command = commandService.getCommand(commandId);
 307 //                                              if(command.isEnabled()) {
 308 //
 309 //                                                      IHandlerService handlerService = (IHandlerService) AbstractUtility.getService(IHandlerService.class);
 310 //
 311 //                                                      try {
 312 //                                                              handlerService.executeCommand(commandId, null);
 313 //                                                      } catch (ExecutionException e) {
 314 //                                                              AbstractUtility.error(this.getClass(), e);
 315 //                                                      } catch (NotDefinedException e) {
 316 //                                                              AbstractUtility.error(this.getClass(), e);
 317 //                                                      } catch (NotEnabledException e) {
 318 //                                                              AbstractUtility.error(this.getClass(), e);
 319 //                                                      } catch (NotHandledException e) {
 320 //                                                              AbstractUtility.error(this.getClass(), e);
 321 //                                                      }
 322 //                                              }
 323 //                                      }
 324 //                              }
 325 //                      }
 326 //              });
 327 //
 328 //              refresh();
 329         }
 330
 331
 332         // This will create the columns for the table
 333         private void createColumns(TableViewer viewer) {
 334                 Table table = viewer.getTable();
 335                 String[] titles = {"Connected", "Name", "Server", "Up", "Type", "Database", "Nomenclatural Code", "Created", "CDM Version", "Compatible", "Notes"};
 336                 int[] bounds = { 24, 200, 100, 50 , 80, 120, 50, 100, 100, 50, 300};
 337
 338                 for (int i = 0; i < titles.length; i++) {
 339                         TableViewerColumn column = new TableViewerColumn(viewer, SWT.NONE);
 340                         column.getColumn().setText(titles[i]);
 341                         column.getColumn().setWidth(bounds[i]);
 342                         column.getColumn().setResizable(true);
 343                         column.getColumn().setMoveable(true);
 344                         column.getColumn().addSelectionListener(getSelectionAdapter(column.getColumn(), i));
 345                         if(i == 1){
 346                                 table.setSortColumn(column.getColumn());
 347                         }
 348                 }
 349                 table.setHeaderVisible(true);
 350                 table.setLinesVisible(true);
 351                 table.setSortDirection(SWT.UP);
 352
 353         }
 354
 355         /**
 356          * <p>refresh</p>
 357          */
 358         public void refresh(){
 359                 getService().schedule(new DataSourceJob("Loading datasources", CdmDataSourceRepository.getAll()), Job.LONG);
 360         }
 361
 362         /** {@inheritDoc} */
 363         @Override
 364         public void dispose() {
 365                 CdmStore.getContextManager().removeContextListener(contextListener);
 366                 super.dispose();
 367         }
 368
 369         /** {@inheritDoc} */
 370         @Override
 371         public void setFocus() {
 372 //              viewer.getControl().setFocus();
 373         }
 374
 375
 376         /* (non-Javadoc)
 377          * @see org.eclipse.ui.part.WorkbenchPart#showBusy(boolean)
 378          */
 379         /** {@inheritDoc} */
 380         @Override
 381         public void showBusy(boolean busy) {
 382                 super.showBusy(busy);
 383 //              viewer.getTable().setEnabled(!busy);
 384                 if(busy){
 385                         partNameCache = getPartName();
 386                         setPartName("Loading datasources");
 387                 }else{
 388                         if(partNameCache != null){
 389                                 setPartName(partNameCache);
 390                         }
 391                 }
 392         }
 393
 394         /**
 395          * <p>Getter for the field <code>viewer</code>.</p>
 396          *
 397          * @return a {@link org.eclipse.jface.viewers.StructuredViewer} object.
 398          */
 399         public StructuredViewer getViewer() {
 400                 return viewer;
 401         }
 402
 403         /**
 404          * <p>Getter for the field <code>service</code>.</p>
 405          *
 406          * @return the service
 407          */
 408         public IWorkbenchSiteProgressService getService() {
 409                 return service;
 410         }
 411
 412         private SelectionAdapter getSelectionAdapter(final TableColumn column,
 413                         final int index) {
 414                 SelectionAdapter selectionAdapter = new SelectionAdapter() {
 415                         @Override
 416                         public void widgetSelected(SelectionEvent e) {
 417                                 comparator.setColumn(index);
 418                                 int dir = viewer.getTable().getSortDirection();
 419                                 if (viewer.getTable().getSortColumn() == column) {
 420                                         dir = dir == SWT.UP ? SWT.DOWN : SWT.UP;
 421                                 } else {
 422                                         dir = SWT.DOWN;
 423                                 }
 424                                 viewer.getTable().setSortDirection(dir);
 425                                 viewer.getTable().setSortColumn(column);
 426                                 viewer.refresh();
 427                         }
 428                 };
 429                 return selectionAdapter;
 430         }
 431
 432 }