eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ShowPherogramHandler.java

   1 package eu.etaxonomy.taxeditor.molecular.handler;
   2
   3
   4 import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;
   5
   6 import java.net.URI;
   7
   8 import org.eclipse.core.commands.AbstractHandler;
   9 import org.eclipse.core.commands.ExecutionEvent;
  10 import org.eclipse.core.commands.ExecutionException;
  11 import org.eclipse.jface.viewers.ISelection;
  12 import org.eclipse.jface.viewers.TreeNode;
  13 import org.eclipse.ui.PartInitException;
  14 import org.eclipse.ui.handlers.HandlerUtil;
  15
  16 import eu.etaxonomy.cdm.model.media.MediaUtils;
  17 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  18 import eu.etaxonomy.taxeditor.editor.EditorUtil;
  19 import eu.etaxonomy.taxeditor.model.MessagingUtils;
  20 import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
  21 import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
  22 import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;
  23
  24
  25
  26 /**
  27  * Displays an undistorted pherogram with {@link PherogramViewPart}.
  28  *
  29  * @author Ben Stöver
  30  *
  31  */
  32 public class ShowPherogramHandler extends AbstractHandler {
  33         public static void showPherogram(PherogramComponentModel model) throws PartInitException {
  34                 PherogramViewPart.createView(model);
  35         }
  36
  37
  38         @Override
  39         public Object execute(ExecutionEvent event) throws ExecutionException {
  40                 ISelection currentSelection = HandlerUtil.getCurrentSelection(event);
  41                 TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);
  42                 if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof SingleRead) {
  43                     //TODO Can the parent node (containing the cut positions) be extracted from SingleRead?
  44                         try {
  45                             SingleRead singleRead = (SingleRead)treeNodeOfSelection.getValue();
  46                             URI uri = null;
  47                             if (singleRead.getPherogram() != null) {  // Pherogram objects without URI are possible.
  48                                 uri = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri();
  49                             }
  50
  51                             if (uri == null) {
  52                         MessagingUtils.messageDialog("No pherogram available", this,
  53                                 "The selected read does not have an associated pherogram.");
  54                             }
  55                             else {
  56                       showPherogram(new PherogramComponentModel(AlignmentEditor.readPherogram(uri)));
  57                             }
  58                         }
  59                 catch (Exception e) {
  60                     MessagingUtils.errorDialog("Error", null, e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID,
  61                             e, false);
  62                 }
  63         }
  64         return null;
  65     }
  66 }