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

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