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

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.taxeditor.molecular.handler;
  10
  11
  12 import java.io.File;
  13 import java.io.IOException;
  14
  15 import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
  16 import org.eclipse.core.commands.AbstractHandler;
  17 import org.eclipse.core.commands.ExecutionEvent;
  18 import org.eclipse.core.commands.ExecutionException;
  19 import org.eclipse.swt.widgets.FileDialog;
  20 import org.eclipse.ui.IEditorPart;
  21
  22 import eu.etaxonomy.taxeditor.model.AbstractUtility;
  23 import eu.etaxonomy.taxeditor.model.MessagingUtils;
  24 import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
  25 import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
  26
  27
  28
  29 /**
  30  * Handler that loads an additional read into the contig alignment displayed by an instance of {@link AlignmentEditor}.
  31  *
  32  * @author Ben Stöver
  33  * @author pplitzner
  34  */
  35 public class LoadPherogramHandler extends AbstractHandler {
  36         //TODO Change so that also URIs which do not point to files can be specified.
  37
  38         /* (non-Javadoc)
  39      * @see org.eclipse.core.commands.IHandler#execute(org.eclipse.core.commands.ExecutionEvent)
  40      */
  41     @Override
  42     public Object execute(ExecutionEvent event) throws ExecutionException {
  43         IEditorPart activeEditor = AbstractUtility.getActiveEditor();
  44         if (activeEditor instanceof AlignmentEditor) {
  45             AlignmentEditor alignmentEditor = (AlignmentEditor)activeEditor;
  46
  47             FileDialog fileDialog = new FileDialog(alignmentEditor.getSite().getShell());
  48             fileDialog.setText("Import pherogram into contig alignment");
  49             fileDialog.setFilterNames(new String[]{"All supported formats", "AB1 pherogram files", "SCF pherogram files", "All files"});
  50             fileDialog.setFilterExtensions(new String[]{"*.ab1;*.scf", "*.ab1", "*.scf", "*.*"});
  51
  52             String path = fileDialog.open();
  53             if (path != null) {
  54                 try {
  55                         alignmentEditor.addRead(new File(path).toURI(), false);
  56                 }
  57                 catch (UnsupportedChromatogramFormatException e) {
  58                     MessagingUtils.errorDialog("Unsupported format", this, "The format of the pherogram file \"" + path +
  59                                 "\" is not supported. (Only AB1 and SCF are supported.)", TaxeditorMolecularPlugin.PLUGIN_ID, e, false);  //TODO set pluginID
  60                 }
  61                 catch (IOException e) {
  62                     MessagingUtils.errorDialog("Unsupported format", this,
  63                                 "An IO error occurred while trying to read the file \"" + path + "\".",
  64                                 TaxeditorMolecularPlugin.PLUGIN_ID, e, false);  //TODO set pluginID
  65                 }
  66             }
  67         }
  68         return null;
  69     }
  70 }