eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/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.editor.handler;
  10
  11
  12 import info.bioinfweb.libralign.AlignmentArea;
  13 import info.bioinfweb.libralign.AlignmentContentArea;
  14 import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
  15 import info.bioinfweb.libralign.pherogram.BioJavaPherogramProvider;
  16 import info.bioinfweb.libralign.sequenceprovider.SequenceDataProvider;
  17
  18 import java.io.File;
  19 import java.io.IOException;
  20
  21 import org.biojava.bio.chromatogram.ChromatogramFactory;
  22 import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
  23 import org.eclipse.core.commands.AbstractHandler;
  24 import org.eclipse.core.commands.ExecutionEvent;
  25 import org.eclipse.core.commands.ExecutionException;
  26 import org.eclipse.swt.widgets.FileDialog;
  27 import org.eclipse.ui.IEditorPart;
  28
  29 import eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor;
  30 import eu.etaxonomy.taxeditor.model.AbstractUtility;
  31 import eu.etaxonomy.taxeditor.model.MessagingUtils;
  32
  33
  34
  35 /**
  36  * Handler that loads an additional read into the contig alignment displayed by an instance of {@link AlignmentEditor}.
  37  *
  38  * @author Ben Stöver
  39  * @author pplitzner
  40  * @date 16.10.2014
  41  */
  42 public class LoadPherogramHandler extends AbstractHandler {
  43         public static final String DEFAULT_READ_NAME_PREFIX = "Read ";
  44
  45
  46         private String newReadName(SequenceDataProvider provider) {
  47                 int index = 1;
  48                 while (provider.sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index) != SequenceDataProvider.NO_SEQUENCE_FOUND) {
  49                         index++;
  50                 }
  51                 return DEFAULT_READ_NAME_PREFIX + index;
  52         }
  53
  54
  55         private void addPherogram(AlignmentContentArea contentArea, File pherogram)
  56                         throws IOException, UnsupportedChromatogramFormatException {
  57
  58                 SequenceDataProvider provider = contentArea.getSequenceProvider();
  59                 BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(pherogram));  // Must happen before a sequence is added, because it might throw an exception.
  60                 String name = newReadName(provider);
  61
  62         // Create sequence:
  63                 provider.addSequence(name);
  64                 int id = provider.sequenceIDByName(name);
  65
  66                 // Copy base call sequence into alignment:
  67                 for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {
  68                         provider.insertTokenAt(id, i, provider.getTokenSet().tokenByKeyChar(
  69                                         pherogramProvider.getBaseCall(i).getUpperedBase().charAt(0)));
  70                 }
  71
  72                 // Add data area:
  73                 PherogramArea pherogramArea = new PherogramArea(contentArea, pherogramProvider);
  74                 contentArea.getDataAreas().getSequenceAreas(id).add(pherogramArea);
  75         }
  76
  77
  78     /* (non-Javadoc)
  79      * @see org.eclipse.core.commands.IHandler#execute(org.eclipse.core.commands.ExecutionEvent)
  80      */
  81     @Override
  82     public Object execute(ExecutionEvent event) throws ExecutionException {
  83         IEditorPart activeEditor = AbstractUtility.getActiveEditor();
  84         if (activeEditor instanceof AlignmentEditor) {
  85             AlignmentEditor alignmentEditor = (AlignmentEditor)activeEditor;
  86
  87             FileDialog fileDialog = new FileDialog(alignmentEditor.getSite().getShell());
  88             fileDialog.setText("Import pherogram into contig alignment");
  89             fileDialog.setFilterNames(new String[]{"All supported formats", "AB1 pherogram files", "SCF pherogram files", "All files"});
  90             fileDialog.setFilterExtensions(new String[]{"*.ab1;*.scf", "*.ab1", "*.scf", "*.*"});
  91
  92             String path = fileDialog.open();
  93             if (path != null) {
  94                 try {
  95                         addPherogram(alignmentEditor.getReadsArea().getContentArea(), new File(path));
  96                 }
  97                 catch (UnsupportedChromatogramFormatException e) {
  98                     MessagingUtils.errorDialog("Unsupported format", this, "The format of the pherogram file \"" + path +
  99                                 "\" is not supported. (Only AB1 and SCF are supported.)", "eu.etaxonomy.taxeditor.editor", e, false);  //TODO set pluginID
 100                 }
 101                 catch (IOException e) {
 102                     MessagingUtils.errorDialog("Unsupported format", this,
 103                                 "An IO error occurred while trying to read the file \"" + path + "\".",
 104                                 "/eu.etaxonomy.taxeditor.editor", e, false);  //TODO set pluginID
 105                 }
 106             }
 107         }
 108         return null;
 109     }
 110 }