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

   1 // $Id$
   2 /**
   3 * Copyright (C) 2016 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 package eu.etaxonomy.taxeditor.molecular.handler;
  11
  12
  13 import info.bioinfweb.jphyloio.JPhyloIOEventWriter;
  14 import info.bioinfweb.jphyloio.ReadWriteParameterMap;
  15 import info.bioinfweb.jphyloio.ReadWriteParameterNames;
  16 import info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter;
  17 import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;
  18 import info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory;
  19
  20 import java.io.File;
  21 import java.io.IOException;
  22
  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.core.runtime.IStatus;
  27 import org.eclipse.jface.viewers.ISelection;
  28 import org.eclipse.jface.viewers.TreeNode;
  29 import org.eclipse.jface.wizard.WizardDialog;
  30 import org.eclipse.ui.handlers.HandlerUtil;
  31
  32 import eu.etaxonomy.cdm.model.molecular.Sequence;
  33 import eu.etaxonomy.taxeditor.editor.EditorUtil;
  34 import eu.etaxonomy.taxeditor.model.MessagingUtils;
  35 import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
  36 import eu.etaxonomy.taxeditor.molecular.io.CDMPherogramAlignmentObjectTranslator;
  37 import eu.etaxonomy.taxeditor.molecular.io.CDMSequenceMatrixAdapter;
  38 import eu.etaxonomy.taxeditor.molecular.io.SingleReadAlignmentRDFXMLConstants;
  39 import eu.etaxonomy.taxeditor.molecular.io.wizard.ExportSingleReadAlignmentWizard;
  40
  41
  42
  43 /**
  44  * Allows to export a single read alignment to various alignment formats using
  45  * <a href="http://bioinfweb.info/JPhyloIO/">JPhyloIO</a>.
  46  *
  47  * @author Ben Stöver
  48  * @date 24.04.2016
  49  */
  50 public class ExportSequenceToFileHandler extends AbstractHandler {
  51     private static final JPhyloIOReaderWriterFactory factory = new JPhyloIOReaderWriterFactory();
  52
  53
  54     @Override
  55     public Object execute(ExecutionEvent event) throws ExecutionException {
  56         ISelection currentSelection = HandlerUtil.getCurrentSelection(event);
  57         TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);
  58         if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence) {
  59             Sequence sequence = (Sequence)treeNodeOfSelection.getValue();
  60
  61             final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard();
  62             final WizardDialog dialog = new WizardDialog(HandlerUtil.getActiveShell(event), wizard);
  63             if (dialog.open() == IStatus.OK) {  //TODO Is the window disposed?
  64                 // Prepare writer parameters:
  65                 ReadWriteParameterMap parameters = new ReadWriteParameterMap();
  66                 ObjectTranslatorFactory translatorFactory = new ObjectTranslatorFactory();
  67                 translatorFactory.addXSDTranslators(true);
  68                 translatorFactory.addTranslator(new CDMPherogramAlignmentObjectTranslator(), true, SingleReadAlignmentRDFXMLConstants.DATA_TYPE_PHERORAGM_ALIGNMENT);
  69                 parameters.put(ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY, translatorFactory);
  70
  71                 // Create writer and document adapters:
  72                 JPhyloIOEventWriter writer = factory.getWriter(wizard.getModel().getFormatInfo().getFormatID());
  73                 ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();
  74                 document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getModel().getConsensusSequenceLabel()));
  75
  76                 // Write document:
  77                 File file = new File(wizard.getModel().getFileName());
  78                 try {
  79                     writer.writeDocument(document, file, parameters);
  80                 }
  81                 catch (IOException e) {
  82                     e.printStackTrace();
  83                     MessagingUtils.errorDialog("IO error", this,
  84                             "An error occured when trying to export a consensus sequence alignment to the file \"" +
  85                             file.getAbsolutePath() + "\".", TaxeditorMolecularPlugin.PLUGIN_ID, e, false);  //TODO set pluginID
  86                             //TODO Use multi language error message.
  87                 }
  88             }
  89         }
  90         return null;
  91     }
  92 }