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.Messages;
  36 import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
  37 import eu.etaxonomy.taxeditor.molecular.io.CDMPherogramAlignmentObjectTranslator;
  38 import eu.etaxonomy.taxeditor.molecular.io.CDMSequenceMatrixAdapter;
  39 import eu.etaxonomy.taxeditor.molecular.io.SingleReadAlignmentRDFXMLConstants;
  40 import eu.etaxonomy.taxeditor.molecular.io.wizard.ExportSingleReadAlignmentWizard;
  41 import eu.etaxonomy.taxeditor.util.ApplicationUtil;
  42
  43
  44
  45 /**
  46  * Allows to export a single read alignment to various alignment formats using
  47  * <a href="http://bioinfweb.info/JPhyloIO/"><i>JPhyloIO</i></a>.
  48  *
  49  * @author Ben Stöver
  50  * @date 24.04.2016
  51  */
  52 public class ExportSequenceToFileHandler extends AbstractHandler {
  53     private static final JPhyloIOReaderWriterFactory factory = new JPhyloIOReaderWriterFactory();
  54
  55
  56     @Override
  57     public Object execute(ExecutionEvent event) throws ExecutionException {
  58         ISelection currentSelection = HandlerUtil.getCurrentSelection(event);
  59         TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);
  60         if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence) {
  61             Sequence sequence = (Sequence)treeNodeOfSelection.getValue();
  62
  63             final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard();
  64             final WizardDialog dialog = new WizardDialog(HandlerUtil.getActiveShell(event), wizard);
  65             if (dialog.open() == IStatus.OK) {
  66                 // Prepare writer parameters:
  67                 ReadWriteParameterMap parameters = new ReadWriteParameterMap();
  68                 parameters.put(ReadWriteParameterNames.KEY_APPLICATION_NAME, ApplicationUtil.getTitle());
  69                 //parameters.put(ReadWriteParameterNames.KEY_APPLICATION_VERSION, ApplicationUtil.getVersion());  // Setting the version unnecessary, since its already contained in the title.
  70                 parameters.put(ReadWriteParameterNames.KEY_APPLICATION_URL, "http://cybertaxonomy.eu/taxeditor/");  //TODO Specify URL obtained from a central class?
  71                 parameters.put(ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN, wizard.getModel().getElongationToken());
  72
  73                 // Create and register object translator for writing pherogram alignment shifts:
  74                 ObjectTranslatorFactory translatorFactory = new ObjectTranslatorFactory();
  75                 translatorFactory.addXSDTranslators(true);
  76                 translatorFactory.addTranslator(new CDMPherogramAlignmentObjectTranslator(), true, SingleReadAlignmentRDFXMLConstants.DATA_TYPE_PHERORAGM_ALIGNMENT);
  77                 parameters.put(ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY, translatorFactory);
  78
  79                 // Create writer and document adapters:
  80                 JPhyloIOEventWriter writer = factory.getWriter(wizard.getModel().getFormatInfo().getFormatID());
  81                 ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();
  82                 document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getModel().getConsensusSequenceLabel(),
  83                         wizard.getModel().isExportConsensusSequence(), wizard.getModel().isExportSingleReads()));
  84
  85                 // Write document:
  86                 File file = new File(wizard.getModel().getFileName());
  87                 if (!file.exists() || MessagingUtils.confirmDialog(Messages.exportSequenceToFileHandlerOverwriteTitle, String.format(
  88                         Messages.exportSequenceToFileHandlerOverwriteText, file.getAbsolutePath()))) {
  89
  90                     try {
  91                         writer.writeDocument(document, file, parameters);
  92                     }
  93                     catch (IOException e) {
  94                         e.printStackTrace();
  95                         MessagingUtils.errorDialog(Messages.exportSequenceToFileHandlerIOErrorTitle, this,
  96                                 String.format(Messages.exportSequenceToFileHandlerIOErrorMessage,
  97                                         file.getAbsolutePath()), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);
  98                     }
  99                 }
 100
 101             }
 102         }
 103         return null;
 104     }
 105 }