eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/e4/handler/ExportSequenceToFileHandlerE4.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.editor.e4.handler;
  11
  12
  13 import java.io.File;
  14 import java.io.IOException;
  15
  16 import javax.inject.Named;
  17
  18 import org.eclipse.core.runtime.IStatus;
  19 import org.eclipse.e4.core.di.annotations.CanExecute;
  20 import org.eclipse.e4.core.di.annotations.Execute;
  21 import org.eclipse.e4.core.di.annotations.Optional;
  22 import org.eclipse.e4.ui.model.application.ui.menu.MHandledMenuItem;
  23 import org.eclipse.e4.ui.services.IServiceConstants;
  24 import org.eclipse.jface.viewers.IStructuredSelection;
  25 import org.eclipse.jface.viewers.TreeNode;
  26 import org.eclipse.jface.wizard.WizardDialog;
  27 import org.eclipse.swt.widgets.Shell;
  28
  29 import eu.etaxonomy.cdm.model.molecular.Sequence;
  30 import eu.etaxonomy.taxeditor.model.MessagingUtils;
  31 import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
  32 import eu.etaxonomy.taxeditor.molecular.io.CDMPherogramAlignmentObjectTranslator;
  33 import eu.etaxonomy.taxeditor.molecular.io.CDMSequenceMatrixAdapter;
  34 import eu.etaxonomy.taxeditor.molecular.io.SingleReadAlignmentRDFXMLConstants;
  35 import eu.etaxonomy.taxeditor.molecular.io.wizard.ExportSingleReadAlignmentWizard;
  36 import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
  37 import eu.etaxonomy.taxeditor.util.ApplicationUtil;
  38 import info.bioinfweb.jphyloio.JPhyloIOEventWriter;
  39 import info.bioinfweb.jphyloio.ReadWriteParameterMap;
  40 import info.bioinfweb.jphyloio.ReadWriteParameterNames;
  41 import info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter;
  42 import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;
  43 import info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory;
  44
  45
  46
  47 /**
  48  * Allows to export a single read alignment to various alignment formats using
  49  * <a href="http://bioinfweb.info/JPhyloIO/"><i>JPhyloIO</i></a>.
  50  *
  51  * @author Ben Stöver
  52  * @date 24.04.2016
  53  */
  54 public class ExportSequenceToFileHandlerE4 {
  55     private static final JPhyloIOReaderWriterFactory factory = new JPhyloIOReaderWriterFactory();
  56
  57
  58     @Execute
  59     public void execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)IStructuredSelection selection,
  60             @Named(IServiceConstants.ACTIVE_SHELL)Shell shell) {
  61         Sequence sequence = (Sequence) ((TreeNode) selection.getFirstElement()).getValue();
  62
  63         final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard();
  64         final WizardDialog dialog = new WizardDialog(shell, 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, "https://cybertaxonomy.org/taxeditor/");  //TODO Specify URL obtained from a central class? //$NON-NLS-1$
  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
 104     @CanExecute
 105     public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) IStructuredSelection selection, MHandledMenuItem menuItem) {
 106         boolean canExecute = false;
 107         canExecute = selection.size()==1
 108                 && selection.getFirstElement() instanceof TreeNode
 109                 && ((TreeNode) selection.getFirstElement()).getValue() instanceof Sequence;
 110         menuItem.setVisible(canExecute);
 111         return canExecute;
 112     }
 113 }