EDIT

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

command.name.EXPORT_SEQUENCE_TO_FILE = Export to alignment file

command.label.EXPORT_SEQUENCE_TO_FILE = Export to alignment file

command.name.EXPORT_SEQUENCE_TO_FILE = Alignmentdatei exportieren

command.label.EXPORT_SEQUENCE_TO_FILE = Alignmentdatei exportieren

         <command

               defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler"

               id="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile"

               name="%command.name.EXPORT_SEQUENCE_TO_FILE">

         </command>

            <command

                  commandId="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile"

                  label="%command.label.EXPORT_SEQUENCE_TO_FILE"

                  style="push">

               <visibleWhen

                     checkEnabled="true">

                  <reference

                        definitionId="isSequence">

                  </reference>

               </visibleWhen>

            </command>

// $Id$

/**

* Copyright (C) 2016 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.taxeditor.molecular.handler;

import info.bioinfweb.jphyloio.JPhyloIOEventWriter;

import info.bioinfweb.jphyloio.ReadWriteParameterMap;

import info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter;

import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;

import info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs;

import java.io.File;

import java.io.IOException;

import org.eclipse.core.commands.AbstractHandler;

import org.eclipse.core.commands.ExecutionEvent;

import org.eclipse.core.commands.ExecutionException;

import org.eclipse.jface.viewers.ISelection;

import org.eclipse.jface.viewers.TreeNode;

import org.eclipse.ui.handlers.HandlerUtil;

import eu.etaxonomy.cdm.model.molecular.Sequence;

import eu.etaxonomy.taxeditor.editor.EditorUtil;

import eu.etaxonomy.taxeditor.model.MessagingUtils;

import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;

import eu.etaxonomy.taxeditor.molecular.io.CDMSequenceMatrixAdapter;

/**

 * Allows to exports a single read alignment to various alignment formats using

 * <a href="http://bioinfweb.info/JPhyloIO/">JPhyloIO</a>.

 *

 * @author Ben Stöver

 * @date 24.04.2016

 */

public class ExportSequenceToFileHandler extends AbstractHandler {

    private static final JPhyloIOReaderWriterFactory factory = new JPhyloIOReaderWriterFactory();

    @Override

    public Object execute(ExecutionEvent event) throws ExecutionException {

        ISelection currentSelection = HandlerUtil.getCurrentSelection(event);

        TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);

        if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence) {

            Sequence sequence = (Sequence)treeNodeOfSelection.getValue();

            //TODO Collect the following information using a wizard.

            File targetFile = new File("O:\\Projects\\Bereich BBI\\EDIT Campanula\\Testdaten\\NeXMLExport.xml");

            String formatID = JPhyloIOFormatIDs.NEXML_FORMAT_ID;

            ReadWriteParameterMap parameters = new ReadWriteParameterMap();

            String consensusSequenceLabel = "Consensus sequence";

            JPhyloIOEventWriter writer = factory.getWriter(formatID);

            ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();

            document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, consensusSequenceLabel));

            try {

                writer.writeDocument(document, targetFile, parameters);

            }

            catch (IOException e) {

                e.printStackTrace();

                MessagingUtils.errorDialog("IO error", this,

                        "An error occured when trying to export a consensus sequence alignment to the file \"" +

                        targetFile.getAbsolutePath() + "\".", TaxeditorMolecularPlugin.PLUGIN_ID, e, false);  //TODO set pluginID

                        //TODO Use multi language error message.

            }

        }

        return null;

    }

}