EDIT

// $Id$

/**

* 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.ReadWriteParameterNames;

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

import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;

import info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory;

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.core.runtime.IStatus;

import org.eclipse.jface.viewers.ISelection;

import org.eclipse.jface.viewers.TreeNode;

import org.eclipse.jface.wizard.WizardDialog;

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.Messages;

import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;

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

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

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

import eu.etaxonomy.taxeditor.molecular.io.wizard.ExportSingleReadAlignmentWizard;

import eu.etaxonomy.taxeditor.util.ApplicationUtil;

/**

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

 * <a href="http://bioinfweb.info/JPhyloIO/"><i>JPhyloIO</i></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();

            final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard();

            final WizardDialog dialog = new WizardDialog(HandlerUtil.getActiveShell(event), wizard);

            if (dialog.open() == IStatus.OK) {

                // Prepare writer parameters:

                ReadWriteParameterMap parameters = new ReadWriteParameterMap();

                parameters.put(ReadWriteParameterNames.KEY_APPLICATION_NAME, ApplicationUtil.getTitle());

                //parameters.put(ReadWriteParameterNames.KEY_APPLICATION_VERSION, ApplicationUtil.getVersion());  // Setting the version unnecessary, since its already contained in the title.

                parameters.put(ReadWriteParameterNames.KEY_APPLICATION_URL, "http://cybertaxonomy.eu/taxeditor/");  //TODO Specify URL obtained from a central class?

                parameters.put(ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN, wizard.getModel().getElongationToken());

                // Create and register object translator for writing pherogram alignment shifts:

                ObjectTranslatorFactory translatorFactory = new ObjectTranslatorFactory();

                translatorFactory.addXSDTranslators(true);

                translatorFactory.addTranslator(new CDMPherogramAlignmentObjectTranslator(), true, SingleReadAlignmentRDFXMLConstants.DATA_TYPE_PHERORAGM_ALIGNMENT);

                parameters.put(ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY, translatorFactory);

                // Create writer and document adapters:

                JPhyloIOEventWriter writer = factory.getWriter(wizard.getModel().getFormatInfo().getFormatID());

                ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();

                document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getModel().getConsensusSequenceLabel(),

                        wizard.getModel().isExportConsensusSequence(), wizard.getModel().isExportSingleReads()));

                // Write document:

                File file = new File(wizard.getModel().getFileName());

                if (!file.exists() || MessagingUtils.confirmDialog(Messages.exportSequenceToFileHandlerOverwriteTitle, String.format(

                        Messages.exportSequenceToFileHandlerOverwriteText, file.getAbsolutePath()))) {

                    try {

                        writer.writeDocument(document, file, parameters);

                    }

                    catch (IOException e) {

                        e.printStackTrace();

                        MessagingUtils.errorDialog(Messages.exportSequenceToFileHandlerIOErrorTitle, this,

                                String.format(Messages.exportSequenceToFileHandlerIOErrorMessage,

                                        file.getAbsolutePath()), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);

                    }

                }

            }

        }

        return null;

    }

}