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.editor.e4.handler;

import java.io.File;

import java.io.IOException;

import javax.inject.Named;

import org.eclipse.core.runtime.IStatus;

import org.eclipse.e4.core.di.annotations.CanExecute;

import org.eclipse.e4.core.di.annotations.Execute;

import org.eclipse.e4.core.di.annotations.Optional;

import org.eclipse.e4.ui.model.application.ui.menu.MHandledMenuItem;

import org.eclipse.e4.ui.services.IServiceConstants;

import org.eclipse.jface.viewers.IStructuredSelection;

import org.eclipse.jface.viewers.TreeNode;

import org.eclipse.jface.wizard.WizardDialog;

import org.eclipse.swt.widgets.Shell;

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

import eu.etaxonomy.taxeditor.model.MessagingUtils;

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.molecular.l10n.Messages;

import eu.etaxonomy.taxeditor.util.ApplicationUtil;

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;

/**

 * 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 ExportSequenceToFileHandlerE4 {

    private static final JPhyloIOReaderWriterFactory factory = new JPhyloIOReaderWriterFactory();

    @Execute

    public void execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)IStructuredSelection selection,

            @Named(IServiceConstants.ACTIVE_SHELL)Shell shell) {

        Sequence sequence = (Sequence) ((TreeNode) selection.getFirstElement()).getValue();

        final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard();

        final WizardDialog dialog = new WizardDialog(shell, 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? //$NON-NLS-1$

            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);

                }

            }

        }

    }

    @CanExecute

    public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) IStructuredSelection selection, MHandledMenuItem menuItem) {

        boolean canExecute = false;

        canExecute = selection.size()==1

                && selection.getFirstElement() instanceof TreeNode

                && ((TreeNode) selection.getFirstElement()).getValue() instanceof Sequence;

        menuItem.setVisible(canExecute);

        return canExecute;

    }

}