EDIT

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

eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java -text

eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/SequenceIDIterator.java -text

 eu.etaxonomy.taxeditor.molecular.handler,

 eu.etaxonomy.taxeditor.molecular.io

// $Id$

/**

* 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 ExportSingleReadAlignmentHandler 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;

    }

}

// $Id$

/**

* 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.io;

import info.bioinfweb.commons.text.StringUtils;

import info.bioinfweb.jphyloio.ReadWriteConstants;

import info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver;

import info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter;

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

import info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent;

import info.bioinfweb.jphyloio.events.SequenceTokensEvent;

import info.bioinfweb.jphyloio.events.type.EventContentType;

import java.io.IOException;

import java.util.Iterator;

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

/**

 * In implementation of {@link MatrixDataAdapter} that delegates to a {@link Sequence} object.

 *

 * @author Ben Stöver

 * @date 29.04.2016

 */

public class CDMSequenceMatrixAdapter extends NoSetsMatrixDataAdapter implements ReadWriteConstants {

    public static final String MATRIX_ID = DEFAULT_MATRIX_ID_PREFIX + "ContigAlignment";

    public static final String SINGLE_READ_SEQUENCE_ID_PREFIX = DEFAULT_SEQUENCE_ID_PREFIX + "SingleRead";

    public static final String CONSENSUS_SEQUENCE_ID= DEFAULT_SEQUENCE_ID_PREFIX + "Consensus";

    private Sequence sequence;

    private String consensusSequenceLabel;

    //TODO Also allow specifying single read labels?

    /**

     * Creates a new instance of this class.

     *

     * @param sequence

     * @param consensusSequenceLabel

     */

    public CDMSequenceMatrixAdapter(Sequence sequence, String consensusSequenceLabel) {

        super();

        this.sequence = sequence;

        this.consensusSequenceLabel = consensusSequenceLabel;

    }

    /**

     * @return the sequence

     */

    public Sequence getCDMSequence() {

        return sequence;

    }

    private int extractSingleReadIndexFromID(String sequenceID) {

        try {

            return Integer.parseInt(sequenceID.substring(SINGLE_READ_SEQUENCE_ID_PREFIX.length()));

        }

        catch (NumberFormatException e) {

            return -1;

        }

    }

    @Override

    public LinkedLabeledIDEvent getStartEvent() {

        return new LinkedLabeledIDEvent(EventContentType.ALIGNMENT, MATRIX_ID, "Contig alignment", null);

                //TODO Use label according to derivate and markers.

    }

    @Override

    public boolean containsLongTokens() {

        return false;

    }

    @Override

    public long getColumnCount() {

        return getCDMSequence().getSequenceString().length();  //TODO Consider that parts of single reads may lie outside of the current consensus sequence. Possibly return -1 in the future.

    }

    @Override

    public long getSequenceCount() {

        return /*sequence.getSingleReadAlignments().size() +*/ 1;

    }

    @Override

    public Iterator<String> getSequenceIDIterator() {

        return new SequenceIDIterator(getCDMSequence().getSingleReadAlignments().size());

    }

    @Override

    public long getSequenceLength(String sequenceID) throws IllegalArgumentException {

        int singleReadIndex = extractSingleReadIndexFromID(sequenceID);

        if (singleReadIndex >= 0) {

            //TODO Determine single read length. (Current problem: Reads are not ordered in the set of the Sequence object.)

            return 0;

        }

        else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {

            return getCDMSequence().getSequenceString().length();

        }

        else {

            throw new IllegalArgumentException("No sequence with the ID \"" + sequenceID + "\" could be found.");

        }

    }

    @Override

    public LinkedLabeledIDEvent getSequenceStartEvent(String sequenceID) {

        int singleReadIndex = extractSingleReadIndexFromID(sequenceID);

        if (singleReadIndex >= 0) {

            return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, "singleRead" + singleReadIndex, null);

                    //TODO Use name displayed in derivate hierarchy or specified name as label instead?

        }

        else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {

            return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, consensusSequenceLabel, null);

        }

        else {

            throw new IllegalArgumentException("No sequence with the ID \"" + sequenceID + "\" could be found.");

        }

    }

    @Override

    public void writeSequencePartContentData(JPhyloIOEventReceiver receiver, String sequenceID, long startColumn,

            long endColumn) throws IOException, IllegalArgumentException {

        int singleReadIndex = extractSingleReadIndexFromID(sequenceID);

        if (singleReadIndex >= 0) {

            //TODO Implement single read output.

        }

        else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {

            if (startColumn == 0) {

                //TODO Add consensus sequence metadata.

                //TODO Possibly export additional properties of sequence (e.g. isBarcode(), getDdbjId(), ...) as metadata.

            }

            receiver.add(new SequenceTokensEvent(StringUtils.charSequenceToStringList(

                    getCDMSequence().getSequenceString().substring((int)startColumn, (int)endColumn))));

        }

        else {

            throw new IllegalArgumentException("No sequence with the ID \"" + sequenceID + "\" could be found.");

        }

    }

}

// $Id$

/**

* 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.io;

import java.util.Iterator;

import java.util.NoSuchElementException;

/**

 * Iterator implementation used internally be {@link CDMSequenceMatrixAdapter}.

 *

 * @author Ben Stöver

 * @date 29.04.2016

 */

public class SequenceIDIterator implements Iterator<String> {

    private int singleReadPos;

    private int singleReadCount;

    /**

     * Creates a new instance of this class.

     *

     * @param singleReadCount the number of single read IDs to be returned by this iterator before the consensus sequence

     */

    public SequenceIDIterator(int singleReadCount) {

        super();

        this.singleReadCount = singleReadCount;

        this.singleReadPos = 0;

    }

    @Override

    public boolean hasNext() {

        return singleReadPos <= singleReadCount;

    }

    @Override

    public String next() {

        if (singleReadPos < singleReadCount) {

            return CDMSequenceMatrixAdapter.SINGLE_READ_SEQUENCE_ID_PREFIX + (singleReadPos++);

        }

        else if (singleReadPos == singleReadCount) {

            singleReadPos++;

            return CDMSequenceMatrixAdapter.CONSENSUS_SEQUENCE_ID;

        }

        else {

            throw new NoSuchElementException("There are no more sequence IDs availble from this iterator.");

        }

    }

    @Override

    public void remove() {

        throw new UnsupportedOperationException("This iterator does not support removing elements.");

    }

}