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.io;

import info.bioinfweb.commons.io.XMLUtils;

import info.bioinfweb.jphyloio.ReaderStreamDataProvider;

import info.bioinfweb.jphyloio.WriterStreamDataProvider;

import info.bioinfweb.jphyloio.objecttranslation.InvalidObjectSourceDataException;

import info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractXMLObjectTranslator;

import java.io.IOException;

import javax.xml.stream.XMLEventReader;

import javax.xml.stream.XMLStreamException;

import javax.xml.stream.XMLStreamWriter;

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

/**

 * <i>JPhyloIO</i> object translator to read and write a shift list of a {@link SingleReadAlignment} object from and

 * to <i>XML</i>.

 *

 * @author Ben Stöver

 * @date 28.10.2016

 */

public class CDMPherogramAlignmentObjectTranslator extends AbstractXMLObjectTranslator<SingleReadAlignment.Shift[]>

        implements SingleReadAlignmentRDFXMLConstants {

    @Override

    public Class<SingleReadAlignment.Shift[]> getObjectClass() {

        return SingleReadAlignment.Shift[].class;

    }

    @Override

    public SingleReadAlignment.Shift[] readXMLRepresentation(XMLEventReader reader, ReaderStreamDataProvider<?> streamDataProvider)

            throws IOException, XMLStreamException, InvalidObjectSourceDataException {

        // TODO implement

        throw new InternalError("Not implemented.");

    }

    @Override

    public void writeXMLRepresentation(XMLStreamWriter writer, Object object, WriterStreamDataProvider<?> streamDataProvider)

            throws IOException, XMLStreamException, ClassCastException {

        SingleReadAlignment.Shift[] shifts = (SingleReadAlignment.Shift[])object;

        XMLUtils.writeStartElement(writer, TAG_SHIFTS);

        for (SingleReadAlignment.Shift shift : shifts) {

            XMLUtils.writeStartElement(writer, TAG_SHIFT);

            XMLUtils.writeAttribute(writer, ATTR_POSITION, Integer.toString(shift.position));

            XMLUtils.writeAttribute(writer, ATTR_SHIFT, Integer.toString(shift.shift));

            writer.writeEndElement();

        }

        writer.writeEndElement();

    }

}