eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMPherogramAlignmentObjectTranslator.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2016 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.taxeditor.molecular.io;
  11
  12
  13 import info.bioinfweb.commons.io.XMLUtils;
  14 import info.bioinfweb.jphyloio.ReaderStreamDataProvider;
  15 import info.bioinfweb.jphyloio.WriterStreamDataProvider;
  16 import info.bioinfweb.jphyloio.objecttranslation.InvalidObjectSourceDataException;
  17 import info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractXMLObjectTranslator;
  18
  19 import java.io.IOException;
  20
  21 import javax.xml.stream.XMLEventReader;
  22 import javax.xml.stream.XMLStreamException;
  23 import javax.xml.stream.XMLStreamWriter;
  24
  25 import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
  26 import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
  27
  28
  29
  30 /**
  31  * <i>JPhyloIO</i> object translator to read and write a shift list of a {@link SingleReadAlignment} object from and
  32  * to <i>XML</i>.
  33  *
  34  * @author Ben Stöver
  35  * @date 28.10.2016
  36  */
  37 public class CDMPherogramAlignmentObjectTranslator extends AbstractXMLObjectTranslator<SingleReadAlignment.Shift[]>
  38         implements SingleReadAlignmentRDFXMLConstants {
  39
  40     @Override
  41     public Class<SingleReadAlignment.Shift[]> getObjectClass() {
  42         return SingleReadAlignment.Shift[].class;
  43     }
  44
  45
  46     @Override
  47     public SingleReadAlignment.Shift[] readXMLRepresentation(XMLEventReader reader, ReaderStreamDataProvider<?> streamDataProvider)
  48             throws IOException, XMLStreamException, InvalidObjectSourceDataException {
  49
  50         // TODO implement
  51         throw new InternalError(Messages.CDMPherogramAlignmentObjectTranslator_NOT_IMPLEMENTED);
  52     }
  53
  54
  55     @Override
  56     public void writeXMLRepresentation(XMLStreamWriter writer, Object object, WriterStreamDataProvider<?> streamDataProvider)
  57             throws IOException, XMLStreamException, ClassCastException {
  58
  59         SingleReadAlignment.Shift[] shifts = (SingleReadAlignment.Shift[])object;
  60         XMLUtils.writeStartElement(writer, TAG_SHIFTS);
  61         for (SingleReadAlignment.Shift shift : shifts) {
  62             XMLUtils.writeStartElement(writer, TAG_SHIFT);
  63             XMLUtils.writeAttribute(writer, ATTR_POSITION, Integer.toString(shift.position));
  64             XMLUtils.writeAttribute(writer, ATTR_SHIFT, Integer.toString(shift.shift));
  65             writer.writeEndElement();
  66         }
  67         writer.writeEndElement();
  68     }
  69 }