001/**
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.bio.seq.io.agave;
022import org.biojava.utils.ChangeVetoException;
023import org.xml.sax.SAXException;
024
025/**
026 * Deals with match_align
027 * @author Hanning Ni    Doubletwist Inc
028 */
029public class AGAVEMatchAlignPropHandler
030               extends StAXPropertyHandler
031{
032  // set up factory method
033  public static final StAXHandlerFactory AGAVE_MATCH_ALIGN_PROP_HANDLER_FACTORY
034    = new StAXHandlerFactory() {
035    public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
036      return new AGAVEMatchAlignPropHandler(staxenv);
037    }
038  };
039
040
041  AGAVEMatchAlignPropHandler(StAXFeatureHandler staxenv) {
042    // execute superclass method to setup environment
043    super(staxenv);
044    setHandlerCharacteristics("match_align", true);
045
046  }
047
048   public void characters(char[] ch, int start, int length)
049        throws SAXException
050  {
051      try{
052          staxenv.featureTemplate.annotation.setProperty("match_align", new String(ch) );
053      }catch (ChangeVetoException cve) {
054        throw new SAXException(" change veto exception ") ;
055    }
056  }
057
058}