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.xml.sax.Attributes;
023import org.xml.sax.SAXException;
024
025/**
026 * Deals with match_region
027 *
028 * @author Hanning Ni    Doubletwist Inc
029 */
030public class AGAVEMatchRegionPropHandler
031               extends StAXPropertyHandler implements AGAVEDbIdCallbackItf, AGAVEEvidenceCallbackItf
032{
033  // set up factory method
034  public static final StAXHandlerFactory AGAVE_MATCH_REGION_PROP_HANDLER_FACTORY
035    = new StAXHandlerFactory() {
036    public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
037      return new AGAVEMatchRegionPropHandler(staxenv);
038    }
039  };
040  private AGAVEMatchRegion match_region = new AGAVEMatchRegion() ;
041
042  AGAVEMatchRegionPropHandler(StAXFeatureHandler staxenv) {
043    // execute superclass method to setup environment
044    super(staxenv);
045    setHandlerCharacteristics("match_region", true);
046
047    super.addHandler(new ElementRecognizer.ByLocalName("db_id"),
048         AGAVEDbIdPropHandler.AGAVE_DBID_PROP_HANDLER_FACTORY);
049    super.addHandler(new ElementRecognizer.ByLocalName("element_id"),
050         AGAVEElementIdPropHandler.AGAVE_ELEMENT_ID_PROP_HANDLER_FACTORY);
051    //bio_sequence
052    //super.addHandler(new ElementRecognizer.ByLocalName("bio_sequence"),
053      //   AGAVEBioSequencePropHandler.AGAVE_BIO_SEQUENCE_PROP_HANDLER_FACTORY);
054
055
056  }
057  public void addDbId( AGAVEDbId id)
058  {
059      match_region.setDbId(id) ;
060  }
061  public void addElementId(String id)
062  {
063      match_region.setElementId( id ) ;
064  }
065  public void startElementHandler(
066                String nsURI,
067                String localName,
068                String qName,
069                Attributes attrs)
070         throws SAXException
071  {
072     match_region.setStart( new Integer( attrs.getValue("start") ) .intValue()  );
073     match_region.setEnd( new Integer( attrs.getValue("end") ) .intValue()  );
074  }
075
076   public void endElementHandler(
077                String nsURI,
078                String localName,
079                String qName,
080                StAXContentHandler handler)
081                throws SAXException
082  {
083      try{
084          staxenv.featureTemplate.annotation.setProperty("match_region", match_region) ;
085      }catch(Exception e){
086          throw new SAXException( e.getMessage() ) ;
087      }
088  }
089
090  }