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 java.util.ListIterator;
023
024import org.xml.sax.Attributes;
025import org.xml.sax.SAXException;
026
027/**
028 *
029 *
030 */
031public class AGAVERelatedAnnotPropHandler extends StAXPropertyHandler implements AGAVEEvidenceCallbackItf{
032
033
034   public static final StAXHandlerFactory AGAVE_RELATED_ANNOT_PROP_HANDLER_FACTORY
035    = new StAXHandlerFactory() {
036    public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
037      return new AGAVERelatedAnnotPropHandler(staxenv);
038    }
039   };
040   private AGAVERelatedAnnot related_annot ;
041   AGAVERelatedAnnotPropHandler(StAXFeatureHandler staxenv) {
042    // execute superclass method to setup environment
043    super(staxenv);
044    setHandlerCharacteristics("related_annot", true);
045
046    super.addHandler(new ElementRecognizer.ByLocalName("element_id"),
047         AGAVEElementIdPropHandler.AGAVE_ELEMENT_ID_PROP_HANDLER_FACTORY);
048    super.addHandler(new ElementRecognizer.ByLocalName("sci_property"),
049         AGAVESciPropertyPropHandler.AGAVE_SCI_PROPERTY_PROP_HANDLER_FACTORY);
050    related_annot = new AGAVERelatedAnnot() ;
051  }
052  public void addElementId(String id)
053  {
054      related_annot.addElementId(id) ;
055  }
056  public void addProperty(AGAVEProperty prop)
057  {
058      related_annot.addProp( prop ) ;
059  }
060  public void startElementHandler(
061                String nsURI,
062                String localName,
063                String qName,
064                Attributes attrs)
065         throws SAXException
066  {
067      related_annot.setScore(attrs.getValue( "score" )  );
068      related_annot.setRel( attrs.getValue( "rel" )   )  ;
069  }
070
071
072  public void endElementHandler(
073                String nsURI,
074                String localName,
075                String qName,
076                StAXContentHandler handler)
077                throws SAXException
078  {
079       int currLevel = staxenv.getLevel();
080       if (currLevel >=1) {
081           ListIterator li = staxenv.getHandlerStackIterator(currLevel);
082           while( li.hasPrevious() )
083          {
084              Object ob =   li.previous() ;
085              if(  ( ob instanceof AGAVECompResultHandler ) ||
086                  ( ob instanceof AGAVESeqFeatureHandler ) )
087              {
088                  ( (AGAVECompResultHandler) ob ).addRelatedAnnot( related_annot ) ;
089                   return ;
090              }
091           }
092       }
093
094  }
095
096
097}