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;
022
023/**
024 *
025 * @author David Huen
026 * @author Hanning Ni     Doubletwist Inc
027 */
028public class AGAVEAssemblyHandler
029               extends StAXFeatureHandler implements SequenceHandler
030
031{
032  public static final StAXHandlerFactory AGAVE_ASSEMBLY_HANDLER_FACTORY
033    = new StAXHandlerFactory() {
034    public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
035      return new AGAVEAssemblyHandler(staxenv);
036    }
037  };
038
039   AGAVEAssemblyHandler(StAXFeatureHandler staxenv) {
040    // setup up environment stuff
041    super( staxenv );
042    featureListener = staxenv.featureListener;
043    setHandlerCharacteristics("assembly", true);
044
045    // setup handlers
046        //
047       super.addHandler(new ElementRecognizer.ByLocalName("bio_sequence"),
048         AGAVEBioSeqHandler.AGAVE_BIO_SEQ_HANDLER_FACTORY);
049       //
050       super.addHandler(new ElementRecognizer.ByLocalName("fragment_order"),
051         AGAVEFragmentOrderHandler.AGAVE_FRAGMENT_ORDER_HANDLER_FACTORY);
052
053  }
054
055}