org.biojava.bio.program.ssbind.HSPStAXHandler Maven / Gradle / Ivy
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.program.ssbind;
import org.biojava.bio.program.xff.ElementRecognizer;
import org.biojava.utils.stax.StAXContentHandler;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
/**
* HSPStAXHandler handles the HSP element of BioJava
* BlastLike XML.
*
* @author Keith James
* @since 1.3
*/
public class HSPStAXHandler extends SeqSimilarityStAXHandler
{
public static final StAXHandlerFactory HSP_HANDLER_FACTORY =
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new HSPStAXHandler(ssContext);
}
};
/**
* Creates a new instance which sends callbacks to the specified
* SeqSimilarityStAXAdapter.
*
* @param ssContext a SeqSimilarityStAXAdapter.
*/
HSPStAXHandler(SeqSimilarityStAXAdapter ssContext)
{
super(ssContext);
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"HSPSummary"),
HSPSummaryStAXHandler.HSPSUMMARY_HANDLER_FACTORY);
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"BlastLikeAlignment"),
AlignmentStAXHandler.ALIGNMENT_HANDLER_FACTORY);
}
protected void handleStartElement(String nsURI,
String localName,
String qName,
Attributes attrs)
throws SAXException
{
ssContext.getSearchContentHandler().startSubHit();
}
protected void handleEndElement(String nsURI,
String localName,
String qName)
throws SAXException
{
ssContext.getSearchContentHandler().endSubHit();
}
}