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/*
* 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.bio.search.SearchContentHandler;
import org.biojava.utils.stax.DelegationManager;
import org.biojava.utils.stax.StAXContentHandler;
import org.biojava.utils.stax.StAXContentHandlerBase;
import org.biojava.utils.stax.StringElementHandlerBase;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
/**
* AlignmentStAXHandler handles the Hit element of
* BioJava BlastLike XML.
*
* @author Keith James
* @since 1.3
*/
public class HitStAXHandler extends SeqSimilarityStAXHandler
{
public static final StAXHandlerFactory HIT_HANDLER_FACTORY =
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new HitStAXHandler(ssContext);
}
};
/**
* Creates a new instance which sends callbacks to the specified
* SeqSimilarityStAXAdapter.
*
* @param ssContext a SeqSimilarityStAXAdapter.
*/
HitStAXHandler(SeqSimilarityStAXAdapter ssContext)
{
super(ssContext);
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"HitId"),
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new HitIDStAXHandler();
}
});
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"QueryId"),
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new QueryIDStAXHandler();
}
});
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"HitDescription"),
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new HitDescriptionStAXHandler();
}
});
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"HSPCollection"),
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new HSPCollectionStAXHandler();
}
});
}
protected void handleStartElement(String nsURI,
String localName,
String qName,
Attributes attrs)
throws SAXException
{
SearchContentHandler sch = ssContext.getSearchContentHandler();
sch.startHit();
if (attrs.getValue("sequenceLength") != null)
{
sch.addHitProperty("subjectSequenceLength",
attrs.getValue("sequenceLength"));
}
}
protected void handleEndElement(String nsURI,
String localName,
String qName)
throws SAXException
{
ssContext.getSearchContentHandler().endHit();
}
/**
* HitIDStAXHandler handles the hit ID.
*/
private class HitIDStAXHandler extends StAXContentHandlerBase
{
public void startElement(String uri,
String localName,
String qName,
Attributes attr,
DelegationManager dm)
throws SAXException
{
ssContext.getSearchContentHandler().addHitProperty("subjectId", attr.getValue("id"));
}
}
/**
* QueryIDStAXHandler handles the query ID.
*/
private class QueryIDStAXHandler extends StAXContentHandlerBase
{
public void startElement(String uri,
String localName,
String qName,
Attributes attr,
DelegationManager dm)
throws SAXException
{
ssContext.getSearchContentHandler().setQueryID(attr.getValue("id"));
}
}
/**
* HitDescriptionStAXHandler handles the hit
* description.
*/
private class HitDescriptionStAXHandler extends StringElementHandlerBase
{
protected void setStringValue(String s)
{
ssContext.getSearchContentHandler().addHitProperty("subjectDescription", s);
}
}
/**
* HSPCollectionStAXHandler handles the HSPCollection
* element.
*/
private class HSPCollectionStAXHandler extends StAXContentHandlerBase
{
public void startElement(String uri,
String localName,
String qName,
Attributes attr,
DelegationManager dm)
throws SAXException
{
if (localName.equals("HSP"))
dm.delegate(HSPStAXHandler.HSP_HANDLER_FACTORY.getHandler(ssContext));
}
}
}
