/*
* 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.StringElementHandlerBase;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
/**
* AlignmentStAXHandler
handles the BlastLikeAlignment
* element of BioJava BlastLike XML.
*
* @author Keith James
* @since 1.3
*/
public class AlignmentStAXHandler extends SeqSimilarityStAXHandler
{
public static final StAXHandlerFactory ALIGNMENT_HANDLER_FACTORY =
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new AlignmentStAXHandler(ssContext);
}
};
/**
* Creates a new instance which sends callbacks to the specified
* SeqSimilarityStAXAdapter
.
*
* @param ssContext a SeqSimilarityStAXAdapter
.
*/
AlignmentStAXHandler(SeqSimilarityStAXAdapter ssContext)
{
super(ssContext);
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"QuerySequence"),
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new QuerySequenceStAXHandler();
}
});
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"HitSequence"),
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new HitSequenceStAXHandler();
}
});
}
/**
* QuerySequenceStAXHandler
handles the query
* sequence.
*/
private class QuerySequenceStAXHandler extends StringElementHandlerBase
{
private SearchContentHandler sch;
public void startElement(String nsURI,
String localName,
String qName,
Attributes attrs,
DelegationManager dm)
throws SAXException
{
super.startElement(nsURI, localName, qName, attrs, dm);
sch = ssContext.getSearchContentHandler();
sch.addSubHitProperty("querySequenceStart",
attrs.getValue("startPosition"));
sch.addSubHitProperty("querySequenceEnd",
attrs.getValue("stopPosition"));
}
protected void setStringValue(String s) throws SAXException
{
sch = ssContext.getSearchContentHandler();
sch.addSubHitProperty("querySequence", s);
}
}
/**
* HitSequenceStAXHandler
handles the hit sequence.
*/
private class HitSequenceStAXHandler extends StringElementHandlerBase
{
private SearchContentHandler sch;
public void startElement(String nsURI,
String localName,
String qName,
Attributes attrs,
DelegationManager dm)
throws SAXException
{
super.startElement(nsURI, localName, qName, attrs, dm);
sch = ssContext.getSearchContentHandler();
sch.addSubHitProperty("subjectSequenceStart",
attrs.getValue("startPosition"));
sch.addSubHitProperty("subjectSequenceEnd",
attrs.getValue("stopPosition"));
}
protected void setStringValue(String s) throws SAXException
{
sch = ssContext.getSearchContentHandler();
sch.addSubHitProperty("subjectSequence", s);
}
}
}