org.biojava.bio.program.ssbind.HeaderStAXHandler 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.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;
/**
* HeaderStAXHandler handles the Header element of
* BioJava BlastLike XML.
*
* @author Keith James
* @author Matthew Pocock
* @since 1.3
*/
public class HeaderStAXHandler extends SeqSimilarityStAXHandler
{
public static final StAXHandlerFactory HEADER_HANDLER_FACTORY =
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new HeaderStAXHandler(ssContext);
}
};
/**
* Creates a new instance which sends callbacks to the specified
* SeqSimilarityStAXAdapter.
*
* @param ssContext a SeqSimilarityStAXAdapter.
*/
HeaderStAXHandler(SeqSimilarityStAXAdapter ssContext)
{
super(ssContext);
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"QueryId"),
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new QueryIDStAXHandler();
}
});
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"QueryDescription"),
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new QueryDescriptionStAXHandler();
}
});
addHandler(new ElementRecognizer.ByNSName(SeqSimilarityStAXAdapter.NAMESPACE,
"DatabaseId"),
new StAXHandlerFactory()
{
public StAXContentHandler getHandler(SeqSimilarityStAXAdapter ssContext)
{
return new DatabaseIDStAXHandler();
}
});
}
/**
* QueryIDStAXHandler handles the query sequence 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"));
if (attr.getValue("queryLength") != null)
{
ssContext.getSearchContentHandler().addSearchProperty("queryLength",
attr.getValue("queryLength"));
}
}
}
/**
* QueryDescriptionStAXHandler handles the hit
* description.
*/
private class QueryDescriptionStAXHandler extends StringElementHandlerBase
{
protected void setStringValue(String s)
{
ssContext.getSearchContentHandler().addSearchProperty("queryDescription", s);
}
}
/**
* DatabaseIDStAXHandler handles the database ID.
*/
private class DatabaseIDStAXHandler extends StAXContentHandlerBase
{
public void startElement(String uri,
String localName,
String qName,
Attributes attr,
DelegationManager dm)
throws SAXException
{
ssContext.getSearchContentHandler().setDatabaseID(attr.getValue("id"));
}
}
}