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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.sax.blastxml;
import java.util.ArrayList;
import java.util.List;
import org.biojava.bio.seq.io.game.ElementRecognizer;
import org.biojava.utils.stax.DelegationManager;
import org.biojava.utils.stax.StAXContentHandler;
import org.biojava.utils.stax.StAXContentHandlerBase;
import org.xml.sax.Attributes;
import org.xml.sax.ContentHandler;
import org.xml.sax.SAXException;
/**
* StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
* It was modified for greater generality. NOTE This class is
* not thread-safe -- it must only be used for one parse at any time.
*
*@author Thomas Down
*@author David Huen
*@created 19 January 2002
*@since 1.8
*/
class StAXFeatureHandler extends StAXContentHandlerBase {
// class variables
/**
* declare namespace
*/
static final String biojavaUri = "http://www.biojava.org";
// static final String biojavaUri = "biojava";
static final String CDATA = "CDATA";
static final String PCDATA = "PCDATA";
static String querySequenceType = null;
static String hitSequenceType = null;
/**
* the SeqIOListener for this object
*/
ContentHandler listener;
/**
* Nesting class that provides callback interfaces to nested class
*/
public StAXFeatureHandler staxenv;
/**
* handler list for delegation
*/
List handlers;
/**
* are we in delegation from current object or is this pass my own?
*/
int level = 0;
/**
* This base class defines default behaviour for a StAX handler including
* delegation.
*/
/**
* the version of constructor called depends on whether there is an
* explicit super(...) in the constructor of the derived class. If there
* is, that specific constructor will be called. If not, the parameterless
* will is called.
*/
StAXFeatureHandler() {
handlers = new ArrayList();
}
/**
* Constructor for the StAXFeatureHandler object
*
*@param staxenv Description of the Parameter
*/
StAXFeatureHandler(StAXFeatureHandler staxenv) {
handlers = new ArrayList();
this.staxenv = staxenv;
}
// Class to implement bindings
/**
* Description of the Class
*
*@author david
*@created 19 January 2002
*/
class Binding {
final ElementRecognizer recognizer;
final StAXHandlerFactory handlerFactory;
/**
* Constructor for the Binding object
*
*@param er Description of the Parameter
*@param hf Description of the Parameter
*/
Binding(ElementRecognizer er, StAXHandlerFactory hf) {
recognizer = er;
handlerFactory = hf;
}
}
// method to add a handler
// we do not distinguish whither it is a feature or property
// handler. The factory method creates the right type subclassed
// from the correct type of handler
/**
* Adds a feature to the Handler attribute of the StAXFeatureHandler object
*
*@param rec The feature to be added to the Handler attribute
*@param handler The feature to be added to the Handler attribute
*/
protected void addHandler(
ElementRecognizer rec,
StAXHandlerFactory handler) {
handlers.add(new Binding(rec, handler));
}
/**
* get the SeqIOListener for this parser
*/
public ContentHandler getListener()
{
// System.out.println("in StAXFeatureHandler. staxenv is " + staxenv);
return staxenv.listener;
}
/**
* Element-specific handler. Subclass this to do something useful!
*
*@param nsURI Description of the Parameter
*@param localName Description of the Parameter
*@param qName Description of the Parameter
*@param attrs Description of the Parameter
*@exception SAXException Description of the Exception
*/
void startElementHandler(
String nsURI,
String localName,
String qName,
Attributes attrs)
throws SAXException { }
/**
* Handles basic entry processing for all feature handlers.
*
*@param nsURI Description of the Parameter
*@param localName Description of the Parameter
*@param qName Description of the Parameter
*@param attrs Description of the Parameter
*@param dm Description of the Parameter
*@exception SAXException Description of the Exception
*/
public void startElement(
String nsURI,
String localName,
String qName,
Attributes attrs,
DelegationManager dm)
throws SAXException {
level++;
// perform delegation
// we must delegate only on features that are directly attached.
// if I do not check that that's so, any element of a kind I delegate
// on will be detected any depth within unrecognized tags.
if (level == 2) {
// System.out.println("StaxFeaturehandler.startElement starting. localName: " + localName + " " + level);
for (int i = handlers.size() - 1; i >= 0; --i) {
Binding b = (Binding) handlers.get(i);
if (b.recognizer.filterStartElement(nsURI, localName, qName, attrs)) {
dm.delegate(b.handlerFactory.getHandler(staxenv));
return;
}
}
}
// call the element specific handler now.
// remember that if we we have a delegation failure we pass here too!
if (level == 1) {
startElementHandler(nsURI, localName, qName, attrs);
}
}
/**
* Element specific exit handler Subclass to do anything useful.
*
*@param nsURI Description of the Parameter
*@param localName Description of the Parameter
*@param qName Description of the Parameter
*@param handler Description of the Parameter
*@exception SAXException Description of the Exception
*/
void endElementHandler(
String nsURI,
String localName,
String qName,
StAXContentHandler handler)
throws SAXException { }
/**
* Handles basic exit processing.
*
*@param nsURI Description of the Parameter
*@param localName Description of the Parameter
*@param qName Description of the Parameter
*@param handler Description of the Parameter
*@exception SAXException Description of the Exception
*/
public void endElement(
String nsURI,
String localName,
String qName,
StAXContentHandler handler)
throws SAXException {
// System.out.println("StAXFeatureHandler endElement called, localName, level: " + localName + " " + stackLevel);
if ((--level) == 0) {
endElementHandler(nsURI, localName, qName, handler);
}
}
}
