Package org.biojava.bio.seq.io.agave

Class StAXPropertyHandler

java.lang.Object

org.biojava.bio.seq.io.agave.StAXContentHandlerBase

org.biojava.bio.seq.io.agave.StAXPropertyHandler

All Implemented Interfaces:

StAXContentHandler

Direct Known Subclasses:

AGAVEAltIdsPropHandler, AGAVEAnnotationsHandler, AGAVEDbIdPropHandler, AGAVEDescPropHandler, AGAVEElementIdPropHandler, AGAVEExonsPropHandler, AGAVEIdAliasPropHandler, AGAVEKeywordPropHandler, AGAVEMapLocationPropHandler, AGAVEMapPositionPropHandler, AGAVEMatchAlignPropHandler, AGAVEMatchDescPropHandler, AGAVEMatchRegionPropHandler, AGAVENotePropHandler, AGAVEQualifierPropHandler, AGAVERelatedAnnotPropHandler, AGAVEResultPropertyPropHandler, AGAVESciPropertyPropHandler, AGAVESeqLocationPropHandler, AGAVESeqPropHandler, AGAVEViewPropHandler, AGAVEXrefPropHandler, AGAVEXrefPropPropHandler, AGAVEXrefsPropHandler

public class StAXPropertyHandler
extends StAXContentHandlerBase

StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. NOTE This class is not thread-safe -- it must only be used for one parse at any time. This class is the basis for classes that do not create a new feature but modify an existing feature. It is not compulsory for property handlers to subclass this class but those that don't but wish to use the handler stack facility need to use the StaxFeatureHandler's push and pop methods.

Author:

copied from Thomas Down, copied from David Huen, Hanning Ni Doubletwist Inc

Field Summary

Fields

Modifier and Type	Field	Description
protected SeqIOListener	featureListener
protected StAXFeatureHandler	staxenv

Method Summary

Modifier and Type	Method	Description
protected void	addHandler(ElementRecognizer rec, StAXHandlerFactory handler)
void	endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
void	endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)	Element specific exit handler Subclass to do anything useful.
protected ListIterator	getHandlerStackIterator()	get iterator for current stack starting at the position below mine.
void	setHandlerCharacteristics(String localName, boolean hasCallback)	Sets the element name that the class responds to.
protected void	setProperty(String name, String value)
void	startElement(String nsURI, String localName, String qName, Attributes attrs, DelegationManager dm)	Override this to do any processing required but call this prior to returning.
void	startElementHandler(String nsURI, String localName, String qName, Attributes attrs)	Element-specific handler.

Methods inherited from class org.biojava.bio.seq.io.agave.StAXContentHandlerBase

characters, endPrefixMapping, endTree, ignorableWhitespace, processingInstruction, setDocumentLocator, skippedEntity, startPrefixMapping, startTree

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

featureListener

protected SeqIOListener featureListener

staxenv

protected StAXFeatureHandler staxenv

Method Detail

setHandlerCharacteristics

public void setHandlerCharacteristics(String localName,
                                      boolean hasCallback)

Sets the element name that the class responds to.

getHandlerStackIterator

protected ListIterator getHandlerStackIterator()
                                        throws ParseException

get iterator for current stack starting at the position below mine.

Throws:

ParseException

addHandler

protected void addHandler(ElementRecognizer rec,
                          StAXHandlerFactory handler)

setProperty

protected void setProperty(String name,
                           String value)

startElementHandler

public void startElementHandler(String nsURI,
                                String localName,
                                String qName,
                                Attributes attrs)
                         throws SAXException

Element-specific handler. Subclass this to do something useful!

Throws:

SAXException

startElement

public void startElement(String nsURI,
                         String localName,
                         String qName,
                         Attributes attrs,
                         DelegationManager dm)
                  throws SAXException

Override this to do any processing required but call this prior to returning. Delegation occurs here!

Specified by:

startElement in interface StAXContentHandler

Overrides:

startElement in class StAXContentHandlerBase

Throws:

SAXException

endElementHandler

public void endElementHandler(String nsURI,
                              String localName,
                              String qName,
                              StAXContentHandler handler)
                       throws SAXException

Element specific exit handler Subclass to do anything useful.

Throws:

SAXException

endElement

public void endElement(String nsURI,
                       String localName,
                       String qName,
                       StAXContentHandler handler)
                throws SAXException

Specified by:

endElement in interface StAXContentHandler

Overrides:

endElement in class StAXContentHandlerBase

Throws:

SAXException