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

Class AGAVEContigHandler

java.lang.Object

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

org.biojava.bio.seq.io.agave.StAXFeatureHandler

org.biojava.bio.seq.io.agave.AGAVEContigHandler

All Implemented Interfaces:

AGAVEContigCallbackItf, SequenceHandler, StAXContentHandler

public class AGAVEContigHandler
extends StAXFeatureHandler
implements AGAVEContigCallbackItf, SequenceHandler

Handles the AGAVE <contig> element

Author:

Hanning Ni Doubletwist Inc, Greg Cox

Field Summary

Fields

Modifier and Type	Field	Description
static StAXHandlerFactory	AGAVE_CONTIG_HANDLER_FACTORY
protected Sequence	sequence

Fields inherited from class org.biojava.bio.seq.io.agave.StAXFeatureHandler

annot, callbackStack, endLoc, featureListener, featureTemplate, myLocalName, stackLevel, startLoc, staxenv, subFeatures

Method Summary

Modifier and Type	Method	Description
void	endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)	Element specific exit handler Subclass to do anything useful.
void	reportDna(String dna)
void	reportSequence(Sequence sequence)
void	startElementHandler(String nsURI, String localName, String qName, Attributes attrs)	Element-specific handler.

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

addFeatureToSequence, addHandler, createTemplate, endElement, getFeatureListener, getHandlerStackIterator, getLevel, pop, push, realizeSubFeatures, setFeatureListener, setHandlerCharacteristics, setProperty, startElement

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

AGAVE_CONTIG_HANDLER_FACTORY

public static final StAXHandlerFactory AGAVE_CONTIG_HANDLER_FACTORY

sequence

protected Sequence sequence

Method Detail

reportSequence

public void reportSequence(Sequence sequence)

Specified by:

reportSequence in interface AGAVEContigCallbackItf

reportDna

public void reportDna(String dna)

Specified by:

reportDna in interface AGAVEContigCallbackItf

startElementHandler

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

Description copied from class: StAXFeatureHandler

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

Overrides:

startElementHandler in class StAXFeatureHandler

Throws:

SAXException

endElementHandler

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

Description copied from class: StAXFeatureHandler

Element specific exit handler Subclass to do anything useful.

Overrides:

endElementHandler in class StAXFeatureHandler

Throws:

SAXException