org.biojava.bio.seq.io.agave

Class AGAVEBioSequenceHandler

java.lang.Object

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

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

org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler

All Implemented Interfaces:

StAXContentHandler

public class AGAVEBioSequenceHandler
extends StAXFeatureHandler

Handles the AGAVE <bio_sequence> element

Author:

David Huen, Hanning Ni Doubletwist Inc

Field Summary

Fields

Modifier and Type	Field and Description
static StAXHandlerFactory	AGAVE_BIO_SEQUENCE_HANDLER_FACTORY

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

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

Method Summary

Methods

Modifier and Type	Method and Description
void	reportFeature(Location loc)
void	reportStrand(StrandedFeature.Strand strand)
void	startElementHandler(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attrs) Element-specific handler.

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

addFeatureToSequence, addHandler, createTemplate, endElement, endElementHandler, 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_BIO_SEQUENCE_HANDLER_FACTORY

public static final StAXHandlerFactory AGAVE_BIO_SEQUENCE_HANDLER_FACTORY

Method Detail

reportStrand

public void reportStrand(StrandedFeature.Strand strand)

reportFeature

public void reportFeature(Location loc)

startElementHandler

public void startElementHandler(java.lang.String nsURI,
                       java.lang.String localName,
                       java.lang.String qName,
                       org.xml.sax.Attributes attrs)
                         throws org.xml.sax.SAXException

Description copied from class: StAXFeatureHandler

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

Overrides:

startElementHandler in class StAXFeatureHandler

Throws:

org.xml.sax.SAXException