org.biojava.bio.seq.io.agave

Class AGAVEBioSeqHandler

java.lang.Object

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

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

org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler

All Implemented Interfaces:

AGAVEBioSeqCallbackItf, SequenceHandler, StAXContentHandler

public class AGAVEBioSeqHandler
extends StAXFeatureHandler
implements AGAVEBioSeqCallbackItf, SequenceHandler

Handles the AGAVE <bio_sequence> element

Author:

David Huen, Hanning Ni Doubletwist Inc, Greg Cox

Field Summary

Fields

Modifier and Type	Field and Description
static StAXHandlerFactory	AGAVE_BIO_SEQ_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

Methods

Modifier and Type	Method and Description
void	endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.
void	reportDna(String dna_seq)
void	reportFeature(Location loc) Allows nesting class that manages a gene template to gain information about its extent from nested elements.
void	reportStrand(StrandedFeature.Strand strand)
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_BIO_SEQ_HANDLER_FACTORY

public static final StAXHandlerFactory AGAVE_BIO_SEQ_HANDLER_FACTORY

sequence

protected Sequence sequence

Method Detail

reportStrand

public void reportStrand(StrandedFeature.Strand strand)

Specified by:

reportStrand in interface AGAVEBioSeqCallbackItf

reportFeature

public void reportFeature(Location loc)

Description copied from interface: AGAVEBioSeqCallbackItf

Allows nesting class that manages a gene template to gain information about its extent from nested elements. Strand is reported separately as some gene features may not have strand.

Specified by:

reportFeature in interface AGAVEBioSeqCallbackItf

reportDna

public void reportDna(String dna_seq)

Specified by:

reportDna in interface AGAVEBioSeqCallbackItf

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