org.biojava.bio.seq.io.agave

Class AGAVEFragmentOrientationHandler

java.lang.Object

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

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

org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler

All Implemented Interfaces:

AGAVEFeatureCallbackItf, StAXContentHandler

public class AGAVEFragmentOrientationHandler
extends StAXFeatureHandler
implements AGAVEFeatureCallbackItf

Author:

Hanning Ni Doubletwist Inc

Field Summary

Fields

Modifier and Type	Field and Description
static StAXHandlerFactory	AGAVE_FRAGMENT_ORIENTATION_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

Modifier and Type	Method and Description
void	reportFeature(Location loc)
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, 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_FRAGMENT_ORIENTATION_HANDLER_FACTORY

public static final StAXHandlerFactory AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY

Method Detail

reportFeature

public void reportFeature(Location loc)

Specified by:

reportFeature in interface AGAVEFeatureCallbackItf

reportStrand

public void reportStrand(StrandedFeature.Strand strand)

Specified by:

reportStrand in interface AGAVEFeatureCallbackItf

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