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

Class AGAVEFragmentOrderHandler

java.lang.Object

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

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

org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler

All Implemented Interfaces:

StAXContentHandler

public class AGAVEFragmentOrderHandler
extends StAXFeatureHandler

Author:

Hanning Ni Doubletwist Inc

Field Summary

Fields

Modifier and Type	Field	Description
static StAXHandlerFactory	AGAVE_FRAGMENT_ORDER_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	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_ORDER_HANDLER_FACTORY

public static final StAXHandlerFactory AGAVE_FRAGMENT_ORDER_HANDLER_FACTORY

Method Detail

reportStrand

public void reportStrand(StrandedFeature.Strand strand)

reportFeature

public void reportFeature(Location loc)

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