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

Class AGAVEHandler

java.lang.Object

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

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

org.biojava.bio.seq.io.agave.AGAVEHandler

All Implemented Interfaces:

AGAVECallbackItf, StAXContentHandler

public class AGAVEHandler
extends StAXFeatureHandler
implements AGAVECallbackItf

Handles the root AGAVE element modified for agave format

Author:

Hanning Ni Doubletwist Inc

Field Summary

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

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

Constructor Summary

Constructors

Constructor	Description
AGAVEHandler()

Method Summary

Modifier and Type	Method	Description
Iterator	getSequences()	get all the top level sequences bio_sequence --> SimpleSequence contig --> SimpleAssembly --> SimpleSequence( if only one sequence ) chromosome -> SimpleAssembly -> SimpleSequence( if only one sequence)
void	reportSequence(Sequence sequence)
void	startElementHandler(String nsURI, String localName, String qName, Attributes attrs, DelegationManager dm)

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, startElementHandler

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

Constructor Detail

AGAVEHandler

public AGAVEHandler()

Method Detail

reportSequence

public void reportSequence(Sequence sequence)

Specified by:

reportSequence in interface AGAVECallbackItf

Parameters:

sequence - from sub-tag <bio_sequence>/<contig>/<chromosome>

 bio_sequence --> SimpleSequence
 contig   --> SimpleAssembly
          --> SimpleSequence( if only one sequence )
 chromosome -> SimpleAssembly
            -> SimpleSequence( if only one sequence)
 

getSequences

public Iterator getSequences()

get all the top level sequences bio_sequence --> SimpleSequence contig --> SimpleAssembly --> SimpleSequence( if only one sequence ) chromosome -> SimpleAssembly -> SimpleSequence( if only one sequence)

startElementHandler

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

Throws:

SAXException