org.biojava.bio.seq.io.agave
Class AGAVEChromosomeHandler

java.lang.Object
  extended byorg.biojava.bio.seq.io.agave.StAXContentHandlerBase
      extended byorg.biojava.bio.seq.io.agave.StAXFeatureHandler
          extended byorg.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
All Implemented Interfaces:
AGAVEChromosomeCallbackItf, SequenceHandler, StAXContentHandler

public class AGAVEChromosomeHandler
extends StAXFeatureHandler
implements AGAVEChromosomeCallbackItf, SequenceHandler

Handles the AGAVE <chromosome> element

Author:
Hanning Ni Doubletwist Inc

Field Summary
static StAXHandlerFactory AGAVE_CHROMOSOME_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
 void endElementHandler(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, StAXContentHandler handler)
          Element specific exit handler Subclass to do anything useful.
 java.util.Iterator getSequences()
           
 void reportSequence(Sequence sequence)
           
 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, 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_CHROMOSOME_HANDLER_FACTORY

public static final StAXHandlerFactory AGAVE_CHROMOSOME_HANDLER_FACTORY
Method Detail

reportSequence

public void reportSequence(Sequence sequence)
Specified by:
reportSequence in interface AGAVEChromosomeCallbackItf

getSequences

public java.util.Iterator getSequences()

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

endElementHandler

public void endElementHandler(java.lang.String nsURI,
                              java.lang.String localName,
                              java.lang.String qName,
                              StAXContentHandler handler)
                       throws org.xml.sax.SAXException
Description copied from class: StAXFeatureHandler
Element specific exit handler Subclass to do anything useful.

Overrides:
endElementHandler in class StAXFeatureHandler
Throws:
org.xml.sax.SAXException