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

java.lang.Object
  extended by org.biojava.bio.seq.io.agave.StAXContentHandlerBase
      extended by org.biojava.bio.seq.io.agave.StAXFeatureHandler
          extended by org.biojava.bio.seq.io.agave.AGAVEContigHandler
All Implemented Interfaces:
AGAVEContigCallbackItf, SequenceHandler, StAXContentHandler

public class AGAVEContigHandler
extends StAXFeatureHandler
implements AGAVEContigCallbackItf, SequenceHandler

Handles the AGAVE <contig> element

Author:
Hanning Ni Doubletwist Inc, Greg Cox

Field Summary
static StAXHandlerFactory AGAVE_CONTIG_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
 void endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
          Element specific exit handler Subclass to do anything useful.
 void reportDna(String dna)
           
 void reportSequence(Sequence sequence)
           
 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_CONTIG_HANDLER_FACTORY

public static final StAXHandlerFactory AGAVE_CONTIG_HANDLER_FACTORY

sequence

protected Sequence sequence
Method Detail

reportSequence

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

reportDna

public void reportDna(String dna)
Specified by:
reportDna in interface AGAVEContigCallbackItf

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