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

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.AGAVEBioSeqHandler
All Implemented Interfaces:
AGAVEBioSeqCallbackItf, SequenceHandler, StAXContentHandler

public class AGAVEBioSeqHandler
extends StAXFeatureHandler
implements AGAVEBioSeqCallbackItf, SequenceHandler

Handles the AGAVE <bio_sequence> element

Author:
David Huen, Hanning Ni Doubletwist Inc, Greg Cox

Field Summary
static StAXHandlerFactory AGAVE_BIO_SEQ_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(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, StAXContentHandler handler)
          Element specific exit handler Subclass to do anything useful.
 void reportDna(java.lang.String dna_seq)
           
 void reportFeature(Location loc)
          Allows nesting class that manages a gene template to gain information about its extent from nested elements.
 void reportStrand(StrandedFeature.Strand strand)
           
 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_BIO_SEQ_HANDLER_FACTORY

public static final StAXHandlerFactory AGAVE_BIO_SEQ_HANDLER_FACTORY

sequence

protected Sequence sequence
Method Detail

reportStrand

public void reportStrand(StrandedFeature.Strand strand)
Specified by:
reportStrand in interface AGAVEBioSeqCallbackItf

reportFeature

public void reportFeature(Location loc)
Description copied from interface: AGAVEBioSeqCallbackItf
Allows nesting class that manages a gene template to gain information about its extent from nested elements. Strand is reported separately as some gene features may not have strand.

Specified by:
reportFeature in interface AGAVEBioSeqCallbackItf

reportDna

public void reportDna(java.lang.String dna_seq)
Specified by:
reportDna in interface AGAVEBioSeqCallbackItf

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