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

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.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
AGAVEHandler()
           
 
Method Summary
 java.util.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(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, org.xml.sax.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 java.util.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(java.lang.String nsURI,
                                java.lang.String localName,
                                java.lang.String qName,
                                org.xml.sax.Attributes attrs,
                                DelegationManager dm)
                         throws org.xml.sax.SAXException
Throws:
org.xml.sax.SAXException