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
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AGAVEHandler
public AGAVEHandler()
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