org.biojava.bio.seq.io.agave
Class AGAVEContigHandler
java.lang.Object
org.biojava.bio.seq.io.agave.StAXContentHandlerBase
org.biojava.bio.seq.io.agave.StAXFeatureHandler
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
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AGAVE_CONTIG_HANDLER_FACTORY
public static final StAXHandlerFactory AGAVE_CONTIG_HANDLER_FACTORY
sequence
protected Sequence sequence
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