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