Package 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
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Field Summary
FieldsFields inherited from class org.biojava.bio.seq.io.agave.StAXFeatureHandler
annot, callbackStack, endLoc, featureListener, featureTemplate, myLocalName, stackLevel, startLoc, staxenv, subFeatures
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Method Summary
Modifier and TypeMethodDescriptionvoid
endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.void
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
(String nsURI, String localName, String qName, 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
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Field Details
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AGAVE_BIO_SEQ_HANDLER_FACTORY
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sequence
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Method Details
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reportStrand
- Specified by:
reportStrand
in interfaceAGAVEBioSeqCallbackItf
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reportFeature
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 interfaceAGAVEBioSeqCallbackItf
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reportDna
- Specified by:
reportDna
in interfaceAGAVEBioSeqCallbackItf
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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 classStAXFeatureHandler
- Throws:
SAXException
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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 classStAXFeatureHandler
- Throws:
SAXException
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