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 -
Method Summary
Modifier and TypeMethodDescriptionvoidendElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.voidvoidreportFeature(Location loc) Allows nesting class that manages a gene template to gain information about its extent from nested elements.voidreportStrand(StrandedFeature.Strand strand) voidstartElementHandler(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, startElementMethods 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:
reportStrandin interfaceAGAVEBioSeqCallbackItf
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reportFeature
Description copied from interface:AGAVEBioSeqCallbackItfAllows 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:
reportFeaturein interfaceAGAVEBioSeqCallbackItf
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reportDna
- Specified by:
reportDnain interfaceAGAVEBioSeqCallbackItf
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startElementHandler
public void startElementHandler(String nsURI, String localName, String qName, Attributes attrs) throws SAXException Description copied from class:StAXFeatureHandlerElement-specific handler. Subclass this to do something useful!- Overrides:
startElementHandlerin 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:StAXFeatureHandlerElement specific exit handler Subclass to do anything useful.- Overrides:
endElementHandlerin classStAXFeatureHandler- Throws:
SAXException
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