Package 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
Handles the root AGAVE element
modified for agave format
- Author:
- Hanning Ni Doubletwist Inc
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Field Summary
Fields inherited from class org.biojava.bio.seq.io.agave.StAXFeatureHandler
annot, callbackStack, endLoc, featureListener, featureTemplate, myLocalName, stackLevel, startLoc, staxenv, subFeatures
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionget all the top level sequences bio_sequence --> SimpleSequence contig --> SimpleAssembly --> SimpleSequence( if only one sequence ) chromosome -> SimpleAssembly -> SimpleSequence( if only one sequence)void
reportSequence
(Sequence sequence) void
startElementHandler
(String nsURI, String localName, String qName, Attributes attrs, DelegationManager dm) 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 org.biojava.bio.seq.io.agave.StAXContentHandlerBase
characters, endPrefixMapping, endTree, ignorableWhitespace, processingInstruction, setDocumentLocator, skippedEntity, startPrefixMapping, startTree
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Constructor Details
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AGAVEHandler
public AGAVEHandler()
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Method Details
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reportSequence
- Specified by:
reportSequence
in interfaceAGAVECallbackItf
- 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)
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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
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