Package org.biojava.bio.seq.io.game
Class GAMEAnnotationHandler
java.lang.Object
org.biojava.utils.stax.StAXContentHandlerBase
org.biojava.bio.seq.io.game.StAXFeatureHandler
org.biojava.bio.seq.io.game.GAMEAnnotationHandler
- All Implemented Interfaces:
GAMEFeatureCallbackItf,StAXContentHandler
Handles the GAME <annotation> element
- Since:
- 1.2
- Author:
- David Huen
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Field Summary
FieldsFields inherited from class org.biojava.bio.seq.io.game.StAXFeatureHandler
callbackStack, endLoc, featureListener, featureTemplate, stackLevel, startLoc -
Method Summary
Modifier and TypeMethodDescriptionprotected Feature.Templategenerates a very basic Template for the feature with SmallAnnotation in the annotation field.voidendElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.voidreportFeature(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.game.StAXFeatureHandler
addHandler, endElement, getFeatureListener, getHandlerStackIterator, getLevel, pop, push, setFeatureListener, setHandlerCharacteristics, startElementMethods inherited from class org.biojava.utils.stax.StAXContentHandlerBase
characters, endPrefixMapping, endTree, ignorableWhitespace, processingInstruction, setDocumentLocator, skippedEntity, startPrefixMapping, startTree
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Field Details
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GAME_ANNOTATION_HANDLER_FACTORY
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Method Details
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createTemplate
Description copied from class:StAXFeatureHandlergenerates a very basic Template for the feature with SmallAnnotation in the annotation field.Override if you wish a more specialised Template.
- Overrides:
createTemplatein classStAXFeatureHandler
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reportFeature
Description copied from interface:GAMEFeatureCallbackItfAllows 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 interfaceGAMEFeatureCallbackItf
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reportStrand
- Specified by:
reportStrandin interfaceGAMEFeatureCallbackItf
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startElementHandler
Description copied from class:StAXFeatureHandlerElement-specific handler. Subclass this to do something useful!- Overrides:
startElementHandlerin classStAXFeatureHandler
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endElementHandler
public void endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) Description copied from class:StAXFeatureHandlerElement specific exit handler Subclass to do anything useful.- Overrides:
endElementHandlerin classStAXFeatureHandler
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