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
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Method Summary
Modifier and TypeMethodDescriptionprotected Feature.Template
generates a very basic Template for the feature with SmallAnnotation in the annotation field.void
endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.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.game.StAXFeatureHandler
addHandler, endElement, getFeatureListener, getHandlerStackIterator, getLevel, pop, push, setFeatureListener, setHandlerCharacteristics, startElement
Methods 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:StAXFeatureHandler
generates a very basic Template for the feature with SmallAnnotation in the annotation field.Override if you wish a more specialised Template.
- Overrides:
createTemplate
in classStAXFeatureHandler
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reportFeature
Description copied from interface:GAMEFeatureCallbackItf
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 interfaceGAMEFeatureCallbackItf
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reportStrand
- Specified by:
reportStrand
in interfaceGAMEFeatureCallbackItf
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startElementHandler
Description copied from class:StAXFeatureHandler
Element-specific handler. Subclass this to do something useful!- Overrides:
startElementHandler
in classStAXFeatureHandler
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endElementHandler
public void endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) Description copied from class:StAXFeatureHandler
Element specific exit handler Subclass to do anything useful.- Overrides:
endElementHandler
in classStAXFeatureHandler
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