Package org.biojava.bio.seq.io.game
Class GAMEFeatureSetHandler
java.lang.Object
org.biojava.utils.stax.StAXContentHandlerBase
org.biojava.bio.seq.io.game.StAXFeatureHandler
org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
- All Implemented Interfaces:
GAMENameCallbackItf
,GAMETranscriptCallbackItf
,StAXContentHandler
public class GAMEFeatureSetHandler
extends StAXFeatureHandler
implements GAMENameCallbackItf, GAMETranscriptCallbackItf
Handles the <feature_set> 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
Callback implemented by nesting class to allow nested class to pass string to nesting class for handling.void
reportExon
(RangeLocation range, StrandedFeature.Strand strand) Allows nesting class that manages a transcript template to gain information about its extent from nested elements that represent exons.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_FEATURESET_HANDLER_FACTORY
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Method Details
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NameSetStringValue
Description copied from interface:GAMENameCallbackItf
Callback implemented by nesting class to allow nested class to pass string to nesting class for handling.- Specified by:
NameSetStringValue
in interfaceGAMENameCallbackItf
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reportExon
Description copied from interface:GAMETranscriptCallbackItf
Allows nesting class that manages a transcript template to gain information about its extent from nested elements that represent exons.- Specified by:
reportExon
in interfaceGAMETranscriptCallbackItf
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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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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) Description copied from class:StAXFeatureHandler
Element specific exit handler Subclass to do anything useful.- Overrides:
endElementHandler
in classStAXFeatureHandler
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