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
-
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.voidCallback implemented by nesting class to allow nested class to pass string to nesting class for handling.voidreportExon(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.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
-
Field Details
-
GAME_FEATURESET_HANDLER_FACTORY
-
-
Method Details
-
NameSetStringValue
Description copied from interface:GAMENameCallbackItfCallback implemented by nesting class to allow nested class to pass string to nesting class for handling.- Specified by:
NameSetStringValuein interfaceGAMENameCallbackItf
-
reportExon
Description copied from interface:GAMETranscriptCallbackItfAllows nesting class that manages a transcript template to gain information about its extent from nested elements that represent exons.- Specified by:
reportExonin interfaceGAMETranscriptCallbackItf
-
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
-
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
-
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
-