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

public class GAMEAnnotationHandler
extends StAXFeatureHandler
implements GAMEFeatureCallbackItf

Handles the GAME <annotation> element

Since:

1.2

Author:

David Huen

Field Summary

Fields

Modifier and Type	Field and Description
static StAXHandlerFactory	GAME_ANNOTATION_HANDLER_FACTORY

Fields inherited from class org.biojava.bio.seq.io.game.StAXFeatureHandler

callbackStack, endLoc, featureListener, featureTemplate, stackLevel, startLoc

Method Summary

Methods

Modifier and Type	Method and Description
protected Feature.Template	createTemplate() 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

GAME_ANNOTATION_HANDLER_FACTORY

public static final StAXHandlerFactory GAME_ANNOTATION_HANDLER_FACTORY

Method Detail

createTemplate

protected Feature.Template 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 class StAXFeatureHandler

reportFeature

public void reportFeature(Location loc)

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 interface GAMEFeatureCallbackItf

reportStrand

public void reportStrand(StrandedFeature.Strand strand)

Specified by:

reportStrand in interface GAMEFeatureCallbackItf

startElementHandler

public void startElementHandler(String nsURI,
                       String localName,
                       String qName,
                       Attributes attrs)

Description copied from class: StAXFeatureHandler

Element-specific handler. Subclass this to do something useful!

Overrides:

startElementHandler in class StAXFeatureHandler

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 class StAXFeatureHandler