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

Fields

Modifier and Type	Field and Description
static StAXHandlerFactory	GAME_FEATURESET_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	NameSetStringValue(String s) 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

Methods inherited from class java.lang.Object

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

Field Detail

GAME_FEATURESET_HANDLER_FACTORY

public static final StAXHandlerFactory GAME_FEATURESET_HANDLER_FACTORY

Method Detail

NameSetStringValue

public void NameSetStringValue(String s)

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 interface GAMENameCallbackItf

reportExon

public void reportExon(RangeLocation range,
              StrandedFeature.Strand strand)

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 interface GAMETranscriptCallbackItf

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

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 class StAXFeatureHandler

Throws:

SAXException

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