org.biojava.bio.seq.io.game
Class GAMEFeatureSetHandler

java.lang.Object
  extended by org.biojava.utils.stax.StAXContentHandlerBase
      extended by org.biojava.bio.seq.io.game.StAXFeatureHandler
          extended by 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
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
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