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

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.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
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
protected  Feature.Template createTemplate()
          generates a very basic Template for the feature with SmallAnnotation in the annotation field.
 void endElementHandler(java.lang.String nsURI, java.lang.String localName, java.lang.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(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, org.xml.sax.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(java.lang.String nsURI,
                                java.lang.String localName,
                                java.lang.String qName,
                                org.xml.sax.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(java.lang.String nsURI,
                              java.lang.String localName,
                              java.lang.String qName,
                              StAXContentHandler handler)
Description copied from class: StAXFeatureHandler
Element specific exit handler Subclass to do anything useful.

Overrides:
endElementHandler in class StAXFeatureHandler