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java.lang.Objectorg.biojava.utils.stax.StAXContentHandlerBase
org.biojava.bio.seq.io.game.StAXFeatureHandler
org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
public class GAMEFeatureSetHandler
Handles the <feature_set> element
Field Summary | |
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static StAXHandlerFactory |
GAME_FEATURESET_HANDLER_FACTORY
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Fields inherited from class org.biojava.bio.seq.io.game.StAXFeatureHandler |
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callbackStack, endLoc, featureListener, featureTemplate, stackLevel, startLoc |
Method Summary | |
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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 |
NameSetStringValue(java.lang.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(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 |
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addHandler, endElement, getFeatureListener, getHandlerStackIterator, getLevel, pop, push, setFeatureListener, setHandlerCharacteristics, startElement |
Methods inherited from class org.biojava.utils.stax.StAXContentHandlerBase |
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characters, endPrefixMapping, endTree, ignorableWhitespace, processingInstruction, setDocumentLocator, skippedEntity, startPrefixMapping, startTree |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final StAXHandlerFactory GAME_FEATURESET_HANDLER_FACTORY
Method Detail |
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public void NameSetStringValue(java.lang.String s)
GAMENameCallbackItf
NameSetStringValue
in interface GAMENameCallbackItf
public void reportExon(RangeLocation range, StrandedFeature.Strand strand)
GAMETranscriptCallbackItf
reportExon
in interface GAMETranscriptCallbackItf
protected Feature.Template createTemplate()
StAXFeatureHandler
Override if you wish a more specialised Template.
createTemplate
in class StAXFeatureHandler
public void startElementHandler(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attrs) throws org.xml.sax.SAXException
StAXFeatureHandler
startElementHandler
in class StAXFeatureHandler
org.xml.sax.SAXException
public void endElementHandler(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, StAXContentHandler handler)
StAXFeatureHandler
endElementHandler
in class StAXFeatureHandler
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