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java.lang.Objectorg.biojava.utils.stax.StAXContentHandlerBase
org.biojava.bio.program.xff.XFFFeatureSetHandler
public class XFFFeatureSetHandler
StAX handler which converts and stream of parse events for an XFF featureSet element into BioJava SeqIO events. NOTE This class is not thread-safe -- it must only be used for one parse at any time.
Field Summary | |
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static java.lang.String |
PROPERTY_XFF_ID
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Constructor Summary | |
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XFFFeatureSetHandler()
Construct a new XFFFeatureSetHandler with the default set of handlers. |
Method Summary | |
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void |
addDetailHandler(ElementRecognizer rec,
XFFPartHandlerFactory handler)
Extend this FeatureSetHandler to delegate certain detail elements to the specified handler type. |
void |
addFeatureHandler(ElementRecognizer rec,
XFFPartHandlerFactory handler)
Extend this FeatureSetHandler to delegate certain feature elements to the specified handler type. |
void |
endElement(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
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StAXContentHandlerBase |
getDetailsHandler()
Return a handler for the XFF details element. |
SeqIOListener |
getFeatureListener()
Return the object which receives startFeature/endFeature notifications. |
Annotation |
getMergeAnnotation()
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void |
setFeatureListener(SeqIOListener siol)
Set the object which receives startFeature/endFeature notifications. |
void |
setMergeAnnotation(Annotation ann)
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void |
startElement(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
org.xml.sax.Attributes attrs,
DelegationManager dm)
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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 java.lang.String PROPERTY_XFF_ID
Constructor Detail |
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public XFFFeatureSetHandler()
Method Detail |
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public void setFeatureListener(SeqIOListener siol)
public SeqIOListener getFeatureListener()
public void setMergeAnnotation(Annotation ann)
public Annotation getMergeAnnotation()
public void addFeatureHandler(ElementRecognizer rec, XFFPartHandlerFactory handler)
rec
- A selector for some sub-set of feature elements.handler
- A factory which returns StAX handlers for matching elements.public void addDetailHandler(ElementRecognizer rec, XFFPartHandlerFactory handler)
rec
- A selector for some sub-set of detail elements.handler
- A factory which returns StAX handlers for matching elements.public void startElement(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attrs, DelegationManager dm) throws org.xml.sax.SAXException
startElement
in interface StAXContentHandler
startElement
in class StAXContentHandlerBase
org.xml.sax.SAXException
public void endElement(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, StAXContentHandler handler)
endElement
in interface StAXContentHandler
endElement
in class StAXContentHandlerBase
public StAXContentHandlerBase getDetailsHandler()
details
element.
This handler will, in turn, delegate to the specific detail
handlers provided with addDetailHandler
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