Package org.biojava.bio.program.xff

Class XFFFeatureSetHandler

java.lang.Object

org.biojava.utils.stax.StAXContentHandlerBase

org.biojava.bio.program.xff.XFFFeatureSetHandler

All Implemented Interfaces:

StAXContentHandler

public class XFFFeatureSetHandler
extends StAXContentHandlerBase

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.

Since:

1.2

Author:

Thomas Down

Field Summary

Fields

Modifier and Type	Field	Description
static String	PROPERTY_XFF_ID

Constructor Summary

Constructors

Constructor	Description
XFFFeatureSetHandler()	Construct a new XFFFeatureSetHandler with the default set of handlers.

Method Summary

Modifier and Type	Method	Description
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(String nsURI, String localName, String qName, StAXContentHandler handler)
StAXContentHandlerBase	getDetailsHandler()	Return a handler for the XFF details element.
SeqIOListener	getFeatureListener()	Return the object which receives startFeature/endFeature notifications.
Annotation	getMergeAnnotation()
void	setFeatureListener(SeqIOListener siol)	Set the object which receives startFeature/endFeature notifications.
void	setMergeAnnotation(Annotation ann)
void	startElement(String nsURI, String localName, String qName, Attributes attrs, DelegationManager dm)

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

PROPERTY_XFF_ID

public static final String PROPERTY_XFF_ID

See Also:

Constant Field Values

Constructor Detail

XFFFeatureSetHandler

public XFFFeatureSetHandler()

Construct a new XFFFeatureSetHandler with the default set of handlers.

Method Detail

setFeatureListener

public void setFeatureListener(SeqIOListener siol)

Set the object which receives startFeature/endFeature notifications.

getFeatureListener

public SeqIOListener getFeatureListener()

Return the object which receives startFeature/endFeature notifications.

setMergeAnnotation

public void setMergeAnnotation(Annotation ann)

getMergeAnnotation

public Annotation getMergeAnnotation()

addFeatureHandler

public void addFeatureHandler(ElementRecognizer rec,
                              XFFPartHandlerFactory handler)

Extend this FeatureSetHandler to delegate certain feature elements to the specified handler type.

Parameters:

rec - A selector for some sub-set of feature elements.

handler - A factory which returns StAX handlers for matching elements.

addDetailHandler

public void addDetailHandler(ElementRecognizer rec,
                             XFFPartHandlerFactory handler)

Extend this FeatureSetHandler to delegate certain detail elements to the specified handler type.

Parameters:

rec - A selector for some sub-set of detail elements.

handler - A factory which returns StAX handlers for matching elements.

startElement

public void startElement(String nsURI,
                         String localName,
                         String qName,
                         Attributes attrs,
                         DelegationManager dm)
                  throws SAXException

Specified by:

startElement in interface StAXContentHandler

Overrides:

startElement in class StAXContentHandlerBase

Throws:

SAXException

endElement

public void endElement(String nsURI,
                       String localName,
                       String qName,
                       StAXContentHandler handler)

Specified by:

endElement in interface StAXContentHandler

Overrides:

endElement in class StAXContentHandlerBase

getDetailsHandler

public StAXContentHandlerBase getDetailsHandler()

Return a handler for the XFF details element. This handler will, in turn, delegate to the specific detail handlers provided with addDetailHandler