Package org.biojava.bio.program.xff

Class FeatureHandler

java.lang.Object

org.biojava.utils.stax.StAXContentHandlerBase

org.biojava.bio.program.xff.FeatureHandler

All Implemented Interfaces:

StAXContentHandler

Direct Known Subclasses:

StrandedFeatureHandler

public class FeatureHandler
extends StAXContentHandlerBase

StAX handler for the basic feature type of XFF. This class can also be subclassed to handle other XFF types.

In general, to handle a feature subclass, you will with to:

• If necessary, override createFeatureTemplate to build the appropriate BioJava Feature.Template
• Add your own startElement and endElement methods which handle extra extra elements in your feature type. These should normally pass on all the standard elements to super.startElement and super.endElement.

Note that, since FeatureHandler does some basic housekeeping, if you `consume' a startElement notification (i.e. don't pass it on to the superclass) you must also consume the matching endElement. Since FeatureHandler silently ignores all unrecognized elements, it is usually safe to pass on all startElement and endElement notifications -- even those which are specific to your feature type.

Since:

1.2

Author:

Thomas Down

Field Summary

Fields

Modifier and Type	Field	Description
static XFFPartHandlerFactory	FEATURE_HANDLER_FACTORY

Constructor Summary

Constructors

Constructor	Description
FeatureHandler(XFFFeatureSetHandler xffenv)	Construct a new Feature handler, passing in an XFF-parsing environment.

Method Summary

Modifier and Type	Method	Description
protected Feature.Template	createFeatureTemplate()	Create a new template of the appropriate type.
void	endElement(String nsURI, String localName, String qName, StAXContentHandler handler)	StAX callback for element ends.
protected void	fireEndFeature()	Fire the endFeature event.
protected void	fireStartFeature()	Fire the startFeature event.
protected Feature.Template	getFeatureTemplate()	Get the template for the feature being constructed.
protected StAXContentHandler	getLocationHandler()
protected StAXContentHandler	getOldIDHandler()
protected StAXContentHandler	getSourceHandler()
protected StAXContentHandler	getTypeHandler()
XFFFeatureSetHandler	getXFFEnvironment()	Return the XFF processing environment passed in when this handler was created.
protected void	setFeatureProperty(Object key, Object value)	Set a property.
void	startElement(String nsURI, String localName, String qName, Attributes attrs, DelegationManager dm)	StAX callback for element starts.

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

FEATURE_HANDLER_FACTORY

public static final XFFPartHandlerFactory FEATURE_HANDLER_FACTORY

Constructor Detail

FeatureHandler

public FeatureHandler(XFFFeatureSetHandler xffenv)

Construct a new Feature handler, passing in an XFF-parsing environment.

Method Detail

getXFFEnvironment

public XFFFeatureSetHandler getXFFEnvironment()

Return the XFF processing environment passed in when this handler was created.

getFeatureTemplate

protected Feature.Template getFeatureTemplate()

Get the template for the feature being constructed. This should usually not be overridden. Delegates to createFeatureTemplate for template construction.

createFeatureTemplate

protected Feature.Template createFeatureTemplate()

Create a new template of the appropriate type. Override this method if you wish to use a template type other than Feature.Template.

fireStartFeature

protected void fireStartFeature()
                         throws ParseException

Fire the startFeature event. You should wrap this method if you want to perform any validation on the Feature.Template before the startFeature is fired.

Throws:

ParseException - if the startFeature notification fails, or if it has already been made.

fireEndFeature

protected void fireEndFeature()
                       throws ParseException

Fire the endFeature event.

Throws:

ParseException

setFeatureProperty

protected void setFeatureProperty(Object key,
                                  Object value)
                           throws ChangeVetoException,
                                  ParseException

Set a property. If the startFeature notification has not yet been fired, the property is added directly to the annotation bundle in the feature template, otherwise an addFeatureProperty event is generated.

Throws:

ChangeVetoException

ParseException

startElement

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

StAX callback for element starts. Wrap this method to handle extra elements within your own feature types.

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)
                throws SAXException

StAX callback for element ends. Wrap this method to handle extra elements within your own feature types.

Specified by:

endElement in interface StAXContentHandler

Overrides:

endElement in class StAXContentHandlerBase

Throws:

SAXException

getTypeHandler

protected StAXContentHandler getTypeHandler()

getSourceHandler

protected StAXContentHandler getSourceHandler()

getOldIDHandler

protected StAXContentHandler getOldIDHandler()

getLocationHandler

protected StAXContentHandler getLocationHandler()