org.biojava.bio.seq.io.agave

Class StAXFeatureHandler

java.lang.Object

org.biojava.bio.seq.io.agave.StAXContentHandlerBase

org.biojava.bio.seq.io.agave.StAXFeatureHandler

All Implemented Interfaces:

StAXContentHandler

Direct Known Subclasses:

AGAVEAssemblyHandler, AGAVEBioSeqHandler, AGAVEBioSequenceHandler, AGAVECdsHandler, AGAVEChromosomeHandler, AGAVEClassificationHandler, AGAVECompResultHandler, AGAVEComputationHandler, AGAVEContigHandler, AGAVEEvidenceHandler, AGAVEFragmentOrderHandler, AGAVEFragmentOrientationHandler, AGAVEGeneHandler, AGAVEHandler, AGAVEMrnaHandler, AGAVEPredictedProteinHandler, AGAVEQueryRegionPropHandler, AGAVEResultGroupHandler, AGAVESeqFeatureHandler, AGAVESeqMapHandler, AGAVETranscriptHandler, AGAVEUnorderedFragmentsHandler

public class StAXFeatureHandler
extends StAXContentHandlerBase

StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. It was modified for greater generality. NOTE This class is not thread-safe -- it must only be used for one parse at any time.

Because AGAVE has nested feature and each feature must attached to some parent feature-holder in biojava, which means we need to generate parents first, so we have to keep the tree structure of features in memory, which is really bad. anyway, we still saved a lot of memory compared with DOM tree . Hanning Ni)

Author:

copied from Thomas Down, copied from David Huen, Hanning Ni Doubletwist Inc

Field Summary

Fields

Modifier and Type	Field and Description
protected SimpleAnnotation	annot
protected List	callbackStack this is the stack of handler objects for the current feature.
protected int	endLoc
protected SeqIOListener	featureListener
protected Feature.Template	featureTemplate
protected String	myLocalName
protected int	stackLevel
protected int	startLoc
protected StAXFeatureHandler	staxenv
protected List	subFeatures

Method Summary

Methods

Modifier and Type	Method and Description
protected void	addFeatureToSequence(Sequence seq)
protected void	addHandler(ElementRecognizer rec, StAXHandlerFactory handler)
protected Feature.Template	createTemplate() generates a very basic Template for the feature with SmallAnnotation in the annotation field.
void	endElement(String nsURI, String localName, String qName, StAXContentHandler handler) Handles basic exit processing.
void	endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.
SeqIOListener	getFeatureListener() Return current feature listener
protected ListIterator	getHandlerStackIterator(int level) return iterator to callbackStack
protected int	getLevel() return current stack level.
protected void	pop() pop a StAXContentHandler off the stack.
protected void	push(StAXContentHandler handler) Push StAXContentHandler object onto stack
protected void	realizeSubFeatures(Feature feature) recursively attach children features to parent
void	setFeatureListener(SeqIOListener siol)
void	setHandlerCharacteristics(String localName, boolean hasCallback) Sets the element name that the class responds to.
protected void	setProperty(String name, String value, boolean forFeature)
void	startElement(String nsURI, String localName, String qName, Attributes attrs, DelegationManager dm) Handles basic entry processing for all feature handlers.
void	startElementHandler(String nsURI, String localName, String qName, Attributes attrs) Element-specific handler.

Methods inherited from class org.biojava.bio.seq.io.agave.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

myLocalName

protected String myLocalName

featureTemplate

protected Feature.Template featureTemplate

staxenv

protected StAXFeatureHandler staxenv

featureListener

protected SeqIOListener featureListener

startLoc

protected int startLoc

endLoc

protected int endLoc

callbackStack

protected List callbackStack

this is the stack of handler objects for the current feature. The base value is the FeatureHandler itself. your feature and property handlers place and remove themselves from this stack. the purpose of all this is to implement context sensitivty for property handlers translucently. Property handlers can pop the stack for other handlers that implement interfaces that process that element. This way the context code is within the object that defines that context rather than in a child property handler.

stackLevel

protected int stackLevel

subFeatures

protected List subFeatures

annot

protected SimpleAnnotation annot

Method Detail

setHandlerCharacteristics

public void setHandlerCharacteristics(String localName,
                             boolean hasCallback)

Sets the element name that the class responds to.

setFeatureListener

public void setFeatureListener(SeqIOListener siol)

addHandler

protected void addHandler(ElementRecognizer rec,
              StAXHandlerFactory handler)

createTemplate

protected Feature.Template createTemplate()

generates a very basic Template for the feature with SmallAnnotation in the annotation field.

Override if you wish a more specialised Template.

realizeSubFeatures

protected void realizeSubFeatures(Feature feature)

recursively attach children features to parent

addFeatureToSequence

protected void addFeatureToSequence(Sequence seq)
                             throws Exception

Throws:

Exception

getLevel

protected int getLevel()

return current stack level. Remember that the stack level is incremented/decremented AFTER the push()/pop() calls and superclass startElement()/StopElement calls.

getHandlerStackIterator

protected ListIterator getHandlerStackIterator(int level)

return iterator to callbackStack

push

protected void push(StAXContentHandler handler)

Push StAXContentHandler object onto stack

pop

protected void pop()

pop a StAXContentHandler off the stack.

getFeatureListener

public SeqIOListener getFeatureListener()

Return current feature listener

setProperty

protected void setProperty(String name,
               String value,
               boolean forFeature)

startElementHandler

public void startElementHandler(String nsURI,
                       String localName,
                       String qName,
                       Attributes attrs)
                         throws SAXException

Element-specific handler. Subclass this to do something useful!

Throws:

SAXException

startElement

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

Handles basic entry processing for all feature handlers.

Specified by:

startElement in interface StAXContentHandler

Overrides:

startElement in class StAXContentHandlerBase

Throws:

SAXException

endElementHandler

public void endElementHandler(String nsURI,
                     String localName,
                     String qName,
                     StAXContentHandler handler)
                       throws SAXException

Element specific exit handler Subclass to do anything useful.

Throws:

SAXException

endElement

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

Handles basic exit processing.

Specified by:

endElement in interface StAXContentHandler

Overrides:

endElement in class StAXContentHandlerBase

Throws:

SAXException