org.biojava.bio.seq.io.game
Class StAXFeatureHandler

java.lang.Object
  extended by org.biojava.utils.stax.StAXContentHandlerBase
      extended by org.biojava.bio.seq.io.game.StAXFeatureHandler
All Implemented Interfaces:
StAXContentHandler
Direct Known Subclasses:
GAMEAnnotationHandler, GAMEFeatureSetHandler, GAMEFeatureSpanHandler, GAMEHandler

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.

Since:
1.8
Author:
Thomas Down, David Huen

Field Summary
protected  java.util.List callbackStack
          this is the stack of handler objects for the current feature.
protected  int endLoc
           
protected  SeqIOListener featureListener
           
protected  Feature.Template featureTemplate
           
protected  int stackLevel
           
protected  int startLoc
           
 
Constructor Summary
StAXFeatureHandler()
           
 
Method Summary
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(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, StAXContentHandler handler)
          Handles basic exit processing.
 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.
 SeqIOListener getFeatureListener()
          Return current feature listener
protected  java.util.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
 void setFeatureListener(SeqIOListener siol)
           
 void setHandlerCharacteristics(java.lang.String localName, boolean hasCallback)
          Sets the element name that the class responds to.
 void startElement(java.lang.String nsURI, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attrs, DelegationManager dm)
          Handles basic entry processing for all feature handlers.
 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.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

featureTemplate

protected Feature.Template featureTemplate

featureListener

protected SeqIOListener featureListener

startLoc

protected int startLoc

endLoc

protected int endLoc

callbackStack

protected java.util.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
Constructor Detail

StAXFeatureHandler

public StAXFeatureHandler()
Method Detail

setHandlerCharacteristics

public void setHandlerCharacteristics(java.lang.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.


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 java.util.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


startElementHandler

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

Throws:
org.xml.sax.SAXException

startElement

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
Handles basic entry processing for all feature handlers.

Specified by:
startElement in interface StAXContentHandler
Overrides:
startElement in class StAXContentHandlerBase
Throws:
org.xml.sax.SAXException

endElementHandler

public void endElementHandler(java.lang.String nsURI,
                              java.lang.String localName,
                              java.lang.String qName,
                              StAXContentHandler handler)
                       throws org.xml.sax.SAXException
Element specific exit handler Subclass to do anything useful.

Throws:
org.xml.sax.SAXException

endElement

public void endElement(java.lang.String nsURI,
                       java.lang.String localName,
                       java.lang.String qName,
                       StAXContentHandler handler)
                throws org.xml.sax.SAXException
Handles basic exit processing.

Specified by:
endElement in interface StAXContentHandler
Overrides:
endElement in class StAXContentHandlerBase
Throws:
org.xml.sax.SAXException