AGAVEFragmentOrientationHandler (biojava-legacy 1.9.7 API)

java.lang.Object

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

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

org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler

All Implemented Interfaces:: AGAVEFeatureCallbackItf, StAXContentHandler

public class AGAVEFragmentOrientationHandler extends StAXFeatureHandler implements AGAVEFeatureCallbackItf

Author:: Hanning Ni Doubletwist Inc

Field Summary

Fields

Modifier and Type

Field

Description

static final StAXHandlerFactory

AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY

Fields inherited from class org.biojava.bio.seq.io.agave.StAXFeatureHandler
annot, callbackStack, endLoc, featureListener, featureTemplate, myLocalName, stackLevel, startLoc, staxenv, subFeatures
Method Summary

Modifier and Type

Method

Description

void

reportFeature(Location loc)

void

reportStrand(StrandedFeature.Strand strand)

void

startElementHandler(String nsURI, String localName, String qName, Attributes attrs)

Element-specific handler.

Methods inherited from class org.biojava.bio.seq.io.agave.StAXFeatureHandler
addFeatureToSequence, addHandler, createTemplate, endElement, endElementHandler, getFeatureListener, getHandlerStackIterator, getLevel, pop, push, realizeSubFeatures, setFeatureListener, setHandlerCharacteristics, setProperty, startElement

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 Details
- AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY
  
  public static final StAXHandlerFactory AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY
Method Details
- reportFeature
  
  public void reportFeature(Location loc)
  
  Specified by:
  
  reportFeature in interface AGAVEFeatureCallbackItf
- reportStrand
  
  public void reportStrand(StrandedFeature.Strand strand)
  
  Specified by:
  
  reportStrand in interface AGAVEFeatureCallbackItf
- startElementHandler
  
  public void startElementHandler(String nsURI, String localName, String qName, Attributes attrs) throws SAXException
  
  Description copied from class: StAXFeatureHandler
  
  Element-specific handler. Subclass this to do something useful!
  
  Overrides:
  
  startElementHandler in class StAXFeatureHandler
  
  Throws:
  
  SAXException