Uses of Interface
org.biojava.bio.seq.io.agave.StAXContentHandler

Packages that use StAXContentHandler
org.biojava.bio.seq.io.agave Classes for converting between AGAVE XML and BioJava objects. 
 

Uses of StAXContentHandler in org.biojava.bio.seq.io.agave
 

Classes in org.biojava.bio.seq.io.agave that implement StAXContentHandler
 class AGAVEAltIdsPropHandler
          Deals with alternate sequence IDs
 class AGAVEAnnotationsHandler
           
 class AGAVEAssemblyHandler
           
 class AGAVEBioSeqHandler
          Handles the AGAVE <bio_sequence> element
 class AGAVEBioSequenceHandler
          Handles the AGAVE <bio_sequence> element
 class AGAVECdsHandler
          Handles the AGAVE <cds> element
 class AGAVEChromosomeHandler
          Handles the AGAVE <chromosome> element
 class AGAVEClassificationHandler
           
 class AGAVECompResultHandler
           
 class AGAVEComputationHandler
           
 class AGAVEContigHandler
          Handles the AGAVE <contig> element
 class AGAVEDbIdPropHandler
          Deals with database crossreferences
 class AGAVEDescPropHandler
          Deals with database crossreferences
 class AGAVEElementIdPropHandler
           
 class AGAVEEvidenceHandler
           
 class AGAVEExonsPropHandler
           
 class AGAVEFragmentOrderHandler
           
 class AGAVEFragmentOrientationHandler
           
 class AGAVEGeneHandler
           
 class AGAVEHandler
          Handles the root AGAVE element modified for agave format
 class AGAVEIdAliasPropHandler
           
 class AGAVEKeywordPropHandler
          Deals with AGAVE keywords
 class AGAVEMapLocationPropHandler
           
 class AGAVEMapPositionPropHandler
           
 class AGAVEMatchAlignPropHandler
          Deals with match_align
 class AGAVEMatchDescPropHandler
          Deals with match_desc
 class AGAVEMatchRegionPropHandler
          Deals with match_region
 class AGAVEMrnaHandler
          Handles the AGAVE <mrna> element
 class AGAVENotePropHandler
          Deals with note
 class AGAVEPredictedProteinHandler
          Handles the AGAVE <predicted_protein> element
 class AGAVEQualifierPropHandler
           
 class AGAVEQueryRegionPropHandler
           
 class AGAVERelatedAnnotPropHandler
           
 class AGAVEResultGroupHandler
           
 class AGAVEResultPropertyPropHandler
           
 class AGAVESciPropertyPropHandler
          sci_property
 class AGAVESeqFeatureHandler
          seq_feature
 class AGAVESeqLocationPropHandler
          seq_location
 class AGAVESeqMapHandler
          sequence_map
 class AGAVESeqPropHandler
          Deals with sequence code
 class AGAVETranscriptHandler
          transcript
 class AGAVEUnorderedFragmentsHandler
          unordered_fragments
 class AGAVEViewPropHandler
          Moves view attributes into annotation properties.
 class AGAVEXrefPropHandler
          handle AGAVE xref
 class AGAVEXrefPropPropHandler
          xref_property
 class AGAVEXrefsPropHandler
          Deals with database crossreferences (xrefs)
 class StAXContentHandlerBase
          Simple implementation of the StAXContentHandler interface, with empty implementations for all the methods.
 class StAXFeatureHandler
          StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
 class StAXPropertyHandler
          StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
 

Methods in org.biojava.bio.seq.io.agave that return StAXContentHandler
 StAXContentHandler StAXHandlerFactory.getHandler(StAXFeatureHandler staxenv)
          Return a suitable StAX content handler.
 

Methods in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandler
 void DelegationManager.delegate(StAXContentHandler handler)
           
 void StAXContentHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate)
           
 void StAXContentHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate)
           
 void StAXFeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
          Handles basic exit processing.
 void StAXPropertyHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEMapLocationPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEMapPositionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEElementIdPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVERelatedAnnotPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void StAXFeatureHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
          Element specific exit handler Subclass to do anything useful.
 void AGAVEDbIdPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVESeqLocationPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void StAXPropertyHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
          Element specific exit handler Subclass to do anything useful.
 void AGAVEXrefPropPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEXrefsPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVESeqPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEEvidenceHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVESciPropertyPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEClassificationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEQueryRegionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEXrefPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEChromosomeHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEResultPropertyPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEBioSeqHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEQualifierPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEMatchRegionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEContigHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void AGAVEIdAliasPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
           
protected  void StAXFeatureHandler.push(StAXContentHandler handler)
          Push StAXContentHandler object onto stack
 

Constructors in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandler
SAX2StAXAdaptor(StAXContentHandler rootHandler)
          Construct a new SAX Content handler which wraps a StAX handler.