Uses of Package
org.biojava.bio.seq.io.agave

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

Classes in org.biojava.bio.seq.io.agave used by org.biojava.bio.seq.io.agave
AGAVEAnnotFilter
          This interface defines mapping from BioJava into AGAVE format.
AGAVEAnnotFilterFactory
           
AGAVEBioSeqCallbackItf
          An interface that can be tested for by nested handlers when trying to do a callback.
AGAVECallbackItf
          An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEChromosomeCallbackItf
          An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEContigCallbackItf
          An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEDbId
          * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEDbIdCallbackItf
          this is the interface implemented by several classes
AGAVEDbIdPropCallbackItf
           
AGAVEEvidenceCallbackItf
           
AGAVEFeatureCallbackItf
          An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEIdAlias
          * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEIdAliasCallbackItf
           
AGAVEMapLocation
          * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEMapPosition
          * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEMatchRegion
          * match_region * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEProperty
           
AGAVEQueryRegion
          * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVERelatedAnnot
          * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AgaveWriter.Indent
          Implements indenting for elements.
AGAVEXref
          xref
AGAVEXrefCallbackItf
           
AGAVEXrefs
          * xrefs * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
DelegationManager
          Interface which exposes delegation services offered by a StAX event source.
ElementRecognizer
          This class is copied to agave package Simple interface for filtering SAX/StAX startElement events
SequenceHandler
          mark interface
SimpleAnnotFilter
          Basic implementation of AGAVEAnnotFilter
StAXContentHandler
          Interface for StAX content handlers.
StAXContentHandlerBase
          Simple implementation of the StAXContentHandler interface, with empty implementations for all the methods.
StAXFeatureHandler
          StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXHandlerFactory
          Factory for StAX content handlers.
StAXPropertyHandler
          StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.