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

Packages that use org.biojava.bio.seq.io.agave

Package	Description
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

Class and Description
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
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
AGAVEIdAliasCallbackItf
AGAVEMapLocation
AGAVEMapPosition
AGAVEMatchRegion match_region
AGAVEProperty
AGAVEQueryRegion
AGAVERelatedAnnot
AgaveWriter.Indent Implements indenting for elements.
AGAVEXref xref
AGAVEXrefCallbackItf
AGAVEXrefs xrefs
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.