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.