Package org.biojava.bio.seq.io.agave
Classes for converting between AGAVE XML and BioJava objects. Use AGAVEHandler with a SAX parser to
parse AGAVE XML into BioJava Sequences, and use AgaveWriter to write BioJava Sequences into AGAVE format.
When writing BioJava to AGAVE we need to specify how the data in BioJava stored.
Two conversion filters are implemented. The Agave2AgaveAnnotFilter helps write data that was parsed from
AGAVE, and Embl2AgaveAnnotFilter helps write data that was parsed from EMBL.
This package uses a modified version of the BioJava StAX parser architecture that
supports nested features.
-
Interface Summary Interface 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.AGAVEDbIdCallbackItf this is the interface implemented by several classesAGAVEDbIdPropCallbackItf AGAVEEvidenceCallbackItf AGAVEFeatureCallbackItf An interface that can be tested for by nested handlers when trying to do a callback.AGAVEIdAliasCallbackItf AGAVEXrefCallbackItf 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 eventsSequenceHandler mark interfaceStAXContentHandler Interface for StAX content handlers.StAXHandlerFactory Factory for StAX content handlers. -
Class Summary Class Description Agave2AgaveAnnotFilter Dumping the data from biojava with source of agave into agave formatAGAVEAltIdsPropHandler Deals with alternate sequence IDsAGAVEAnnotationsHandler AGAVEAssemblyHandler AGAVEBioSeqHandler Handles the AGAVE <bio_sequence> elementAGAVEBioSequenceHandler Handles the AGAVE <bio_sequence> elementAGAVECdsHandler Handles the AGAVE <cds> elementAGAVEChromosomeHandler Handles the AGAVE <chromosome> elementAGAVEClassificationHandler AGAVECompResultHandler AGAVEComputationHandler AGAVEContigHandler Handles the AGAVE <contig> elementAGAVEDbId AGAVEDbIdPropHandler Deals with database crossreferencesAGAVEDescPropHandler Deals with database crossreferencesAGAVEElementIdPropHandler AGAVEEvidenceHandler AGAVEExonsPropHandler AGAVEFragmentOrderHandler AGAVEFragmentOrientationHandler AGAVEGeneHandler AGAVEHandler Handles the root AGAVE element modified for agave formatAGAVEIdAlias AGAVEIdAliasPropHandler AGAVEKeywordPropHandler Deals with AGAVE keywordsAGAVEMapLocation AGAVEMapLocationPropHandler AGAVEMapPosition AGAVEMapPositionPropHandler AGAVEMatchAlignPropHandler Deals with match_alignAGAVEMatchDescPropHandler Deals with match_descAGAVEMatchRegion match_regionAGAVEMatchRegionPropHandler Deals with match_regionAGAVEMrnaHandler Handles the AGAVE <mrna> elementAGAVENotePropHandler Deals with noteAGAVEPredictedProteinHandler Handles the AGAVE <predicted_protein> elementAGAVEProperty AGAVEQualifierPropHandler AGAVEQueryRegion AGAVEQueryRegionPropHandler AGAVERelatedAnnot AGAVERelatedAnnotPropHandler AGAVEResultGroupHandler AGAVEResultPropertyPropHandler AGAVESciPropertyPropHandler sci_propertyAGAVESeqFeatureHandler seq_featureAGAVESeqLocationPropHandler seq_locationAGAVESeqMapHandler sequence_mapAGAVESeqPropHandler Deals with sequence codeAGAVETranscriptHandler transcriptAGAVEUnorderedFragmentsHandler unordered_fragmentsAGAVEViewPropHandler Moves view attributes into annotation properties.AgaveWriter Writes Sequence into AGAVE XML document.AGAVEXref xrefAGAVEXrefPropHandler handle AGAVE xrefAGAVEXrefPropPropHandler xref_propertyAGAVEXrefs xrefsAGAVEXrefsPropHandler Deals with database crossreferences (xrefs)ElementRecognizer.AllElementRecognizer ElementRecognizer.ByLocalName Filter elements by local name (not recommended).ElementRecognizer.ByNSName Filter elements by name and namespace.ElementRecognizer.HasAttribute Filter elements on the existence of a specified attribute.Embl2AgaveAnnotFilter Map EMBL data into AGAVE formatSAX2StAXAdaptor Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services.SimpleAnnotFilter Basic implementation of AGAVEAnnotFilterStAXContentHandlerBase Simple implementation of theStAXContentHandlerinterface, with empty implementations for all the methods.StAXFeatureHandler StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.StAXPropertyHandler StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.UtilHelper Just make the property follow the common case