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

Classes for converting between AGAVE XML and BioJava objects.

See: Description

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 classes
AGAVEDbIdPropCallbackItf
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 events
SequenceHandler	mark interface
StAXContentHandler	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 format
AGAVEAltIdsPropHandler	Deals with alternate sequence IDs
AGAVEAnnotationsHandler
AGAVEAssemblyHandler
AGAVEBioSeqHandler	Handles the AGAVE <bio_sequence> element
AGAVEBioSequenceHandler	Handles the AGAVE <bio_sequence> element
AGAVECdsHandler	Handles the AGAVE <cds> element
AGAVEChromosomeHandler	Handles the AGAVE <chromosome> element
AGAVEClassificationHandler
AGAVECompResultHandler
AGAVEComputationHandler
AGAVEContigHandler	Handles the AGAVE <contig> element
AGAVEDbId
AGAVEDbIdPropHandler	Deals with database crossreferences
AGAVEDescPropHandler	Deals with database crossreferences
AGAVEElementIdPropHandler
AGAVEEvidenceHandler
AGAVEExonsPropHandler
AGAVEFragmentOrderHandler
AGAVEFragmentOrientationHandler
AGAVEGeneHandler
AGAVEHandler	Handles the root AGAVE element modified for agave format
AGAVEIdAlias
AGAVEIdAliasPropHandler
AGAVEKeywordPropHandler	Deals with AGAVE keywords
AGAVEMapLocation
AGAVEMapLocationPropHandler
AGAVEMapPosition
AGAVEMapPositionPropHandler
AGAVEMatchAlignPropHandler	Deals with match_align
AGAVEMatchDescPropHandler	Deals with match_desc
AGAVEMatchRegion	match_region
AGAVEMatchRegionPropHandler	Deals with match_region
AGAVEMrnaHandler	Handles the AGAVE <mrna> element
AGAVENotePropHandler	Deals with note
AGAVEPredictedProteinHandler	Handles the AGAVE <predicted_protein> element
AGAVEProperty
AGAVEQualifierPropHandler
AGAVEQueryRegion
AGAVEQueryRegionPropHandler
AGAVERelatedAnnot
AGAVERelatedAnnotPropHandler
AGAVEResultGroupHandler
AGAVEResultPropertyPropHandler
AGAVESciPropertyPropHandler	sci_property
AGAVESeqFeatureHandler	seq_feature
AGAVESeqLocationPropHandler	seq_location
AGAVESeqMapHandler	sequence_map
AGAVESeqPropHandler	Deals with sequence code
AGAVETranscriptHandler	transcript
AGAVEUnorderedFragmentsHandler	unordered_fragments
AGAVEViewPropHandler	Moves view attributes into annotation properties.
AgaveWriter	Writes Sequence into AGAVE XML document.
AGAVEXref	xref
AGAVEXrefPropHandler	handle AGAVE xref
AGAVEXrefPropPropHandler	xref_property
AGAVEXrefs	xrefs
AGAVEXrefsPropHandler	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 format
SAX2StAXAdaptor	Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services.
SimpleAnnotFilter	Basic implementation of AGAVEAnnotFilter
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.
StAXPropertyHandler	StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
UtilHelper	Just make the property follow the common case

Package org.biojava.bio.seq.io.agave Description

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.