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

Classes for converting between AGAVE XML and BioJava objects.

See:
          Description

Interface Summary
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
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 * @author Hanning Ni Doubletwist Inc * @author Greg Cox
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 * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEIdAliasPropHandler  
AGAVEKeywordPropHandler Deals with AGAVE keywords
AGAVEMapLocation * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEMapLocationPropHandler  
AGAVEMapPosition * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEMapPositionPropHandler  
AGAVEMatchAlignPropHandler Deals with match_align
AGAVEMatchDescPropHandler Deals with match_desc
AGAVEMatchRegion * match_region * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
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 * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVEQueryRegionPropHandler  
AGAVERelatedAnnot * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
AGAVERelatedAnnotPropHandler  
AGAVEResultGroupHandler  
AGAVEResultPropertyPropHandler  
AGAVESciPropertyPropHandler sci_property
AGAVESeqFeatureHandler seq_feature
AGAVESeqLocationPropHandler seq_location
AGAVESeqMapHandler sequence_map
AGAVESeqPropHandler * Deals with sequence code * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
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 * * @author Hanning Ni Doubletwist Inc * @author Greg Cox
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.