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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 |
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.
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