Package org.biojava.bio.seq.io.agave
Interface AGAVEAnnotFilter
- All Known Implementing Classes:
Agave2AgaveAnnotFilter
,Embl2AgaveAnnotFilter
,SimpleAnnotFilter
public interface AGAVEAnnotFilter
This interface defines mapping from BioJava into AGAVE format. As data from different sources is stored differently in BioJava it is impossible to define universal mapping from BioJava to Agave. Currently I implemented two mappings:
( embl -> )biojava -> agave
( agave -> )biojava -> agave
- Author:
- Hanning Ni Doubletwist Inc
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
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Method Summary
Modifier and TypeMethodDescriptiongetAccession
(Annotation annot) getAlignLength
(Annotation annot) getAlignUnits
(Annotation annot) getAltIds
(Annotation annot) getChromNum
(Annotation annot) getChromosome
(Annotation annot) getClassifyId
(Annotation annot) getClassifySystem
(Annotation annot) getClassifyType
(Annotation annot) getCloneId
(Annotation annot) getCloneLibrary
(Annotation annot) getConfidence
(Annotation annot) getCreateDate
(Annotation annot) getDbId
(Annotation annot) getDescription
(Annotation annot) getEcNumber
(Annotation annot) getElementId
(Annotation annot) String[]
getElementIds
(Annotation annot) String[]
getExonIds
(Annotation annot) getFeatureType
(Annotation annot) getGroupOrder
(Annotation annot) getIdAlias
(Annotation annot) getKeyword
(Annotation annot) getLabel
(Annotation annot) getMapLocation
(Annotation annot) getMapPosition
(Annotation annot) getMatchAlign
(Annotation annot) getMatchDesc
(Annotation annot) getMatchRegion
(Annotation annot) getMolType
(Annotation annot) getNote
(Annotation annot) getOrganism
(Annotation annot) getOS
(Annotation annot) getProperty
(Annotation annot, String type) getQueryRegion
(Annotation annot) getRelatedAnnot
(Annotation annot) getResultType
(Annotation annot) getSequenceId
(Annotation annot) getTaxonId
(Annotation annot) getUpdateDate
(Annotation annot) getVersion
(Annotation annot) getXrefs
(Annotation annot)
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Field Details
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FORWARD
- See Also:
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COMPLEMENT
- See Also:
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BOTH_FORWARD_COMPLEMENT
- See Also:
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Method Details
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getAccession
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getLabel
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getElementId
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getSequenceId
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getKeyword
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getOrganism
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getDescription
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getNote
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getVersion
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getOS
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getMolType
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getTaxonId
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getCloneId
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getCloneLibrary
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getChromosome
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getMapPosition
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getEcNumber
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getCreateDate
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getUpdateDate
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getAltIds
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getXrefs
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getMapLocation
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getRelatedAnnot
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getElementIds
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getExonIds
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getChromNum
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getProperty
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getDbId
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getGroupOrder
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getFeatureType
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getResultType
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getConfidence
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getAlignLength
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getAlignUnits
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getMatchDesc
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getMatchAlign
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getQueryRegion
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getMatchRegion
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getIdAlias
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getClassifySystem
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getClassifyId
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getClassifyType
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