Package org.biojava.bio.seq.io.agave
Interface AGAVEAnnotFilter
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- 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
Fields Modifier and Type Field Description static int
BOTH_FORWARD_COMPLEMENT
static int
COMPLEMENT
static int
FORWARD
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.String
getAccession(Annotation annot)
java.lang.String
getAlignLength(Annotation annot)
java.lang.String
getAlignUnits(Annotation annot)
AGAVEDbId[]
getAltIds(Annotation annot)
java.lang.String
getChromNum(Annotation annot)
java.lang.String
getChromosome(Annotation annot)
java.lang.String
getClassifyId(Annotation annot)
java.lang.String
getClassifySystem(Annotation annot)
java.lang.String
getClassifyType(Annotation annot)
java.lang.String
getCloneId(Annotation annot)
java.lang.String
getCloneLibrary(Annotation annot)
java.lang.String
getConfidence(Annotation annot)
java.lang.String
getCreateDate(Annotation annot)
AGAVEDbId
getDbId(Annotation annot)
java.lang.String
getDescription(Annotation annot)
java.lang.String
getEcNumber(Annotation annot)
java.lang.String
getElementId(Annotation annot)
java.lang.String[]
getElementIds(Annotation annot)
java.lang.String[]
getExonIds(Annotation annot)
java.lang.String
getFeatureType(Annotation annot)
java.lang.String
getGroupOrder(Annotation annot)
AGAVEIdAlias[]
getIdAlias(Annotation annot)
java.lang.String
getKeyword(Annotation annot)
java.lang.String
getLabel(Annotation annot)
AGAVEMapLocation[]
getMapLocation(Annotation annot)
java.lang.String
getMapPosition(Annotation annot)
java.lang.String
getMatchAlign(Annotation annot)
java.lang.String
getMatchDesc(Annotation annot)
AGAVEMatchRegion
getMatchRegion(Annotation annot)
java.lang.String
getMolType(Annotation annot)
java.lang.String
getNote(Annotation annot)
java.lang.String
getOrganism(Annotation annot)
java.lang.String
getOS(Annotation annot)
AGAVEProperty[]
getProperty(Annotation annot, java.lang.String type)
AGAVEQueryRegion
getQueryRegion(Annotation annot)
AGAVERelatedAnnot[]
getRelatedAnnot(Annotation annot)
java.lang.String
getResultType(Annotation annot)
java.lang.String
getSequenceId(Annotation annot)
java.lang.String
getTaxonId(Annotation annot)
java.lang.String
getUpdateDate(Annotation annot)
java.lang.String
getVersion(Annotation annot)
AGAVEXrefs[]
getXrefs(Annotation annot)
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Field Detail
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FORWARD
static final int FORWARD
- See Also:
- Constant Field Values
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COMPLEMENT
static final int COMPLEMENT
- See Also:
- Constant Field Values
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BOTH_FORWARD_COMPLEMENT
static final int BOTH_FORWARD_COMPLEMENT
- See Also:
- Constant Field Values
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Method Detail
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getAccession
java.lang.String getAccession(Annotation annot)
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getLabel
java.lang.String getLabel(Annotation annot)
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getElementId
java.lang.String getElementId(Annotation annot)
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getSequenceId
java.lang.String getSequenceId(Annotation annot)
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getKeyword
java.lang.String getKeyword(Annotation annot)
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getOrganism
java.lang.String getOrganism(Annotation annot)
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getDescription
java.lang.String getDescription(Annotation annot)
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getNote
java.lang.String getNote(Annotation annot)
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getVersion
java.lang.String getVersion(Annotation annot)
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getOS
java.lang.String getOS(Annotation annot)
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getMolType
java.lang.String getMolType(Annotation annot)
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getTaxonId
java.lang.String getTaxonId(Annotation annot)
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getCloneId
java.lang.String getCloneId(Annotation annot)
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getCloneLibrary
java.lang.String getCloneLibrary(Annotation annot)
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getChromosome
java.lang.String getChromosome(Annotation annot)
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getMapPosition
java.lang.String getMapPosition(Annotation annot)
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getEcNumber
java.lang.String getEcNumber(Annotation annot)
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getCreateDate
java.lang.String getCreateDate(Annotation annot)
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getUpdateDate
java.lang.String getUpdateDate(Annotation annot)
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getAltIds
AGAVEDbId[] getAltIds(Annotation annot)
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getXrefs
AGAVEXrefs[] getXrefs(Annotation annot)
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getMapLocation
AGAVEMapLocation[] getMapLocation(Annotation annot)
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getRelatedAnnot
AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
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getElementIds
java.lang.String[] getElementIds(Annotation annot)
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getExonIds
java.lang.String[] getExonIds(Annotation annot)
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getChromNum
java.lang.String getChromNum(Annotation annot)
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getProperty
AGAVEProperty[] getProperty(Annotation annot, java.lang.String type)
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getDbId
AGAVEDbId getDbId(Annotation annot)
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getGroupOrder
java.lang.String getGroupOrder(Annotation annot)
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getFeatureType
java.lang.String getFeatureType(Annotation annot)
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getResultType
java.lang.String getResultType(Annotation annot)
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getConfidence
java.lang.String getConfidence(Annotation annot)
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getAlignLength
java.lang.String getAlignLength(Annotation annot)
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getAlignUnits
java.lang.String getAlignUnits(Annotation annot)
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getMatchDesc
java.lang.String getMatchDesc(Annotation annot)
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getMatchAlign
java.lang.String getMatchAlign(Annotation annot)
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getQueryRegion
AGAVEQueryRegion getQueryRegion(Annotation annot)
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getMatchRegion
AGAVEMatchRegion getMatchRegion(Annotation annot)
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getIdAlias
AGAVEIdAlias[] getIdAlias(Annotation annot)
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getClassifySystem
java.lang.String getClassifySystem(Annotation annot)
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getClassifyId
java.lang.String getClassifyId(Annotation annot)
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getClassifyType
java.lang.String getClassifyType(Annotation annot)
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