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
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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
String getAccession(Annotation annot)
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getLabel
String getLabel(Annotation annot)
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getElementId
String getElementId(Annotation annot)
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getSequenceId
String getSequenceId(Annotation annot)
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getKeyword
String getKeyword(Annotation annot)
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getOrganism
String getOrganism(Annotation annot)
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getDescription
String getDescription(Annotation annot)
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getNote
String getNote(Annotation annot)
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getVersion
String getVersion(Annotation annot)
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getOS
String getOS(Annotation annot)
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getMolType
String getMolType(Annotation annot)
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getTaxonId
String getTaxonId(Annotation annot)
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getCloneId
String getCloneId(Annotation annot)
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getCloneLibrary
String getCloneLibrary(Annotation annot)
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getChromosome
String getChromosome(Annotation annot)
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getMapPosition
String getMapPosition(Annotation annot)
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getEcNumber
String getEcNumber(Annotation annot)
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getCreateDate
String getCreateDate(Annotation annot)
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getUpdateDate
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
String[] getElementIds(Annotation annot)
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getExonIds
String[] getExonIds(Annotation annot)
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getChromNum
String getChromNum(Annotation annot)
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getProperty
AGAVEProperty[] getProperty(Annotation annot, String type)
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getDbId
AGAVEDbId getDbId(Annotation annot)
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getGroupOrder
String getGroupOrder(Annotation annot)
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getFeatureType
String getFeatureType(Annotation annot)
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getResultType
String getResultType(Annotation annot)
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getConfidence
String getConfidence(Annotation annot)
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getAlignLength
String getAlignLength(Annotation annot)
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getAlignUnits
String getAlignUnits(Annotation annot)
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getMatchDesc
String getMatchDesc(Annotation annot)
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getMatchAlign
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
String getClassifySystem(Annotation annot)
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getClassifyId
String getClassifyId(Annotation annot)
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getClassifyType
String getClassifyType(Annotation annot)
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