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
FORWARD
static final int FORWARD
- See Also:
- Constant Field Values
COMPLEMENT
static final int COMPLEMENT
- See Also:
- Constant Field Values
BOTH_FORWARD_COMPLEMENT
static final int BOTH_FORWARD_COMPLEMENT
- See Also:
- Constant Field Values
getAccession
java.lang.String getAccession(Annotation annot)
getLabel
java.lang.String getLabel(Annotation annot)
getElementId
java.lang.String getElementId(Annotation annot)
getSequenceId
java.lang.String getSequenceId(Annotation annot)
getKeyword
java.lang.String getKeyword(Annotation annot)
getOrganism
java.lang.String getOrganism(Annotation annot)
getDescription
java.lang.String getDescription(Annotation annot)
getNote
java.lang.String getNote(Annotation annot)
getVersion
java.lang.String getVersion(Annotation annot)
getOS
java.lang.String getOS(Annotation annot)
getMolType
java.lang.String getMolType(Annotation annot)
getTaxonId
java.lang.String getTaxonId(Annotation annot)
getCloneId
java.lang.String getCloneId(Annotation annot)
getCloneLibrary
java.lang.String getCloneLibrary(Annotation annot)
getChromosome
java.lang.String getChromosome(Annotation annot)
getMapPosition
java.lang.String getMapPosition(Annotation annot)
getEcNumber
java.lang.String getEcNumber(Annotation annot)
getCreateDate
java.lang.String getCreateDate(Annotation annot)
getUpdateDate
java.lang.String getUpdateDate(Annotation annot)
getAltIds
AGAVEDbId[] getAltIds(Annotation annot)
getXrefs
AGAVEXrefs[] getXrefs(Annotation annot)
getMapLocation
AGAVEMapLocation[] getMapLocation(Annotation annot)
getRelatedAnnot
AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
getElementIds
java.lang.String[] getElementIds(Annotation annot)
getExonIds
java.lang.String[] getExonIds(Annotation annot)
getChromNum
java.lang.String getChromNum(Annotation annot)
getProperty
AGAVEProperty[] getProperty(Annotation annot,
java.lang.String type)
getDbId
AGAVEDbId getDbId(Annotation annot)
getGroupOrder
java.lang.String getGroupOrder(Annotation annot)
getFeatureType
java.lang.String getFeatureType(Annotation annot)
getResultType
java.lang.String getResultType(Annotation annot)
getConfidence
java.lang.String getConfidence(Annotation annot)
getAlignLength
java.lang.String getAlignLength(Annotation annot)
getAlignUnits
java.lang.String getAlignUnits(Annotation annot)
getMatchDesc
java.lang.String getMatchDesc(Annotation annot)
getMatchAlign
java.lang.String getMatchAlign(Annotation annot)
getQueryRegion
AGAVEQueryRegion getQueryRegion(Annotation annot)
getMatchRegion
AGAVEMatchRegion getMatchRegion(Annotation annot)
getIdAlias
AGAVEIdAlias[] getIdAlias(Annotation annot)
getClassifySystem
java.lang.String getClassifySystem(Annotation annot)
getClassifyId
java.lang.String getClassifyId(Annotation annot)
getClassifyType
java.lang.String getClassifyType(Annotation annot)