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