## 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

Field Summary
`static int` `BOTH_FORWARD_COMPLEMENT`
`static int` `COMPLEMENT`
`static int` `FORWARD`

Method Summary
`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)`

Field Detail

### 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

Method Detail

### 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)