## 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

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

    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

Method Detail

### 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)