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
 String getAccession(Annotation annot)
           
 String getAlignLength(Annotation annot)
           
 String getAlignUnits(Annotation annot)
           
 AGAVEDbId[] getAltIds(Annotation annot)
           
 String getChromNum(Annotation annot)
           
 String getChromosome(Annotation annot)
           
 String getClassifyId(Annotation annot)
           
 String getClassifySystem(Annotation annot)
           
 String getClassifyType(Annotation annot)
           
 String getCloneId(Annotation annot)
           
 String getCloneLibrary(Annotation annot)
           
 String getConfidence(Annotation annot)
           
 String getCreateDate(Annotation annot)
           
 AGAVEDbId getDbId(Annotation annot)
           
 String getDescription(Annotation annot)
           
 String getEcNumber(Annotation annot)
           
 String getElementId(Annotation annot)
           
 String[] getElementIds(Annotation annot)
           
 String[] getExonIds(Annotation annot)
           
 String getFeatureType(Annotation annot)
           
 String getGroupOrder(Annotation annot)
           
 AGAVEIdAlias[] getIdAlias(Annotation annot)
           
 String getKeyword(Annotation annot)
           
 String getLabel(Annotation annot)
           
 AGAVEMapLocation[] getMapLocation(Annotation annot)
           
 String getMapPosition(Annotation annot)
           
 String getMatchAlign(Annotation annot)
           
 String getMatchDesc(Annotation annot)
           
 AGAVEMatchRegion getMatchRegion(Annotation annot)
           
 String getMolType(Annotation annot)
           
 String getNote(Annotation annot)
           
 String getOrganism(Annotation annot)
           
 String getOS(Annotation annot)
           
 AGAVEProperty[] getProperty(Annotation annot, String type)
           
 AGAVEQueryRegion getQueryRegion(Annotation annot)
           
 AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
           
 String getResultType(Annotation annot)
           
 String getSequenceId(Annotation annot)
           
 String getTaxonId(Annotation annot)
           
 String getUpdateDate(Annotation annot)
           
 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

String getAccession(Annotation annot)

getLabel

String getLabel(Annotation annot)

getElementId

String getElementId(Annotation annot)

getSequenceId

String getSequenceId(Annotation annot)

getKeyword

String getKeyword(Annotation annot)

getOrganism

String getOrganism(Annotation annot)

getDescription

String getDescription(Annotation annot)

getNote

String getNote(Annotation annot)

getVersion

String getVersion(Annotation annot)

getOS

String getOS(Annotation annot)

getMolType

String getMolType(Annotation annot)

getTaxonId

String getTaxonId(Annotation annot)

getCloneId

String getCloneId(Annotation annot)

getCloneLibrary

String getCloneLibrary(Annotation annot)

getChromosome

String getChromosome(Annotation annot)

getMapPosition

String getMapPosition(Annotation annot)

getEcNumber

String getEcNumber(Annotation annot)

getCreateDate

String getCreateDate(Annotation annot)

getUpdateDate

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

String[] getElementIds(Annotation annot)

getExonIds

String[] getExonIds(Annotation annot)

getChromNum

String getChromNum(Annotation annot)

getProperty

AGAVEProperty[] getProperty(Annotation annot,
                            String type)

getDbId

AGAVEDbId getDbId(Annotation annot)

getGroupOrder

String getGroupOrder(Annotation annot)

getFeatureType

String getFeatureType(Annotation annot)

getResultType

String getResultType(Annotation annot)

getConfidence

String getConfidence(Annotation annot)

getAlignLength

String getAlignLength(Annotation annot)

getAlignUnits

String getAlignUnits(Annotation annot)

getMatchDesc

String getMatchDesc(Annotation annot)

getMatchAlign

String getMatchAlign(Annotation annot)

getQueryRegion

AGAVEQueryRegion getQueryRegion(Annotation annot)

getMatchRegion

AGAVEMatchRegion getMatchRegion(Annotation annot)

getIdAlias

AGAVEIdAlias[] getIdAlias(Annotation annot)

getClassifySystem

String getClassifySystem(Annotation annot)

getClassifyId

String getClassifyId(Annotation annot)

getClassifyType

String getClassifyType(Annotation annot)