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

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

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 String getAccession(Annotation annot)

getLabel

public String getLabel(Annotation annot)

getElementId

public String getElementId(Annotation annot)

getSequenceId

public String getSequenceId(Annotation annot)

getKeyword

public String getKeyword(Annotation annot)

getOrganism

public String getOrganism(Annotation annot)

getDescription

public String getDescription(Annotation annot)

getNote

public String getNote(Annotation annot)

getVersion

public String getVersion(Annotation annot)

getOS

public String getOS(Annotation annot)

getMolType

public String getMolType(Annotation annot)

getTaxonId

public String getTaxonId(Annotation annot)

getCloneId

public String getCloneId(Annotation annot)

getCloneLibrary

public String getCloneLibrary(Annotation annot)

getChromosome

public String getChromosome(Annotation annot)

getMapPosition

public String getMapPosition(Annotation annot)

getEcNumber

public String getEcNumber(Annotation annot)

getCreateDate

public String getCreateDate(Annotation annot)

getUpdateDate

public 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 String[] getElementIds(Annotation annot)

getExonIds

public String[] getExonIds(Annotation annot)

getChromNum

public String getChromNum(Annotation annot)

getProperty

public AGAVEProperty[] getProperty(Annotation annot,
                                   String type)

getDbId

public AGAVEDbId getDbId(Annotation annot)

getGroupOrder

public String getGroupOrder(Annotation annot)

getFeatureType

public String getFeatureType(Annotation annot)

getResultType

public String getResultType(Annotation annot)

getConfidence

public String getConfidence(Annotation annot)

getAlignLength

public String getAlignLength(Annotation annot)

getAlignUnits

public String getAlignUnits(Annotation annot)

getMatchDesc

public String getMatchDesc(Annotation annot)

getMatchAlign

public String getMatchAlign(Annotation annot)

getQueryRegion

public AGAVEQueryRegion getQueryRegion(Annotation annot)

getMatchRegion

public AGAVEMatchRegion getMatchRegion(Annotation annot)

getIdAlias

public AGAVEIdAlias[] getIdAlias(Annotation annot)

getClassifySystem

public String getClassifySystem(Annotation annot)

getClassifyId

public String getClassifyId(Annotation annot)

getClassifyType

public String getClassifyType(Annotation annot)