Package org.biojava.bio.seq.io.agave

Class Embl2AgaveAnnotFilter

java.lang.Object

org.biojava.bio.seq.io.agave.SimpleAnnotFilter

org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter

All Implemented Interfaces:

AGAVEAnnotFilter

public class Embl2AgaveAnnotFilter
extends SimpleAnnotFilter

Map EMBL data into AGAVE format

Author:

Hanning Ni Doubletwist Inc

Field Summary

Fields

Modifier and Type	Field	Description
static AGAVEAnnotFilterFactory	EMBL_AGAVE_ANNOT_FILTER_FACTORY

Fields inherited from class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

SIMPLE_ANNOT_FILTER_FACTORY

Fields inherited from interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter

BOTH_FORWARD_COMPLEMENT, COMPLEMENT, FORWARD

Method Summary

Modifier and Type	Method	Description
String	getAccession(Annotation annot)
AGAVEDbId	getDbId(Annotation annot)
String	getDescription(Annotation annot)
String	getKeyword(Annotation annot)
String	getMolType(Annotation annot)
String	getNote(Annotation annot)
String	getOrganism(Annotation annot)
String	getOS(Annotation annot)
String	getVersion(Annotation annot)

Methods inherited from class org.biojava.bio.seq.io.agave.SimpleAnnotFilter

getAlignLength, getAlignUnits, getAltIds, getChromNum, getChromosome, getClassifyId, getClassifySystem, getClassifyType, getCloneId, getCloneLibrary, getConfidence, getCreateDate, getEcNumber, getElementId, getElementIds, getExonIds, getFeatureType, getGroupOrder, getIdAlias, getLabel, getMapLocation, getMapPosition, getMatchAlign, getMatchDesc, getMatchRegion, getProperty, getQueryRegion, getRelatedAnnot, getResultType, getSequenceId, getTaxonId, getUpdateDate, getXrefs

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

EMBL_AGAVE_ANNOT_FILTER_FACTORY

public static final AGAVEAnnotFilterFactory EMBL_AGAVE_ANNOT_FILTER_FACTORY

Method Detail

getAccession

public String getAccession(Annotation annot)

Specified by:

getAccession in interface AGAVEAnnotFilter

Overrides:

getAccession in class SimpleAnnotFilter

getKeyword

public String getKeyword(Annotation annot)

Specified by:

getKeyword in interface AGAVEAnnotFilter

Overrides:

getKeyword in class SimpleAnnotFilter

getOrganism

public String getOrganism(Annotation annot)

Specified by:

getOrganism in interface AGAVEAnnotFilter

Overrides:

getOrganism in class SimpleAnnotFilter

getDescription

public String getDescription(Annotation annot)

Specified by:

getDescription in interface AGAVEAnnotFilter

Overrides:

getDescription in class SimpleAnnotFilter

getNote

public String getNote(Annotation annot)

Specified by:

getNote in interface AGAVEAnnotFilter

Overrides:

getNote in class SimpleAnnotFilter

getVersion

public String getVersion(Annotation annot)

Specified by:

getVersion in interface AGAVEAnnotFilter

Overrides:

getVersion in class SimpleAnnotFilter

getOS

public String getOS(Annotation annot)

Specified by:

getOS in interface AGAVEAnnotFilter

Overrides:

getOS in class SimpleAnnotFilter

getMolType

public String getMolType(Annotation annot)

Specified by:

getMolType in interface AGAVEAnnotFilter

Overrides:

getMolType in class SimpleAnnotFilter

getDbId

public AGAVEDbId getDbId(Annotation annot)

Specified by:

getDbId in interface AGAVEAnnotFilter

Overrides:

getDbId in class SimpleAnnotFilter