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

java.lang.Object
  extended by org.biojava.bio.seq.io.agave.SimpleAnnotFilter
      extended by 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
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
 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