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 final 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 Details
- EMBL_AGAVE_ANNOT_FILTER_FACTORY
  
  public static final AGAVEAnnotFilterFactory EMBL_AGAVE_ANNOT_FILTER_FACTORY
Method Details
- 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

Class Embl2AgaveAnnotFilter

Field Summary

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

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

Method Summary

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

Methods inherited from class java.lang.Object

Field Details

EMBL_AGAVE_ANNOT_FILTER_FACTORY

Method Details

getAccession

getKeyword

getOrganism

getDescription

getNote

getVersion

getOS

getMolType

getDbId