java.lang.Object

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

org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter

All Implemented Interfaces:: AGAVEAnnotFilter

public class Agave2AgaveAnnotFilter extends SimpleAnnotFilter

Dumping the data from biojava with source of agave into agave format

Author:: Hanning Ni Doubletwist Inc

Field Summary

Fields

Modifier and Type

Field

Description

static final AGAVEAnnotFilterFactory

AGAVE_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)

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)

ThomasD made this a bit safer...

AGAVEQueryRegion

getQueryRegion(Annotation annot)

AGAVERelatedAnnot[]

getRelatedAnnot(Annotation annot)

String

getResultType(Annotation annot)

String

getTaxonId(Annotation annot)

String

getUpdateDate(Annotation annot)

String

getVersion(Annotation annot)

AGAVEXrefs[]

getXrefs(Annotation annot)

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- AGAVE_AGAVE_ANNOT_FILTER_FACTORY
  
  public static final AGAVEAnnotFilterFactory AGAVE_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
- getElementId
  
  public String getElementId(Annotation annot)
  
  Specified by:
  
  getElementId in interface AGAVEAnnotFilter
  
  Overrides:
  
  getElementId in class SimpleAnnotFilter
- getLabel
  
  public String getLabel(Annotation annot)
  
  Specified by:
  
  getLabel in interface AGAVEAnnotFilter
  
  Overrides:
  
  getLabel 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
- getTaxonId
  
  public String getTaxonId(Annotation annot)
  
  Specified by:
  
  getTaxonId in interface AGAVEAnnotFilter
  
  Overrides:
  
  getTaxonId in class SimpleAnnotFilter
- getCloneId
  
  public String getCloneId(Annotation annot)
  
  Specified by:
  
  getCloneId in interface AGAVEAnnotFilter
  
  Overrides:
  
  getCloneId in class SimpleAnnotFilter
- getCloneLibrary
  
  public String getCloneLibrary(Annotation annot)
  
  Specified by:
  
  getCloneLibrary in interface AGAVEAnnotFilter
  
  Overrides:
  
  getCloneLibrary in class SimpleAnnotFilter
- getChromosome
  
  public String getChromosome(Annotation annot)
  
  Specified by:
  
  getChromosome in interface AGAVEAnnotFilter
  
  Overrides:
  
  getChromosome in class SimpleAnnotFilter
- getMapPosition
  
  public String getMapPosition(Annotation annot)
  
  Specified by:
  
  getMapPosition in interface AGAVEAnnotFilter
  
  Overrides:
  
  getMapPosition in class SimpleAnnotFilter
- getEcNumber
  
  public String getEcNumber(Annotation annot)
  
  Specified by:
  
  getEcNumber in interface AGAVEAnnotFilter
  
  Overrides:
  
  getEcNumber in class SimpleAnnotFilter
- getCreateDate
  
  public String getCreateDate(Annotation annot)
  
  Specified by:
  
  getCreateDate in interface AGAVEAnnotFilter
  
  Overrides:
  
  getCreateDate in class SimpleAnnotFilter
- getUpdateDate
  
  public String getUpdateDate(Annotation annot)
  
  Specified by:
  
  getUpdateDate in interface AGAVEAnnotFilter
  
  Overrides:
  
  getUpdateDate in class SimpleAnnotFilter
- getXrefs
  
  public AGAVEXrefs[] getXrefs(Annotation annot)
  
  Specified by:
  
  getXrefs in interface AGAVEAnnotFilter
  
  Overrides:
  
  getXrefs in class SimpleAnnotFilter
- getRelatedAnnot
  
  public AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
  
  Specified by:
  
  getRelatedAnnot in interface AGAVEAnnotFilter
  
  Overrides:
  
  getRelatedAnnot in class SimpleAnnotFilter
- getGroupOrder
  
  public String getGroupOrder(Annotation annot)
  
  Specified by:
  
  getGroupOrder in interface AGAVEAnnotFilter
  
  Overrides:
  
  getGroupOrder in class SimpleAnnotFilter
- getFeatureType
  
  public String getFeatureType(Annotation annot)
  
  Specified by:
  
  getFeatureType in interface AGAVEAnnotFilter
  
  Overrides:
  
  getFeatureType in class SimpleAnnotFilter
- getResultType
  
  public String getResultType(Annotation annot)
  
  Specified by:
  
  getResultType in interface AGAVEAnnotFilter
  
  Overrides:
  
  getResultType in class SimpleAnnotFilter
- getConfidence
  
  public String getConfidence(Annotation annot)
  
  Specified by:
  
  getConfidence in interface AGAVEAnnotFilter
  
  Overrides:
  
  getConfidence in class SimpleAnnotFilter
- getMatchAlign
  
  public String getMatchAlign(Annotation annot)
  
  Specified by:
  
  getMatchAlign in interface AGAVEAnnotFilter
  
  Overrides:
  
  getMatchAlign in class SimpleAnnotFilter
- getMatchRegion
  
  public AGAVEMatchRegion getMatchRegion(Annotation annot)
  
  Specified by:
  
  getMatchRegion in interface AGAVEAnnotFilter
  
  Overrides:
  
  getMatchRegion in class SimpleAnnotFilter
- getQueryRegion
  
  public AGAVEQueryRegion getQueryRegion(Annotation annot)
  
  Specified by:
  
  getQueryRegion in interface AGAVEAnnotFilter
  
  Overrides:
  
  getQueryRegion in class SimpleAnnotFilter
- getAlignUnits
  
  public String getAlignUnits(Annotation annot)
  
  Specified by:
  
  getAlignUnits in interface AGAVEAnnotFilter
  
  Overrides:
  
  getAlignUnits in class SimpleAnnotFilter
- getMatchDesc
  
  public String getMatchDesc(Annotation annot)
  
  Specified by:
  
  getMatchDesc in interface AGAVEAnnotFilter
  
  Overrides:
  
  getMatchDesc in class SimpleAnnotFilter
- getElementIds
  
  public String[] getElementIds(Annotation annot)
  
  Specified by:
  
  getElementIds in interface AGAVEAnnotFilter
  
  Overrides:
  
  getElementIds in class SimpleAnnotFilter
- getMapLocation
  
  public AGAVEMapLocation[] getMapLocation(Annotation annot)
  
  Specified by:
  
  getMapLocation in interface AGAVEAnnotFilter
  
  Overrides:
  
  getMapLocation in class SimpleAnnotFilter
- getAltIds
  
  public AGAVEDbId[] getAltIds(Annotation annot)
  
  Specified by:
  
  getAltIds in interface AGAVEAnnotFilter
  
  Overrides:
  
  getAltIds in class SimpleAnnotFilter
- getClassifySystem
  
  public String getClassifySystem(Annotation annot)
  
  Specified by:
  
  getClassifySystem in interface AGAVEAnnotFilter
  
  Overrides:
  
  getClassifySystem in class SimpleAnnotFilter
- getClassifyId
  
  public String getClassifyId(Annotation annot)
  
  Specified by:
  
  getClassifyId in interface AGAVEAnnotFilter
  
  Overrides:
  
  getClassifyId in class SimpleAnnotFilter
- getClassifyType
  
  public String getClassifyType(Annotation annot)
  
  Specified by:
  
  getClassifyType in interface AGAVEAnnotFilter
  
  Overrides:
  
  getClassifyType in class SimpleAnnotFilter
- getDbId
  
  public AGAVEDbId getDbId(Annotation annot)
  
  Specified by:
  
  getDbId in interface AGAVEAnnotFilter
  
  Overrides:
  
  getDbId in class SimpleAnnotFilter
- getIdAlias
  
  public AGAVEIdAlias[] getIdAlias(Annotation annot)
  
  Specified by:
  
  getIdAlias in interface AGAVEAnnotFilter
  
  Overrides:
  
  getIdAlias in class SimpleAnnotFilter
- getExonIds
  
  public String[] getExonIds(Annotation annot)
  
  Specified by:
  
  getExonIds in interface AGAVEAnnotFilter
  
  Overrides:
  
  getExonIds in class SimpleAnnotFilter
- getChromNum
  
  public String getChromNum(Annotation annot)
  
  Specified by:
  
  getChromNum in interface AGAVEAnnotFilter
  
  Overrides:
  
  getChromNum in class SimpleAnnotFilter
- getProperty
  
  public AGAVEProperty[] getProperty(Annotation annot, String type)
  
  Description copied from class: SimpleAnnotFilter
  
  ThomasD made this a bit safer...
  
  Specified by:
  
  getProperty in interface AGAVEAnnotFilter
  
  Overrides:
  
  getProperty in class SimpleAnnotFilter

Class Agave2AgaveAnnotFilter

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

AGAVE_AGAVE_ANNOT_FILTER_FACTORY

Method Details

getAccession

getKeyword

getOrganism

getElementId

getLabel

getDescription

getNote

getVersion

getOS

getMolType

getTaxonId

getCloneId

getCloneLibrary

getChromosome

getMapPosition

getEcNumber

getCreateDate

getUpdateDate

getXrefs

getRelatedAnnot

getGroupOrder

getFeatureType

getResultType

getConfidence

getMatchAlign

getMatchRegion

getQueryRegion

getAlignUnits

getMatchDesc

getElementIds

getMapLocation

getAltIds

getClassifySystem

getClassifyId

getClassifyType

getDbId

getIdAlias

getExonIds

getChromNum

getProperty