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

java.lang.Object
  extended byorg.biojava.bio.seq.io.agave.SimpleAnnotFilter
      extended byorg.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
static 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
 java.lang.String getAccession(Annotation annot)
           
 java.lang.String getAlignUnits(Annotation annot)
           
 AGAVEDbId[] getAltIds(Annotation annot)
           
 java.lang.String getChromNum(Annotation annot)
           
 java.lang.String getChromosome(Annotation annot)
           
 java.lang.String getClassifyId(Annotation annot)
           
 java.lang.String getClassifySystem(Annotation annot)
           
 java.lang.String getClassifyType(Annotation annot)
           
 java.lang.String getCloneId(Annotation annot)
           
 java.lang.String getCloneLibrary(Annotation annot)
           
 java.lang.String getConfidence(Annotation annot)
           
 java.lang.String getCreateDate(Annotation annot)
           
 AGAVEDbId getDbId(Annotation annot)
           
 java.lang.String getDescription(Annotation annot)
           
 java.lang.String getEcNumber(Annotation annot)
           
 java.lang.String getElementId(Annotation annot)
           
 java.lang.String[] getElementIds(Annotation annot)
           
 java.lang.String[] getExonIds(Annotation annot)
           
 java.lang.String getFeatureType(Annotation annot)
           
 java.lang.String getGroupOrder(Annotation annot)
           
 AGAVEIdAlias[] getIdAlias(Annotation annot)
           
 java.lang.String getKeyword(Annotation annot)
           
 java.lang.String getLabel(Annotation annot)
           
 AGAVEMapLocation[] getMapLocation(Annotation annot)
           
 java.lang.String getMapPosition(Annotation annot)
           
 java.lang.String getMatchAlign(Annotation annot)
           
 java.lang.String getMatchDesc(Annotation annot)
           
 AGAVEMatchRegion getMatchRegion(Annotation annot)
           
 java.lang.String getMolType(Annotation annot)
           
 java.lang.String getNote(Annotation annot)
           
 java.lang.String getOrganism(Annotation annot)
           
 java.lang.String getOS(Annotation annot)
           
 AGAVEProperty[] getProperty(Annotation annot, java.lang.String type)
          ThomasD made this a bit safer...
 AGAVEQueryRegion getQueryRegion(Annotation annot)
           
 AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
           
 java.lang.String getResultType(Annotation annot)
           
 java.lang.String getTaxonId(Annotation annot)
           
 java.lang.String getUpdateDate(Annotation annot)
           
 java.lang.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 Detail

AGAVE_AGAVE_ANNOT_FILTER_FACTORY

public static final AGAVEAnnotFilterFactory AGAVE_AGAVE_ANNOT_FILTER_FACTORY
Method Detail

getAccession

public java.lang.String getAccession(Annotation annot)
Specified by:
getAccession in interface AGAVEAnnotFilter
Overrides:
getAccession in class SimpleAnnotFilter

getKeyword

public java.lang.String getKeyword(Annotation annot)
Specified by:
getKeyword in interface AGAVEAnnotFilter
Overrides:
getKeyword in class SimpleAnnotFilter

getOrganism

public java.lang.String getOrganism(Annotation annot)
Specified by:
getOrganism in interface AGAVEAnnotFilter
Overrides:
getOrganism in class SimpleAnnotFilter

getElementId

public java.lang.String getElementId(Annotation annot)
Specified by:
getElementId in interface AGAVEAnnotFilter
Overrides:
getElementId in class SimpleAnnotFilter

getLabel

public java.lang.String getLabel(Annotation annot)
Specified by:
getLabel in interface AGAVEAnnotFilter
Overrides:
getLabel in class SimpleAnnotFilter

getDescription

public java.lang.String getDescription(Annotation annot)
Specified by:
getDescription in interface AGAVEAnnotFilter
Overrides:
getDescription in class SimpleAnnotFilter

getNote

public java.lang.String getNote(Annotation annot)
Specified by:
getNote in interface AGAVEAnnotFilter
Overrides:
getNote in class SimpleAnnotFilter

getVersion

public java.lang.String getVersion(Annotation annot)
Specified by:
getVersion in interface AGAVEAnnotFilter
Overrides:
getVersion in class SimpleAnnotFilter

getOS

public java.lang.String getOS(Annotation annot)
Specified by:
getOS in interface AGAVEAnnotFilter
Overrides:
getOS in class SimpleAnnotFilter

getMolType

public java.lang.String getMolType(Annotation annot)
Specified by:
getMolType in interface AGAVEAnnotFilter
Overrides:
getMolType in class SimpleAnnotFilter

getTaxonId

public java.lang.String getTaxonId(Annotation annot)
Specified by:
getTaxonId in interface AGAVEAnnotFilter
Overrides:
getTaxonId in class SimpleAnnotFilter

getCloneId

public java.lang.String getCloneId(Annotation annot)
Specified by:
getCloneId in interface AGAVEAnnotFilter
Overrides:
getCloneId in class SimpleAnnotFilter

getCloneLibrary

public java.lang.String getCloneLibrary(Annotation annot)
Specified by:
getCloneLibrary in interface AGAVEAnnotFilter
Overrides:
getCloneLibrary in class SimpleAnnotFilter

getChromosome

public java.lang.String getChromosome(Annotation annot)
Specified by:
getChromosome in interface AGAVEAnnotFilter
Overrides:
getChromosome in class SimpleAnnotFilter

getMapPosition

public java.lang.String getMapPosition(Annotation annot)
Specified by:
getMapPosition in interface AGAVEAnnotFilter
Overrides:
getMapPosition in class SimpleAnnotFilter

getEcNumber

public java.lang.String getEcNumber(Annotation annot)
Specified by:
getEcNumber in interface AGAVEAnnotFilter
Overrides:
getEcNumber in class SimpleAnnotFilter

getCreateDate

public java.lang.String getCreateDate(Annotation annot)
Specified by:
getCreateDate in interface AGAVEAnnotFilter
Overrides:
getCreateDate in class SimpleAnnotFilter

getUpdateDate

public java.lang.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 java.lang.String getGroupOrder(Annotation annot)
Specified by:
getGroupOrder in interface AGAVEAnnotFilter
Overrides:
getGroupOrder in class SimpleAnnotFilter

getFeatureType

public java.lang.String getFeatureType(Annotation annot)
Specified by:
getFeatureType in interface AGAVEAnnotFilter
Overrides:
getFeatureType in class SimpleAnnotFilter

getResultType

public java.lang.String getResultType(Annotation annot)
Specified by:
getResultType in interface AGAVEAnnotFilter
Overrides:
getResultType in class SimpleAnnotFilter

getConfidence

public java.lang.String getConfidence(Annotation annot)
Specified by:
getConfidence in interface AGAVEAnnotFilter
Overrides:
getConfidence in class SimpleAnnotFilter

getMatchAlign

public java.lang.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 java.lang.String getAlignUnits(Annotation annot)
Specified by:
getAlignUnits in interface AGAVEAnnotFilter
Overrides:
getAlignUnits in class SimpleAnnotFilter

getMatchDesc

public java.lang.String getMatchDesc(Annotation annot)
Specified by:
getMatchDesc in interface AGAVEAnnotFilter
Overrides:
getMatchDesc in class SimpleAnnotFilter

getElementIds

public java.lang.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 java.lang.String getClassifySystem(Annotation annot)
Specified by:
getClassifySystem in interface AGAVEAnnotFilter
Overrides:
getClassifySystem in class SimpleAnnotFilter

getClassifyId

public java.lang.String getClassifyId(Annotation annot)
Specified by:
getClassifyId in interface AGAVEAnnotFilter
Overrides:
getClassifyId in class SimpleAnnotFilter

getClassifyType

public java.lang.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 java.lang.String[] getExonIds(Annotation annot)
Specified by:
getExonIds in interface AGAVEAnnotFilter
Overrides:
getExonIds in class SimpleAnnotFilter

getChromNum

public java.lang.String getChromNum(Annotation annot)
Specified by:
getChromNum in interface AGAVEAnnotFilter
Overrides:
getChromNum in class SimpleAnnotFilter

getProperty

public AGAVEProperty[] getProperty(Annotation annot,
                                   java.lang.String type)
Description copied from class: SimpleAnnotFilter
ThomasD made this a bit safer...

Specified by:
getProperty in interface AGAVEAnnotFilter
Overrides:
getProperty in class SimpleAnnotFilter