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

java.lang.Object
  extended byorg.biojava.bio.seq.io.agave.SimpleAnnotFilter
All Implemented Interfaces:
AGAVEAnnotFilter
Direct Known Subclasses:
Agave2AgaveAnnotFilter, Embl2AgaveAnnotFilter

public class SimpleAnnotFilter
extends java.lang.Object
implements AGAVEAnnotFilter

Basic implementation of AGAVEAnnotFilter

Author:
Hanning Ni Doubletwist Inc

Field Summary
static AGAVEAnnotFilterFactory 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 getAlignLength(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 getSequenceId(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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

SIMPLE_ANNOT_FILTER_FACTORY

public static final AGAVEAnnotFilterFactory SIMPLE_ANNOT_FILTER_FACTORY
Method Detail

getAccession

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

getKeyword

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

getElementId

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

getOrganism

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

getLabel

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

getDescription

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

getMatchAlign

public java.lang.String getMatchAlign(Annotation annot)
Specified by:
getMatchAlign in interface AGAVEAnnotFilter

getMatchRegion

public AGAVEMatchRegion getMatchRegion(Annotation annot)
Specified by:
getMatchRegion in interface AGAVEAnnotFilter

getQueryRegion

public AGAVEQueryRegion getQueryRegion(Annotation annot)
Specified by:
getQueryRegion in interface AGAVEAnnotFilter

getClassifySystem

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

getClassifyId

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

getClassifyType

public java.lang.String getClassifyType(Annotation annot)
Specified by:
getClassifyType in interface AGAVEAnnotFilter

getExonIds

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

getChromNum

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

getIdAlias

public AGAVEIdAlias[] getIdAlias(Annotation annot)
Specified by:
getIdAlias in interface AGAVEAnnotFilter

getNote

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

getAltIds

public AGAVEDbId[] getAltIds(Annotation annot)
Specified by:
getAltIds in interface AGAVEAnnotFilter

getMapLocation

public AGAVEMapLocation[] getMapLocation(Annotation annot)
Specified by:
getMapLocation in interface AGAVEAnnotFilter

getRelatedAnnot

public AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
Specified by:
getRelatedAnnot in interface AGAVEAnnotFilter

getElementIds

public java.lang.String[] getElementIds(Annotation annot)
Specified by:
getElementIds in interface AGAVEAnnotFilter

getGroupOrder

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

getMatchDesc

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

getFeatureType

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

getResultType

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

getConfidence

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

getAlignLength

public java.lang.String getAlignLength(Annotation annot)
Specified by:
getAlignLength in interface AGAVEAnnotFilter

getAlignUnits

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

getXrefs

public AGAVEXrefs[] getXrefs(Annotation annot)
Specified by:
getXrefs in interface AGAVEAnnotFilter

getVersion

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

getSequenceId

public java.lang.String getSequenceId(Annotation annot)
Specified by:
getSequenceId in interface AGAVEAnnotFilter

getTaxonId

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

getCloneId

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

getCloneLibrary

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

getChromosome

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

getMapPosition

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

getEcNumber

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

getCreateDate

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

getUpdateDate

public java.lang.String getUpdateDate(Annotation annot)
Specified by:
getUpdateDate in interface AGAVEAnnotFilter

getOS

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

getMolType

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

getDbId

public AGAVEDbId getDbId(Annotation annot)
Specified by:
getDbId in interface AGAVEAnnotFilter

getProperty

public AGAVEProperty[] getProperty(Annotation annot,
                                   java.lang.String type)
ThomasD made this a bit safer...

Specified by:
getProperty in interface AGAVEAnnotFilter