Package org.biojava.bio.seq.io.agave

Class Agave2AgaveAnnotFilter

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 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 Detail

AGAVE_AGAVE_ANNOT_FILTER_FACTORY

public static final AGAVEAnnotFilterFactory AGAVE_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

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