Package org.biojava.bio.seq.io.agave
Class Agave2AgaveAnnotFilter
- java.lang.Object
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- org.biojava.bio.seq.io.agave.SimpleAnnotFilter
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- org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
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- 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
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Field Summary
Fields Modifier and Type Field Description static AGAVEAnnotFilterFactory
AGAVE_AGAVE_ANNOT_FILTER_FACTORY
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Fields inherited from class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
SIMPLE_ANNOT_FILTER_FACTORY
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Fields inherited from interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
BOTH_FORWARD_COMPLEMENT, COMPLEMENT, FORWARD
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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)
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Methods inherited from class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAlignLength, getSequenceId
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Field Detail
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AGAVE_AGAVE_ANNOT_FILTER_FACTORY
public static final AGAVEAnnotFilterFactory AGAVE_AGAVE_ANNOT_FILTER_FACTORY
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Method Detail
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getAccession
public java.lang.String getAccession(Annotation annot)
- Specified by:
getAccession
in interfaceAGAVEAnnotFilter
- Overrides:
getAccession
in classSimpleAnnotFilter
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getKeyword
public java.lang.String getKeyword(Annotation annot)
- Specified by:
getKeyword
in interfaceAGAVEAnnotFilter
- Overrides:
getKeyword
in classSimpleAnnotFilter
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getOrganism
public java.lang.String getOrganism(Annotation annot)
- Specified by:
getOrganism
in interfaceAGAVEAnnotFilter
- Overrides:
getOrganism
in classSimpleAnnotFilter
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getElementId
public java.lang.String getElementId(Annotation annot)
- Specified by:
getElementId
in interfaceAGAVEAnnotFilter
- Overrides:
getElementId
in classSimpleAnnotFilter
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getLabel
public java.lang.String getLabel(Annotation annot)
- Specified by:
getLabel
in interfaceAGAVEAnnotFilter
- Overrides:
getLabel
in classSimpleAnnotFilter
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getDescription
public java.lang.String getDescription(Annotation annot)
- Specified by:
getDescription
in interfaceAGAVEAnnotFilter
- Overrides:
getDescription
in classSimpleAnnotFilter
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getNote
public java.lang.String getNote(Annotation annot)
- Specified by:
getNote
in interfaceAGAVEAnnotFilter
- Overrides:
getNote
in classSimpleAnnotFilter
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getVersion
public java.lang.String getVersion(Annotation annot)
- Specified by:
getVersion
in interfaceAGAVEAnnotFilter
- Overrides:
getVersion
in classSimpleAnnotFilter
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getOS
public java.lang.String getOS(Annotation annot)
- Specified by:
getOS
in interfaceAGAVEAnnotFilter
- Overrides:
getOS
in classSimpleAnnotFilter
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getMolType
public java.lang.String getMolType(Annotation annot)
- Specified by:
getMolType
in interfaceAGAVEAnnotFilter
- Overrides:
getMolType
in classSimpleAnnotFilter
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getTaxonId
public java.lang.String getTaxonId(Annotation annot)
- Specified by:
getTaxonId
in interfaceAGAVEAnnotFilter
- Overrides:
getTaxonId
in classSimpleAnnotFilter
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getCloneId
public java.lang.String getCloneId(Annotation annot)
- Specified by:
getCloneId
in interfaceAGAVEAnnotFilter
- Overrides:
getCloneId
in classSimpleAnnotFilter
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getCloneLibrary
public java.lang.String getCloneLibrary(Annotation annot)
- Specified by:
getCloneLibrary
in interfaceAGAVEAnnotFilter
- Overrides:
getCloneLibrary
in classSimpleAnnotFilter
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getChromosome
public java.lang.String getChromosome(Annotation annot)
- Specified by:
getChromosome
in interfaceAGAVEAnnotFilter
- Overrides:
getChromosome
in classSimpleAnnotFilter
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getMapPosition
public java.lang.String getMapPosition(Annotation annot)
- Specified by:
getMapPosition
in interfaceAGAVEAnnotFilter
- Overrides:
getMapPosition
in classSimpleAnnotFilter
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getEcNumber
public java.lang.String getEcNumber(Annotation annot)
- Specified by:
getEcNumber
in interfaceAGAVEAnnotFilter
- Overrides:
getEcNumber
in classSimpleAnnotFilter
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getCreateDate
public java.lang.String getCreateDate(Annotation annot)
- Specified by:
getCreateDate
in interfaceAGAVEAnnotFilter
- Overrides:
getCreateDate
in classSimpleAnnotFilter
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getUpdateDate
public java.lang.String getUpdateDate(Annotation annot)
- Specified by:
getUpdateDate
in interfaceAGAVEAnnotFilter
- Overrides:
getUpdateDate
in classSimpleAnnotFilter
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getXrefs
public AGAVEXrefs[] getXrefs(Annotation annot)
- Specified by:
getXrefs
in interfaceAGAVEAnnotFilter
- Overrides:
getXrefs
in classSimpleAnnotFilter
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getRelatedAnnot
public AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
- Specified by:
getRelatedAnnot
in interfaceAGAVEAnnotFilter
- Overrides:
getRelatedAnnot
in classSimpleAnnotFilter
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getGroupOrder
public java.lang.String getGroupOrder(Annotation annot)
- Specified by:
getGroupOrder
in interfaceAGAVEAnnotFilter
- Overrides:
getGroupOrder
in classSimpleAnnotFilter
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getFeatureType
public java.lang.String getFeatureType(Annotation annot)
- Specified by:
getFeatureType
in interfaceAGAVEAnnotFilter
- Overrides:
getFeatureType
in classSimpleAnnotFilter
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getResultType
public java.lang.String getResultType(Annotation annot)
- Specified by:
getResultType
in interfaceAGAVEAnnotFilter
- Overrides:
getResultType
in classSimpleAnnotFilter
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getConfidence
public java.lang.String getConfidence(Annotation annot)
- Specified by:
getConfidence
in interfaceAGAVEAnnotFilter
- Overrides:
getConfidence
in classSimpleAnnotFilter
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getMatchAlign
public java.lang.String getMatchAlign(Annotation annot)
- Specified by:
getMatchAlign
in interfaceAGAVEAnnotFilter
- Overrides:
getMatchAlign
in classSimpleAnnotFilter
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getMatchRegion
public AGAVEMatchRegion getMatchRegion(Annotation annot)
- Specified by:
getMatchRegion
in interfaceAGAVEAnnotFilter
- Overrides:
getMatchRegion
in classSimpleAnnotFilter
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getQueryRegion
public AGAVEQueryRegion getQueryRegion(Annotation annot)
- Specified by:
getQueryRegion
in interfaceAGAVEAnnotFilter
- Overrides:
getQueryRegion
in classSimpleAnnotFilter
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getAlignUnits
public java.lang.String getAlignUnits(Annotation annot)
- Specified by:
getAlignUnits
in interfaceAGAVEAnnotFilter
- Overrides:
getAlignUnits
in classSimpleAnnotFilter
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getMatchDesc
public java.lang.String getMatchDesc(Annotation annot)
- Specified by:
getMatchDesc
in interfaceAGAVEAnnotFilter
- Overrides:
getMatchDesc
in classSimpleAnnotFilter
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getElementIds
public java.lang.String[] getElementIds(Annotation annot)
- Specified by:
getElementIds
in interfaceAGAVEAnnotFilter
- Overrides:
getElementIds
in classSimpleAnnotFilter
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getMapLocation
public AGAVEMapLocation[] getMapLocation(Annotation annot)
- Specified by:
getMapLocation
in interfaceAGAVEAnnotFilter
- Overrides:
getMapLocation
in classSimpleAnnotFilter
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getAltIds
public AGAVEDbId[] getAltIds(Annotation annot)
- Specified by:
getAltIds
in interfaceAGAVEAnnotFilter
- Overrides:
getAltIds
in classSimpleAnnotFilter
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getClassifySystem
public java.lang.String getClassifySystem(Annotation annot)
- Specified by:
getClassifySystem
in interfaceAGAVEAnnotFilter
- Overrides:
getClassifySystem
in classSimpleAnnotFilter
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getClassifyId
public java.lang.String getClassifyId(Annotation annot)
- Specified by:
getClassifyId
in interfaceAGAVEAnnotFilter
- Overrides:
getClassifyId
in classSimpleAnnotFilter
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getClassifyType
public java.lang.String getClassifyType(Annotation annot)
- Specified by:
getClassifyType
in interfaceAGAVEAnnotFilter
- Overrides:
getClassifyType
in classSimpleAnnotFilter
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getDbId
public AGAVEDbId getDbId(Annotation annot)
- Specified by:
getDbId
in interfaceAGAVEAnnotFilter
- Overrides:
getDbId
in classSimpleAnnotFilter
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getIdAlias
public AGAVEIdAlias[] getIdAlias(Annotation annot)
- Specified by:
getIdAlias
in interfaceAGAVEAnnotFilter
- Overrides:
getIdAlias
in classSimpleAnnotFilter
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getExonIds
public java.lang.String[] getExonIds(Annotation annot)
- Specified by:
getExonIds
in interfaceAGAVEAnnotFilter
- Overrides:
getExonIds
in classSimpleAnnotFilter
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getChromNum
public java.lang.String getChromNum(Annotation annot)
- Specified by:
getChromNum
in interfaceAGAVEAnnotFilter
- Overrides:
getChromNum
in classSimpleAnnotFilter
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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 interfaceAGAVEAnnotFilter
- Overrides:
getProperty
in classSimpleAnnotFilter
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