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
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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 String getAccession(Annotation annot)
- Specified by:
getAccession
in interfaceAGAVEAnnotFilter
- Overrides:
getAccession
in classSimpleAnnotFilter
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getKeyword
public String getKeyword(Annotation annot)
- Specified by:
getKeyword
in interfaceAGAVEAnnotFilter
- Overrides:
getKeyword
in classSimpleAnnotFilter
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getOrganism
public String getOrganism(Annotation annot)
- Specified by:
getOrganism
in interfaceAGAVEAnnotFilter
- Overrides:
getOrganism
in classSimpleAnnotFilter
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getElementId
public String getElementId(Annotation annot)
- Specified by:
getElementId
in interfaceAGAVEAnnotFilter
- Overrides:
getElementId
in classSimpleAnnotFilter
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getLabel
public String getLabel(Annotation annot)
- Specified by:
getLabel
in interfaceAGAVEAnnotFilter
- Overrides:
getLabel
in classSimpleAnnotFilter
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getDescription
public String getDescription(Annotation annot)
- Specified by:
getDescription
in interfaceAGAVEAnnotFilter
- Overrides:
getDescription
in classSimpleAnnotFilter
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getNote
public String getNote(Annotation annot)
- Specified by:
getNote
in interfaceAGAVEAnnotFilter
- Overrides:
getNote
in classSimpleAnnotFilter
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getVersion
public String getVersion(Annotation annot)
- Specified by:
getVersion
in interfaceAGAVEAnnotFilter
- Overrides:
getVersion
in classSimpleAnnotFilter
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getOS
public String getOS(Annotation annot)
- Specified by:
getOS
in interfaceAGAVEAnnotFilter
- Overrides:
getOS
in classSimpleAnnotFilter
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getMolType
public String getMolType(Annotation annot)
- Specified by:
getMolType
in interfaceAGAVEAnnotFilter
- Overrides:
getMolType
in classSimpleAnnotFilter
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getTaxonId
public String getTaxonId(Annotation annot)
- Specified by:
getTaxonId
in interfaceAGAVEAnnotFilter
- Overrides:
getTaxonId
in classSimpleAnnotFilter
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getCloneId
public String getCloneId(Annotation annot)
- Specified by:
getCloneId
in interfaceAGAVEAnnotFilter
- Overrides:
getCloneId
in classSimpleAnnotFilter
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getCloneLibrary
public String getCloneLibrary(Annotation annot)
- Specified by:
getCloneLibrary
in interfaceAGAVEAnnotFilter
- Overrides:
getCloneLibrary
in classSimpleAnnotFilter
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getChromosome
public String getChromosome(Annotation annot)
- Specified by:
getChromosome
in interfaceAGAVEAnnotFilter
- Overrides:
getChromosome
in classSimpleAnnotFilter
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getMapPosition
public String getMapPosition(Annotation annot)
- Specified by:
getMapPosition
in interfaceAGAVEAnnotFilter
- Overrides:
getMapPosition
in classSimpleAnnotFilter
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getEcNumber
public String getEcNumber(Annotation annot)
- Specified by:
getEcNumber
in interfaceAGAVEAnnotFilter
- Overrides:
getEcNumber
in classSimpleAnnotFilter
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getCreateDate
public String getCreateDate(Annotation annot)
- Specified by:
getCreateDate
in interfaceAGAVEAnnotFilter
- Overrides:
getCreateDate
in classSimpleAnnotFilter
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getUpdateDate
public 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 String getGroupOrder(Annotation annot)
- Specified by:
getGroupOrder
in interfaceAGAVEAnnotFilter
- Overrides:
getGroupOrder
in classSimpleAnnotFilter
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getFeatureType
public String getFeatureType(Annotation annot)
- Specified by:
getFeatureType
in interfaceAGAVEAnnotFilter
- Overrides:
getFeatureType
in classSimpleAnnotFilter
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getResultType
public String getResultType(Annotation annot)
- Specified by:
getResultType
in interfaceAGAVEAnnotFilter
- Overrides:
getResultType
in classSimpleAnnotFilter
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getConfidence
public String getConfidence(Annotation annot)
- Specified by:
getConfidence
in interfaceAGAVEAnnotFilter
- Overrides:
getConfidence
in classSimpleAnnotFilter
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getMatchAlign
public 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 String getAlignUnits(Annotation annot)
- Specified by:
getAlignUnits
in interfaceAGAVEAnnotFilter
- Overrides:
getAlignUnits
in classSimpleAnnotFilter
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getMatchDesc
public String getMatchDesc(Annotation annot)
- Specified by:
getMatchDesc
in interfaceAGAVEAnnotFilter
- Overrides:
getMatchDesc
in classSimpleAnnotFilter
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getElementIds
public 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 String getClassifySystem(Annotation annot)
- Specified by:
getClassifySystem
in interfaceAGAVEAnnotFilter
- Overrides:
getClassifySystem
in classSimpleAnnotFilter
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getClassifyId
public String getClassifyId(Annotation annot)
- Specified by:
getClassifyId
in interfaceAGAVEAnnotFilter
- Overrides:
getClassifyId
in classSimpleAnnotFilter
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getClassifyType
public 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 String[] getExonIds(Annotation annot)
- Specified by:
getExonIds
in interfaceAGAVEAnnotFilter
- Overrides:
getExonIds
in classSimpleAnnotFilter
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getChromNum
public String getChromNum(Annotation annot)
- Specified by:
getChromNum
in interfaceAGAVEAnnotFilter
- Overrides:
getChromNum
in classSimpleAnnotFilter
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getProperty
public AGAVEProperty[] getProperty(Annotation annot, 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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