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
Dumping the data from biojava with source of agave into agave format
- Author:
- Hanning Ni Doubletwist Inc
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Field Summary
FieldsFields 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
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Method Summary
Modifier and TypeMethodDescriptiongetAccession
(Annotation annot) getAlignUnits
(Annotation annot) getAltIds
(Annotation annot) getChromNum
(Annotation annot) getChromosome
(Annotation annot) getClassifyId
(Annotation annot) getClassifySystem
(Annotation annot) getClassifyType
(Annotation annot) getCloneId
(Annotation annot) getCloneLibrary
(Annotation annot) getConfidence
(Annotation annot) getCreateDate
(Annotation annot) getDbId
(Annotation annot) getDescription
(Annotation annot) getEcNumber
(Annotation annot) getElementId
(Annotation annot) String[]
getElementIds
(Annotation annot) String[]
getExonIds
(Annotation annot) getFeatureType
(Annotation annot) getGroupOrder
(Annotation annot) getIdAlias
(Annotation annot) getKeyword
(Annotation annot) getLabel
(Annotation annot) getMapLocation
(Annotation annot) getMapPosition
(Annotation annot) getMatchAlign
(Annotation annot) getMatchDesc
(Annotation annot) getMatchRegion
(Annotation annot) getMolType
(Annotation annot) getNote
(Annotation annot) getOrganism
(Annotation annot) getOS
(Annotation annot) getProperty
(Annotation annot, String type) ThomasD made this a bit safer...getQueryRegion
(Annotation annot) getRelatedAnnot
(Annotation annot) getResultType
(Annotation annot) getTaxonId
(Annotation annot) getUpdateDate
(Annotation annot) getVersion
(Annotation annot) getXrefs
(Annotation annot) Methods inherited from class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAlignLength, getSequenceId
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Field Details
-
AGAVE_AGAVE_ANNOT_FILTER_FACTORY
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-
Method Details
-
getAccession
- Specified by:
getAccession
in interfaceAGAVEAnnotFilter
- Overrides:
getAccession
in classSimpleAnnotFilter
-
getKeyword
- Specified by:
getKeyword
in interfaceAGAVEAnnotFilter
- Overrides:
getKeyword
in classSimpleAnnotFilter
-
getOrganism
- Specified by:
getOrganism
in interfaceAGAVEAnnotFilter
- Overrides:
getOrganism
in classSimpleAnnotFilter
-
getElementId
- Specified by:
getElementId
in interfaceAGAVEAnnotFilter
- Overrides:
getElementId
in classSimpleAnnotFilter
-
getLabel
- Specified by:
getLabel
in interfaceAGAVEAnnotFilter
- Overrides:
getLabel
in classSimpleAnnotFilter
-
getDescription
- Specified by:
getDescription
in interfaceAGAVEAnnotFilter
- Overrides:
getDescription
in classSimpleAnnotFilter
-
getNote
- Specified by:
getNote
in interfaceAGAVEAnnotFilter
- Overrides:
getNote
in classSimpleAnnotFilter
-
getVersion
- Specified by:
getVersion
in interfaceAGAVEAnnotFilter
- Overrides:
getVersion
in classSimpleAnnotFilter
-
getOS
- Specified by:
getOS
in interfaceAGAVEAnnotFilter
- Overrides:
getOS
in classSimpleAnnotFilter
-
getMolType
- Specified by:
getMolType
in interfaceAGAVEAnnotFilter
- Overrides:
getMolType
in classSimpleAnnotFilter
-
getTaxonId
- Specified by:
getTaxonId
in interfaceAGAVEAnnotFilter
- Overrides:
getTaxonId
in classSimpleAnnotFilter
-
getCloneId
- Specified by:
getCloneId
in interfaceAGAVEAnnotFilter
- Overrides:
getCloneId
in classSimpleAnnotFilter
-
getCloneLibrary
- Specified by:
getCloneLibrary
in interfaceAGAVEAnnotFilter
- Overrides:
getCloneLibrary
in classSimpleAnnotFilter
-
getChromosome
- Specified by:
getChromosome
in interfaceAGAVEAnnotFilter
- Overrides:
getChromosome
in classSimpleAnnotFilter
-
getMapPosition
- Specified by:
getMapPosition
in interfaceAGAVEAnnotFilter
- Overrides:
getMapPosition
in classSimpleAnnotFilter
-
getEcNumber
- Specified by:
getEcNumber
in interfaceAGAVEAnnotFilter
- Overrides:
getEcNumber
in classSimpleAnnotFilter
-
getCreateDate
- Specified by:
getCreateDate
in interfaceAGAVEAnnotFilter
- Overrides:
getCreateDate
in classSimpleAnnotFilter
-
getUpdateDate
- Specified by:
getUpdateDate
in interfaceAGAVEAnnotFilter
- Overrides:
getUpdateDate
in classSimpleAnnotFilter
-
getXrefs
- Specified by:
getXrefs
in interfaceAGAVEAnnotFilter
- Overrides:
getXrefs
in classSimpleAnnotFilter
-
getRelatedAnnot
- Specified by:
getRelatedAnnot
in interfaceAGAVEAnnotFilter
- Overrides:
getRelatedAnnot
in classSimpleAnnotFilter
-
getGroupOrder
- Specified by:
getGroupOrder
in interfaceAGAVEAnnotFilter
- Overrides:
getGroupOrder
in classSimpleAnnotFilter
-
getFeatureType
- Specified by:
getFeatureType
in interfaceAGAVEAnnotFilter
- Overrides:
getFeatureType
in classSimpleAnnotFilter
-
getResultType
- Specified by:
getResultType
in interfaceAGAVEAnnotFilter
- Overrides:
getResultType
in classSimpleAnnotFilter
-
getConfidence
- Specified by:
getConfidence
in interfaceAGAVEAnnotFilter
- Overrides:
getConfidence
in classSimpleAnnotFilter
-
getMatchAlign
- Specified by:
getMatchAlign
in interfaceAGAVEAnnotFilter
- Overrides:
getMatchAlign
in classSimpleAnnotFilter
-
getMatchRegion
- Specified by:
getMatchRegion
in interfaceAGAVEAnnotFilter
- Overrides:
getMatchRegion
in classSimpleAnnotFilter
-
getQueryRegion
- Specified by:
getQueryRegion
in interfaceAGAVEAnnotFilter
- Overrides:
getQueryRegion
in classSimpleAnnotFilter
-
getAlignUnits
- Specified by:
getAlignUnits
in interfaceAGAVEAnnotFilter
- Overrides:
getAlignUnits
in classSimpleAnnotFilter
-
getMatchDesc
- Specified by:
getMatchDesc
in interfaceAGAVEAnnotFilter
- Overrides:
getMatchDesc
in classSimpleAnnotFilter
-
getElementIds
- Specified by:
getElementIds
in interfaceAGAVEAnnotFilter
- Overrides:
getElementIds
in classSimpleAnnotFilter
-
getMapLocation
- Specified by:
getMapLocation
in interfaceAGAVEAnnotFilter
- Overrides:
getMapLocation
in classSimpleAnnotFilter
-
getAltIds
- Specified by:
getAltIds
in interfaceAGAVEAnnotFilter
- Overrides:
getAltIds
in classSimpleAnnotFilter
-
getClassifySystem
- Specified by:
getClassifySystem
in interfaceAGAVEAnnotFilter
- Overrides:
getClassifySystem
in classSimpleAnnotFilter
-
getClassifyId
- Specified by:
getClassifyId
in interfaceAGAVEAnnotFilter
- Overrides:
getClassifyId
in classSimpleAnnotFilter
-
getClassifyType
- Specified by:
getClassifyType
in interfaceAGAVEAnnotFilter
- Overrides:
getClassifyType
in classSimpleAnnotFilter
-
getDbId
- Specified by:
getDbId
in interfaceAGAVEAnnotFilter
- Overrides:
getDbId
in classSimpleAnnotFilter
-
getIdAlias
- Specified by:
getIdAlias
in interfaceAGAVEAnnotFilter
- Overrides:
getIdAlias
in classSimpleAnnotFilter
-
getExonIds
- Specified by:
getExonIds
in interfaceAGAVEAnnotFilter
- Overrides:
getExonIds
in classSimpleAnnotFilter
-
getChromNum
- Specified by:
getChromNum
in interfaceAGAVEAnnotFilter
- Overrides:
getChromNum
in classSimpleAnnotFilter
-
getProperty
Description copied from class:SimpleAnnotFilter
ThomasD made this a bit safer...- Specified by:
getProperty
in interfaceAGAVEAnnotFilter
- Overrides:
getProperty
in classSimpleAnnotFilter
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