Package org.biojava.bio.seq.io.agave
Class Embl2AgaveAnnotFilter
- java.lang.Object
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- org.biojava.bio.seq.io.agave.SimpleAnnotFilter
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- org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
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- All Implemented Interfaces:
AGAVEAnnotFilter
public class Embl2AgaveAnnotFilter extends SimpleAnnotFilter
Map EMBL data into AGAVE format- Author:
- Hanning Ni Doubletwist Inc
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Field Summary
Fields Modifier and Type Field Description static AGAVEAnnotFilterFactory
EMBL_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 String
getAccession(Annotation annot)
AGAVEDbId
getDbId(Annotation annot)
String
getDescription(Annotation annot)
String
getKeyword(Annotation annot)
String
getMolType(Annotation annot)
String
getNote(Annotation annot)
String
getOrganism(Annotation annot)
String
getOS(Annotation annot)
String
getVersion(Annotation annot)
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Methods inherited from class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAlignLength, getAlignUnits, getAltIds, getChromNum, getChromosome, getClassifyId, getClassifySystem, getClassifyType, getCloneId, getCloneLibrary, getConfidence, getCreateDate, getEcNumber, getElementId, getElementIds, getExonIds, getFeatureType, getGroupOrder, getIdAlias, getLabel, getMapLocation, getMapPosition, getMatchAlign, getMatchDesc, getMatchRegion, getProperty, getQueryRegion, getRelatedAnnot, getResultType, getSequenceId, getTaxonId, getUpdateDate, getXrefs
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Field Detail
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EMBL_AGAVE_ANNOT_FILTER_FACTORY
public static final AGAVEAnnotFilterFactory EMBL_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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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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getDbId
public AGAVEDbId getDbId(Annotation annot)
- Specified by:
getDbId
in interfaceAGAVEAnnotFilter
- Overrides:
getDbId
in classSimpleAnnotFilter
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