public class Agave2AgaveAnnotFilter extends SimpleAnnotFilter
Modifier and Type | Field and Description |
---|---|
static AGAVEAnnotFilterFactory |
AGAVE_AGAVE_ANNOT_FILTER_FACTORY |
SIMPLE_ANNOT_FILTER_FACTORY
BOTH_FORWARD_COMPLEMENT, COMPLEMENT, FORWARD
getAlignLength, getSequenceId
public static final AGAVEAnnotFilterFactory AGAVE_AGAVE_ANNOT_FILTER_FACTORY
public String getAccession(Annotation annot)
getAccession
in interface AGAVEAnnotFilter
getAccession
in class SimpleAnnotFilter
public String getKeyword(Annotation annot)
getKeyword
in interface AGAVEAnnotFilter
getKeyword
in class SimpleAnnotFilter
public String getOrganism(Annotation annot)
getOrganism
in interface AGAVEAnnotFilter
getOrganism
in class SimpleAnnotFilter
public String getElementId(Annotation annot)
getElementId
in interface AGAVEAnnotFilter
getElementId
in class SimpleAnnotFilter
public String getLabel(Annotation annot)
getLabel
in interface AGAVEAnnotFilter
getLabel
in class SimpleAnnotFilter
public String getDescription(Annotation annot)
getDescription
in interface AGAVEAnnotFilter
getDescription
in class SimpleAnnotFilter
public String getNote(Annotation annot)
getNote
in interface AGAVEAnnotFilter
getNote
in class SimpleAnnotFilter
public String getVersion(Annotation annot)
getVersion
in interface AGAVEAnnotFilter
getVersion
in class SimpleAnnotFilter
public String getOS(Annotation annot)
getOS
in interface AGAVEAnnotFilter
getOS
in class SimpleAnnotFilter
public String getMolType(Annotation annot)
getMolType
in interface AGAVEAnnotFilter
getMolType
in class SimpleAnnotFilter
public String getTaxonId(Annotation annot)
getTaxonId
in interface AGAVEAnnotFilter
getTaxonId
in class SimpleAnnotFilter
public String getCloneId(Annotation annot)
getCloneId
in interface AGAVEAnnotFilter
getCloneId
in class SimpleAnnotFilter
public String getCloneLibrary(Annotation annot)
getCloneLibrary
in interface AGAVEAnnotFilter
getCloneLibrary
in class SimpleAnnotFilter
public String getChromosome(Annotation annot)
getChromosome
in interface AGAVEAnnotFilter
getChromosome
in class SimpleAnnotFilter
public String getMapPosition(Annotation annot)
getMapPosition
in interface AGAVEAnnotFilter
getMapPosition
in class SimpleAnnotFilter
public String getEcNumber(Annotation annot)
getEcNumber
in interface AGAVEAnnotFilter
getEcNumber
in class SimpleAnnotFilter
public String getCreateDate(Annotation annot)
getCreateDate
in interface AGAVEAnnotFilter
getCreateDate
in class SimpleAnnotFilter
public String getUpdateDate(Annotation annot)
getUpdateDate
in interface AGAVEAnnotFilter
getUpdateDate
in class SimpleAnnotFilter
public AGAVEXrefs[] getXrefs(Annotation annot)
getXrefs
in interface AGAVEAnnotFilter
getXrefs
in class SimpleAnnotFilter
public AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
getRelatedAnnot
in interface AGAVEAnnotFilter
getRelatedAnnot
in class SimpleAnnotFilter
public String getGroupOrder(Annotation annot)
getGroupOrder
in interface AGAVEAnnotFilter
getGroupOrder
in class SimpleAnnotFilter
public String getFeatureType(Annotation annot)
getFeatureType
in interface AGAVEAnnotFilter
getFeatureType
in class SimpleAnnotFilter
public String getResultType(Annotation annot)
getResultType
in interface AGAVEAnnotFilter
getResultType
in class SimpleAnnotFilter
public String getConfidence(Annotation annot)
getConfidence
in interface AGAVEAnnotFilter
getConfidence
in class SimpleAnnotFilter
public String getMatchAlign(Annotation annot)
getMatchAlign
in interface AGAVEAnnotFilter
getMatchAlign
in class SimpleAnnotFilter
public AGAVEMatchRegion getMatchRegion(Annotation annot)
getMatchRegion
in interface AGAVEAnnotFilter
getMatchRegion
in class SimpleAnnotFilter
public AGAVEQueryRegion getQueryRegion(Annotation annot)
getQueryRegion
in interface AGAVEAnnotFilter
getQueryRegion
in class SimpleAnnotFilter
public String getAlignUnits(Annotation annot)
getAlignUnits
in interface AGAVEAnnotFilter
getAlignUnits
in class SimpleAnnotFilter
public String getMatchDesc(Annotation annot)
getMatchDesc
in interface AGAVEAnnotFilter
getMatchDesc
in class SimpleAnnotFilter
public String[] getElementIds(Annotation annot)
getElementIds
in interface AGAVEAnnotFilter
getElementIds
in class SimpleAnnotFilter
public AGAVEMapLocation[] getMapLocation(Annotation annot)
getMapLocation
in interface AGAVEAnnotFilter
getMapLocation
in class SimpleAnnotFilter
public AGAVEDbId[] getAltIds(Annotation annot)
getAltIds
in interface AGAVEAnnotFilter
getAltIds
in class SimpleAnnotFilter
public String getClassifySystem(Annotation annot)
getClassifySystem
in interface AGAVEAnnotFilter
getClassifySystem
in class SimpleAnnotFilter
public String getClassifyId(Annotation annot)
getClassifyId
in interface AGAVEAnnotFilter
getClassifyId
in class SimpleAnnotFilter
public String getClassifyType(Annotation annot)
getClassifyType
in interface AGAVEAnnotFilter
getClassifyType
in class SimpleAnnotFilter
public AGAVEDbId getDbId(Annotation annot)
getDbId
in interface AGAVEAnnotFilter
getDbId
in class SimpleAnnotFilter
public AGAVEIdAlias[] getIdAlias(Annotation annot)
getIdAlias
in interface AGAVEAnnotFilter
getIdAlias
in class SimpleAnnotFilter
public String[] getExonIds(Annotation annot)
getExonIds
in interface AGAVEAnnotFilter
getExonIds
in class SimpleAnnotFilter
public String getChromNum(Annotation annot)
getChromNum
in interface AGAVEAnnotFilter
getChromNum
in class SimpleAnnotFilter
public AGAVEProperty[] getProperty(Annotation annot, String type)
SimpleAnnotFilter
getProperty
in interface AGAVEAnnotFilter
getProperty
in class SimpleAnnotFilter
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