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