org.biojava.bio.seq.io.agave
Class SimpleAnnotFilter
java.lang.Object
org.biojava.bio.seq.io.agave.SimpleAnnotFilter
- All Implemented Interfaces:
- AGAVEAnnotFilter
- Direct Known Subclasses:
- Agave2AgaveAnnotFilter, Embl2AgaveAnnotFilter
public class SimpleAnnotFilter
- extends Object
- implements AGAVEAnnotFilter
Basic implementation of AGAVEAnnotFilter
- Author:
- Hanning Ni Doubletwist Inc
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SIMPLE_ANNOT_FILTER_FACTORY
public static final AGAVEAnnotFilterFactory SIMPLE_ANNOT_FILTER_FACTORY
getAccession
public String getAccession(Annotation annot)
- Specified by:
getAccession
in interface AGAVEAnnotFilter
getKeyword
public String getKeyword(Annotation annot)
- Specified by:
getKeyword
in interface AGAVEAnnotFilter
getElementId
public String getElementId(Annotation annot)
- Specified by:
getElementId
in interface AGAVEAnnotFilter
getOrganism
public String getOrganism(Annotation annot)
- Specified by:
getOrganism
in interface AGAVEAnnotFilter
getLabel
public String getLabel(Annotation annot)
- Specified by:
getLabel
in interface AGAVEAnnotFilter
getDescription
public String getDescription(Annotation annot)
- Specified by:
getDescription
in interface AGAVEAnnotFilter
getMatchAlign
public String getMatchAlign(Annotation annot)
- Specified by:
getMatchAlign
in interface AGAVEAnnotFilter
getMatchRegion
public AGAVEMatchRegion getMatchRegion(Annotation annot)
- Specified by:
getMatchRegion
in interface AGAVEAnnotFilter
getQueryRegion
public AGAVEQueryRegion getQueryRegion(Annotation annot)
- Specified by:
getQueryRegion
in interface AGAVEAnnotFilter
getClassifySystem
public String getClassifySystem(Annotation annot)
- Specified by:
getClassifySystem
in interface AGAVEAnnotFilter
getClassifyId
public String getClassifyId(Annotation annot)
- Specified by:
getClassifyId
in interface AGAVEAnnotFilter
getClassifyType
public String getClassifyType(Annotation annot)
- Specified by:
getClassifyType
in interface AGAVEAnnotFilter
getExonIds
public String[] getExonIds(Annotation annot)
- Specified by:
getExonIds
in interface AGAVEAnnotFilter
getChromNum
public String getChromNum(Annotation annot)
- Specified by:
getChromNum
in interface AGAVEAnnotFilter
getIdAlias
public AGAVEIdAlias[] getIdAlias(Annotation annot)
- Specified by:
getIdAlias
in interface AGAVEAnnotFilter
getNote
public String getNote(Annotation annot)
- Specified by:
getNote
in interface AGAVEAnnotFilter
getAltIds
public AGAVEDbId[] getAltIds(Annotation annot)
- Specified by:
getAltIds
in interface AGAVEAnnotFilter
getMapLocation
public AGAVEMapLocation[] getMapLocation(Annotation annot)
- Specified by:
getMapLocation
in interface AGAVEAnnotFilter
getRelatedAnnot
public AGAVERelatedAnnot[] getRelatedAnnot(Annotation annot)
- Specified by:
getRelatedAnnot
in interface AGAVEAnnotFilter
getElementIds
public String[] getElementIds(Annotation annot)
- Specified by:
getElementIds
in interface AGAVEAnnotFilter
getGroupOrder
public String getGroupOrder(Annotation annot)
- Specified by:
getGroupOrder
in interface AGAVEAnnotFilter
getMatchDesc
public String getMatchDesc(Annotation annot)
- Specified by:
getMatchDesc
in interface AGAVEAnnotFilter
getFeatureType
public String getFeatureType(Annotation annot)
- Specified by:
getFeatureType
in interface AGAVEAnnotFilter
getResultType
public String getResultType(Annotation annot)
- Specified by:
getResultType
in interface AGAVEAnnotFilter
getConfidence
public String getConfidence(Annotation annot)
- Specified by:
getConfidence
in interface AGAVEAnnotFilter
getAlignLength
public String getAlignLength(Annotation annot)
- Specified by:
getAlignLength
in interface AGAVEAnnotFilter
getAlignUnits
public String getAlignUnits(Annotation annot)
- Specified by:
getAlignUnits
in interface AGAVEAnnotFilter
getXrefs
public AGAVEXrefs[] getXrefs(Annotation annot)
- Specified by:
getXrefs
in interface AGAVEAnnotFilter
getVersion
public String getVersion(Annotation annot)
- Specified by:
getVersion
in interface AGAVEAnnotFilter
getSequenceId
public String getSequenceId(Annotation annot)
- Specified by:
getSequenceId
in interface AGAVEAnnotFilter
getTaxonId
public String getTaxonId(Annotation annot)
- Specified by:
getTaxonId
in interface AGAVEAnnotFilter
getCloneId
public String getCloneId(Annotation annot)
- Specified by:
getCloneId
in interface AGAVEAnnotFilter
getCloneLibrary
public String getCloneLibrary(Annotation annot)
- Specified by:
getCloneLibrary
in interface AGAVEAnnotFilter
getChromosome
public String getChromosome(Annotation annot)
- Specified by:
getChromosome
in interface AGAVEAnnotFilter
getMapPosition
public String getMapPosition(Annotation annot)
- Specified by:
getMapPosition
in interface AGAVEAnnotFilter
getEcNumber
public String getEcNumber(Annotation annot)
- Specified by:
getEcNumber
in interface AGAVEAnnotFilter
getCreateDate
public String getCreateDate(Annotation annot)
- Specified by:
getCreateDate
in interface AGAVEAnnotFilter
getUpdateDate
public String getUpdateDate(Annotation annot)
- Specified by:
getUpdateDate
in interface AGAVEAnnotFilter
getOS
public String getOS(Annotation annot)
- Specified by:
getOS
in interface AGAVEAnnotFilter
getMolType
public String getMolType(Annotation annot)
- Specified by:
getMolType
in interface AGAVEAnnotFilter
getDbId
public AGAVEDbId getDbId(Annotation annot)
- Specified by:
getDbId
in interface AGAVEAnnotFilter
getProperty
public AGAVEProperty[] getProperty(Annotation annot,
String type)
- ThomasD made this a bit safer...
- Specified by:
getProperty
in interface AGAVEAnnotFilter