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 java.lang.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 java.lang.String getAccession(Annotation annot)
- Specified by:
getAccession
in interface AGAVEAnnotFilter
getKeyword
public java.lang.String getKeyword(Annotation annot)
- Specified by:
getKeyword
in interface AGAVEAnnotFilter
getElementId
public java.lang.String getElementId(Annotation annot)
- Specified by:
getElementId
in interface AGAVEAnnotFilter
getOrganism
public java.lang.String getOrganism(Annotation annot)
- Specified by:
getOrganism
in interface AGAVEAnnotFilter
getLabel
public java.lang.String getLabel(Annotation annot)
- Specified by:
getLabel
in interface AGAVEAnnotFilter
getDescription
public java.lang.String getDescription(Annotation annot)
- Specified by:
getDescription
in interface AGAVEAnnotFilter
getMatchAlign
public java.lang.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 java.lang.String getClassifySystem(Annotation annot)
- Specified by:
getClassifySystem
in interface AGAVEAnnotFilter
getClassifyId
public java.lang.String getClassifyId(Annotation annot)
- Specified by:
getClassifyId
in interface AGAVEAnnotFilter
getClassifyType
public java.lang.String getClassifyType(Annotation annot)
- Specified by:
getClassifyType
in interface AGAVEAnnotFilter
getExonIds
public java.lang.String[] getExonIds(Annotation annot)
- Specified by:
getExonIds
in interface AGAVEAnnotFilter
getChromNum
public java.lang.String getChromNum(Annotation annot)
- Specified by:
getChromNum
in interface AGAVEAnnotFilter
getIdAlias
public AGAVEIdAlias[] getIdAlias(Annotation annot)
- Specified by:
getIdAlias
in interface AGAVEAnnotFilter
getNote
public java.lang.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 java.lang.String[] getElementIds(Annotation annot)
- Specified by:
getElementIds
in interface AGAVEAnnotFilter
getGroupOrder
public java.lang.String getGroupOrder(Annotation annot)
- Specified by:
getGroupOrder
in interface AGAVEAnnotFilter
getMatchDesc
public java.lang.String getMatchDesc(Annotation annot)
- Specified by:
getMatchDesc
in interface AGAVEAnnotFilter
getFeatureType
public java.lang.String getFeatureType(Annotation annot)
- Specified by:
getFeatureType
in interface AGAVEAnnotFilter
getResultType
public java.lang.String getResultType(Annotation annot)
- Specified by:
getResultType
in interface AGAVEAnnotFilter
getConfidence
public java.lang.String getConfidence(Annotation annot)
- Specified by:
getConfidence
in interface AGAVEAnnotFilter
getAlignLength
public java.lang.String getAlignLength(Annotation annot)
- Specified by:
getAlignLength
in interface AGAVEAnnotFilter
getAlignUnits
public java.lang.String getAlignUnits(Annotation annot)
- Specified by:
getAlignUnits
in interface AGAVEAnnotFilter
getXrefs
public AGAVEXrefs[] getXrefs(Annotation annot)
- Specified by:
getXrefs
in interface AGAVEAnnotFilter
getVersion
public java.lang.String getVersion(Annotation annot)
- Specified by:
getVersion
in interface AGAVEAnnotFilter
getSequenceId
public java.lang.String getSequenceId(Annotation annot)
- Specified by:
getSequenceId
in interface AGAVEAnnotFilter
getTaxonId
public java.lang.String getTaxonId(Annotation annot)
- Specified by:
getTaxonId
in interface AGAVEAnnotFilter
getCloneId
public java.lang.String getCloneId(Annotation annot)
- Specified by:
getCloneId
in interface AGAVEAnnotFilter
getCloneLibrary
public java.lang.String getCloneLibrary(Annotation annot)
- Specified by:
getCloneLibrary
in interface AGAVEAnnotFilter
getChromosome
public java.lang.String getChromosome(Annotation annot)
- Specified by:
getChromosome
in interface AGAVEAnnotFilter
getMapPosition
public java.lang.String getMapPosition(Annotation annot)
- Specified by:
getMapPosition
in interface AGAVEAnnotFilter
getEcNumber
public java.lang.String getEcNumber(Annotation annot)
- Specified by:
getEcNumber
in interface AGAVEAnnotFilter
getCreateDate
public java.lang.String getCreateDate(Annotation annot)
- Specified by:
getCreateDate
in interface AGAVEAnnotFilter
getUpdateDate
public java.lang.String getUpdateDate(Annotation annot)
- Specified by:
getUpdateDate
in interface AGAVEAnnotFilter
getOS
public java.lang.String getOS(Annotation annot)
- Specified by:
getOS
in interface AGAVEAnnotFilter
getMolType
public java.lang.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,
java.lang.String type)
- ThomasD made this a bit safer...
- Specified by:
getProperty
in interface AGAVEAnnotFilter