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