owltools.gaf
Class GeneAnnotation
java.lang.Object
owltools.gaf.GeneAnnotation
public class GeneAnnotation
- extends Object
Representation of a gene annotation.
GAF_Date_Format
public static final ThreadLocal<DateFormat> GAF_Date_Format
- Provide a thread-safe formatter for a GAF date.
GeneAnnotation
public GeneAnnotation()
GeneAnnotation
public GeneAnnotation(GeneAnnotation ann)
toString
public String toString()
- Overrides:
toString
in class Object
getBioentity
public String getBioentity()
setBioentity
public void setBioentity(String bioentity)
getRelation
public String getRelation()
setRelation
public void setRelation(String relation)
getCls
public String getCls()
setCls
public void setCls(String cls)
getReferenceIds
public List<String> getReferenceIds()
addReferenceId
public void addReferenceId(String referenceId)
addReferenceIds
public void addReferenceIds(Collection<String> referenceIds)
getEcoEvidenceCls
public String getEcoEvidenceCls()
getShortEvidence
public String getShortEvidence()
setEvidence
public void setEvidence(String shortEvidence,
String ecoEvidenceCls)
getActsOnTaxonId
public org.apache.commons.lang3.tuple.Pair<String,String> getActsOnTaxonId()
setAspect
public void setAspect(String inAspect)
getAspect
public String getAspect()
setActsOnTaxonId
public void setActsOnTaxonId(String actsOnTaxonId)
setActsOnTaxonId
public void setActsOnTaxonId(org.apache.commons.lang3.tuple.Pair<String,String> taxonRelPair)
getLastUpdateDate
public String getLastUpdateDate()
setLastUpdateDate
public void setLastUpdateDate(Date date)
setLastUpdateDate
public void setLastUpdateDate(String lastUpdateDate)
getAssignedBy
public String getAssignedBy()
setAssignedBy
public void setAssignedBy(String assignedBy)
getExtensionExpressions
public List<List<ExtensionExpression>> getExtensionExpressions()
setExtensionExpressions
public void setExtensionExpressions(List<List<ExtensionExpression>> expressions)
getGeneProductForm
public String getGeneProductForm()
setGeneProductForm
public void setGeneProductForm(String geneProductForm)
getBioentityObject
public Bioentity getBioentityObject()
setBioentityObject
public void setBioentityObject(Bioentity bioentityObject)
getIsContributesTo
public boolean getIsContributesTo()
setIsContributesTo
public void setIsContributesTo(boolean isContributesTo)
getIsIntegralTo
public boolean getIsIntegralTo()
setIsIntegralTo
public void setIsIntegralTo(boolean isIntegralTo)
setIsNegated
public void setIsNegated(boolean isNegated)
isNegated
public boolean isNegated()
setWithInfos
public void setWithInfos(Collection<String> withInfoList)
getWithInfos
public Collection<String> getWithInfos()
setCompositeQualifiers
public void setCompositeQualifiers(List<String> compositeQualifiers)
getCompositeQualifiers
public List<String> getCompositeQualifiers()
- Retrieve the list of qualifiers. Split the composite string, if
necessary.
- Returns:
- list, never null
getSource
public AnnotationSource getSource()
setSource
public void setSource(AnnotationSource annotationSource)
addProperty
public void addProperty(String key,
String value)
getProperties
public List<org.apache.commons.lang3.tuple.Pair<String,String>> getProperties()
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