owltools.gaf
Class GeneAnnotation

java.lang.Object
  extended by owltools.gaf.GeneAnnotation

public class GeneAnnotation
extends Object

Representation of a gene annotation.


Field Summary
static ThreadLocal<DateFormat> GAF_Date_Format
          Provide a thread-safe formatter for a GAF date.
 
Constructor Summary
GeneAnnotation()
           
GeneAnnotation(GeneAnnotation ann)
           
 
Method Summary
 void addProperty(String key, String value)
           
 void addReferenceId(String referenceId)
           
 void addReferenceIds(Collection<String> referenceIds)
           
 org.apache.commons.lang3.tuple.Pair<String,String> getActsOnTaxonId()
           
 String getAspect()
           
 String getAssignedBy()
           
 String getBioentity()
           
 Bioentity getBioentityObject()
           
 String getCls()
           
 List<String> getCompositeQualifiers()
          Retrieve the list of qualifiers.
 String getEcoEvidenceCls()
           
 List<List<ExtensionExpression>> getExtensionExpressions()
           
 String getGeneProductForm()
           
 boolean getIsContributesTo()
           
 boolean getIsIntegralTo()
           
 String getLastUpdateDate()
           
 List<org.apache.commons.lang3.tuple.Pair<String,String>> getProperties()
           
 List<String> getReferenceIds()
           
 String getRelation()
           
 String getShortEvidence()
           
 AnnotationSource getSource()
           
 Collection<String> getWithInfos()
           
 boolean isNegated()
           
 void setActsOnTaxonId(org.apache.commons.lang3.tuple.Pair<String,String> taxonRelPair)
           
 void setActsOnTaxonId(String actsOnTaxonId)
           
 void setAspect(String inAspect)
           
 void setAssignedBy(String assignedBy)
           
 void setBioentity(String bioentity)
           
 void setBioentityObject(Bioentity bioentityObject)
           
 void setCls(String cls)
           
 void setCompositeQualifiers(List<String> compositeQualifiers)
           
 void setEvidence(String shortEvidence, String ecoEvidenceCls)
           
 void setExtensionExpressions(List<List<ExtensionExpression>> expressions)
           
 void setGeneProductForm(String geneProductForm)
           
 void setIsContributesTo(boolean isContributesTo)
           
 void setIsIntegralTo(boolean isIntegralTo)
           
 void setIsNegated(boolean isNegated)
           
 void setLastUpdateDate(Date date)
           
 void setLastUpdateDate(String lastUpdateDate)
           
 void setRelation(String relation)
           
 void setSource(AnnotationSource annotationSource)
           
 void setWithInfos(Collection<String> withInfoList)
           
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

GAF_Date_Format

public static final ThreadLocal<DateFormat> GAF_Date_Format
Provide a thread-safe formatter for a GAF date.

Constructor Detail

GeneAnnotation

public GeneAnnotation()

GeneAnnotation

public GeneAnnotation(GeneAnnotation ann)
Method Detail

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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