public interface AnnotationRule
Modifier and Type | Method and Description |
---|---|
Date |
getDate()
Get the status date of this rule.
|
String |
getDescription()
Get the description for a rule.
|
Date |
getGrandFatheringDate()
Return the cut-off date for grand fathering the rule.
|
String |
getName()
Return the name of the rule.
|
List<Prediction> |
getPredictedAnnotations(GafDocument gafDoc,
OWLGraphWrapper graph)
Given a whole
GafDocument in plan and OWL format, check for
possible new inferred annotations (Prediction ). |
String |
getRuleId()
Get the ruleId.
|
Set<AnnotationRuleViolation> |
getRuleViolations(GafDocument gafDoc)
Given a whole
GafDocument , find the set of violations using the rule |
Set<AnnotationRuleViolation> |
getRuleViolations(GafDocument gafDoc,
OWLGraphWrapper graph)
Given a whole
GafDocument in OWL, find the set of violations using the rule |
Set<AnnotationRuleViolation> |
getRuleViolations(GeneAnnotation a)
Given an annotation, find the set of violations using the rule
|
String |
getStatus()
Get the status of this rule.
|
boolean |
hasGrandFathering()
Indicate the use of grand fathering, meaning do not report violations for
this rule for annotations older than the given grand fathering date
cut-off.
|
boolean |
isAnnotationLevel() |
boolean |
isDocumentLevel() |
boolean |
isInferringAnnotations() |
boolean |
isOwlDocumentLevel() |
void |
setDate(Date date)
Set the status date for this rule.
|
void |
setDescription(String description)
Set the description for this rule.
|
void |
setGrandFatheringDate(Date date)
Set the cut-off date for grand fathering the rule.
|
void |
setName(String name)
Set the name for the rule.
|
void |
setRuleId(String ruleId)
Set the rule id
|
void |
setStatus(String status)
Set the status for this rule.
|
Set<AnnotationRuleViolation> getRuleViolations(GeneAnnotation a)
a
- annotationisAnnotationLevel()
Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc)
GafDocument
, find the set of violations using the rulegafDoc
- isDocumentLevel()
Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc, OWLGraphWrapper graph)
GafDocument
in OWL, find the set of violations using the rulegafDoc
- graph
- isOwlDocumentLevel()
List<Prediction> getPredictedAnnotations(GafDocument gafDoc, OWLGraphWrapper graph)
GafDocument
in plan and OWL format, check for
possible new inferred annotations (Prediction
).gafDoc
- graph
- void setRuleId(String ruleId)
ruleId
- String getRuleId()
String getName()
void setName(String name)
name
- Date getDate()
void setDate(Date date)
date
- String getStatus()
void setStatus(String status)
status
- String getDescription()
void setDescription(String description)
description
- boolean isAnnotationLevel()
GeneAnnotation
.getRuleViolations(GeneAnnotation)
boolean isDocumentLevel()
getRuleViolations(GafDocument)
boolean isOwlDocumentLevel()
getRuleViolations(GafDocument, OWLGraphWrapper)
boolean isInferringAnnotations()
getPredictedAnnotations(GafDocument, OWLGraphWrapper)
boolean hasGrandFathering()
getGrandFatheringDate()
Date getGrandFatheringDate()
hasGrandFathering()
is true.hasGrandFathering()
void setGrandFatheringDate(Date date)
date
- hasGrandFathering()
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