|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
public interface AnnotationRule
Method Summary | |
---|---|
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(GeneAnnotation a)
Given an annotation, find the set of violations using the rule |
Set<AnnotationRuleViolation> |
getRuleViolations(OWLGraphWrapper graph)
Given a whole GafDocument in OWL, 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. |
Method Detail |
---|
Set<AnnotationRuleViolation> getRuleViolations(GeneAnnotation a)
a
- annotation
isAnnotationLevel()
Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc)
GafDocument
, find the set of violations using the rule
gafDoc
-
isDocumentLevel()
Set<AnnotationRuleViolation> getRuleViolations(OWLGraphWrapper graph)
GafDocument
in OWL, find the set of violations using the rule
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(OWLGraphWrapper)
boolean isInferringAnnotations()
getPredictedAnnotations(GafDocument, OWLGraphWrapper)
boolean hasGrandFathering()
getGrandFatheringDate()
Date getGrandFatheringDate()
hasGrandFathering()
is true.
hasGrandFathering()
void setGrandFatheringDate(Date date)
date
- hasGrandFathering()
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |