public abstract class AbstractAnnotationRule extends Object implements AnnotationRule
Constructor and Description |
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AbstractAnnotationRule() |
Modifier and Type | Method and Description |
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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 |
abstract 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.
|
public abstract Set<AnnotationRuleViolation> getRuleViolations(GeneAnnotation a)
AnnotationRule
getRuleViolations
in interface AnnotationRule
a
- annotationAnnotationRule.isAnnotationLevel()
public Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc)
AnnotationRule
GafDocument
, find the set of violations using the rulegetRuleViolations
in interface AnnotationRule
AnnotationRule.isDocumentLevel()
public Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc, OWLGraphWrapper graph)
AnnotationRule
GafDocument
in OWL, find the set of violations using the rulegetRuleViolations
in interface AnnotationRule
AnnotationRule.isOwlDocumentLevel()
public List<Prediction> getPredictedAnnotations(GafDocument gafDoc, OWLGraphWrapper graph)
AnnotationRule
GafDocument
in plan and OWL format, check for
possible new inferred annotations (Prediction
).getPredictedAnnotations
in interface AnnotationRule
public void setRuleId(String ruleId)
AnnotationRule
setRuleId
in interface AnnotationRule
public String getRuleId()
AnnotationRule
getRuleId
in interface AnnotationRule
public String getName()
AnnotationRule
getName
in interface AnnotationRule
public void setName(String name)
AnnotationRule
setName
in interface AnnotationRule
public Date getDate()
AnnotationRule
getDate
in interface AnnotationRule
public void setDate(Date date)
AnnotationRule
setDate
in interface AnnotationRule
public String getStatus()
AnnotationRule
getStatus
in interface AnnotationRule
public void setStatus(String status)
AnnotationRule
setStatus
in interface AnnotationRule
public String getDescription()
AnnotationRule
getDescription
in interface AnnotationRule
public void setDescription(String description)
AnnotationRule
setDescription
in interface AnnotationRule
public boolean isAnnotationLevel()
isAnnotationLevel
in interface AnnotationRule
GeneAnnotation
.AnnotationRule.getRuleViolations(GeneAnnotation)
public boolean isDocumentLevel()
isDocumentLevel
in interface AnnotationRule
AnnotationRule.getRuleViolations(GafDocument)
public boolean isOwlDocumentLevel()
isOwlDocumentLevel
in interface AnnotationRule
AnnotationRule.getRuleViolations(GafDocument, OWLGraphWrapper)
public boolean isInferringAnnotations()
isInferringAnnotations
in interface AnnotationRule
AnnotationRule.getPredictedAnnotations(GafDocument, OWLGraphWrapper)
public boolean hasGrandFathering()
AnnotationRule
hasGrandFathering
in interface AnnotationRule
AnnotationRule.getGrandFatheringDate()
public Date getGrandFatheringDate()
AnnotationRule
AnnotationRule.hasGrandFathering()
is true.getGrandFatheringDate
in interface AnnotationRule
AnnotationRule.hasGrandFathering()
public void setGrandFatheringDate(Date date)
AnnotationRule
setGrandFatheringDate
in interface AnnotationRule
AnnotationRule.hasGrandFathering()
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