owltools.gaf.rules
Interface AnnotationRule

All Known Implementing Classes:
AbstractAnnotationRule, AnnotationRegularExpressionFromXMLRule, AnnotationTaxonRule, BasicChecksRule, GenericReasonerValidationCheck, GoAnnotationExperimentalPredictionRule, GoAnnotationPredictionRule, GoAnnotationTaxonRule, GoBindingCheckWithFieldRule, GoClassReferenceAnnotationRule, GoICAnnotationRule, GoIDAAnnotationRule, GoIEPRestrictionsRule, GoIPIAnnotationRule, GoIPICatalyticActivityRestrictionsRule, GoMultipleTaxonRule, GoNDAnnotationRule, GoNoHighLevelTermAnnotationRule, GoNoISSProteinBindingRule, GOReciprocalAnnotationRule

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(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.
 

Method Detail

getRuleViolations

Set<AnnotationRuleViolation> getRuleViolations(GeneAnnotation a)
Given an annotation, find the set of violations using the rule

Parameters:
a - annotation
Returns:
set of violations
See Also:
isAnnotationLevel()

getRuleViolations

Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc)
Given a whole GafDocument , find the set of violations using the rule

Parameters:
gafDoc -
Returns:
set of violations
See Also:
isDocumentLevel()

getRuleViolations

Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc,
                                               OWLGraphWrapper graph)
Given a whole GafDocument in OWL, find the set of violations using the rule

Parameters:
gafDoc -
graph -
Returns:
set of violations
See Also:
isOwlDocumentLevel()

getPredictedAnnotations

List<Prediction> getPredictedAnnotations(GafDocument gafDoc,
                                         OWLGraphWrapper graph)
Given a whole GafDocument in plan and OWL format, check for possible new inferred annotations (Prediction).

Parameters:
gafDoc -
graph -
Returns:
set of inferred annotation predictions

setRuleId

void setRuleId(String ruleId)
Set the rule id

Parameters:
ruleId -

getRuleId

String getRuleId()
Get the ruleId.

Returns:
ruleId

getName

String getName()
Return the name of the rule.

Returns:
name

setName

void setName(String name)
Set the name for the rule.

Parameters:
name -

getDate

Date getDate()
Get the status date of this rule.

Returns:
status date or null

setDate

void setDate(Date date)
Set the status date for this rule.

Parameters:
date -

getStatus

String getStatus()
Get the status of this rule.

Returns:
status

setStatus

void setStatus(String status)
Set the status for this rule.

Parameters:
status -

getDescription

String getDescription()
Get the description for a rule. May be null.

Returns:
string or null

setDescription

void setDescription(String description)
Set the description for this rule.

Parameters:
description -

isAnnotationLevel

boolean isAnnotationLevel()
Returns:
true if the rule has to be applied to a GeneAnnotation.
See Also:
getRuleViolations(GeneAnnotation)

isDocumentLevel

boolean isDocumentLevel()
Returns:
true if the rule has to be applied to the whole GA document.
See Also:
getRuleViolations(GafDocument)

isOwlDocumentLevel

boolean isOwlDocumentLevel()
Returns:
true if the rule has to be applied to the whole OWL document.
See Also:
getRuleViolations(GafDocument, OWLGraphWrapper)

isInferringAnnotations

boolean isInferringAnnotations()
Returns:
true, if the rule is also capable of inferring new annotations.
See Also:
getPredictedAnnotations(GafDocument, OWLGraphWrapper)

hasGrandFathering

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.

Returns:
true, if the rule requires grand fathering
See Also:
getGrandFatheringDate()

getGrandFatheringDate

Date getGrandFatheringDate()
Return the cut-off date for grand fathering the rule. Has only a valid value if hasGrandFathering() is true.

Returns:
date
See Also:
hasGrandFathering()

setGrandFatheringDate

void setGrandFatheringDate(Date date)
Set the cut-off date for grand fathering the rule. A null value deactivates the grand fathering.

Parameters:
date -
See Also:
hasGrandFathering()


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