owltools.gaf.rules
Interface AnnotationRule

All Known Implementing Classes:
AbstractAnnotationRule, AnnotationRegularExpressionFromXMLRule, AnnotationTaxonRule, BasicChecksRule, GenericReasonerValidationCheck, GoAnnotationTaxonRule, GoBindingCheckWithFieldRule, GoClassReferenceAnnotationRule, GoICAnnotationRule, GoIDAAnnotationRule, GoIEPRestrictionsRule, GoIPIAnnotationRule, GoIPICatalyticActivityRestrictionsRule, GoNoISSProteinBindingRule

public interface AnnotationRule


Method Summary
 Date getDate()
          Get the status date of this rule.
 String getDescription()
          Get the description for a rule.
 String getName()
          Return the name of the rule.
 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 isAnnotationLevel()
           
 boolean isDocumentLevel()
           
 boolean isOwlDocumentLevel()
           
 void setDate(Date date)
          Set the status date for this rule.
 void setDescription(String description)
          Set the description for this 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(OWLGraphWrapper graph)
Given a whole GafDocument in OWL, find the set of violations using the rule

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

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(OWLGraphWrapper)


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