Package | Description |
---|---|
owltools.gaf.rules | |
owltools.gaf.rules.go |
Modifier and Type | Class and Description |
---|---|
class |
AbstractAnnotationRule |
class |
AnnotationRegularExpressionFromXMLRule
This class implements execution of the regular expression rules.
|
class |
AnnotationTaxonRule
Checks if an annotation is valid according to taxon constraints.
|
class |
GenericReasonerValidationCheck
This check using the
ElkReasoner will not detect unsatisfiable
classes, which result from inverse_of object properties. |
Modifier and Type | Method and Description |
---|---|
protected AnnotationRule |
AnnotationRulesFactoryImpl.getClassForName(String className) |
AnnotationRule |
AnnotationRulesEngine.getRule(String id)
Retrieve the corresponding rule for a given rule id.
|
Modifier and Type | Method and Description |
---|---|
List<AnnotationRule> |
AnnotationRulesFactoryImpl.getExperimentalInferenceRules() |
List<AnnotationRule> |
AnnotationRulesFactory.getExperimentalInferenceRules()
Get the list of rules, which check for inferred annotations.
|
List<AnnotationRule> |
AnnotationRulesFactoryImpl.getGafDocumentRules() |
List<AnnotationRule> |
AnnotationRulesFactory.getGafDocumentRules()
Get the list of rules, which require a global view of the GAF (
GafDocument ). |
List<AnnotationRule> |
AnnotationRulesFactoryImpl.getGeneAnnotationRules() |
List<AnnotationRule> |
AnnotationRulesFactory.getGeneAnnotationRules()
Get the list of rules to be applied for each
GeneAnnotation |
List<AnnotationRule> |
AnnotationRulesFactoryImpl.getInferenceRules() |
List<AnnotationRule> |
AnnotationRulesFactory.getInferenceRules()
Get the list of rules, which check for inferred annotations.
|
List<AnnotationRule> |
AnnotationRulesFactoryImpl.getOwlRules() |
List<AnnotationRule> |
AnnotationRulesFactory.getOwlRules()
Get the list of rules, which require a global view of the GAF (
GafDocument ) and OWL. |
Modifier and Type | Method and Description |
---|---|
protected void |
AnnotationRulesFactoryImpl.handleAdditionalRules(List<AnnotationRule> annotationRules,
List<AnnotationRule> documentRules,
List<AnnotationRule> owlRules,
List<AnnotationRule> inferenceRules,
List<AnnotationRule> experimentalInferenceRules) |
protected void |
AnnotationRulesFactoryImpl.handleAdditionalRules(List<AnnotationRule> annotationRules,
List<AnnotationRule> documentRules,
List<AnnotationRule> owlRules,
List<AnnotationRule> inferenceRules,
List<AnnotationRule> experimentalInferenceRules) |
protected void |
AnnotationRulesFactoryImpl.handleAdditionalRules(List<AnnotationRule> annotationRules,
List<AnnotationRule> documentRules,
List<AnnotationRule> owlRules,
List<AnnotationRule> inferenceRules,
List<AnnotationRule> experimentalInferenceRules) |
protected void |
AnnotationRulesFactoryImpl.handleAdditionalRules(List<AnnotationRule> annotationRules,
List<AnnotationRule> documentRules,
List<AnnotationRule> owlRules,
List<AnnotationRule> inferenceRules,
List<AnnotationRule> experimentalInferenceRules) |
protected void |
AnnotationRulesFactoryImpl.handleAdditionalRules(List<AnnotationRule> annotationRules,
List<AnnotationRule> documentRules,
List<AnnotationRule> owlRules,
List<AnnotationRule> inferenceRules,
List<AnnotationRule> experimentalInferenceRules) |
Modifier and Type | Class and Description |
---|---|
class |
BasicChecksRule
This class performs basic checks.
|
class |
GoAnnotationExperimentalPredictionRule |
class |
GoAnnotationPredictionRule |
class |
GoAnnotationTaxonRule
Checks if an annotation is valid according to GO taxon constraints.
|
class |
GoBindingCheckWithFieldRule
GO_AR:0000003
|
class |
GoClassReferenceAnnotationRule
Checks to see if an annotation uses a class that is not in the current ontology, and that
the class has not been obsoleted
|
class |
GoICAnnotationRule
GO_AR:0000016
|
class |
GoIDAAnnotationRule
GO_AR:0000017
|
class |
GoIEPRestrictionsRule
GO_AR:0000006
|
class |
GoIPIAnnotationRule
GO_AR:0000018
|
class |
GoIPICatalyticActivityRestrictionsRule
GO_AR:0000007
|
class |
GoMultipleTaxonRule
GO_AR:0000015
|
class |
GoNDAnnotationRule
GO_AR:0000011
|
class |
GoNoHighLevelTermAnnotationRule
GO_AR:0000008
|
class |
GoNoISSProteinBindingRule
GO_AR:0000005
|
class |
GOReciprocalAnnotationRule
GO_AR:0000004
|
Modifier and Type | Method and Description |
---|---|
protected AnnotationRule |
GoAnnotationRulesFactoryImpl.getClassForName(String className) |
Modifier and Type | Method and Description |
---|---|
protected void |
GoAnnotationRulesFactoryImpl.handleAdditionalRules(List<AnnotationRule> annotationRules,
List<AnnotationRule> documentRules,
List<AnnotationRule> owlRules,
List<AnnotationRule> inferenceRules,
List<AnnotationRule> experimentalInferenceRules) |
protected void |
GoAnnotationRulesFactoryImpl.handleAdditionalRules(List<AnnotationRule> annotationRules,
List<AnnotationRule> documentRules,
List<AnnotationRule> owlRules,
List<AnnotationRule> inferenceRules,
List<AnnotationRule> experimentalInferenceRules) |
protected void |
GoAnnotationRulesFactoryImpl.handleAdditionalRules(List<AnnotationRule> annotationRules,
List<AnnotationRule> documentRules,
List<AnnotationRule> owlRules,
List<AnnotationRule> inferenceRules,
List<AnnotationRule> experimentalInferenceRules) |
protected void |
GoAnnotationRulesFactoryImpl.handleAdditionalRules(List<AnnotationRule> annotationRules,
List<AnnotationRule> documentRules,
List<AnnotationRule> owlRules,
List<AnnotationRule> inferenceRules,
List<AnnotationRule> experimentalInferenceRules) |
protected void |
GoAnnotationRulesFactoryImpl.handleAdditionalRules(List<AnnotationRule> annotationRules,
List<AnnotationRule> documentRules,
List<AnnotationRule> owlRules,
List<AnnotationRule> inferenceRules,
List<AnnotationRule> experimentalInferenceRules) |
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