- GAF_Date_Format - Static variable in class owltools.gaf.GeneAnnotation
-
Provide a thread-safe formatter for a GAF date.
- GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI - Static variable in class owltools.gaf.owl.GAFOWLBridge
-
- gafdocs - Variable in class owltools.gaf.godb.Dumper
-
- GafDocument - Class in owltools.gaf
-
Representation of a gene annotation file (GAF).
- GafDocument(String, String) - Constructor for class owltools.gaf.GafDocument
-
Create a new document instance.
- GafDocument(String, String, Map<String, Bioentity>) - Constructor for class owltools.gaf.GafDocument
-
Create a new document instance.
- gafDocumentSizeInBytes - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
-
- GafObjectsBuilder - Class in owltools.gaf.parser
-
- GafObjectsBuilder() - Constructor for class owltools.gaf.parser.GafObjectsBuilder
-
- GafObjectsBuilder(int) - Constructor for class owltools.gaf.parser.GafObjectsBuilder
-
- GAFOWLBridge - Class in owltools.gaf.owl
-
- GAFOWLBridge(OWLGraphWrapper) - Constructor for class owltools.gaf.owl.GAFOWLBridge
-
- GAFOWLBridge(OWLGraphWrapper, OWLOntology) - Constructor for class owltools.gaf.owl.GAFOWLBridge
-
The ontology generated from the gaf will be placed in tgtOnt
The graphwrapper object should include ontologies required to resolve certain entities,
including the relations used in col16.
- GAFOWLBridge.BioentityMapping - Enum in owltools.gaf.owl
-
- GAFOWLBridge.GAFDescription - Class in owltools.gaf.owl
-
- GAFOWLBridge.GAFDescription(OWLObjectSomeValuesFrom, String) - Constructor for class owltools.gaf.owl.GAFOWLBridge.GAFDescription
-
- GAFOWLBridge.Vocab - Enum in owltools.gaf.owl
-
- GAFParser - Class in owltools.gaf.parser
-
- GAFParser() - Constructor for class owltools.gaf.parser.GAFParser
-
- GafWriter - Class in owltools.gaf.io
-
Write a Gene Annotation File to a given stream or file.
- GafWriter() - Constructor for class owltools.gaf.io.GafWriter
-
- GafWriter.BufferedGafWriter - Class in owltools.gaf.io
-
Helper class to create a list of all
GeneAnnotation
lines,
excluding any headers.
Can be used for sorting.
- GafWriter.BufferedGafWriter() - Constructor for class owltools.gaf.io.GafWriter.BufferedGafWriter
-
- GENE_PRODUCT_ISOFORM - Static variable in class owltools.gaf.parser.GAFParser
-
- GeneAnnotation - Class in owltools.gaf
-
Representation of a gene annotation.
- GeneAnnotation() - Constructor for class owltools.gaf.GeneAnnotation
-
- GeneAnnotation(GeneAnnotation) - Constructor for class owltools.gaf.GeneAnnotation
-
- generateAssociations(OWLOntology) - Method in class owltools.gaf.owl.SimpleABoxToGAF
-
- generateAssociations(OWLNamedIndividual, OWLOntology) - Method in class owltools.gaf.owl.SimpleABoxToGAF
-
- GenericReasonerValidationCheck - Class in owltools.gaf.rules
-
This check using the ElkReasoner
will not detect unsatisfiable
classes, which result from inverse_of object properties.
- GenericReasonerValidationCheck() - Constructor for class owltools.gaf.rules.GenericReasonerValidationCheck
-
- get(OWLClass, OWLClass) - Method in class owltools.gaf.inference.ClassTaxonMatrix
-
- getActsOnTaxonId() - Method in class owltools.gaf.GeneAnnotation
-
- getAllEcoClassesForCode(String) - Method in interface owltools.gaf.eco.EcoMapper
-
Retrieve the ECO classes for the given GO evidence code.
- getAllEcoClassesForCode(String) - Method in class owltools.gaf.eco.EcoMapperImpl
-
- getAllPredictions() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
-
- getAllPredictions() - Method in interface owltools.gaf.inference.AnnotationPredictor
-
- getAllValidEvidenceIds(String, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper
-
Get all strings which are valid identifiers for a given evidence code.
- getAllValidEvidenceIds(Set<String>, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper
-
Get all strings which are valid identifiers for the given evidence codes.
- getAllValidEvidenceIds(String, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
-
- getAllValidEvidenceIds(Set<String>, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
-
- getAncestors(Set<OWLClass>, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper
-
Traversing method for the ECO ontology.
- getAncestors(OWLClass, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper
-
Traversing method for the ECO ontology.
- getAncestors(Set<OWLClass>, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
-
- getAncestors(OWLClass, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
-
- getAncestors(Set<OWLClass>, boolean) - Method in class owltools.gaf.EcoTools
-
Deprecated.
Wrapper method for the reasoner.
- getAncestors(OWLClass, boolean) - Method in class owltools.gaf.TaxonTools
-
Wrapper method for the reasoner.
- getAnnotation_Extension() - Method in class owltools.gaf.parser.GpadParser
-
- getAnnotation_Properties() - Method in class owltools.gaf.parser.GpadParser
-
- getAnnotationCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
-
- getAnnotationExtension() - Method in class owltools.gaf.parser.GAFParser
-
- getAnnotationRow() - Method in class owltools.gaf.rules.AnnotationRuleViolation
-
- getAnnotationRuleViolations() - Method in class owltools.gaf.parser.GAFParser
-
- getAnnotations() - Method in class owltools.gaf.Bioentity
-
- getAspect() - Method in class owltools.gaf.GeneAnnotation
-
- getAspect(String) - Method in class owltools.gaf.parser.DefaultAspectProvider
-
- getAspect() - Method in class owltools.gaf.parser.GAFParser
-
- getAspect(String) - Method in interface owltools.gaf.parser.GpadGpiObjectsBuilder.AspectProvider
-
- getAssigned_by() - Method in class owltools.gaf.parser.GpadParser
-
- getAssignedBy() - Method in class owltools.gaf.GeneAnnotation
-
- getAssignedBy() - Method in class owltools.gaf.parser.GAFParser
-
- getBioentities() - Method in class owltools.gaf.BioentityDocument
-
- getBioentities() - Method in class owltools.gaf.GafDocument
-
- getBioentity(String) - Method in class owltools.gaf.GafDocument
-
Retrieve the
Bioentity
object for the given id.
- getBioentity() - Method in class owltools.gaf.GeneAnnotation
-
- getBioentityMapping() - Method in class owltools.gaf.owl.GAFOWLBridge
-
- getBioentityObject() - Method in class owltools.gaf.GeneAnnotation
-
- getChildren() - Method in class owltools.gaf.Bioentity
-
- getClassesForGoCode(String) - Method in class owltools.gaf.EcoTools
-
Deprecated.
Retrieve the ECO classes for the given GO annotation codes.
- getClassesForGoCodes(OWLGraphWrapper, String...) - Static method in class owltools.gaf.EcoTools
-
Deprecated.
Retrieve the ECO classes for the given GO annotation codes.
- getClassesForGoCodes(OWLGraphWrapper, Set<String>) - Static method in class owltools.gaf.EcoTools
-
Deprecated.
Retrieve the ECO classes for the given GO annotation codes.
- getClassForName(String) - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
-
- getClassForName(String) - Method in class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
-
- getCls() - Method in class owltools.gaf.ExtensionExpression
-
- getCls() - Method in class owltools.gaf.GeneAnnotation
-
- getCodes(Set<OWLClass>, OWLGraphWrapper) - Static method in class owltools.gaf.EcoTools
-
Deprecated.
- getCodes(Set<OWLClass>, OWLGraphWrapper, boolean) - Static method in class owltools.gaf.EcoTools
-
Deprecated.
Retrieve the set of codes for a given set of ECO classes.
- getCodesForEcoClasses() - Method in interface owltools.gaf.eco.EcoMapper
-
Retrieve the mapping from ECO classes to GO evidence codes.
- getCodesForEcoClasses() - Method in class owltools.gaf.eco.EcoMapperImpl
-
- getColumn(GpadParser.GpadColumns) - Method in class owltools.gaf.parser.GpadParser
-
- getColumn(GpiParser.GpiColumns) - Method in class owltools.gaf.parser.GpiParser
-
- getComments() - Method in class owltools.gaf.BioentityDocument
-
Get the current set of comments.
- getComments() - Method in class owltools.gaf.GafDocument
-
Get the current set of comments.
- getCurrentRow() - Method in class owltools.gaf.parser.GAFParser
-
- getDate() - Method in class owltools.gaf.parser.GAFParser
-
- getDate() - Method in class owltools.gaf.parser.GpadParser
-
- getDate() - Method in class owltools.gaf.rules.AbstractAnnotationRule
-
- getDate() - Method in interface owltools.gaf.rules.AnnotationRule
-
Get the status date of this rule.
- getDb() - Method in class owltools.gaf.Bioentity
-
- getDb() - Method in class owltools.gaf.parser.GAFParser
-
- getDB() - Method in class owltools.gaf.parser.GpadParser
-
- getDB_Object_ID() - Method in class owltools.gaf.parser.GpadParser
-
- getDB_Object_ID() - Method in class owltools.gaf.parser.GpiParser
-
- getDB_Object_Name() - Method in class owltools.gaf.parser.GpiParser
-
- getDB_Object_Symbol() - Method in class owltools.gaf.parser.GpiParser
-
- getDB_Object_Synonym() - Method in class owltools.gaf.parser.GpiParser
-
- getDB_Object_Type() - Method in class owltools.gaf.parser.GpiParser
-
- getDB_Reference() - Method in class owltools.gaf.parser.GpadParser
-
- getDB_Xref() - Method in class owltools.gaf.parser.GpiParser
-
- getDBID() - Method in class owltools.gaf.Bioentity
-
- getDbObjectId() - Method in class owltools.gaf.parser.GAFParser
-
- getDbObjectName() - Method in class owltools.gaf.parser.GAFParser
-
- getDbObjectSymbol() - Method in class owltools.gaf.parser.GAFParser
-
- getDbObjectSynonym() - Method in class owltools.gaf.parser.GAFParser
-
- getDBObjectType() - Method in class owltools.gaf.parser.GAFParser
-
- getDBs() - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo
-
Retrieve the databases for which there are identifiers for the protein.
- getDbXrefs() - Method in class owltools.gaf.Bioentity
-
- getDefaultDbToTaxon() - Static method in class owltools.gaf.bioentities.ProteinTools
-
Retrieve the default mapping from db name to the numeric part of the NCBI
taxon id.
- getDescendents(Set<OWLClass>, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper
-
Traversing method for the ECO ontology.
- getDescendents(OWLClass, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper
-
Traversing method for the ECO ontology.
- getDescendents(Set<OWLClass>, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
-
- getDescendents(OWLClass, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
-
- getDescendents(Set<OWLClass>, boolean) - Method in class owltools.gaf.EcoTools
-
Deprecated.
Wrapper method for the reasoner
- getDescendents(Set<OWLClass>, boolean) - Method in class owltools.gaf.TaxonTools
-
Wrapper method for the reasoner
- getDescription(GeneAnnotation) - Method in class owltools.gaf.owl.GAFOWLBridge
-
- getDescription() - Method in class owltools.gaf.rules.AbstractAnnotationRule
-
- getDescription() - Method in interface owltools.gaf.rules.AnnotationRule
-
Get the description for a rule.
- getDirectLinkedClasses(OWLClass, String, OWLGraphWrapper) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator
-
Lookup relation super classes in graph g for a given sub class c and property p.
- getDirectLinkedClasses(OWLClass, Set<OWLObjectProperty>, OWLGraphWrapper, Set<OWLClass>) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator
-
Lookup relation super classes in graph g for a given sub class c and property p.
- getDocumentPath() - Method in class owltools.gaf.GafDocument
-
Retrieve the source path for this document
- getEco(String, String) - Method in interface owltools.gaf.eco.SimpleEcoMapper
-
- getEco(String, Collection<String>) - Method in interface owltools.gaf.eco.SimpleEcoMapper
-
- getEco(String, String) - Method in class owltools.gaf.eco.SimpleEcoMapperImpl
-
- getEco(String, Collection<String>) - Method in class owltools.gaf.eco.SimpleEcoMapperImpl
-
- getEcoClassForCode(String) - Method in interface owltools.gaf.eco.EcoMapper
-
Retrieve the equivalent ECO class for the given GO evidence code.
- getEcoClassForCode(String, String) - Method in interface owltools.gaf.eco.EcoMapper
-
Retrieve the ECO class for the given GO evidence code and reference.
- getEcoClassForCode(String) - Method in class owltools.gaf.eco.EcoMapperImpl
-
- getEcoClassForCode(String, String) - Method in class owltools.gaf.eco.EcoMapperImpl
-
- getEcoEvidenceCls() - Method in class owltools.gaf.GeneAnnotation
-
- getErrorCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
-
- getErrorMessage() - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
-
- getErrors() - Method in class owltools.gaf.parser.IssueListener.DefaultIssueListener
-
- getEvidence() - Method in class owltools.gaf.parser.GAFParser
-
- getEvidence_Code() - Method in class owltools.gaf.parser.GpadParser
-
- getExpectedColumnCount() - Method in class owltools.gaf.parser.GpadParser
-
- getExpectedColumnCount() - Method in class owltools.gaf.parser.GpiParser
-
- getExperimentalInferenceRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory
-
Get the list of rules, which check for inferred annotations.
- getExperimentalInferenceRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
-
- getExtensionExpressions() - Method in class owltools.gaf.GeneAnnotation
-
- getFileName() - Method in class owltools.gaf.AnnotationSource
-
- getFoldedClassMap() - Method in class owltools.gaf.owl.AnnotationExtensionFolder
-
- getFullName() - Method in class owltools.gaf.Bioentity
-
- getGafdocs() - Method in class owltools.gaf.godb.Dumper
-
- getGafDocument() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
-
- getGafDocument() - Method in class owltools.gaf.rules.AnnotationRuleViolation
-
- getGafDocumentRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory
-
Get the list of rules, which require a global view of the GAF (
GafDocument
).
- getGafDocumentRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
-
- getGene_Product_Properties() - Method in class owltools.gaf.parser.GpiParser
-
- getGeneAnnotation() - Method in class owltools.gaf.inference.Prediction
-
- getGeneAnnotationByLineNumber(int) - Method in class owltools.gaf.GafDocument
-
Retrieve the (first) annotation for the given line number or null.
- getGeneAnnotationRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory
-
- getGeneAnnotationRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
-
- getGeneAnnotations() - Method in class owltools.gaf.GafDocument
-
Get all annotations from this document.
- getGeneAnnotations(String) - Method in class owltools.gaf.GafDocument
-
Get all annotations for a given
Bioentity
id.
- getGeneAnnotationsByDirectGoCls(String) - Method in class owltools.gaf.GafDocument
-
Search for all annotations with the given cls String.
- getGeneId() - Method in class owltools.gaf.Bioentity
-
- getGeneProductForm() - Method in class owltools.gaf.GeneAnnotation
-
- getGeneProjectFormId() - Method in class owltools.gaf.parser.GAFParser
-
- getGO_ID() - Method in class owltools.gaf.parser.GpadParser
-
- getGoCode(String) - Method in interface owltools.gaf.eco.SimpleEcoMapper
-
- getGoCode(String) - Method in class owltools.gaf.eco.SimpleEcoMapperImpl
-
- getGOId() - Method in class owltools.gaf.parser.GAFParser
-
- getGoSubOntology(OWLClass, OWLGraphWrapper) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
-
Get the specific sub ontology.
- getGrandFatheringDate() - Method in class owltools.gaf.rules.AbstractAnnotationRule
-
- getGrandFatheringDate() - Method in interface owltools.gaf.rules.AnnotationRule
-
Return the cut-off date for grand fathering the rule.
- getGraph() - Method in class owltools.gaf.eco.EcoMapperFactory.OntologyMapperPair
-
- getGraph() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
-
- getGraph() - Method in interface owltools.gaf.rules.AnnotationRulesFactory
-
Get the underlying ontology graph for this rule factory.
- getGraph() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
-
- getId() - Method in class owltools.gaf.Bioentity
-
- getId() - Method in class owltools.gaf.BioentityDocument
-
- getId() - Method in class owltools.gaf.GafDocument
-
- getId(String, Object) - Method in class owltools.gaf.godb.DatabaseDumper
-
- getId(String, Object, boolean) - Method in class owltools.gaf.godb.DatabaseDumper
-
- getId(String) - Method in class owltools.gaf.io.XgmmlWriter
-
- getIds(String) - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo
-
Retrieve all identifier of a protein for the given database.
- getInferenceRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory
-
Get the list of rules, which check for inferred annotations.
- getInferenceRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
-
- getInteracting_Taxon_ID() - Method in class owltools.gaf.parser.GpadParser
-
- getIsaPartofSuperClassClosure(Collection<OWLClass>, OWLGraphWrapper, OWLReasoner) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator
-
- getLastUpdateDate() - Method in class owltools.gaf.GeneAnnotation
-
- getLineNumber() - Method in class owltools.gaf.AnnotationSource
-
- getLineNumber() - Method in class owltools.gaf.parser.GAFParser
-
- getLineNumber() - Method in class owltools.gaf.rules.AnnotationRuleViolation
-
- getLines() - Method in class owltools.gaf.io.GafWriter.BufferedGafWriter
-
- getLocalId() - Method in class owltools.gaf.Bioentity
-
- getMappedErrors() - Method in class owltools.gaf.parser.IssueListener.DefaultIssueListener
-
- getMappedWarnings() - Method in class owltools.gaf.parser.IssueListener.DefaultIssueListener
-
- getMapper() - Method in class owltools.gaf.eco.EcoMapperFactory.OntologyMapperPair
-
- getMappingSource() - Method in class owltools.gaf.IdMapping
-
- getMessage() - Method in class owltools.gaf.rules.AnnotationRuleViolation
-
- getName() - Method in class owltools.gaf.rules.AbstractAnnotationRule
-
- getName() - Method in interface owltools.gaf.rules.AnnotationRule
-
Return the name of the rule.
- getNamespace() - Method in class owltools.gaf.parser.GpiParser
-
- getNcbiTaxonId() - Method in class owltools.gaf.Bioentity
-
- getNextSplitDocument() - Method in class owltools.gaf.parser.GafObjectsBuilder
-
- getNonRedundantLinkedClasses(OWLClass, Set<OWLObjectProperty>, OWLGraphWrapper, OWLReasoner, Set<OWLClass>, Map<Set<OWLClass>, Set<OWLClass>>) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator
-
Retrieve the non redundant set of linked classes using the given
relation.
- getObjectPropertyByShorthand(String) - Method in class owltools.gaf.owl.GAFOWLBridge
-
- getOWLClass(String) - Method in class owltools.gaf.inference.CompositionalClassPredictor
-
Deprecated.
- getOWLClass(String) - Method in class owltools.gaf.owl.GAFOWLBridge
-
- getOwlRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory
-
Get the list of rules, which require a global view of the GAF (
GafDocument
) and OWL.
- getOwlRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
-
- getPaintId() - Method in class owltools.gaf.Bioentity
-
- getParent() - Method in class owltools.gaf.Bioentity
-
- getParent_Object_ID() - Method in class owltools.gaf.parser.GpiParser
-
- getParser() - Method in class owltools.gaf.parser.GafObjectsBuilder
-
- getPattern() - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
-
- getPersistantNodeID() - Method in class owltools.gaf.Bioentity
-
- getPredictedAnnotations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.AbstractAnnotationRule
-
- getPredictedAnnotations(GafDocument, OWLGraphWrapper) - Method in interface owltools.gaf.rules.AnnotationRule
-
Given a whole
GafDocument
in plan and OWL format, check for
possible new inferred annotations (
Prediction
).
- getPredictedAnnotations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
-
- getPredictedAnnotations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.go.GoAnnotationPredictionRule
-
- getPrediction(OWLClass, String, String) - Method in class owltools.gaf.inference.CompositionalClassPredictor
-
Deprecated.
- getPrediction(GeneAnnotation, OWLClass, String, String) - Method in class owltools.gaf.inference.FoldBasedPredictor
-
- getPrintStream(String) - Method in class owltools.gaf.godb.DatabaseDumper
-
- getPrintStream(String, boolean) - Method in class owltools.gaf.godb.DatabaseDumper
-
- getProperties() - Method in class owltools.gaf.Bioentity
-
- getProperties() - Method in class owltools.gaf.GeneAnnotation
-
- getQualifier() - Method in class owltools.gaf.parser.GAFParser
-
- getQualifier() - Method in class owltools.gaf.parser.GpadParser
-
- getQualifiers() - Method in class owltools.gaf.GeneAnnotation
-
- getReason() - Method in class owltools.gaf.inference.Prediction
-
- getRecommendationCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
-
- getReference() - Method in class owltools.gaf.parser.GAFParser
-
- getReferenceIds() - Method in class owltools.gaf.GeneAnnotation
-
- getRegex() - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
-
- getRelation() - Method in class owltools.gaf.ExtensionExpression
-
- getRelation() - Method in class owltools.gaf.GeneAnnotation
-
- getRelationship() - Method in class owltools.gaf.IdMapping
-
- getRow() - Method in class owltools.gaf.AnnotationSource
-
- getRule(String) - Method in class owltools.gaf.rules.AnnotationRulesEngine
-
Retrieve the corresponding rule for a given rule id.
- getRuleId() - Method in class owltools.gaf.rules.AbstractAnnotationRule
-
- getRuleId() - Method in interface owltools.gaf.rules.AnnotationRule
-
Get the ruleId.
- getRuleId() - Method in class owltools.gaf.rules.AnnotationRuleViolation
-
- getRules() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.AbstractAnnotationRule
-
- getRuleViolations(GafDocument) - Method in class owltools.gaf.rules.AbstractAnnotationRule
-
- getRuleViolations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.AbstractAnnotationRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
-
- getRuleViolations(GeneAnnotation) - Method in interface owltools.gaf.rules.AnnotationRule
-
Given an annotation, find the set of violations using the rule
- getRuleViolations(GafDocument) - Method in interface owltools.gaf.rules.AnnotationRule
-
Given a whole
GafDocument
, find the set of violations using the rule
- getRuleViolations(GafDocument, OWLGraphWrapper) - Method in interface owltools.gaf.rules.AnnotationRule
-
Given a whole
GafDocument
in OWL, find the set of violations using the rule
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.AnnotationTaxonRule
-
- getRuleViolations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.AnnotationTaxonRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.GenericReasonerValidationCheck
-
- getRuleViolations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.GenericReasonerValidationCheck
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.BasicChecksRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoAnnotationPredictionRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoBindingCheckWithFieldRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoClassReferenceAnnotationRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoICAnnotationRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoIDAAnnotationRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoIEPRestrictionsRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoIPIAnnotationRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoIPICatalyticActivityRestrictionsRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoMultipleTaxonRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoNDAnnotationRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoNoHighLevelTermAnnotationRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoNoISSProteinBindingRule
-
- getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
-
- getRuleViolations(GafDocument) - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
-
- getSeqDb() - Method in class owltools.gaf.Bioentity
-
- getSeqId() - Method in class owltools.gaf.Bioentity
-
- getSequence() - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo
-
- getShortEvidence() - Method in class owltools.gaf.GeneAnnotation
-
- getSource() - Method in class owltools.gaf.GeneAnnotation
-
- getSourceAnnotation() - Method in class owltools.gaf.rules.AnnotationRuleViolation
-
- getSourceId() - Method in class owltools.gaf.IdMapping
-
- getSpeciesLabel() - Method in class owltools.gaf.Bioentity
-
- getSplitSize() - Method in class owltools.gaf.parser.GafObjectsBuilder
-
- getStatus() - Method in class owltools.gaf.rules.AbstractAnnotationRule
-
- getStatus() - Method in interface owltools.gaf.rules.AnnotationRule
-
Get the status of this rule.
- getStream() - Method in class owltools.gaf.io.GafWriter
-
- getSubOntology(OWLClass) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
-
- getSuggestedReplacements() - Method in class owltools.gaf.rules.AnnotationRuleViolation
-
- getSymbol() - Method in class owltools.gaf.Bioentity
-
- getSynonyms() - Method in class owltools.gaf.Bioentity
-
- getTargetDirectory() - Method in class owltools.gaf.godb.Dumper
-
- getTargetId() - Method in class owltools.gaf.IdMapping
-
- getTargetOntology() - Method in class owltools.gaf.owl.GAFOWLBridge
-
- getTaxon() - Method in class owltools.gaf.parser.GAFParser
-
- getTaxon() - Method in class owltools.gaf.parser.GpiParser
-
- getType() - Method in class owltools.gaf.rules.AnnotationRuleViolation
-
- getTypeCls() - Method in class owltools.gaf.Bioentity
-
- getTypes() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
-
- getViolations(AnnotationRuleViolation.ViolationType) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
-
- getWarningCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
-
- getWarnings() - Method in class owltools.gaf.parser.IssueListener.DefaultIssueListener
-
- getWith() - Method in class owltools.gaf.parser.GAFParser
-
- getWith() - Method in class owltools.gaf.parser.GpadParser
-
- getWithInfos() - Method in class owltools.gaf.GeneAnnotation
-
- GoAnnotationExperimentalPredictionRule - Class in owltools.gaf.rules.go
-
- GoAnnotationExperimentalPredictionRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
-
- GoAnnotationPredictionRule - Class in owltools.gaf.rules.go
-
- GoAnnotationPredictionRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoAnnotationPredictionRule
-
- GoAnnotationRulesFactoryImpl - Class in owltools.gaf.rules.go
-
- GoAnnotationRulesFactoryImpl(ParserWrapper, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
-
- GoAnnotationRulesFactoryImpl(String, String, ParserWrapper, String, String, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
-
Deprecated.
- GoAnnotationRulesFactoryImpl(String, String, ParserWrapper, List<String>, String, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
-
- GoAnnotationRulesFactoryImpl(OWLGraphWrapper, TraversingEcoMapper, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
-
- GoAnnotationRulesFactoryImpl(String, String, OWLGraphWrapper, TraversingEcoMapper, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
-
- GoAnnotationTaxonRule - Class in owltools.gaf.rules.go
-
Checks if an annotation is valid according to GO taxon constraints.
- GoAnnotationTaxonRule(OWLGraphWrapper, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationTaxonRule
-
- GoBindingCheckWithFieldRule - Class in owltools.gaf.rules.go
-
GO_AR:0000003
- GoBindingCheckWithFieldRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoBindingCheckWithFieldRule
-
- GoClassReferenceAnnotationRule - Class in owltools.gaf.rules.go
-
Checks to see if an annotation uses a class that is not in the current ontology, and that
the class has not been obsoleted
- GoClassReferenceAnnotationRule(OWLGraphWrapper, String...) - Constructor for class owltools.gaf.rules.go.GoClassReferenceAnnotationRule
-
- GoICAnnotationRule - Class in owltools.gaf.rules.go
-
GO_AR:0000016
- GoICAnnotationRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoICAnnotationRule
-
- GOID - Static variable in class owltools.gaf.parser.GAFParser
-
- GoIDAAnnotationRule - Class in owltools.gaf.rules.go
-
GO_AR:0000017
- GoIDAAnnotationRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoIDAAnnotationRule
-
- GoIEPRestrictionsRule - Class in owltools.gaf.rules.go
-
GO_AR:0000006
- GoIEPRestrictionsRule(OWLGraphWrapper, TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoIEPRestrictionsRule
-
- GoIPIAnnotationRule - Class in owltools.gaf.rules.go
-
GO_AR:0000018
- GoIPIAnnotationRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoIPIAnnotationRule
-
- GoIPICatalyticActivityRestrictionsRule - Class in owltools.gaf.rules.go
-
GO_AR:0000007
- GoIPICatalyticActivityRestrictionsRule(OWLGraphWrapper, TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoIPICatalyticActivityRestrictionsRule
-
- GoMultipleTaxonRule - Class in owltools.gaf.rules.go
-
GO_AR:0000015
- GoMultipleTaxonRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoMultipleTaxonRule
-
- GoMySQLDatabaseDumper - Class in owltools.gaf.godb
-
implements DatabaseDumper for GO MySQL db
- GoMySQLDatabaseDumper(OWLGraphWrapper) - Constructor for class owltools.gaf.godb.GoMySQLDatabaseDumper
-
- GoMySQLDatabaseDumper.GOMySQLTable - Enum in owltools.gaf.godb
-
- GoNDAnnotationRule - Class in owltools.gaf.rules.go
-
GO_AR:0000011
- GoNDAnnotationRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoNDAnnotationRule
-
- GoNoHighLevelTermAnnotationRule - Class in owltools.gaf.rules.go
-
GO_AR:0000008
- GoNoHighLevelTermAnnotationRule(OWLGraphWrapper, TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoNoHighLevelTermAnnotationRule
-
- GoNoISSProteinBindingRule - Class in owltools.gaf.rules.go
-
GO_AR:0000005
- GoNoISSProteinBindingRule(TraversingEcoMapper, AnnotationRuleViolation.ViolationType) - Constructor for class owltools.gaf.rules.go.GoNoISSProteinBindingRule
-
- GoNoISSProteinBindingRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoNoISSProteinBindingRule
-
- GOReciprocalAnnotationRule - Class in owltools.gaf.rules.go
-
GO_AR:0000004
- GOReciprocalAnnotationRule(OWLGraphWrapper, TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GOReciprocalAnnotationRule
-
- GpadGpiObjectsBuilder - Class in owltools.gaf.parser
-
- GpadGpiObjectsBuilder(SimpleEcoMapper) - Constructor for class owltools.gaf.parser.GpadGpiObjectsBuilder
-
- GpadGpiObjectsBuilder.AspectProvider - Interface in owltools.gaf.parser
-
- GpadParser - Class in owltools.gaf.parser
-
- GpadParser() - Constructor for class owltools.gaf.parser.GpadParser
-
- GpadWriter - Class in owltools.gaf.io
-
- GpadWriter(PrintWriter, double) - Constructor for class owltools.gaf.io.GpadWriter
-
- GpiParser - Class in owltools.gaf.parser
-
- GpiParser() - Constructor for class owltools.gaf.parser.GpiParser
-
- GpiWriter - Class in owltools.gaf.io
-
- GpiWriter(PrintWriter, double) - Constructor for class owltools.gaf.io.GpiWriter
-
- graph - Variable in class owltools.gaf.godb.Dumper
-
- graph - Variable in class owltools.gaf.owl.GAFOWLBridge
-
- parse(InputStream) - Method in class owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser
-
Parse the content of the stream with an event-based XML parser.
Content is only provided to registered listeners.
- parse(Reader) - Method in class owltools.gaf.parser.GAFParser
-
- parse(String) - Method in class owltools.gaf.parser.GAFParser
-
- parse(File) - Method in class owltools.gaf.parser.GAFParser
-
- parseCompositeQualifier(String) - Static method in class owltools.gaf.parser.BuilderTools
-
Parse the string into a list of qualifier strings
- parseExtensionExpression(String) - Static method in class owltools.gaf.parser.BuilderTools
-
- parserError(String, String, int) - Method in interface owltools.gaf.parser.ParserListener
-
Report a parser error.
- ParserListener - Interface in owltools.gaf.parser
-
- parserWarning(String, String, int) - Method in interface owltools.gaf.parser.ParserListener
-
Report a parser warning.
- parseTaxonRelationshipPair(String) - Static method in class owltools.gaf.parser.BuilderTools
-
- parseVersion(String) - Method in class owltools.gaf.parser.GpadParser
-
- parseVersion(String) - Method in class owltools.gaf.parser.GpiParser
-
- parseWithInfo(String) - Static method in class owltools.gaf.parser.BuilderTools
-
Parse the string into a collection of with strings
- parsing(String, int) - Method in interface owltools.gaf.parser.ParserListener
-
The current line is parsed.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.GenericReasonerValidationCheck
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.BasicChecksRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoAnnotationPredictionRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoAnnotationTaxonRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoBindingCheckWithFieldRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoClassReferenceAnnotationRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoICAnnotationRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoIDAAnnotationRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoIEPRestrictionsRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoIPIAnnotationRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoIPICatalyticActivityRestrictionsRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoMultipleTaxonRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoNDAnnotationRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoNoHighLevelTermAnnotationRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoNoISSProteinBindingRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
-
The string to identify this class in the annotation_qc.xml and related factories.
- predict(String) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
-
- predict(String) - Method in interface owltools.gaf.inference.AnnotationPredictor
-
- predictForBioEntity(Bioentity, Collection<GeneAnnotation>) - Method in interface owltools.gaf.inference.AnnotationPredictor
-
- predictForBioEntity(Bioentity, Collection<GeneAnnotation>) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
-
- predictForBioEntity(Bioentity, Collection<GeneAnnotation>) - Method in class owltools.gaf.inference.CompositionalClassPredictor
-
Deprecated.
- predictForBioEntity(Bioentity, Collection<GeneAnnotation>) - Method in class owltools.gaf.inference.FoldBasedPredictor
-
- Prediction - Class in owltools.gaf.inference
-
- Prediction(GeneAnnotation) - Constructor for class owltools.gaf.inference.Prediction
-
- predictionReportWriter - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
-
- predictionWriter - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
-
- print(String) - Method in class owltools.gaf.io.AbstractGafWriter
-
Append an arbitrary string.
- print(String) - Method in class owltools.gaf.io.GafWriter.BufferedGafWriter
-
- print(String) - Method in class owltools.gaf.io.GafWriter
-
- print(String) - Method in class owltools.gaf.io.GpadWriter
-
Append an arbitrary string.
- print(String) - Method in class owltools.gaf.io.GpiWriter
-
Append an arbitrary string.
- problems - Variable in class owltools.gaf.godb.Dumper
-
- ProteinTools - Class in owltools.gaf.bioentities
-
- ProteinTools() - Constructor for class owltools.gaf.bioentities.ProteinTools
-
- PseudoRdfXmlWriter - Class in owltools.gaf.io
-
Java implementation to create a legacy pseudo RDF XML file for GO
terms and gene annotations.
- PseudoRdfXmlWriter() - Constructor for class owltools.gaf.io.PseudoRdfXmlWriter
-
- PseudoRdfXmlWriter.ProgressReporter - Interface in owltools.gaf.io
-