A B C D E F G H I L M N O P Q R S T V W X

A

AbstractAnnotationPredictor - Class in owltools.gaf.inference
 
AbstractAnnotationPredictor(GafDocument, OWLGraphWrapper) - Constructor for class owltools.gaf.inference.AbstractAnnotationPredictor
 
AbstractAnnotationRule - Class in owltools.gaf.rules
 
AbstractAnnotationRule() - Constructor for class owltools.gaf.rules.AbstractAnnotationRule
 
AbstractXmlWriter - Class in owltools.gaf.io
Helper to write properly formated XML using an XMLStreamWriter.
AbstractXmlWriter(String) - Constructor for class owltools.gaf.io.AbstractXmlWriter
 
actsOnTaxonId - Variable in class owltools.gaf.GeneAnnotation
 
add(boolean, OWLClass, OWLClass) - Method in class owltools.gaf.inference.ClassTaxonMatrix
 
addBioentity(Bioentity) - Method in class owltools.gaf.GafDocument
 
addCompositeQualifier(CompositeQualifier) - Method in class owltools.gaf.GafDocument
 
addExtensionExpression(ExtensionExpression) - Method in class owltools.gaf.GafDocument
 
addGeneAnnotation(GeneAnnotation) - Method in class owltools.gaf.GafDocument
 
addParserListener(GafParserListener) - Method in class owltools.gaf.GAFParser
 
addWithInfo(WithInfo) - Method in class owltools.gaf.GafDocument
 
ANNOTATION_XP - Static variable in class owltools.gaf.GAFParser
 
AnnotationPredictor - Interface in owltools.gaf.inference
given a bioentity, predict a set of annotations
AnnotationRegularExpressionFromXMLRule - Class in owltools.gaf.rules
This class implements execution of the regular expression rules.
AnnotationRegularExpressionFromXMLRule() - Constructor for class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
 
AnnotationRule - Interface in owltools.gaf.rules
 
AnnotationRulesEngine - Class in owltools.gaf.rules
 
AnnotationRulesEngine(AnnotationRulesFactory) - Constructor for class owltools.gaf.rules.AnnotationRulesEngine
 
AnnotationRulesEngine.AnnotationRuleCheckException - Exception in owltools.gaf.rules
This exception is thrown when an exception occurs during the execution of annotation rules.
AnnotationRulesEngine.AnnotationRuleCheckException() - Constructor for exception owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException
 
AnnotationRulesEngine.AnnotationRuleCheckException(String) - Constructor for exception owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException
 
AnnotationRulesEngine.AnnotationRuleCheckException(Throwable) - Constructor for exception owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException
 
AnnotationRulesEngine.AnnotationRuleCheckException(String, Throwable) - Constructor for exception owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException
 
AnnotationRulesEngine.AnnotationRulesEngineResult - Class in owltools.gaf.rules
Results for a run of the AnnotationRulesEngine.
AnnotationRulesFactory - Interface in owltools.gaf.rules
 
AnnotationRulesFactoryImpl - Class in owltools.gaf.rules
This class reads the annotation_qc.xml file and builds AnnotationRule objects from the qc file.
AnnotationRulesFactoryImpl(String, OWLGraphWrapper) - Constructor for class owltools.gaf.rules.AnnotationRulesFactoryImpl
 
AnnotationRuleViolation - Class in owltools.gaf.rules
Data associated with a rule violation
AnnotationRuleViolation(String, String) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation
Create a simple violation from with a given message.
AnnotationRuleViolation(String, String, GeneAnnotation) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation
Create a violation object with a message and a the corresponding source annotation.
AnnotationRuleViolation(String, String, GeneAnnotation, AnnotationRuleViolation.ViolationType) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation
Create a violation object with a message and a the corresponding source annotation.
AnnotationRuleViolation(String, String, String) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation
Create a violation object with a message and a the corresponding annotation row.
AnnotationRuleViolation(String, String, String, AnnotationRuleViolation.ViolationType) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation
Create a violation object with a message and a the corresponding annotation row and AnnotationRuleViolation.ViolationType.
AnnotationRuleViolation.ViolationType - Enum in owltools.gaf.rules
 
annotations - Variable in class owltools.gaf.GafDocument
 
AnnotationSource - Class in owltools.gaf
 
AnnotationSource(String, int, String) - Constructor for class owltools.gaf.AnnotationSource
 
annotationSource - Variable in class owltools.gaf.GeneAnnotation
 
AnnotationTaxonRule - Class in owltools.gaf.rules
Checks if an annotation is valid according to taxon constraints.
AnnotationTaxonRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.AnnotationTaxonRule
 
ASPECT - Static variable in class owltools.gaf.GAFParser
 
ASSIGNED_BY - Static variable in class owltools.gaf.GAFParser
 
assignedBy - Variable in class owltools.gaf.GeneAnnotation
 

B

BasicAnnotationPropagator - Class in owltools.gaf.inference
TODO: this class has not yet been tested! This performs basic annotation inferences involving propagation between the 3 sub-ontologies in GO MF -> MP over part_of BP -> CC over occurs_in TODO: reimplement using OWL semantics and reasoning
BasicAnnotationPropagator(GafDocument, OWLGraphWrapper) - Constructor for class owltools.gaf.inference.BasicAnnotationPropagator
 
BasicChecksRule - Class in owltools.gaf.rules.go
This class performs basic checks.
BasicChecksRule(String) - Constructor for class owltools.gaf.rules.go.BasicChecksRule
 
bioentities - Variable in class owltools.gaf.GafDocument
 
Bioentity - Class in owltools.gaf
 
Bioentity() - Constructor for class owltools.gaf.Bioentity
 
Bioentity(String, String, String, String, String, String, String) - Constructor for class owltools.gaf.Bioentity
 
bioentity - Variable in class owltools.gaf.GeneAnnotation
 
bioentityObject - Variable in class owltools.gaf.GeneAnnotation
 
buildDocument(Reader, String, String) - Method in class owltools.gaf.GafObjectsBuilder
 
buildDocument(String, String, String) - Method in class owltools.gaf.GafObjectsBuilder
 
buildDocument(File) - Method in class owltools.gaf.GafObjectsBuilder
 
buildDocument(String) - Method in class owltools.gaf.GafObjectsBuilder
 
buildRow() - Method in class owltools.gaf.GeneAnnotation
this method generates/updates the tab separated row of a gene annotation.

C

ClassTaxonMatrix - Class in owltools.gaf.inference
Matrix representing the applicability of classes and taxa.
ClassTaxonMatrix(int, int) - Constructor for class owltools.gaf.inference.ClassTaxonMatrix
 
cls - Variable in class owltools.gaf.ExtensionExpression
 
cls - Variable in class owltools.gaf.GeneAnnotation
 
CompositeQualifier - Class in owltools.gaf
 
CompositeQualifier() - Constructor for class owltools.gaf.CompositeQualifier
 
CompositeQualifier(String, String) - Constructor for class owltools.gaf.CompositeQualifier
 
compositeQualifier - Variable in class owltools.gaf.GeneAnnotation
 
compositeQualifierList - Variable in class owltools.gaf.GeneAnnotation
 
compositeQualifiers - Variable in class owltools.gaf.GafDocument
 
CompositionalClassPredictor - Class in owltools.gaf.inference
Given an annotation to classes c1, c2, ..., cn, we generate suggestions of annotations to class D if D EquivalentTo d1 and d2 and dm and forall d in d1..dm, there exists a class c in c1...cn such that: Path(c,d) OR d = r some e, and Path(c,e) (i.e.
CompositionalClassPredictor(GafDocument, OWLGraphWrapper) - Constructor for class owltools.gaf.inference.CompositionalClassPredictor
 
countViolations(AnnotationRuleViolation.ViolationType) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
create(OWLGraphWrapper, Collection<OWLClass>, String...) - Static method in class owltools.gaf.inference.ClassTaxonMatrix
Create a new taxon-class-matrix for the given classes and taxa.
create(OWLGraphWrapper, Collection<OWLClass>, Collection<OWLClass>) - Static method in class owltools.gaf.inference.ClassTaxonMatrix
Create a new taxon-class-matrix for the given classes and taxa.
createWriter(OutputStream) - Method in class owltools.gaf.io.AbstractXmlWriter
 

D

DATE - Static variable in class owltools.gaf.GAFParser
 
db - Variable in class owltools.gaf.Bioentity
 
DB - Static variable in class owltools.gaf.GAFParser
 
DB_OBJECT_ID - Static variable in class owltools.gaf.GAFParser
 
DB_OBJECT_NAME - Static variable in class owltools.gaf.GAFParser
 
DB_OBJECT_SYMBOL - Static variable in class owltools.gaf.GAFParser
 
DB_OBJECT_SYNONYM - Static variable in class owltools.gaf.GAFParser
 
DB_OBJECT_TYPE - Static variable in class owltools.gaf.GAFParser
 
dispose() - Method in class owltools.gaf.EcoTools
Clean up the internal data structures, usually done as last operation.
dispose() - Method in class owltools.gaf.TaxonTools
Clean up the internal data structures, usually done as last operation.
documentPath - Variable in class owltools.gaf.GafDocument
 
dtFormat - Static variable in class owltools.gaf.rules.go.BasicChecksRule
 

E

ECO_PURL - Static variable in class owltools.gaf.EcoTools
 
EcoTools - Class in owltools.gaf
Methods to simplify the work with the evidence code ontology (ECO).
EcoTools(OWLGraphWrapper, OWLReasoner, boolean) - Constructor for class owltools.gaf.EcoTools
Create an instance for the given graph and reasoner.
EcoTools(ParserWrapper) - Constructor for class owltools.gaf.EcoTools
Create a new instance using the given ParserWrapper to load the ECO.
EcoTools(OWLGraphWrapper) - Constructor for class owltools.gaf.EcoTools
Create a new instance using the ECO graph wrapper.
equals(Object) - Method in class owltools.gaf.CompositeQualifier
 
equals(Object) - Method in class owltools.gaf.ExtensionExpression
 
equals(Object) - Method in class owltools.gaf.WithInfo
 
EVIDENCE - Static variable in class owltools.gaf.GAFParser
 
evidenceCls - Variable in class owltools.gaf.GeneAnnotation
 
ExtensionExpression - Class in owltools.gaf
Corresponds to col16 in GAF2.0
ExtensionExpression() - Constructor for class owltools.gaf.ExtensionExpression
 
ExtensionExpression(String, String, String) - Constructor for class owltools.gaf.ExtensionExpression
 
extensionExpression - Variable in class owltools.gaf.GeneAnnotation
 
extensionExpressionList - Variable in class owltools.gaf.GeneAnnotation
 
extensionExpressions - Variable in class owltools.gaf.GafDocument
 

F

fullName - Variable in class owltools.gaf.Bioentity
 

G

GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI - Static variable in class owltools.gaf.owl.GAFOWLBridge
 
gafDocument - Variable in class owltools.gaf.Bioentity
 
GafDocument - Class in owltools.gaf
 
GafDocument() - Constructor for class owltools.gaf.GafDocument
 
GafDocument(String, String) - Constructor for class owltools.gaf.GafDocument
 
gafDocument - Variable in class owltools.gaf.GeneAnnotation
 
gafDocumentObject - Variable in class owltools.gaf.GeneAnnotation
 
GafObjectsBuilder - Class in owltools.gaf
The class builds GafDocument a gaf file.
GafObjectsBuilder() - Constructor for class owltools.gaf.GafObjectsBuilder
 
GafObjectsBuilder(int) - Constructor for class owltools.gaf.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.Vocab - Enum in owltools.gaf.owl
 
GAFParser - Class in owltools.gaf
 
GAFParser() - Constructor for class owltools.gaf.GAFParser
 
GafParserListener - Interface in owltools.gaf
 
GENE_PRODUCT_ISOFORM - Static variable in class owltools.gaf.GAFParser
 
GeneAnnotation - Class in owltools.gaf
 
GeneAnnotation() - Constructor for class owltools.gaf.GeneAnnotation
 
GeneAnnotation(String, boolean, boolean, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class owltools.gaf.GeneAnnotation
 
geneProductForm - Variable in class owltools.gaf.GeneAnnotation
 
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
 
getAllPredictions() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
getAllPredictions() - Method in interface owltools.gaf.inference.AnnotationPredictor
 
getAncestors(Set<OWLClass>, boolean) - Method in class owltools.gaf.EcoTools
Wrapper method for the reasoner.
getAncestors(OWLClass, boolean) - Method in class owltools.gaf.TaxonTools
Wrapper method for the reasoner.
getAnnotationCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
getAnnotationExtension() - Method in class owltools.gaf.GAFParser
 
getAnnotationRow() - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
getAnnotationRuleViolations() - Method in class owltools.gaf.GAFParser
 
getAspect() - Method in class owltools.gaf.GAFParser
 
getAssignedBy() - Method in class owltools.gaf.GAFParser
 
getAssignedBy() - Method in class owltools.gaf.GeneAnnotation
 
getBioentities() - Method in class owltools.gaf.GafDocument
 
getBioentity(String) - Method in class owltools.gaf.GafDocument
 
getBioentity() - Method in class owltools.gaf.GeneAnnotation
 
getBioentityMapping() - Method in class owltools.gaf.owl.GAFOWLBridge
 
getBioentityObject() - Method in class owltools.gaf.GeneAnnotation
 
getClassesForGoCode(String) - Method in class owltools.gaf.EcoTools
Retrieve the ECO classes for the given GO annotation codes.
getClassesForGoCodes(OWLGraphWrapper, String...) - Static method in class owltools.gaf.EcoTools
Retrieve the ECO classes for the given GO annotation codes.
getClassesForGoCodes(OWLGraphWrapper, Set<String>) - Static method in class owltools.gaf.EcoTools
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
 
getCodes(Set<OWLClass>, OWLGraphWrapper, boolean) - Static method in class owltools.gaf.EcoTools
Retrieve the set of codes for a given set of ECO classes.
getCompositeQualifier() - Method in class owltools.gaf.GeneAnnotation
 
getCompositeQualifiers(String) - Method in class owltools.gaf.GafDocument
 
getCompositeQualifiers() - Method in class owltools.gaf.GeneAnnotation
 
getCompositeQualifiersIds() - Method in class owltools.gaf.GafDocument
 
getCurrentRow() - Method in class owltools.gaf.GAFParser
 
getDate() - Method in class owltools.gaf.GAFParser
 
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.GAFParser
 
getDbObjectId() - Method in class owltools.gaf.GAFParser
 
getDbObjectName() - Method in class owltools.gaf.GAFParser
 
getDbObjectSymbol() - Method in class owltools.gaf.GAFParser
 
getDbObjectSynonym() - Method in class owltools.gaf.GAFParser
 
getDBObjectType() - Method in class owltools.gaf.GAFParser
 
getDescendents(Set<OWLClass>, boolean) - Method in class owltools.gaf.EcoTools
Wrapper method for the reasoner
getDescendents(Set<OWLClass>, boolean) - Method in class owltools.gaf.TaxonTools
Wrapper method for the reasoner
getDescription() - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
getDescription() - Method in interface owltools.gaf.rules.AnnotationRule
Get the description for a rule.
getDocumentPath() - Method in class owltools.gaf.GafDocument
 
getErrorCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
getErrorMessage() - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
 
getEvidence() - Method in class owltools.gaf.GAFParser
 
getEvidenceCls() - Method in class owltools.gaf.GeneAnnotation
 
getExpressions(String) - Method in class owltools.gaf.GafDocument
 
getExtensionExpression() - Method in class owltools.gaf.GeneAnnotation
 
getExtensionExpressionIds() - Method in class owltools.gaf.GafDocument
 
getExtensionExpressions() - Method in class owltools.gaf.GeneAnnotation
 
getFileName() - Method in class owltools.gaf.AnnotationSource
 
getFullName() - Method in class owltools.gaf.Bioentity
 
getGafDocument() - Method in class owltools.gaf.Bioentity
 
getGafDocument() - Method in class owltools.gaf.GafObjectsBuilder
 
getGafDocument() - Method in class owltools.gaf.GeneAnnotation
 
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
 
getGeneAnnotation() - Method in class owltools.gaf.inference.Prediction
 
getGeneAnnotationRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory
Get the list of rules to be applied for each GeneAnnotation
getGeneAnnotationRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
 
getGeneAnnotations() - Method in class owltools.gaf.GafDocument
 
getGeneAnnotations(String) - Method in class owltools.gaf.GafDocument
 
getGeneAnnotationsByDirectGoCls(String) - Method in class owltools.gaf.GafDocument
 
getGeneProductForm() - Method in class owltools.gaf.GeneAnnotation
 
getGeneProjectFormId() - Method in class owltools.gaf.GAFParser
 
getGOId() - Method in class owltools.gaf.GAFParser
 
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.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.CompositeQualifier
 
getId() - Method in class owltools.gaf.ExtensionExpression
 
getId() - Method in class owltools.gaf.GafDocument
 
getId(String) - Method in class owltools.gaf.io.XgmmlWriter
 
getId() - Method in class owltools.gaf.WithInfo
 
getIsContributesTo() - Method in class owltools.gaf.GeneAnnotation
 
getIsIntegralTo() - Method in class owltools.gaf.GeneAnnotation
 
getLastUpdateDate() - Method in class owltools.gaf.GeneAnnotation
 
getLineNumber() - Method in class owltools.gaf.AnnotationSource
 
getLineNumber() - Method in class owltools.gaf.GAFParser
 
getLineNumber() - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
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.
getNcbiTaxonId() - Method in class owltools.gaf.Bioentity
 
getNextSplitDocument() - Method in class owltools.gaf.GafObjectsBuilder
When this variable reaches the splitSize count, the algorithm in the GafObjectsBuilder.getNextSplitDocument() method stops calling next method of the GafParser and returns the GafDocument object build with the number of rows
getOWLClass(String) - Method in class owltools.gaf.inference.CompositionalClassPredictor
 
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
 
getParser() - Method in class owltools.gaf.GafObjectsBuilder
 
getPattern() - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
 
getPrediction(OWLClass, String, String) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
 
getPrediction(OWLClass, String, String) - Method in class owltools.gaf.inference.CompositionalClassPredictor
 
getQualifier() - Method in class owltools.gaf.GAFParser
 
getQualifierObj() - Method in class owltools.gaf.CompositeQualifier
 
getRecommendationCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
getReference() - Method in class owltools.gaf.GAFParser
 
getReferenceId() - 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(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(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(OWLGraphWrapper) - Method in class owltools.gaf.rules.AnnotationTaxonRule
 
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.GenericReasonerValidationCheck
 
getRuleViolations(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.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.GoNoISSProteinBindingRule
 
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
 
getRuleViolations(GafDocument) - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
 
getSource() - Method in class owltools.gaf.GeneAnnotation
 
getSourceAnnotation() - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
getSourceId() - Method in class owltools.gaf.IdMapping
 
getSplitSize() - Method in class owltools.gaf.GafObjectsBuilder
 
getStatus() - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
getStatus() - Method in interface owltools.gaf.rules.AnnotationRule
Get the status of this rule.
getSuggestedReplacements() - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
getSymbol() - Method in class owltools.gaf.Bioentity
 
getTargetId() - Method in class owltools.gaf.IdMapping
 
getTargetOntology() - Method in class owltools.gaf.owl.GAFOWLBridge
 
getTaxon() - Method in class owltools.gaf.GAFParser
 
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
Retrieve all violations for a given AnnotationRuleViolation.ViolationType.
getWarningCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
getWith() - Method in class owltools.gaf.GAFParser
 
getWithExpression() - Method in class owltools.gaf.GeneAnnotation
 
getWithInfos(String) - Method in class owltools.gaf.GafDocument
 
getWithInfos() - Method in class owltools.gaf.GeneAnnotation
 
getWithInfosIds() - Method in class owltools.gaf.GafDocument
 
getWithXref() - Method in class owltools.gaf.WithInfo
 
GoAnnotationRulesFactoryImpl - Class in owltools.gaf.rules.go
 
GoAnnotationRulesFactoryImpl(ParserWrapper) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
 
GoAnnotationRulesFactoryImpl(String, String, ParserWrapper, String, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
 
GoAnnotationRulesFactoryImpl(OWLGraphWrapper, OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
 
GoAnnotationRulesFactoryImpl(String, String, OWLGraphWrapper, OWLGraphWrapper) - 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) - Constructor for class owltools.gaf.rules.go.GoAnnotationTaxonRule
 
GoBindingCheckWithFieldRule - Class in owltools.gaf.rules.go
GO_AR:0000003
GoBindingCheckWithFieldRule(OWLGraphWrapper) - 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) - Constructor for class owltools.gaf.rules.go.GoClassReferenceAnnotationRule
 
GoICAnnotationRule - Class in owltools.gaf.rules.go
GO_AR:0000016
GoICAnnotationRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoICAnnotationRule
 
GOID - Static variable in class owltools.gaf.GAFParser
 
GoIDAAnnotationRule - Class in owltools.gaf.rules.go
GO_AR:0000017
GoIDAAnnotationRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoIDAAnnotationRule
 
GoIEPRestrictionsRule - Class in owltools.gaf.rules.go
GO_AR:0000006
GoIEPRestrictionsRule(OWLGraphWrapper, OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoIEPRestrictionsRule
 
GoIPIAnnotationRule - Class in owltools.gaf.rules.go
GO_AR:0000018
GoIPIAnnotationRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoIPIAnnotationRule
 
GoIPICatalyticActivityRestrictionsRule - Class in owltools.gaf.rules.go
GO_AR:0000007
GoIPICatalyticActivityRestrictionsRule(OWLGraphWrapper, OWLGraphWrapper) - 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
 
GoNDAnnotationRule - Class in owltools.gaf.rules.go
GO_AR:0000011
GoNDAnnotationRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoNDAnnotationRule
 
GoNoISSProteinBindingRule - Class in owltools.gaf.rules.go
GO_AR:0000005
GoNoISSProteinBindingRule(OWLGraphWrapper, AnnotationRuleViolation.ViolationType) - Constructor for class owltools.gaf.rules.go.GoNoISSProteinBindingRule
 
GoNoISSProteinBindingRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoNoISSProteinBindingRule
 
GOReciprocalAnnotationRule - Class in owltools.gaf.rules.go
GO_AR:0000004
GOReciprocalAnnotationRule(OWLGraphWrapper, OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GOReciprocalAnnotationRule
 

H

hasErrors() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
hasGrandFathering() - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
hasGrandFathering() - Method in interface owltools.gaf.rules.AnnotationRule
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.
hashCode() - Method in class owltools.gaf.CompositeQualifier
 
hashCode() - Method in class owltools.gaf.ExtensionExpression
 
hashCode() - Method in class owltools.gaf.WithInfo
 
hasRecommendations() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
hasType(AnnotationRuleViolation.ViolationType) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
hasWarnings() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 

I

id - Variable in class owltools.gaf.Bioentity
 
id - Variable in class owltools.gaf.CompositeQualifier
 
id - Variable in class owltools.gaf.ExtensionExpression
 
id - Variable in class owltools.gaf.GafDocument
 
id - Variable in class owltools.gaf.WithInfo
 
IdMapping - Class in owltools.gaf
 
IdMapping() - Constructor for class owltools.gaf.IdMapping
 
IdMapping(String, String, String, String) - Constructor for class owltools.gaf.IdMapping
 
index() - Method in class owltools.gaf.GafDocument
 
init() - Method in class owltools.gaf.GAFParser
 
init() - Method in interface owltools.gaf.rules.AnnotationRulesFactory
Initialize the factory.
init() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
 
isAnnotationLevel() - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
isAnnotationLevel() - Method in interface owltools.gaf.rules.AnnotationRule
 
isAnnotationLevel() - Method in class owltools.gaf.rules.GenericReasonerValidationCheck
 
isAnnotationLevel() - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
 
isChanged - Variable in class owltools.gaf.GeneAnnotation
If value of this variable is true then toString is re-calculated
isClassApplicable(String, String) - Method in class owltools.gaf.inference.TaxonConstraintsEngine
Deprecated.  
isClassApplicable(OWLClass, OWLClass) - Method in class owltools.gaf.inference.TaxonConstraintsEngine
Deprecated. returns true if testOntologyCls is applicable for testTax
isClassApplicable(OWLClass, OWLClass, Set<OWLGraphEdge>, Set<OWLObject>) - Method in class owltools.gaf.inference.TaxonConstraintsEngine
Deprecated.  
isContributesTo - Variable in class owltools.gaf.GeneAnnotation
 
isDocumentLevel() - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
isDocumentLevel() - Method in interface owltools.gaf.rules.AnnotationRule
 
isDocumentLevel() - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
 
isDocumentSplitted() - Method in class owltools.gaf.GafObjectsBuilder
 
isEmpty() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
isGenerateIndividuals() - Method in class owltools.gaf.owl.GAFOWLBridge
 
isIntegralTo - Variable in class owltools.gaf.GeneAnnotation
 
isOwlDocumentLevel() - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
isOwlDocumentLevel() - Method in interface owltools.gaf.rules.AnnotationRule
 
isOwlDocumentLevel() - Method in class owltools.gaf.rules.AnnotationTaxonRule
 
isOwlDocumentLevel() - Method in class owltools.gaf.rules.GenericReasonerValidationCheck
 
isRedundantWithExistingAnnotations() - Method in class owltools.gaf.inference.Prediction
 
isRedundantWithOtherPredictions() - Method in class owltools.gaf.inference.Prediction
 

L

lastUpdateDate - Variable in class owltools.gaf.GeneAnnotation
 
loadECO(ParserWrapper) - Static method in class owltools.gaf.EcoTools
Load the evidence code ontology (ECO) from its default PURL.
LOG - Static variable in class owltools.gaf.GAFParser
 
LOG - Static variable in class owltools.gaf.inference.AbstractAnnotationPredictor
 
LOG - Static variable in class owltools.gaf.inference.BasicAnnotationPropagator
 
LOG - Static variable in class owltools.gaf.inference.CompositionalClassPredictor
 

M

mappingSource - Variable in class owltools.gaf.IdMapping
 

N

ncbiTaxonId - Variable in class owltools.gaf.Bioentity
 
next() - Method in class owltools.gaf.GAFParser
Method declaration

O

owltools.gaf - package owltools.gaf
Processing of GO Gene Association Files
owltools.gaf.inference - package owltools.gaf.inference
Perform inference on Gene Associations
owltools.gaf.io - package owltools.gaf.io
 
owltools.gaf.owl - package owltools.gaf.owl
 
owltools.gaf.rules - package owltools.gaf.rules
 
owltools.gaf.rules.go - package owltools.gaf.rules.go
 

P

parse(Reader) - Method in class owltools.gaf.GAFParser
 
parse(String) - Method in class owltools.gaf.GAFParser
 
parse(File) - Method in class owltools.gaf.GAFParser
 
parserError(String, String, int) - Method in interface owltools.gaf.GafParserListener
Report a parser error.
parserWarning(String, String, int) - Method in interface owltools.gaf.GafParserListener
Report a parser warning.
parsing(String, int) - Method in interface owltools.gaf.GafParserListener
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.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.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 interface owltools.gaf.inference.AnnotationPredictor
 
predict(String) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
 
predict(String) - Method in class owltools.gaf.inference.CompositionalClassPredictor
 
Prediction - Class in owltools.gaf.inference
 
Prediction() - Constructor for class owltools.gaf.inference.Prediction
 
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
 

Q

QUALIFIER - Static variable in class owltools.gaf.GAFParser
 
qualifierObj - Variable in class owltools.gaf.CompositeQualifier
 

R

REFERENCE - Static variable in class owltools.gaf.GAFParser
 
referenceId - Variable in class owltools.gaf.GeneAnnotation
 
relation - Variable in class owltools.gaf.ExtensionExpression
 
relation - Variable in class owltools.gaf.GeneAnnotation
 
relationship - Variable in class owltools.gaf.IdMapping
 
remoteParserListener(GafParserListener) - Method in class owltools.gaf.GAFParser
 
render(OWLPrettyPrinter) - Method in class owltools.gaf.inference.Prediction
 
renderViolations(AnnotationRulesEngine.AnnotationRulesEngineResult, AnnotationRulesEngine, PrintWriter) - Static method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
A simple tab delimited print-out of the result.
renderViolations(AnnotationRulesEngine.AnnotationRulesEngineResult, AnnotationRulesEngine, PrintWriter, PrintWriter) - Static method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
A simple tab delimited print-out of the result and a simple summary.
reportWarnings() - Method in interface owltools.gaf.GafParserListener
 

S

setActsOnTaxonId(String) - Method in class owltools.gaf.GeneAnnotation
 
setAndFilterRedundantPredictions(Set<Prediction>, Set<OWLClass>) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
side-effects: removes redundant predictions
setAnnotationCount(int) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
setAnnotationRow(String) - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
setAssignedBy(String) - Method in class owltools.gaf.GeneAnnotation
 
setBioentity(String) - Method in class owltools.gaf.GeneAnnotation
 
setBioentityMapping(GAFOWLBridge.BioentityMapping) - Method in class owltools.gaf.owl.GAFOWLBridge
 
setBioentityObject(Bioentity) - Method in class owltools.gaf.GeneAnnotation
 
setCls(String) - Method in class owltools.gaf.ExtensionExpression
 
setCls(String) - Method in class owltools.gaf.GeneAnnotation
 
setCompositeQualifier(String) - Method in class owltools.gaf.GeneAnnotation
 
setDate(Date) - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
setDate(Date) - Method in interface owltools.gaf.rules.AnnotationRule
Set the status date for this rule.
setDb(String) - Method in class owltools.gaf.Bioentity
 
setDescription(String) - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
setDescription(String) - Method in interface owltools.gaf.rules.AnnotationRule
Set the description for this rule.
setDocumentPath(String) - Method in class owltools.gaf.GafDocument
 
setErrorMessage(String) - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
 
setEvidenceCls(String) - Method in class owltools.gaf.GeneAnnotation
 
setExtensionExpression(String) - Method in class owltools.gaf.GeneAnnotation
 
setFullName(String) - Method in class owltools.gaf.Bioentity
 
setGafDocument(String) - Method in class owltools.gaf.Bioentity
 
setGafDocument(String) - Method in class owltools.gaf.GeneAnnotation
 
setGafDocument(GafDocument) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
setGafDoument(String) - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
setGeneAnnotation(GeneAnnotation) - Method in class owltools.gaf.inference.Prediction
 
setGeneProductForm(String) - Method in class owltools.gaf.GeneAnnotation
 
setGenerateIndividuals(boolean) - Method in class owltools.gaf.owl.GAFOWLBridge
 
setGrandFatheringDate(Date) - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
setGrandFatheringDate(Date) - Method in interface owltools.gaf.rules.AnnotationRule
Set the cut-off date for grand fathering the rule.
setGraph(OWLGraphWrapper) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
setId(String) - Method in class owltools.gaf.Bioentity
 
setId(String) - Method in class owltools.gaf.CompositeQualifier
 
setId(String) - Method in class owltools.gaf.ExtensionExpression
 
setId(String) - Method in class owltools.gaf.GafDocument
 
setId(String) - Method in class owltools.gaf.WithInfo
 
setIsContributesTo(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setIsIntegralTo(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setLastUpdateDate(String) - Method in class owltools.gaf.GeneAnnotation
 
setLineNumber(int) - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
setMappingSource(String) - Method in class owltools.gaf.IdMapping
 
setName(String) - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
setName(String) - Method in interface owltools.gaf.rules.AnnotationRule
Set the name for the rule.
setNcbiTaxonId(String) - Method in class owltools.gaf.Bioentity
 
setPattern(Pattern) - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
 
setQualifierObj(String) - Method in class owltools.gaf.CompositeQualifier
 
setRedundantWithExistingAnnotations(boolean) - Method in class owltools.gaf.inference.Prediction
 
setRedundantWithOtherPredictions(boolean) - Method in class owltools.gaf.inference.Prediction
 
setReferenceId(String) - Method in class owltools.gaf.GeneAnnotation
 
setRegex(String) - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
 
setRelation(String) - Method in class owltools.gaf.ExtensionExpression
 
setRelation(String) - Method in class owltools.gaf.GeneAnnotation
 
setRelationship(String) - Method in class owltools.gaf.IdMapping
 
setRuleId(String) - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
setRuleId(String) - Method in interface owltools.gaf.rules.AnnotationRule
Set the rule id
setSourceAnnotation(GeneAnnotation) - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
setSourceId(String) - Method in class owltools.gaf.IdMapping
 
setStatus(String) - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
setStatus(String) - Method in interface owltools.gaf.rules.AnnotationRule
Set the status for this rule.
setSuggestedReplacements(Set<GeneAnnotation>) - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
setSymbol(String) - Method in class owltools.gaf.Bioentity
 
setTargetId(String) - Method in class owltools.gaf.IdMapping
 
setTargetOntology(OWLOntology) - Method in class owltools.gaf.owl.GAFOWLBridge
 
setType(AnnotationRuleViolation.ViolationType) - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
setTypeCls(String) - Method in class owltools.gaf.Bioentity
 
setWithExpression(String) - Method in class owltools.gaf.GeneAnnotation
 
setWithXref(String) - Method in class owltools.gaf.WithInfo
 
sourceId - Variable in class owltools.gaf.IdMapping
 
status_df - Static variable in class owltools.gaf.rules.AnnotationRulesFactoryImpl
 
symbol - Variable in class owltools.gaf.Bioentity
 

T

targetId - Variable in class owltools.gaf.IdMapping
 
TAXON - Static variable in class owltools.gaf.GAFParser
 
TAXON_PURL - Static variable in class owltools.gaf.TaxonTools
 
TaxonConstraintsEngine - Class in owltools.gaf.inference
Deprecated. There is now a taxon checks using an OWL resoner. This implementation may over-report violations, i.e. taxon constrains should not be propagated over regulates relations.
TaxonConstraintsEngine(OWLGraphWrapper) - Constructor for class owltools.gaf.inference.TaxonConstraintsEngine
Deprecated.  
TaxonTools - Class in owltools.gaf
Methods to simplify the work with the evidence code ontology (ECO).
TaxonTools(OWLGraphWrapper, OWLReasoner, boolean) - Constructor for class owltools.gaf.TaxonTools
Create an instance for the given graph and reasoner.
toString() - Method in class owltools.gaf.Bioentity
 
toString - Variable in class owltools.gaf.GeneAnnotation
 
toString() - Method in class owltools.gaf.GeneAnnotation
 
toString() - Method in class owltools.gaf.inference.Prediction
 
toString() - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
toString() - Method in class owltools.gaf.WithInfo
 
translate(GafDocument) - Method in class owltools.gaf.owl.GAFOWLBridge
 
typeCls - Variable in class owltools.gaf.Bioentity
 

V

validateAnnotations(GafDocument) - Method in class owltools.gaf.rules.AnnotationRulesEngine
Validate the given GafDocument.
valueOf(String) - Static method in enum owltools.gaf.owl.GAFOWLBridge.BioentityMapping
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gaf.owl.GAFOWLBridge.Vocab
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gaf.rules.AnnotationRuleViolation.ViolationType
Returns the enum constant of this type with the specified name.
values() - Static method in enum owltools.gaf.owl.GAFOWLBridge.BioentityMapping
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gaf.owl.GAFOWLBridge.Vocab
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gaf.rules.AnnotationRuleViolation.ViolationType
Returns an array containing the constants of this enum type, in the order they are declared.

W

WITH - Static variable in class owltools.gaf.GAFParser
 
withExpression - Variable in class owltools.gaf.GeneAnnotation
 
WithInfo - Class in owltools.gaf
 
WithInfo() - Constructor for class owltools.gaf.WithInfo
 
WithInfo(String, String) - Constructor for class owltools.gaf.WithInfo
 
withInfoList - Variable in class owltools.gaf.GeneAnnotation
 
withInfos - Variable in class owltools.gaf.GafDocument
 
withXref - Variable in class owltools.gaf.WithInfo
 
write(ClassTaxonMatrix, OWLGraphWrapper, BufferedWriter) - Static method in class owltools.gaf.inference.ClassTaxonMatrix
Write a ClassTaxonMatrix using the default delimiter.
write(ClassTaxonMatrix, OWLGraphWrapper, char, BufferedWriter) - Static method in class owltools.gaf.inference.ClassTaxonMatrix
Write a ClassTaxonMatrix using the specified delimiter.
write(OutputStream, OWLGraphWrapper, List<GafDocument>) - Method in class owltools.gaf.io.PseudoRdfXmlWriter
Write a pseudo RDF XML for the given ontology and gene annotations.
write(OutputStream, OWLGraphWrapper, List<GafDocument>) - Method in class owltools.gaf.io.XgmmlWriter
Write a pseudo RDF XML for the given ontology and gene annotations.

X

XgmmlWriter - Class in owltools.gaf.io
Generates Xgmml for import into Cytoscape
XgmmlWriter() - Constructor for class owltools.gaf.io.XgmmlWriter
 

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