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

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
 
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() - Constructor for class owltools.gaf.rules.AnnotationRulesEngine
 
AnnotationRulesEngine(int, 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
 
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) - 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, String) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation
Create a violation object with a message and a the corresponding annotation row.
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, String, String) - 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 generate a tab separated row of a gene annotation

C

check(String, String) - Method in class owltools.gaf.rules.AnnotationTaxonRule
 
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
 
compositeQualifierEmptyList - Static 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
 
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.

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
 
documentPath - Variable in class owltools.gaf.GafDocument
 

E

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
 
extensionExpressionEmptyList - Static 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

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.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
 
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
 
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
 
getBioentityObject() - Method in class owltools.gaf.GeneAnnotation
 
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
 
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
 
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
 
getDocumentPath() - Method in class owltools.gaf.GafDocument
 
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
 
getGeneAnnotation() - Method in class owltools.gaf.inference.Prediction
 
getGeneAnnotations() - Method in class owltools.gaf.GafDocument
 
getGeneAnnotations(String) - Method in class owltools.gaf.GafDocument
 
getGeneAnnotationsByGoCls(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
 
getGraph() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
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() - 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
 
getNcbiTaxonId() - Method in class owltools.gaf.Bioentity
 
getNextSplitDocument() - Method in class owltools.gaf.GafObjectsBuilder
when this variable reaches at splitSize then the algorithm in the getNextSplitDocument method stops calling next method of the GafParser and return the GafDocument object build with the number of rows
getOWLClass(String) - Method in class owltools.gaf.inference.CompositionalClassPredictor
 
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
 
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
 
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 interface owltools.gaf.rules.AnnotationRulesFactory
 
getRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
 
getRuleViolations(GeneAnnotation) - 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(GeneAnnotation) - Method in class owltools.gaf.rules.AnnotationTaxonRule
 
getRuleViolations(String, String) - Method in class owltools.gaf.rules.AnnotationTaxonRule
 
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.BasicChecksRule
 
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoClassReferenceAnnotationRule
 
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
 
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
 
getTypeCls() - Method in class owltools.gaf.Bioentity
 
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() - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
 
GoAnnotationRulesFactoryImpl(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
 
GoAnnotationRulesFactoryImpl(String, String, List<String>) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
 
GoAnnotationRulesFactoryImpl(String, String, 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
 
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
 
GOID - Static variable in class owltools.gaf.GAFParser
 

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
 
init() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
 
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
 
isClassApplicable(OWLClass, OWLClass) - Method in class owltools.gaf.inference.TaxonConstraintsEngine
returns true if testOntologyCls is applicable for testTax
isClassApplicable(OWLClass, OWLClass, Set<OWLGraphEdge>, Set<OWLObject>) - Method in class owltools.gaf.inference.TaxonConstraintsEngine
 
isContributesTo - Variable in class owltools.gaf.GeneAnnotation
 
isDocumentSplitted() - Method in class owltools.gaf.GafObjectsBuilder
 
isGenerateIndividuals() - Method in class owltools.gaf.owl.GAFOWLBridge
 
isIntegralTo - Variable in class owltools.gaf.GeneAnnotation
 
isRedundantWithExistingAnnotations() - Method in class owltools.gaf.inference.Prediction
 
isRedundantWithOtherPredictions() - Method in class owltools.gaf.inference.Prediction
 

L

lastUpdateDate - Variable in class owltools.gaf.GeneAnnotation
 
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
 
LOG - Static variable in class owltools.gaf.inference.TaxonConstraintsEngine
 

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.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
 
parsing(String, int) - Method in interface owltools.gaf.GafParserListener
 
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
 

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
 

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
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
 
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
 
setDb(String) - Method in class owltools.gaf.Bioentity
 
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
 
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
 
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
 
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
 
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
 
symbol - Variable in class owltools.gaf.Bioentity
 

T

targetId - Variable in class owltools.gaf.IdMapping
 
TAXON - Static variable in class owltools.gaf.GAFParser
 
TaxonConstraintsEngine - Class in owltools.gaf.inference
 
TaxonConstraintsEngine(OWLGraphWrapper) - Constructor for class owltools.gaf.inference.TaxonConstraintsEngine
 
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
 
valueOf(String) - Static method in enum owltools.gaf.owl.GAFOWLBridge.Vocab
Returns the enum constant of this type with the specified name.
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.

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
 
withInfoEmptyList - Static variable in class owltools.gaf.GeneAnnotation
 
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.

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