A B C D E F G H I K L M N O P Q R S T U 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
 
AbstractGafWriter - Class in owltools.gaf.io
General utility to write a GafDocument or GeneAnnotation.
AbstractGafWriter() - Constructor for class owltools.gaf.io.AbstractGafWriter
 
AbstractXmlWriter - Class in owltools.gaf.io
Helper to write properly formated XML using an XMLStreamWriter.
AbstractXmlWriter(String) - Constructor for class owltools.gaf.io.AbstractXmlWriter
 
accept(String, int, T) - Method in interface owltools.gaf.parser.LineFilter
Given a line in a annotation file, decide whether to load the line.
activityEdgeSet - Variable in class owltools.gaf.lego.NetworkInferenceEngine.ActivityNetwork
Deprecated.
 
activityNetwork - Variable in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
EA ⊆ A x A x TA
activitySet - Variable in class owltools.gaf.lego.NetworkInferenceEngine.ActivityNetwork
Deprecated.
 
add(boolean, OWLClass, OWLClass) - Method in class owltools.gaf.inference.ClassTaxonMatrix
 
add(Bioentity) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
Adds a single Bioentity to a model
add(GeneAnnotation) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
Adds a single GeneAnnotation to a model
add(NetworkInferenceEngine.Activity) - Method in class owltools.gaf.lego.NetworkInferenceEngine.ActivityNetwork
Deprecated.
 
addAnnotation(GeneAnnotation) - Method in class owltools.gaf.Bioentity
 
addAnnotations(String, ModelContainer, OWLNamedIndividual, Collection<OWLAnnotation>, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
addAnnotations(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set<OWLAnnotation>, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
addAnnotations(String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
addAnnotations(String, String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
addAnnotations(String, String, String, String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
addAxioms(Set<OWLAxiom>) - Method in class owltools.gaf.owl.GAFOWLBridge
 
addBioentity(Bioentity) - Method in class owltools.gaf.BioentityDocument
Add a Bioentity object to the document.
addBioentity(Bioentity) - Method in class owltools.gaf.GafDocument
Add a Bioentity object to the document.
addComment(String) - Method in class owltools.gaf.BioentityDocument
Add a comment line.
addComment(String) - Method in class owltools.gaf.GafDocument
Add a comment line.
addCommentListener(CommentListener) - Method in class owltools.gaf.parser.GAFParser
 
addDbXref(String) - Method in class owltools.gaf.Bioentity
 
addEdge(NetworkInferenceEngine.Activity, NetworkInferenceEngine.Activity, OWLObjectPropertyExpression) - Method in class owltools.gaf.lego.NetworkInferenceEngine.ActivityNetwork
Deprecated.
 
addEdge(NetworkInferenceEngine.InstanceNode, NetworkInferenceEngine.InstanceNode) - Method in class owltools.gaf.lego.NetworkInferenceEngine.Partonomy
Deprecated.
 
addEnabledBy(String, String, String) - Method in class owltools.gaf.lego.MolecularModelManager
Deprecated.
addEnabledBy(String, OWLNamedIndividual, OWLClassExpression) - Method in class owltools.gaf.lego.MolecularModelManager
Deprecated.
addExperimentalInferences(List<Prediction>) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set<OWLAnnotation>, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Adds triple (i,p,j) to specified model
addFact(String, OBOUpperVocabulary, OWLNamedIndividual, OWLNamedIndividual, Set<OWLAnnotation>, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
addFact(String, String, String, String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
addFact(String, OBOUpperVocabulary, String, String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
addFactNonReasoning(String, String, String, String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
addFilter(LineFilter<GAFParser>) - Method in class owltools.gaf.parser.GafObjectsBuilder
Add a filter to object builder.
addGafDocument(GafDocument) - Method in class owltools.gaf.godb.Dumper
 
addGeneAnnotation(GeneAnnotation) - Method in class owltools.gaf.GafDocument
Add a single annotation to the document.
addGenes(String, Collection<String>) - Method in class owltools.gaf.lego.LegoModelGenerator
 
addGenes(OWLClass) - Method in class owltools.gaf.lego.LegoModelGenerator
 
addGenes(OWLClass, Collection<String>) - Method in class owltools.gaf.lego.LegoModelGenerator
Create initial activation node set A for a process P and a set of seed genes for all g ∈ Gseed, add a = to A where f = argmax(p) { t : t ∈ TA, p=Prob( t | g) }
addGpadFilter(LineFilter<GpadParser>) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
addGpiFilter(LineFilter<GpiParser>) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
addHeaderInfo(GafDocument) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
Adds header info from a GAF, use the comments from the GafDocument.
addImports(Iterable<String>) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Add additional import declarations for any newly generated model.
addInferences(List<Prediction>) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
addIssueListener(IssueListener) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
addListener(QuestForOrthologsSeqXMLParser.ProteinListener) - Method in class owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser
addListener(QuestForOrthologsSeqXMLParser.MoreInfoProteinListener) - Method in class owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser
addObsoleteImportIRIs(Collection<IRI>) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Mark the given imports as obsolete.
addObsoleteImports(Iterable<String>) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Mark the given imports as obsolete.
addOccursIn(String, String, String) - Method in class owltools.gaf.lego.MolecularModelManager
Deprecated.
addOccursIn(String, OWLNamedIndividual, OWLClassExpression) - Method in class owltools.gaf.lego.MolecularModelManager
Deprecated.
addParserListener(ParserListener) - Method in class owltools.gaf.parser.GAFParser
 
addPartOf(String, String, String, Collection<Pair<String, String>>) - Method in class owltools.gaf.lego.MolecularModelManager
Deprecated.
addPartOf(String, OWLNamedIndividual, OWLNamedIndividual, Set<OWLAnnotation>) - Method in class owltools.gaf.lego.MolecularModelManager
Deprecated.
addProblem(String) - Method in class owltools.gaf.godb.Dumper
 
addProperty(String, String) - Method in class owltools.gaf.Bioentity
 
addProperty(String, String) - Method in class owltools.gaf.GeneAnnotation
 
addReferenceId(String) - Method in class owltools.gaf.GeneAnnotation
 
addReferenceIds(Collection<String>) - Method in class owltools.gaf.GeneAnnotation
 
addSpeciesLabel(String) - Method in class owltools.gaf.Bioentity
 
addSynonym(String) - Method in class owltools.gaf.Bioentity
 
addToHistory(String, ModelContainer, List<OWLOntologyChange>, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Hook for implementing an undo and redo.
addToHistory(String, ModelContainer, List<OWLOntologyChange>, UndoAwareMolecularModelManager.UndoMetadata) - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager
 
addType(String, OWLNamedIndividual, OWLClass, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Adds ClassAssertion(c,i) to specified model
addType(String, OWLNamedIndividual, OWLObjectPropertyExpression, OWLClassExpression, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Adds a ClassAssertion, where the class expression instantiated is an ObjectSomeValuesFrom expression Example: Individual: i Type: enabledBy some PRO_123
addType(String, String, String, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
addType(String, String, String, String, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
addTypeNonReasoning(String, String, OWLClassExpression, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
addTypeNonReasoning(String, String, String, OWLClassExpression, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
addViolations(Iterable<AnnotationRuleViolation>) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
annotatedEntityCount - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
 
ANNOTATION_XP - Static variable in class owltools.gaf.parser.GAFParser
 
annotationCount - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
 
annotationCountExcludingIEA - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
 
AnnotationDocumentMetadata - Class in owltools.gaf.metadata
 
AnnotationDocumentMetadata() - Constructor for class owltools.gaf.metadata.AnnotationDocumentMetadata
 
AnnotationExtensionFolder - Class in owltools.gaf.owl
 
AnnotationExtensionFolder(OWLGraphWrapper) - Constructor for class owltools.gaf.owl.AnnotationExtensionFolder
 
AnnotationExtensionUnfolder - Class in owltools.gaf.owl
 
AnnotationExtensionUnfolder(OWLGraphWrapper) - Constructor for class owltools.gaf.owl.AnnotationExtensionUnfolder
 
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, boolean, boolean) - 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.
AnnotationRulesEngine.AnnotationRulesEngineResult() - Constructor for class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
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
 
AnnotationRulesReportWriter - Class in owltools.gaf.rules
Write reports for the results of annotations validation and prediction.
AnnotationRulesReportWriter(String, String, String, String, String, String) - Constructor for class owltools.gaf.rules.AnnotationRulesReportWriter
 
AnnotationRulesReportWriter(File, File, File, File, File, File) - Constructor for class owltools.gaf.rules.AnnotationRulesReportWriter
 
AnnotationRulesReportWriter(PrintWriter, PrintWriter, PrintStream, PrintWriter, PrintStream, PrintWriter) - Constructor for class owltools.gaf.rules.AnnotationRulesReportWriter
 
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
 
AnnotationSource - Class in owltools.gaf
 
AnnotationSource(String, int, String) - Constructor for class owltools.gaf.AnnotationSource
 
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
 
anonymizeMaterialEntities() - Method in class owltools.gaf.lego.LegoModelGenerator
Example: if we have triples: This will generate: ClassAssertion( occurs_in some Nucleus, p123)
applyChanges(List<OWLOntologyChange>, OWLOntologyManager) - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager
 
ASPECT - Static variable in class owltools.gaf.parser.GAFParser
 
ASSIGNED_BY - Static variable in class owltools.gaf.parser.GAFParser
 

B

BasicABox - Class in owltools.gaf.owl.mapping
 
BasicABox(OWLGraphWrapper) - Constructor for class owltools.gaf.owl.mapping.BasicABox
 
BasicAnnotationPropagator - Class in owltools.gaf.inference
This performs basic annotation inferences involving propagation between the 3 sub-ontologies in GO MF -> BP over part_of BP -> CC over occurs_in This approach pre-computes the possible non-redundant propagations classes for each class during the setup.
BasicAnnotationPropagator(GafDocument, OWLGraphWrapper, boolean) - Constructor for class owltools.gaf.inference.BasicAnnotationPropagator
Create instance.
BasicChecksRule - Class in owltools.gaf.rules.go
This class performs basic checks.
BasicChecksRule(String, TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.BasicChecksRule
 
bioentities - Variable in class owltools.gaf.BioentityDocument
 
Bioentity - Class in owltools.gaf
 
Bioentity() - Constructor for class owltools.gaf.Bioentity
 
Bioentity(String, String, String, String, String, String) - Constructor for class owltools.gaf.Bioentity
 
BioentityDocument - Class in owltools.gaf
 
BioentityDocument(String) - Constructor for class owltools.gaf.BioentityDocument
 
BioentityDocument(String, List<Bioentity>) - Constructor for class owltools.gaf.BioentityDocument
 
buildDocument(Reader, String, String) - Method in class owltools.gaf.parser.GafObjectsBuilder
 
buildDocument(String, String, String) - Method in class owltools.gaf.parser.GafObjectsBuilder
 
buildDocument(File) - Method in class owltools.gaf.parser.GafObjectsBuilder
 
buildDocument(String) - Method in class owltools.gaf.parser.GafObjectsBuilder
 
BuilderTools - Class in owltools.gaf.parser
 
BuilderTools() - Constructor for class owltools.gaf.parser.BuilderTools
 
buildExtensionExpression(List<List<ExtensionExpression>>) - Static method in class owltools.gaf.parser.BuilderTools
 
buildGafQualifierString(GeneAnnotation) - Static method in class owltools.gaf.parser.BuilderTools
 
buildGpadQualifierString(GeneAnnotation) - Static method in class owltools.gaf.parser.BuilderTools
 
buildNetwork(OWLClass, Collection<String>) - Method in class owltools.gaf.lego.LegoModelGenerator
Performs all steps to seed activation network.
buildNetwork(String, Collection<String>) - Method in class owltools.gaf.lego.LegoModelGenerator
buildNetwork(OWLClass, Set<String>) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
Performs all steps to build activation network
buildNetwork(String, Set<String>) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
buildPropertyExpression(List<Pair<String, String>>) - Static method in class owltools.gaf.parser.BuilderTools
 
buildReferenceIdsString(List<String>) - Static method in class owltools.gaf.parser.BuilderTools
 
buildTaxonString(String, Pair<String, String>) - Static method in class owltools.gaf.parser.BuilderTools
 
buildTaxonString(Pair<String, String>) - Static method in class owltools.gaf.parser.BuilderTools
 
buildWithString(Collection<String>) - Static method in class owltools.gaf.parser.BuilderTools
 
buildWithString(Collection<String>, String) - Static method in class owltools.gaf.parser.BuilderTools
 

C

calculateConditionalProbaility(OWLClass, OWLClass) - Method in class owltools.gaf.lego.LegoModelGenerator
Pr( F | P ) = Pr(F,P) / Pr(P)
calculateConditionalProbaility(OWLClass, OWLClass) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
Pr( F | P ) = Pr(F,P) / Pr(P)
calculatePairwiseEnrichment(OWLClass, OWLClass) - Method in class owltools.gaf.lego.LegoModelGenerator
 
calculatePairwiseEnrichment(OWLClass, OWLClass, int) - Method in class owltools.gaf.lego.LegoModelGenerator
 
checkModelId(String) - Method in class owltools.gaf.lego.MolecularModelManager
 
classExpression - Variable in class owltools.gaf.owl.GAFOWLBridge.GAFDescription
 
ClassTaxonMatrix - Class in owltools.gaf.inference
Matrix representing the applicability of classes and taxa.
ClassTaxonMatrix(int, int) - Constructor for class owltools.gaf.inference.ClassTaxonMatrix
 
cleanup() - Method in class owltools.gaf.godb.DatabaseDumper
 
close() - Method in class owltools.gaf.io.GafWriter
 
close() - Method in class owltools.gaf.rules.AnnotationRulesReportWriter
 
closeAllPrintStreams() - Method in class owltools.gaf.godb.DatabaseDumper
 
closePrintStream(String) - Method in class owltools.gaf.godb.DatabaseDumper
 
cls - Variable in class owltools.gaf.ExtensionExpression
 
COLOCATES_WITH_MASK - Static variable in class owltools.gaf.GeneAnnotation
 
CommentListener - Interface in owltools.gaf.parser
 
CompositionalClassPredictor - Class in owltools.gaf.inference
Deprecated.
CompositionalClassPredictor(GafDocument, OWLGraphWrapper) - Constructor for class owltools.gaf.inference.CompositionalClassPredictor
Deprecated.
 
connectGraph() - Method in class owltools.gaf.lego.LegoModelGenerator
Add default edges based on PPI network add ( a1 , a2 ) to E where ( g1 , g2 ) is in PPI, and a = (g, _) is in A
connectGraph() - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
Add default edges based on PPI network add ( a1 , a2 ) to E where ( g1 , g2 ) is in PPI, and a = (g, _) is in A
CONTRIBUTES_TO_MASK - Static variable in class owltools.gaf.GeneAnnotation
 
convertLegoModelToAllIndividuals(ModelContainer, String) - Method in class owltools.gaf.lego.format.LegoModelVersionConverter
 
CoreMolecularModelManager<METADATA> - Class in owltools.gaf.lego
Manager and core operations for in memory MolecularModels (aka lego diagrams).
CoreMolecularModelManager(OWLGraphWrapper) - Constructor for class owltools.gaf.lego.CoreMolecularModelManager
 
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.
CREATE_EXPLANATIONS - Static variable in class owltools.gaf.rules.GenericReasonerValidationCheck
 
createAspectProvider(OWLGraphWrapper, Map<String, String>, OWLReasoner) - Static method in class owltools.gaf.parser.DefaultAspectProvider
Create a new aspect provider from the given super classes and aspects.
createDefaultAspectMap(OWLGraphWrapper) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
Create the mapping from the sub ontology to the aspect in the GAF.
createEcoMapper() - Static method in class owltools.gaf.eco.EcoMapperFactory
Create an instance of a EcoMapper.
createEcoMapper(OWLOntologyManager) - Static method in class owltools.gaf.eco.EcoMapperFactory
Create an instance of a EcoMapper.
createEcoMapper(ParserWrapper) - Static method in class owltools.gaf.eco.EcoMapperFactory
Create an instance of a EcoMapper.
createEcoMapper(ParserWrapper, String) - Static method in class owltools.gaf.eco.EcoMapperFactory
Create an instance of a EcoMapper.
createEcoMapper(OWLGraphWrapper) - Static method in class owltools.gaf.eco.EcoMapperFactory
Create an instance of a EcoMapper.
createFact(ModelContainer, OWLObjectPropertyExpression, OWLIndividual, OWLIndividual, Set<OWLAnnotation>) - Static method in class owltools.gaf.lego.CoreMolecularModelManager
 
createIndividual(String, ModelContainer, OWLClass, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
createIndividual(String, ModelContainer, OWLClassExpression, Set<OWLAnnotation>) - Static method in class owltools.gaf.lego.CoreMolecularModelManager
 
createIndividual(String, String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
createIndividualNonReasoning(String, String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
createModel(GafDocument) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
Generate an RDF model from a GAF Document
createPartonomy(OWLClass) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
Generate M = N x N where N ∈ P or N ∈ A Basic idea: we want to create a partonomy that breaks down a large process into smaller chunks and ultimately partonomic leaves - activities.
createPrediction(OWLClass, String, String, GeneAnnotation) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
 
createPropagationRules(OWLGraphWrapper, OWLReasoner) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
Create the default propagation rule set tailored for the GeneOntology.
createProteinClassesFromQuestForOrthologs(OWLOntology, InputStream, OWLClass) - Static method in class owltools.gaf.bioentities.ProteinTools
Add a named class for each protein extracted from the InputStream.
createProteinLabelOntology(OWLOntologyManager, IRI, File) - Static method in class owltools.gaf.bioentities.ProteinTools
Create a new ontology (with the given ID) for all proteins in the given Quest for Orthlogs seq XML file.
createProteinOntologies(Set<String>, String, String, String) - Static method in class owltools.gaf.bioentities.ProteinTools
Create protein ontologies from the qfo files.
createProteinOntologyIRI(String) - Static method in class owltools.gaf.bioentities.ProteinTools
Create an protein ontology IRI for the given subset name.
createSimple() - Static method in class owltools.gaf.eco.EcoMapperFactory
Create a new SimpleEcoMapper with from the mapping loaded from the PURL.
createSimple(String) - Static method in class owltools.gaf.eco.EcoMapperFactory
Create a new SimpleEcoMapper with from the mapping loaded from the given source.
createTraversingEcoMapper() - Static method in class owltools.gaf.eco.EcoMapperFactory
Create a TraversingEcoMapper instance using a new ParserWrapper to load ECO.
createTraversingEcoMapper(ParserWrapper) - Static method in class owltools.gaf.eco.EcoMapperFactory
Create a TraversingEcoMapper instance using the given ParserWrapper to load ECO.
createTraversingEcoMapper(ParserWrapper, String) - Static method in class owltools.gaf.eco.EcoMapperFactory
Create a TraversingEcoMapper instance using the given ParserWrapper to load ECO from the given location.
createTraversingEcoMapper(OWLGraphWrapper, OWLReasoner, boolean) - Static method in class owltools.gaf.eco.EcoMapperFactory
Create a TraversingEcoMapper instance using the given OWLGraphWrapper.
createType(ModelContainer, OWLIndividual, OWLClassExpression) - Static method in class owltools.gaf.lego.CoreMolecularModelManager
 
createWriter(OutputStream) - Method in class owltools.gaf.io.AbstractXmlWriter
 
CUT_MASK - Static variable in class owltools.gaf.GeneAnnotation
 

D

DatabaseDumper - Class in owltools.gaf.godb
Generates a relational database dump.
DatabaseDumper() - Constructor for class owltools.gaf.godb.DatabaseDumper
 
DATE - Static variable in class owltools.gaf.parser.GAFParser
 
DB - Static variable in class owltools.gaf.parser.GAFParser
 
DB_OBJECT_ID - Static variable in class owltools.gaf.parser.GAFParser
 
DB_OBJECT_NAME - Static variable in class owltools.gaf.parser.GAFParser
 
DB_OBJECT_SYMBOL - Static variable in class owltools.gaf.parser.GAFParser
 
DB_OBJECT_SYNONYM - Static variable in class owltools.gaf.parser.GAFParser
 
DB_OBJECT_TYPE - Static variable in class owltools.gaf.parser.GAFParser
 
dbname - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
 
DefaultAspectProvider - Class in owltools.gaf.parser
 
DefaultAspectProvider(Map<String, String>) - Constructor for class owltools.gaf.parser.DefaultAspectProvider
Create a new aspect provider with the given (complete) id-aspect mappings.
deleteIndividual(String, ModelContainer, OWLNamedIndividual, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Deletes an individual
deleteIndividual(String, String, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
Deletes an individual
deleteIndividualNonReasoning(String, String, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
Deletes an individual
deleteModel(String) - Method in class owltools.gaf.lego.MolecularModelManager
 
dispose() - Method in interface owltools.gaf.eco.TraversingEcoMapper
Dispose this instance
dispose() - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
 
dispose() - Method in class owltools.gaf.EcoTools
Deprecated.
Clean up the internal data structures, usually done as last operation.
dispose() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
dispose() - Method in interface owltools.gaf.inference.AnnotationPredictor
 
dispose() - Method in class owltools.gaf.inference.BasicAnnotationPropagator
 
dispose() - Method in class owltools.gaf.inference.FoldBasedPredictor
 
dispose() - Method in class owltools.gaf.lego.CoreMolecularModelManager
internal method to cleanup this instance
dispose() - Method in class owltools.gaf.parser.GafObjectsBuilder
 
dispose() - Method in class owltools.gaf.parser.GAFParser
 
dispose() - Method in class owltools.gaf.TaxonTools
Clean up the internal data structures, usually done as last operation.
dtFormat - Static variable in class owltools.gaf.rules.go.BasicChecksRule
 
dump() - Method in class owltools.gaf.godb.Dumper
dumps all data
dump() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumps all tables
dumpAssociationModule() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpAssociationRowsForGaf(PrintStream, GafDocument) - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpAssociationTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpDbxrefTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
Dumper - Class in owltools.gaf.godb
Generates a dump of a combined set of ontologies, annotations and related data Currently there is one implementing subclass, for dumping a relational database.
Dumper() - Constructor for class owltools.gaf.godb.Dumper
 
dumpGeneProductRowsForGaf(PrintStream, GafDocument) - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpGraphModule() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpGraphPathTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpMetaModule() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpOptModule() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpRow(PrintStream, Object...) - Method in class owltools.gaf.godb.DatabaseDumper
 
dumpSpeciesRow(PrintStream, String) - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpSpeciesTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpTerm2TermTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpTermSubsetTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 
dumpTermTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
 

E

ECO_MAPPING_PURL - Static variable in interface owltools.gaf.eco.EcoMapper
Permanent URL for the mapping of GO evidence codes to ECO classes
ECO_PURL - Static variable in interface owltools.gaf.eco.EcoMapper
Permanent URL for the evidence code ontology (ECO) owl file.
ECO_PURL - Static variable in class owltools.gaf.EcoTools
Deprecated.
 
ECO_PURL_IRI - Static variable in interface owltools.gaf.eco.EcoMapper
IRI for the evidence code ontology (ECO) owl file.
EcoMapper - Interface in owltools.gaf.eco
 
EcoMapperFactory - Class in owltools.gaf.eco
Factory to create instances of EcoMapper and TraversingEcoMapper.
EcoMapperFactory.OntologyMapperPair<MAPPER extends EcoMapper> - Class in owltools.gaf.eco
 
EcoMapperImpl - Class in owltools.gaf.eco
 
EcoTools - Class in owltools.gaf
EcoTools(OWLGraphWrapper, OWLReasoner, boolean) - Constructor for class owltools.gaf.EcoTools
Deprecated.
Create an instance for the given graph and reasoner.
EcoTools(ParserWrapper) - Constructor for class owltools.gaf.EcoTools
Deprecated.
Create a new instance using the given ParserWrapper to load the ECO.
EcoTools(OWLGraphWrapper) - Constructor for class owltools.gaf.EcoTools
Deprecated.
Create a new instance using the ECO graph wrapper.
edgeSet - Variable in class owltools.gaf.lego.NetworkInferenceEngine.Partonomy
Deprecated.
 
end() - Method in class owltools.gaf.io.AbstractGafWriter
Called after the writing of a GafDocument has been finished.
end() - Method in class owltools.gaf.io.GafWriter.BufferedGafWriter
 
end() - Method in class owltools.gaf.io.GafWriter
 
end() - Method in class owltools.gaf.io.GpadWriter
Called after the writing of a GafDocument has been finished.
end() - Method in class owltools.gaf.io.GpiWriter
Called after the writing of a GafDocument has been finished.
equals(Object) - Method in class owltools.gaf.ExtensionExpression
 
equals(Object) - Method in class owltools.gaf.inference.Prediction
 
equals(Object) - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager.UndoMetadata
 
EVIDENCE - Static variable in class owltools.gaf.parser.GAFParser
 
experimentalPredictionReportWriter - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
 
experimentalPredictionWriter - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
 
exportModel(String, ModelContainer, OWLOntologyFormat) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Export the ABox, will try to set the ontologyID to the given modelId (to ensure import assumptions are met)
exportModel(String, ModelContainer) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Export the ABox for the given modelId in the default OWLOntologyFormat.
exportModel(String, ModelContainer, String) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Export the ABox for the given modelId in the given ontology format.
Warning: The mapping from String to OWLOntologyFormat does not map every format!
exportModel(String) - Method in class owltools.gaf.lego.MolecularModelManager
Export the ABox for the given modelId in the default OWLOntologyFormat.
exportModelLegacy(String, ModelContainer, String) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Export the model (ABox) in a legacy format, such as GAF or GPAD.
exportModelLegacy(String, String) - Method in class owltools.gaf.lego.MolecularModelManager
Export the model (ABox) for the given modelId in a legacy format, such as GAF or GPAD.
ExtensionExpression - Class in owltools.gaf
Corresponds to col16 in GAF2.0
ExtensionExpression() - Constructor for class owltools.gaf.ExtensionExpression
 
ExtensionExpression(String, String) - Constructor for class owltools.gaf.ExtensionExpression
 

F

fetchScoredCandidateProcesses(OWLClass, Integer) - Method in class owltools.gaf.lego.LegoModelGenerator
 
FileBasedMolecularModelManager<METADATA> - Class in owltools.gaf.lego
Layer for retrieving and storing models as OWL files.
FileBasedMolecularModelManager(OWLGraphWrapper) - Constructor for class owltools.gaf.lego.FileBasedMolecularModelManager
 
fold(GafDocument) - Method in class owltools.gaf.owl.AnnotationExtensionFolder
 
fold(GafDocument, boolean) - Method in class owltools.gaf.owl.AnnotationExtensionFolder
 
fold(GafDocument, GeneAnnotation) - Method in class owltools.gaf.owl.AnnotationExtensionFolder
given an annotation to a pre-existing term, this will return a set of zero or more annotations to new terms that are generated from folding the annotation extensions into newly created term
FoldBasedPredictor - Class in owltools.gaf.inference
Use a reasoner to find more specific named classes for annotations with extension expressions.
FoldBasedPredictor(GafDocument, OWLGraphWrapper, boolean) - Constructor for class owltools.gaf.inference.FoldBasedPredictor
 
foldedClassMap - Variable in class owltools.gaf.owl.AnnotationExtensionFolder
 

G

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
The class builds GafDocument a gaf file.
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
 
GafToLegoTranslator - Class in owltools.gaf.lego
Given a set of gene associations, this procedure will generate LEGO individuals.
GafToLegoTranslator(OWLGraphWrapper, Map<String, String>) - Constructor for class owltools.gaf.lego.GafToLegoTranslator
 
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 - Variable in class owltools.gaf.lego.NetworkInferenceEngine.Activity
Deprecated.
 
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
 
generateBlankModel(String, METADATA) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Generates a new model taking as input a database D.
generateBlankModelWithTaxon(String, METADATA) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Generates a new blank model, add protein label for the given as import.
generateDerivedModel(String, METADATA) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
 
generateDot(String) - Method in class owltools.gaf.lego.MolecularModelManager
Deprecated.
generateImage(String) - Method in class owltools.gaf.lego.MolecularModelManager
Deprecated.
generateModel(OWLClass, String, METADATA) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Generates a new model taking as input a biological process P and a database D.
generateModel(String, String, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
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
 
getActivityTypes(String) - Method in class owltools.gaf.lego.LegoModelGenerator
Get all activity types a gene enables (i.e.
getActivityTypes(String) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
Get all activity types a gene enables (i.e.
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
 
getAnnotationProperty() - Method in enum owltools.gaf.lego.MolecularModelManager.LegoAnnotationType
 
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
 
getAvailableModelIds() - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Retrieve a collection of all available model ids.
Note: Models may not be loaded at this point.
getBioentities() - Method in class owltools.gaf.BioentityDocument
Get all Bioentity objects.
getBioentities() - Method in class owltools.gaf.GafDocument
Get all registered Bioentity objects.
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
 
getChanges() - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager.ChangeEvent
 
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.
getCreatedClasses() - Method in class owltools.gaf.lego.ManchesterSyntaxTool
 
getCurrentModelIds() - Method in class owltools.gaf.lego.CoreMolecularModelManager
Retrieve a collection of all model ids currently in memory.
getCurrentModelIds() - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Retrieve a collection of all model ids currently in memory.
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
 
getGaf(String) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
 
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
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
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
 
getGenes(OWLClass) - Method in class owltools.gaf.lego.LegoModelGenerator
Gets all genes annotated to cls or descendant via involved-in relations
getGenes(OWLClass) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
Gets all genes that enable a given activity type (i.e.
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 class owltools.gaf.lego.CoreMolecularModelManager
 
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
 
getGraphStatistics() - Method in class owltools.gaf.lego.LegoModelGenerator
 
getGraphStatistics() - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
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
 
getId(OWLNamedObject, OWLGraphWrapper) - Static method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
getId(IRI) - Static method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
getIdLabelPair(Object) - Method in class owltools.gaf.lego.LegoModelGenerator
 
getIds(String) - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo
Retrieve all identifier of a protein for the given database.
getImports() - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
getIndividuals(String) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
getIndividualsByQuery(String, OWLClassExpression) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
getIndividualsByQuery(String, String) - Method in class owltools.gaf.lego.MolecularModelManager
 
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
 
getInferredRelationshipsForGene(String) - Method in class owltools.gaf.lego.LegoModelGenerator
 
getInferredTypes(String) - Method in class owltools.gaf.lego.LegoModelGenerator
 
getInteracting_Taxon_ID() - Method in class owltools.gaf.parser.GpadParser
 
getIRI(String, OWLGraphWrapper) - Static method in class owltools.gaf.lego.MolecularModelJsonRenderer
getIsaPartofSuperClassClosure(Collection<OWLClass>, OWLGraphWrapper, OWLReasoner) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator
 
getLabel(Object) - Method in class owltools.gaf.lego.LegoModelGenerator
 
getLabel(OWLNamedObject, String) - Method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
getLabel(Object) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
getLastUpdateDate() - Method in class owltools.gaf.GeneAnnotation
 
getLegoType(IRI) - Static method in enum owltools.gaf.lego.MolecularModelManager.LegoAnnotationType
 
getLegoType(String) - Static method in enum owltools.gaf.lego.MolecularModelManager.LegoAnnotationType
 
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
 
getModel(String) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Fetches a model by its Id
getModelAbox(String) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Retrieve the abox ontology.
getModelIds() - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
getMostLikelyActivityForGene(String, OWLClass) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
getMostSpecificActivityTypes(String) - Method in class owltools.gaf.lego.LegoModelGenerator
 
getMostSpecificActivityTypes(String) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
getMostSpecificProcessTypes(String) - Method in class owltools.gaf.lego.LegoModelGenerator
 
getName() - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
getName() - Method in interface owltools.gaf.rules.AnnotationRule
Return the name of the rule.
getNamedIndividual(String, String) - Method in class owltools.gaf.lego.MolecularModelManager
 
getNamespace() - Method in class owltools.gaf.parser.GpiParser
 
getNcbiTaxonId() - Method in class owltools.gaf.Bioentity
 
getNextSplitDocument() - Method in class owltools.gaf.parser.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
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.
getNumberOfGenes() - Method in class owltools.gaf.lego.LegoModelGenerator
 
getNumberOfGenes() - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
getObjectPropertyByShorthand(String) - Method in class owltools.gaf.owl.GAFOWLBridge
 
getOntology() - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
getOWLClass(String) - Method in class owltools.gaf.inference.CompositionalClassPredictor
Deprecated.
 
getOWLClass(String) - Method in class owltools.gaf.owl.GAFOWLBridge
 
getOWLDataFactory(String) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
getOWLOntologyManager(String) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
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
 
getPathToGafs() - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
 
getPathToOWLFiles() - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Note this may move to an implementation-specific subclass in future
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
 
getProcessTypes(String) - Method in class owltools.gaf.lego.LegoModelGenerator
 
getProcessTypes(String) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
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.
getStoredModelIds() - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Retrieve a collection of all file/stored model ids found in the repo.
Note: Models may not be loaded at this point.
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
 
getTboxIRI(OWLGraphWrapper) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Executed before the init call CoreMolecularModelManager.init().
getTime() - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager.ChangeEvent
 
getType() - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
getTypeCls() - Method in class owltools.gaf.Bioentity
 
getTypes() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
getUndoRedoEvents(String) - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager
Retrieve the current available undo and redo events.
getUserId() - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager.ChangeEvent
 
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
 
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, boolean) - 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, boolean) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
 
GoAnnotationRulesFactoryImpl(OWLGraphWrapper, TraversingEcoMapper, boolean) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
 
GoAnnotationRulesFactoryImpl(String, String, OWLGraphWrapper, TraversingEcoMapper, boolean) - 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
 

H

handleAdditionalRules(List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>) - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
 
handleAdditionalRules(List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>) - Method in class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
 
handleHeaderMetaData(String) - Method in class owltools.gaf.parser.GpiParser
 
handleProtein(String, String, String, String, String, String, QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo) - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener
 
handleProtein(String, String, String, String, String, String) - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.ProteinListener
 
handleUnsatisfiable(Set<OWLClass>, OWLOntology) - Method in class owltools.gaf.rules.AnnotationTaxonRule
 
handleUnsatisfiable(Set<OWLClass>, OWLOntology) - Method in class owltools.gaf.rules.go.GoAnnotationTaxonRule
 
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.ExtensionExpression
 
hashCode() - Method in class owltools.gaf.inference.Prediction
 
hashCode() - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager.UndoMetadata
 
hasQualifiers() - Method in class owltools.gaf.GeneAnnotation
 
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

IdMapping - Class in owltools.gaf
 
IdMapping() - Constructor for class owltools.gaf.IdMapping
 
IdMapping(String, String, String, String) - Constructor for class owltools.gaf.IdMapping
 
importModel(String) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Try to load (or replace) a model with the given ontology.
incrementallyLoadedTables - Variable in class owltools.gaf.godb.DatabaseDumper
 
index() - Method in class owltools.gaf.GafDocument
Index all current annotations of this document.
inferLocations() - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
init() - Method in class owltools.gaf.inference.FoldBasedPredictor
 
init() - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
init() - Method in class owltools.gaf.parser.GAFParser
 
init() - Method in interface owltools.gaf.rules.AnnotationRulesFactory
Initialize the factory.
init() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
 
initialize(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.lego.LegoModelGenerator
 
initialize(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
INSTANCE - Static variable in class owltools.gaf.lego.ReverseChangeGenerator
 
INTEGRAL_TO_MASK - Static variable in class owltools.gaf.GeneAnnotation
 
invertChanges(List<OWLOntologyChange>) - Static method in class owltools.gaf.lego.ReverseChangeGenerator
 
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.GoAnnotationExperimentalPredictionRule
 
isAnnotationLevel() - Method in class owltools.gaf.rules.go.GoAnnotationPredictionRule
 
isAnnotationLevel() - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
 
isBasicAboxMapping() - Method in class owltools.gaf.owl.GAFOWLBridge
 
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.
 
isColocatesWith() - Method in class owltools.gaf.GeneAnnotation
 
isConsistent(String) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
isContributesTo() - Method in class owltools.gaf.GeneAnnotation
 
isCut() - Method in class owltools.gaf.GeneAnnotation
 
isDirectNot() - Method 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.parser.GafObjectsBuilder
 
isEmpty() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
isFormatDeclaration(String) - Method in class owltools.gaf.parser.GpadParser
 
isFormatDeclaration(String) - Method in class owltools.gaf.parser.GpiParser
 
isGenerateIndividuals() - Method in class owltools.gaf.owl.GAFOWLBridge
 
isGoEvidenceCode(String) - Method in interface owltools.gaf.eco.EcoMapper
Check that the given GO code is a valid code with an existing mapping to ECO
isGoEvidenceCode(String) - Method in class owltools.gaf.eco.EcoMapperImpl
 
isGpadIncludeUnknowBioentities() - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
isGpadIncludeUnmappedECO() - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
isHeaderMetaData(String) - Method in class owltools.gaf.parser.GpadParser
 
isHeaderMetaData(String) - Method in class owltools.gaf.parser.GpiParser
 
isInferringAnnotations() - Method in class owltools.gaf.rules.AbstractAnnotationRule
 
isInferringAnnotations() - Method in interface owltools.gaf.rules.AnnotationRule
 
isInferringAnnotations() - Method in class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
 
isInferringAnnotations() - Method in class owltools.gaf.rules.go.GoAnnotationPredictionRule
 
isInitialized() - Method in interface owltools.gaf.inference.AnnotationPredictor
 
isInitialized() - Method in class owltools.gaf.inference.BasicAnnotationPropagator
 
isInitialized() - Method in class owltools.gaf.inference.CompositionalClassPredictor
Deprecated.
 
isInitialized() - Method in class owltools.gaf.inference.FoldBasedPredictor
 
isIntegralTo() - Method in class owltools.gaf.GeneAnnotation
 
isLeaf() - Method in class owltools.gaf.Bioentity
 
isMRC() - Method in class owltools.gaf.GeneAnnotation
 
isNegated() - Method 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
 
isPruned() - Method in class owltools.gaf.Bioentity
 
isRedundantWithExistingAnnotations() - Method in class owltools.gaf.inference.Prediction
 
isRedundantWithOtherPredictions() - Method in class owltools.gaf.inference.Prediction
 
isReplaceGenus - Variable in class owltools.gaf.owl.AnnotationExtensionUnfolder
 
isSkipNotAnnotations() - Method in class owltools.gaf.owl.GAFOWLBridge
 
isStrict - Variable in class owltools.gaf.godb.DatabaseDumper
 
IssueListener - Interface in owltools.gaf.parser
 
IssueListener.DefaultIssueListener - Class in owltools.gaf.parser
 
IssueListener.DefaultIssueListener() - Constructor for class owltools.gaf.parser.IssueListener.DefaultIssueListener
 
isTerminus() - Method in class owltools.gaf.Bioentity
 
isThrowOnMultipleExpressions - Variable in class owltools.gaf.owl.AnnotationExtensionUnfolder
 

K

KEY_FACTS - Static variable in class owltools.gaf.lego.MolecularModelJsonRenderer
 
KEY_INDIVIDUALS - Static variable in class owltools.gaf.lego.MolecularModelJsonRenderer
 
KEY_INDIVIDUALS_INFERENCES - Static variable in class owltools.gaf.lego.MolecularModelJsonRenderer
 
KEY_PROPERTIES - Static variable in class owltools.gaf.lego.MolecularModelJsonRenderer
 

L

label - Variable in class owltools.gaf.lego.NetworkInferenceEngine.InstanceNode
Deprecated.
 
LegoAllIndividualToGeneAnnotationTranslator - Class in owltools.gaf.lego.legacy
 
LegoAllIndividualToGeneAnnotationTranslator(OWLGraphWrapper, OWLReasoner, SimpleEcoMapper) - Constructor for class owltools.gaf.lego.legacy.LegoAllIndividualToGeneAnnotationTranslator
 
LegoAnnotationTypeDateFormat - Static variable in class owltools.gaf.lego.MolecularModelManager
 
LegoModelGenerator - Class in owltools.gaf.lego
Generates an augmented Minimal Model (aka LEGO) graph for a given process, given an ontology and a set of annotations.
LegoModelGenerator(ModelContainer) - Constructor for class owltools.gaf.lego.LegoModelGenerator
 
LegoModelVersionConverter - Class in owltools.gaf.lego.format
 
LegoModelVersionConverter() - Constructor for class owltools.gaf.lego.format.LegoModelVersionConverter
 
LegoToGeneAnnotationTranslator - Class in owltools.gaf.lego.legacy
 
LegoToGeneAnnotationTranslator(OWLGraphWrapper, OWLReasoner, SimpleEcoMapper) - Constructor for class owltools.gaf.lego.legacy.LegoToGeneAnnotationTranslator
 
LineFilter<T> - Interface in owltools.gaf.parser
 
loadECO(ParserWrapper) - Static method in class owltools.gaf.EcoTools
Deprecated.
Load the evidence code ontology (ECO) from its default PURL.
loadGaf(String) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
loads/register a Gaf document
loadGaf(String, File) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Loads and caches a GAF document from a specified location
loadGpadGpi(File, File) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
loadModel(String, boolean) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
loadModel(String, boolean) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
 
loadModelABox(String) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
loadModelABox(String) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
 
loadOntologyIRI(IRI, boolean) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
locations - Variable in class owltools.gaf.lego.NetworkInferenceEngine.InstanceNode
Deprecated.
 
LOG - Static variable in class owltools.gaf.inference.BasicAnnotationPropagator
 
LOG - Static variable in class owltools.gaf.inference.CompositionalClassPredictor
Deprecated.
 
LOG - Static variable in class owltools.gaf.parser.GAFParser
 
lookupByActivityType(OWLClassExpression) - Method in class owltools.gaf.lego.NetworkInferenceEngine.ActivityNetwork
Deprecated.
 
lookupByGene(String) - Method in class owltools.gaf.lego.NetworkInferenceEngine.ActivityNetwork
Deprecated.
 

M

ManchesterSyntaxTool - Class in owltools.gaf.lego
Wrapper for parsing OWL Manchester Syntax using a OWLGraphWrapper.
ManchesterSyntaxTool(OWLGraphWrapper, boolean) - Constructor for class owltools.gaf.lego.ManchesterSyntaxTool
Create new instance.
mapExt(OWLClass, List<ExtensionExpression>) - Method in class owltools.gaf.owl.AnnotationExtensionFolder
 
mappingSource - Variable in class owltools.gaf.IdMapping
 
minimizedTranslate(GafDocument) - Method in class owltools.gaf.lego.GafToLegoTranslator
Translate the given GafDocument into an OWL representation of the LEGO model.
mmg - Variable in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
MolecularModelJsonRenderer - Class in owltools.gaf.lego
A Renderer that takes a MolecularModel (an OWL ABox) and generates Map objects that can be translated to JSON using Gson.
MolecularModelJsonRenderer(ModelContainer) - Constructor for class owltools.gaf.lego.MolecularModelJsonRenderer
 
MolecularModelJsonRenderer(OWLOntology) - Constructor for class owltools.gaf.lego.MolecularModelJsonRenderer
 
MolecularModelJsonRenderer(OWLGraphWrapper) - Constructor for class owltools.gaf.lego.MolecularModelJsonRenderer
 
MolecularModelJsonRenderer.KEY - Enum in owltools.gaf.lego
JSON-LD keywords for elements of different vocabularies: RDF OWL GO RO TODO: use a complex enum to generate IRIs for each
MolecularModelJsonRenderer.VAL - Enum in owltools.gaf.lego
merge with KEY?
MolecularModelManager<METADATA> - Class in owltools.gaf.lego
Convenience layer for operations on collections of MolecularModels (aka lego diagrams) This manager is intended to be used within a web server.
MolecularModelManager(OWLGraphWrapper) - Constructor for class owltools.gaf.lego.MolecularModelManager
 
MolecularModelManager.LegoAnnotationType - Enum in owltools.gaf.lego
 
MolecularModelManager.LegoStringDotRenderer - Class in owltools.gaf.lego
Deprecated.
MolecularModelManager.LegoStringDotRenderer(OWLGraphWrapper, OWLReasoner) - Constructor for class owltools.gaf.lego.MolecularModelManager.LegoStringDotRenderer
Deprecated.
 
MolecularModelManager.UnknownIdentifierException - Exception in owltools.gaf.lego
 
MolecularModelManager.UnknownIdentifierException(String, Throwable) - Constructor for exception owltools.gaf.lego.MolecularModelManager.UnknownIdentifierException
 
MolecularModelManager.UnknownIdentifierException(String) - Constructor for exception owltools.gaf.lego.MolecularModelManager.UnknownIdentifierException
 

N

NCBI - Static variable in class owltools.gaf.TaxonTools
 
NetworkInferenceEngine - Class in owltools.gaf.lego
Deprecated.
NetworkInferenceEngine() - Constructor for class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
NetworkInferenceEngine.Activity - Class in owltools.gaf.lego
Deprecated.
A ⊆ G x TA
An instance of an activity that is enabled by some gene/product
NetworkInferenceEngine.Activity(OWLClassExpression, String, String) - Constructor for class owltools.gaf.lego.NetworkInferenceEngine.Activity
Deprecated.
 
NetworkInferenceEngine.ActivityNetwork - Class in owltools.gaf.lego
Deprecated.
NA = (A, EA)
A network/graph of activity nodes
NetworkInferenceEngine.ActivityNetwork() - Constructor for class owltools.gaf.lego.NetworkInferenceEngine.ActivityNetwork
Deprecated.
 
NetworkInferenceEngine.Edge<T extends NetworkInferenceEngine.InstanceNode,U extends NetworkInferenceEngine.InstanceNode> - Class in owltools.gaf.lego
Deprecated.

EdgeType can be null for unknown (i.e.
NetworkInferenceEngine.Edge(T, U, OWLObjectPropertyExpression) - Constructor for class owltools.gaf.lego.NetworkInferenceEngine.Edge
Deprecated.
 
NetworkInferenceEngine.Edge(T, U, String) - Constructor for class owltools.gaf.lego.NetworkInferenceEngine.Edge
Deprecated.
 
NetworkInferenceEngine.InstanceNode - Class in owltools.gaf.lego
Deprecated.
 
NetworkInferenceEngine.InstanceNode() - Constructor for class owltools.gaf.lego.NetworkInferenceEngine.InstanceNode
Deprecated.
 
NetworkInferenceEngine.Partonomy - Class in owltools.gaf.lego
Deprecated.
M : Merelogy (partonomy), from activity instances to process instances, and between process instances.
NetworkInferenceEngine.Partonomy() - Constructor for class owltools.gaf.lego.NetworkInferenceEngine.Partonomy
Deprecated.
 
NetworkInferenceEngine.Process - Class in owltools.gaf.lego
Deprecated.
 
NetworkInferenceEngine.Process(OWLClassExpression, String) - Constructor for class owltools.gaf.lego.NetworkInferenceEngine.Process
Deprecated.
 
next() - Method in class owltools.gaf.parser.GAFParser
Try to parse a next line, may skip lines until a line is parsed successfully or the file ends.
nl() - Method in class owltools.gaf.io.AbstractGafWriter
Append the separator between rows.
nl() - Method in class owltools.gaf.io.GafWriter.BufferedGafWriter
 
nl() - Method in class owltools.gaf.io.GpadWriter
Append the separator between rows.
nl() - Method in class owltools.gaf.io.GpiWriter
Append the separator between rows.
normalizeDirections() - Method in class owltools.gaf.lego.LegoModelGenerator
Reroute all has_parts to part_ofs
NOT_MASK - Static variable in class owltools.gaf.GeneAnnotation
 
numParents - Variable in class owltools.gaf.lego.NetworkInferenceEngine.InstanceNode
Deprecated.
 

O

object - Variable in class owltools.gaf.lego.NetworkInferenceEngine.Edge
Deprecated.
 
objLastIdMap - Variable in class owltools.gaf.godb.DatabaseDumper
 
OpenAnnotationRDFWriter - Class in owltools.gaf.io
Generates and writes RDF Models conforming to http://www.openannotation.org/spec/core/core.html from GeneAnnotation objects.
OpenAnnotationRDFWriter() - Constructor for class owltools.gaf.io.OpenAnnotationRDFWriter
Creates a new writer, using the default output format (turtle)
OpenAnnotationRDFWriter(String) - Constructor for class owltools.gaf.io.OpenAnnotationRDFWriter
 
owlObject - Variable in class owltools.gaf.lego.NetworkInferenceEngine.Edge
Deprecated.
 
owlObject - Variable in class owltools.gaf.lego.NetworkInferenceEngine.InstanceNode
Deprecated.
 
owlOntologyManager - Variable in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
owltools.gaf - package owltools.gaf
Processing of GO Gene Association Files
owltools.gaf.bioentities - package owltools.gaf.bioentities
 
owltools.gaf.eco - package owltools.gaf.eco
 
owltools.gaf.godb - package owltools.gaf.godb
This will replace go-db-perl MySQL loader
owltools.gaf.inference - package owltools.gaf.inference
Perform inference on Gene Associations
owltools.gaf.io - package owltools.gaf.io
 
owltools.gaf.lego - package owltools.gaf.lego
 
owltools.gaf.lego.format - package owltools.gaf.lego.format
 
owltools.gaf.lego.legacy - package owltools.gaf.lego.legacy
 
owltools.gaf.metadata - package owltools.gaf.metadata
 
owltools.gaf.owl - package owltools.gaf.owl
 
owltools.gaf.owl.mapping - package owltools.gaf.owl.mapping
 
owltools.gaf.parser - package owltools.gaf.parser
 
owltools.gaf.rules - package owltools.gaf.rules
 
owltools.gaf.rules.go - package owltools.gaf.rules.go
 

P

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
 
parseClassExpression(String, OWLGraphWrapper) - Static method in class owltools.gaf.lego.MolecularModelManager
Deprecated.
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
 
parseManchesterExpression(String) - Method in class owltools.gaf.lego.ManchesterSyntaxTool
Parse a class expression in Manchester syntax.
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.
partonomy - Variable in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
M ⊆ N x N, N = A ∪ P
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
 
processClassSet - Variable in class owltools.gaf.lego.LegoModelGenerator
 
processClassSet - Variable in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
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
 

Q

QUALIFIER - Static variable in class owltools.gaf.parser.GAFParser
 
QuestForOrthologsSeqXMLParser - Class in owltools.gaf.bioentities
This is an event based parser for the seq XML produced by the Quest for Orthologs project.

Add listeners to retrieve the information.
QuestForOrthologsSeqXMLParser() - Constructor for class owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser
 
QuestForOrthologsSeqXMLParser.MoreInfoProteinListener - Interface in owltools.gaf.bioentities
QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo - Interface in owltools.gaf.bioentities
Additional data about a protein.
QuestForOrthologsSeqXMLParser.ProteinListener - Interface in owltools.gaf.bioentities

R

readingComment(String, String, int) - Method in interface owltools.gaf.parser.CommentListener
 
redo(String, String) - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager
Redo latest change for the given model.
redo(String, ModelContainer, String) - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager
Redo latest change for the given model.
reduceToNonRedundant(Set<OWLClass>, OWLReasoner) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator
Given a set of classes, create a new non-redundant set with respect to the inferred super class hierarchy.
REFERENCE - Static variable in class owltools.gaf.parser.GAFParser
 
ReferentialIntegrityException - Exception in owltools.gaf.godb
 
ReferentialIntegrityException(String, Object) - Constructor for exception owltools.gaf.godb.ReferentialIntegrityException
 
relation - Variable in class owltools.gaf.ExtensionExpression
 
relationship - Variable in class owltools.gaf.IdMapping
 
remoteParserListener(ParserListener) - Method in class owltools.gaf.parser.GAFParser
 
removeAnnotations(String, ModelContainer, OWLNamedIndividual, Collection<OWLAnnotation>, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
removeAnnotations(String, String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
removeAnnotations(String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
removeAnnotations(String, String, String, String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
removeCommentListener(CommentListener) - Method in class owltools.gaf.parser.GAFParser
 
removeFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
removeFact(String, String, String, String, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
removeFactNonReasoning(String, String, String, String, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
removePrefix(String, char) - Static method in class owltools.gaf.parser.BuilderTools
 
removeType(String, OWLNamedIndividual, OWLClass, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
remove ClassAssertion(c,i) to specified model
removeType(String, OWLNamedIndividual, OWLObjectPropertyExpression, OWLClassExpression, METADATA) - Method in class owltools.gaf.lego.CoreMolecularModelManager
Removes a ClassAssertion, where the class expression instantiated is an ObjectSomeValuesFrom expression
removeType(String, String, String, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
removeTypeNonReasoning(String, String, OWLClassExpression, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
 
render(OWLPrettyPrinter) - Method in class owltools.gaf.inference.Prediction
 
renderEngineResult(AnnotationRulesEngine.AnnotationRulesEngineResult, AnnotationRulesEngine) - Method in class owltools.gaf.rules.AnnotationRulesReportWriter
A print-out of the results, summaries, and preditions.
renderEvidences(MolecularModelManager<?>) - Static method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderEvidences(OWLOntologyManager) - Static method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderIndividuals(Collection<OWLNamedIndividual>) - Method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderInferences(Collection<OWLNamedIndividual>, Map<Object, Object>, OWLReasoner) - Method in class owltools.gaf.lego.MolecularModelJsonRenderer
Add the inferences for the given individuals to the JSON map.
renderModel() - Method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderModelAnnotations(OWLOntology) - Static method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderModelInferences(Map<Object, Object>, OWLReasoner) - Method in class owltools.gaf.lego.MolecularModelJsonRenderer
Add the available inferences to the given JSON map.
renderObject(OWLNamedIndividual) - Method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderObject(OWLObjectPropertyAssertionAxiom) - Method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderObject(OWLObjectProperty) - Method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderRelations(MolecularModelManager<?>, Set<OWLObjectProperty>) - Static method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderToJson(OWLOntology) - Static method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderToJson(OWLOntology, boolean) - Static method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderToJson(OWLOntology, boolean, boolean) - Static method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
renderViolations(AnnotationRulesEngine.AnnotationRulesEngineResult, AnnotationRulesEngine, PrintWriter) - Static method in class owltools.gaf.rules.AnnotationRulesReportWriter
A simple tab delimited print-out of the validation results.
report(int, int) - Method in interface owltools.gaf.io.PseudoRdfXmlWriter.ProgressReporter
 
reportError(String, GeneAnnotation) - Method in class owltools.gaf.lego.GafToLegoTranslator
 
reportEvidenceIssue(String, String, boolean) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
reportIssue(String, String, boolean) - Method in class owltools.gaf.parser.IssueListener.DefaultIssueListener
 
reportIssue(String, String, boolean) - Method in interface owltools.gaf.parser.IssueListener
 
reportProblems() - Method in class owltools.gaf.godb.Dumper
 
reportUnknowBioentityId(String, boolean) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
reportWarn(String, GeneAnnotation) - Method in class owltools.gaf.lego.GafToLegoTranslator
 
reportWarnings() - Method in interface owltools.gaf.parser.ParserListener
 
requestToken - Variable in class owltools.gaf.lego.UndoAwareMolecularModelManager.UndoMetadata
 
ReverseChangeGenerator - Class in owltools.gaf.lego
Create the reverse of an OWLOntologyChange.

S

saveAllModels(Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Save all models to disk.
saveModel(String, ModelContainer, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Save a model to disk.
saveModel(String, Collection<Pair<String, String>>, METADATA) - Method in class owltools.gaf.lego.MolecularModelManager
Save a model to disk.
sb - Variable in class owltools.gaf.lego.MolecularModelManager.LegoStringDotRenderer
Deprecated.
 
searchModels(Collection<String>) - Method in class owltools.gaf.lego.MolecularModelManager
 
seedGraph(OWLClass, Set<String>) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
Create initial activation node set A for a process P and a set of seed genes for all g ∈ Gseed, add a = to A where f = argmax(p) { t : t ∈ TA, p=Prob( t | g) }
seedGraph(String, Set<String>) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
seedGraph(OWLClass) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
sep() - Method in class owltools.gaf.io.AbstractGafWriter
Append a the separator between columns.
sep() - Method in class owltools.gaf.io.GpadWriter
Append a the separator between columns.
sep() - Method in class owltools.gaf.io.GpiWriter
Append a the separator between columns.
setActsOnTaxonId(String) - Method in class owltools.gaf.GeneAnnotation
 
setActsOnTaxonId(Pair<String, String>) - Method in class owltools.gaf.GeneAnnotation
 
setAndFilterRedundantPredictions(Set<Prediction>, Set<OWLClass>) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
side-effects: removes redundant predictions over all relationships
setAndFilterRedundantPredictions(Set<Prediction>, Set<OWLClass>, Set<OWLPropertyExpression>) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
side-effects: removes redundant predictions over a set of relationships.
setAnnotationCount(int) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
 
setAnnotationRow(String) - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
setAnnotations(List<GeneAnnotation>) - Method in class owltools.gaf.Bioentity
 
setAspect(String) - Method in class owltools.gaf.GeneAnnotation
 
setAspectProvider(GpadGpiObjectsBuilder.AspectProvider) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
setAssignedBy(String) - Method in class owltools.gaf.GeneAnnotation
 
setBasicAboxMapping(boolean) - Method in class owltools.gaf.owl.GAFOWLBridge
 
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
 
setChildren(List<Bioentity>) - Method in class owltools.gaf.Bioentity
 
setCls(String) - Method in class owltools.gaf.ExtensionExpression
 
setCls(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.
setDirectMRC(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setDirectNot(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setDistanceFromParent(float) - Method in class owltools.gaf.Bioentity
 
setErrorMessage(String) - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
 
setEvidence(String, String) - Method in class owltools.gaf.GeneAnnotation
 
setExtensionExpressions(List<List<ExtensionExpression>>) - Method in class owltools.gaf.GeneAnnotation
 
setFoldedClassMap(Map<OWLClass, OWLClassExpression>) - Method in class owltools.gaf.owl.AnnotationExtensionFolder
 
setFullName(String) - Method in class owltools.gaf.Bioentity
 
setGafdocs(Set<GafDocument>) - Method in class owltools.gaf.godb.Dumper
 
setGafDocument(GafDocument) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
setGafMode() - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
If set, calling {OpenAnnotationRDFWriter.write(GafDocument, File) generates bioentities plus annotations (as in a GAF file)
setGeneAnnotations(List<GeneAnnotation>) - Method in class owltools.gaf.GafDocument
Replace the current set of annotations with the given list.
setGeneId(String) - Method in class owltools.gaf.Bioentity
 
setGeneProductForm(String) - Method in class owltools.gaf.GeneAnnotation
 
setGenerateIndividuals(boolean) - Method in class owltools.gaf.owl.GAFOWLBridge
 
setGpadfMode() - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
If set, calling {OpenAnnotationRDFWriter.write(GafDocument, File) generates annotations only (as in a GPAD file) This is the default
setGpadIncludeUnknowBioentities(boolean) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
setGpadIncludeUnmappedECO(boolean) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
 
setGpifMode() - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
If set, calling {OpenAnnotationRDFWriter.write(GafDocument, File) generates bioentities only (as in a GPI file)
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
 
setIncludeObjectPropertyValues(boolean) - Method in class owltools.gaf.lego.MolecularModelJsonRenderer
 
setIsColocatesWith(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setIsContributesTo(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setIsCut(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setIsIntegralTo(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setIsNegated(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setLastUpdateDate(Date) - Method in class owltools.gaf.GeneAnnotation
 
setLastUpdateDate(String) - Method in class owltools.gaf.GeneAnnotation
 
setLineNumber(int) - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
setLocation(OWLClass) - Method in class owltools.gaf.lego.NetworkInferenceEngine.InstanceNode
Deprecated.
 
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
 
setOriginalChildrenToCurrentChildren() - Method in class owltools.gaf.Bioentity
 
setPaintId(String) - Method in class owltools.gaf.Bioentity
 
setParent(Bioentity) - Method in class owltools.gaf.Bioentity
 
setPathToGafs(String) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
Can either be an HTTP prefix, or an absolute file path
setPathToOWLFiles(String) - Method in class owltools.gaf.lego.FileBasedMolecularModelManager
 
setPattern(Pattern) - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
 
setPersistantNodeID(String, String) - Method in class owltools.gaf.Bioentity
 
setProgressReporter(PseudoRdfXmlWriter.ProgressReporter) - Method in class owltools.gaf.io.PseudoRdfXmlWriter
 
setPrune(boolean) - Method in class owltools.gaf.Bioentity
 
setQualifiers(int) - Method in class owltools.gaf.GeneAnnotation
 
setReason(String) - Method in class owltools.gaf.inference.Prediction
 
setRedundantWithExistingAnnotations(boolean) - Method in class owltools.gaf.inference.Prediction
 
setRedundantWithOtherPredictions(boolean) - Method in class owltools.gaf.inference.Prediction
 
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
setSeqId(String, String) - Method in class owltools.gaf.Bioentity
 
setSkipNotAnnotations(boolean) - Method in class owltools.gaf.owl.GAFOWLBridge
 
setSource(AnnotationSource) - Method in class owltools.gaf.GeneAnnotation
 
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.
setStream(PrintStream) - Method in class owltools.gaf.io.GafWriter
 
setStream(String) - Method in class owltools.gaf.io.GafWriter
 
setStream(File) - Method in class owltools.gaf.io.GafWriter
 
setSuggestedReplacements(Set<GeneAnnotation>) - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
setSymbol(String) - Method in class owltools.gaf.Bioentity
 
setSynonyms(List<String>) - Method in class owltools.gaf.Bioentity
 
setTargetDirectory(String) - Method in class owltools.gaf.godb.Dumper
 
setTargetId(String) - Method in class owltools.gaf.IdMapping
 
setTargetOntology(OWLOntology) - Method in class owltools.gaf.owl.GAFOWLBridge
 
setType(String) - Method in class owltools.gaf.Bioentity
 
setType(AnnotationRuleViolation.ViolationType) - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
setTypeCls(String) - Method in class owltools.gaf.Bioentity
 
setWithInfos(Collection<String>) - Method in class owltools.gaf.GeneAnnotation
 
showStats() - Method in class owltools.gaf.godb.DatabaseDumper
 
SimpleABoxToGAF - Class in owltools.gaf.owl
Translates a set of ClassAssertion axioms to a minimal GAF
SimpleABoxToGAF() - Constructor for class owltools.gaf.owl.SimpleABoxToGAF
 
SimpleEcoMapper - Interface in owltools.gaf.eco
 
SimpleEcoMapperImpl - Class in owltools.gaf.eco
 
SKIP_IEA - Static variable in class owltools.gaf.inference.BasicAnnotationPropagator
 
sortByValue(Map<K, V>) - Static method in class owltools.gaf.lego.LegoModelGenerator
 
sourceId - Variable in class owltools.gaf.IdMapping
 
status_df - Static variable in class owltools.gaf.rules.AnnotationRulesFactoryImpl
 
stream - Variable in class owltools.gaf.io.GafWriter
 
strength - Variable in class owltools.gaf.lego.NetworkInferenceEngine.Activity
Deprecated.
 
subject - Variable in class owltools.gaf.lego.NetworkInferenceEngine.Edge
Deprecated.
 
submissionDate - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
 
summaryWriter - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
 

T

tableObjIdMap - Variable in class owltools.gaf.godb.DatabaseDumper
 
targetDirectory - Variable in class owltools.gaf.godb.Dumper
 
targetId - Variable in class owltools.gaf.IdMapping
 
TAXON - Static variable in class owltools.gaf.parser.GAFParser
 
TAXON_PREFIX - Static variable in class owltools.gaf.TaxonTools
 
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 taxons.
TaxonTools(OWLReasoner, boolean) - Constructor for class owltools.gaf.TaxonTools
Create an instance for the given reasoner.
toString() - Method in class owltools.gaf.Bioentity
 
toString() - Method in class owltools.gaf.ExtensionExpression
 
toString() - Method in class owltools.gaf.GeneAnnotation
 
toString() - Method in class owltools.gaf.inference.Prediction
 
toString() - Method in class owltools.gaf.rules.AnnotationRuleViolation
 
translate(GafDocument) - Method in class owltools.gaf.lego.GafToLegoTranslator
Translate the given GafDocument into an OWL representation of the LEGO model.
translate(Collection<GeneAnnotation>) - Method in class owltools.gaf.lego.GafToLegoTranslator
Translate the given annotations (GeneAnnotation) into an OWL representation of the LEGO model.
translate(OWLOntology, GafDocument, BioentityDocument, List<String>) - Method in class owltools.gaf.lego.legacy.LegoAllIndividualToGeneAnnotationTranslator
 
translate(OWLOntology, GafDocument, BioentityDocument, List<String>) - Method in class owltools.gaf.lego.legacy.LegoToGeneAnnotationTranslator
 
translate(GafDocument) - Method in class owltools.gaf.owl.GAFOWLBridge
 
translateBioentity(Bioentity) - Method in class owltools.gaf.owl.GAFOWLBridge
 
translateBioentity(Bioentity) - Method in class owltools.gaf.owl.mapping.BasicABox
 
translateGeneAnnotation(GeneAnnotation) - Method in class owltools.gaf.owl.GAFOWLBridge
 
translateGeneAnnotation(GeneAnnotation) - Method in class owltools.gaf.owl.mapping.BasicABox
 
translateNetworkToOWL() - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
translateNetworkToOWL(OWLOntology) - Method in class owltools.gaf.lego.NetworkInferenceEngine
Deprecated.
 
TraversingEcoMapper - Interface in owltools.gaf.eco
 
TraversingEcoMapperImpl - Class in owltools.gaf.eco
 
type - Variable in class owltools.gaf.lego.NetworkInferenceEngine.Edge
Deprecated.
 
typeOf - Variable in class owltools.gaf.lego.NetworkInferenceEngine.InstanceNode
Deprecated.
 

U

undo(String, String) - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager
Undo latest change for the given model.
undo(String, ModelContainer, String) - Method in class owltools.gaf.lego.UndoAwareMolecularModelManager
Undo latest change for the given model.
UndoAwareMolecularModelManager - Class in owltools.gaf.lego
Provide undo and redo operations for the MolecularModelManager.
UndoAwareMolecularModelManager(OWLGraphWrapper) - Constructor for class owltools.gaf.lego.UndoAwareMolecularModelManager
 
UndoAwareMolecularModelManager.ChangeEvent - Class in owltools.gaf.lego
Details for a change in a model.
UndoAwareMolecularModelManager.ChangeEvent(String, List<OWLOntologyChange>, long) - Constructor for class owltools.gaf.lego.UndoAwareMolecularModelManager.ChangeEvent
 
UndoAwareMolecularModelManager.UndoMetadata - Class in owltools.gaf.lego
 
UndoAwareMolecularModelManager.UndoMetadata(String) - Constructor for class owltools.gaf.lego.UndoAwareMolecularModelManager.UndoMetadata
 
unfold(GafDocument) - Method in class owltools.gaf.owl.AnnotationExtensionUnfolder
 
unfold(GafDocument, GeneAnnotation) - Method in class owltools.gaf.owl.AnnotationExtensionUnfolder
given an annotation to a pre-existing term, this will return a set of zero or more annotations to new terms that are generated from folding the annotation extensions into newly created term
unlinkModel(String) - Method in class owltools.gaf.lego.CoreMolecularModelManager
 
updateImports(String, ModelContainer) - Method in class owltools.gaf.lego.CoreMolecularModelManager
This method will check the given model and update the import declarations.
updateImports(String) - Method in class owltools.gaf.lego.MolecularModelManager
This method will check the given model and update the import declarations.
userId - Variable in class owltools.gaf.lego.UndoAwareMolecularModelManager.UndoMetadata
 

V

validateAnnotations(GafDocument) - Method in class owltools.gaf.rules.AnnotationRulesEngine
Validate the given GafDocument.
valueOf(String) - Static method in enum owltools.gaf.godb.GoMySQLDatabaseDumper.GOMySQLTable
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gaf.lego.MolecularModelJsonRenderer.KEY
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gaf.lego.MolecularModelJsonRenderer.VAL
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gaf.lego.MolecularModelManager.LegoAnnotationType
Returns the enum constant of this type with the specified name.
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.godb.GoMySQLDatabaseDumper.GOMySQLTable
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gaf.lego.MolecularModelJsonRenderer.KEY
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gaf.lego.MolecularModelJsonRenderer.VAL
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gaf.lego.MolecularModelManager.LegoAnnotationType
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.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.
visit(AddAxiom) - Method in class owltools.gaf.lego.ReverseChangeGenerator
 
visit(RemoveAxiom) - Method in class owltools.gaf.lego.ReverseChangeGenerator
 
visit(SetOntologyID) - Method in class owltools.gaf.lego.ReverseChangeGenerator
 
visit(AddImport) - Method in class owltools.gaf.lego.ReverseChangeGenerator
 
visit(RemoveImport) - Method in class owltools.gaf.lego.ReverseChangeGenerator
 
visit(AddOntologyAnnotation) - Method in class owltools.gaf.lego.ReverseChangeGenerator
 
visit(RemoveOntologyAnnotation) - Method in class owltools.gaf.lego.ReverseChangeGenerator
 

W

WITH - Static variable in class owltools.gaf.parser.GAFParser
 
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(GafDocument) - Method in class owltools.gaf.io.AbstractGafWriter
Write a full GAF.
write(GeneAnnotation) - Method in class owltools.gaf.io.AbstractGafWriter
Write a single GeneAnnotation.
write(GafDocument) - Method in class owltools.gaf.io.GpadWriter
Write a full GAF.
write(GeneAnnotation) - Method in class owltools.gaf.io.GpadWriter
Write a single GeneAnnotation.
write(BioentityDocument) - Method in class owltools.gaf.io.GpiWriter
 
write(Collection<Bioentity>) - Method in class owltools.gaf.io.GpiWriter
Write a full GAF.
write(Bioentity) - Method in class owltools.gaf.io.GpiWriter
Write a single Bioentity.
write(GafDocument, PrintStream) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
Writes associations from GAF document as RDF on out
write(GafDocument, File) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
 
write(GafDocument, String) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
 
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.
writeHeader(GafDocument) - Method in class owltools.gaf.io.AbstractGafWriter
Write a header of a GAF, use the comments from the GafDocument.
writeHeader(List<String>) - Method in class owltools.gaf.io.AbstractGafWriter
Write a header for a GAF, header comments are optional.
writeHeader(List<String>) - Method in class owltools.gaf.io.GafWriter.BufferedGafWriter
 
writeHeader(GafDocument) - Method in class owltools.gaf.io.GpadWriter
Write a header of a GAF, use the comments from the GafDocument.
writeHeader(List<String>) - Method in class owltools.gaf.io.GpadWriter
Write a header for a GAF, header comments are optional.
writeHeader(Collection<Bioentity>) - Method in class owltools.gaf.io.GpiWriter
Write a header of a GPI.
writeHeader(List<String>, Collection<Bioentity>) - Method in class owltools.gaf.io.GpiWriter
Write a header for a GAF, header comments are optional.
writeLego(OWLOntology, String, String) - Method in class owltools.gaf.lego.MolecularModelManager
Deprecated.
writer - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
 

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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