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

A

aboutCommand() - Method in class owltools.web.OWLHandler
information about an ontology object (class, property, individual)
AbstractAnnotationPredictor - Class in owltools.gaf.inference
 
AbstractAnnotationPredictor(GafDocument, OWLGraphWrapper) - Constructor for class owltools.gaf.inference.AbstractAnnotationPredictor
 
AbstractClosureReader - Class in owltools.io
 
AbstractClosureReader(InputStream) - Constructor for class owltools.io.AbstractClosureReader
 
AbstractClosureReader(String) - Constructor for class owltools.io.AbstractClosureReader
 
AbstractClosureReader(OWLGraphWrapper) - Constructor for class owltools.io.AbstractClosureReader
 
AbstractClosureRenderer - Class in owltools.io
Renders the graph closure - i.e.
AbstractClosureRenderer(PrintStream) - Constructor for class owltools.io.AbstractClosureRenderer
 
AbstractClosureRenderer(String) - Constructor for class owltools.io.AbstractClosureRenderer
 
AbstractMappingParser - Class in owltools.idmap
Parses the IDMapping file available here: ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz
AbstractMappingParser() - Constructor for class owltools.idmap.AbstractMappingParser
 
AbstractSolrLoader - Class in owltools.solrj
root class for loading ontologies or ontology-related data into a solr server using web services and the solrj library
AbstractSolrLoader(SolrServer) - Constructor for class owltools.solrj.AbstractSolrLoader
 
AbstractSolrLoader(String) - Constructor for class owltools.solrj.AbstractSolrLoader
 
actsOnTaxonId - Variable in class owltools.gaf.GeneAnnotation
 
add(SolrInputDocument) - Method in class owltools.solrj.AbstractSolrLoader
 
add(E) - Method in class owltools.util.BloomFilter
Adds an object to the Bloom filter.
addAll(Collection<SolrInputDocument>) - Method in class owltools.solrj.AbstractSolrLoader
 
addAll(Collection<? extends E>) - Method in class owltools.util.BloomFilter
Adds all elements from a Collection to the Bloom filter.
addAllAndCommit() - Method in class owltools.solrj.AbstractSolrLoader
 
addAllObjects() - Method in class owltools.gfx.OWLGraphLayoutRenderer
Adds all objects from the OGW into the rendered graph CAUTION: do this only for small ontologies
addBioentity(Bioentity) - Method in class owltools.gaf.GafDocument
 
addBridgeOntology(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
addCompositeQualifier(CompositeQualifier) - Method in class owltools.gaf.GafDocument
 
addEdge(OWLGraphEdge) - Method in class owltools.gfx.OWLGraphLayoutRenderer
Adds an edge to the graph.
addExtensionExpression(ExtensionExpression) - Method in class owltools.gaf.GafDocument
 
addGeneAnnotation(GeneAnnotation) - Method in class owltools.gaf.GafDocument
 
addImport(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
adds an imports declaration between the source ontology and extOnt
addImport(String) - Method in class owltools.mooncat.Mooncat
Deprecated. 
AddImportTest - Class in owltools.test
 
AddImportTest() - Constructor for class owltools.test.AddImportTest
 
addObject(OWLObject) - Method in class owltools.gfx.OWLGraphLayoutRenderer
Adds an object to the graph to be rendered This will also add all ancestors of the focusObj, and all direct edges from each ancestor
addObjects(Set<OWLObject>) - Method in class owltools.gfx.OWLGraphLayoutRenderer
 
addParserListener(GafParserListener) - Method in class owltools.gaf.GAFParser
 
addPath(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
addQueryOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
addReferencedOntology(OWLOntology) - Method in class owltools.mooncat.Mooncat
 
addResultsToOWLOntology(OWLOntology) - Method in class owltools.sim.Similarity
translates similarity results into OWL Axioms and saves axioms into an OWL Ontology
addRow(String[]) - Method in class owltools.io.TableToAxiomConverter
 
addRow(OWLOntology, String[]) - Method in class owltools.io.TableToAxiomConverter
 
addSourceOntologyPrefix(String) - Method in class owltools.mooncat.Mooncat
Add a source ontology prefix to the internal set.
addSourceOntologyPrefix(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
addSupportOntologiesFromImportsClosure() - Method in class owltools.graph.OWLGraphWrapper
Each ontology in the import closure of the source ontology is added to the list of support ontologies
addSupportOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
 
addValues(String, Collection<String>) - Static method in class owltools.ontologyrelease.OortConfiguration
Only public for testing purposes.
addWithInfo(WithInfo) - Method in class owltools.gaf.GafDocument
 
afterClass() - Static method in class owltools.ontologyrelease.test.OortConfigurationTest
 
AfterLoading - Annotation Type in owltools.ontologyverification.annotations
 
afterLoading(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler
Run tests for the ontology after loading it.
AfterMireot - Annotation Type in owltools.ontologyverification.annotations
 
afterMireot(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler
Run tests for the ontology after mireoting.
AfterReasoning - Annotation Type in owltools.ontologyverification.annotations
 
afterReasoning(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler
Run tests for the ontology after reasoning.
allowFileOverwrite(File) - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner
Hook method to handle an unexpected file overwrite request.
allSubClassOfCommand() - Method in class owltools.web.OWLHandler
 
alternativeCode - Variable in enum owltools.gfx.RelationType
 
AncestorsTest - Class in owltools.graph.test
 
AncestorsTest() - Constructor for class owltools.graph.test.AncestorsTest
 
AncestorsTest - Class in owltools.ontologyrelease.test
 
AncestorsTest() - Constructor for class owltools.ontologyrelease.test.AncestorsTest
 
AncestorsTest2 - Class in owltools.graph.test
 
AncestorsTest2() - Constructor for class owltools.graph.test.AncestorsTest2
 
ANNOTATION_XP - Static variable in class owltools.gaf.GAFParser
 
annotationIRI(String) - Method in class owltools.sim.Similarity
 
AnnotationPredictor - Interface in owltools.gaf.inference
given a bioentity, predict a set of annotations
annotations - Variable in class owltools.gaf.GafDocument
 
AnnotationSource - Class in owltools.gaf
 
AnnotationSource(String, int, String) - Constructor for class owltools.gaf.AnnotationSource
 
annotationSource - Variable in class owltools.gaf.GeneAnnotation
 
AsbtractSimEngineTest - Class in owltools.sim.test
 
AsbtractSimEngineTest() - Constructor for class owltools.sim.test.AsbtractSimEngineTest
 
aScore - Variable in class owltools.sim.MultiSimilarity
 
ASPECT - Static variable in class owltools.gaf.GAFParser
 
ASSIGNED_BY - Static variable in class owltools.gaf.GAFParser
 
assignedBy - Variable in class owltools.gaf.GeneAnnotation
 
AsymmetricJaccardSimilarity - Class in owltools.sim
 
AsymmetricJaccardSimilarity() - Constructor for class owltools.sim.AsymmetricJaccardSimilarity
 
Attribute - Class in owltools.phenolog
Represents a characteristic of an individual.
Attribute(String, String) - Constructor for class owltools.phenolog.Attribute
 
Attribute(String) - Constructor for class owltools.phenolog.Attribute
 
AvgInformationContentBestMatchesSimilarity - Class in owltools.sim
Deprecated. 
AvgInformationContentBestMatchesSimilarity() - Constructor for class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.  
AvgInformationContentLCSSimilarity - Class in owltools.sim
Deprecated. 
AvgInformationContentLCSSimilarity() - Constructor for class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.  
axiomType - Variable in class owltools.io.TableToAxiomConverter.Config
 

B

BasicAnnotationPropagator - Class in owltools.gaf.inference
TODO: this class has not yet been tested! This performs basic annotation inferences involving propagation between the 3 sub-ontologies in GO MF -> MP over part_of BP -> CC over occurs_in TODO: reimplement using OWL semantics and reasoning
BasicAnnotationPropagator(GafDocument, OWLGraphWrapper) - Constructor for class owltools.gaf.inference.BasicAnnotationPropagator
 
before() - Method in class owltools.test.TaxonGraphTest
 
beforeClass() - Static method in class owltools.ontologyrelease.test.OortConfigurationTest
 
belongsToSource(OWLEntity) - Method in class owltools.mooncat.Mooncat
 
bestSubsumers - Variable in class owltools.sim.ConjunctiveSetSimilarity
 
bestSubsumers - Variable in class owltools.sim.DisjunctiveSetSimilarity
 
bestSubsumers - Variable in class owltools.sim.MaximumInformationContentSimilarity
 
bioentities - Variable in class owltools.gaf.GafDocument
 
Bioentity - Class in owltools.gaf
 
Bioentity() - Constructor for class owltools.gaf.Bioentity
 
Bioentity(String, String, String, String, String, String, String) - Constructor for class owltools.gaf.Bioentity
 
bioentity - Variable in class owltools.gaf.GeneAnnotation
 
bioentityObject - Variable in class owltools.gaf.GeneAnnotation
 
bloomFilter - Variable in class owltools.sim.SimSearch
 
BloomFilter<E> - Class in owltools.util
Implementation of a Bloom-filter, as described here: http://en.wikipedia.org/wiki/Bloom_filter Inspired by the SimpleBloomFilter-class written by Ian Clarke.
BloomFilter(double, int, int) - Constructor for class owltools.util.BloomFilter
Constructs an empty Bloom filter.
BloomFilter(int, int) - Constructor for class owltools.util.BloomFilter
Constructs an empty Bloom filter.
BloomFilter(double, int) - Constructor for class owltools.util.BloomFilter
Constructs an empty Bloom filter with a given false positive probability.
BloomFilter(int, int, int, BitSet) - Constructor for class owltools.util.BloomFilter
Construct a new Bloom filter based on existing Bloom filter data.
border - Variable in class owltools.gfx.OWLGraphLayoutNode
 
bottom() - Method in class owltools.gfx.OWLGraphLayoutNode
 
bottom - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
bScore - Variable in class owltools.sim.MultiSimilarity
 
buildClassMap(OWLGraphWrapper) - Method in class owltools.io.TableToAxiomConverter
 
buildDescription(OWLObject, OWLObject) - Method in class owltools.sim.DescriptionTreeSimilarity
Recursively build a class expression that subsumes a and b.
buildDescription(OWLObject, OWLObject, Set<OWLObject>) - Method in class owltools.sim.DescriptionTreeSimilarity
 
buildDocument(Reader, String, String) - Method in class owltools.gaf.GafObjectsBuilder
 
buildDocument(String, String, String) - Method in class owltools.gaf.GafObjectsBuilder
 
buildDocument(File) - Method in class owltools.gaf.GafObjectsBuilder
 
buildDocument(String) - Method in class owltools.gaf.GafObjectsBuilder
 
buildInferences() - Method in class owltools.InferenceBuilder
 
buildInferences(boolean) - Method in class owltools.InferenceBuilder
if alwaysAssertSuperClasses then ensure that superclasses are always asserted for every equivalence axiom, except in the case where a more specific superclass is already in the set of inferences.
buildRow() - Method in class owltools.gaf.GeneAnnotation
this method generate a tab separated row of a gene annotation
BuildVersionId - Class in owltools.ontologyrelease
Deprecated. 
BuildVersionId() - Constructor for class owltools.ontologyrelease.BuildVersionId
Deprecated.  

C

cacheEdges() - Method in class owltools.graph.OWLGraphWrapper
caches full outgoing and incoming edges in general you should not need to call this directly; used internally by this class.
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.AsymmetricJaccardSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.  
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.  
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.CombinedSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.CombinedSimilarity2
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.ConjunctiveSetSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.DescriptionTreeSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.DisjunctiveSetSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.JaccardBloomSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.JaccardSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.MaximumInformationContentSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.MultiSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.OverlapSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.Similarity
 
calculate_overlap(Pheno, Pheno, HashMap<String, IndividualPair>) - Static method in class owltools.phenolog.Main
 
calculateAllSimilarity(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
calculateSimilarity(Similarity, OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
Calculates the similarity between two OWLObjects this is the core method of the SimEngine
calculateSimilarity(OWLObject, OWLObject) - Method in interface owltools.sim.SimilarityCalculator
given two objects, calculate their similarity, returning a number between zero (no similarity) and 1 (equivalence)
calculateSimilarityAllByAll(String, Double) - Method in class owltools.sim.SimEngine
 
calculateSimilarityScore(Similarity, OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
candidates - Variable in class owltools.sim.SimSearch
 
CaroDotTest - Class in owltools.gfx.test
 
CaroDotTest() - Constructor for class owltools.gfx.test.CaroDotTest
 
ChadoGraphClosureRenderer - Class in owltools.io
implements a graph closure writer suitable for imports into Chado; in particular: (i) all identifiers are translated to OBO IDs (ii) relationship chains of length > 1 are ignored (iii) SUBCLASS is written as is_a, and only existential restrictions are emitted
ChadoGraphClosureRenderer(PrintStream) - Constructor for class owltools.io.ChadoGraphClosureRenderer
 
ChadoGraphClosureRenderer(String) - Constructor for class owltools.io.ChadoGraphClosureRenderer
 
ChainTest - Class in owltools.graph.test
 
ChainTest() - Constructor for class owltools.graph.test.ChainTest
 
ChainTestRegulation - Class in owltools.test
 
ChainTestRegulation() - Constructor for class owltools.test.ChainTestRegulation
 
Check - Annotation Type in owltools.ontologyverification.annotations
 
checkAnnotationCardinality(OWLOntology, OntologyMetaDataTools.AnnotationCardinalityConfictHandler) - Static method in class owltools.mooncat.OntologyMetaDataTools
Check the annotations for cardinality violations.
checkAnnotationCardinality(OWLOntology) - Static method in class owltools.mooncat.OntologyMetaDataTools
Check the annotations for cardinality violations.
checkNew(File) - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner
Check whether the file is new.
CheckResult - Class in owltools.ontologyverification
 
CheckResult.Status - Enum in owltools.ontologyverification
 
childArrowShape - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
classMap - Variable in class owltools.io.TableToAxiomConverter.Config
 
clear() - Method in class owltools.util.BloomFilter
Sets all bits to false in the Bloom filter.
ClosureTestCARO - Class in owltools.test
 
ClosureTestCARO() - Constructor for class owltools.test.ClosureTestCARO
 
cls - Variable in class owltools.gaf.ExtensionExpression
 
cls - Variable in class owltools.gaf.GeneAnnotation
 
code - Variable in enum owltools.gfx.RelationType
 
COL_SUBSET - Variable in class owltools.idmap.IDMappingPIRParser
 
colIxSubset - Variable in class owltools.idmap.IDMappingPIRParser
 
collect(OWLObject) - Method in class owltools.solrj.OntologySolrLoader
 
color - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
color - Variable in enum owltools.gfx.RelationType
 
colour - Variable in class owltools.gfx.OWLGraphStrokeEdge.SVGEdge
 
COLS - Static variable in class owltools.idmap.IDMappingPIRParser
 
CombinedJaccardConjunctiveSetSimilarity - Class in owltools.sim
 
CombinedJaccardConjunctiveSetSimilarity() - Constructor for class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
 
CombinedJaccardConjunctiveSetSimilarityTest - Class in owltools.sim.test
 
CombinedJaccardConjunctiveSetSimilarityTest() - Constructor for class owltools.sim.test.CombinedJaccardConjunctiveSetSimilarityTest
 
CombinedSimilarity - Class in owltools.sim
 
CombinedSimilarity() - Constructor for class owltools.sim.CombinedSimilarity
 
CombinedSimilarity2 - Class in owltools.sim
 
CombinedSimilarity2() - Constructor for class owltools.sim.CombinedSimilarity2
 
combineEdgePair(OWLObject, OWLGraphEdge, OWLGraphEdge, int) - Method in class owltools.graph.OWLGraphWrapper
Composes two graph edges into a new edge, using axioms in the ontology to determine the correct composition For examole, Edge(x,SUBCLASS_OF,y) * Edge(y,SUBCLASS_OF,z) yields Edge(x,SUBCLASS_OF,z) Note that property chains of length>2 are currently ignored
CommandLineInterface - Class in owltools.cli
 
CommandLineInterface() - Constructor for class owltools.cli.CommandLineInterface
 
CommandRunner - Class in owltools.cli
An instance of this class can execute owltools commands in sequence.
CommandRunner() - Constructor for class owltools.cli.CommandRunner
 
CommandRunner.OptionException - Exception in owltools.cli
 
CommandRunner.OptionException(String) - Constructor for exception owltools.cli.CommandRunner.OptionException
 
CommandRunner.Opts - Class in owltools.cli
 
CommandRunner.Opts(String[]) - Constructor for class owltools.cli.CommandRunner.Opts
 
CommandRunner.Opts(List<String>) - Constructor for class owltools.cli.CommandRunner.Opts
 
CompactGraphClosureReader - Class in owltools.io
Note that the ontology must be loaded prior to restored a closure table
CompactGraphClosureReader(OWLGraphWrapper) - Constructor for class owltools.io.CompactGraphClosureReader
 
CompactGraphClosureRenderer - Class in owltools.io
Similar to GraphClosureRenderer, writes in a more compact format
CompactGraphClosureRenderer(PrintStream) - Constructor for class owltools.io.CompactGraphClosureRenderer
 
CompactGraphClosureRenderer(String) - Constructor for class owltools.io.CompactGraphClosureRenderer
 
compareTo(GenePheno) - Method in class owltools.phenolog.GenePheno
 
compareTo(Individual) - Method in class owltools.phenolog.Individual
 
compareTo(IndividualPair) - Method in class owltools.phenolog.IndividualPair
 
compareTo(Pheno) - Method in class owltools.phenolog.Pheno
 
comparisonClass - Variable in class owltools.sim.SimEngine
 
comparisonProperty - Variable in class owltools.sim.SimEngine
 
comparisonSuperclass - Variable in class owltools.sim.SimEngine
 
CompositeQualifier - Class in owltools.gaf
 
CompositeQualifier() - Constructor for class owltools.gaf.CompositeQualifier
 
CompositeQualifier(String, String) - Constructor for class owltools.gaf.CompositeQualifier
 
compositeQualifier - Variable in class owltools.gaf.GeneAnnotation
 
compositeQualifierEmptyList - Static variable in class owltools.gaf.GeneAnnotation
 
compositeQualifierList - Variable in class owltools.gaf.GeneAnnotation
 
compositeQualifiers - Variable in class owltools.gaf.GafDocument
 
CompositionalClassPredictor - Class in owltools.gaf.inference
Given an annotation to classes c1, c2, ..., cn, we generate suggestions of annotations to class D if D EquivalentTo d1 and d2 and dm and forall d in d1..dm, there exists a class c in c1...cn such that: Path(c,d) OR d = r some e, and Path(c,e) (i.e.
CompositionalClassPredictor(GafDocument, OWLGraphWrapper) - Constructor for class owltools.gaf.inference.CompositionalClassPredictor
 
config - Variable in class owltools.io.TableToAxiomConverter
 
ConjunctiveSetInformationContentRatioSimilarity - Class in owltools.sim
score is the IC of the intersection of all attributes divided my min IC of a or b it's recommended this used as a sub-method of a MultiSimilarity check
ConjunctiveSetInformationContentRatioSimilarity() - Constructor for class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
ConjunctiveSetSimilarity - Class in owltools.sim
score is the IC of the intersection of all attributes; it's recommended this used as a sub-method of a MultiSimilarity check
ConjunctiveSetSimilarity() - Constructor for class owltools.sim.ConjunctiveSetSimilarity
 
ConjunctiveSetSimilarityTest - Class in owltools.sim.test
 
ConjunctiveSetSimilarityTest() - Constructor for class owltools.sim.test.ConjunctiveSetSimilarityTest
 
contains(E) - Method in class owltools.util.BloomFilter
Returns true if the element could have been inserted into the Bloom filter.
containsAll(Collection<? extends E>) - Method in class owltools.util.BloomFilter
Returns true if all the elements of a Collection could have been inserted into the Bloom filter.
convert(OWLObject) - Method in class owltools.io.OWLGsonRenderer
 
convert(OWLOntology) - Method in class owltools.io.OWLGsonRenderer
 
convert(OWLAxiom) - Method in class owltools.io.OWLGsonRenderer
 
convert(OWLGraphEdge) - Method in class owltools.io.OWLGsonRenderer
 
CopyOfCommandLineInterface - Class in owltools.cli
 
CopyOfCommandLineInterface() - Constructor for class owltools.cli.CopyOfCommandLineInterface
 
count() - Method in class owltools.util.BloomFilter
Returns the number of elements added to the Bloom filter after it was constructed or after clear() was called.
createError(String) - Static method in class owltools.ontologyverification.CheckResult
 
createError(List<String>) - Static method in class owltools.ontologyverification.CheckResult
 
createHash(String, Charset) - Static method in class owltools.util.BloomFilter
Generates a digest based on the contents of a String.
createHash(String) - Static method in class owltools.util.BloomFilter
Generates a digest based on the contents of a String.
createHash(byte[]) - Static method in class owltools.util.BloomFilter
Generates a digest based on the contents of an array of bytes.
createNonBufferingReasoner(OWLOntology) - Method in class owltools.reasoner.GraphReasonerFactory
 
createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.GraphReasonerFactory
 
createNonBufferingReasoner(OWLOntology) - Method in class owltools.reasoner.PlaceholderJcelFactory
 
createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.PlaceholderJcelFactory
 
createOortConfig(Properties) - Static method in class owltools.ontologyrelease.OortConfiguration
Create an OortConfiguration from the given Properties.
createOWLOntologyFromResults() - Method in class owltools.sim.Similarity
 
createProperties(OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration
Create a Properties object for the given configuration.
createReasoner(OWLOntology) - Method in class owltools.reasoner.GraphReasonerFactory
 
createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.GraphReasonerFactory
 
createReasoner(OWLOntology) - Method in class owltools.reasoner.PlaceholderJcelFactory
 
createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.PlaceholderJcelFactory
 
createRelease(Vector<String>) - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner
 
createSuccess() - Static method in class owltools.ontologyverification.CheckResult
 
createSuccess(String) - Static method in class owltools.ontologyverification.CheckResult
 
createUnionExpression(OWLObject, OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
createWarning(String) - Static method in class owltools.ontologyverification.CheckResult
 
createWarning(List<String>) - Static method in class owltools.ontologyverification.CheckResult
 
crender(OWLObject) - Method in class owltools.io.CompactGraphClosureRenderer
 
currentCols - Variable in class owltools.idmap.AbstractMappingParser
 
currentRow - Variable in class owltools.idmap.AbstractMappingParser
 
CycleTest - Class in owltools.test
 
CycleTest() - Constructor for class owltools.test.CycleTest
 

D

DATE - Static variable in class owltools.gaf.GAFParser
 
db - Variable in class owltools.gaf.Bioentity
 
DB - Static variable in class owltools.gaf.GAFParser
 
DB_OBJECT_ID - Static variable in class owltools.gaf.GAFParser
 
DB_OBJECT_NAME - Static variable in class owltools.gaf.GAFParser
 
DB_OBJECT_SYMBOL - Static variable in class owltools.gaf.GAFParser
 
DB_OBJECT_SYNONYM - Static variable in class owltools.gaf.GAFParser
 
DB_OBJECT_TYPE - Static variable in class owltools.gaf.GAFParser
 
deepSimMethods - Variable in class owltools.sim.MultiSimilarity
 
DEFAULT_HANDLER - Static variable in class owltools.mooncat.OntologyMetaDataTools
 
DEFAULT_INSTANCE - Static variable in class owltools.ontologyverification.OntologyCheckHandler
Default instance for convenient use.
DEFAULT_IRI_PREFIX - Static variable in class owltools.graph.OWLGraphWrapper
 
defaultCol1 - Variable in class owltools.io.TableToAxiomConverter.Config
 
defaultCol2 - Variable in class owltools.io.TableToAxiomConverter.Config
 
DefaultOntologyChecks - Class in owltools.ontologyverification
 
DefaultOntologyChecks() - Constructor for class owltools.ontologyverification.DefaultOntologyChecks
 
demo() - Method in class owltools.test.FlyTutorial
 
description - Variable in enum owltools.gfx.RelationType
 
DescriptionTreeSimilarity - Class in owltools.sim
A similarity between two entities constructed by threading two description trees together.
DescriptionTreeSimilarity() - Constructor for class owltools.sim.DescriptionTreeSimilarity
 
disableReleaseButton() - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
 
DisjunctiveSetSimilarity - Class in owltools.sim
 
DisjunctiveSetSimilarity() - Constructor for class owltools.sim.DisjunctiveSetSimilarity
 
dispose() - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
 
dispose() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
DLLikeQueryTest - Class in owltools.graph.test
 
DLLikeQueryTest() - Constructor for class owltools.graph.test.DLLikeQueryTest
 
documentPath - Variable in class owltools.gaf.GafDocument
 
DrawAllCAROTest - Class in owltools.gfx.test
 
DrawAllCAROTest() - Constructor for class owltools.gfx.test.DrawAllCAROTest
 
DrawCAROTest - Class in owltools.gfx.test
 
DrawCAROTest() - Constructor for class owltools.gfx.test.DrawCAROTest
 
DrawOmmatidiumTest - Class in owltools.gfx.test
 
DrawOmmatidiumTest() - Constructor for class owltools.gfx.test.DrawOmmatidiumTest
 
DuplicateDefinitionMooncatTest - Class in owltools.mooncat.test
Test for Mooncat and OntologyMetaDataTools.
DuplicateDefinitionMooncatTest() - Constructor for class owltools.mooncat.test.DuplicateDefinitionMooncatTest
 

E

edgeSetToExpression(Set<OWLGraphEdge>) - Method in class owltools.sim.SimEngine
 
edgeToTargetExpression(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapper
pack/translate an edge (either asserted or a graph closure edge) into an OWL class expression according to the OWLGraph to OWLOntology translation rules.
enableReleaseButton() - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
 
endTaskNotify(String) - Method in class owltools.profile.Profiler
 
enforceEL(OWLGraphWrapper) - Static method in class owltools.InferenceBuilder
Create an ontology with EL as description logic profile.
equals(Object) - Method in class owltools.graph.OWLGraphEdge
 
equals(Object) - Method in class owltools.graph.OWLQuantifiedProperty
 
equals(Object) - Method in class owltools.phenolog.GenePheno
 
equals(Object) - Method in class owltools.phenolog.Individual
 
equals(Object) - Method in class owltools.phenolog.IndividualPair
 
equals(Object) - Method in class owltools.phenolog.Pheno
 
equals(Object) - Method in class owltools.sim.OWLObjectPair
 
equals(Object) - Method in class owltools.util.BloomFilter
Compares the contents of two instances to see if they are equal.
escape(String, char) - Static method in class owltools.ontologyrelease.OortConfiguration
Only public for testing purposes.
EVIDENCE - Static variable in class owltools.gaf.GAFParser
 
evidenceCls - Variable in class owltools.gaf.GeneAnnotation
 
excludeClassesInComparison - Variable in class owltools.sim.SimEngine
 
excludeMetaClass - Variable in class owltools.graph.OWLGraphWrapper.Config
 
excludeProperty(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper.Config
Deprecated. 
execute() - Method in class owltools.ontologyrelease.BuildVersionId
Deprecated. Run task.
execute() - Method in class owltools.ontologyrelease.GetOntologyId
Deprecated.  
execute() - Method in class owltools.ontologyrelease.OboProperty
Deprecated.  
executeRelease(OortGuiConfiguration) - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
Execute the actual release.
expectedFalsePositiveProbability() - Method in class owltools.util.BloomFilter
Calculates the expected probability of false positives based on the number of expected filter elements and the size of the Bloom filter.
expectedNumCols - Variable in class owltools.idmap.AbstractMappingParser
 
ExpressionMaterializingReasoner - Class in owltools.reasoner
 
ExpressionMaterializingReasoner(OWLOntology, OWLReasonerConfiguration, BufferingMode) - Constructor for class owltools.reasoner.ExpressionMaterializingReasoner
 
ExpressionMaterializingReasoner(OWLOntology) - Constructor for class owltools.reasoner.ExpressionMaterializingReasoner
 
ExtensionExpression - Class in owltools.gaf
Corresponds to col16 in GAF2.0
ExtensionExpression() - Constructor for class owltools.gaf.ExtensionExpression
 
ExtensionExpression(String, String, String) - Constructor for class owltools.gaf.ExtensionExpression
 
extensionExpression - Variable in class owltools.gaf.GeneAnnotation
 
extensionExpressionEmptyList - Static variable in class owltools.gaf.GeneAnnotation
 
extensionExpressionList - Variable in class owltools.gaf.GeneAnnotation
 
extensionExpressions - Variable in class owltools.gaf.GafDocument
 

F

FactPPTest - Class in owltools.test
Tests the various wrapper get* methods in OWLGraphWrapper
FactPPTest() - Constructor for class owltools.test.FactPPTest
 
FactPPTest() - Method in class owltools.test.FactPPTest
 
fail() - Method in class owltools.cli.CommandRunner.Opts
 
featureToAttributeMap - Variable in class owltools.sim.MultiSimilarity
 
fill - Variable in class owltools.gfx.GraphStyle
 
fill - Variable in class owltools.gfx.OWLGraphLayoutNode
 
filterObjects(Set<OWLObject>) - Method in class owltools.sim.SimEngine
 
filterWhere - Variable in class owltools.idmap.IDMappingPIRParser
 
findCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findCommonSubsumersAsEdges(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findLeastCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findLeastCommonSubsumersAsEdges(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findRelations() - Method in class owltools.graph.test.RetrieveRelationByLabelTest
 
flush() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
FlyTest - Class in owltools.test
 
FlyTest() - Constructor for class owltools.test.FlyTest
 
FlyTutorial - Class in owltools.test
 
FlyTutorial() - Constructor for class owltools.test.FlyTutorial
 
FlyXPTest - Class in owltools.test
 
FlyXPTest() - Constructor for class owltools.test.FlyXPTest
 
font - Variable in class owltools.gfx.OWLGraphLayoutNode
 
fontName - Variable in class owltools.gfx.GraphStyle
 
fontSize - Variable in class owltools.gfx.GraphStyle
 
forceReflexivePropertyCreation - Variable in class owltools.sim.DescriptionTreeSimilarity
 
forCodes(String) - Static method in enum owltools.gfx.RelationType
 
formalCode - Variable in enum owltools.gfx.RelationType
 
format(Date) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Format a date into the canonical format of YYYY-MM-DD.
fullName - Variable in class owltools.gaf.Bioentity
 

G

g - Variable in class owltools.gfx.OWLGraphLayoutRenderer
 
gafDocument - Variable in class owltools.gaf.Bioentity
 
GafDocument - Class in owltools.gaf
 
GafDocument() - Constructor for class owltools.gaf.GafDocument
 
GafDocument(String, String) - Constructor for class owltools.gaf.GafDocument
 
gafDocument - Variable in class owltools.gaf.GeneAnnotation
 
gafDocumentObject - Variable in class owltools.gaf.GeneAnnotation
 
GAFInferenceTest - Class in owltools.gaf.test
 
GAFInferenceTest() - Constructor for class owltools.gaf.test.GAFInferenceTest
 
GafObjectsBuilder - Class in owltools.gaf
The class builds GafDocument a gaf file.
GafObjectsBuilder() - Constructor for class owltools.gaf.GafObjectsBuilder
 
GafObjectsBuilder(int) - Constructor for class owltools.gaf.GafObjectsBuilder
 
GafObjectsBuilderTest - Class in owltools.gaf.test
 
GafObjectsBuilderTest() - Constructor for class owltools.gaf.test.GafObjectsBuilderTest
 
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
 
GAFOWLBridge.Vocab - Enum in owltools.gaf.owl
 
GAFOWLBridgeTest - Class in owltools.gaf.owl.test
 
GAFOWLBridgeTest() - Constructor for class owltools.gaf.owl.test.GAFOWLBridgeTest
 
GAFParser - Class in owltools.gaf
 
GAFParser() - Constructor for class owltools.gaf.GAFParser
 
GafParserListener - Interface in owltools.gaf
 
GAFParserTest - Class in owltools.gaf.test
 
GAFParserTest() - Constructor for class owltools.gaf.test.GAFParserTest
 
GafSolrDocumentLoader - Class in owltools.solrj
 
GafSolrDocumentLoader(String) - Constructor for class owltools.solrj.GafSolrDocumentLoader
 
GENE_PRODUCT_ISOFORM - Static variable in class owltools.gaf.GAFParser
 
GeneAnnotation - Class in owltools.gaf
 
GeneAnnotation() - Constructor for class owltools.gaf.GeneAnnotation
 
GeneAnnotation(String, boolean, boolean, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class owltools.gaf.GeneAnnotation
 
GenePheno - Class in owltools.phenolog
Represents a characteristic of an individual.
GenePheno(String, String, String, String) - Constructor for class owltools.phenolog.GenePheno
 
GenePheno(String, String) - Constructor for class owltools.phenolog.GenePheno
 
GenePhenoTsvParser - Class in owltools.phenolog
 
GenePhenoTsvParser() - Constructor for class owltools.phenolog.GenePhenoTsvParser
 
geneProductForm - Variable in class owltools.gaf.GeneAnnotation
 
generate(OWLGraphWrapper) - Method in class owltools.ontologyrelease.OntologyMetadata
 
getA() - Method in class owltools.sim.OWLObjectPair
 
getActsOnTaxonId() - Method in class owltools.gaf.GeneAnnotation
 
getAdvancedPanel() - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
Retrieve advanced panel, create new if it not exists.
getAllOntologies() - Method in class owltools.graph.OWLGraphWrapper
in general application code need not call this - it is mostly used internally
getAllOntologies() - Method in class owltools.mooncat.Mooncat
 
getAllOWLObjects() - Method in class owltools.graph.OWLGraphWrapper
fetches all classes, individuals and object properties in all ontologies
getAllPredictions() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
getAllPredictions() - Method in interface owltools.gaf.inference.AnnotationPredictor
 
getAllSimilarityAlgorithmClasses() - Method in class owltools.sim.SimEngine
 
getAllUsedSubsets() - Method in class owltools.graph.OWLGraphWrapper
fetches all subset names that are used
getAltIds(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the values of the alt_id tag
getAncestors(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
returns all ancestors of an object.
getAncestors(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapper
returns all ancestors that can be reached over subclass or the specified set of relations
getancestors() - Method in class owltools.phenolog.Pheno
 
getAncestorsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getAncestorsReflexive(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapper
 
getAnnotationExtension() - Method in class owltools.gaf.GAFParser
 
getAnnotationProperty(String) - Method in class owltools.graph.OWLGraphWrapper
It translates a oboformat tag into an OWL annotation property
getAnnotationRuleViolations() - Method in class owltools.gaf.GAFParser
 
getAnnotationValue(OWLObject, OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapper
fetches the value of a single-valued annotation property for an OWLObject TODO: provide a flag that determines behavior in the case of >1 value
getAnnotationValues(OWLObject, OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapper
gets the values of all annotation assertions to an OWLObject for a particular annotation property
getAspect() - Method in class owltools.gaf.GAFParser
 
getAssignedBy() - Method in class owltools.gaf.GAFParser
 
getAssignedBy() - Method in class owltools.gaf.GeneAnnotation
 
getAttributeClosureFor(OWLObject) - Method in class owltools.sim.SimEngine
 
getAttributes() - Method in class owltools.phenolog.Individual
 
getAttributesFor(OWLObject) - Method in class owltools.sim.SimEngine
 
getAxiomsForSubset(Set<OWLObject>) - Method in class owltools.mooncat.Mooncat
"slim down" an ontology.
getB() - Method in class owltools.sim.OWLObjectPair
 
getBase() - Method in class owltools.ontologyrelease.OortConfiguration
 
getBioentities() - Method in class owltools.gaf.GafDocument
 
getBioentity(String) - Method in class owltools.gaf.GafDocument
 
getBioentity() - Method in class owltools.gaf.GeneAnnotation
 
getBioentityObject() - Method in class owltools.gaf.GeneAnnotation
 
getBit(int) - Method in class owltools.util.BloomFilter
Read a single bit from the Bloom filter.
getBitSet() - Method in class owltools.util.BloomFilter
Return the bit set used to store the Bloom filter.
getBitsPerElement() - Method in class owltools.util.BloomFilter
Get actual number of bits per element based on the number of elements that have currently been inserted and the length of the Bloom filter.
getBottomClassNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getBottomClassNode() - Method in class owltools.reasoner.GraphReasoner
 
getBottomDataPropertyNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getBottomDataPropertyNode() - Method in class owltools.reasoner.GraphReasoner
 
getBottomObjectPropertyNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getBottomObjectPropertyNode() - Method in class owltools.reasoner.GraphReasoner
 
getBridgeOntologies() - Method in class owltools.ontologyrelease.OortConfiguration
 
getBufferingMode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getBuiltin(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
getCategory() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
 
getCategory() - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
getCheckName() - Method in class owltools.ontologyverification.CheckResult
 
getClosest() - Method in class owltools.phenolog.Pheno
 
getClosestDistance() - Method in class owltools.phenolog.Pheno
 
getClosestOverlap() - Method in class owltools.phenolog.Pheno
 
getClosestOverlapPairs() - Method in class owltools.phenolog.Pheno
 
getClosureAxiomsOfExternalReferencedEntities() - Method in class owltools.mooncat.Mooncat
find all axioms in closure of external referenced entities.
getClosureOfExternalReferencedEntities() - Method in class owltools.mooncat.Mooncat
finds the full closure of all external referenced entities.
getCls() - Method in class owltools.gaf.ExtensionExpression
 
getCls() - Method in class owltools.gaf.GeneAnnotation
 
getCommandName() - Method in class owltools.web.OWLHandler
 
getComment(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
gets the value of rdfs:comment for an OWLObject
getCommonSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getCommonSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getCompositeQualifier() - Method in class owltools.gaf.GeneAnnotation
 
getCompositeQualifiers(String) - Method in class owltools.gaf.GafDocument
 
getCompositeQualifiers() - Method in class owltools.gaf.GeneAnnotation
 
getCompositeQualifiersIds() - Method in class owltools.gaf.GafDocument
 
getConfig() - Method in class owltools.graph.OWLGraphWrapper
 
getConsider(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the consider tag.
getCorpusSize() - Method in class owltools.sim.SimEngine
 
getCreatedBy(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the created_by tag
getCurrentRow() - Method in class owltools.gaf.GAFParser
 
getDanglingAxioms(OWLOntology) - Method in class owltools.mooncat.Mooncat
 
getDanglingClasses() - Method in class owltools.mooncat.Mooncat
 
getDanglingClasses(OWLOntology) - Method in class owltools.mooncat.Mooncat
finds all classes for which Mooncat.isDangling(OWLOntology, OWLEntity) is true
getDataFactory() - Method in class owltools.graph.OWLGraphWrapper
 
getDataPropertyDomains(OWLDataProperty, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDataPropertyDomains(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getDataPropertyValues(OWLNamedIndividual, OWLDataProperty) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDataPropertyValues(OWLNamedIndividual, OWLDataProperty) - Method in class owltools.reasoner.GraphReasoner
 
getDate() - Method in class owltools.gaf.GAFParser
 
getDb() - Method in class owltools.gaf.Bioentity
 
getDb() - Method in class owltools.gaf.GAFParser
 
getDbObjectId() - Method in class owltools.gaf.GAFParser
 
getDbObjectName() - Method in class owltools.gaf.GAFParser
 
getDbObjectSymbol() - Method in class owltools.gaf.GAFParser
 
getDbObjectSynonym() - Method in class owltools.gaf.GAFParser
 
getDBObjectType() - Method in class owltools.gaf.GAFParser
 
getDef(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Gets the textual definition of an OWLObject assumes zero or one def It returns the definition text (encoded as def in obo format and IAO_0000115 annotation property in OWL format) of a class
getDefaultFormat() - Method in class owltools.ontologyrelease.OortConfiguration
 
getDefXref(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Get the definition xrefs (IAO_0000115)
getDescendants(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
gets all descendants d of x, where d is reachable by any path.
getDescendantsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
gets all reflexive descendants d of x, where d is reachable by any path.
getDifferentIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDifferentIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.GraphReasoner
 
getDisjointClasses(OWLClassExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDisjointClasses(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
 
getDisjointDataProperties(OWLDataPropertyExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDisjointDataProperties(OWLDataPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
 
getDisjointObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDisjointObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
 
getDistance() - Method in class owltools.graph.OWLGraphEdge
 
getDocumentPath() - Method in class owltools.gaf.GafDocument
 
getDomain(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the domain tag
getEdgesBetween(OWLObject, OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getEquivalentClasses(OWLClassExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getEquivalentClasses(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
 
getEquivalentDataProperties(OWLDataProperty) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getEquivalentDataProperties(OWLDataProperty) - Method in class owltools.reasoner.GraphReasoner
 
getEquivalentNamedClassPairs() - Method in class owltools.InferenceBuilder
 
getEquivalentObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getEquivalentObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
 
getEvidence() - Method in class owltools.gaf.GAFParser
 
getEvidenceCls() - Method in class owltools.gaf.GeneAnnotation
 
getExcludedLabels() - Method in class owltools.sim.SimEngine
any class whose label matches any of the strings returned here will be excluded from any analysis.
getExpectedBitsPerElement() - Method in class owltools.util.BloomFilter
Get expected number of bits per element when the Bloom filter is full.
getExpectedNumberOfElements() - Method in class owltools.util.BloomFilter
Returns the expected number of elements to be inserted into the filter.
getExplaination(String, String, OWLQuantifiedProperty.Quantifier) - Method in class owltools.InferenceBuilder
 
getExpressions(String) - Method in class owltools.gaf.GafDocument
 
getExtensionExpression() - Method in class owltools.gaf.GeneAnnotation
 
getExtensionExpressionIds() - Method in class owltools.gaf.GafDocument
 
getExtensionExpressions() - Method in class owltools.gaf.GeneAnnotation
 
getExternalReferencedEntities() - Method in class owltools.mooncat.Mooncat
returns set of entities that belong to a referenced ontology that are referenced in the source ontology.
getFalsePositiveProbability(double) - Method in class owltools.util.BloomFilter
Calculate the probability of a false positive given the specified number of inserted elements.
getFalsePositiveProbability() - Method in class owltools.util.BloomFilter
Get the current probability of a false positive.
getFile() - Method in class owltools.ontologyrelease.GetOntologyId
Deprecated.  
getFileName() - Method in class owltools.gaf.AnnotationSource
 
getFinalQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
 
getFirstQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
 
getFormat() - Method in class owltools.web.OWLHandler
 
getFrequency(OWLObject) - Method in class owltools.sim.SimEngine
 
getFrequency(Set<OWLObject>) - Method in class owltools.sim.SimEngine
as getFrequency(obj), treats objs as a conjunction
getFreshEntityPolicy() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getFullName() - Method in class owltools.gaf.Bioentity
 
getGafDocument() - Method in class owltools.gaf.Bioentity
 
getGafDocument() - Method in class owltools.gaf.GafObjectsBuilder
 
getGafDocument() - Method in class owltools.gaf.GeneAnnotation
 
getGafDocument() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
getGafDocument() - Method in class owltools.solrj.GafSolrDocumentLoader
 
getGeneAnnotation() - Method in class owltools.gaf.inference.Prediction
 
getGeneAnnotations() - Method in class owltools.gaf.GafDocument
 
getGeneAnnotations(String) - Method in class owltools.gaf.GafDocument
 
getGeneAnnotationsByGoCls(String) - Method in class owltools.gaf.GafDocument
 
getGeneProductForm() - Method in class owltools.gaf.GeneAnnotation
 
getGeneProjectFormId() - Method in class owltools.gaf.GAFParser
 
getGOId() - Method in class owltools.gaf.GAFParser
 
getGraph() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
getGraph() - Method in class owltools.mooncat.Mooncat
 
getGraph() - Method in class owltools.sim.SimEngine
 
getGraph() - Method in interface owltools.sim.SimilarityCalculator
 
getGraph() - Method in class owltools.solrj.AbstractSolrLoader
 
getGraph(String) - Method in class owltools.test.OWLToolsTestBasics
 
getHeight() - Method in class owltools.gfx.OWLGraphLayoutNode
 
getHint() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
gethmp() - Method in class owltools.phenolog.PhenoTransitiveClosure
 
gethmpair() - Method in class owltools.phenolog.PhenoTransitiveClosure
 
gethsp() - Method in class owltools.phenolog.PhenoTransitiveClosure
 
getId() - Method in class owltools.gaf.Bioentity
 
getId() - Method in class owltools.gaf.CompositeQualifier
 
getId() - Method in class owltools.gaf.ExtensionExpression
 
getId() - Method in class owltools.gaf.GafDocument
 
getId() - Method in class owltools.gaf.WithInfo
 
getId() - Method in class owltools.phenolog.Attribute
 
getid() - Method in class owltools.phenolog.GenePheno
 
getId() - Method in class owltools.phenolog.Individual
 
getId() - Method in class owltools.phenolog.Pheno
 
getIdentifier(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
gets the OBO-style ID of the specified object.
getIdentifier(IRI) - Method in class owltools.graph.OWLGraphWrapper
gets the OBO-style ID of the specified object.
getIncomingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getIncomingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
gets all inferred edges coming in to the target edge for every s, if t is reachable from s, then include the inferred edge between s and t.
getIndividualDescendants(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
return all individuals i where x is reachable from i
getIndividualNodeSetPolicy() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getIndividualPairs() - Method in class owltools.phenolog.PhenologEngine
 
getIndividuals() - Method in class owltools.phenolog.Pheno
 
getInformationContent(OWLObject) - Method in class owltools.sim.SimEngine
The IC of an OWLObject is freq(Obj)/corpusSize here the frequency of an object is the number of individuals with a graph path up to the object, and the corpus size is the number of individuals in the graph
getInformationContent(Set<OWLObject>) - Method in class owltools.sim.SimEngine
 
getInstanceChainsFromClosure(OWLClass) - Method in class owltools.graph.OWLGraphWrapper
Finds all edges between an instance i and he given class c.
getInstances(OWLClassExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getInstances(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getInstancesFromClosure(OWLClass) - Method in class owltools.graph.OWLGraphWrapper
Find all edges of the form [i INST c] in the graph closure.
getInverseObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getInverseObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
 
getIRIByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapper
 
getIRIByLabel(String) - Method in class owltools.graph.OWLGraphWrapper
fetches an OWL IRI by rdfs:label
getIRIByLabel(String, boolean) - Method in class owltools.graph.OWLGraphWrapper
fetches an OWL IRI by rdfs:label, optionally testing for uniqueness TODO: index labels.
getIsAnonymous(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
getIsAntiSymmetric(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the is_anti_symmetric tag or IAO_0000427 annotation
getIsContributesTo() - Method in class owltools.gaf.GeneAnnotation
 
getIsCyclic(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the is_cyclic tag
getisFromTC() - Method in class owltools.phenolog.Pheno
 
getIsFunctional(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
true if c is functional in the source ontology
getIsIntegralTo() - Method in class owltools.gaf.GeneAnnotation
 
getIsInverseFunctional(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
 
getIsMetaTag(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the is_metadata_tag tag.
getIsObsolete(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the is-obsolete tag.
getIsReflexive(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
 
getIsSymmetric(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
 
getIsTransitive(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
true if c is transitive in the source ontology
getK() - Method in class owltools.util.BloomFilter
Returns the value chosen for K.

K is the optimal number of hash functions based on the size of the Bloom filter and the expected number of inserted elements.
getLabel(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
fetches the rdfs:label for an OWLObject assumes zero or one rdfs:label
getLabel() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
 
getLabel() - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
getLabel() - Method in class owltools.phenolog.Attribute
 
getlabel() - Method in class owltools.phenolog.GenePheno
 
getLabel() - Method in class owltools.phenolog.Individual
 
getLabel() - Method in class owltools.phenolog.Pheno
 
getLabelOrDisplayId(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getLastQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
 
getLastUpdateDate() - Method in class owltools.gaf.GeneAnnotation
 
getLCS() - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
getLeastCommonSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
note that this performs caching by default
getLeastCommonSubsumerSimpleClassExpression(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getLeastCommonSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getLineNumber() - Method in class owltools.gaf.AnnotationSource
 
getLineNumber() - Method in class owltools.gaf.GAFParser
 
getMacroStrategy() - Method in class owltools.ontologyrelease.OortConfiguration
 
getManager() - Method in class owltools.graph.OWLGraphWrapper
 
getManager() - Method in class owltools.io.ParserWrapper
 
getManager() - Method in class owltools.mooncat.Mooncat
 
getMappingSource() - Method in class owltools.gaf.IdMapping
 
getMaxCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
 
getMaxHits() - Method in class owltools.sim.SimSearch
 
getMember1() - Method in class owltools.phenolog.IndividualPair
 
getMember2() - Method in class owltools.phenolog.IndividualPair
 
getMessage() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
getMessages() - Method in class owltools.ontologyverification.CheckResult
 
getMinCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
 
getNamedAncestors(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Gets all ancestors that are OWLNamedObjects i.e.
getNamedAncestorsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getNamespace(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the OBO-namespace tag Example: if the OWLObject is the GO class GO:0008150, this would return "biological_process"
getNcbiTaxonId() - Method in class owltools.gaf.Bioentity
 
getNextSplitDocument() - Method in class owltools.gaf.GafObjectsBuilder
when this variable reaches at splitSize then the algorithm in the getNextSplitDocument method stops calling next method of the GafParser and return the GafDocument object build with the number of rows
getNode(OWLObject) - Method in class owltools.gfx.OWLGraphLayoutRenderer
fetch a layout node via the cognate OWLObject make private?
getNonTCIndividualSize() - Method in class owltools.phenolog.Pheno
 
getObjectPropertyDomains(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getObjectPropertyDomains(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getObjectPropertyRanges(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getObjectPropertyRanges(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getObjectPropertyValues(OWLNamedIndividual, OWLObjectPropertyExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getObjectPropertyValues(OWLNamedIndividual, OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
 
GetObjectsTest - Class in owltools.test
Tests the various wrapper get* methods in OWLGraphWrapper
GetObjectsTest() - Constructor for class owltools.test.GetObjectsTest
 
getOBOdoc() - Method in class owltools.io.ParserWrapper
 
getOboInOWLVersion(OWLOntology) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Retrieve the ontology version from the OboInOwl remark.
getOboInOWLVersionDate(OWLOntology) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Retrieve the ontology version from the OboInOwl remark and parse as Date.
getobolink() - Method in class owltools.phenolog.PhenoTransitiveClosure
 
getOBOSynonyms(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns array of synonyms as encoded by OBO2OWL.
getOntology() - Method in class owltools.graph.OWLGraphEdge
 
getOntology() - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
getOntology() - Method in class owltools.mooncat.Mooncat
 
getOntologyId() - Method in class owltools.graph.OWLGraphWrapper
gets the OBO-style ID of the source ontology IRI.
GetOntologyId - Class in owltools.ontologyrelease
Deprecated. 
GetOntologyId() - Constructor for class owltools.ontologyrelease.GetOntologyId
Deprecated.  
getOntologyVersion(OWLOntology) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Retrieve the ontology version as string.
getOntologyVersionDate(OWLOntology) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Retrieve the ontology version as Date.
getOntologyVersionIRI(OWLOntology) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Retrieve the ontology version as IRI.
getOntologyWrapper(String) - Method in class owltools.sim.test.AsbtractSimEngineTest
 
getOntologyWrapperFromURL(String) - Method in class owltools.sim.test.AsbtractSimEngineTest
 
getOrthologs() - Method in class owltools.phenolog.Individual
 
getOutgoingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
retrieves direct edges from a source to the direct **named** target e.g.
getOutgoingEdges(OWLObject, boolean, boolean) - Method in class owltools.graph.OWLGraphWrapper
 
getOutgoingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Retrieves the graph closure originating from source.
getOutgoingEdgesClosureReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
as getOutgoingEdgesClosure(s), but also includes an identity edge
getOutgoingEdgesCommand() - Method in class owltools.web.OWLHandler
 
getOWLClass(String) - Method in class owltools.gaf.inference.CompositionalClassPredictor
 
getOWLClass(String) - Method in class owltools.graph.OWLGraphWrapper
Returns an OWLClass given an IRI string the class must be declared in either the source ontology, or in a support ontology, otherwise null is returned
getOWLClass(IRI) - Method in class owltools.graph.OWLGraphWrapper
Returns an OWLClass given an IRI the class must be declared in either the source ontology, or in a support ontology, otherwise null is returned
getOWLClass(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getOWLClassByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapper
Given an OBO-style ID, return the corresponding OWLClass, if it is declared - otherwise null
getOWLClassesInSubset(String) - Method in class owltools.graph.OWLGraphWrapper
given a subset name, find all OWLClasses assigned to that subset
getOWLGraphWrapper() - Method in class owltools.InferenceBuilder
 
getOWLIndividual(IRI) - Method in class owltools.graph.OWLGraphWrapper
Returns an OWLNamedIndividual with this IRI if it has been declared in the source or support ontologies.
getOWLIndividual(String) - Method in class owltools.graph.OWLGraphWrapper
 
getOWLIndividualByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapper
Given an OBO-style ID, return the corresponding OWLNamedIndividual, if it is declared - otherwise null
getOwlObject() - Method in class owltools.gfx.OWLGraphLayoutNode
 
getOWLObject(String) - Method in class owltools.graph.OWLGraphWrapper
Returns the OWLObject with this IRI (where IRI is specified as a string - e.g http://purl.obolibrary.org/obo/GO_0008150)
getOWLObjectByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapper
Given an OBO-style ID, return the corresponding OWLObject, if it is declared - otherwise null
getOWLObjectByLabel(String) - Method in class owltools.graph.OWLGraphWrapper
fetches an OWL Object by rdfs:label if there is >1 match, return the first one encountered
getOWLObjectProperty(String) - Method in class owltools.graph.OWLGraphWrapper
Returns the OWLObjectProperty with this IRI Must have been declared in one of the ontologies
getOWLObjectProperty(IRI) - Method in class owltools.graph.OWLGraphWrapper
 
getOWLObjectPropertyByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapper
Given an OBO-style ID, return the corresponding OWLObjectProperty, if it is declared - otherwise null
getOWLObjectsInSubset(String) - Method in class owltools.graph.OWLGraphWrapper
given a subset name, find all OWLObjects (typically OWLClasses) assigned to that subset
getOwlXMLFormat() - Method in class owltools.ontologyrelease.OortConfiguration
 
getParser() - Method in class owltools.gaf.GafObjectsBuilder
 
getPaths() - Method in class owltools.ontologyrelease.OortConfiguration
 
getPendingAxiomAdditions() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getPendingAxiomRemovals() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getPendingChanges() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getpermutedgenes(int, int, ArrayList<Individual>) - Static method in class owltools.phenolog.Main
 
getphenoid() - Method in class owltools.phenolog.GenePheno
 
getphenolabel() - Method in class owltools.phenolog.GenePheno
 
getPrecomputableInferenceTypes() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getPrecomputableInferenceTypes() - Method in class owltools.reasoner.GraphReasoner
 
getPrediction(OWLClass, String, String) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
 
getPrediction(OWLClass, String, String) - Method in class owltools.gaf.inference.CompositionalClassPredictor
 
getprefix() - Method in class owltools.phenolog.PhenoTransitiveClosure
 
getPreSimMethod() - Method in class owltools.sim.MultiSimilarity
 
getPrimitiveOutgoingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
primitive edges connect any combination of named objects and expressions e.g.
getProfiler() - Method in class owltools.graph.OWLGraphWrapper
 
getProperty() - Method in class owltools.graph.OWLQuantifiedProperty
 
getPropertyId() - Method in class owltools.graph.OWLQuantifiedProperty
 
getQualifier() - Method in class owltools.gaf.GAFParser
 
getQualifierObj() - Method in class owltools.gaf.CompositeQualifier
 
getQuantifiedPropertyList() - Method in class owltools.graph.OWLGraphEdge
 
getQuantifier() - Method in class owltools.graph.OWLQuantifiedProperty
 
getRange(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the range tag
getReasoner() - Method in class owltools.graph.OWLGraphWrapper
 
getReasoner(String) - Method in class owltools.web.OWLServer
 
getReasonerName() - Method in class owltools.ontologyrelease.OortConfiguration
 
getReasonerName() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getReasonerName() - Method in class owltools.reasoner.GraphReasoner
 
getReasonerName() - Method in class owltools.reasoner.GraphReasonerFactory
 
getReasonerName() - Method in class owltools.reasoner.PlaceholderJcelFactory
 
getReasonerVersion() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getReasonerVersion() - Method in class owltools.reasoner.GraphReasoner
 
getReasons() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
getRedundantAxioms() - Method in class owltools.InferenceBuilder
 
getReference() - Method in class owltools.gaf.GAFParser
 
getReferencedOntologies() - Method in class owltools.mooncat.Mooncat
delegates to OWLGraphWrapper support ontologies
getReferenceId() - Method in class owltools.gaf.GeneAnnotation
 
getRelation() - Method in class owltools.gaf.ExtensionExpression
 
getRelationship() - Method in class owltools.gaf.IdMapping
 
getReplacedBy(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the replaced_by tag or IAO_0100001 annotation.
getResource(String) - Method in class owltools.test.OWLToolsTestBasics
 
getResourceIRI(String) - Method in class owltools.test.OWLToolsTestBasics
 
getResourceIRIString(String) - Method in class owltools.test.OWLToolsTestBasics
 
getRootOntology() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getRow() - Method in class owltools.gaf.AnnotationSource
 
getSameIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSameIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.GraphReasoner
 
getScope() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
 
getScope() - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
getScore() - Method in class owltools.sim.Similarity
 
getShortForm(OWLEntity) - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
 
getSimEngine() - Method in class owltools.sim.SimSearch
 
getSimilarityAlgorithm(String) - Method in class owltools.sim.SimEngine
factory class for generating a Similarity instance based on its name
getSimilarityAlgorithm(Class) - Method in class owltools.sim.SimEngine
 
getSingleQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
 
getSource() - Method in class owltools.gaf.GeneAnnotation
 
getSource() - Method in class owltools.graph.OWLGraphEdge
 
getSourceId() - Method in class owltools.gaf.IdMapping
 
getSourceId() - Method in class owltools.graph.OWLGraphEdge
 
getSourceOntology() - Method in class owltools.graph.OWLGraphWrapper
Every OWLGraphWrapper objects wraps zero or one source ontologies.
getSourceOntologyPrefixes() - Method in class owltools.mooncat.Mooncat
E.g.
getSourceOntologyPrefixes() - Method in class owltools.ontologyrelease.OortConfiguration
 
getSplitSize() - Method in class owltools.gaf.GafObjectsBuilder
 
getStatus() - Method in class owltools.ontologyverification.CheckResult
 
getStream() - Method in class owltools.io.AbstractClosureReader
 
getStream() - Method in class owltools.io.AbstractClosureRenderer
 
getSubClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSubClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSubClassesNames(OWLClass) - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
getSubDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSubDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSubObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSubObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSubsets(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the subset tag.
getSubSimMethod() - Method in class owltools.sim.MultiSimilarity
 
getSubsumersFromClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
find the set of classes or class expressions subsuming source, using the graph closure.
getSuperClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSuperClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSuperClassesCommand() - Method in class owltools.web.OWLHandler
 
getSuperClassExpressions(OWLClassExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
note that this is not a standard reasoner method
getSuperClassExpressions(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
note that this is not a standard reasoner method
getSuperClassExpressions(OWLClassExpression, boolean) - Method in interface owltools.reasoner.OWLExtendedReasoner
 
getSuperDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSuperDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSuperObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSuperObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSuperPropertiesOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapper
returns parent properties of p in all ontologies
getSupportOntologySet() - Method in class owltools.graph.OWLGraphWrapper
all operations are over a set of ontologies - the source ontology plus any number of supporting ontologies.
getSymbol() - Method in class owltools.gaf.Bioentity
 
getSynonymStrings(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
getTarget() - Method in class owltools.graph.OWLGraphEdge
 
getTargetId() - Method in class owltools.gaf.IdMapping
 
getTargetId() - Method in class owltools.graph.OWLGraphEdge
 
getTaxon() - Method in class owltools.gaf.GAFParser
 
getTimeOut() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getTopClassNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getTopClassNode() - Method in class owltools.reasoner.GraphReasoner
 
getTopDataPropertyNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getTopDataPropertyNode() - Method in class owltools.reasoner.GraphReasoner
 
getTopObjectPropertyNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getTopObjectPropertyNode() - Method in class owltools.reasoner.GraphReasoner
 
getTypeCls() - Method in class owltools.gaf.Bioentity
 
getTypes(OWLNamedIndividual, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getTypes(OWLNamedIndividual, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getUnionSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getUnionSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getUnsatisfiableClasses() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getUnsatisfiableClasses() - Method in class owltools.reasoner.GraphReasoner
 
getWidth() - Method in class owltools.gfx.OWLGraphLayoutNode
 
getWith() - Method in class owltools.gaf.GAFParser
 
getWithExpression() - Method in class owltools.gaf.GeneAnnotation
 
getWithInfos(String) - Method in class owltools.gaf.GafDocument
 
getWithInfos() - Method in class owltools.gaf.GeneAnnotation
 
getWithInfosIds() - Method in class owltools.gaf.GafDocument
 
getWithXref() - Method in class owltools.gaf.WithInfo
 
getWrappedReasoner() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getXref(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
get the values of of the obo xref tag
getXrefs() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
 
getXrefs() - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
GOID - Static variable in class owltools.gaf.GAFParser
 
graph - Variable in class owltools.io.AbstractClosureRenderer
 
graph - Variable in class owltools.io.TableToAxiomConverter
 
graph - Variable in class owltools.sim.SimEngine
 
graph - Variable in class owltools.solrj.AbstractSolrLoader
 
GraphClosureRenderer - Class in owltools.io
 
GraphClosureRenderer(PrintStream) - Constructor for class owltools.io.GraphClosureRenderer
 
GraphClosureRenderer(String) - Constructor for class owltools.io.GraphClosureRenderer
 
graphEdgeExcludeSet - Variable in class owltools.graph.OWLGraphWrapper.Config
 
graphEdgeIncludeSet - Variable in class owltools.graph.OWLGraphWrapper.Config
 
GraphicsConfig - Class in owltools.gfx
 
GraphicsConfig() - Constructor for class owltools.gfx.GraphicsConfig
 
graphicsConfig - Variable in class owltools.gfx.OWLGraphLayoutRenderer
 
GraphicsConfig.RelationConfig - Class in owltools.gfx
 
GraphicsConfig.RelationConfig() - Constructor for class owltools.gfx.GraphicsConfig.RelationConfig
 
GraphImportsClosureTest - Class in owltools.graph.test
 
GraphImportsClosureTest() - Constructor for class owltools.graph.test.GraphImportsClosureTest
 
GraphReader - Interface in owltools.io
 
GraphReasoner - Class in owltools.reasoner
incomplete.
GraphReasoner(OWLOntology, OWLReasonerConfiguration, BufferingMode) - Constructor for class owltools.reasoner.GraphReasoner
 
GraphReasonerFactory - Class in owltools.reasoner
 
GraphReasonerFactory() - Constructor for class owltools.reasoner.GraphReasonerFactory
 
GraphRenderer - Interface in owltools.io
 
GraphStyle - Class in owltools.gfx
hacked crudely from QuickGO
GraphStyle() - Constructor for class owltools.gfx.GraphStyle
 
GraphStyle(Map<String, String>) - Constructor for class owltools.gfx.GraphStyle
 

H

handle(String, Request, HttpServletRequest, HttpServletResponse) - Method in class owltools.web.OWLServer
 
handleChanges(Set<OWLAxiom>, Set<OWLAxiom>) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
handleChanges(Set<OWLAxiom>, Set<OWLAxiom>) - Method in class owltools.reasoner.GraphReasoner
 
handleConflict(OWLEntity, OWLAnnotationProperty, Collection<OWLAnnotationAssertionAxiom>) - Method in interface owltools.mooncat.OntologyMetaDataTools.AnnotationCardinalityConfictHandler
Resolve a conflict for a given annotation property and axioms.
handler - Variable in class owltools.idmap.IDMappingPIRParser
 
hasArgs() - Method in class owltools.cli.CommandRunner.Opts
 
hashCode() - Method in class owltools.graph.OWLGraphEdge
 
hashCode() - Method in class owltools.phenolog.GenePheno
 
hashCode() - Method in class owltools.phenolog.Individual
 
hashCode() - Method in class owltools.phenolog.IndividualPair
 
hashCode() - Method in class owltools.phenolog.Pheno
 
hashCode() - Method in class owltools.sim.OWLObjectPair
 
hashCode() - Method in class owltools.util.BloomFilter
Calculates a hash code for this class.
hasInformationContent(OWLObject) - Method in class owltools.sim.SimEngine
 
hasOpt(String) - Method in class owltools.cli.CommandRunner.Opts
 
hasOpts() - Method in class owltools.cli.CommandRunner.Opts
 
hasProperty() - Method in class owltools.graph.OWLQuantifiedProperty
 
headerHTML() - Method in class owltools.web.OWLHandler
 
headerImage(String) - Method in class owltools.web.OWLHandler
 
headerOWL() - Method in class owltools.web.OWLHandler
 
headerText() - Method in class owltools.web.OWLHandler
 
height - Variable in class owltools.gfx.GraphStyle
 
height - Variable in class owltools.gfx.OWLGraphLayoutNode
 
help() - Method in class owltools.cli.CommandRunner
 
help() - Static method in class owltools.cli.CopyOfCommandLineInterface
 
helpCommand() - Method in class owltools.web.OWLHandler
 
helpFooter() - Method in class owltools.cli.CommandRunner
 
helpFooter() - Static method in class owltools.cli.CopyOfCommandLineInterface
 
hideIds() - Method in class owltools.io.OWLPrettyPrinter
 

I

id - Variable in class owltools.gaf.Bioentity
 
id - Variable in class owltools.gaf.CompositeQualifier
 
id - Variable in class owltools.gaf.ExtensionExpression
 
id - Variable in class owltools.gaf.GafDocument
 
id - Variable in class owltools.gaf.WithInfo
 
id - Variable in class owltools.gfx.OWLGraphLayoutNode
 
idColour - Variable in class owltools.gfx.OWLGraphLayoutNode
 
idMap - Variable in class owltools.idmap.UniProtIDMapParser
 
IDMapHandler - Class in owltools.idmap
 
IDMapHandler() - Constructor for class owltools.idmap.IDMapHandler
 
IDMapPairWriter - Class in owltools.idmap
 
IDMapPairWriter() - Constructor for class owltools.idmap.IDMapPairWriter
 
IdMapping - Class in owltools.gaf
 
IdMapping() - Constructor for class owltools.gaf.IdMapping
 
IdMapping(String, String, String, String) - Constructor for class owltools.gaf.IdMapping
 
IDMappingPIRParser - Class in owltools.idmap
Parses the IDMapping file available here: ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz
IDMappingPIRParser() - Constructor for class owltools.idmap.IDMappingPIRParser
 
IDMappingPIRParser.Types - Enum in owltools.idmap
 
idTypes - Variable in class owltools.idmap.UniProtIDMapParser
 
ImportPropertyMooncatTest - Class in owltools.mooncat.test
Tests for the detection of import properties during mireot with Mooncat.
ImportPropertyMooncatTest() - Constructor for class owltools.mooncat.test.ImportPropertyMooncatTest
 
ImportTest - Class in owltools.gfx.test
 
ImportTest() - Constructor for class owltools.gfx.test.ImportTest
 
index() - Method in class owltools.gaf.GafDocument
 
Individual - Class in owltools.phenolog
represents an attribute-bearing entity; for example, a gene.
Individual(String, String, Set<Attribute>) - Constructor for class owltools.phenolog.Individual
 
Individual(String, Set<Attribute>) - Constructor for class owltools.phenolog.Individual
 
Individual(String, String) - Constructor for class owltools.phenolog.Individual
 
Individual(String, String, int) - Constructor for class owltools.phenolog.Individual
 
Individual(String) - Constructor for class owltools.phenolog.Individual
 
IndividualPair - Class in owltools.phenolog
 
IndividualPair() - Constructor for class owltools.phenolog.IndividualPair
 
IndividualPair(Individual, Individual) - Constructor for class owltools.phenolog.IndividualPair
 
individualsType - Variable in class owltools.io.TableToAxiomConverter.Config
 
InferenceBuilder - Class in owltools
This class build inferred axioms of an ontology.
InferenceBuilder(OWLGraphWrapper) - Constructor for class owltools.InferenceBuilder
 
InferenceBuilder(OWLGraphWrapper, String) - Constructor for class owltools.InferenceBuilder
 
InferenceBuilder(OWLGraphWrapper, String, boolean) - Constructor for class owltools.InferenceBuilder
 
InferenceBuilder(OWLGraphWrapper, OWLReasonerFactory, boolean) - Constructor for class owltools.InferenceBuilder
 
inferredEdgeBySource - Variable in class owltools.graph.OWLGraphWrapper
 
info(String, String) - Method in class owltools.cli.CommandRunner.Opts
 
info(String) - Method in class owltools.web.OWLHandler
 
init() - Method in class owltools.gaf.GAFParser
 
init() - Method in class owltools.idmap.IDMapHandler
 
init() - Method in class owltools.idmap.IDMapPairWriter
 
interrupt() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
interrupt() - Method in class owltools.reasoner.GraphReasoner
 
intersection(Collection<E>) - Method in class owltools.util.BloomFilter
 
iriPrefixMap - Variable in class owltools.io.TableToAxiomConverter.Config
 
isAboveMinScore() - Method in class owltools.sim.Similarity
 
isAllowEquivalentNamedClassPairs() - Method in class owltools.ontologyrelease.OortConfiguration
 
isAllowFileOverWrite() - Method in class owltools.ontologyrelease.OortConfiguration
 
isAllValuesFrom() - Method in class owltools.graph.OWLQuantifiedProperty
 
isAsserted() - Method in class owltools.ontologyrelease.OortConfiguration
 
isAutoDetectBridgingOntology() - Method in class owltools.ontologyrelease.OortConfiguration
 
isCacheClosure - Variable in class owltools.graph.OWLGraphWrapper.Config
 
isCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
 
isChain - Variable in class owltools.io.ChadoGraphClosureRenderer
 
isChanged - Variable in class owltools.gaf.GeneAnnotation
If value of this variable is true then toString is re-calculated
isCheckConsistency() - Method in class owltools.ontologyrelease.OortConfiguration
 
isClassApplicable(String, String) - Method in class owltools.gaf.inference.TaxonConstraintsEngine
 
isClassApplicable(OWLClass, OWLClass) - Method in class owltools.gaf.inference.TaxonConstraintsEngine
returns true if testOntologyCls is applicable for testTax
isClassApplicable(OWLClass, OWLClass, Set<OWLGraphEdge>, Set<OWLObject>) - Method in class owltools.gaf.inference.TaxonConstraintsEngine
 
isClassApplicableForTaxonCommand() - Method in class owltools.web.OWLHandler
tests which of a set of input classes (specified using id) is applicable for a set of taxa (specified using taxid)
isConsistent() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isConsistent() - Method in class owltools.reasoner.GraphReasoner
 
isContributesTo - Variable in class owltools.gaf.GeneAnnotation
 
isDangling(OWLOntology, OWLEntity) - Method in class owltools.mooncat.Mooncat
Here a dangling entity is one that has no annotation assertions; this is not a perfect test, as conceivable a class could lack assertions; however, this would not be the case for any ontology following obo library principles.
isDeprecated(OWLClass, OWLOntology, OWLAnnotationProperty) - Method in class owltools.ontologyrelease.OntologyMetadata
 
isDocumentSplitted() - Method in class owltools.gaf.GafObjectsBuilder
 
isEnforceEL() - Method in class owltools.ontologyrelease.OortConfiguration
 
isEntailed(OWLAxiom) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isEntailed(Set<? extends OWLAxiom>) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isEntailed(OWLAxiom) - Method in class owltools.reasoner.GraphReasoner
 
isEntailed(Set<? extends OWLAxiom>) - Method in class owltools.reasoner.GraphReasoner
 
isEntailmentCheckingSupported(AxiomType<?>) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isEntailmentCheckingSupported(AxiomType<?>) - Method in class owltools.reasoner.GraphReasoner
 
isEq(Object, Object) - Method in class owltools.graph.OWLGraphEdge
 
isExcludedFromAnalysis(OWLObject) - Method in class owltools.sim.SimEngine
A class is excluded from the analysis if: it is a named entity, and the label for that entity matches the exclude labels list OR: it is a class expression, and the signature contains an excluded class
isExecuteOntologyChecks() - Method in class owltools.ontologyrelease.OortConfiguration
 
isExpandMacros() - Method in class owltools.ontologyrelease.OortConfiguration
 
isExpandShortcutRelations() - Method in class owltools.ontologyrelease.OortConfiguration
 
isExpandXrefs() - Method in class owltools.ontologyrelease.OortConfiguration
 
isFollowComplementOfInClosure - Variable in class owltools.graph.OWLGraphWrapper.Config
 
isForceRelease() - Method in class owltools.ontologyrelease.OortConfiguration
 
isHasValue() - Method in class owltools.graph.OWLQuantifiedProperty
 
isIdentity() - Method in class owltools.graph.OWLQuantifiedProperty
 
isImportMarkedEntity(OWLNamedObject, OWLOntology) - Static method in class owltools.mooncat.Mooncat
Check, if the named object has the annotation property IAO:0000412, declaring the object as imported.
isIncludeClassExpressionsInClosure - Variable in class owltools.graph.OWLGraphWrapper.Config
 
isInferred() - Method in class owltools.graph.OWLQuantifiedProperty
 
isInstanceOf() - Method in class owltools.graph.OWLQuantifiedProperty
 
isIntegralTo - Variable in class owltools.gaf.GeneAnnotation
 
isInverseOf() - Method in class owltools.graph.OWLQuantifiedProperty
 
isJustifyAssertedSubclasses() - Method in class owltools.ontologyrelease.OortConfiguration
 
isMonitorMemory - Variable in class owltools.graph.OWLGraphWrapper.Config
 
isOboIdentifiers - Variable in class owltools.io.TableToAxiomConverter.Config
 
isOBOOntologyVersion(String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Check, whether the given version string is an OBO-specific IRI.
isObsolete(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
tests if an OWLObject has been declared obsolete in the source ontology
isPrecomputed(InferenceType) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isPrecomputed(InferenceType) - Method in class owltools.reasoner.GraphReasoner
 
isPropertyAssertion() - Method in class owltools.graph.OWLQuantifiedProperty
 
isQuantified() - Method in class owltools.graph.OWLQuantifiedProperty
 
isRecreateMireot() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRedundantWithExistingAnnotations() - Method in class owltools.gaf.inference.Prediction
 
isRedundantWithOtherPredictions() - Method in class owltools.gaf.inference.Prediction
 
isRepairAnnotationCardinality() - Method in class owltools.ontologyrelease.OortConfiguration
 
isSatisfiable(OWLClassExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isSatisfiable(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
 
isSimple() - Method in class owltools.ontologyrelease.OortConfiguration
 
isSomeValuesFrom() - Method in class owltools.graph.OWLQuantifiedProperty
 
isSourceNamedObject() - Method in class owltools.graph.OWLGraphEdge
 
isSubClassOf() - Method in class owltools.graph.OWLQuantifiedProperty
 
isSwitchSubjectObject - Variable in class owltools.io.TableToAxiomConverter.Config
 
isTargetNamedObject() - Method in class owltools.graph.OWLGraphEdge
 
isWriteELOntology() - Method in class owltools.ontologyrelease.OortConfiguration
 
isWriteMetadata() - Method in class owltools.ontologyrelease.OortConfiguration
 
isWriteSubsets() - Method in class owltools.ontologyrelease.OortConfiguration
 

J

JaccardBloomSimilarity - Class in owltools.sim
 
JaccardBloomSimilarity() - Constructor for class owltools.sim.JaccardBloomSimilarity
 
JaccardSimilarity - Class in owltools.sim
 
JaccardSimilarity() - Constructor for class owltools.sim.JaccardSimilarity
 
JSONPrinter - Class in owltools.io
Deprecated. 
JSONPrinter(PrintWriter) - Constructor for class owltools.io.JSONPrinter
Deprecated.  

K

key - Variable in class owltools.gfx.GraphStyle
 

L

label - Variable in class owltools.gfx.OWLGraphLayoutNode
 
label(OWLObject) - Method in class owltools.sim.SimEngine
 
lastUpdateDate - Variable in class owltools.gaf.GeneAnnotation
 
lcsExpressionCommand() - Method in class owltools.web.OWLHandler
 
lcsIntersectionSet - Variable in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
LCSTestCARO - Class in owltools.test
 
LCSTestCARO() - Constructor for class owltools.test.LCSTestCARO
 
left() - Method in class owltools.gfx.OWLGraphLayoutNode
 
left - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
line - Variable in class owltools.gfx.OWLGraphLayoutNode
 
lineNumber - Variable in class owltools.idmap.AbstractMappingParser
 
load() - Method in class owltools.solrj.AbstractSolrLoader
 
load() - Method in class owltools.solrj.GafSolrDocumentLoader
 
load() - Method in class owltools.solrj.OntologySolrLoader
 
loadConfig(File, OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration
Load the configuration from a property file into the given OortConfiguration.
loadOortConfig(Properties, OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration
Load the given Properties into the OortConfiguration.
LOG - Static variable in class owltools.gaf.GAFParser
 
LOG - Static variable in class owltools.gaf.inference.AbstractAnnotationPredictor
 
LOG - Static variable in class owltools.gaf.inference.BasicAnnotationPropagator
 
LOG - Static variable in class owltools.gaf.inference.CompositionalClassPredictor
 
LOG - Static variable in class owltools.gaf.inference.TaxonConstraintsEngine
 
log(StringBuilder, Level) - Method in class owltools.ontologyverification.OntologyCheckHandler
 
logger - Static variable in class owltools.InferenceBuilder
 
logger - Static variable in class owltools.ontologyrelease.OboOntologyReleaseRunner
 
logger - Static variable in class owltools.OWLReasonerRunner
 

M

main(String[]) - Static method in class owltools.cli.CommandLineInterface
 
main(String[]) - Static method in class owltools.cli.CopyOfCommandLineInterface
 
main(String[]) - Static method in class owltools.gfx.GraphStyle
 
main(String[]) - Static method in class owltools.gfx.SampleGraphDraw
 
main(String[]) - Static method in class owltools.io.OWLGsonRenderer
 
main(String[]) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunner
 
main(String[]) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
 
main(String[]) - Static method in class owltools.OWLReasonerRunner
 
Main - Class in owltools.phenolog
Author : Neeral Beladia Date Created : September 5, 2010 Class Purpose : The Main Class is the kickoff Class consisting of Main() method Methods : Main() printhash() Program Logic : 1.
Main() - Constructor for class owltools.phenolog.Main
 
main(String[]) - Static method in class owltools.phenolog.Main
 
makeEdge(OWLGraphEdge) - Method in class owltools.gfx.OWLGraphLayoutRenderer
Make a layout edge from a OWLGraphEdge make private?
makeIntersectionPair(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.SimEngine
 
makeNonRedundant(Set<OWLObject>) - Method in class owltools.sim.SimEngine
An object x is redundant with a set S if: there exists an element y of S, such that ymakeNonRedundant(Set<OWLObject>, boolean) - Method in class owltools.sim.SimEngine
 
makeSubsetOntology(Set<OWLClass>, IRI) - Method in class owltools.mooncat.Mooncat
Given a set of classes (e.g.
makeSubsetOntologyCommand() - Method in class owltools.web.OWLHandler
generates a sub-ontology consisting only of classes specified using the id param.
makeUnionPair(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.SimEngine
 
mappingSource - Variable in class owltools.gaf.IdMapping
 
materializeExpressions(OWLOntology) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
materializeExpressions() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
maxDepthChain - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
maxDepthTotal - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
maxHits - Variable in class owltools.sim.SimSearch
 
MaximumInformationContentSimilarity - Class in owltools.sim
 
MaximumInformationContentSimilarity() - Constructor for class owltools.sim.MaximumInformationContentSimilarity
 
mergeIntoReferenceOntology(OWLOntology) - Method in class owltools.mooncat.Mooncat
 
mergeOntologies() - Method in class owltools.mooncat.Mooncat
merge minimal subset of referenced ontologies into the source ontology.
mergeOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
Adds all axioms from extOnt into source ontology
minIC - Variable in class owltools.sim.SimSearch
 
minimumIC - Variable in class owltools.sim.SimEngine
 
minScore - Variable in class owltools.sim.Similarity
 
minScore - Variable in class owltools.sim.SimSearch
 
MireotTest2 - Class in owltools.mooncat.test
 
MireotTest2() - Constructor for class owltools.mooncat.test.MireotTest2
 
MireotTest3 - Class in owltools.mooncat.test
 
MireotTest3() - Constructor for class owltools.mooncat.test.MireotTest3
 
Mooncat - Class in owltools.mooncat
Given one source ontology referencing one or more referenced ontologies (e.g.
Mooncat(OWLOntologyManager, OWLDataFactory, OWLOntology) - Constructor for class owltools.mooncat.Mooncat
 
Mooncat(OWLGraphWrapper) - Constructor for class owltools.mooncat.Mooncat
 
MooncatTest - Class in owltools.mooncat.test
 
MooncatTest() - Constructor for class owltools.mooncat.test.MooncatTest
 
MPClosureTest - Class in owltools.test
 
MPClosureTest() - Constructor for class owltools.test.MPClosureTest
 
MPVizTest - Class in owltools.gfx.test
 
MPVizTest() - Constructor for class owltools.gfx.test.MPVizTest
 
MultiSimilarity - Class in owltools.sim
This is the standard method to use when comparing entities with multiple attributes.
MultiSimilarity() - Constructor for class owltools.sim.MultiSimilarity
 

N

ncbiTaxonId - Variable in class owltools.gaf.Bioentity
 
next() - Method in class owltools.gaf.GAFParser
Method declaration
next() - Method in class owltools.idmap.IDMappingPIRParser
 
nextArgIsHelp() - Method in class owltools.cli.CommandRunner.Opts
 
nextEq(String) - Method in class owltools.cli.CommandRunner.Opts
 
nextEq(Collection<String>) - Method in class owltools.cli.CommandRunner.Opts
 
nextList() - Method in class owltools.cli.CommandRunner.Opts
 
nextOpt() - Method in class owltools.cli.CommandRunner.Opts
 
nl() - Method in class owltools.io.AbstractClosureRenderer
 
nonSignificantObjects() - Method in class owltools.sim.SimEngine
 

O

OboOntologyReleaseRunner - Class in owltools.ontologyrelease
This class is a command line utility which builds an ontology release.
OboOntologyReleaseRunner(OortConfiguration, File) - Constructor for class owltools.ontologyrelease.OboOntologyReleaseRunner
 
OboOntologyReleaseRunnerCheckException - Exception in owltools.ontologyrelease
OORT Exception indicating a failed check during the release process.
OboOntologyReleaseRunnerCheckException(String) - Constructor for exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
OboOntologyReleaseRunnerCheckException(String, List<String>) - Constructor for exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
OboOntologyReleaseRunnerCheckException(String, List<String>, String) - Constructor for exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
OboOntologyReleaseRunnerGui - Class in owltools.ontologyrelease
GUI access for ontology release runner.
OboOntologyReleaseRunnerGui() - Constructor for class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
 
OboProperty - Class in owltools.ontologyrelease
Deprecated. 
OboProperty() - Constructor for class owltools.ontologyrelease.OboProperty
Deprecated.  
OboProperty(boolean, Project) - Constructor for class owltools.ontologyrelease.OboProperty
Deprecated.  
OboProperty(boolean) - Constructor for class owltools.ontologyrelease.OboProperty
Deprecated.  
OntologyCheckHandler - Class in owltools.ontologyverification
Handle the ontology checks for an ontology and its reporting via a Logger.
OntologyCheckHandler(boolean, Class<?>...) - Constructor for class owltools.ontologyverification.OntologyCheckHandler
Create a new instance.
OntologyCheckRunner - Class in owltools.ontologyverification
Identify and run ontology checks for an ontology (OWLGraphWrapper).
OntologyCheckRunnerTest - Class in owltools.ontologyverification
Tests for OntologyCheckRunner.
OntologyCheckRunnerTest() - Constructor for class owltools.ontologyverification.OntologyCheckRunnerTest
 
OntologyMetadata - Class in owltools.ontologyrelease
 
OntologyMetadata(PrintWriter) - Constructor for class owltools.ontologyrelease.OntologyMetadata
 
OntologyMetadata() - Constructor for class owltools.ontologyrelease.OntologyMetadata
 
OntologyMetadata.MetadataField - Enum in owltools.ontologyrelease
 
OntologyMetadata.MetadataQualifier - Enum in owltools.ontologyrelease
 
OntologyMetaDataTools - Class in owltools.mooncat
Tools for checking and managing ontology data.
OntologyMetaDataTools() - Constructor for class owltools.mooncat.OntologyMetaDataTools
 
OntologyMetaDataTools.AnnotationCardinalityConfictHandler - Interface in owltools.mooncat
Functor for resolving conflicts for an annotation property and its cardinality constraint.
OntologyMetaDataTools.AnnotationCardinalityException - Exception in owltools.mooncat
Exception indication a non-resolvable conflict for an annotation property and its cardinality constraint.
OntologyMetaDataTools.AnnotationCardinalityException(String, Throwable) - Constructor for exception owltools.mooncat.OntologyMetaDataTools.AnnotationCardinalityException
Create a new Exception.
OntologyMetaDataTools.AnnotationCardinalityException(String) - Constructor for exception owltools.mooncat.OntologyMetaDataTools.AnnotationCardinalityException
Create a new Exception.
OntologySolrLoader - Class in owltools.solrj
 
OntologySolrLoader(String) - Constructor for class owltools.solrj.OntologySolrLoader
 
OntologyVersionTools - Class in owltools.ontologyrelease
Tools to handle the writing and reading of version information of owl ontology files.
OortConfiguration - Class in owltools.ontologyrelease
Parameters for OboOntologyReleaseRunner.
OortConfiguration() - Constructor for class owltools.ontologyrelease.OortConfiguration
 
OortConfiguration.MacroStrategy - Enum in owltools.ontologyrelease
 
OortConfigurationTest - Class in owltools.ontologyrelease.test
Tests for OortConfiguration.
OortConfigurationTest() - Constructor for class owltools.ontologyrelease.test.OortConfigurationTest
 
OortGuiAdvancedPanel - Class in owltools.ontologyrelease.gui
Panel containing advanced options for the release manager.
OortGuiAdvancedPanel(OortConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiAdvancedPanel
Create the panel with the given default values.
OortGuiConfiguration - Class in owltools.ontologyrelease.gui
Parameters for OboOntologyReleaseRunnerGui with different default values.
OortGuiConfiguration() - Constructor for class owltools.ontologyrelease.gui.OortGuiConfiguration
 
OortGuiMainFrame - Class in owltools.ontologyrelease.gui
GUI main frame, calls all constructors for the sub components.
OortGuiMainFrame() - Constructor for class owltools.ontologyrelease.gui.OortGuiMainFrame
Default constructor, required only for testing the GUI as bean.
OortGuiMainFrame(BlockingQueue<String>) - Constructor for class owltools.ontologyrelease.gui.OortGuiMainFrame
Main constructor.
OortGuiMainPanel - Class in owltools.ontologyrelease.gui
GUI component for the minimum number of configurations required for the release manager.
OortGuiMainPanel(Frame, OortConfiguration, OortGuiAdvancedPanel) - Constructor for class owltools.ontologyrelease.gui.OortGuiMainPanel
Constructor allows to build a panel with default values.
OortGuiMenuBar - Class in owltools.ontologyrelease.gui
Menu bar for OORT.
OortGuiMenuBar(OortGuiMainFrame, OortConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiMenuBar
Create a new menu instance.
OverlapSimilarity - Class in owltools.sim
 
OverlapSimilarity() - Constructor for class owltools.sim.OverlapSimilarity
 
OWLExtendedReasoner - Interface in owltools.reasoner
Extends standard OWL reasoning to allow for querying of ancestor class expressions
OWLGraphEdge - Class in owltools.graph
 
OWLGraphEdge(OWLObject, OWLObject, OWLOntology, OWLQuantifiedProperty) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLRestriction, OWLObject, OWLQuantifiedProperty, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, List<OWLQuantifiedProperty>, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, OWLObjectPropertyExpression, OWLQuantifiedProperty.Quantifier, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, OWLQuantifiedProperty.Quantifier) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphLayoutNode - Class in owltools.gfx
 
OWLGraphLayoutNode(OWLGraphWrapper, OWLObject) - Constructor for class owltools.gfx.OWLGraphLayoutNode
 
OWLGraphLayoutNode(OWLGraphWrapper, OWLObject, GraphStyle) - Constructor for class owltools.gfx.OWLGraphLayoutNode
 
OWLGraphLayoutNode.SVGRectangle - Class in owltools.gfx
 
OWLGraphLayoutNode.SVGRectangle() - Constructor for class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
OWLGraphLayoutRenderer - Class in owltools.gfx
Render a portion of an ontology using the QuickGO graphics code This should be capable of rendering relationships between any OWLObjects - as well as class hierarchies, also object property hierarchies.
OWLGraphLayoutRenderer(OWLGraphWrapper) - Constructor for class owltools.gfx.OWLGraphLayoutRenderer
 
OWLGraphStrokeEdge - Class in owltools.gfx
Represents an edge in a layour graph Adapted from QuickGO
OWLGraphStrokeEdge(OWLGraphLayoutNode, OWLGraphLayoutNode, OWLGraphEdge) - Constructor for class owltools.gfx.OWLGraphStrokeEdge
 
OWLGraphStrokeEdge.SVGEdge - Class in owltools.gfx
 
OWLGraphUtil - Class in owltools.graph
general static methods for additional graph operations
OWLGraphUtil() - Constructor for class owltools.graph.OWLGraphUtil
 
OWLGraphvizRenderer - Class in owltools.gfx
IN-PROGRESS GraphViz renderer TODO - make a common abstract class for all renderers
OWLGraphvizRenderer(OWLGraphWrapper) - Constructor for class owltools.gfx.OWLGraphvizRenderer
 
owlGraphWrapper - Variable in class owltools.gfx.OWLGraphLayoutRenderer
 
OWLGraphWrapper - Class in owltools.graph
Wraps one or more OWLOntology objects providing convenient OBO-like operations
OWLGraphWrapper(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapper
Create a new wrapper for an OWLOntology
OWLGraphWrapper(OWLOntology, boolean) - Constructor for class owltools.graph.OWLGraphWrapper
Deprecated.  
OWLGraphWrapper(String) - Constructor for class owltools.graph.OWLGraphWrapper
creates a new OWLOntology as the source ontology
OWLGraphWrapper.Config - Class in owltools.graph
Configuration options.
OWLGraphWrapper.Config() - Constructor for class owltools.graph.OWLGraphWrapper.Config
 
OWLGraphWrapper.ISynonym - Interface in owltools.graph
 
OWLGraphWrapper.Synonym - Class in owltools.graph
 
OWLGraphWrapper.Synonym(String, String, String, Set<String>) - Constructor for class owltools.graph.OWLGraphWrapper.Synonym
 
OWLGraphWrapperTest - Class in owltools.graph.test
 
OWLGraphWrapperTest() - Constructor for class owltools.graph.test.OWLGraphWrapperTest
 
OWLGsonRenderer - Class in owltools.io
 
OWLGsonRenderer(PrintWriter) - Constructor for class owltools.io.OWLGsonRenderer
 
OWLGsonRenderer() - Constructor for class owltools.io.OWLGsonRenderer
 
OWLGsonRendererTest - Class in owltools.io.test
 
OWLGsonRendererTest() - Constructor for class owltools.io.test.OWLGsonRendererTest
 
OWLHandler - Class in owltools.web
 
OWLHandler(OWLServer, OWLGraphWrapper, HttpServletRequest, HttpServletResponse) - Constructor for class owltools.web.OWLHandler
 
OWLHandler.Param - Enum in owltools.web
 
OWLHandler.ResultType - Enum in owltools.web
 
owlObject - Variable in class owltools.gfx.OWLGraphLayoutNode
 
owlObject - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
OWLObjectPair - Class in owltools.sim
 
OWLObjectPair(OWLObject, OWLObject) - Constructor for class owltools.sim.OWLObjectPair
 
OWLObjectPair(OWLObject, OWLObject, boolean) - Constructor for class owltools.sim.OWLObjectPair
 
OWLPrettyPrinter - Class in owltools.io
 
OWLPrettyPrinter(OWLGraphWrapper) - Constructor for class owltools.io.OWLPrettyPrinter
 
OWLPrettyPrinter.LabelProvider - Class in owltools.io
 
OWLPrettyPrinter.LabelProvider(OWLGraphWrapper) - Constructor for class owltools.io.OWLPrettyPrinter.LabelProvider
 
OWLQuantifiedProperty - Class in owltools.graph
 
OWLQuantifiedProperty(OWLObjectPropertyExpression, OWLQuantifiedProperty.Quantifier) - Constructor for class owltools.graph.OWLQuantifiedProperty
 
OWLQuantifiedProperty() - Constructor for class owltools.graph.OWLQuantifiedProperty
 
OWLQuantifiedProperty(OWLQuantifiedProperty.Quantifier) - Constructor for class owltools.graph.OWLQuantifiedProperty
 
OWLQuantifiedProperty.Quantifier - Enum in owltools.graph
 
OWLReasonerRunner - Class in owltools
Adapted from Matthew Horridge's OWLAPI examples by Chris Mungall.
OWLReasonerRunner() - Constructor for class owltools.OWLReasonerRunner
 
OWLServer - Class in owltools.web
 
OWLServer(OWLGraphWrapper) - Constructor for class owltools.web.OWLServer
 
owltools - package owltools
OWLTools - an OWL API wrapper
owltools.cli - package owltools.cli
CLI - Command Line Interface
owltools.gaf - package owltools.gaf
Processing of GO Gene Association Files
owltools.gaf.inference - package owltools.gaf.inference
Perform inference on Gene Associations
owltools.gaf.owl - package owltools.gaf.owl
 
owltools.gaf.owl.test - package owltools.gaf.owl.test
 
owltools.gaf.test - package owltools.gaf.test
 
owltools.gfx - package owltools.gfx
GFX - OWL Graphics and Visualization
owltools.gfx.test - package owltools.gfx.test
 
owltools.graph - package owltools.graph
OWLGraph -- OBO-like Graph Wrapper for OWL Ontologies
owltools.graph.test - package owltools.graph.test
 
owltools.idmap - package owltools.idmap
 
owltools.io - package owltools.io
IO - Input/Output
owltools.io.test - package owltools.io.test
 
owltools.mooncat - package owltools.mooncat
Mooncat -- Multiple OWL ONtology Catenation
owltools.mooncat.test - package owltools.mooncat.test
 
owltools.ontologyrelease - package owltools.ontologyrelease
Oort - OBO Ontology Release Tool (OORT)
owltools.ontologyrelease.gui - package owltools.ontologyrelease.gui
 
owltools.ontologyrelease.test - package owltools.ontologyrelease.test
 
owltools.ontologyverification - package owltools.ontologyverification
 
owltools.ontologyverification.annotations - package owltools.ontologyverification.annotations
 
owltools.phenolog - package owltools.phenolog
Phenolog - Calculation of class similarity based on instance data
owltools.profile - package owltools.profile
 
owltools.reasoner - package owltools.reasoner
 
owltools.sim - package owltools.sim
OWLSim -- Semantic Similarity over OWL ontologies
owltools.sim.test - package owltools.sim.test
 
owltools.solrj - package owltools.solrj
 
owltools.test - package owltools.test
 
owltools.util - package owltools.util
 
owltools.web - package owltools.web
OWLTools Web Services
OWLToolsTestBasics - Class in owltools.test
 
OWLToolsTestBasics() - Constructor for class owltools.test.OWLToolsTestBasics
 

P

parentArrowShape - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
parse(Reader) - Method in class owltools.gaf.GAFParser
 
parse(String) - Method in class owltools.gaf.GAFParser
 
parse(File) - Method in class owltools.gaf.GAFParser
 
parse(String) - Method in class owltools.idmap.AbstractMappingParser
 
parse(Reader) - Method in class owltools.idmap.AbstractMappingParser
 
parse(File) - Method in class owltools.idmap.AbstractMappingParser
 
parse(Reader) - Method in class owltools.idmap.IDMappingPIRParser
 
parse(Reader) - Method in class owltools.idmap.UniProtIDMapParser
 
parse(String) - Method in class owltools.io.ParserWrapper
 
parse(String) - Method in class owltools.io.TableToAxiomConverter
 
parse(String) - Method in class owltools.phenolog.GenePhenoTsvParser
 
parseArgString(String) - Method in class owltools.cli.CommandRunner
 
parseOBO(String) - Method in class owltools.io.ParserWrapper
 
parseOBOFiles(List<String>) - Method in class owltools.io.ParserWrapper
 
parseOWL(String) - Method in class owltools.io.ParserWrapper
 
parseOWL(IRI) - Method in class owltools.io.ParserWrapper
 
parserError(String, String, int) - Method in interface owltools.gaf.GafParserListener
 
ParserWrapper - Class in owltools.io
Convenience class wrapping org.oboformat that abstracts away underlying details of ontology format or location
ParserWrapper() - Constructor for class owltools.io.ParserWrapper
 
parseToOWLGraph(String) - Method in class owltools.io.ParserWrapper
 
parseToOWLGraph(String, boolean) - Method in class owltools.io.ParserWrapper
 
parseVersion(String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Try to parse the string as a Date using the both patterns for version IRI and OboInOwl.
parsing(String, int) - Method in interface owltools.gaf.GafParserListener
 
peekArg() - Method in class owltools.cli.CommandRunner.Opts
 
performConsistencyChecks() - Method in class owltools.InferenceBuilder
 
performtransiviteclosure() - Method in class owltools.phenolog.PhenoTransitiveClosure
 
performtransiviteclosure(String, String, HashSet<Pheno>, HashMap<String, Pheno>, HashMap<String, IndividualPair>) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
Pheno - Class in owltools.phenolog
represents an attribute-bearing entity; for example, a phenotype.
Pheno() - Constructor for class owltools.phenolog.Pheno
 
Pheno(String) - Constructor for class owltools.phenolog.Pheno
 
Pheno(String, String) - Constructor for class owltools.phenolog.Pheno
 
Pheno(String, String, HashSet<Individual>) - Constructor for class owltools.phenolog.Pheno
 
Pheno(String, String, HashSet<Individual>, boolean) - Constructor for class owltools.phenolog.Pheno
 
PhenologEngine - Class in owltools.phenolog
 
PhenologEngine() - Constructor for class owltools.phenolog.PhenologEngine
 
PhenologSimTest - Class in owltools.sim.test
 
PhenologSimTest() - Constructor for class owltools.sim.test.PhenologSimTest
 
PhenoTransitiveClosure - Class in owltools.phenolog
 
PhenoTransitiveClosure() - Constructor for class owltools.phenolog.PhenoTransitiveClosure
 
PHYSICAL_IRI - Static variable in class owltools.OWLReasonerRunner
 
PKBTest - Class in owltools.graph.test
 
PKBTest() - Constructor for class owltools.graph.test.PKBTest
 
PlaceholderJcelFactory - Class in owltools.reasoner
 
PlaceholderJcelFactory() - Constructor for class owltools.reasoner.PlaceholderJcelFactory
 
polarity - Variable in enum owltools.gfx.RelationType
 
precomputeInferences(InferenceType...) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
precomputeInferences(InferenceType...) - Method in class owltools.reasoner.GraphReasoner
 
predict(String) - Method in interface owltools.gaf.inference.AnnotationPredictor
 
predict(String) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
 
predict(String) - Method in class owltools.gaf.inference.CompositionalClassPredictor
 
Prediction - Class in owltools.gaf.inference
 
Prediction() - Constructor for class owltools.gaf.inference.Prediction
 
preSimMethod - Variable in class owltools.sim.MultiSimilarity
 
prettyPrinter - Variable in class owltools.io.AbstractClosureRenderer
 
print(OWLObject) - Method in class owltools.io.AbstractClosureRenderer
 
print(String) - Method in class owltools.io.AbstractClosureRenderer
 
print(OWLObject) - Method in class owltools.io.OWLPrettyPrinter
 
print(Set<OWLAxiom>) - Method in class owltools.io.OWLPrettyPrinter
 
print(String) - Method in class owltools.io.OWLPrettyPrinter
 
print(PrintStream) - Method in class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.  
print(PrintStream) - Method in class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.  
print(PrintStream) - Method in class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
 
print(PrintStream) - Method in class owltools.sim.CombinedSimilarity
 
print(PrintStream) - Method in class owltools.sim.CombinedSimilarity2
 
print(PrintStream) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
print(PrintStream) - Method in class owltools.sim.ConjunctiveSetSimilarity
 
print(PrintStream) - Method in class owltools.sim.DescriptionTreeSimilarity
 
print(PrintStream) - Method in class owltools.sim.DisjunctiveSetSimilarity
 
print(PrintStream) - Method in class owltools.sim.MultiSimilarity
 
print() - Method in class owltools.sim.Similarity
 
print(PrintStream) - Method in class owltools.sim.Similarity
 
print(PrintStream, OWLObject) - Method in class owltools.sim.Similarity
 
printCachedObjects() - Method in class owltools.web.OWLHandler
 
printDescription(PrintStream, OWLObject) - Method in class owltools.sim.Similarity
 
printDescription(PrintStream, OWLObject, int) - Method in class owltools.sim.Similarity
 
printresults(String, ArrayList<Pheno>, double, int) - Static method in class owltools.phenolog.Main
 
printX(PrintStream, OWLObject) - Method in class owltools.sim.DescriptionTreeSimilarity
 
printX(PrintStream, OWLObject, int) - Method in class owltools.sim.DescriptionTreeSimilarity
 
process(String[]) - Method in class owltools.idmap.IDMapHandler
 
process(String[]) - Method in class owltools.idmap.IDMapPairWriter
 
process(String[]) - Method in class owltools.idmap.IDMappingPIRParser
 
Profiler - Class in owltools.profile
 
Profiler() - Constructor for class owltools.profile.Profiler
 
property - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
property - Variable in class owltools.io.TableToAxiomConverter.Config
 

Q

QUALIFIER - Static variable in class owltools.gaf.GAFParser
 
qualifierObj - Variable in class owltools.gaf.CompositeQualifier
 
queryDescendants(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapper
 
queryDescendants(OWLClassExpression) - Method in class owltools.graph.OWLGraphWrapper
Performs a closed-world query using a DL expression as a set of boolean database-style constraints.
queryDescendants(OWLClassExpression, boolean, boolean) - Method in class owltools.graph.OWLGraphWrapper
 
quickScore(Set<OWLObject>, Set<OWLObject>) - Method in class owltools.sim.DescriptionTreeSimilarity
 
qvizCommand() - Method in class owltools.web.OWLHandler
visualize using QuickGO graphdraw.

R

read(String) - Method in class owltools.io.AbstractClosureReader
 
read() - Method in class owltools.io.AbstractClosureReader
 
read() - Method in class owltools.io.CompactGraphClosureReader
 
read() - Method in interface owltools.io.GraphReader
 
read(String) - Method in interface owltools.io.GraphReader
 
readConfig(File) - Static method in class owltools.ontologyrelease.OortConfiguration
Read from a configuration property file and load it into a new OortConfiguration object.
reader - Variable in class owltools.idmap.AbstractMappingParser
 
REASONER_ELK - Static variable in class owltools.InferenceBuilder
 
REASONER_HERMIT - Static variable in class owltools.InferenceBuilder
 
REASONER_JCEL - Static variable in class owltools.InferenceBuilder
 
REASONER_PELLET - Static variable in class owltools.InferenceBuilder
 
REFERENCE - Static variable in class owltools.gaf.GAFParser
 
referenceId - Variable in class owltools.gaf.GeneAnnotation
 
relation - Variable in class owltools.gaf.ExtensionExpression
 
relationConfigMap - Variable in class owltools.gfx.GraphicsConfig
 
relationship - Variable in class owltools.gaf.IdMapping
 
RelationType - Enum in owltools.gfx
hacked crudely from QuickGO TODO: use config object to map relationship types to colors
RelationType.Polarity - Enum in owltools.gfx
 
ReleaseInferenceTest - Class in owltools.ontologyrelease.test
 
ReleaseInferenceTest() - Constructor for class owltools.ontologyrelease.test.ReleaseInferenceTest
 
remoteParserListener(GafParserListener) - Method in class owltools.gaf.GAFParser
 
removeDanglingAxioms(OWLOntology) - Method in class owltools.mooncat.Mooncat
Removes any axiom from ont if that axiom contains a dangling reference - i.e.
removeDanglingAxioms() - Method in class owltools.mooncat.Mooncat
 
removeExternalOntologyClasses(boolean) - Method in class owltools.mooncat.Mooncat
 
removeSubsetComplementClasses(Set<OWLClass>, boolean) - Method in class owltools.mooncat.Mooncat
Remove all classes *not* in subset.
removeSupportOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
 
render(OWLPrettyPrinter) - Method in class owltools.gaf.inference.Prediction
 
render(Graphics2D) - Method in class owltools.gfx.OWLGraphLayoutNode
 
render(OWLGraphWrapper) - Method in class owltools.io.AbstractClosureRenderer
 
render(OWLGraphEdge) - Method in class owltools.io.AbstractClosureRenderer
 
render(OWLGraphEdge) - Method in class owltools.io.ChadoGraphClosureRenderer
 
render(OWLGraphWrapper) - Method in class owltools.io.CompactGraphClosureRenderer
 
render(OWLGraphEdge) - Method in class owltools.io.CompactGraphClosureRenderer
 
render(OWLGraphEdge) - Method in class owltools.io.GraphClosureRenderer
 
render(OWLGraphWrapper) - Method in interface owltools.io.GraphRenderer
 
render(String) - Method in class owltools.io.JSONPrinter
Deprecated.  
render(Set) - Method in class owltools.io.JSONPrinter
Deprecated.  
render(OWLObject) - Method in class owltools.io.JSONPrinter
Deprecated.  
render(OWLAxiom) - Method in class owltools.io.JSONPrinter
Deprecated.  
render(OWLGraphEdge) - Method in class owltools.io.JSONPrinter
Deprecated.  
render(OWLAxiom) - Method in class owltools.io.OWLGsonRenderer
 
render(OWLGraphEdge) - Method in class owltools.io.OWLGsonRenderer
 
render(OWLOntology) - Method in class owltools.io.OWLGsonRenderer
 
render(Set) - Method in class owltools.io.OWLGsonRenderer
 
render(OWLObject) - Method in class owltools.io.OWLPrettyPrinter
 
render(OWLAxiom) - Method in class owltools.io.OWLPrettyPrinter
 
render(OWLGraphEdge) - Method in class owltools.io.OWLPrettyPrinter
 
renderDot() - Method in class owltools.gfx.OWLGraphvizRenderer
 
renderHTML() - Method in class owltools.gfx.OWLGraphLayoutRenderer
generates both HTML and a PNG
renderID(Graphics2D) - Method in class owltools.gfx.OWLGraphLayoutNode
 
renderId(String) - Method in class owltools.io.OWLPrettyPrinter
 
renderImage(String, OutputStream) - Method in class owltools.gfx.OWLGraphLayoutRenderer
renders the graph in the specified format
renderImage(String, OutputStream) - Method in class owltools.gfx.OWLGraphvizRenderer
 
renderMessageString() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
Render the exception in an human readable form and suitable for appending to a logger.
renderOBO(OBODoc) - Static method in class owltools.test.OWLToolsTestBasics
 
report(StringBuilder, CheckResult, CheckResult.Status) - Method in class owltools.ontologyverification.OntologyCheckHandler
 
report() - Method in class owltools.profile.Profiler
 
report(Reporter) - Method in class owltools.sim.AsymmetricJaccardSimilarity
 
report(Reporter) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
report(Reporter) - Method in class owltools.sim.JaccardSimilarity
 
report(Reporter) - Method in class owltools.sim.MultiSimilarity
 
report(Object...) - Method in class owltools.sim.Reporter
 
report(Reporter) - Method in class owltools.sim.Similarity
 
Reporter - Class in owltools.sim
 
Reporter(PrintStream, OWLGraphWrapper) - Constructor for class owltools.sim.Reporter
 
Reporter(OWLGraphWrapper) - Constructor for class owltools.sim.Reporter
 
reporter - Variable in class owltools.sim.SimSearch
 
reportHeader(StringBuilder) - Method in class owltools.ontologyverification.OntologyCheckHandler
 
resolveClass(String) - Method in class owltools.cli.CommandRunner
 
resolveClass(OWLGraphWrapper, String) - Static method in class owltools.cli.CopyOfCommandLineInterface
 
resolveEntity(CommandRunner.Opts) - Method in class owltools.cli.CommandRunner
 
resolveEntity(String) - Method in class owltools.cli.CommandRunner
 
resolveEntity(OWLGraphWrapper, CopyOfCommandLineInterface.Opts) - Static method in class owltools.cli.CopyOfCommandLineInterface
 
resolveEntity(OWLGraphWrapper, String) - Static method in class owltools.cli.CopyOfCommandLineInterface
 
resolveObjectProperty(String) - Method in class owltools.cli.CommandRunner
 
resolveObjectProperty(OWLGraphWrapper, String) - Static method in class owltools.cli.CopyOfCommandLineInterface
 
RestrictToELTest - Class in owltools.test
 
RestrictToELTest() - Constructor for class owltools.test.RestrictToELTest
 
RetrieveRelationByLabelTest - Class in owltools.graph.test
 
RetrieveRelationByLabelTest() - Constructor for class owltools.graph.test.RetrieveRelationByLabelTest
 
right() - Method in class owltools.gfx.OWLGraphLayoutNode
 
right - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
rowToAxioms(String[]) - Method in class owltools.io.TableToAxiomConverter
 
run(String[]) - Method in class owltools.cli.CommandRunner
 
run(CommandRunner.Opts) - Method in class owltools.cli.CommandRunner
 
run(OWLGraphWrapper, Similarity, OWLObject, OWLObject) - Method in class owltools.sim.test.AsbtractSimEngineTest
 

S

SampleGraphDraw - Class in owltools.gfx
Draw an example graph.
SampleGraphDraw() - Constructor for class owltools.gfx.SampleGraphDraw
 
saveOWL(OWLOntology, String) - Method in class owltools.io.ParserWrapper
 
saveOWL(OWLOntology, OWLOntologyFormat, String) - Method in class owltools.io.ParserWrapper
 
saveOWL(OWLOntology, OWLOntologyFormat, OutputStream) - Method in class owltools.io.ParserWrapper
 
search(OWLObject) - Method in class owltools.sim.SimSearch
Given a query object (e.g.
selfReferenceInDefinition(OWLGraphWrapper) - Method in class owltools.ontologyverification.DefaultOntologyChecks
Check, whether the class is defined using the class itself.
sep() - Method in class owltools.io.AbstractClosureRenderer
 
serialise() - Method in class owltools.gfx.OWLGraphLayoutNode
 
serialise() - Method in class owltools.gfx.OWLGraphStrokeEdge
 
setActsOnTaxonId(String) - Method in class owltools.gaf.GeneAnnotation
 
setAllowEquivalentNamedClassPairs(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setAllowFileOverWrite(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
Set allowFileOverWrite
setAllowOverwrite(boolean) - Method in class owltools.ontologyrelease.gui.OortGuiAdvancedPanel
 
setancestors(HashSet<Pheno>) - Method in class owltools.phenolog.Pheno
 
setAndFilterRedundantPredictions(Set<Prediction>, Set<OWLClass>) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
side-effects: removes redundant predictions
setAsserted(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
Set asserted
setAssignedBy(String) - Method in class owltools.gaf.GeneAnnotation
 
setAttributes(Set<Attribute>) - Method in class owltools.phenolog.Individual
 
setAutoDetectBridgingOntology(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setAxiomType(String) - Method in class owltools.io.TableToAxiomConverter.Config
 
setBase(File) - Method in class owltools.ontologyrelease.OortConfiguration
 
setBioentity(String) - Method in class owltools.gaf.GeneAnnotation
 
setBioentityObject(Bioentity) - Method in class owltools.gaf.GeneAnnotation
 
setBit(int, boolean) - Method in class owltools.util.BloomFilter
Set a single bit in the Bloom filter.
setBridgeOntologies(List<String>) - Method in class owltools.ontologyrelease.OortConfiguration
 
setCandidates(Set<OWLObject>) - Method in class owltools.sim.SimSearch
 
setCheckConsistency(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setClosest(Pheno) - Method in class owltools.phenolog.Pheno
 
setClosestDistance(double) - Method in class owltools.phenolog.Pheno
 
setClosestOverlap(int) - Method in class owltools.phenolog.Pheno
 
setClosestOverlapPairs(HashSet<IndividualPair>) - Method in class owltools.phenolog.Pheno
 
setCls(String) - Method in class owltools.gaf.ExtensionExpression
 
setCls(String) - Method in class owltools.gaf.GeneAnnotation
 
setCommandName(String) - Method in class owltools.web.OWLHandler
 
setCompositeQualifier(String) - Method in class owltools.gaf.GeneAnnotation
 
setConfig(OWLGraphWrapper.Config) - Method in class owltools.graph.OWLGraphWrapper
 
setConfigForFlyMine() - Method in class owltools.phenolog.GenePhenoTsvParser
 
setConfigForMGIPhenoGeno() - Method in class owltools.phenolog.GenePhenoTsvParser
 
setDataFactory(OWLDataFactory) - Method in class owltools.graph.OWLGraphWrapper
 
setDb(String) - Method in class owltools.gaf.Bioentity
 
setDistance(int) - Method in class owltools.graph.OWLGraphEdge
 
setDocumentPath(String) - Method in class owltools.gaf.GafDocument
 
setEnforceEL(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setEvidenceCls(String) - Method in class owltools.gaf.GeneAnnotation
 
setExecuteOntologyChecks(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setExpandMacros(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setExpandShortcutRelations(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setExpandXrefs(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
Set export bridges
setExtensionExpression(String) - Method in class owltools.gaf.GeneAnnotation
 
setFile(File) - Method in class owltools.ontologyrelease.BuildVersionId
Deprecated. The file in which the build number is stored.
setFile(String) - Method in class owltools.ontologyrelease.GetOntologyId
Deprecated.  
setForceRelease(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setFormat(String) - Method in class owltools.web.OWLHandler
 
setFullName(String) - Method in class owltools.gaf.Bioentity
 
setGafDocument(String) - Method in class owltools.gaf.Bioentity
 
setGafDocument(String) - Method in class owltools.gaf.GeneAnnotation
 
setGafDocument(GafDocument) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
setGafDocument(GafDocument) - Method in class owltools.solrj.GafSolrDocumentLoader
 
setGeneAnnotation(GeneAnnotation) - Method in class owltools.gaf.inference.Prediction
 
setGeneProductForm(String) - Method in class owltools.gaf.GeneAnnotation
 
setGraph(OWLGraphWrapper) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
 
setGraph(OWLGraphWrapper) - Method in class owltools.mooncat.Mooncat
 
setGraph(OWLGraphWrapper) - Method in class owltools.sim.SimEngine
 
setGraph(OWLGraphWrapper) - Method in interface owltools.sim.SimilarityCalculator
 
setGraph(OWLGraphWrapper) - Method in class owltools.solrj.AbstractSolrLoader
 
sethmp(HashMap<String, Pheno>) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
sethmpair(HashMap<String, IndividualPair>) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
sethsp(HashSet<Pheno>) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
setId(String) - Method in class owltools.gaf.Bioentity
 
setId(String) - Method in class owltools.gaf.CompositeQualifier
 
setId(String) - Method in class owltools.gaf.ExtensionExpression
 
setId(String) - Method in class owltools.gaf.GafDocument
 
setId(String) - Method in class owltools.gaf.WithInfo
 
setId(String) - Method in class owltools.phenolog.Attribute
 
setid(String) - Method in class owltools.phenolog.GenePheno
 
setId(String) - Method in class owltools.phenolog.Individual
 
setId(String) - Method in class owltools.phenolog.Pheno
 
setIndividualPairs(Set<IndividualPair>) - Method in class owltools.phenolog.PhenologEngine
 
setIndividuals(HashSet<Individual>) - Method in class owltools.phenolog.Pheno
 
setInferred(boolean) - Method in class owltools.graph.OWLQuantifiedProperty
 
setInverseOf(boolean) - Method in class owltools.graph.OWLQuantifiedProperty
 
setIsContributesTo(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setisFromTC(boolean) - Method in class owltools.phenolog.Pheno
 
setIsIntegralTo(boolean) - Method in class owltools.gaf.GeneAnnotation
 
setJustifyAssertedSubclasses(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setLabel(String) - Method in class owltools.phenolog.Attribute
 
setlabel(String) - Method in class owltools.phenolog.GenePheno
 
setLabel(String) - Method in class owltools.phenolog.Individual
 
setLabel(String) - Method in class owltools.phenolog.Pheno
 
setLastUpdateDate(String) - Method in class owltools.gaf.GeneAnnotation
 
setLocation(int, int) - Method in class owltools.gfx.OWLGraphLayoutNode
 
setMacroStrategy(OortConfiguration.MacroStrategy) - Method in class owltools.ontologyrelease.OortConfiguration
Set the OortConfiguration.MacroStrategy
setManager(OWLOntologyManager) - Method in class owltools.graph.OWLGraphWrapper
 
setManager(OWLOntologyManager) - Method in class owltools.io.ParserWrapper
 
setManager(OWLOntologyManager) - Method in class owltools.mooncat.Mooncat
 
setMappingSource(String) - Method in class owltools.gaf.IdMapping
 
setMaxCardinality(Integer) - Method in class owltools.graph.OWLQuantifiedProperty
 
setMaxHits(int) - Method in class owltools.sim.SimSearch
 
setMember1(Individual) - Method in class owltools.phenolog.IndividualPair
 
setMember2(Individual) - Method in class owltools.phenolog.IndividualPair
 
setMinCardinality(Integer) - Method in class owltools.graph.OWLQuantifiedProperty
 
setNcbiTaxonId(String) - Method in class owltools.gaf.Bioentity
 
setNonTCIndividualSize(int) - Method in class owltools.phenolog.Pheno
 
setOboInOWLVersion(OWLOntology, String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Set the OboInOWL remark to the given ontology version.
setOboInOWLVersion(OWLOntology, Date) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Set the OboInOWL remark to the given date.
setobolink(String) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
setOntology(OWLOntology) - Method in class owltools.graph.OWLGraphEdge
 
setOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
setOntology(OWLOntology) - Method in class owltools.mooncat.Mooncat
 
setOntologyVersion(OWLOntology, String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Set the ontology version IRI in the OntologyID to the given string.
setOntologyVersion(OWLOntology, Date, String, String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Set the ontology version IRI in the OntologyID.
setOntologyVersion(OWLOntology, IRI) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Set the ontology version IRI in the OntologyID.
setOrthologs(int) - Method in class owltools.phenolog.Individual
 
setOWLGraphWrapper(OWLGraphWrapper) - Method in class owltools.InferenceBuilder
 
setPair(String, String) - Method in class owltools.idmap.IDMapPairWriter
 
setphenoid(String) - Method in class owltools.phenolog.GenePheno
 
setphenolabel(String) - Method in class owltools.phenolog.GenePheno
 
setprefix(String) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
setPreSimMethod(String) - Method in class owltools.sim.MultiSimilarity
 
setProfiler(Profiler) - Method in class owltools.graph.OWLGraphWrapper
 
setProperty(OWLObjectProperty) - Method in class owltools.graph.OWLQuantifiedProperty
 
setPropertyToComment() - Method in class owltools.io.TableToAxiomConverter.Config
 
setPropertyToLabel() - Method in class owltools.io.TableToAxiomConverter.Config
 
setQualifierObj(String) - Method in class owltools.gaf.CompositeQualifier
 
setQuantifiedPropertyList(List<OWLQuantifiedProperty>) - Method in class owltools.graph.OWLGraphEdge
 
setQuantifier(OWLQuantifiedProperty.Quantifier) - Method in class owltools.graph.OWLQuantifiedProperty
 
setReasoner(OWLReasoner) - Method in class owltools.graph.OWLGraphWrapper
 
setReasoner(OWLReasoner) - Method in class owltools.InferenceBuilder
 
setReasonerName(String) - Method in class owltools.ontologyrelease.OortConfiguration
Set the reasoner name
setRecreateMireot(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
Set recreateMireot
setRedundantWithExistingAnnotations(boolean) - Method in class owltools.gaf.inference.Prediction
 
setRedundantWithOtherPredictions(boolean) - Method in class owltools.gaf.inference.Prediction
 
setReferencedOntologies(Set<OWLOntology>) - Method in class owltools.mooncat.Mooncat
Deprecated. 
setReferenceId(String) - Method in class owltools.gaf.GeneAnnotation
 
setRelation(String) - Method in class owltools.gaf.ExtensionExpression
 
setRelationship(String) - Method in class owltools.gaf.IdMapping
 
setRelationType() - Method in class owltools.gfx.OWLGraphStrokeEdge
Sets the value of relType based on OWLGraphEdge properties TODO : this is too hacky.
setRepairAnnotationCardinality(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setScore(Double) - Method in class owltools.sim.Similarity
 
setScore(int) - Method in class owltools.sim.Similarity
 
setSimEngine(SimEngine) - Method in class owltools.sim.SimSearch
 
setSimple(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
Set simple.
setSingleQuantifiedProperty(OWLQuantifiedProperty) - Method in class owltools.graph.OWLGraphEdge
 
setSource(OWLObject) - Method in class owltools.graph.OWLGraphEdge
 
setSourceId(String) - Method in class owltools.gaf.IdMapping
 
setSourceOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
 
setSourceOntologyPrefixes(Set<String>) - Method in class owltools.mooncat.Mooncat
Set the source ontology prefixes.
setSourceOntologyPrefixes(Set<String>) - Method in class owltools.ontologyrelease.OortConfiguration
 
setStream(InputStream) - Method in class owltools.io.AbstractClosureReader
 
setStream(String) - Method in class owltools.io.AbstractClosureReader
 
setStream(PrintStream) - Method in class owltools.io.AbstractClosureRenderer
 
setStream(String) - Method in class owltools.io.AbstractClosureRenderer
 
setSubSimMethod(String) - Method in class owltools.sim.MultiSimilarity
 
setSupportOntologySet(Set<OWLOntology>) - Method in class owltools.graph.OWLGraphWrapper
 
setSymbol(String) - Method in class owltools.gaf.Bioentity
 
setTarget(OWLObject) - Method in class owltools.graph.OWLGraphEdge
 
setTargetId(String) - Method in class owltools.gaf.IdMapping
 
setTypeCls(String) - Method in class owltools.gaf.Bioentity
 
setWithExpression(String) - Method in class owltools.gaf.GeneAnnotation
 
setWithXref(String) - Method in class owltools.gaf.WithInfo
 
setWrappedReasoner(OWLReasoner) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
setWriteELOntology(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setWriteMetadata(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setWriteSubsets(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
SharedLabelException - Exception in owltools.graph
 
SharedLabelException(String, IRI, IRI) - Constructor for exception owltools.graph.SharedLabelException
 
showMemory() - Static method in class owltools.OWLReasonerRunner
 
SimEngine - Class in owltools.sim
SimEngine provides access to multiple similarity calculation procedures (see Similarity).
SimEngine(OWLGraphWrapper) - Constructor for class owltools.sim.SimEngine
 
simEngine - Variable in class owltools.sim.SimSearch
 
SimEngine.SimilarityAlgorithmException - Exception in owltools.sim
 
SimEngine.SimilarityAlgorithmException(String) - Constructor for exception owltools.sim.SimEngine.SimilarityAlgorithmException
 
SimEngineTest - Class in owltools.sim.test
 
SimEngineTest() - Constructor for class owltools.sim.test.SimEngineTest
 
SimEngineTest2 - Class in owltools.sim.test
 
SimEngineTest2() - Constructor for class owltools.sim.test.SimEngineTest2
 
SimEngineTest3 - Class in owltools.sim.test
 
SimEngineTest3() - Constructor for class owltools.sim.test.SimEngineTest3
 
SimEngineTest4 - Class in owltools.sim.test
 
SimEngineTest4() - Constructor for class owltools.sim.test.SimEngineTest4
 
Similarity - Class in owltools.sim
Represents a pairwise similarity between two OWLObjects.
Similarity() - Constructor for class owltools.sim.Similarity
 
SimilarityCalculator - Interface in owltools.sim
 
SimSearch - Class in owltools.sim
quick search for best matches
SimSearch(SimEngine) - Constructor for class owltools.sim.SimSearch
 
SimSearch(SimEngine, Reporter) - Constructor for class owltools.sim.SimSearch
 
size() - Method in class owltools.util.BloomFilter
Returns the number of bits in the Bloom filter.
slimColours - Variable in class owltools.gfx.GraphStyle
 
sortMapByScore(Map<OWLObject, Similarity>) - Method in class owltools.sim.MultiSimilarity
 
sourceId - Variable in class owltools.gaf.IdMapping
 
SparqlDLQueryTest - Class in owltools.graph.test
This basic examples show how to load an ontology, to initialize the SPARQL-DL query engine as well as to execute some simple queries.
SparqlDLQueryTest() - Constructor for class owltools.graph.test.SparqlDLQueryTest
 
split(String) - Method in class owltools.idmap.IDMapHandler
 
splitIRI(IRI) - Method in class owltools.sim.Similarity
 
startTaskNotify(String) - Method in class owltools.profile.Profiler
 
stream - Variable in class owltools.io.AbstractClosureReader
 
stream - Variable in class owltools.io.AbstractClosureRenderer
 
subSimMethod - Variable in class owltools.sim.MultiSimilarity
 
subsumes(OWLQuantifiedProperty) - Method in class owltools.graph.OWLQuantifiedProperty
 
summarizeOntology(OWLOntology) - Method in class owltools.cli.CommandRunner
 
summarizeOntology(OWLOntology) - Static method in class owltools.cli.CopyOfCommandLineInterface
 
summary(int, int, int, int, int) - Method in class owltools.ontologyverification.OntologyCheckHandler
 
svgPath - Variable in class owltools.gfx.OWLGraphStrokeEdge.SVGEdge
 
symbol - Variable in class owltools.gaf.Bioentity
 

T

t1 - Variable in class owltools.idmap.IDMapPairWriter
 
t2 - Variable in class owltools.idmap.IDMapPairWriter
 
TableToAxiomConverter - Class in owltools.io
reads in a table (e.g.
TableToAxiomConverter(OWLGraphWrapper) - Constructor for class owltools.io.TableToAxiomConverter
 
TableToAxiomConverter.Config - Class in owltools.io
If AxiomType is ClassAssertion, then axioms will be of form ClassAssertion(sub obj) If AxiomType is SubClassOf, then axioms will be of form SubClassOf(sub obj) if a property P is specified, then obj is transformed to a class expression "P some obj'" where obj' is the original value for obj
TableToAxiomConverter.Config() - Constructor for class owltools.io.TableToAxiomConverter.Config
 
targetId - Variable in class owltools.gaf.IdMapping
 
TAXON - Static variable in class owltools.gaf.GAFParser
 
TaxonConstraintsEngine - Class in owltools.gaf.inference
 
TaxonConstraintsEngine(OWLGraphWrapper) - Constructor for class owltools.gaf.inference.TaxonConstraintsEngine
 
TaxonGraphTest - Class in owltools.test
 
TaxonGraphTest() - Constructor for class owltools.test.TaxonGraphTest
 
termIds - Variable in class owltools.gfx.GraphStyle
 
testAnc() - Method in class owltools.graph.test.PKBTest
 
testAncestorsQuery() - Method in class owltools.graph.test.AncestorsTest
 
testAncestorsQuery() - Method in class owltools.ontologyrelease.test.AncestorsTest
 
testAncestorsQuery() - Method in class owltools.ontologyrelease.test.ReleaseInferenceTest
 
testAxioms() - Method in class owltools.io.test.OWLGsonRendererTest
 
testBuildDocument() - Method in class owltools.gaf.test.GafObjectsBuilderTest
 
testCARO() - Method in class owltools.sim.test.SimEngineTest
 
testCARO() - Method in class owltools.sim.test.SimEngineTest2
 
testClosure() - Method in class owltools.graph.test.GraphImportsClosureTest
 
testClosureIntra() - Method in class owltools.graph.test.GraphImportsClosureTest
 
testConvertXPs() - Method in class owltools.test.ChainTestRegulation
 
testConvertXPs() - Method in class owltools.test.ClosureTestCARO
 
testConvertXPs() - Method in class owltools.test.CycleTest
 
testConvertXPs() - Method in class owltools.test.FlyTest
 
testConvertXPs() - Method in class owltools.test.FlyXPTest
 
testConvertXPs() - Method in class owltools.test.LCSTestCARO
 
testConvertXPs() - Method in class owltools.test.MPClosureTest
 
testDef() - Method in class owltools.graph.test.OWLGraphWrapperTest
 
testDescendants() - Method in class owltools.graph.test.AncestorsTest
 
testDescendants() - Method in class owltools.graph.test.AncestorsTest2
 
testDescendants() - Method in class owltools.graph.test.ChainTest
 
testDescendants() - Method in class owltools.ontologyrelease.test.AncestorsTest
 
testDescendants() - Method in class owltools.ontologyrelease.test.ReleaseInferenceTest
 
testDescendantsQuery() - Method in class owltools.graph.test.AncestorsTest
 
testDescendantsQuery() - Method in class owltools.graph.test.AncestorsTest2
 
testDescendantsQuery() - Method in class owltools.ontologyrelease.test.AncestorsTest
 
testDescendantsQuery() - Method in class owltools.ontologyrelease.test.ReleaseInferenceTest
 
testEnforceEL() - Method in class owltools.test.RestrictToELTest
Simple test for InferenceBuilder.enforceEL(OWLGraphWrapper).
testEscape() - Method in class owltools.ontologyrelease.test.OortConfigurationTest
Tests for OortConfiguration.escape(String, char)
testExclusion() - Method in class owltools.graph.test.AncestorsTest2
 
testGEdges() - Method in class owltools.io.test.OWLGsonRendererTest
 
testGetEntity() - Method in class owltools.test.GetObjectsTest
 
testGetOBOSynonymsMultipleScopes() - Method in class owltools.graph.test.OWLGraphWrapperTest
 
testGetOBOSynonymsWithXrefs() - Method in class owltools.graph.test.OWLGraphWrapperTest
 
testHippocampusLCS() - Method in class owltools.sim.test.SimEngineTest3
 
testImportProperties() - Method in class owltools.mooncat.test.ImportPropertyMooncatTest
Test a conflict in a relation with a direct import (rel_f is both declared in D and F).
testImportProperties2() - Method in class owltools.mooncat.test.ImportPropertyMooncatTest
Test a conflict in a relation with an direct and indirect import (rel_f is declared in D, E, and F).
testIntersectionsReturnedInClosure() - Method in class owltools.graph.test.AncestorsTest2
 
testIntersectionsReturnedInClosure() - Method in class owltools.graph.test.DLLikeQueryTest
 
testMakeImport() - Method in class owltools.test.AddImportTest
 
testMireot() - Method in class owltools.mooncat.test.DuplicateDefinitionMooncatTest
 
testMireot() - Method in class owltools.mooncat.test.MireotTest2
 
testMireot() - Method in class owltools.mooncat.test.MireotTest3
 
testMireot() - Method in class owltools.mooncat.test.MooncatTest
 
testOnt() - Method in class owltools.io.test.OWLGsonRendererTest
 
testOntologyCheckRunner() - Method in class owltools.ontologyverification.OntologyCheckRunnerTest
 
testParser() - Method in class owltools.gaf.owl.test.GAFOWLBridgeTest
 
testParser() - Method in class owltools.gaf.test.GAFInferenceTest
 
testParser() - Method in class owltools.gaf.test.GAFParserTest
 
testQuery() - Method in class owltools.graph.test.DLLikeQueryTest
 
testQuery() - Method in class owltools.graph.test.SparqlDLQueryTest
 
testReadWriteConfig() - Method in class owltools.ontologyrelease.test.OortConfigurationTest
Tests for OortConfiguration.writeConfig(File, OortConfiguration) and OortConfiguration.readConfig(File).
testRenderCARO() - Method in class owltools.gfx.test.CaroDotTest
 
testRenderCARO() - Method in class owltools.gfx.test.DrawAllCAROTest
 
testRenderCARO() - Method in class owltools.gfx.test.DrawCAROTest
 
testRenderCARO() - Method in class owltools.gfx.test.DrawOmmatidiumTest
 
testRenderCARO() - Method in class owltools.gfx.test.ImportTest
 
testRenderCARO() - Method in class owltools.gfx.test.MPVizTest
 
testRestrictionQuery() - Method in class owltools.graph.test.DLLikeQueryTest
 
testRestrictionQuery2() - Method in class owltools.graph.test.DLLikeQueryTest
 
testRestrictionsReturnedInClosure() - Method in class owltools.graph.test.AncestorsTest2
 
testRetainDeprecated() - Method in class owltools.test.RestrictToELTest
Test whether the ontology still has deprecation annotations after the conversion.
testRetainOntologyId() - Method in class owltools.test.RestrictToELTest
Test whether the ontology has the same ontology id after the conversion.
testSim() - Method in class owltools.sim.test.CombinedJaccardConjunctiveSetSimilarityTest
 
testSim() - Method in class owltools.sim.test.ConjunctiveSetSimilarityTest
 
testSim() - Method in class owltools.sim.test.PhenologSimTest
 
testSim() - Method in class owltools.sim.test.SimEngineTest3
 
testSim() - Method in class owltools.sim.test.SimEngineTest4
 
testSimEq() - Method in class owltools.sim.test.SimEngineTest3
 
testSplitBuildDocument() - Method in class owltools.gaf.test.GafObjectsBuilderTest
 
testSplitList() - Method in class owltools.ontologyrelease.test.OortConfigurationTest
Tests for OortConfiguration.addValues(String, java.util.Collection)
testSubClassesNames() - Method in class owltools.graph.test.OWLGraphWrapperTest
 
testSynonyms() - Method in class owltools.graph.test.OWLGraphWrapperTest
 
testUnescape() - Method in class owltools.ontologyrelease.test.OortConfigurationTest
Tests for OortConfiguration.unescape(String)
testUnion() - Method in class owltools.test.TaxonGraphTest
 
top - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
top() - Method in class owltools.gfx.OWLGraphLayoutNode
 
topCommand() - Method in class owltools.web.OWLHandler
 
topLine - Variable in class owltools.gfx.OWLGraphLayoutNode
 
toString() - Method in class owltools.gaf.Bioentity
 
toString - Variable in class owltools.gaf.GeneAnnotation
 
toString() - Method in class owltools.gaf.GeneAnnotation
 
toString() - Method in class owltools.gaf.inference.Prediction
 
toString() - Method in class owltools.gaf.WithInfo
 
toString() - Method in class owltools.graph.OWLGraphEdge
 
toString() - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
toString() - Method in class owltools.graph.OWLQuantifiedProperty
 
toString() - Method in class owltools.ontologyrelease.OortConfiguration
 
toString() - Method in class owltools.ontologyverification.CheckResult
 
toString() - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
toString() - Method in class owltools.sim.ConjunctiveSetSimilarity
 
toString() - Method in class owltools.sim.DisjunctiveSetSimilarity
 
toString() - Method in class owltools.sim.MaximumInformationContentSimilarity
 
toString() - Method in class owltools.sim.OWLObjectPair
 
toString() - Method in class owltools.sim.Similarity
 
translate(GafDocument) - Method in class owltools.gaf.owl.GAFOWLBridge
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.AsymmetricJaccardSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.  
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.  
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.CombinedSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.CombinedSimilarity2
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.ConjunctiveSetSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.DescriptionTreeSimilarity
adds additional axioms specific to this method.
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.DisjunctiveSetSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.JaccardBloomSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.JaccardSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.MaximumInformationContentSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.MultiSimilarity
adds additional axioms specific to this method.
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.OverlapSimilarity
 
translateResultsToOWLAxioms() - Method in class owltools.sim.Similarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.Similarity
 
typeCls - Variable in class owltools.gaf.Bioentity
 
typeIxMap - Variable in class owltools.idmap.IDMappingPIRParser
 
typeMap - Variable in class owltools.idmap.IDMapHandler
 

U

unescape(String) - Static method in class owltools.ontologyrelease.OortConfiguration
Only public for testing purposes.
UniProtIDMapParser - Class in owltools.idmap
 
UniProtIDMapParser() - Constructor for class owltools.idmap.UniProtIDMapParser
 
useImportClosureForQueries() - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 

V

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.gfx.RelationType.Polarity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gfx.RelationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.graph.OWLQuantifiedProperty.Quantifier
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.idmap.IDMappingPIRParser.Types
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataField
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataQualifier
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyrelease.OortConfiguration.MacroStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyverification.CheckResult.Status
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.web.OWLHandler.Param
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.web.OWLHandler.ResultType
Returns the enum constant of this type with the specified name.
values() - Static method in enum owltools.gaf.owl.GAFOWLBridge.Vocab
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gfx.RelationType.Polarity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gfx.RelationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.graph.OWLQuantifiedProperty.Quantifier
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.idmap.IDMappingPIRParser.Types
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataField
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataQualifier
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyrelease.OortConfiguration.MacroStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyverification.CheckResult.Status
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.web.OWLHandler.Param
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.web.OWLHandler.ResultType
Returns an array containing the constants of this enum type, in the order they are declared.

W

width - Variable in class owltools.gfx.GraphStyle
 
width - Variable in class owltools.gfx.OWLGraphLayoutNode
 
WITH - Static variable in class owltools.gaf.GAFParser
 
withExpression - Variable in class owltools.gaf.GeneAnnotation
 
WithInfo - Class in owltools.gaf
 
WithInfo() - Constructor for class owltools.gaf.WithInfo
 
WithInfo(String, String) - Constructor for class owltools.gaf.WithInfo
 
withInfoEmptyList - Static variable in class owltools.gaf.GeneAnnotation
 
withInfoList - Variable in class owltools.gaf.GeneAnnotation
 
withInfos - Variable in class owltools.gaf.GafDocument
 
withXref - Variable in class owltools.gaf.WithInfo
 
writeConfig(File, OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration
Write the given OortConfiguration into the file as properties.

X

x - Variable in class owltools.gfx.OWLGraphLayoutNode
 

Y

y - Variable in class owltools.gfx.OWLGraphLayoutNode
 

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