Index (Uberon ROBOT plugin 0.5.1-SNAPSHOT API)

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A

addPreservedPrefix(String) - Method in class org.incenp.obofoundry.uberon.util.EquivalenceSetMerger: Add a preserved prefix.

B

BasePlugin - Class in org.incenp.obofoundry.uberon: Helper base class for ROBOT commands.
BasePlugin(String, String, String) - Constructor for class org.incenp.obofoundry.uberon.BasePlugin: Creates a new command.

D

DefaultSpeciesSubsetter - Class in org.incenp.obofoundry.uberon.util: The “default” strategy to create a taxon-specific subset.
DefaultSpeciesSubsetter() - Constructor for class org.incenp.obofoundry.uberon.util.DefaultSpeciesSubsetter
DELETE - Enum constant in enum class org.incenp.obofoundry.uberon.util.SpeciesMerger.GCAMergeMode: Delete general class axioms that refer to a to-be-merged class.

E

EquivalenceSetMerger - Class in org.incenp.obofoundry.uberon.util: A helper class to merge classes that are inferred to be equivalent.
EquivalenceSetMerger() - Constructor for class org.incenp.obofoundry.uberon.util.EquivalenceSetMerger
execute(CommandState, String[]) - Method in class org.incenp.obofoundry.uberon.BasePlugin

G

getDescription() - Method in class org.incenp.obofoundry.uberon.BasePlugin
getIOHelper() - Method in class org.incenp.obofoundry.uberon.BasePlugin
getIRI(String, String) - Method in class org.incenp.obofoundry.uberon.BasePlugin: Create an IRI from a user-specified source.
getName() - Method in class org.incenp.obofoundry.uberon.BasePlugin
getOptions() - Method in class org.incenp.obofoundry.uberon.BasePlugin
getSubset(OWLOntology, OWLReasoner, Collection<IRI>, IRI) - Method in class org.incenp.obofoundry.uberon.util.DefaultSpeciesSubsetter
getSubset(OWLOntology, OWLReasoner, Collection<IRI>, IRI) - Method in interface org.incenp.obofoundry.uberon.util.ISpeciesSubsetStrategy: Creates a taxon-specific subset of the given ontology.
getSubset(OWLOntology, OWLReasoner, Collection<IRI>, IRI) - Method in class org.incenp.obofoundry.uberon.util.PreciseSpeciesSubsetter
getUsage() - Method in class org.incenp.obofoundry.uberon.BasePlugin

I

IN_TAXON - Static variable in interface org.incenp.obofoundry.uberon.util.ISpeciesSubsetStrategy
InferenceDiffCommand - Class in org.incenp.obofoundry.uberon: A command to produce a report on the consequences of logical changes between two versions of the same ontology.
InferenceDiffCommand() - Constructor for class org.incenp.obofoundry.uberon.InferenceDiffCommand
ISpeciesSubsetStrategy - Interface in org.incenp.obofoundry.uberon.util: Represents a strategy to create a taxon-specific subset of an ontology.

M

main(String[]) - Method in class org.incenp.obofoundry.uberon.BasePlugin
merge(IRI, IRI, String, List<IRI>) - Method in class org.incenp.obofoundry.uberon.util.SpeciesMerger: Unfold classes for the specified taxon over the specified linking property.
merge(OWLOntology, OWLReasoner) - Method in class org.incenp.obofoundry.uberon.util.EquivalenceSetMerger: Merge inferred equivalent classes in an ontology.
MergeEquivalentSetsCommand - Class in org.incenp.obofoundry.uberon: A command to merge sets of equivalent classes across ontologies.
MergeEquivalentSetsCommand() - Constructor for class org.incenp.obofoundry.uberon.MergeEquivalentSetsCommand
MergeSpeciesCommand - Class in org.incenp.obofoundry.uberon: A command to fold species-specific classes to form a “composite” ontology.
MergeSpeciesCommand() - Constructor for class org.incenp.obofoundry.uberon.MergeSpeciesCommand

O

options - Variable in class org.incenp.obofoundry.uberon.BasePlugin
org.incenp.obofoundry.uberon - package org.incenp.obofoundry.uberon
org.incenp.obofoundry.uberon.util - package org.incenp.obofoundry.uberon.util
ORIGINAL - Enum constant in enum class org.incenp.obofoundry.uberon.util.SpeciesMerger.GCAMergeMode: Keep general class axioms as they are.

P

performOperation(CommandState, CommandLine) - Method in class org.incenp.obofoundry.uberon.BasePlugin: Perform whatever operation the command is supposed to do.
performOperation(CommandState, CommandLine) - Method in class org.incenp.obofoundry.uberon.InferenceDiffCommand
performOperation(CommandState, CommandLine) - Method in class org.incenp.obofoundry.uberon.MergeEquivalentSetsCommand
performOperation(CommandState, CommandLine) - Method in class org.incenp.obofoundry.uberon.MergeSpeciesCommand
performOperation(CommandState, CommandLine) - Method in class org.incenp.obofoundry.uberon.SpeciesSubsetCommand
PreciseSpeciesSubsetter - Class in org.incenp.obofoundry.uberon.util: A “precise” strategy to create a taxon-specific subset, as an alternative to the strategy implemented in DefaultSpeciesSubsetter.
PreciseSpeciesSubsetter() - Constructor for class org.incenp.obofoundry.uberon.util.PreciseSpeciesSubsetter

R

ReasoningException - Exception in org.incenp.obofoundry.uberon.util: This exception may be thrown by other classes in this package if an error occurs when reasoning over an ontology (for example, if the ontology is unexpectedly inconsistent).
ReasoningException(String) - Constructor for exception org.incenp.obofoundry.uberon.util.ReasoningException: Creates a new instance.
ReasoningException(String, Set<OWLClass>) - Constructor for exception org.incenp.obofoundry.uberon.util.ReasoningException: Creates a new instance for cases where classes were found to be unsatisfiable.

S

setAddEquivalenceAxioms(boolean) - Method in class org.incenp.obofoundry.uberon.util.EquivalenceSetMerger: Enable or disable the generation of cross-reference annotations.
setExtendedTranslation(boolean) - Method in class org.incenp.obofoundry.uberon.util.SpeciesMerger: Enables or disables the translation of more class expressions.
setGCAMode(SpeciesMerger.GCAMergeMode) - Method in class org.incenp.obofoundry.uberon.util.SpeciesMerger: Sets the behaviour for general class axioms (GCAs) that have one (or more) merged class in their signature.
setPrefixScore(String, Double) - Method in class org.incenp.obofoundry.uberon.util.EquivalenceSetMerger: Set the priority score for a given prefix.
setPropertyPrefixScore(OWLAnnotationProperty, String, Double) - Method in class org.incenp.obofoundry.uberon.util.EquivalenceSetMerger: Set a property-specific score for a given prefix.
setRemoveDeclarationAxiom(boolean) - Method in class org.incenp.obofoundry.uberon.util.SpeciesMerger: Enables or disables removal of declaration axioms for classes that have been replaced by a translated expression.
SpeciesMerger - Class in org.incenp.obofoundry.uberon.util: This class may be used to create multi-species ontologies following the "composite/merger" strategy described in Uberon's wiki.
SpeciesMerger(OWLOntology, OWLReasoner) - Constructor for class org.incenp.obofoundry.uberon.util.SpeciesMerger: Creates a new instance.
SpeciesMerger.GCAMergeMode - Enum Class in org.incenp.obofoundry.uberon.util: Mode of operation for general class axioms.
SpeciesSubsetCommand - Class in org.incenp.obofoundry.uberon: A command to create a taxon-specific subset of an ontology, that is a subset containing only the classes that are valid for a given taxon.
SpeciesSubsetCommand() - Constructor for class org.incenp.obofoundry.uberon.SpeciesSubsetCommand

T

TRANSLATE - Enum constant in enum class org.incenp.obofoundry.uberon.util.SpeciesMerger.GCAMergeMode: Translate general class axioms that refer to a to-be-merged class.

V

valueOf(String) - Static method in enum class org.incenp.obofoundry.uberon.util.SpeciesMerger.GCAMergeMode: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.incenp.obofoundry.uberon.util.SpeciesMerger.GCAMergeMode: Returns an array containing the constants of this enum class, in the order they are declared.
visit(OWLAnnotationAssertionAxiom) - Method in class org.incenp.obofoundry.uberon.util.SpeciesMerger
visit(OWLEquivalentClassesAxiom) - Method in class org.incenp.obofoundry.uberon.util.SpeciesMerger
visit(OWLSubClassOfAxiom) - Method in class org.incenp.obofoundry.uberon.util.SpeciesMerger

A B D E G I M O P R S T V
All Classes and Interfaces|All Packages|Serialized Form