Index

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A

addCommandLineOptions(Options) - Method in interface org.phyloref.jphyloref.commands.Command

A list of valid command line options.

addCommandLineOptions(Options) - Method in class org.phyloref.jphyloref.commands.ResolveCommand

Add command-line options specific to this command.

addCommandLineOptions(Options) - Method in class org.phyloref.jphyloref.commands.TestCommand

Add command-line options specific to this command.

addCommandLineOptions(Options) - Method in class org.phyloref.jphyloref.commands.WebserverCommand

Add command-line options specific to this command.

addCommandLineOptions(Options) - Static method in class org.phyloref.jphyloref.helpers.ReasonerHelper

Add command line options that can be read by getReasonerFromCmdLine()

C

Command - Interface in org.phyloref.jphyloref.commands

Commands provide commands for jphyloref to run.

createRDFParserForOntology(OWLOntology) - Static method in class org.phyloref.jphyloref.helpers.JSONLDHelper

Create an RDFParser for JSON-LD files.

E

execute(String[]) - Method in class org.phyloref.jphyloref.JPhyloRef

Interpret the command line arguments to determine which command to execute.

execute(CommandLine) - Method in interface org.phyloref.jphyloref.commands.Command

Execute this command with the provided command line options, and provide an exit value to return to the operating system.

execute(CommandLine) - Method in class org.phyloref.jphyloref.commands.ResolveCommand

Set up a webserver to listen on the provided hostname and port (or their defaults).

execute(CommandLine) - Method in class org.phyloref.jphyloref.commands.TestCommand

Given an input ontology, reason over it and determine if nodes are identified correctly.

execute(CommandLine) - Method in class org.phyloref.jphyloref.commands.WebserverCommand

Set up a webserver to listen on the provided hostname and port (or their defaults).

G

getAnnotationLiteralsForEntity(OWLOntology, OWLEntity, OWLAnnotationProperty) - Static method in class org.phyloref.jphyloref.helpers.OWLHelper

Return a Map that contains all known values for a given annotation property for a given OWL entity, grouped by language tags.

getAnnotationLiteralsForEntity(OWLOntology, OWLEntity, OWLAnnotationProperty, List<String>) - Static method in class org.phyloref.jphyloref.helpers.OWLHelper

Extract literal values for an annotation property applied to an OWL entity in an ontology for a particular set of languages.

getDescription() - Method in interface org.phyloref.jphyloref.commands.Command

A one-line description of this command.

getDescription() - Method in class org.phyloref.jphyloref.commands.ResolveCommand

A description of the Resolve command.

getDescription() - Method in class org.phyloref.jphyloref.commands.TestCommand

A description of the Test command.

getDescription() - Method in class org.phyloref.jphyloref.commands.WebserverCommand

A description of the Webserver command.

getIntervalEnd() - Method in class org.phyloref.jphyloref.helpers.PhylorefHelper.PhylorefStatus

getIntervalStart() - Method in class org.phyloref.jphyloref.helpers.PhylorefHelper.PhylorefStatus

getLabelProperty(OWLOntology) - Static method in class org.phyloref.jphyloref.helpers.OWLHelper

Returns OWL property rdfs:label, using a cache so we don't need to load the property using the data property.

getLabelsInEnglish(OWLNamedIndividual, OWLOntology) - Static method in class org.phyloref.jphyloref.helpers.OWLHelper

Return a list of labels for an OWLNamedIndividual in English or (if no such label is known) with no language provided.

getName() - Method in interface org.phyloref.jphyloref.commands.Command

The name of this command.

getName() - Method in class org.phyloref.jphyloref.commands.ResolveCommand

This command is named "resolve".

getName() - Method in class org.phyloref.jphyloref.commands.TestCommand

This command is named "test".

getName() - Method in class org.phyloref.jphyloref.commands.WebserverCommand

This command is named "webserver".

getNodesInClass(OWLClass, OWLOntology, OWLReasoner) - Static method in class org.phyloref.jphyloref.helpers.PhylorefHelper

Get the set of named individuals in a particular OWL class.

getPhyloref() - Method in class org.phyloref.jphyloref.helpers.PhylorefHelper.PhylorefStatus

getPhyloreferences(OWLOntology, OWLReasoner) - Static method in class org.phyloref.jphyloref.helpers.PhylorefHelper

Get a list of phyloreferences in this ontology.

getPhyloreferencesWithoutReasoning(OWLOntology) - Static method in class org.phyloref.jphyloref.helpers.PhylorefHelper

Get a list of phyloreferences in this ontology without reasoning.

getReasonerFactories() - Static method in class org.phyloref.jphyloref.helpers.ReasonerHelper

Get all reasoner factories.

getReasonerFactory(String) - Static method in class org.phyloref.jphyloref.helpers.ReasonerHelper

Get reasoner factory by name.

getReasonerFactoryFromCmdLine(CommandLine) - Static method in class org.phyloref.jphyloref.helpers.ReasonerHelper

Return an OWLReasoner based on the command-line settings.

getReasonerNameAndVersion(OWLReasonerFactory) - Static method in class org.phyloref.jphyloref.helpers.ReasonerHelper

getStatus() - Method in class org.phyloref.jphyloref.helpers.PhylorefHelper.PhylorefStatus

getStatusesForPhyloref(OWLClass, OWLOntology) - Static method in class org.phyloref.jphyloref.helpers.PhylorefHelper

Return a list of PhylorefStatuses associated with a particular phyloreference in the provided ontology.

I

IRI_CDAO_NODE - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for OWL class Phylogeny

IRI_OBI_HAS_SPECIFIED_INPUT - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for the OBI has_specified_input property.

IRI_OBI_IS_SPECIFIED_OUTPUT_OF - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for the OBI is_specified_output_of property.

IRI_PHYLOREFERENCE - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for OWL class Phyloreference

IRI_PSO_DRAFT - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for the publication status of "Draft"

IRI_PSO_HOLDS_STATUS_IN_TIME - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for the OWL object property that associates a publication with its publication status at a particular time.

IRI_PSO_PUBLISHED - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for the publication status of "Published"

IRI_PSO_SUBMITTED - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for the publication status of "Submitted"

IRI_PSO_WITH_STATUS - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for the OWL object property that indicates the publication status of a publication status at a particular time.

IRI_TIMEINT_HAS_INTERVAL_END_DATE - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for the OWL data property that indicates when a publication status time ends

IRI_TIMEINT_HAS_INTERVAL_START_DATE - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for the OWL data property that indicates when a publication status time begins

IRI_TVC_AT_TIME - Static variable in class org.phyloref.jphyloref.helpers.PhylorefHelper

IRI for the OWL object property that associates a publication status at a particular time with a particular time.

J

JPhyloRef - Class in org.phyloref.jphyloref

Main class for JPhyloRef.

JPhyloRef() - Constructor for class org.phyloref.jphyloref.JPhyloRef

JSONLDHelper - Class in org.phyloref.jphyloref.helpers

JSONLDHelper provides methods to help read and process JSON-LD files.

JSONLDHelper() - Constructor for class org.phyloref.jphyloref.helpers.JSONLDHelper

M

main(String[]) - Static method in class org.phyloref.jphyloref.JPhyloRef

Main method for JPhyloRef.

O

org.phyloref.jphyloref - package org.phyloref.jphyloref

org.phyloref.jphyloref.commands - package org.phyloref.jphyloref.commands

org.phyloref.jphyloref.helpers - package org.phyloref.jphyloref.helpers

OWLHelper - Class in org.phyloref.jphyloref.helpers

OWLHelper contains methods simplify accessing information from the OWL API.

OWLHelper() - Constructor for class org.phyloref.jphyloref.helpers.OWLHelper

P

PhylorefHelper - Class in org.phyloref.jphyloref.helpers

A Phyloreference helper class.

PhylorefHelper() - Constructor for class org.phyloref.jphyloref.helpers.PhylorefHelper

PhylorefHelper.PhylorefStatus - Class in org.phyloref.jphyloref.helpers

A wrapper for a phyloref status at a particular point in time.

PhylorefStatus(OWLClass, IRI, Instant, Instant) - Constructor for class org.phyloref.jphyloref.helpers.PhylorefHelper.PhylorefStatus

Create a PhylorefStatus.

R

ReasonerHelper - Class in org.phyloref.jphyloref.helpers

The ReasonerHelper provides methods to help create and manage OWL Reasoners, and to allow the user to choose a different reasoner to carry out any specified task.

ReasonerHelper() - Constructor for class org.phyloref.jphyloref.helpers.ReasonerHelper

ResolveCommand - Class in org.phyloref.jphyloref.commands

Resolve an ontology of phyloreferences provided on the command line, and report on the resolution of each clade definition.

ResolveCommand() - Constructor for class org.phyloref.jphyloref.commands.ResolveCommand

T

TestCommand - Class in org.phyloref.jphyloref.commands

Test whether the phyloreferences in the provided ontology resolve correctly.

TestCommand() - Constructor for class org.phyloref.jphyloref.commands.TestCommand

toString() - Method in class org.phyloref.jphyloref.helpers.PhylorefHelper.PhylorefStatus

V

VERSION - Static variable in class org.phyloref.jphyloref.JPhyloRef

Version of JPhyloRef.

W

WebserverCommand - Class in org.phyloref.jphyloref.commands

Sets up a webserver that allows reasoning over phyloreferences over HTTP.

WebserverCommand() - Constructor for class org.phyloref.jphyloref.commands.WebserverCommand

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