Index (robot-command 1.8.3 API)

A C D E F G H M O P Q R S T U V
All Classes All Packages

A

addCommand(String, Command) - Method in class org.obolibrary.robot.CommandManager: Add a new command to this manager.
AnnotateCommand - Class in org.obolibrary.robot: Add and remove annotations from an ontology.
AnnotateCommand() - Constructor for class org.obolibrary.robot.AnnotateCommand: Initialize the command.

C

cleanAxiomStrings(CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line, get the 'axioms' option(s) and make sure all are properly split and return one axiom selector per list entry.
CollapseCommand - Class in org.obolibrary.robot
CollapseCommand() - Constructor for class org.obolibrary.robot.CollapseCommand: Initialize the command.
Command - Interface in org.obolibrary.robot: A simple interface for all ROBOT commands.
CommandLineHelper - Class in org.obolibrary.robot: Convenience methods for working with command line options.
CommandLineHelper() - Constructor for class org.obolibrary.robot.CommandLineHelper
CommandLineInterface - Class in org.obolibrary.robot: Entry point for ROBOT command-line interface.
CommandLineInterface() - Constructor for class org.obolibrary.robot.CommandLineInterface
CommandManager - Class in org.obolibrary.robot: Execute collections of commands.
CommandManager() - Constructor for class org.obolibrary.robot.CommandManager: Initialze the command.
CommandState - Class in org.obolibrary.robot: A simple state container for communicating between Commands.
CommandState() - Constructor for class org.obolibrary.robot.CommandState
ConvertCommand - Class in org.obolibrary.robot: Save ontology to a different format.
ConvertCommand() - Constructor for class org.obolibrary.robot.ConvertCommand: Initialize the command.

D

DiffCommand - Class in org.obolibrary.robot: A command to get the differences between two ontology files.
DiffCommand() - Constructor for class org.obolibrary.robot.DiffCommand: Initialze the command.

E

ExceptionHelper - Class in org.obolibrary.robot: Convenience class to handle formatting error messages and returning links to user support.
ExceptionHelper() - Constructor for class org.obolibrary.robot.ExceptionHelper
execute(String[]) - Static method in class org.obolibrary.robot.CommandLineInterface: Execute the given command-line arguments, throwing any exceptions.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.AnnotateCommand: Given an input state and command line arguments, add or remove ontology annotations and return the modified state.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.CollapseCommand
execute(CommandState, String[]) - Method in interface org.obolibrary.robot.Command: All commands offer an execute method that can be chained from previous commands.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.CommandManager: Given an input state and command-line arguments, execute one or more commands.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.ConvertCommand: Given an input state and command line arguments, save the ontology to a new format and return the state unchanged.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.DiffCommand: Given an input state and command line arguments, report on the differences between ontologies, if any, and return the state unchanged.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.ExplainCommand
execute(CommandState, String[]) - Method in class org.obolibrary.robot.ExportCommand: Given an input state and command line arguments, build a new ontology from the given template, and return a state with the new ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.ExportPrefixesCommand: Given an input state and command line arguments, export the current prefixes and return the state unchanged.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.ExtractCommand: Given an input state and command line arguments, extract a new ontology and return an new state.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.FilterCommand: Given an input state and command line arguments, filter axioms from its ontology, modifying it, and return a state with the modified ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.MaterializeCommand: Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.MeasureCommand: Given an input state and command line arguments, compute metrics in ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.MergeCommand: Given an input state and command line arguments, merge all ontology axioms into the first ontology and return a state with the merged ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.MirrorCommand: Mirrors the input ontologgy and its imports closure.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.PythonCommand: Runs ROBOT accessible via Python.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.QueryCommand: Given an input state and command line arguments, query the ontolgy.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.ReasonCommand: Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.ReduceCommand: Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.RelaxCommand: Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.RemoveCommand: Given an input state and command line arguments, create a new ontology with removed axioms and return a new state.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.RenameCommand: Given an input state and command line arguments, rename the entity IRIs in the ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.RepairCommand: Given an input state and command line arguments, repair a new ontology and return an new state.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.ReportCommand: Given an input state and command line arguments, report a new ontology and return an new state.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.TemplateCommand: Given an input state and command line arguments, build a new ontology from the given template, and return a state with the new ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.UnmergeCommand: Given an input state and command line arguments, unmerge all ontology axioms into the first ontology and return a state with the unmerged ontology.
execute(CommandState, String[]) - Method in class org.obolibrary.robot.ValidateProfileCommand
execute(CommandState, String[]) - Method in class org.obolibrary.robot.VerifyCommand: Given an input state and command line arguments, verify that the SPARQL queries return no results.
executeCommand(CommandState, List<String>, List<String>) - Method in class org.obolibrary.robot.CommandManager: Given an input state, global option strings, and remaining command-line argument strings, use as many arguments as needed to execute a single command.
ExplainCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the ExplainOperation.
ExplainCommand() - Constructor for class org.obolibrary.robot.ExplainCommand
ExportCommand - Class in org.obolibrary.robot
ExportCommand() - Constructor for class org.obolibrary.robot.ExportCommand: Initialize the command.
ExportPrefixesCommand - Class in org.obolibrary.robot: Export prefixes to a file.
ExportPrefixesCommand() - Constructor for class org.obolibrary.robot.ExportPrefixesCommand: Initialze the command.
ExtendedPosixParser - Class in org.obolibrary.robot: Deprecated.
ExtendedPosixParser(boolean) - Constructor for class org.obolibrary.robot.ExtendedPosixParser: Deprecated.
ExtractCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the ExtractOperation.
ExtractCommand() - Constructor for class org.obolibrary.robot.ExtractCommand: Initialze the command.

F

FilterCommand - Class in org.obolibrary.robot: Create a subset of an ontology based on a series of inputs.
FilterCommand() - Constructor for class org.obolibrary.robot.FilterCommand: Initialize the command.

G

getAddPrefixes(CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line, get a map of all prefixes to use and add to the output.
getAxiomValues(CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Deprecated.
split into methods CommandLineHelper.cleanAxiomStrings(CommandLine) and others in RelatedObjectsHelper
getBaseNamespaces(CommandLine, IOHelper) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line and an IOHelper, return a list of base namespaces from the '--base-iri' option.
getBooleanValue(CommandLine, String, boolean) - Static method in class org.obolibrary.robot.CommandLineHelper: Get the boolean value of a command-line option with the given name.
getBooleanValue(CommandLine, String, boolean, boolean) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line, an argument name, the boolean default value, and boolean if the arg is optional, return the value of the command-line option 'name'.
getCatalogPath() - Method in class org.obolibrary.robot.CommandState: Get the catalog path.
getCommand(CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line, return its first argument, which should be the name of the command to execute.
getCommandLine(String, Options, String[]) - Static method in class org.obolibrary.robot.CommandLineHelper: Parse the command line, handle help and other common options, (May exit!) and return a CommandLine.
getCommonOptions() - Static method in class org.obolibrary.robot.CommandLineHelper: Create a new Options object with shared options for 'help' and 'version'.
getDefaultValue(CommandLine, String, String) - Static method in class org.obolibrary.robot.CommandLineHelper: Get the value of the command-line option with the given name, or return a default value if the option is not found.
getDescription() - Method in class org.obolibrary.robot.AnnotateCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.CollapseCommand: Brief description of the command.
getDescription() - Method in interface org.obolibrary.robot.Command: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.CommandManager: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.ConvertCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.DiffCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.ExplainCommand
getDescription() - Method in class org.obolibrary.robot.ExportCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.ExportPrefixesCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.ExtractCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.FilterCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.MaterializeCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.MeasureCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.MergeCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.MirrorCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.PythonCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.QueryCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.ReasonCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.ReduceCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.RelaxCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.RemoveCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.RenameCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.RepairCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.ReportCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.TemplateCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.UnmergeCommand: Brief description of the command.
getDescription() - Method in class org.obolibrary.robot.ValidateProfileCommand
getDescription() - Method in class org.obolibrary.robot.VerifyCommand: Brief description of the command.
getIndexValue(CommandLine, int) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line and an index, return the argument at that index.
getInputOntologies(IOHelper, CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given an IOHelper and a command line, check input options and return a list of loaded input ontologies.
getInputOntologies(IOHelper, CommandLine, boolean) - Static method in class org.obolibrary.robot.CommandLineHelper: Given an IOHelper and a command line, check for required options and return a list of loaded input ontologies.
getInputOntologies(IOHelper, CommandLine, String) - Static method in class org.obolibrary.robot.CommandLineHelper: Given an IOHelper, a command line, and the path to a catalog file, check input options and return a list of loaded input ontologies with the catalog file.
getInputOntology(IOHelper, CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given an IOHelper and a command line, check for required options and return a loaded input ontology.
getInputOntology(IOHelper, CommandLine, String) - Static method in class org.obolibrary.robot.CommandLineHelper: Given an IOHelper, a command line, and a path to a catalog, return an OWLOntology loaded from input or input-iri using the specified catalog (or null).
getIOHelper(CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line, return an initialized IOHelper.
getName() - Method in class org.obolibrary.robot.AnnotateCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.CollapseCommand: Name of the command.
getName() - Method in interface org.obolibrary.robot.Command: Name of the command.
getName() - Method in class org.obolibrary.robot.CommandManager: Name of the command.
getName() - Method in class org.obolibrary.robot.ConvertCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.DiffCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.ExplainCommand
getName() - Method in class org.obolibrary.robot.ExportCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.ExportPrefixesCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.ExtractCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.FilterCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.MaterializeCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.MeasureCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.MergeCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.MirrorCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.PythonCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.QueryCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.ReasonCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.ReduceCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.RelaxCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.RemoveCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.RenameCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.RepairCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.ReportCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.TemplateCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.UnmergeCommand: Name of the command.
getName() - Method in class org.obolibrary.robot.ValidateProfileCommand
getName() - Method in class org.obolibrary.robot.VerifyCommand: Name of the command.
getObjects(CommandLine, IOHelper, OWLOntology, List<List<String>>) - Static method in class org.obolibrary.robot.RemoveCommand: Given a command line, an IOHelper, an ontology, and a list of select groups, return the objects from the ontology based on the select groups.
getOntology() - Method in class org.obolibrary.robot.CommandState: Get the ontology (not a copy).
getOntologyPath() - Method in class org.obolibrary.robot.CommandState: Get the ontology path.
getOptionalValue(CommandLine, String) - Static method in class org.obolibrary.robot.CommandLineHelper: Get the value of the command-line option with the given name.
getOptionalValues(CommandLine, String) - Static method in class org.obolibrary.robot.CommandLineHelper: Get the value of the command-line options with the given name.
getOptionArgs(Options, List<String>) - Method in class org.obolibrary.robot.CommandManager: Given some Options and some arguments, collect all the options until the first non-option argument, then remove those used argument strings from the arguments list and return the used arguments as a new list.
getOptions() - Method in class org.obolibrary.robot.AnnotateCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.CollapseCommand: Command-line options for the command.
getOptions() - Method in interface org.obolibrary.robot.Command: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.CommandManager: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.ConvertCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.DiffCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.ExplainCommand
getOptions() - Method in class org.obolibrary.robot.ExportCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.ExportPrefixesCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.ExtractCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.FilterCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.MaterializeCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.MeasureCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.MergeCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.MirrorCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.PythonCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.QueryCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.ReasonCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.ReduceCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.RelaxCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.RemoveCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.RenameCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.RepairCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.ReportCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.TemplateCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.UnmergeCommand: Command-line options for the command.
getOptions() - Method in class org.obolibrary.robot.ValidateProfileCommand
getOptions() - Method in class org.obolibrary.robot.VerifyCommand: Command-line options for the command.
getOptionValues(CommandLine, String) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line, return the values for an option as a list.
getOutputFile(CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line, check for the required options and return a File for saving data.
getOutputIRI(CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line, check for the required options and return an IRI to be used as the OntologyIRI for the output ontology.
getReasonerFactory(CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a string of a reasoner name from user input, return the reasoner factory.
getReasonerFactory(CommandLine, boolean) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a string of a reasoner name from user input, return the reasoner factory.
getRequiredValue(CommandLine, String, String) - Static method in class org.obolibrary.robot.CommandLineHelper: Get the value of the command-line option with the given name, or throw an IllegalArgumentException with a given message if the option is not found.
getTerms(IOHelper, CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given an IOHelper and a command line, check for the required options and return a set of IRIs for terms.
getTerms(IOHelper, CommandLine, boolean) - Static method in class org.obolibrary.robot.CommandLineHelper: As getTerms, but allow the list to be empty.
getTerms(IOHelper, CommandLine, String, String) - Static method in class org.obolibrary.robot.CommandLineHelper: Given an IOHelper and a command line, and the names of two options, check for the required options and return a set of IRIs for terms.
getUsage() - Method in class org.obolibrary.robot.AnnotateCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.CollapseCommand: Command-line usage for the command.
getUsage() - Method in interface org.obolibrary.robot.Command: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.CommandManager: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.ConvertCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.DiffCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.ExplainCommand
getUsage() - Method in class org.obolibrary.robot.ExportCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.ExportPrefixesCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.ExtractCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.FilterCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.MaterializeCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.MeasureCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.MergeCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.MirrorCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.PythonCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.QueryCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.ReasonCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.ReduceCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.RelaxCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.RemoveCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.RenameCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.RepairCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.ReportCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.TemplateCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.UnmergeCommand: Command-line usage for the command.
getUsage() - Method in class org.obolibrary.robot.ValidateProfileCommand
getUsage() - Method in class org.obolibrary.robot.VerifyCommand: Command-line usage for the command.
global - Static variable in interface org.obolibrary.robot.Command

H

handleException(Exception) - Static method in class org.obolibrary.robot.CommandLineHelper: Shared method for dealing with exceptions, printing help, and exiting.
handleException(Exception) - Static method in class org.obolibrary.robot.ExceptionHelper: Prints the exception details as errors, including help URL (if the exception message contains a valid exception ID).
handleException(String, Options, Exception) - Static method in class org.obolibrary.robot.CommandLineHelper: Shared method for dealing with exceptions, printing help, and exiting.
hasFlagOrCommand(CommandLine, String) - Static method in class org.obolibrary.robot.CommandLineHelper: Return true if a command line include the option with the given name, or the command with the given name.

M

main(String[]) - Method in class org.obolibrary.robot.AnnotateCommand: Handle the command-line and file operations for the command.
main(String[]) - Method in class org.obolibrary.robot.CollapseCommand: Handle the command-line and file operations for the ReasonOperation.
main(String[]) - Method in interface org.obolibrary.robot.Command: All commands can be call from the Java command line with an array of strings as arguments.
main(String[]) - Static method in class org.obolibrary.robot.CommandLineInterface: Execute the given command-line arguments, catching any exceptions.
main(String[]) - Method in class org.obolibrary.robot.CommandManager: Given command-line arguments, execute one or more commands.
main(String[]) - Method in class org.obolibrary.robot.ConvertCommand: Handle the command-line and file operations for the ReasonOperation.
main(String[]) - Method in class org.obolibrary.robot.DiffCommand: Handle the command-line and file operations for the DiffOperation.
main(String[]) - Method in class org.obolibrary.robot.ExplainCommand: Handle the command-line and file operations for the ExplainOperation.
main(String[]) - Method in class org.obolibrary.robot.ExportCommand: Handle the command-line and file operations for the TemplateOperation.
main(String[]) - Method in class org.obolibrary.robot.ExportPrefixesCommand: Handle the command-line and file operations for the command.
main(String[]) - Method in class org.obolibrary.robot.ExtractCommand: Handle the command-line and file operations for the ExtractOperation.
main(String[]) - Method in class org.obolibrary.robot.FilterCommand: Handle the command-line and file operations.
main(String[]) - Method in class org.obolibrary.robot.MaterializeCommand: Handle the command-line and file operations for the ReasonOperation.
main(String[]) - Method in class org.obolibrary.robot.MeasureCommand: Handle the command-line and file operations for the MeasureOperation.
main(String[]) - Method in class org.obolibrary.robot.MergeCommand: Handle the command-line and file operations for the MergeOperation.
main(String[]) - Method in class org.obolibrary.robot.MirrorCommand: Handle the command-line and file operations for the ReasonOperation.
main(String[]) - Method in class org.obolibrary.robot.PythonCommand: Handle the command-line and file operations for the ReasonOperation.
main(String[]) - Method in class org.obolibrary.robot.QueryCommand: Handle the command-line and file operations for the QueryOperation.
main(String[]) - Method in class org.obolibrary.robot.ReasonCommand: Handle the command-line and file operations for the ReasonOperation.
main(String[]) - Method in class org.obolibrary.robot.ReduceCommand: Handle the command-line and file operations for the reduceOperation.
main(String[]) - Method in class org.obolibrary.robot.RelaxCommand: Handle the command-line and file operations for the relaxOperation.
main(String[]) - Method in class org.obolibrary.robot.RemoveCommand: Handle the command-line and file operations.
main(String[]) - Method in class org.obolibrary.robot.RenameCommand: Handle the command-line and file operations.
main(String[]) - Method in class org.obolibrary.robot.RepairCommand: Handle the command-line and file operations for the RepairOperation.
main(String[]) - Method in class org.obolibrary.robot.ReportCommand: Handle the command-line and file operations for the reportOperation.
main(String[]) - Method in class org.obolibrary.robot.TemplateCommand: Handle the command-line and file operations for the TemplateOperation.
main(String[]) - Method in class org.obolibrary.robot.UnmergeCommand: Handle the command-line and file operations for the UnergeOperation.
main(String[]) - Method in class org.obolibrary.robot.ValidateProfileCommand
main(String[]) - Method in class org.obolibrary.robot.VerifyCommand: Handle the command-line and file operations for the VerifyOperation.
MaterializeCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the MaterializeOperation.
MaterializeCommand() - Constructor for class org.obolibrary.robot.MaterializeCommand: Initialize the command.
maybeCreateIRI(IOHelper, String, String) - Static method in class org.obolibrary.robot.CommandLineHelper: Try to create an IRI from a string input.
maybeGetCommandLine(String, Options, String[], boolean) - Static method in class org.obolibrary.robot.CommandLineHelper: Parse the command line, handle help and other common options, and return null or a CommandLine.
maybeSaveOutput(CommandLine, OWLOntology) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a command line and an ontology, for each `--output` option (if any), save a copy of the ontology to the specified path.
MeasureCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the MeasureOperation.
MeasureCommand() - Constructor for class org.obolibrary.robot.MeasureCommand: Initialze the command.
MergeCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the MergeOperation.
MergeCommand() - Constructor for class org.obolibrary.robot.MergeCommand: Initialize the command.
MirrorCommand - Class in org.obolibrary.robot: Mirrors an ontology plus its imports closure locally.
MirrorCommand() - Constructor for class org.obolibrary.robot.MirrorCommand: Initialize the command.
missingFileError - Static variable in interface org.obolibrary.robot.Command

O

org.obolibrary.robot - package org.obolibrary.robot

P

parseArgList(String) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a single string, return a list of strings split at whitespace but allowing for quoted values, as a command-line parser does.
parseArgs(String) - Static method in class org.obolibrary.robot.CommandLineHelper: Given a single string, return an array of strings split at whitespace but allowing for quoted values, as a command-line parser does.
printHelp() - Method in class org.obolibrary.robot.CommandManager: Print general help plus a list of available commands.
printHelp(String, Options) - Static method in class org.obolibrary.robot.CommandLineHelper: Print a help message for a command.
printHelpEntry(String, String) - Method in class org.obolibrary.robot.CommandManager: Print a help entry for a single command.
printHelpEntry(Map.Entry<String, Command>) - Method in class org.obolibrary.robot.CommandManager: Print a help entry for a single command.
printVersion() - Static method in class org.obolibrary.robot.CommandLineHelper: Print the ROBOT version
processOption(String, ListIterator<String>) - Method in class org.obolibrary.robot.ExtendedPosixParser: Deprecated.
PythonCommand - Class in org.obolibrary.robot: Starts a gateway server for Py4J to execute ROBOT operations via Python.
PythonCommand() - Constructor for class org.obolibrary.robot.PythonCommand: Initialize the command.

Q

QueryCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the QueryOperation.
QueryCommand() - Constructor for class org.obolibrary.robot.QueryCommand: Initialze the command.

R

ReasonCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the ReasonOperation.
ReasonCommand() - Constructor for class org.obolibrary.robot.ReasonCommand: Initialize the command.
ReduceCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the ReduceOperation.
ReduceCommand() - Constructor for class org.obolibrary.robot.ReduceCommand: Initialize the command.
RelaxCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the RelaxOperation.
RelaxCommand() - Constructor for class org.obolibrary.robot.RelaxCommand: Initialize the command.
RemoveCommand - Class in org.obolibrary.robot: Remove axioms from an ontology based on a series of inputs.
RemoveCommand() - Constructor for class org.obolibrary.robot.RemoveCommand: Initialze the command.
RenameCommand - Class in org.obolibrary.robot
RenameCommand() - Constructor for class org.obolibrary.robot.RenameCommand: Initialze the command.
RepairCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the RepairOperation.
RepairCommand() - Constructor for class org.obolibrary.robot.RepairCommand: Initialze the command.
ReportCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the ReportOperation.
ReportCommand() - Constructor for class org.obolibrary.robot.ReportCommand: Initialze the command.

S

setCatalogPath(String) - Method in class org.obolibrary.robot.CommandState: Set the catalog path.
setOntology(OWLOntology) - Method in class org.obolibrary.robot.CommandState: Set the ontology.
setOntologyPath(String) - Method in class org.obolibrary.robot.CommandState: Set the ontology path.
splitSelects(String) - Static method in class org.obolibrary.robot.CommandLineHelper: Given an input string, return a list of the string split on whitespace, while ignoring any whitespace in single string quotes.

T

TemplateCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the TemplateOperation.
TemplateCommand() - Constructor for class org.obolibrary.robot.TemplateCommand: Initialize the command.

U

UnmergeCommand - Class in org.obolibrary.robot: Handles inputs and outputs for the UnmergeOperation.
UnmergeCommand() - Constructor for class org.obolibrary.robot.UnmergeCommand: Initialize the command.
updateInputOntology(IOHelper, CommandState, CommandLine) - Static method in class org.obolibrary.robot.CommandLineHelper: Given an IOHelper, a state object, and a command line, update the state with the ontology.
updateInputOntology(IOHelper, CommandState, CommandLine, boolean) - Static method in class org.obolibrary.robot.CommandLineHelper: Given an IOHelper, a state object, a command line, and a "required" flag, update the state with the ontology.

V

ValidateProfileCommand - Class in org.obolibrary.robot
ValidateProfileCommand() - Constructor for class org.obolibrary.robot.ValidateProfileCommand: Initialize the command.
VerifyCommand - Class in org.obolibrary.robot: Command that runs a sparql query expecting zero results.
VerifyCommand() - Constructor for class org.obolibrary.robot.VerifyCommand: Initialze the command.

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