A C D E F G H M O P Q R S T U V
All Classes All Packages
All Classes All Packages
All Classes All Packages
A
- addCommand(String, Command) - Method in class org.obolibrary.robot.CommandManager
-
Add a new command to this manager.
- addPluggableCommands(CommandManager) - Method in class org.obolibrary.robot.PluginManager
-
Find pluggable commands and add them to a CommandManager.
- 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.ExpandCommand
-
Given an input state and command line arguments, expand macro relations, and add axioms to the input ontology, returning a state with the updated ontology.
- 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.
- ExpandCommand - Class in org.obolibrary.robot
-
Handles inputs and outputs for the
ExpandOperation
. - ExpandCommand() - Constructor for class org.obolibrary.robot.ExpandCommand
-
Initialize the 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 inRelatedObjectsHelper
- 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.ExpandCommand
-
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.ExpandCommand
-
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.ExpandCommand
-
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.ExpandCommand
-
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.ExpandCommand
-
Handle the command-line and file operations for the ExpandOperation.
- 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.
- PluginManager - Class in org.obolibrary.robot
-
Pluggable commands loader.
- PluginManager() - Constructor for class org.obolibrary.robot.PluginManager
- 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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