- 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(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(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.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.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
-
- 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
-
A custom CommandLineParser that ignores unrecognized options without throwing an exeception.
- ExtendedPosixParser(boolean) - Constructor for class org.obolibrary.robot.ExtendedPosixParser
-
Extend constructor to accept ignore option.
- ExtractCommand - Class in org.obolibrary.robot
-
- ExtractCommand() - Constructor for class org.obolibrary.robot.ExtractCommand
-
Initialze the command.
- 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
-
- 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, 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'.
- 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.
- 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.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, 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) - 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, 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.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.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.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
-
- 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.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
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Handle the command-line and file operations for the reportOperation.
- main(String[]) - Method in class org.obolibrary.robot.TemplateCommand
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Handle the command-line and file operations for the TemplateOperation.
- main(String[]) - Method in class org.obolibrary.robot.UnmergeCommand
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Handle the command-line and file operations for the UnergeOperation.
- main(String[]) - Method in class org.obolibrary.robot.ValidateProfileCommand
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- main(String[]) - Method in class org.obolibrary.robot.VerifyCommand
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Handle the command-line and file operations for the VerifyOperation.
- MaterializeCommand - Class in org.obolibrary.robot
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- MaterializeCommand() - Constructor for class org.obolibrary.robot.MaterializeCommand
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Initialize the command.
- maybeCreateIRI(IOHelper, String, String) - Static method in class org.obolibrary.robot.CommandLineHelper
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Try to create an IRI from a string input.
- maybeGetCommandLine(String, Options, String[], boolean) - Static method in class org.obolibrary.robot.CommandLineHelper
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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
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Given a command line and an ontology, for each `--output` option (if any), save a copy of the
ontology to the specified path.
- MergeCommand - Class in org.obolibrary.robot
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- MergeCommand() - Constructor for class org.obolibrary.robot.MergeCommand
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Initialize the command.
- MirrorCommand - Class in org.obolibrary.robot
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Mirrors an ontology plus its imports closure locally.
- MirrorCommand() - Constructor for class org.obolibrary.robot.MirrorCommand
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Initialize the command.
- missingFileError - Static variable in interface org.obolibrary.robot.Command
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