Package org.incenp.obofoundry.uberon

Class SpeciesSubsetCommand

java.lang.Object

org.incenp.obofoundry.uberon.BasePlugin

org.incenp.obofoundry.uberon.SpeciesSubsetCommand

All Implemented Interfaces:

org.obolibrary.robot.Command

public class SpeciesSubsetCommand
extends BasePlugin

A command to create a taxon-specific subset of an ontology, that is a subset containing only the classes that are valid for a given taxon.

This command is intended to replace OWLTools’ --make-species-subset. It provides two different strategies to create the subset:

• the strategy used by the original OWLTools command (default), which basically consists in asserting owl:Thing in_taxon some THE_TAXON and excluding all classes that are unsatisfiable as a result of that assertion;
• an alternative strategy (precise), which basically consists in including each class for which the expression THE_CLASS and in_taxon some THE_TAXON is satisfiable.

Field Summary

Fields inherited from class org.incenp.obofoundry.uberon.BasePlugin

options

Fields inherited from interface org.obolibrary.robot.Command

global, missingFileError

Constructor Summary

Constructors

Constructor	Description
SpeciesSubsetCommand()

Method Summary

Modifier and Type	Method	Description
void	performOperation(org.obolibrary.robot.CommandState state, org.apache.commons.cli.CommandLine line)	Perform whatever operation the command is supposed to do.

Methods inherited from class org.incenp.obofoundry.uberon.BasePlugin

execute, getDescription, getIOHelper, getIRI, getName, getOptions, getUsage, main

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SpeciesSubsetCommand

public SpeciesSubsetCommand()

Method Details

performOperation

public void performOperation(org.obolibrary.robot.CommandState state,
 org.apache.commons.cli.CommandLine line)
                      throws Exception

Description copied from class: BasePlugin

Perform whatever operation the command is supposed to do.

Specified by:

performOperation in class BasePlugin

Parameters:

state - The internal state of ROBOT.

line - The command line used to invoke the command.

Throws:

Exception - If any error occurred when attempting to execute the operation.