| Name | Description | Type | Package | Framework |
| AbstractParserControl | Class to inherit from so when in future when new controls are added clients will no have to implement them. | Class | org.apache.commons.cli.avalon | CytoScape |
| CLArgsParser | Parser for command line arguments. | Class | org.apache.commons.cli.avalon | CytoScape |
| CLOption | Basic class describing an instance of option. | Class | org.apache.commons.cli.avalon | CytoScape |
| CLOptionDescriptor | Basic class describing an type of option. | Class | org.apache.commons.cli.avalon | CytoScape |
| CLUtil | CLUtil offers basic utility operations for use both internal and external to package. | Class | org.apache.commons.cli.avalon | CytoScape |
| ParserControl | ParserControl is used to control particular behaviour of the parser. | Interface | org.apache.commons.cli.avalon | CytoScape |