## *Core App*: Command Line Impl ### Note: This app is pre-installed in Cytoscape 3.3 or later **_You should not download this app_ from the store yourself. If Cytoscape detects that a new version is available in the App Store, it will notify you as it's starting and will give you a chance to download it directly.** **_You should not download this app_ if your Cytoscape is earlier than 3.3. An earlier version of this app is pre-installed in your Cytoscape, and this app cannot replace it.** The Command Line Implementation core app provides a simple command-line interface to Cytoscape using the org.cytoscape.command APIs. Any app that registers task factories with command namespaces and commands will be available through the Command Line Dialog provided by this implementation that allows the user to type commands into Cytoscape and see the results in a "Reply Log". These commands are the same commands that may be added to a Cytoscape script file. Each line in the script file is a command that is handled by Cytoscape or the appropriate App. Script files may be entered on the Cytoscape command line using the "-S" flag to Cytoscape, or through the "Execute Command File..." menu item under Tools. commandDialog uses the AvailableCommands API to provide help. "help" by itself will list all of the command classes (or namespaces) and "help " followed by a namespace will list all of the commands supported by that namespace. Details of a specific command are available by typing "help" followed by the namespace and command (e.g. "help layout force-directed").