Managing modules

Users will be able to use Mesquite more effectively if they become familar with the concepts of modules and how they interact. An understanding of the modular system will help the user more effectively give commands to Mesquite via menus and scripting, and interpret the results obtained.

The page on how Mesquite works introduces modules and how they cooperate. In brief, modules link together to perform calculations and display the results to the user. The linkage of modules is in the form of a tree, with the root module being the "trunk" Mesquite module itself. Which modules are currently active depends on the files the program has read and the calculations the user has requested.

Installed versus loaded versus running modules

An installed module is one available to be used: it is sitting as a file or a series of files on your disk or web server. Mesquite can find these modules and, if approprate, can get them started up. Among the installed modules might be some that you never use, because you don't happen to need their calculations.

Not all installed modules are available to a user during a Mesquite run. The reason is that, although a module might be physically installed, it might not be loaded by Mesquite at startup. An installed module might not be loaded if, for instance, the user has chosen a configuration to control the loaded packages (see Activate/Deactivate Packages in the File manue). The configuration file might indicate that only some of the packages are to be loaded and available.

When Mesquite starts up, or when the user requests new windows, calculations, and so on, some of the loaded modules are started up to do the work. These are the running modules.

This characterization is a bit misleading, however, since many active copies of a single module on disk can be running at once. That is, the installed module on disk can be thought of as a blueprint for a machine, and each time Mesquite needs to start up a module, the machine is built and started. If Mesquite needs another machine of the same sort, it can build a new one from the blueprint. Many machines (running modules) from a single blueprint (loaded module) can be built and be running simultaneously.

(To the programmer, the loaded modules are the available classes that are subclasses of the basic module class; an active module is an object instantiated from one of these classes.)

Where modules are installed

To be installed and found by the Mesquite system, a module must be within the mesquite directory of Mesquite_Folder. Furthermore, the active configuration must specify that the module's package be loaded. Be default, all installed packages are loaded.

Thus, if you open up the Mesquite_Folder, you might see the following

• com
• corejava
• docs
• documentation.html
• edu
• examples
• images
• Jama
• JSci
• lesser.txt
• pal
• mesquite. In this directory, you might see:
• ancstates
• assoc
• basic
• batchArch
• categ
• charMatrices
• charts
• coalesce
• configs
• cont
• distance
• genesis
• io
• jama
• jsci
• lib
• lists
• Mesquite.class
• minimal
• molec
• ornamental
• pairwise
• pal
• parsimony
• rhetenor
• search
• stochchar
• treefarm
• trees
• trunk

Each of the items in bold above is a directory (folder) that contains modules. Within minimal, you might see:

• BasicFileCoordinator
• Defaults
• DrawHierarchy
• InterpretNEXUS
• ManageForeignBlocks
• (and so on)

Each of these directories is for one module. For a module to be found and used by Mesquite, it must be present in a directory whose name is the same as the class file for the module (e.g., the class file for the module "Basic File Coordinator", BasicFileCoordinator.class, must be in a directory named BasicFileCoordinator).

Modules currently in use

While Mesquite is running you may want to learn what modules are currently running. In the Help menu the Active Module Tree menu item displays a window that displays the modules currently running. You can also see the modules responsible for any window by touching on the Modules tab in the window's information bar.

If you touch on the name of the module in theses module tree displays, a menu will drop down that allows you to find out information about the module.

Information pages and Manuals for modules

Mesquite gathers information about each module and summarizes it in an information page for each module. These are linked from the page available via the Modules Loaded menu item in the Help menu while Mesquite is running. As well, some individual modules have their own manuals in the form of web pages. These are also linked from the Modules Loaded web page.