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(updated August 2000)
Mesquite menus include a few constant ones (File, Edit, Windows) and various other menus that change as different modules are used. This situation could be confusing to the user. For instance, menu items for particular modules may appear in different places depending on the context.
Below is a list of the standard menu items that should appear in most configurations of Mesquite. There will likely be other menus and menu items in addition to these.
Mesquite can automatically generate documentation for the current menu configuration and present it to the user as a web page. This can be done by selecting the Menu & Control Explanations menu item from the Windows menu of Mesquite.
— Show a data editor for a character matrix
— Show the list of characters for a particular character data matrix
— Make a new character data matrix by copying an existing matrix or filling the matrix from a special source (e.g., simulated characters)
— Make a new model of character evolution
— Edit an existing model of character evolution
— Show a list of the sets of assignments of parsimony models for a particular character data matrix
— Show a list of the sets of assignments of probability models for a particular character data matrix
— Show the character sets for a particular character data matrix
— Show the character inclusions sets for a particular character data matrix
— Show the character partitions for a particular character data matrix
— Show a tree window for a particular set of taxa
— Show a list of taxa for a particular set of taxa
— Show a list of trees in a tree block in the file
Other menus come and go depending on which window is in front and what calculations are in use. Thus, the standard Tree Window has a Tree menu.
As the user requests calculations and output of results, the menus change. The reason for this is that different menus are appropriate in different circumstances. Thus, if the user requests the Balls and Sticks method to draw trees, a menu item "Spot size" appears in the Tree menu. Spot size controls the size of the balls drawn at the nodes of the tree.
Exactly where a menu item appears may at first be confusing to the user, but there is a certain logic to it that hopefully won't be too obscure (technical details are available in the developer's documentation). The "Spot size" menu item belongs to the module that draws trees in the Balls and Sticks fashion, since that module wants the user to be able to control the size of the balls. That menu item appears within the menu of the modules that employ it to draw trees. Since the Tree menu belongs to the Tree Window, and it is the tree window module that (indirectly) is employing Balls and Sticks to draw the tree, the menu items belonging to Balls and Sticks appear in the Tree window. On the other hand, the Spot Size menu item won't always appear in the Tree menu: some module other than the tree window module might have reason to draw a tree, and it might employ Balls and Sticks to do it, and thus Spot Size would appear in that other module's menu, whatever it might be called.
A module can also have its own menu, as does the Tree Window. Thus, the menu items of a module (usually) appear in the menu belonging to its closest employer module that has its own menu. We say "closest" because sometimes a module will have a menu item, but its immediate employer won't have a menu to put it in. The menu item drifts upward in the employment hierarchy until it finds an employer that has a menu that can house it..
This system means that menu items appear in an appropriate context, but that that context is sometimes unpredictable. That is, a manual for a module can't say "The Spot size menu item will appear in the Tree menu", because if Balls and Sticks were hired by a module other than the Tree Window, its menu item might be housed in a menu of a different name.