Mesquite's Windows
Some basic Mesquite windows are:
- Startup window - the colorful window with
the mesquite leaf, the progress bar indicating modules loading,
and the banners at right for installed and loaded packages.
- Mesquite log - the text window showing the
log of Mesquite activity
- Project and files - the window at left showing
open projects/files and their components
- Tree Window - the
window to view and edit trees
- Character Matrix Editor
- a spreadsheet editor for character matrices
- List Windows -
show lists of characters, taxa, trees, models and other objects.
On this page are explanations of the general features of windows,
as well as issues specific to list windows.
Common features of windows
Windows in Mesquite have a consistent structure, with these components
commonly appearing:
Here are brief descriptions of some of these:
Window information bar
Windows can have an information bar that allows you to access
information about the window, its calculations, and the modules
involved in them. If the information bar is not showing and you
wish to see it, select "Show Information bar"
in the Window menu. The information bar can be turned off
by clicking the triangle at its left.
The tabs in the information bar choose the different modes of
display of the window. The first two of these (the graphics tab,
and the text version tab), cause the window to display its basic
output (e.g., the spreadsheet data editor, the tree drawn in a
tree window) in either a graphics form or a textual form. The
remaining tabs give information of other sorts.
The window modes are:
- Grapical version of output — The standard output
of the window showing results and analyses.
- Textual version of output — A textual version
of the results and analyses.
- Parameters of modules — A list of the current
settings and parameters of the modules involved in producing
the window and its contained results.
- Tree of Modules — Shows the employee tree of all
modules participating in the window
- Citations for modules — Gives citations for some
of the modules participating in the window.
Mini scrolls
Mini scrolls are used to scroll among trees, characters and
other items. The small blue button right of the text edit box,
when
hit, tells the scroll to enter and use the number within the
edit box. Otherwise you can use the arrows to scroll forward
or back.
If the change is not acceptable (e.g., because you are already
at the minimum or maximum value) the arrow is dimmed.
Tool palettes
In various windows are tool palettes that look something like
this:
The button of the current tool is shown darker. Usually in the
explanation area of the window, an explanation is shown for a
tool when
you
click on it. Some tools (whose buttons may show a small inverted
triangle) when double clicked, right-clicked or control-clicked,
show a menu in which options can be chosen.
Annotation area
The white annotation area shows footnotes or other annotations
stored for taxa, trees, characters or other objects. These annotations
are sometimes editable. At its left are two buttons, a minus and
a plus arrow. These reduce and increase the height of the annotation
area.
Explanation area
The explanation area, below the annotation area, shows explanations
for tools, modules, objects in files, and so on. Its height
can be contolled by the minus and plus arrows.
List Windows
In the Characters and the Taxa&Trees menus are available
various windows that give lists of objects with information
about
each, including the List of Characters and the List of Taxa Windows.
Other List Windows present lists of tree blocks, taxa blocks,
character matrices, character models, parsimony model sets, and
so on. These List Windows have a consistent interface: you can
select rows and columns, show and hide columns, and possibly
rename and delete objects.
At left of the List Window is a tool palette. The arrow
tool allows you to select columns or
rows. The I-beam tool allows you
to edit the name of an object. The magic wand tool selects
all rows that have the same or similar value in the column touched.
The magic wand tool has alternative selection criteria that can
be chosen by clicking and holding the cursor on the tool in
the
tool palette. The sort tool reorders the objects listed according
the column on which you touch. Thus, if you touch on the leftmost
column showing names, the objects would be sorted alphabetically.
If you touch on a column showing a numerical result, the objects
are sorted in ascending or descending order of the number. The
sort tool sorts in ascending order by default, but by descending
order if the option or ALT key is held down.
Each List Window has a List menu, with which you can show or
hide columns. Some columns merely inform you of some quality of
the object. Others may represent analyses. For instance, the column
may show the value of some statistic for each of the characters
listed in the List of Characters window.
For some of the List Windows, you can ask to delete the objects
whose rows are selected by choosing "Delete Selected"
from the List menu.
