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The Wisconsin Package Interface
(WPI) is a windowing environment layered
on top of the command line interface used so far with
GCG. In contrast to personal
computer windowing systems, which use Microsoft Windows or the
Macintosh Finder to
display windows, WPI uses the so-called
X-Windows
system to send data
from the host computer to your display.
Therefore, you need an X-Windows
display, such as an X-terminal, an X-server running on a microcomputer,
or a
workstation that runs X-Windows, if you want to use WPI. You may have used X-Windows already
to display GCG graphics on the screen.
As in the GCG command line version, WPI graphics
can be produced on various output devices such as printers,
plotters and the screen.
WPI is neither a replacement for GCG, nor does it offer programs which are
not available
in the GCG command line version. WPI adds the convenience of
window-oriented software usage.
WPI does not change or alter the
way how results are produced by the GCG package.
IMPORTANT NOTE: To run WPI, your PC or Mac must be connected to the
campus network and run sufficiently fast. A colour screen
of at least 16 inch
and high resolution is recommended. Personal computers running X-Windows
are known to require well more than 8 MByte of RAM.
In contrast to the GCG command line interface, WPI allows you to define
and store the set of
sequences you want to work with. I.e., you no longer need to remember
which sequence files
are of current interest. WPI will collect sequence files for you when
you 'add' them to the list. If you start WPI for the very first time, this list is empty.
The pull-down of the menu 'Sequence' allows you to 'Add' sequences to the list from either
'Adding' sequences to the "main list window" neither alters
sequences nor
changes their location. The purpose of 'adding' sequences to the list
is just
to register the sequences within the WPI interface to utilise them more easily.
With the GCG command line version,
you type the name of a program, feed it
with parameters, and wait for the completion of the
program. In contrast, WPI allows
you to continue to work while another program is running in
the background.
This is different from the 'batch' option. The programs are executed like the
ones you
started by typing the command. In a way, WPI does the command
typing for you. There
are several types of output:
The results may be viewed or processed according to their character, e.g., a graphics file
can be plotted as a figure, and a list of file names can be added to the
"main list window".
The "output manager window" allows
you to trigger these actions, including deletion and other
file handling commands.
Instead of waiting for a result, WPI allows you
to continue to work while another program is
running in the background. The "job manager window"
lists the execution status of all the jobs
that you have started. Programs running in the background
may generate output, in particular
if they do not run as expected. Error messages are
displayed in the
"job manager window".
WPI allows you to have more than
one window open. Instead of
sequentially opening and closing all the windows, you should try
to keep at
least the "main list window" and the "output manager window" open
simultaneously.
Given the proper configuration of the environment
, it is sufficient to type
% wpi &
WPI can be configured in a sophisticated fashion. In contrast to the
GCG command line interface, WPI uses so-called "sets" of sequences which hold additional data
such as start/end and other information.
If you plan to use WPI in parallel to the GCG command line interface,
it is important
to remember two important items:
================================= Begin Exercise 1
A small WPI exercise: Run a 'fasta' search of a database sequence against the SWISSPROT
database.
Proceed as follows:
================================= End Exercise 1
Small Computer Screens and WPI
If you feel that the screen of your personal computer is too small, you can
either configure your X-Windows server program to display scroll bars or
start WPI with smaller
characters (recommended) to get a smaller window
size. The latter can be done by typing
% wpi -small
WPI Timing
The option to run jobs in the background may affect the
timing of your session. WPI itself
will time out if you do not work for
an extended period of time, i.e., you need to restart
WPI after
returning from lunch or similar elongated pauses.
At some sites system managers
have configured a time out
for idle sessions on the entire computer system. If you did not save
your current
list in the "main list window",
this list will be lost if your session times
out. Therefore,
better save your working list occasionally.
Subsection 4.4.2 WPI Details: The Concept of "Lists"
Subsection 4.4.3 More WPI Details: The Concept of an "Output Manager"
Subsection 4.4.4 Even more WPI Details: The Concept of a "Job Manager"
Subsection 4.4.5 Interaction of WPI Windows
Subsection 4.4.6 Starting WPI
Subsection 4.4.7 WPI and the User
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