PROGRAPH Program Description??

Dan Jacobson danj at welchgate.welch.jhu.edu
Fri May 7 18:20:40 EST 1993


In article <Roberts_D-070593105233 at riversend.bms.com> Roberts_D at BMS.COM (Dan Roberts) writes:
>Does anyone out there have a description of the IBM platform PROGRAPH
>program that they could send me??..Thanks...:-)..Dan
>

This is a clip from the (extensive) documentation that comes
with prograph.  Note this is a little out of date - there's newer
docs that come with the present version.


Best of luck,

Dan Jacobson

danj at welchgate.welch.jhu.edu

----------------------------------------------------------



A graphical protein analysis tool


V 1.3    October 1991


A.      What is PROFILEGRAPH
PROFILEGRAPH is a public-domain program for helping with the analysis of
protein sequences. It does so by plotting profiles of the sequence to the
screen or to various output devices. These profiles are derived from the
sequence by application of amino-acid specific parameters, a well known
example for such a profile is the hydrophobicity plot.
One of my main concerns in writing PROFILEGRAPH was to include a lot of
options for influencing the calculation of the profile and to make
PROFILEGRAPH able to do everything that is possible with such profiles.
Of course this goal was not achieved in many ways, but I hope the
features I did implement are a reasonable subset of all possible ones.
Another main concern besides making PROFILEGRAPH as flexible as possible
was to make it comfortable and relatively fast. One obvious reason for
including a comfortable user-interface is that such a program is more fun
to work with. Another reason is that all the nice options I included
would almost never be used if they were hidden behind cryptic command
line options or the like.
I hope that by providing a sufficiently fast and easy interface the
usefulness of the program will be improved and that even some less
obvious profile analyses will be carried out which are likely to give no

show something unexpected (and I believe that the unexpected features are
the most interesting ones).

For a first introduction and a short guided tour through the menus of
PROFILEGRAPH, read chapter E.  of this file.
For a more detailed description of each menu-choice, please read chapter
D. of this documentation.

If you like to contact me, feel free to do so, my address is:

          Kay Oliver Hofmann
          Institut fuer Biochemie (med. Fak.)
          Universitaet Koeln
          Joseph Stelzmann Str. 52
          D-5000 Koeln 41 (West Germany)

        Tel +49 221 478-6980
        Fax +49 221 478-6979
        INTERNET: khofmann at cipvax.biolan.uni-koeln.de

I am extremely interested in bug reports, suggestions for future
versions, proposed modifications of PROFILEGRAPH or any other comments.
B. Hardware and software requirements
Because PROFILEGRAPH works fully in graphics mode, a graphics adapter in
combination with an appropriate monitor is required. Almost any available
adapter type is supported. The program has been written in TURBO PASCALTM
and it uses the BORLAND GRAPHICS INTERFACETM. Therefore the correct .BGI-
graphics driver must be present. Driver files for hercules, EGA, VGA and
SVGA adapters are supplied together with the executables of PROFILEGRAPH.
A complete set of drivers is shipped with newer versions of all TURBO-
languages from BORLAND.
A high-resolution color graphics adapter is highly desirable but hercules
graphics will also do. There is a problem with CGA-graphics where some

A most critical feature of PROFILEGRAPH V1.3 is that use of a mouse is
highly recommended. (See chapter D.) The executable files run only with a
MICROSOFTTM compatible mouse if there is an appropriate mouse-driver
installed. If you plan to recompile the sources, it will be easy to
replace the unit MOUSE by another one supporting other rodents like
MOUSE-SYSTEMSTM mice etc.
The memory requirements are not clearly defined because the program makes
extensive use of dynamically allocated memory. I only tried running the
program on ATs with more than 640kB, it is possible that less memory is
also sufficient when using a low-resolution graphics card. Extended or
expanded memory is supported only for overlay management at the moment.
The program is suited for running under MS-WINDOWS as a non-windows
application. I have tested it with WINDOWS 3.0, corresponding PIF and ICO
files are provided with the executables of PROFILEGRAPH.
Running PROFILEGRAPH under WINDOWS offers the advantage of cutting and
pasting to the clipboard and, of course, switching between multiple
applications.
In the executable version of PROFILEGRAPH V1.3, a numerical coprocessor
is not supported. If you recompile the pascal sources, it will be most
easy to switch on a compiler option to include 80x87-code.
I you like to recompile the program, you need a current version of the
TURBO-PASCAL compiler. The executables distributed have been compiled by
release 5.5 of the compiler, in contrast to the previous release, TP5.5
specific code is used.
C. Installation
The release version V1.3 of PROFILEGRAPH consist of the following files:

executable section:
- PG_READ .ME       last minute informations
- PROGRAPH.EXE      the main program
- PROGRAPH.TAB      the startup amino-acid parameter table
-     *   .TAB      perhaps some additional tables
- PROGRAPH.ANA      standard analysis file

- PROGRAPH.ICO      Icon file for use with MS-WINDOWS 3.0
- PG256   .CFG      demo configuration file for 256 color SVGA
- PG16S   .CFG      demo configuration file for 16 color SVGA
- PG16    .CFG      demo configuration file for 16 color EGA/VGA
- PG2     .CFG      demo configuration file for b/w
-     *   .BGI      graphics drivers (copyright BORLAND)
- SVGABGI .ZIP      SVGA drivers (copyright Jordan Hargrave)
- MYPR$HUM.DAT      test sequence file in UWGCG-format
- TPGLVIEW.EXE      TPGL file viewer
- TPGLTOPS.EXE      TPGL to POSTSCRIPTTM - Converter
- TPGLPRT .BAT      needed for 'special print' feature

documentation section
- PG_READ .ME       last minute informations
- PGDOC   .TXT      documentation in ASCII-format
- PGDOC   .DOC      documentation in MS-WinWord format
- PGDOC   .PS       documentation in POSTSCRIPTTM format
- PG_PAPER.DOC      paper decribing PROFILEGRAPH in MS-WinWord format

source code section:
- PG_READ .ME       last minute informations
- PROGRAPH.PAS      the main program
- PG_TYPE .PAS      type declaration unit
- PG_INIT .PAS      variable initialization unit
- PG_CALC .PAS      calculation unit
- PG_WHEEL.PAS      helical wheel unit
- POPUP   .PAS      pop-up menu unit
- POPAPP  .PAS      pop-up menu applications unit
- GRUTIL  .PAS      graphics utility unit
- FILUTIL .PAS      file utility unit
- OVR_INIT.PAS      overlay initialization unit
- SEQ     .PAS      sequence utility unit
- HCOPY   .PAS      hard copy utility unit

- TPGL    .PAS      TPGL-creation unit
- UREADSEQ.PAS      Don Gilbert's READSEQ unit (converted for
                    use with TP5)
- TPGLVIEW.PAS      TPGL file viewer
- TPGLTOPS.PAS      TPGL to POSTSCRIPTTM converter
                                                                      


And much more - this is just the start...




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