Read Me

README to MSGRAPH V2.1
2021-10-30, JHa
======================

NAME

MSGraph - a program to facilitate qualitative analysis of mass
          spectrometric data, especially those obtained in LC/MS.



DESCRIPTION

MSGraph is a program designed for the fast, qualitative analysis of mass
spectrometric data. It is a convenient tool to provide fast and simple
access to all the information contained in an LC/MS analysis run.

The program was first published 1993 as a paper in Spectrochimica Acta
(J. Hau and M. Linscheid. MSGraph: A Program for the Display of LC/MS Data.
Spectrochimica Acta 48B (1993), E1047-E1051). The version given here is a
thoroughly revised, almost completely re-written and in many details
improved version of the initial program.

MSGraph is different from today's Windows-type applications. The program
was developed for MS-DOS, which was the standard operating system at that
time ... and this has not changed since. Being `non Windows' may seem
inconvenient at first glance, but some functions of MSGraph are so
straightforward that they will still contrast to other software. To name a
few features:

* Direct call to most functions with a single keystroke or mouse click.

* The 'eagle's view' (2D) display allows visualisation of all the
  information of an analysis run: time, scan number, m/z and signal
  intensity at the same time.

* CODA component detection algorithm, enabling 'intelligent' background
  subtraction.

* Rapid zoom by a point-and-draw action of the mouse.

* Switch between all displays with just ONE mouse click or keystroke.

* Browse spectra and mass chromatograms with one keystroke or mouse
  click. Simple and straightforward mouse-controlled integration of
  mass chromatograms.

* Get graphical data in high-quality Postscript format, including color
  Postscript for the 2D display.

* Send numerical data - mass spectra, mass chromatogram, integration
  results and even 2D - to ASCII files, e.g. for use with graphics
  or spreadsheet software.

* Data conversion to JCAMP-DX format.

* ... and with version 2.1 (2004-10) it became Free Software, published
  under the GNU Public License (GPL)!



DEJA VU ?

If you have used an old version of MSGraph before, READ THE MANUAL. 
There are many things that have changed with version 2.x - command line 
options, keyboard shortcuts, file formats, and much more.



LICENSE

This program and its documentation are Copyright (C) by Joerg Hau.

This program is free software; you can redistribute it and/or modify it
under the terms of version 2 of the GNU General Public License as published
by the Free Software Foundation. See the file LICENSE for details (and make
sure that you have entirely read and understood it!)

Please note in particular that, if you use this program, or ANY part of it
- even a single line of code - in another application, the resulting application
becomes also GPL. In other words, GPL is a "contaminating" license.

If you do not understand any portion of this notice, please seek appropriate
professional legal advice. If you do not or - for any reason - you can not
accept ALL of these conditions, then you must not use nor distribute this program.

This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
(file LICENSE) for more details.

The origin of this software must not be misrepresented; you must not claim that
you wrote the original software. Altered source versions must be clearly marked
as such, and must not be misrepresented as being the original software.

This notice must not be removed or altered from any source distribution.



CITATIONS

Usage is free of charge, however, the author requests that the user
credit the author and/or the software in any publication that results
from the use or application of this software (an appropriate place would
be the 'Materials and Methods' section).

As of 2009, the appropriate reference is:

  J. Hau and M. Linscheid. MSGraph: A Program for the Display of LC/MS
  Data. Spectrochimica Acta 48B (1993), E1047-E1051. Revised version
  online at http://msgraph.sourceforge.net/.



OBTAINING THE PROGRAM

The latest version can be obtained from the MSGraph project page on sourceforge.net:

    http://msgraph.sourceforge.net/



OPERATING SYSTEM, FILES, INSTALLATION, ...

See the User's Manual. The program has been tested using MS-DOS 6.22,
but it should work under earlier versions (is anyone still using them?)
and it will work in a 'DOS box' of the Microsoft Windows environment -
which was successfully tested with MS Windows 3.11, 95b, 98SE, NT4 and
2000.

MSGraph runs nicely, even in the high-resolution graphic modes, under
Linux DOSEMU and in virtual environments such as VirtualBox.



HISTORY

since 1.0:

- ASCII export allows to select any delimiter character
- export of integration results possible
- can read Teknivent MID data
- directory and drive handling completely via mouse
- safe 'drive-ready' detection (TCC 'access()' has a bug)
- faster reading of spectra
- color switching in 2D display
- faster drawing routines
- normalisation of display possible
- smoothing of chromatograms possible
- write "interesting" m/z to file using the SPACE key
- HPGL output in 2D
- bugfix in 2D PS driver that caused wrong colour shading
- bugfix in reading data file that caused a memory leak
- improved error handling
- and numerous little bugfixes.


New in V2.0:

- CODA processing
- a number of new command line options
- can now open a file from cmd line
- changed filename extensions for data and integration files
- averaging of spectra
- new JCAMP output (5.0)
- new look of main page, shows all paths and free memory
- code largely revised, partially rewritten and condensed
- Hi-Res SVGA driver (read the manual!)
- PostScript output now supports 33 standard fonts
- manual entirely rewritten
- CDF converter available (extra package, under GPL)
- etc. etc.

New in V2.01:

- the F10 key does no longer switch CODA processing off.


New in V2.02:

- the comment lines of the MCQ files are now Linux/Unix-compatible.
  The old mcq files are no longer compatible.
- mzXML converter available (extra package, under GPL)


New in V2.03:

- If MCQ data are used, the number of mass traces used to "compose"
  a given mass chromatogram is now shown in the header.


New in V2.1:

- Software released under GPL. Added the corresponding comments in
  the source code and updated the documentation. No changes to the
  code functionality "as such".

2004-10-04, Manual and file LICENSE in the binary distribution
  updated. No changes to the code.

2009-03-02: Now hosted at sourceforge.net. Updated most of the documentation;
no code changes.

2021-10-30: Updated documentation, renamed manual. No code changes.



IF YOU WANT TO RE-COMPILE ...

The original distribution was developed and compiled using the IDE of
Borland C++ 3.0. The PRJ-file (as I use it on my development machine,
which still uses MS-DOS 6.22) is provided, and the MAKEfile was generated
by using Borland's PRJ2MAK.

Be aware that a lot of the older comments are in German.

At the time I started writing MSGraph, portability was not much of an issue.
Thus, the code makes intensive use of Borland-specific extensions. If you
run into problems using another compiler, do not blame me ;-)

The SVGA driver was written by Ullrich von Bassewitz and is available at
http://www.von-bassewitz.de/uz/bgi.html.



EXTENSIONS

Please note that, for several years now, MSGraph is in a stable state.

If you want me to include your extensions or changes, make absolutely
sure that you do not impact other functions (and there are quite some!).
This concerns in particular:

- i/o routines
- menus, mouse & keyboard stuff
- printing routines
- file format
- check the return value of *everything* you do, in particular memory management.
- all changes *must* be backward-compatible to existing data files.



BUGS

If you find any bugs or observe some "behaviour" that is not mentioned in 
the manual, please file a bug report via the sourceforge.net project page.

If possible, submit not only a bug report but also a bug fix ;-),

Please note that the URL given above is the only "official" source for MSGraph.
If you obtained your copy from another source and you run into bugs, please
recompile from the "official" sources first before you blame me ;-)



AUTHOR

	Dr Jörg Hau, PMP
	Route du Marchairuz 29
	CH-1188 St-George
	Switzerland
	code at schweizerschrauber.ch


Thank you for your interest, and ... have fun!

--eof--