JAM language released

Reinhard Doelz doelz at comp.bioz.unibas.ch
Sat Oct 8 13:19:51 EST 1994

Survival Guide Project (survival at comp.bioz.unibas.ch) wrote:

: another  metafile)  which allows to include site-specific items, and 
: alternative  documentation for either VMS or UNIX. The new guide has 
: the  potential  to  become  a  collaborative  project,  and  will be 
: available mid-october in JAM source code, together with the  program
: required  to prepare either printed or on-line versions of the docu-
: ment.  I would need some comments on a preliminary version, which is 

This is just to announce that the JAM language is now released. 

Today, documentation in Biocomputing must be  available in various  formats. 
Users who have never used computers for this purpose before will not  easily 
adopt all-electronic information and require professionally printed material. 
Colleagues at remote sites who wish to print the text locally in chapters,or 
send  it  around in electronic Mail messages, require a simple ASCII-type of 
format. Electronic hypertext systems, on the other hand, have become increa-
singly  popular  in  recent years and have the tremendous advantage that the 
cross-references will  be  much more intuitive and easy to follow.Previously, 
the  use  of  translators provided a preliminary way of switching in between
worlds. There  are various elements of text structuring and cross-references
which  are  similar in between the formats discussed above, however, the de-
tailed spelling and presentation to the user is different and depends on the 
presentation context. The following example shall illustrate this. 

   RTF source 
   This program (see also under keyword seqed _i_seqed_;_)  has been discu...
   Wordprocessor text  
   This program (also under keyword seqed) has been discussed earlier.   

   LaTEX source 
   This program (see also, \pageref{seqed}) has been discussed earlier.  

   LaTEX appearance: 
   This program (see also, page 35) has been discussed earlier. 
   html source 
   This <a href=editing#seqed> program </a> has been discussed earlier.  

   html appearance 
   This program has been discussed earlier.  

In order to avoid the obvious shortcomings of translators, which were unable 
to create the explanatory wrappers for cross-links as depicted above,we have 
created the JAM format in order to produce different formats from one single 

The  JAM  source  code  contains several configurable files (extension .STE) 
which hold site-specific information such as contact addresses for the local 
computing center, which editor to use, and  similar  localized elements. The 
local information, as well as the residual text, allows the adaption of both 
UNIX- and VMS type of environments. 

The format has several classes of statements: 
   comments    - simple lines to structure text. not processed. 
   conditional statements - extremely simple, similar to the C-preprocessor 
              and expanded before the formatting statements. Rules are: 
                       1st column is a pound sign (#) 
                       immediately after the pond sign there is either 
                             o ifdef  
                             o else  
                             o endif   
                             o include 
   formatting statements -  is  required to display four different types of 
              non-flow text. These are 
                       verbatim (i.e., all is printed as written) 
                       itemized (such as this text) 
                       special (i.e., different font but not verbatim) 
              Each  formatting  statement starts with a dash (-), a letter, 
              and another dash at column 1, e.g. -V- starts  Verbatim.  End 
              of formatting is indicated using the same syntax (-v-). 
   structuring statements -  processed after the conditional and formatting 
              statements and auomatically numbered.The text structure is in 
              three levels. Chapters, Sections, and Headlines are implemen-
              ted using asterices embraced in dashes: 
                       *       is a chapter   
                       -*-     is a section   
                       -**-    is a Headline   
   referencing statements - to allow indexing and transparent reference in-
              sertion. The following items are allowed: 
              Type                 Symbol          Expansion to   
              Index entry          #|text|#        entry in index   
              Reference point      +|text|+        word being referenced  
              Hint to reference    *|text|cleartext|*  hypertext link (html)   
                                                   'see also, ...' (LaTEX)   
                                                   'see keyword...' (RTF) 
              HASSLE receptor      [|text|cleartext|]  hypertext link  to 
                                                   command, or only <strong>
                                                   (html, depending on conf.)
                                                   boxed word (LaTEX)
                                                   bold italic (RTF) 

We call  this a  'beta' version. If you find any problems, please let us 
know.  We would be very interested in hearing your comments on this project. 

<a href= http://www.ch.embnet.org/jam/jam.html > Jam Page </a>.
The ftp archive  is bioftp.unibas.ch, directory survival/ . Please
note that you should only use the survival/ directory. Thank you.

Acknowledgements: The  program  writing  was  supported  by Basel
University, and the  Swiss  National Science Foundation  (NF).

 R.Doelz         Klingelbergstr.70| Tel. x41 61 267 2247  Fax x41 61 267 2078|
 Biocomputing        CH 4056 Basel| electronic Mail    doelz at ubaclu.unibas.ch|
 Biozentrum der Universitaet Basel|-------------- Switzerland ---------------|
<a href=http://beta.embnet.unibas.ch/>EMBnet Switzerland:info at ch.embnet.org</a> 

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net