Delila Program: shell

shell program

Documentation for the shell program is below, with links to related programs in the "see also" section.

{   version = 3.01; (* of shell.p 2014 Nov 23}

(* begin module *)
   shell: One line description: Example Delila System program (an empty shell)

   shell(afile: in, shellp: in, bfile: out, output: out)


   afile:  multiple line detailed description of the first file.

   bfile:  multiple line detailed description of the second file.

   shellp:  parameters to control the program.  The file must contain the
      following parameters, one per line:

      parameterversion: The version number of the program.  This allows the
         user to be warned if an old parameter file is used.

      The convention is that the name of the parameter file is formed by
      taking the name of the program and adding a 'p' on the end.

      Usually there are many parameters.  Parameters are left justified when
      characters.  Numbers can have spaces in front.  Anything to the right
      is a comment.  A useful trick is to insert a new temporary parameter on
      the left side while trying something out.  For example, in makelogo
      there is a range parameter, which is two integers (from - to in bases
      for the sequence logo).  So one might have:

-20 +20    FROM to TO range to make the logo over

      The trick then would be to set the range bigger with

-200 +200 -20 +20    FROM to TO range to make the logo over

      This way one can simply delete the new range to put it back the way it
      was.  (Note that the "+" is not necessary, but often helps in visually
      identifying that a pair of numbers is a range.)

makelogop: parameters for the makelogo program, version 8.76 or higher

  Be sure to check out the
      atchange program (see a link to it in the See Also section below).

   output: messages to the user


   The purpose and use of the program.
   This page is intended to be copied and edited for making new programs.  To
   make it easy to add information later, do not delete sections, just leave
   them blank if they are not in use.
   Here are descriptions of each section of the documentation:
   The name section is a single line, always less than 78 characters,
   that briefly describes what the program does.
   The synopsis defines the input (":in") and output (":out") files of the
   program.  In rare cases there is also an input/output file ("inout").
   Starting 2000 Dec 4 I will indicate one more kind of input, "stdin".
   This applies to any file named 'input', which is treated specially
   by pascal to mean the keyboard.  Under unix operating systems it
   is the standard input file.  For programs that use stdin, one
   can pipe the results into the program or redirect it.  For example,
        rb < myfile > myfile.without.extra.blanks
   The file section describes each file in detail.  Delila programs
   frequently use many input and output files in parallel.  The name given in
   the documentation must corresponds to a file in the current directory.
   This is a feature of Pascal that is either a blessing or a curse.  It is a
   blessing because one can always identify the file by name.  It is a curse
   because the name is not descriptive.  So, for example, an input file to
   the Delila program is the inst file (instructions).  This is not very
   descriptive!  So I will often work with a descriptive name, fis.inst, for
   example.  But Delila won't read that file, so it would be painful to keep
   copying fis.inst to inst.  This is where the atchange program (see link
   below) comes in handy.  I just work on the inst.fis file and have atchange
   copy it over to inst and then run delila automatically.
   Any file that is mentioned as an "in" in the synopsis will need to be in
   your current working directory (under Unix).  You do not need to make the
   output files, they will be generated automatically.  Be sure that you
   don't overwrite something important.  (RTFM to see which files are
   required by any particular program.  RTFM stands for "Read The Manual", an
   old joke from MIT ;-)
   The description section explains how to use the program.  In the case of
   the shell program, it describes how to use Delila programs in general.
   Examples are often worked out for you.  They usually will
   correspond to examples in the See Also section.
   Documentation is usually publications.
   The See Also section contains active web links.
   I'm putting those silly dashes on the left side so that this entire
   section is one paragraph.  This allows me to delete the paragraph with the
   command "d}" in the text editor vi.


   An example of the use of this form is module describe.lister.  See the
   link to the lister program below.

   Parts of documentation:
   see also
   technical notes


   Other sources of information or documents on the program.

see also

   Example program with extensive documentation: lister.p

   In this section, text inside curlie brackets is copied
   and text outside become web links by the program htmlink.p .

   The ergonomic and fast vi program is described at

   The atchange program will automate your world:

   makelogo.p uses the ranges mentioned in the section above about

   delila.p is the main program of the Delila system.

   Information about ranges is in the glossary:

   The rb program mentioned above is: rb.p


   Thomas Dana Schneider


   problems with the program and how to get around them (if known).

technical notes

   Details about the implementation that may be relevant to a user.

(* end module *)
{This manual page was created by makman 1.44}
{created by htmlink 1.55}
U.S. Department of Health and Human Services  |  National Institutes of Health  |  National Cancer Institute  |  | 
Policies  |  Viewing Files  |  Accessibility  |  FOIA