Modification for MSF files

[Rick Westerman]

						July, 1993
						Rick Westerman
						westerm at aclcb.purdue.edu

   How long have we had MSF (multiple sequence format) files within
the GCG package? Two or three years by now. And so why do I have to keep
telling my users over and over that if they wish to use MSF files they 
must append "{*}" to the end of the file name? Even experienced users
seem to forget. Sigh. 

   I finally have gotten tired enough of the above problem that I modified
the GCG package. Now my users no longer need to append the "{*}" to their 
MSF files. In other words, instead of having to do:

   $ pretty pileup.msf{*}

they can now do:

   $ pretty pileup.msf

additionally, they can still use the "{*}" or "{sequence}" forms. The 
modification effects all GCG programs because it changes one of the
base routines -- NEXTFILE.

   The downside of the modification is that any file that ends with ".msf"
is considered to be a MSF file. To implement the modification, change your
directory to where you keep modified GCG source code and:

   1) $ GCGSupport

   2) $ copy GENLIB:NEXTFILE.FOR []

   3) Edit NEXTFILE.FOR and put in the changes below.

   4) $ FORTRAN NEXTFILE.FOR

   5) $ ToGenLib NEXTFILE.OBJ

   6) $ MakeShare

   7) If you have shared libraries installed,
      $ @GenCom:GCGIMAGE REPLACE


   If you wish to test out the modification before installing it, I 
suggest that after step #4, you do:

   4A) $ library/create test.olb nextfile.obj

   4B) $ copy GENSOURCE:PRETTY.FOR []

   4C) $ fortran PRETTY.FOR

   4C) $ genlink pretty.obj test.olb

   4D) $ run pretty 
       This runs the pretty program with the modified code


   While I and my users have tested this code, there are no guarantees. Use
at your own risk.

   The source code modifications to NEXTFILE are:

   1) Change the line:

      	Character WildName(*), ThisFName(*)

      To:

   	Character WName(*), ThisFName(*),  WildName(256)
   	Integer StrConcat, RPW

   2) After the line:

        Integer StrFind

      Add the following:

        Call StrCopy(WildName,WName)
  
        If  (((StrFind('.MSF',WildName).gt.1)  .or.
     &        (StrFind('.msf',WildName).gt.1)  .or.
     &        (StrFind('.Msf',WildName).gt.1)) .and.
     &        (StrFind('{',WildName).eq.0))
     &      RPW = StrConcat(WildName,'{*}')


   3) Make sure the "&"s in the above are in column 6. Add comments as
      desired. That's all there is to it. Basically, whenever the program
      sees a file that ends in ".MSF", ".msf", or ".Msf" and there is 
      no "{" in the file name, then "{*}" is appended to the file name.


-- Rick

Rick Westerman                System Manager of the AIDS Center Laboratory
westerm at aclcb.purdue.edu      for Computational Biochemistry (ACLCB), BCHM
Phone: (317) 494-0505         bldg., Purdue University, W. Lafayette, IN 47907
  FAX: (317) 494-7897