
STRMAT -  Version 1.5 Notes.


   IMPORTANT NOTE:  This software is for internal use only.  This is
   --------------   NOT a completed software product available for
                    distribution.  Copies should only be made for 
                    personal or class use.

                    Also, there are most likely a number of bugs
                    and undocumented (or incompletely documented)
                    features in this program.  That is because this
                    is not a finished product, and is only the current
                    version of an ongoing production. 


Getting Started:  To run this program all you need to type "strmat".
                  If strmat does not exist then type "make" to get
                  this file.

General conventions:
  To simplify using the interface I have included the following 
  conventions:

    Typing 0 (when available) will return you to the previous menu.

    Typing * (when available) will bring you to the utilities menu.

    Typing Control-D (when available) during an operation will abort
    the operation and return you to the last menu.

    Strmat keeps a list of sequences which can be used as input to
    the various algorithms.  The utilities menu contains operations
    to add, delete and print the sequences in the list.

    Output is pipelined though a more interface developed by
    James Knight.  When given the -More- prompt:
	Type 'q' to stop printing.
	Type <space> to display next page.
       	Type <return> to display next line.


Selecting Algorithm at Main Menu:
  The algorithms are grouped into categories.  Select a number 
  corresponding with the type of algorithms you wish to execute.  


Selecting Algorithm:
  Select an algorithm by number (and optionally a letter).

  You will then be asked to select the input sequences (i.e., a 
  single sequence, a pattern plus a text, a set of patterns plus
  a text, ...). During the selection, you are also able to access the
  utilities menu as well as read in files and list the current
  sequences that are available.


Using Utilites Menu:
  Here you are given a list of utilites:
  1) Reads a formatted file created by strmat.  (Look in the "doc"
     sub-directory for a description of the file format.)
  2) Reads an the sequence from a file after prompting you for
     the name and type of alphabet.  If the alphabet is ASCII, all of
     the characters are assumed to be part of the sequence.  If not,
     only the file characters in the alphabet are considered part of
     the sequence.
  3) Creates a new sequence.  Same as option 2, but here you
     are prompted to type in the sequence.
  4) Lists title, length, alphabet and identification number of
     all the sequences.
  5) Print out the sequence of your choice.
  6) Saves sequences to a file.  Enter sequences numbers as you do 
     for option 3 and 5.
  7) Delete sequences from the list in memory.  Enter sequence
     numbers as you would for option 3.
  8) Allows you to set display options.  Here you can opt to 
     suppress the printing of statistics as well as redirect 
     the output to a file.


Warning about cross alphabet matching:
  Strmat allows you to compare sequences that contain different
  alphabets by mapping all the sequences to the union of the
  characters in the different alphabets.

  This has not been tested thoroughly.


If you have any problems, questions or suggestions please e-mail:
   knight@cs.ucdavis.edu
