//    Copyright (c) 1997-99 by Arthur Delcher, Steven Salzberg, Simon
//    Kasif, and Owen White.  All rights reserved.  Redistribution
//    is not permitted without the express written permission of
//    the authors.

Program  build-icm.c  creates and outputs an interpolated Markov
model (IMM) as described in the paper
  A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg.
  Improved Microbial Gene Identification with Glimmer.  
  Nucleic Acids Research, 1999, in press.
Please reference this paper if you use the system as part of any
published research.

Input comes from the file named on the command-line.  Format should be
one string per line.  Each line has an ID string followed by white space
followed by the sequence itself.  The script run-glimmer2 generates
an input file in the correct format using the 'extract' program.

The IMM is constructed as follows: For a given context, say
acgtta, we want to estimate the probability distribution of the
next character.  We shall do this as a linear combination of the
observed probability distributions for this context and all of
its suffixes, i.e., cgtta, gtta, tta, ta, a and empty.  By
observed distributions I mean the counts of the number of
occurrences of these strings in the training set.  The linear
combination is determined by a set of probabilities, lambda, one
for each context string.  For context acgtta the linear combination
coefficients are:
    lambda (acgtta)
    (1 - lambda (acgtta)) x lambda (cgtta)
    (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x lambda (gtta)
    (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta)) x lambda (tta)
                   :
    (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta)) 
             x (1 - lambda (tta))  x (1 - lambda (ta))  x (1 - lambda (a))

We compute the lambda values for each context as follows:
  - If the number of observations in the training set is >= the constant
    SAMPLE_SIZE_BOUND, the lambda for that context is 1.0
  - Otherwise, do a chi-square test on the observations for this context
    compared to the distribution predicted for the one-character shorter
    suffix context.
    If the chi-square significance < 0.5, set the lambda for this context to 0.0
    Otherwise set the lambda for this context to:
       (chi-square significance) x (# observations) / SAMPLE_WEIGHT

To compile the program:

      g++ build-icm.c -lm -o build-icm

  Uses include files  delcher.h  context.h  strarray.h  gene.h

To run the program:

      build-icm <train.seq >train.model

  This will use the training data in train.seq to produce the file
  train.model, containing your IMM.