double
get_lambda(int **pam2p, int n0, int nsq, char *aa0) {
double lambda, H;
double *pr, tot, sum;
int i, ioff, j, min, max;
/* get min and max scores */
min = BIGNUM;
max = -BIGNUM;
if(pam2p[0][1] == -BIGNUM) {
ioff = 1;
n0++;
} else {
ioff = 0;
}
for (i = ioff ; i < n0 ; i++) {
for (j = 1; j <= nsq ; j++) {
if (min > pam2p[i][j])
min = pam2p[i][j];
if (max < pam2p[i][j])
max = pam2p[i][j];
}
}
/* fprintf(stderr, "min: %d\tmax:%d\n", min, max); */
if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) {
fprintf(stderr, "Couldn't allocate memory for score probabilities: %d\n", max - min + 1);
exit(1);
}
tot = (double) rrtotal * (double) rrtotal * (double) n0;
for (i = ioff ; i < n0 ; i++) {
for (j = 1; j <= nsq ; j++) {
pr[pam2p[i][j] - min] +=
(double) ((double) rrcounts[aascii[aa0[i]]] * (double) rrcounts[j]) / tot;
}
}
sum = 0.0;
for(i = 0 ; i <= max-min ; i++) {
sum += pr[i];
/* fprintf(stderr, "%3d: %g %g\n", i+min, pr[i], sum); */
}
/* fprintf(stderr, "sum: %g\n", sum); */
for(i = 0 ; i <= max-min ; i++) { pr[i] /= sum; }
if (!karlin(min, max, pr, &lambda, &H)) {
fprintf(stderr, "Karlin lambda estimation failed\n");
}
/* fprintf(stderr, "lambda: %g\n", lambda); */
free(pr);
return lambda;
}
MATRIX_T *convert_score_to_target(
MATRIX_T *score, /* score matrix */
ARRAY_T *prob /* letter frequencies */
)
{
int i, j;
KARLIN_INPUT_T *karlin_input;
double lambda, K, H;
MATRIX_T *target; /* target freq. matrix */
int alen = get_num_rows(score); /* alphabet length */
/* make input for karlin() */
karlin_input = make_karlin_input(score, prob);
/* get lambda */
karlin(karlin_input->low, karlin_input->high, karlin_input->prob->items,
&lambda, &K, &H);
/*printf("lambda %f K %f H %f\n", lambda, K, H);*/
/* calculate target frequencies */
target = allocate_matrix(alen, alen);
for (i=0; i<alen; i++) {
for (j=0; j<alen; j++) {
double pi = get_array_item(i, prob);
double pj = get_array_item(j, prob);
double sij = get_matrix_cell(i, j, score);
double f = pi * pj * exp(lambda * sij);
set_matrix_cell(i, j, f, target);
}
}
// Free local dynamic memory.
free_array(karlin_input->prob);
myfree(karlin_input);
return(target);
} /* convert_score_to_target */
