/***********************************************************************
* Normalize an array in log space.
***********************************************************************/
void log_normalize
(ATYPE close_enough,
ARRAY_T* array)
{
int i_item;
int num_items;
ATYPE total;
ATYPE this_value;
/* Get the sum of the elements. */
total = log_array_total(array);
/* If the array already sums to zero, don't bother. */
if (almost_equal(total, 0.0, close_enough)) {
return;
}
/* If there's nothing in the array, then return all zeroes. */
if (total < LOG_SMALL) {
init_array(LOG_ZERO, array);
return;
}
num_items = get_array_length(array);
for (i_item = 0; i_item < num_items; i_item++) {
this_value = get_array_item(i_item, array) - total;
/* If this value is small enough, just make it zero. */
if (this_value < LOG_SMALL) {
set_array_item(i_item, LOG_ZERO, array);
} else {
set_array_item(i_item, this_value, array);
}
}
}
BOOLEAN_T verify_trans_matrix
(BOOLEAN_T log_form, /* Is the transition matrix in log form? */
int num_states, /* Number of states in the (square) matrix. */
MATRIX_T* trans) /* The matrix. */
{
int i_state;
PROB_T total;
for (i_state = 0; i_state < num_states - 1; i_state++) {
/* Cf. Rabiner, formula (43b), p. 265. */
if (log_form) {
total = log_array_total(get_matrix_row(i_state, trans));
if ((!almost_equal(total, 0.0, SLOP)) &&
(!almost_equal(total, 1.0, SLOP)) && // Allow for FIMS.
(!almost_equal(EXP2(total), 0.0, SLOP))) {
fprintf(stderr,
"Warning: Row %d of transition matrix differs from 0.0 by %g.\n",
i_state, EXP2(total));
return(FALSE);
}
} else {
total = array_total(get_matrix_row(i_state, trans));
if ((!almost_equal(total, 1.0, SLOP)) &&
(!almost_equal(total, 2.0, SLOP)) && // Allow FIMs.
(!almost_equal(total, 0.0, SLOP))) { // Allow inaccessible motifs.
fprintf(stderr,
"Warning: Row %d of transition matrix differs from 1.0 by %g.\n",
i_state, 1.0 - total);
return(FALSE);
}
}
/* All transitions from the end state must be zero. */
if ((log_form) &&
(get_matrix_cell(num_states - 1, i_state, trans) > LOG_SMALL)) {
fprintf(stderr,
"Warning: Transition %d from end state is non-zero (%g).\n",
i_state, get_matrix_cell(num_states - 1, i_state, trans));
return(FALSE);
} else if (!(log_form) &&
(!almost_equal(get_matrix_cell(num_states - 1, i_state, trans),
0.0, SLOP))) {
fprintf(stderr,
"Warning: Transition %d from end state is non-zero (%g).\n",
i_state, get_matrix_cell(num_states - 1, i_state, trans));
return(FALSE);
}
}
return(TRUE);
}
