extern void get_not_o(
DATASET *dataset, /* the dataset */
int w, /* width of motif */
BOOLEAN get_log /* compute log_not_o if true */
)
{
int i,j,k;
int n_samples = dataset->n_samples;
SAMPLE **samples = dataset->samples;
for (i=0; i < n_samples; i++){ /* sequence */
SAMPLE *s = samples[i];
int lseq = s->length;
double *weights = s->weights; /* prb not in a previous site */
double *not_o = s->not_o; /* prb not overlapping a site */
int *log_not_o = s->log_not_o; /* prb not overlapping a site */
for (j=0; j <= lseq - w; j++) { /* site start */
not_o[j] = 1.0; /* assume not overlapping */
for (k=j; k < j+w; k++) { /* position in sequence */
if (weights[k] < not_o[j]) not_o[j] = weights[k];
}
if (get_log) log_not_o[j] = INT_LOG(not_o[j]);
}
for (j=lseq-w+1; j < lseq ; j++) { /* beyond possible site starts */
not_o[j] = 1;
if (get_log) log_not_o[j] = 0;
}
}
}
extern void get_not_o(
DATASET *dataset, // the dataset
int w // motif width
)
{
int i,j,k;
int n_samples = dataset->n_samples;
SAMPLE **samples = dataset->samples;
for (i=0; i<n_samples; i++){ /* sequence */
SAMPLE *s = samples[i];
int lseq = s->length;
double *weights = s->weights; /* prb not in a previous site */
double *not_o = s->not_o; /* prb not overlapping a site */
int *log_not_o = s->log_not_o; /* log prb not overlapping a site */
if (lseq < w) continue; /* sequence to short for motif */
for (j=0; j <= lseq - w; j++) { /* site start */
not_o[j] = 1.0; /* assume not overlapping */
for (k=j; k < j+w; k++) { /* position in sequence */
if (weights[k] < not_o[j]) not_o[j] = weights[k];
}
log_not_o[j] = INT_LOG(not_o[j]);
} /* for j */
for (j=lseq-w+1; j < lseq; j++) { /* beyond possible site starts */
not_o[j] = 1;
log_not_o[j] = 0;
}
} /* for i */
} /* get_not_o */
/**
* convert_to_lmap
*
* Converts a matrix of sequence to theta probability mappings into a
* matrix containing the int logs of those probabilities. Also sets up
* a vector for mapping an "X" character to a vector of letter probabilities.
* Those probabilities are uniform across all letters.
*/
extern void convert_to_lmap (
THETA map,
int lmap[MAXALPH][MAXALPH],
int alength
)
{
/*
Set up the matrix of frequency vectors for each letter in the alphabet.
Column and row for the "match-anything" character X are set to 1.0/alength
so that such matches are neither favored nor disfavored, and where
they match is irrelevant:
*/
int i,j;
for (i=0; i<alength+1; i++) {
for (j=0; j<alength; j++) {
lmap[i][j] = (i<alength) ? INT_LOG(map[j][i]) : INT_LOG(1.0/alength);
}
lmap[i][j] = INT_LOG(1.0/alength); /* X */
}
}
/**
* convert_to_ltheta
*
* Convert the entries in the specified matrix motif model from doubles to INT
* LOG values.
*/
extern void convert_to_ltheta (
double matrix_ds[MAXSITE][MAXALPH], ///< The input matrix of doubles
int matrix_il[MAXSITE][MAXALPH], ///< The output matrix of int logs
int nrows,
int ncols
)
{
int row_idx;
for (row_idx = 0; row_idx < nrows; row_idx++) {
int col_idx;
for (col_idx = 0; col_idx < ncols; col_idx++) {
matrix_il[row_idx][col_idx] = INT_LOG(matrix_ds[row_idx][col_idx]);
fprintf(stderr, "%i ", matrix_il[row_idx][col_idx]);
}
fprintf(stderr, "\n");
}
}
