/*************************************************************************
* Output JSON data for a motif
*************************************************************************/
static void output_motif_json(JSONWR_T* json, MOTIF_STATS_T* stats,
SITE_COUNTS_T* counts) {
//vars
MOTIF_T *motif;
MATRIX_T *freqs;
int i, j, mlen, asize, end;
motif = stats->motif;
freqs = get_motif_freqs(motif);
asize = alph_size(get_motif_alph(motif), ALPH_SIZE);
jsonwr_start_object_value(json);
jsonwr_lng_prop(json, "db", stats->db->id);
jsonwr_str_prop(json, "id", get_motif_id(motif));
if (*(get_motif_id2(motif))) {
jsonwr_str_prop(json, "alt", get_motif_id2(motif));
}
mlen = get_motif_length(motif);
jsonwr_lng_prop(json, "len", mlen);
jsonwr_dbl_prop(json, "motif_evalue", get_motif_evalue(motif));
jsonwr_dbl_prop(json, "motif_nsites", get_motif_nsites(motif));
if (get_motif_url(motif) && *get_motif_url(motif)) {
jsonwr_str_prop(json, "url", get_motif_url(motif));
}
jsonwr_property(json, "pwm");
jsonwr_start_array_value(json);
for (i = 0; i < mlen; i++) {
jsonwr_start_array_value(json);
for (j = 0; j < asize; j++) {
jsonwr_dbl_value(json, get_matrix_cell(i, j, freqs));
}
jsonwr_end_array_value(json);
}
jsonwr_end_array_value(json);
jsonwr_lng_prop(json, "bin_width", stats->central_window+1);
jsonwr_dbl_prop(json, "bin_sites", stats->central_sites);
jsonwr_lng_prop(json, "total_sites", counts->total_sites);
jsonwr_dbl_prop(json, "log_pvalue", stats->log_adj_pvalue);
jsonwr_dbl_prop(json, "max_prob", stats->max_prob);
jsonwr_property(json, "sites");
jsonwr_start_array_value(json);
end = counts->allocated - (mlen - 1);
for (i = (mlen - 1); i < end; i += 2) {
jsonwr_dbl_value(json, counts->sites[i]);
}
jsonwr_end_array_value(json);
jsonwr_end_object_value(json);
}
/***********************************************************************
* Should the given motif be inserted into the model?
* FIXME: These tests needn't be mutually exclusive.
***********************************************************************/
static BOOLEAN_T retain_motif(
STRING_LIST_T* requested_motifs, // IDs of motifs to include.
double e_threshold, // E-value to include motifs.
double complexity_threshold, // Complexity threshold to include.
ORDER_T* order_spacing, // Motif order and spacing (linear HMM).
MOTIF_T* motif // The motif.
) {
int num_requested;
int i;
char* motif_id;
/* Method 1: Select motifs by index. */
num_requested = get_num_strings(requested_motifs);
if (num_requested > 0) {
motif_id = get_motif_id(motif);
for (i = 0; i < num_requested; i++) {
if (strcmp(get_nth_string(i, requested_motifs), motif_id) == 0) {
return(TRUE);
}
}
return(FALSE);
}
/* Method 2: Select motifs below a certain E-value threshold. */
else if (e_threshold != 0.0) {
return (get_motif_evalue(motif) <= e_threshold);
}
/* Method 3: Select motifs that are included in the order string. */
else if (order_spacing != NULL) {
return order_contains(get_motif_id(motif), order_spacing);
}
// Method 4: Select motifs by their complexity score.
else if (complexity_threshold != 0.0) {
return(motif->complexity >= complexity_threshold);
}
/* Default is to include all motifs. */
return(TRUE);
}
