/*
* Get a background distribution
* - by reading values from a file if filename is given, or
* - equal to the NRDB frequencies if filename is NULL.
*/
ARRAY_T* get_background(ALPH_T alph, char* bg_filename) {
ARRAY_T* background;
if ((bg_filename == NULL) || (strcmp(bg_filename, "nrdb") == 0)) {
background = get_nrdb_frequencies(alph, NULL);
} else {
background = get_file_frequencies(&alph, bg_filename, NULL);
}
return(background);
}
/*
* Sets the background for the pseudo-counts
* but requires the alphabet to do it.
*/
static void set_pseudo_bg(MREAD_T *mread) {
ALPH_T alph;
alph = mread->formats->get_alphabet(mread->formats->data);
assert(alph != INVALID_ALPH);
if (!mread->other_bg) {
// no change to other_bg
if (mread->other_bg_src == NULL ||
strcmp(mread->other_bg_src, "--nrdb--") == 0) {
mread->other_bg = get_nrdb_frequencies(alph, NULL);
} else if (strcmp(mread->other_bg_src, "--uniform--") == 0) {
mread->other_bg = get_uniform_frequencies(alph, NULL);
} else if (strcmp(mread->other_bg_src, "--motif--") == 0 ||
strcmp(mread->other_bg_src, "motif-file") == 0) {
// motif_bg is loaded elsewhere
} else {
mread->other_bg = get_file_frequencies(&(alph), mread->other_bg_src, NULL);
}
}
if (mread->other_bg) mread->pseudo_bg = mread->other_bg;
else mread->pseudo_bg = mread->motif_bg;
}
ARRAY_T* ramen_load_background() {
ALPH_T alph = DNA_ALPH;
ARRAY_T* freqs;
switch (args.bg_format) {
case UNIFORM_BG:
freqs = get_uniform_frequencies(alph, NULL);
break;
case MOTIF_BG:
//We've previously read in the freqs when we read the motif list
freqs = motifs.bg_freqs; //so we're just copying a pointer address so that we use them.
break;
case FILE_BG:
freqs = get_file_frequencies(&alph, args.bg_filename, NULL);
break;
default:
die("Illegal background option");
freqs = NULL; // make compiler happy
}
return freqs;
}
