//setting this out to allow for other types of setting
static void set_branch_length_sliding_window(nodeptr p, int numBranches,state * s, boolean record_tmp_bl)
{
int i;
double new_value;
double r,mx,mn;
for(i = 0; i < numBranches; i++)
{
assert(p->z[i] == p->back->z[i]);
if(record_tmp_bl)
p->z_tmp[i] = p->back->z_tmp[i] = p->z[i]; /* keep current value */
r = (double)rand()/(double)RAND_MAX;
mn = p->z[i]-(s->bl_sliding_window_w/2);
mx = p->z[i]+(s->bl_sliding_window_w/2);
new_value = fabs(mn + r * (mx-mn));
/* Ensure always you stay within this range */
if(new_value > zmax) new_value = zmax;
if(new_value < zmin) new_value = zmin;
assert(new_value <= zmax && new_value >= zmin);
p->z[i] = p->back->z[i] = new_value;
//assuming this will be visiting each node, and multiple threads won't be accessing this
s->bl_prior += log(exp_pdf(s->bl_prior_exp_lambda,new_value));
//s->bl_prior += 1;
}
}
int32
s2_mixing_weights(float32 ***out_mixw,
const char *hmm_file_name)
{
int magic; /* SPHINX-II hmm file magic number */
int n_cw; /* number of codewords for the model */
int n_omatrix; /* number of output pdfs in the model */
int32 *tmp_opdf;
uint32 i;
FILE *fp;
fp = fopen(hmm_file_name, "rb");
if (fp == NULL) {
fflush(stdout);
fprintf(stderr, "%s(%d): ERROR cannot open HMM file %s for reading\n",
__FILE__, __LINE__, hmm_file_name);
perror(hmm_file_name);
fflush(stderr);
return S3_ERROR;
}
magic = ckd_read_int32(fp);
if (!IS_MAGIC(magic)) {
fflush(stdout);
fprintf(stderr, "%s(%d): ERROR invalid magic number found. Byteorder? Not an HMM?\n", __FILE__, __LINE__);
fflush(stderr);
return S3_ERROR;
}
n_cw = ckd_read_int32(fp);
assert(n_cw == S2_N_CODEWORD);
tmp_opdf = (int32 *)ckd_calloc(n_cw, sizeof(int32));
n_omatrix = ckd_read_int32(fp);
assert(n_omatrix == S2_N_STATE-1);
if ((magic == COUNT_F) || (magic == PROB_F)) {
for (i = 0; i < n_omatrix; i++) {
read_opdf(tmp_opdf, n_cw, fp);
if (COUNT_P(magic))
normalize_opdf(tmp_opdf, n_cw);
exp_pdf(out_mixw[i][0], tmp_opdf, n_cw);
}
for (i = 0; i < n_omatrix; i++) {
read_opdf(tmp_opdf, n_cw, fp);
if (COUNT_P(magic))
normalize_opdf(tmp_opdf, n_cw);
exp_pdf(out_mixw[i][1], tmp_opdf, n_cw);
}
for (i = 0; i < n_omatrix; i++) {
read_opdf(tmp_opdf, n_cw, fp);
if (COUNT_P(magic))
normalize_opdf(tmp_opdf, n_cw);
exp_pdf(out_mixw[i][2], tmp_opdf, n_cw);
}
for (i = 0; i < n_omatrix; i++) {
read_opdf(tmp_opdf, n_cw, fp);
if (COUNT_P(magic))
normalize_opdf(tmp_opdf, n_cw);
exp_pdf(out_mixw[i][3], tmp_opdf, n_cw);
}
}
ckd_free(tmp_opdf);
return 0;
}
