void init_dp(data *d) {
const int width = d->m.width;
int i;
d->dp_seqlen = 0;
d->dp_mat = xmalloc2(width+1, 1 * sizeof(double));
d->forbidden = xmalloc2(width+1, 1);
/* boundary conditions for short-in-long alignment: */
d->dp_mat[0][0] = 0;
for (i = 0; i < width; ++i)
d->dp_mat[i+1][0] = d->delete_scores[i] + d->dp_mat[i][0];
}
unsigned int *
headint32(struct rpmhead *h, int tag, int *cnt)
{
unsigned int i, o, *r;
unsigned char *d, taga[4];
d = h->data;
taga[0] = tag >> 24;
taga[1] = tag >> 16;
taga[2] = tag >> 8;
taga[3] = tag;
for (i = 0; i < h->cnt; i++, d += 16)
if (d[3] == taga[3] && d[2] == taga[2] && d[1] == taga[1] && d[0] == taga[0])
break;
if (i >= h->cnt)
return 0;
if (d[4] != 0 || d[5] != 0 || d[6] != 0 || d[7] != 4)
return 0;
o = d[8] << 24 | d[9] << 16 | d[10] << 8 | d[11];
i = d[12] << 24 | d[13] << 16 | d[14] << 8 | d[15];
if (o + 4 * i > h->dcnt)
return 0;
d = h->dp + o;
r = xmalloc2(i ? i : 1, sizeof(unsigned int));
if (cnt)
*cnt = i;
for (o = 0; o < i; o++, d += 4)
r[o] = d[0] << 24 | d[1] << 16 | d[2] << 8 | d[3];
return r;
}
extern "C" void *
xcalloc(size_t n, size_t size)
{
void* ptr = xmalloc2(n, size);
memset(ptr, 0, n * size);
return ptr;
}
static VALUE
rb_buffer_read(VALUE self, SEL sel, VALUE queue)
{
int i;
cl_int err;
cl_command_queue q = (cl_command_queue) rb_ivar_get(queue, rb_intern("queue"));
float* d = xmalloc2(ROpenCLBuffer(self)->size, sizeof(float));
err = clEnqueueReadBuffer(q, ROpenCLBuffer(self)->buffer, CL_TRUE, 0, sizeof(float)*ROpenCLBuffer(self)->size, d, 0, NULL, NULL);
if(err != CL_SUCCESS)
rb_raise(rb_eArgError, "Failed with error `%d'", err);
VALUE res = rb_ary_new2(ROpenCLBuffer(self)->size);
for(i=0; i<ROpenCLBuffer(self)->size; i++) {
rb_ary_push(res, rb_float_new(d[i]));
}
return res;
}
static VALUE
rb_buffer_write(VALUE self, SEL sel, VALUE queue, VALUE data)
{
int i;
cl_int err;
cl_command_queue q = (cl_command_queue) rb_ivar_get(queue, rb_intern("queue"));
float* d = xmalloc2(ROpenCLBuffer(self)->size, sizeof(float));
for(i=0; i<ROpenCLBuffer(self)->size; i++) {
d[i] = NUM2DBL(rb_ary_entry(data, i));
}
err = clEnqueueWriteBuffer(q, ROpenCLBuffer(self)->buffer, CL_TRUE, 0, sizeof(double)*ROpenCLBuffer(self)->size, d, 0, NULL, NULL);
if(err != CL_SUCCESS)
rb_raise(rb_eArgError, "Failed with error `%d'", err);
return Qnil;
}
void init_scores(data *d) {
const int alph_size = d->m.alph_size;
const int width = d->m.width;
const double *bg = d->alph.prob;
glam2_scorer *s = &d->scorer;
int i, j;
d->match_scores = xmalloc2(width, (alph_size+1) * sizeof(double));
XMALLOC(d->delete_scores, width);
XMALLOC(d->insert_scores, width);
for (i = 0; i < width; ++i) {
const int *residue_counts = d->m.residue_counts[i];
const int match_count = sum_int(residue_counts, alph_size);
const int delete_count = d->m.delete_counts[i];
const int insert_count = d->m.insert_counts[i];
const int aligned_seq = match_count + delete_count;
const double ds = beta_ratio_a(&s->d_prior, delete_count, match_count);
const double ms = beta_ratio_b(&s->d_prior, delete_count, match_count);
const double is = beta_ratio_a(&s->i_prior, insert_count, aligned_seq);
const double js = beta_ratio_b(&s->i_prior, insert_count, aligned_seq);
dmix_ratios(&s->e_prior, d->match_scores[i], residue_counts);
if (i+1 < width) {
for (j = 0; j < alph_size; ++j)
d->match_scores[i][j] = xlog(js * ms * d->match_scores[i][j] / bg[j]);
d->delete_scores[i] = xlog(ds * js);
d->insert_scores[i] = xlog(is);
} else { /* no insertions after last column: special case */
for (j = 0; j < alph_size; ++j)
d->match_scores[i][j] = xlog(ms * d->match_scores[i][j] / bg[j]);
d->delete_scores[i] = xlog(ds);
d->insert_scores[i] = -DBL_MAX; /* overflow risk? */
}
/* overflow risk? */
d->match_scores[i][alph_size] = -DBL_MAX; /* mask character forbidden */
}
}
