inline Vector speed_test(
void test(size_t size, size_t repeat),
const Vector& size_vec ,
double time_min )
{
// check that size_vec is a simple vector with size_t elements
CheckSimpleVector<size_t, Vector>();
size_t n = size_vec.size();
Vector rate_vec(n);
size_t i;
for(i = 0; i < n; i++)
{ size_t size = size_vec[i];
size_t repeat = 1;
double s0 = elapsed_seconds();
double s1 = elapsed_seconds();
while( s1 - s0 < time_min )
{ repeat = 2 * repeat;
s0 = elapsed_seconds();
test(size, repeat);
s1 = elapsed_seconds();
}
rate_vec[i] = (size_t)(.5 + repeat / (s1 - s0));
}
return rate_vec;
}
bool speed_test(void)
{ bool ok = true;
// size of the test cases
vector<size_t> size_vec(2);
size_vec[0] = 40;
size_vec[1] = 80;
// minimum amount of time to run test
double time_min = 0.5;
// run the test cases
vector<size_t> rate_vec(2);
rate_vec = CppAD::speed_test(test, size_vec, time_min);
// time per repeat loop (note counting setup or teardown)
double time_0 = 1. / double(rate_vec[0]);
double time_1 = 1. / double(rate_vec[1]);
// for this case, time should be linear w.r.t size
double check = double(size_vec[1]) * time_0 / double(size_vec[0]);
double rel_diff = (check - time_1) / time_1;
ok &= (std::fabs(rel_diff) <= .1);
if( ! ok )
std::cout << std::endl << "rel_diff = " << rel_diff << std::endl;
a.clear();
b.clear();
c.clear();
return ok;
}
vector<double> ribo_model::build_rate_vec(rid_t t)
{
vector<double> rate_vec(codon_vec_len(t),0);
// build elongation rate vector
for (size_t i=0; i!=rate_vec.size(); ++i)
rate_vec[i] = get_erate(model[t].codon_id_map[i]);
// insert initiation rate at the beginning of rate vector
rate_vec.insert(rate_vec.begin(), get_irate(t));
return rate_vec;
}
void ribo_model::update_profile(const ribo_profile& rprofile, bool ignore_no_map, int nproc)
{
omp_set_num_threads(nproc);
#pragma omp parallel for schedule(static)
for (size_t t=0; t<rprofile.number_of_transcripts(); ++t) {
if (ignore_no_map and rprofile.get_tot_count(t) == 0) continue;
tmodel& m = get_model_ref(t);
if (get_obj(t)<0) continue;
vector<double> rate_vec(build_rate_vec(t));
double trate = compute_profile(rate_vec, m.profile);
if (trate>0)
set_trate(t, trate);
else
compute_translation_rate(t, rate_vec);
compute_transcript_abundance(t, rprofile.get_read_assignments(t));
}
}
