def _prepare_simulation(self, parameters):
self._set_parameters(parameters)
#recalculate PCR mixture
mixture = self._searcher.matches_to_mixture(WorkCounter(),
self._seq_name,
self._matches_list,
self._PCR_ProductsFinder)
if mixture is None: return None, None
register_tmp_file(mixture)
self._update_side_reactions(parameters)
pcr = SinglePCR(self._abort_event, self._primers_concentrations,
self._elongation_time, self._polymerase,
self._with_exonuclease, self._num_cycles,
self._side_reactions, self._side_concentrations)
ovc = compute_objective_value(pcr, self._product_bounds, self._purity)
return ovc, mixture
def _prepare_simulation(self, parameters):
self._set_parameters(parameters)
#recalculate PCR mixture
mixture = self._searcher.matches_to_mixture(WorkCounter(),
self._seq_name,
self._matches_list,
self._PCR_ProductsFinder)
if mixture is None: return None, None
register_tmp_file(mixture)
self._update_side_reactions(parameters)
pcr = SinglePCR(self._abort_event,
self._primers_concentrations,
self._elongation_time,
self._polymerase,
self._with_exonuclease,
self._num_cycles,
self._side_reactions, self._side_concentrations)
ovc = compute_objective_value(pcr, self._product_bounds, self._purity)
return ovc, mixture
def add_mixture(self, reaction_id, mixture_path):
self._reactions_ids.add(reaction_id)
self._PCR_mixtures[reaction_id] = mixture_path
register_tmp_file(mixture_path)
def add_mixture(self, reaction_id, mixture_path):
self._reactions_ids.add(reaction_id)
self._PCR_mixtures[reaction_id] = mixture_path
register_tmp_file(mixture_path)