void OutputRepertoire(string output_fname) const {
ofstream out(output_fname.c_str());
size_t id = 1;
for(auto it = begin(); it != end(); it++) {
for(size_t i = 0; i < it->Multiplicity(); i++) {
out << ">antibody_" << id << "_multiplicity_" << it->Multiplicity() << "_copy_" << i + 1 << endl;
out << it->Sequence() << endl;
}
id++;
}
out.close();
}
HC_Repertoire_Ptr CreateMutatedHCRepertoire(HC_InputParams params, HC_Repertoire_Ptr base_repertoire) {
HC_Repertoire_Ptr mutated_repertoire(new HC_Repertoire());
// mutated multiplicity creator
// HC_ExponentialMultiplicityCreator mutated_multiplicity_creator(base_repertoire->NumberAntibodies(),
// params.basic_repertoire_params.final_repertoire_size);
HC_PowerLawMultiplicityCreator mutated_multiplicity_creator(base_repertoire->NumberAntibodies(),
params.basic_repertoire_params.final_repertoire_size);
// shm creator
HC_RgywWrcySHMStrategy shm_creation_strategy1(params.pattern_shm_params.min_number_pattern_shm,
params.pattern_shm_params.max_number_pattern_shm,
params.pattern_shm_params.substitution_propability);
HC_CDRBasedRandomSHMStrategy shm_creation_strategy2(params.cdr_shm_params.min_number_mutations,
params.cdr_shm_params.max_number_mutations,
params.cdr_shm_params.mutation_in_fr_prop);
HC_CompositeSHMCreationStrategy composite_shm_strategy(shm_creation_strategy1, shm_creation_strategy2);
HC_SHMCreator shm_creator(composite_shm_strategy);
for(auto it = base_repertoire->begin(); it != base_repertoire->end(); it++) {
for(size_t i = 0; i < it->Multiplicity(); i++) {
auto variable_region_ptr = it->IgVariableRegion()->Clone();
variable_region_ptr = shm_creator.CreateSHM(variable_region_ptr);
size_t multiplicity = mutated_multiplicity_creator.AssignMultiplicity(variable_region_ptr);
mutated_repertoire->Add(HC_Cluster(variable_region_ptr, multiplicity));
}
}
return mutated_repertoire;
}
void PrintBaseHCRepertoire(HC_Repertoire_Ptr base_repertoire) {
for(auto it = base_repertoire->begin(); it != base_repertoire->end(); it++) {
cout << it->IgVariableRegion()->VDJ_Recombination()->Sequence() << " " << it->Multiplicity() << endl;
cout << it->IgVariableRegion()->GetCDRSettings();
}
}
void PrintMutatedHCRepertoire(HC_Repertoire_Ptr mutated_repertoire) {
for(auto it = mutated_repertoire->begin(); it != mutated_repertoire->end(); it++) {
cout << it->IgVariableRegion()->VDJ_Recombination()->Sequence() << " " << it->Multiplicity() << endl;
}
}
void OutputMultiplicities(string output_fname) const {
ofstream out(output_fname.c_str());
for(auto it = begin(); it != end(); it++)
out << it->Multiplicity() << endl;
out.close();
}
size_t NumberAntibodies() {
size_t size = 0;
for(auto it = begin(); it != end(); it++)
size += it->Multiplicity();
return size;
}
