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/*
* Bestscenarioscounter.cpp
*
* Created on: Aug 19, 2016
* Author: Quentin Marcou
*
* This source code is distributed as part of the IGoR software.
* IGoR (Inference and Generation of Repertoires) is a versatile software to analyze and model immune receptors
* generation, selection, mutation and all other processes.
* Copyright (C) 2017 Quentin Marcou
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
#include "Bestscenarioscounter.h"
using namespace std;
Best_scenarios_counter::Best_scenarios_counter(size_t n_scenarios): Counter(), n_scenarios_counted(n_scenarios) {
}
Best_scenarios_counter::Best_scenarios_counter(size_t n_scenarios , bool is_last_iter_only): Best_scenarios_counter(n_scenarios) {
this->last_iter_only = is_last_iter_only;
}
Best_scenarios_counter::Best_scenarios_counter(size_t n_scenarios , string path): Counter(path) , n_scenarios_counted(n_scenarios) {
}
Best_scenarios_counter::Best_scenarios_counter(size_t n_scenarios , string path , bool is_last_iter_only) : Best_scenarios_counter(n_scenarios , path) {
this->last_iter_only = is_last_iter_only;
}
Best_scenarios_counter::Best_scenarios_counter():Best_scenarios_counter(1,true) {
// TODO Auto-generated constructor stub
}
Best_scenarios_counter::~Best_scenarios_counter() {
// TODO Auto-generated destructor stub
}
void Best_scenarios_counter::count_scenario(long double scenario_seq_joint_proba , double scenario_probability , const string& original_sequence , Seq_type_str_p_map& constructed_sequences , const Seq_offsets_map& seq_offsets , const unordered_map<tuple<Event_type,Gene_class,Seq_side>, shared_ptr<Rec_Event>>& events_map , Mismatch_vectors_map& mismatches_lists){
if(this->best_scenarios_vec.size()<this->n_scenarios_counted){
for(forward_list<shared_ptr<const Rec_Event>>::const_iterator iter = this->event_fw_list.begin() ; iter != this->event_fw_list.end() ; ++iter){
this->single_scenario_realizations_queue.push((*iter)->get_current_realizations_index_vec());
}
// Get mismatches and add them to the mismatch list
if(mismatches_lists.exist(V_gene_seq)){
const vector<int>& v_mismatch_list = *mismatches_lists.at(V_gene_seq);
single_scenario_mismatches_list.insert(single_scenario_mismatches_list.end() , v_mismatch_list.begin() , v_mismatch_list.end());
}
if(mismatches_lists.exist(D_gene_seq)){
const vector<int>& d_mismatch_list = *mismatches_lists[D_gene_seq];
single_scenario_mismatches_list.insert(single_scenario_mismatches_list.end() , d_mismatch_list.begin() , d_mismatch_list.end());
}
if(mismatches_lists.exist(J_gene_seq)){
const vector<int>& j_mismatch_list = *mismatches_lists.at(J_gene_seq);
single_scenario_mismatches_list.insert(single_scenario_mismatches_list.end() , j_mismatch_list.begin() , j_mismatch_list.end());
}
if(this->best_scenarios_vec.empty()){
this->best_scenarios_vec.emplace_back(scenario_seq_joint_proba,const_cast<queue<vector<int>>&>(this->single_scenario_realizations_queue),single_scenario_mismatches_list);
}
else{
vector<tuple<double,queue<vector<int>>,list<int>>>::iterator jter = this->best_scenarios_vec.begin();
while( (scenario_seq_joint_proba>get<0>(*jter)) and (jter != this->best_scenarios_vec.end()) ){
++jter;
}
this->best_scenarios_vec.emplace(jter , scenario_seq_joint_proba,const_cast<queue<vector<int>>&>(this->single_scenario_realizations_queue),single_scenario_mismatches_list);
}
}
else{
if(scenario_seq_joint_proba > get<0>(this->best_scenarios_vec[0])){
for(forward_list<shared_ptr<const Rec_Event>>::const_iterator iter = this->event_fw_list.begin() ; iter != this->event_fw_list.end() ; ++iter){
this->single_scenario_realizations_queue.push((*iter)->get_current_realizations_index_vec());
}
// Get mismatches and add them to the mismatch list
if(mismatches_lists.exist(V_gene_seq)){
const vector<int>& v_mismatch_list = *mismatches_lists.at(V_gene_seq);
single_scenario_mismatches_list.insert(single_scenario_mismatches_list.end() , v_mismatch_list.begin() , v_mismatch_list.end());
}
if(mismatches_lists.exist(D_gene_seq)){
const vector<int>& d_mismatch_list = *mismatches_lists[D_gene_seq];
single_scenario_mismatches_list.insert(single_scenario_mismatches_list.end() , d_mismatch_list.begin() , d_mismatch_list.end());
}
if(mismatches_lists.exist(J_gene_seq)){
const vector<int>& j_mismatch_list = *mismatches_lists.at(J_gene_seq);
single_scenario_mismatches_list.insert(single_scenario_mismatches_list.end() , j_mismatch_list.begin() , j_mismatch_list.end());
}
auto jter = this->best_scenarios_vec.begin()+1;
while( (scenario_seq_joint_proba>get<0>(*jter)) and (jter != this->best_scenarios_vec.end()) ){
++jter;
}
this->best_scenarios_vec.emplace(jter , scenario_seq_joint_proba,this->single_scenario_realizations_queue , single_scenario_mismatches_list);
this->best_scenarios_vec.erase(this->best_scenarios_vec.begin());
}
}
while(not this->single_scenario_realizations_queue.empty()){
this->single_scenario_realizations_queue.pop();
}
single_scenario_mismatches_list.clear();
}
void Best_scenarios_counter::count_sequence(double seq_likelihood , const Model_marginals& single_seq_marginals , const Model_Parms& single_seq_model_parms){
for(vector<tuple<double,queue<vector<int>>,list<int>>>::iterator iter = this->best_scenarios_vec.begin() ; iter!=this->best_scenarios_vec.end() ; ++iter){
get<0>(*iter)/=seq_likelihood;
//If an exception is thrown here there is a problem upstream
}
}
void Best_scenarios_counter::initialize_counter(const Model_Parms& parms , const Model_marginals& marginals){
if(not fstreams_created){
output_scenario_file_ptr = shared_ptr<ofstream>(new ofstream);
this->output_scenario_file_ptr->open(path_to_file + "best_scenarios_counts.csv");
//Create the header
(*this->output_scenario_file_ptr.get())<<"seq_index;scenario_rank;scenario_proba_cond_seq";
auto event_queue = parms.get_model_queue();
while(not event_queue.empty()){
shared_ptr<Rec_Event> event_ptr = event_queue.front();
(*this->output_scenario_file_ptr.get())<<";"<<event_ptr->get_name();
this->event_fw_list.emplace_front( event_ptr);
event_queue.pop();
}
event_fw_list.reverse();
(*this->output_scenario_file_ptr.get())<<";Mismatches"<<endl;
fstreams_created = true;
}
else{
//Still need to fill in the fw list
auto event_queue = parms.get_model_queue();
while(not event_queue.empty()){
shared_ptr<Rec_Event> event_ptr = event_queue.front();
this->event_fw_list.emplace_front( event_ptr);
event_queue.pop();
}
event_fw_list.reverse();
}
}
void Best_scenarios_counter::add_checked(shared_ptr<Counter> counter){
return ;
}
void Best_scenarios_counter::dump_sequence_data(int seq_index , int iteration_n){
size_t counter = 1;
for(vector<tuple<double,queue<vector<int>>,list<int>>>::reverse_iterator iter = this->best_scenarios_vec.rbegin() ; iter!=this->best_scenarios_vec.rend() ; ++iter){
(*this->output_scenario_file_ptr.get())<<seq_index<<";"<<counter<<";"<<get<0>(*iter);
queue<vector<int>>& scenario_queue = get<1>(*iter);
//Loop over events
while(not scenario_queue.empty()){
const vector<int>& real_vec = scenario_queue.front();
(*this->output_scenario_file_ptr.get())<<";(";
//Loop over event realizations
for(vector<int>::const_iterator jter = real_vec.begin() ; jter!= real_vec.end() ; ++jter){
(*this->output_scenario_file_ptr.get())<<(*jter);
if(jter!=real_vec.end() -1){
(*this->output_scenario_file_ptr.get())<<",";
}
}
(*this->output_scenario_file_ptr.get())<<")";
scenario_queue.pop();
}
(*this->output_scenario_file_ptr.get())<<";(";
//Loop over mismatches
list<int>& mismatches_list = get<2>(*iter);
list<int>::const_iterator util_iter = mismatches_list.end();
--util_iter;
for(list<int>::const_iterator kter = mismatches_list.begin() ; kter!= mismatches_list.end() ; ++kter){
(*this->output_scenario_file_ptr.get())<<(*kter);
if(kter!=util_iter){
(*this->output_scenario_file_ptr.get())<<",";
}
}
(*this->output_scenario_file_ptr.get())<<")"<<endl;
++counter;
}
best_scenarios_vec.clear();
}
shared_ptr<Counter> Best_scenarios_counter::copy() const{
shared_ptr<Best_scenarios_counter> counter_copy_ptr (new Best_scenarios_counter(this->n_scenarios_counted));
counter_copy_ptr->fstreams_created = this->fstreams_created;
if(this->fstreams_created){
counter_copy_ptr->output_scenario_file_ptr = this->output_scenario_file_ptr;
}
else{
throw runtime_error("Counters should not be copied before stream initalization");
}
return counter_copy_ptr;
}
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