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/*
* Insertion.h
*
* Created on: Dec 9, 2014
* 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/>.
*
*/
#ifndef INSERTION_H_
#define INSERTION_H_
#include "Rec_Event.h"
#include "Utils.h"
#include <forward_list>
#include <unordered_map>
#include <string>
#include <list>
#include <queue>
#include <utility>
#include "Errorrate.h"
#include <random>
#include <map>
/**
* \class Insertion Insertion.h
* \brief Insertion recombination events.
* \author Q.Marcou
* \version 1.0
*
* The Insertion RecEvent models the distribution of junctional insertion length during the V(D)J recombination process.
*
*/
class Insertion: public Rec_Event {
public:
//Constructors
Insertion();
Insertion(Gene_class,std::pair<int,int>);
Insertion(Gene_class,std::forward_list<int>);
Insertion(Gene_class );
Insertion(Gene_class , std::unordered_map<std::string , Event_realization>&);
//Destructor
virtual ~Insertion();
//virtual methods
std::shared_ptr<Rec_Event> copy();
inline void iterate(double& , Downstream_scenario_proba_bound_map& , const std::string& , const Int_Str& , Index_map& , const std::unordered_map<Rec_Event_name,std::vector<std::pair<std::shared_ptr<const Rec_Event>,int>>>& , std::shared_ptr<Next_event_ptr>& , Marginal_array_p& , const Marginal_array_p& , const std::unordered_map<Gene_class , std::vector<Alignment_data>>& , Seq_type_str_p_map& , Seq_offsets_map& , std::shared_ptr<Error_rate>& , std::map<size_t,std::shared_ptr<Counter>>& , const std::unordered_map<std::tuple<Event_type,Gene_class,Seq_side>, std::shared_ptr<Rec_Event>> & , Safety_bool_map& , Mismatch_vectors_map& , double& , double&);
bool add_realization(int);
std::queue<int> draw_random_realization( const Marginal_array_p& , std::unordered_map<Rec_Event_name,int>& , const std::unordered_map<Rec_Event_name,std::vector<std::pair<std::shared_ptr<const Rec_Event>,int>>>& , std::unordered_map<Seq_type , std::string>& , std::mt19937_64&)const ;
void write2txt(std::ofstream&);
void initialize_event( std::unordered_set<Rec_Event_name>& , const std::unordered_map<std::tuple<Event_type,Gene_class,Seq_side>, std::shared_ptr<Rec_Event>>& , const std::unordered_map<Rec_Event_name,std::vector<std::pair<std::shared_ptr<const Rec_Event>,int>>>& , Downstream_scenario_proba_bound_map& , Seq_type_str_p_map& , Safety_bool_map& , std::shared_ptr<Error_rate> ,Mismatch_vectors_map&,Seq_offsets_map&,Index_map&);
void add_to_marginals(long double , Marginal_array_p&) const;
void set_crude_upper_bound_proba(size_t , size_t , Marginal_array_p&) ;
void initialize_crude_scenario_proba_bound(double& , std::forward_list<double*>& ,const std::unordered_map<std::tuple<Event_type,Gene_class,Seq_side>, std::shared_ptr<Rec_Event>>&);
//Proba bound related computation methods
bool has_effect_on(Seq_type) const;
void iterate_initialize_Len_proba( Seq_type considered_junction , std::map<int,double>& length_best_proba_map , std::queue<std::shared_ptr<Rec_Event>>& model_queue , double& scenario_proba , const Marginal_array_p& model_parameters_point , Index_map& base_index_map , Seq_type_str_p_map& constructed_sequences , int& seq_len ) const ;
void initialize_Len_proba_bound(std::queue<std::shared_ptr<Rec_Event>>& model_queue , const Marginal_array_p& model_parameters_point , Index_map& base_index_map );
private:
inline double iterate_common(double , int , int , Index_map& ,const std::unordered_map<Rec_Event_name,std::vector<std::pair<std::shared_ptr<const Rec_Event>,int>>>& ,const Marginal_array_p&);
std::map<int,Event_realization> ordered_realization_map;
std::map<int,double> junction_length_best_proba_map;
mutable Int_Str inserted_str;
mutable int base_index;
double new_scenario_proba;
double proba_contribution;
int insertions;
int new_index;
std::map<int,double> upper_bound_per_ins; //Contains the probability upper bound for each number of insertions
int previous_index;
//Iterate common
int realization_index;
std::string insertions_str;
double* dinuc_updated_bound;
int memory_layer_proba_map_junction;
//Pre create pairs to call seq_offsets (otherwise cost of creating a pair at each call)
//std::pair<Seq_type,Seq_side> d_5_pair = std::make_pair (D_gene_seq,Five_prime);
//std::pair<Seq_type,Seq_side> v_3_pair = std::make_pair (V_gene_seq,Three_prime);
//std::pair<Seq_type,Seq_side> j_5_pair = std::make_pair (J_gene_seq,Five_prime);
//std::pair<Seq_type,Seq_side> d_3_pair = std::make_pair (D_gene_seq,Three_prime);
};
#endif /* INSERTION_H_ */
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