/*
 * Utils.cpp

 *
 *  Created on: Apr 9, 2015
 *      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 "Utils.h"

using namespace std;

/////Utilitaries
ostream& operator<<(ostream& os , Gene_class gc){
	switch(gc){
	case V_gene:os<<"V_gene";break;
	case VD_genes:os<<"VD_genes";break;
	case D_gene:os<<"D_gene";break;
	case DJ_genes:os<<"DJ_gene";break;
	case VJ_genes:os<<"VJ_gene";break;
	case J_gene:os<<"J_gene";break;
	case VDJ_genes:os<<"VDJ_genes";break;
	case Undefined_gene: os<<"Undefined_gene";break;

	default:
		throw invalid_argument("Unknown Gene_class in operator<< ");
	}
	return os;
}

ostream& operator<<(ostream& os , Seq_side ss){
	switch(ss){
	case Five_prime:os<<"Five_prime";break;
	case Three_prime:os<<"Three_prime";break;
	case Undefined_side:os<<"Undefined_side";break;

	default:
		throw invalid_argument("Unknown Seq_side in operator << ");
	}
	return os;
}

string operator+(const string& str , Gene_class gc){
	string next_str;
	switch(gc){
	case V_gene:next_str="V_gene";break;
	case VD_genes:next_str="VD_genes";break;
	case D_gene:next_str="D_gene";break;
	case DJ_genes:next_str="DJ_gene";break;
	case VJ_genes:next_str="VJ_gene";break;
	case J_gene:next_str="J_gene";break;
	case VDJ_genes:next_str="VDJ_genes";break;
	case Undefined_gene: next_str="Undefined_gene";break;
	}
	return str+next_str;
}

string operator+(const string& str , Seq_side ss){
	string next_str;
	switch(ss){
	case Five_prime:next_str="Five_prime";break;
	case Three_prime:next_str="Three_prime";break;
	case Undefined_side:next_str="Undefined_side";break;
	}
	return str+next_str;
}

string operator+(const string& str , Event_type et){
	string next_str;
	switch(et){
	case GeneChoice_t:next_str="GeneChoice";break;
	case Deletion_t:next_str="Deletion";break;
	case Insertion_t:next_str="Insertion";break;
	case Dinuclmarkov_t:next_str="DinucMarkov";break;
	}
	return str+next_str;
}

/**
 * \brief Creates a Gene_class object from a string.
 * \author Q.Marcou
 * \version 1.0.0
 */
Gene_class str2GeneClass(const string str){
	Gene_class gene_class;
	if(str == "V_gene"){gene_class = V_gene;}
	else if(str == "VD_genes"){gene_class = VD_genes;}
	else if(str == "D_gene"){gene_class = D_gene;}
	else if(str == "DJ_gene"){gene_class = DJ_genes;}
	else if(str == "VJ_gene"){gene_class = VJ_genes;}
	else if(str == "J_gene"){gene_class = J_gene;}
	else if(str == "VDJ_genes"){gene_class = VDJ_genes;}
	else if(str == "Undefined_gene"){gene_class = Undefined_gene;}
	else{
		throw runtime_error("Unknown Gene_class in str2GeneClass");
	}
	return gene_class;
}

/**
 * \brief Overloads std::to_string to convert Gene_class object to string.
 * \author Q.Marcou
 * \version 1.2.0
 */
string to_string(const Gene_class gc){
	switch(gc){
	case V_gene:return "V_gene";
	case VD_genes:return "VD_genes";
	case D_gene:return "D_gene";
	case DJ_genes:return "DJ_gene";
	case VJ_genes:return "VJ_gene";
	case J_gene:return "J_gene";
	case VDJ_genes:return "VDJ_genes";
	case Undefined_gene:return "Undefined_gene";

	default:
		throw invalid_argument("Unknown Gene_class in to_string(const Gene_class).");
	}
}

/**
 * \brief Creates a Seq_side object from a string.
 * \author Q.Marcou
 * \version 1.0.0
 */
Seq_side str2SeqSide(const string str){
	Seq_side seq_side;
	if(str == "Five_prime"){seq_side = Five_prime;}
		else if(str == "Three_prime"){seq_side = Three_prime;}
		else if(str == "Undefined_side"){seq_side = Undefined_side;}
	else{
		throw runtime_error("Unknown event_side in str2SeqSide");
	}
	return seq_side;
}

/**
 * \brief Overloads std::to_string to convert Seq_side object to string.
 * \author Q.Marcou
 * \version 1.2.0
 */
string to_string(const Seq_side ss){
	switch(ss){
	case Five_prime:return "Five_prime";
	case Three_prime:return "Three_prime";
	case Undefined_side:return "Undefined_side";

	default:
		throw invalid_argument("Unknown Seq_side in to_string(const Seq_side).");
	}

}

//Seq_type_str_p_map::Seq_type_str_p_map(): Enum_fast_memory_map<Seq_type,Str_ptr>(6){}

//Implementing Seq_type_str_p_map methods

//template<typename K, typename V>

/*Enum_fast_memory_map::Enum_fast_memory_map(int defined_range) : max_layer(0),range(defined_range){


		str_ptr_arr =  new Str_ptr [range];
		memory_layer_ptr = new int [range];

		for(size_t i = 0 ; i!=range ; i++){
			str_ptr_arr[i] = nullptr;
		}

		for(size_t i = 0 ; i!=range ; i++){
			this->memory_layer_ptr[i] = -1;
		}
	};

Enum_fast_memory_map::~Enum_fast_memory_map(){
		delete [] str_ptr_arr;
		delete [] memory_layer_ptr;
	}


	 * Access operator without bound checks, once called the position is considered initialized

	Str_ptr& Seq_type_str_p_map::operator[](const Seq_type& seq_type){
		std::cout<<"operator[]"<<std::endl;
		for(size_t j=0 ; j!=(max_layer+1) ; j++){
						for(size_t i = 0 ; i!=range ; i++){
							std::cout<<(*(str_ptr_arr+i+range*j))<<";";
						}
						std::cout<<std::endl;
					}
					std::cout<<std::endl;


		if(seq_type>range-1){throw std::out_of_range("Unknown seq type in Seq_type_str_p_map::operator(Seq_type)");}
		if(memory_layer_ptr[seq_type]>-1){
			return (*(str_ptr_arr+seq_type + memory_layer_ptr[seq_type]*range));
		}
		else{
			memory_layer_ptr[seq_type] = 0;
			return (*(str_ptr_arr+seq_type));
		}

	}

	void update(){
		for(size_t i = 0 ; i!=range ; i++){
			if(tmp_modif_bool_array[i]){
				str_ptr_arr[i] = str_ptr_arr_tmp[i];
				tmp_modif_bool_array[i]=false;
				init_bool_array[i] = true;
			}
		}
	}


	 * This method returns the current memory layer at the given position

	int Seq_type_str_p_map::get_current_memory_layer(Seq_type seq_type){
		return memory_layer_ptr[seq_type];
	}


	 * Requesting a memory layer at a position adds a layer to that position

	void Seq_type_str_p_map::request_memory_layer(Seq_type seq_type){
		//Get current memory layer at this position
		if(memory_layer_ptr[seq_type]<max_layer){
			memory_layer_ptr[seq_type]++;
		}
		else{
			max_layer++;
			Str_ptr* new_str_ptr = new Str_ptr [range*(max_layer+1)];
			for(size_t i = 0 ; i!=range ; i++){
				for(size_t j=0 ; j!=(max_layer+1) ; j++){
					(*(new_str_ptr + i+j*range)) = (*(str_ptr_arr + i+j*range));
				}
			}
			delete [] str_ptr_arr;
			str_ptr_arr = new_str_ptr;
			memory_layer_ptr[seq_type]++;
		}
	}

	void Seq_type_str_p_map::set_value(Seq_type seq_type, Str_ptr value , int memory_layer){
		if(seq_type>range-1){throw std::out_of_range("Unknown seq type in Seq_type_str_p_map::operator(Seq_type)");}
		//Cannot fill memory layer without filling the ones downstream
		if(memory_layer<=(memory_layer_ptr[seq_type]+1)){
			(*(str_ptr_arr + seq_type + memory_layer*range)) = value;
			//Setting a value at a given layer invalidate upper layers
			memory_layer_ptr[seq_type] = memory_layer;
		}
		else{
			throw out_of_range("Trying to access incorrect memory layer");
		}

	}

	 * Access operator with bounds checks, prevent access to uninitialized positions

	Str_ptr& Seq_type_str_p_map::at(const Seq_type& seq_type){

		if(seq_type>range-1){
			throw std::out_of_range("Unknown seq type in Seq_type_str_p_map::operator(Seq_type)");
		}
		else{
			if(memory_layer_ptr[seq_type]>-1){
				return (*(str_ptr_arr + seq_type + memory_layer_ptr[seq_type]*range));
			}
			else{
				throw std::out_of_range("Trying to access unintialized position in Seq_type_str_p_map::at()");
			}
		}

	}


	Str_ptr& Seq_type_str_p_map::at(const Seq_type& seq_type , int memory_layer){

		if(seq_type>range-1){
			throw std::out_of_range("Unknown seq type in Seq_type_str_p_map::operator(Seq_type)");
		}
		else{
			if(memory_layer<=(memory_layer_ptr[seq_type]+1)){
				memory_layer_ptr[seq_type] = memory_layer;
				return (*(str_ptr_arr + seq_type + memory_layer*range));
			}
			else{
				throw std::out_of_range("Trying to access unintialized position in Seq_type_str_p_map::at()");
			}
		}

	}*/
/*
	 * Assignment operator,provides a shallow copy of the non tmp array

	Seq_type_str_p_map& operator=(const Seq_type_str_p_map& other){
		this->str_ptr_arr = other.str_ptr_arr;
		this->init_bool_array = other.init_bool_array;
		for(size_t i = 0 ; i!=range ; i++){
			if(other.tmp_modif_bool_array[i]){
				str_ptr_arr[i] = str_ptr_arr_tmp[i];

				init_bool_array[i] = true;
			}
		}
		return *this;
	}*/

	/*
	 * Copy constructor
	 * Provides a deep copy of the object

	Seq_type_str_p_map(const Seq_type_str_p_map& other){
		//Provides a deep copy of the "map"
		this->str_ptr_arr = new std::string* [range];

		this->init_bool_array = new bool [range];


		for(size_t i = 0 ; i!=range ; i++){
			this->str_ptr_arr[i] = other.str_ptr_arr[i];
			this->init_bool_array[i] = other.init_bool_array[i];
		}
	}*/

/**
 * \brief A handy function to extract separated fields in a string (e.g csv)
 * \author Q.Marcou
 * \version 1.2.0
 *
 * \param [in] total_string The original string
 * \param [in] separator the string separator
 *
 * \return A vector containing the separated fields in order of appearance.
 */
vector<string> extract_string_fields(const string total_string ,const string separator){
	vector<string> output_vector;
	int sep_index = -1;
	int next_sep_index = total_string.find(separator);
	while(next_sep_index>0){
		output_vector.emplace_back(total_string.substr(sep_index+1,next_sep_index));
		sep_index = next_sep_index;
		next_sep_index = total_string.find(separator,sep_index+1);
	}
	output_vector.emplace_back(total_string.substr(sep_index+1,string::npos));
	return output_vector;
}

/**
 * \brief A handy function to show/update a progress bar in a stream
 * \author Q.Marcou
 * \version 1.2.0
 *
 * \param [in,out] output_stream The stream (file or console) to interact with
 * \param [in] progress the current progress of the considered task. Should be comprised between 0 and 1.
 * \param [in] prefix_message Prefix message to the progress bar
 * \param [in] progress_bar_size number of divisions in the progress bar. Default is 50.
 *
 * \bug Although not really a bug, no test will be to check that progress is indeed between 0 and 1.
 *
 * Note this function's call should eventually be followed by a call to close_progress_bar
 *
 */
void show_progress_bar(std::ostream& output_stream , double progress, std::string prefix_message /*= ""*/, size_t progress_bar_size /*= 50*/){
	output_stream << prefix_message <<" [";
	size_t pos = progress_bar_size * progress;
	for(size_t i=0 ; i!=progress_bar_size ; ++i){
		if(i<pos) output_stream<<"|";
		else output_stream<<" ";
	}
	output_stream<< "] " << to_string(progress * 100.0).substr(0,5) << " %\r";
	output_stream.flush();
}

/**
 * \brief A handy function to show a full progress bar labeled as 'Done'
 * \author Q.Marcou
 * \version 1.2.0
 *
 * \param [in,out] output_stream The stream (file or console) to interact with
 * \param [in] prefix_message Prefix message to the progress bar
 * \param [in] progress_bar_size number of divisions in the progress bar. Default is 50.
 *
 *
 * Note this function's output needs to be terminated by \endl.
 *
 */
void close_progress_bar(std::ostream& output_stream , std::string prefix_message /*= ""*/, size_t progress_bar_size /*= 50*/){
	output_stream << prefix_message <<" [";
	for(size_t i=0 ; i!=progress_bar_size ; ++i){
		output_stream<<"|";
	}
	output_stream<< "] " << " Done." << " \r";
	output_stream.flush();
	output_stream<<endl;
}

/**
 * \brief A function drawing a random 64 bits integer seed.
 * \author Q.Marcou
 * \version 1.2.0
 *
 * Draws a random 64 bits integer seed trying to be as close as possible from the guidelines given in http://www0.cs.ucl.ac.uk/staff/D.Jones/GoodPracticeRNG.pdf
 * If a random device is available (e.g /dev/random) is available, two 32 bits integers are drawn from it and combined as a 64 bit one.
 * If no random device is available a 64 bits random seed is computed from time, process id, etc...
 */
uint64_t draw_random_64bits_seed(){
	uint64_t random_seed;
	try{
		// Use a random device (e.g /dev/random)
		random_device rd;
		// Draw two different 32 bits seeds
		uint32_t subseed1 = rd();
		uint32_t subseed2 = rd();
		// Combine them in a single 64 bit unsigned integer.
		uint32_t* begin_ptr = (uint32_t*)&random_seed;
		*begin_ptr = subseed1;
		*(begin_ptr+1) = subseed2;
	}
	catch (exception& e){
		cerr<<"Exception caught trying to initialize random_device to generate a random seed in draw_random_64bits_seed"<<endl;
		cerr<<"A lesser quality seed based on date,time,PID,... has been provided instead."<<endl;
		//Get today's time
		typedef std::chrono::high_resolution_clock myclock;
		myclock::time_point time = myclock::now();
		chrono::duration<uint64_t,nano> dur1 (time -  myclock::time_point::min());
		chrono::duration<uint64_t,nano> dur2 (myclock::time_point::max() - time);
		uint64_t time1 = dur1.count();
		uint64_t time2 = dur2.count();
		// Get process ID
		int pid = ::getpid();
		// Get host ID
		long int hid = ::gethostid();
		//Get a somewhat random timing (will vary of the order of micro seconds)
		chrono::duration<uint64_t,nano> dur3 (myclock::now() - time);
		uint64_t time3 = dur3.count();

		//Now combine them
		uint64_t rd_id = pid*hid-pid;
			//Perform a somewhat random circular shift
				rd_id = (rd_id << rd_id%17) | (rd_id >> (64 - rd_id%17));
				time1 = (time1 << time1%23) | (time1 >> (64 - time1%23));
				time2 = (time2 << time2%13) | (time2 >> (64 - time2%13));
				time3 = (time3 << time3%7) | (time3 >> (64 - time3%7));
		uint64_t rd_time = time1^((time2<<1)^(time3>>1)>>1);
		random_seed = (rd_id>>1)^(rd_time<<1)<<1;
	}
	return random_seed;
}


UMCodonTable CodonTableStandard = {
	{"TTT", "F"}, {"TTC", "F"}, {"TTA", "L"}, {"TTG", "L"}, 
	{"TCT", "S"}, {"TCC", "S"}, {"TCA", "S"}, {"TCG", "S"}, 
	{"TAT", "Y"}, {"TAC", "Y"}, {"TGT", "C"}, {"TGC", "C"}, 
	{"TGG", "W"}, {"CTT", "L"}, {"CTC", "L"}, {"CTA", "L"}, 
	{"CTG", "L"}, {"CCT", "P"}, {"CCC", "P"}, {"CCA", "P"}, 
	{"CCG", "P"}, {"CAT", "H"}, {"CAC", "H"}, {"CAA", "Q"}, 
	{"CAG", "Q"}, {"CGT", "R"}, {"CGC", "R"}, {"CGA", "R"}, 
	{"CGG", "R"}, {"ATT", "I"}, {"ATC", "I"}, {"ATA", "I"}, 
	{"ATG", "M"}, {"ACT", "T"}, {"ACC", "T"}, {"ACA", "T"}, 
	{"ACG", "T"}, {"AAT", "N"}, {"AAC", "N"}, {"AAA", "K"}, 
	{"AAG", "K"}, {"AGT", "S"}, {"AGC", "S"}, {"AGA", "R"}, 
	{"AGG", "R"}, {"GTT", "V"}, {"GTC", "V"}, {"GTA", "V"}, 
	{"GTG", "V"}, {"GCT", "A"}, {"GCC", "A"}, {"GCA", "A"}, 
	{"GCG", "A"}, {"GAT", "D"}, {"GAC", "D"}, {"GAA", "E"}, 
	{"GAG", "E"}, {"GGT", "G"}, {"GGC", "G"}, {"GGA", "G"}, 
	{"GGG", "G"},
	// Stop  codon
	{"TAA", "*"}, {"TAG", "*"}, {"TGA", "*"},
	// Start codon
	{"TTG", "s"}, {"CTG", "s"}, {"ATG", "s"}
};


/**
 * \param seq: DNA sequence to translate.
 * \return amino acid sequence. 
 */
string translate(string seq){
	size_t codonPos = 0;
	const size_t codonLen = 3;
	size_t seqLen = seq.length();
	string strCodon = "";
	string AA ="";
	string AAChain ="";
	bool stopCodonQ = false;
	if (seqLen % codonLen == 0){
			while ((codonPos < seqLen) ){
			strCodon = seq.substr(codonPos, codonLen);
	//		cout << strCodon << " codonPos: " << codonPos << endl;
			codonPos += codonLen; 
			AA = CodonTableStandard[strCodon];
			if (AA == "*"){
				stopCodonQ = true;
			}
			AAChain +=  AA;			
		}
		return AAChain;
	}else{
		// FIXME: Add a message? or leave it blank?
		return AAChain;
	}
}