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228
DEC_GUI/DEC-0.0/processor/Settings.cpp
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228
DEC_GUI/DEC-0.0/processor/Settings.cpp
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#include "Settings.h"
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#include <vector>
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#include <iostream>
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#include <fstream>
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#include <cstdio>
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#include <boost/algorithm/string.hpp>
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#include <boost/tokenizer.hpp>
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#include <QVector>
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#include <qmath.h>
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#ifdef LINUX
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#define sscanf_s sscanf
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#endif
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#define sscanf_s sscanf
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// Default parameters
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bool Settings::WRITE_FULL_STATISTICS_TO_FILE = false;
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int Settings::Iterations = 10;
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long int Settings::InitPopSize = 10;
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float Settings::InitRatioBetweenPops = 1.f;
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double Settings::BirthRate = 0.01;
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double Settings::NaturalDeathRate = 0.01;
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long int Settings::KMaxParameter = 10000;
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int Settings::OffspringsMean = 3;
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float Settings::CoadaptiveThreshold = 0;
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float Settings::CoadaptiveMinimumP = 0.2f;
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float Settings::CoadaptiveMaximumTrait = 15.f;
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float Settings::DiseaseThreshold = 1;
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std::string Settings::CoadaptiveGenesInteraction = "onechromosome";
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std::string Settings::DiseaseGenesInteraction = "add";
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std::string Settings::BreedingStrategy = "default";
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std::string Settings::GenToPhenStrategy = "default";
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std::string Settings::PhenToFitStrategy = "default";
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std::string Settings::RecombinationStrategy = "default";
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double Settings::ProbMtDNARecomb = 0.0;
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int Settings::PopulationHomoInitSize = 1000;
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int Settings::PopulationAncientInitSize = 1000;
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double Settings::migrationPartHomoToAncient = 0.1;
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double Settings::migrationPartAncientToHomo = 0.1;
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int Settings::generationsPerMigration = 100;
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int Settings::locusLength = 60;
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double Settings::percentDiffLoci = 0.1;
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int Settings::numLoci = 50;
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// (END) Default parameters
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int Settings::globalGenerations;
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int Settings::maxYval;
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int Settings::minYval;
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QVector<double> Settings::homoCommonSize;
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QVector<double> Settings::homoFemaleSize;
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QVector<double> Settings::homoMaleSize;
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QVector<double> Settings::ancientCommonSize;
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QVector<double> Settings::ancientFemaleSize;
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QVector<double> Settings::ancientMaleSize;
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QVector<double> Settings::generations;
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std::vector<std::string> Settings::initMtDNA;
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std::vector<std::string> Settings::initMtDNA_ancient;
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std::vector<std::string> Settings::calcScript;
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QVector<QVector<double> > Settings::malesGene;
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QVector<QVector<double> > Settings::femalesGene;
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QVector<std::string> Settings::geneName;
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void Settings::initGUIvect()
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{
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// Settings::globalGenerations = 1;
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// Settings::maxYval = 0;
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// Settings::minYval = 0;
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// Settings::homoCommonSize.clear();
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// Settings::homoFemaleSize.clear();
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// Settings::homoMaleSize.clear();
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// Settings::ancientCommonSize.clear();
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// Settings::ancientFemaleSize.clear();
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// Settings::ancientMaleSize.clear();
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// Settings::generations.clear();
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// Settings::initMtDNA.clear();
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// Settings::initMtDNA_ancient.clear();
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// Settings::calcScript.clear();
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Settings::generations.push_back(0);
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Settings::homoCommonSize.push_back(Settings::PopulationHomoInitSize);
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Settings::homoFemaleSize.push_back(Settings::PopulationHomoInitSize / 2);
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Settings::homoMaleSize.push_back(Settings::PopulationHomoInitSize / 2);
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Settings::ancientCommonSize.push_back(Settings::PopulationAncientInitSize);
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Settings::ancientFemaleSize.push_back(Settings::PopulationAncientInitSize / 2);
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Settings::ancientMaleSize.push_back(Settings::PopulationAncientInitSize / 2);
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}
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void Settings::fillVectors(BisexualPopulation* pop_Sapiens, BisexualPopulation* pop_Ancient)
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{
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Settings::globalGenerations++;
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Settings::generations.push_back(Settings::globalGenerations);
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Settings::ancientCommonSize.push_back(pop_Ancient->females.size() + pop_Ancient->males.size());
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Settings::homoCommonSize.push_back(pop_Sapiens->females.size() + pop_Sapiens->males.size());
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Settings::ancientMaleSize.push_back(pop_Ancient->males.size());
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Settings::ancientFemaleSize.push_back(pop_Ancient->females.size());
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Settings::homoMaleSize.push_back(pop_Sapiens->males.size());
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Settings::homoFemaleSize.push_back(pop_Sapiens->females.size());
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Settings::maxYval = qMax(pop_Ancient->females.size() + pop_Ancient->males.size(), pop_Sapiens->females.size() + pop_Sapiens->males.size());
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Settings::minYval = qMin(pop_Ancient->females.size() + pop_Ancient->males.size(), pop_Sapiens->females.size() + pop_Sapiens->males.size());
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}
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void Settings::initScript(std::string fileName){
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std::vector<std::string> script;
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std::ifstream file(fileName.c_str());
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std::string str;
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while(getline(file,str)){
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if(str.length() > 2)
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script.push_back(str);
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}
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file.close();
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// process Script
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unsigned int curLine;
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for(curLine = 0; curLine < script.size(); curLine++){
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if(script.at(curLine).at(0) == '/' || script.at(curLine).at(0) == '#')
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continue;
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std::vector<std::string > tokensVector; // Search for tokens
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boost::split(tokensVector, script.at(curLine), boost::is_any_of("=") );
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std::string instr = tokensVector.at(0);
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boost::to_lower(instr);
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boost::trim(instr);
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// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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if(instr == "fullstat"){
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int flag = 0;
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sscanf_s(tokensVector.at(1).c_str(),"%d", &flag);
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if(flag != 0)
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Settings::WRITE_FULL_STATISTICS_TO_FILE = true;
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}
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else if(instr == "generations" || instr == "iterations" ){
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int iter = Settings::Iterations;
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sscanf_s(tokensVector.at(1).c_str(),"%d", &iter);
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Settings::Iterations = iter;
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}
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else if(instr == "initpopsize" || instr == "init_pop_size" || instr == "popsize" ){
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long int size = Settings::InitPopSize;
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sscanf_s(tokensVector.at(1).c_str(),"%ld", &size);
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Settings::InitPopSize = size;
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}
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else if(instr == "initratio" || instr == "init_ratio" || instr == "init_ratio_between_pop_size" ){
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float size = Settings::InitRatioBetweenPops;
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sscanf_s(tokensVector.at(1).c_str(),"%f", &size);
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Settings::InitRatioBetweenPops = size;
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}
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else if(instr == "birth" || instr == "birthrate" || instr == "birth_rate" ){
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double rate = Settings::BirthRate;
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sscanf_s(tokensVector.at(1).c_str(),"%lg", &rate);
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Settings::BirthRate = rate;
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}
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else if(instr == "death" || instr == "deathrate" || instr == "death_rate" ){
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double rate = Settings::NaturalDeathRate;
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sscanf_s(tokensVector.at(1).c_str(),"%lg", &rate);
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Settings::NaturalDeathRate = rate;
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}
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else if(instr == "kmax"){
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long int kMax = Settings::KMaxParameter;
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sscanf_s(tokensVector.at(1).c_str(),"%ld", &kMax);
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Settings::KMaxParameter = kMax;
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}
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else if(instr == "offsprings" || instr == "offsprings_mean" ){
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int offsprings = Settings::OffspringsMean;
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sscanf_s(tokensVector.at(1).c_str(),"%d", &offsprings);
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Settings::OffspringsMean = offsprings;
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}
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else if(instr == "coadaptivet" || instr == "coadaptive_threshold" ){
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float coadaptive = Settings::CoadaptiveThreshold;
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sscanf_s(tokensVector.at(1).c_str(),"%f", &coadaptive);
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Settings::CoadaptiveThreshold = coadaptive;
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}
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else if(instr == "coadaptivemax" || instr == "coadaptive_maximum_trait" ){
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float coadaptive = Settings::CoadaptiveMaximumTrait;
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sscanf_s(tokensVector.at(1).c_str(),"%f", &coadaptive);
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Settings::CoadaptiveMaximumTrait = coadaptive;
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}
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else if(instr == "coadaptivemin" || instr == "coadaptive_minimum_p" ){
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float coadaptive = Settings::CoadaptiveMinimumP;
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sscanf_s(tokensVector.at(1).c_str(),"%f", &coadaptive);
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Settings::CoadaptiveMinimumP = coadaptive;
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}
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else if(instr == "diseaset" || instr == "disease_threshold" ){
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float disease = Settings::DiseaseThreshold;
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sscanf_s(tokensVector.at(1).c_str(),"%f", &disease);
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Settings::DiseaseThreshold = disease;
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}
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else if(instr == "coadaptivegenesinteract" || instr == "cgi"){
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//long int kMax = Settings::KMaxParameter;
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//sscanf_s(tokensVector.at(1).c_str(),"%ld", &kMax);
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std::string cgi = tokensVector.at(1);
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boost::to_lower(cgi);
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boost::trim(cgi);
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Settings::CoadaptiveGenesInteraction = cgi;
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}
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else if(instr == "diseasegenesinteract" || instr == "dgi"){
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//long int kMax = Settings::KMaxParameter;
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//sscanf_s(tokensVector.at(1).c_str(),"%ld", &kMax);
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std::string dgi = tokensVector.at(1);
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boost::to_lower(dgi);
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boost::trim(dgi);
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Settings::DiseaseGenesInteraction = dgi;
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}
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//*****************************
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else if(instr == "breedings"){
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//long int kMax = Settings::KMaxParameter;
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//sscanf_s(tokensVector.at(1).c_str(),"%ld", &kMax);
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std::string strategy = tokensVector.at(1);
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boost::to_lower(strategy);
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boost::trim(strategy);
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Settings::BreedingStrategy = strategy;
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}
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} // (END) for(curLine = 0; curLine < script.size(); curLine++)
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}
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