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parms.h
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parms.h
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//
// parms.h
// frequencyDependentSimulation
//
// Created by Nicholas Croucher on 28/09/2015.
// Copyright (c) 2015 Imperial College. All rights reserved.
//
#ifndef frequencyDependentSimulation_parms_h
#define frequencyDependentSimulation_parms_h
#include <iostream>
#include <string>
#include <fstream>
#include <getopt.h>
#include <string.h>
#include <vector>
// structure for storing parameters
struct parms {
std::string programme;
double fSelection;
double vSelection;
double immigrationRate;
int immigrationType;
double upperLimit;
double lowerLimit;
double selectedProp;
double lowerSelection;
double higherSelection;
double transformationProportion;
double transformationRate;
double transformationAsymmetryLoci;
double transformationAsymmetryMarker;
int popSize;
int numGen;
int genotypeSampleSize;
double decayRate;
std::string het_mode;
int densdepMode;
};
// structure for isolate objects
struct isolate {
std::string id;
int year;
int sc;
std::string serotype;
bool vt;
bool latent_vt;
std::vector<bool> genotype;
std::vector<bool> markers;
double fitness;
// new constructor for struct 'isolate'
// isolate(std::string init_id, int init_year, int init_sc, std::string init_serotype, bool init_vt, bool second_vt, std::vector<bool> *init_genotype, std::vector<bool> *init_markers) : id(init_id),year(init_year),sc(init_sc),serotype(init_serotype),vt(init_vt),latent_vt(second_vt),genotype(*init_genotype),markers(*init_markers) {}
// constructor for struct 'isolate'
isolate(std::string init_id, int init_year, int init_sc, std::string init_serotype, bool init_vt, bool second_vt, std::vector<bool> *init_genotype, std::vector<bool> *init_markers, double init_fitness) {
id = init_id;
year = init_year;
sc = init_sc;
serotype = init_serotype;
vt = init_vt;
latent_vt = second_vt;
genotype = (*init_genotype);
markers = (*init_markers);
fitness = init_fitness;
};
// destructor for struct 'isolate'
// ~isolate() {
// genotype.clear();
// genotype.shrink_to_fit();
// markers.clear();
// markers.shrink_to_fit();
// }
//
// // copy constructor for struct 'isolate'
// isolate(const isolate& other): id(other.id),year(other.year),sc(other.sc),serotype(other.serotype),vt(other.vt),latent_vt(other.latent_vt),genotype(other.genotype),markers(other.markers) {}
//
// // copy assignment operator
// isolate& operator=(const isolate& other) {
// // check for self-assignment
// if (&other != this) {
// id = other.id;
// year = other.year;
// sc = other.sc;
// serotype = other.serotype;
// vt = other.vt;
// latent_vt = other.latent_vt;
// genotype = other.genotype;
// markers = other.markers;
// }
// return *this;
// }
//
// // move constructor
// isolate(isolate&& other) {
//
// id = other.id;
// other.id = nullptr;
// year = other.year;
// other.year = nullptr;
// sc = other.sc;
// other.sc = nullptr;
// serotype = other.serotype;
// other.serotype = nullptr;
// vt = other.vt;
// other.vt = nullptr;
// latent_vt = other.latent_vt;
// other.latent_vt = nullptr;
// genotype = other.genotype;
// other.genotype = nullptr;
// markers = other.markers;
// other.markers = nullptr;
//
// }
// move assignment operator
// isolate& operator=(isolate&& other) {
// if (&other != this) {
// delete p;
// p = other.p;
// other.p = nullptr;
//
// }
// return *this;
// }
};
// constructor
//isolate::isolate(std::string init_id, int init_year, int init_sc, std::string init_serotype, bool init_vt, bool second_vt, std::vector<bool> *init_genotype, std::vector<bool> *init_markers) {
// id = init_id;
// year = init_year;
// sc = init_sc;
// serotype = init_serotype;
// vt = init_vt;
// latent_vt = second_vt;
// genotype = (*init_genotype);
// markers = (*init_markers);
//}
// destructor
//isolate::~isolate() {
//// delete[] genotype;
// genotype = nullptr;
//// delete[] markers;
// markers = nullptr;
//}
// structure for COG objects
struct cog {
std::string id;
bool vt;
double weight;
double currentFreq;
double eqFreq;
std::vector<double> actualFreq;
std::vector<double> simFreq;
// constructor for struct 'cog'
cog(std::string init_id, int init_vt, double init_weight, double init_eqFreq, std::vector<double> *init_actualFreq) {
id = init_id;
vt = init_vt;
weight = init_weight;
currentFreq = 0.0;
eqFreq = init_eqFreq;
actualFreq = (*init_actualFreq);
std::vector<double> tmpSimFreq(actualFreq.size(),0.0);
simFreq = tmpSimFreq;
};
// copy constructor for struct 'cog'
cog(const cog& other): id(other.id),vt(other.vt),weight(other.weight),currentFreq(other.currentFreq),actualFreq(other.actualFreq),simFreq(other.simFreq) {}
};
#endif