Program Listing for File parameters.h

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//This file is part of necsim project which is released under MIT license.
//See file **LICENSE.txt** or visit https://opensource.org/licenses/MIT) for full license details.
#ifndef NECSIM_PARAMETERS_H
#define NECSIM_PARAMETERS_H

#include <cstring>
#include <stdexcept>
#include <string>
#include <memory>
#include <vector>
#include "double_comparison.h"

using namespace std;
namespace necsim
{
    struct ProtractedSpeciationParameters
    {
        double min_speciation_gen;
        double max_speciation_gen;

        ProtractedSpeciationParameters() : min_speciation_gen(0), max_speciation_gen(0)
        { };

        bool operator==(const ProtractedSpeciationParameters &p1) const
        {
            return (doubleCompare(p1.min_speciation_gen, min_speciation_gen, 0.00000001)
                    && doubleCompare(p1.max_speciation_gen, max_speciation_gen, 0.00000001));
        }

    };

    struct CommunityParameters
    {
        unsigned long reference;
        long double speciation_rate;
        long double time;
        bool fragment;
        unsigned long metacommunity_reference; // will be 0 if no metacommunity used.
        // protracted speciation current_metacommunity_parameters
        ProtractedSpeciationParameters protracted_parameters;
        bool updated; // set to true if the fragment reference needs updating in the database

        CommunityParameters() : reference(0), speciation_rate(0.0), time(0), fragment(false),
                                metacommunity_reference(0), protracted_parameters(), updated(false)
        { }

        ~CommunityParameters() = default;

        CommunityParameters(unsigned long reference_in, long double speciation_rate_in, long double time_in,
                            bool fragment_in, unsigned long metacommunity_reference_in,
                            const ProtractedSpeciationParameters &protracted_params);

        void setup(unsigned long reference_in, long double speciation_rate_in, long double time_in, bool fragment_in,
                   unsigned long metacommunity_reference_in, const ProtractedSpeciationParameters &protracted_params);

        bool compare(long double speciation_rate_in, long double time_in, bool fragment_in,
                     unsigned long metacommunity_reference_in, const ProtractedSpeciationParameters &protracted_params);

        bool compare(long double speciation_rate_in, long double time_in, unsigned long metacommunity_reference_in,
                     const ProtractedSpeciationParameters &protracted_params);

        bool compare(unsigned long reference_in);
    };

    struct CommunitiesArray
    {
        vector<shared_ptr<CommunityParameters>> comm_parameters;

        CommunitiesArray();

        ~CommunitiesArray() = default;

        void pushBack(unsigned long reference, long double speciation_rate, long double time, bool fragment,
                      unsigned long metacommunity_reference, const ProtractedSpeciationParameters &protracted_params);

        void pushBack(shared_ptr<CommunityParameters> tmp_param);

        shared_ptr<CommunityParameters> addNew(long double speciation_rate, long double time, bool fragment,
                                               unsigned long metacommunity_reference,
                                               const ProtractedSpeciationParameters &protracted_params);

        bool hasPair(long double speciation_rate, double time, bool fragment, unsigned long metacommunity_reference,
                     const ProtractedSpeciationParameters &protracted_params);

    };

    struct MetacommunityParameters
    {
        unsigned long reference{};
        unsigned long metacommunity_size{};
        long double speciation_rate{};
        string option;
        unsigned long external_reference{};

        MetacommunityParameters();

        ~MetacommunityParameters() = default;

        MetacommunityParameters(const unsigned long &reference_in, const unsigned long &metacommunity_size_in,
                                const long double &speciation_rate_in, const string &option_in,
                                const unsigned long &external_reference_in);

        bool compare(unsigned long metacommunity_size_in, long double speciation_rate_in, const string &option_in,
                     const unsigned long &ext_reference_in);

        bool compare(const MetacommunityParameters &metacomm_in);

        bool compare(unsigned long reference_in);

        bool isMetacommunityOption() const;

        void clear();

        MetacommunityParameters &operator=(const MetacommunityParameters &parameters);

        bool operator==(const MetacommunityParameters &parameters);

        bool operator!=(const MetacommunityParameters &parameters);
    };

    struct MetacommunitiesArray
    {
        vector<shared_ptr<MetacommunityParameters>> metacomm_parameters;

        MetacommunitiesArray();

        ~MetacommunitiesArray() = default;

        vector<shared_ptr<MetacommunityParameters>>::iterator begin();

        vector<shared_ptr<MetacommunityParameters>>::iterator end();

        vector<shared_ptr<MetacommunityParameters>>::const_iterator begin() const;

        vector<shared_ptr<MetacommunityParameters>>::const_iterator end() const;

        void pushBack(const unsigned long &reference, const unsigned long &metacommunity_size,
                      const long double &speciation_rate, const string &option,
                      const unsigned long &external_reference);

        void pushBack(shared_ptr<MetacommunityParameters> tmp_param);

        void clear();

        unsigned long size();

        bool empty();

        unsigned long addNew(const unsigned long &metacommunity_size, const long double &speciation_rate,
                             const string &option, const unsigned long &external_reference);

        unsigned long addNew(const MetacommunityParameters &metacomm_in);

        bool hasOption(const unsigned long &metacommunity_size, const long double &speciation_rate,
                       const string &option, const unsigned long &external_reference);

        bool hasOption(unsigned long reference);

        bool hasOption(const MetacommunityParameters &metacomm_in);

        unsigned long getReference(const unsigned long &metacommunity_size, const long double &speciation_rate,
                                   const string &option, const unsigned long &external_reference);

        unsigned long getReference(const MetacommunityParameters &metacomm_parameters);

        void addNull();

        bool hasMetacommunityOption();
    };
}
#endif //NECSIM_PARAMETERS_H