Program Listing for File parameters.cpp

↰ Return to documentation for file (necsim/parameters.cpp)

//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.
#include "parameters.h"
#include "custom_exceptions.h"
namespace necsim
{
    CommunityParameters::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)
    {
        setup(reference_in, speciation_rate_in, time_in, fragment_in, metacommunity_reference_in, protracted_params);
    }

    void CommunityParameters::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)
    {
        time = time_in;
        speciation_rate = speciation_rate_in;
        fragment = fragment_in;
        reference = reference_in;
        metacommunity_reference = metacommunity_reference_in;
        protracted_parameters = protracted_params;
        updated = false;

    }

    bool CommunityParameters::compare(long double speciation_rate_in, long double time_in, bool fragment_in,
                                      unsigned long metacommunity_reference_in,
                                      const ProtractedSpeciationParameters &protracted_params)
    {
        if(doubleCompare(double(time_in), double(0.0), 0.00001))
        {
#ifdef DEBUG
            stringstream os;
            os << "Detected generation at t=0.0." << endl;
            writeLog(10, os);
#endif // DEBUG
            return doubleCompare(speciation_rate, speciation_rate_in, speciation_rate * 0.000001)
                   && fragment == fragment_in && metacommunity_reference == metacommunity_reference_in
                   && protracted_params == protracted_parameters;
        }
        return doubleCompare(speciation_rate, speciation_rate_in, speciation_rate * 0.000001)
               && doubleCompare(time, time_in, time * 0.0000000001) && fragment == fragment_in
               && metacommunity_reference == metacommunity_reference_in && protracted_params == protracted_parameters;
    }

    bool CommunityParameters::compare(long double speciation_rate_in, long double time_in,
                                      unsigned long metacommunity_reference_in,
                                      const ProtractedSpeciationParameters &protracted_params)
    {
        return doubleCompare(speciation_rate, speciation_rate_in, speciation_rate * 0.000001)
               && doubleCompare(time, time_in, 0.0000000001) && metacommunity_reference == metacommunity_reference_in
               && protracted_params == protracted_parameters;
    }

    bool CommunityParameters::compare(unsigned long reference_in)
    {
        return reference == reference_in;
    }

    CommunitiesArray::CommunitiesArray() : comm_parameters()
    { };

    void CommunitiesArray::pushBack(unsigned long reference, long double speciation_rate, long double time,
                                    bool fragment, unsigned long metacommunity_reference,
                                    const ProtractedSpeciationParameters &protracted_params)
    {
        auto tmp_param = make_shared<CommunityParameters>(reference, speciation_rate, time, fragment,
                                                          metacommunity_reference, protracted_params);
        comm_parameters.emplace_back(tmp_param);
    }

    void CommunitiesArray::pushBack(shared_ptr<CommunityParameters> tmp_param)
    {
        comm_parameters.emplace_back(tmp_param);
    }

    shared_ptr<CommunityParameters> CommunitiesArray::addNew(long double speciation_rate, long double time,
                                                             bool fragment, unsigned long metacommunity_reference,
                                                             const ProtractedSpeciationParameters &protracted_params)
    {
        unsigned long max_reference = 1;
        for(auto &i : comm_parameters)
        {
            if(i->compare(speciation_rate, time, metacommunity_reference, protracted_params))
            {
                if(i->fragment == fragment || !fragment)
                {
                    stringstream ss;
                    ss << "Non-unique parameter set: " << endl;
                    ss << "-speciation rate: " << speciation_rate << endl;
                    ss << "-time: " << time << endl;
                    ss << "-fragment: " << fragment << endl;
                    ss << "-metacommunity reference: " << metacommunity_reference << endl;
                    ss << "-protracted speciation min: " << protracted_params.min_speciation_gen << endl;
                    ss << "-protracted speciation max: " << protracted_params.max_speciation_gen << endl;
                    writeCritical(ss.str());
                    throw FatalException("Tried to get reference for non-unique parameter set in communities. "
                                         "Please report this bug.");
                }
                else
                {
                    i->fragment = true;
                    i->updated = true;
                    return i;
                }
            }
            else
            {
                if(i->reference >= max_reference)
                {
                    max_reference = i->reference + 1;
                }
            }
        }
        auto tmp_param = make_shared<CommunityParameters>(max_reference, speciation_rate, time, fragment,
                                                          metacommunity_reference, protracted_params);
        comm_parameters.emplace_back(tmp_param);
        return comm_parameters.back();
    }

    bool CommunitiesArray::hasPair(long double speciation_rate, double time, bool fragment,
                                   unsigned long metacommunity_reference,
                                   const ProtractedSpeciationParameters &protracted_params)
    {
        for(auto &i : comm_parameters)
        {
            if(i->compare(speciation_rate, time, fragment, metacommunity_reference, protracted_params))
            {
                return true;
            }
        }
        return false;
    }

    MetacommunityParameters::MetacommunityParameters()
    {
        reference = 0;
        metacommunity_size = 0;
        speciation_rate = 0.0;
        option = "none";
        external_reference = 0;
    }

    MetacommunityParameters::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)
    {
        reference = reference_in;
        metacommunity_size = metacommunity_size_in;
        speciation_rate = speciation_rate_in;
        option = option_in;
        external_reference = external_reference_in;
    }

    bool MetacommunityParameters::compare(unsigned long metacommunity_size_in, long double speciation_rate_in,
                                          const string &option_in, const unsigned long &ext_reference_in)
    {
        if(option_in == "none" && metacommunity_size == 0)
        {
            return option == "none" && metacommunity_size == 0;
        }
        if(option_in == "simulated" || option_in == "analytical")
        {
            return doubleCompare(speciation_rate, speciation_rate_in, speciation_rate * 0.000001)
                   && metacommunity_size == metacommunity_size_in && option == option_in;
        }
        else
        {
            return option == option_in && external_reference == ext_reference_in;
        }
    }

    bool MetacommunityParameters::compare(const MetacommunityParameters &metacomm_in)
    {
        return compare(metacomm_in.metacommunity_size, metacomm_in.speciation_rate, metacomm_in.option,
                       metacomm_in.external_reference);
    }

    bool MetacommunityParameters::compare(unsigned long reference_in)
    {
        return reference == reference_in;
    }

    bool MetacommunityParameters::isMetacommunityOption() const
    {
        if(metacommunity_size > 0 && speciation_rate > 0)
        {
            if(option != "simulated" && option != "analytical")
            {
                throw FatalException(
                        "Must use simulation or analytical solutions when supplying a metacommunity size and "
                        "speciation rate.");
            }
            return true;
        }
        if(option != "simulated" && option != "analytical" && option != "none")
        {
            if(external_reference == 0)
            {
                throw FatalException(
                        "External reference cannot be 0 when reading metacommunity from external database.");
            }
            return true;
        }
        return false;
    }

    void MetacommunityParameters::clear()
    {
        reference = 0;
        metacommunity_size = 0;
        speciation_rate = 0.0;
        option = "none";
        external_reference = 0;
    }

    MetacommunityParameters &MetacommunityParameters::operator=(const MetacommunityParameters &parameters)
    {
        reference = parameters.reference;
        metacommunity_size = parameters.metacommunity_size;
        speciation_rate = parameters.speciation_rate;
        option = parameters.option;
        external_reference = parameters.external_reference;
        return *this;
    }

    bool MetacommunityParameters::operator==(const MetacommunityParameters &parameters)
    {
        return compare(parameters);
    }

    bool MetacommunityParameters::operator!=(const MetacommunityParameters &parameters)
    {
        return !compare(parameters);
    }

    MetacommunitiesArray::MetacommunitiesArray() : metacomm_parameters()
    {

    }

    vector<shared_ptr<MetacommunityParameters>>::iterator MetacommunitiesArray::begin()
    {
        return metacomm_parameters.begin();
    }

    vector<shared_ptr<MetacommunityParameters>>::iterator MetacommunitiesArray::end()
    {
        return metacomm_parameters.end();
    }

    vector<shared_ptr<MetacommunityParameters>>::const_iterator MetacommunitiesArray::begin() const
    {
        return metacomm_parameters.begin();
    }

    vector<shared_ptr<MetacommunityParameters>>::const_iterator MetacommunitiesArray::end() const
    {
        return metacomm_parameters.end();
    }

    void MetacommunitiesArray::pushBack(const unsigned long &reference, const unsigned long &metacommunity_size,
                                        const long double &speciation_rate, const string &option,
                                        const unsigned long &external_reference)
    {
        auto tmp_param = make_shared<MetacommunityParameters>(reference, speciation_rate, metacommunity_size, option,
                                                              external_reference);
        metacomm_parameters.emplace_back(tmp_param);
    }

    void MetacommunitiesArray::pushBack(shared_ptr<MetacommunityParameters> tmp_param)
    {
        metacomm_parameters.emplace_back(tmp_param);
    }

    void MetacommunitiesArray::clear()
    {
        metacomm_parameters.clear();
    }

    unsigned long MetacommunitiesArray::size()
    {
        return metacomm_parameters.size();
    }

    bool MetacommunitiesArray::empty()
    {
        return metacomm_parameters.empty();
    }

    unsigned long MetacommunitiesArray::addNew(const unsigned long &metacommunity_size,
                                               const long double &speciation_rate, const string &option,
                                               const unsigned long &external_reference)
    {
        unsigned long max_reference = 1;
        for(auto &i : metacomm_parameters)
        {
            if(i->compare(metacommunity_size, speciation_rate, option, external_reference))
            {
                stringstream ss;
                ss << "Duplicate metacommunity parameters: " << endl;
                ss << "Size: " << metacommunity_size << endl;
                ss << "Speciation rate: " << speciation_rate << endl;
                ss << "Option: " << option << endl;
                ss << "External reference: " << external_reference << endl;
                writeCritical(ss.str());
                throw FatalException("Tried to get reference for non-unique parameter set in metacommunities. "
                                     "Please report this bug.");
            }
            else
            {
                if(i->reference >= max_reference)
                {
                    max_reference = i->reference + 1;
                }
            }
        }
        auto tmp_param = make_shared<MetacommunityParameters>(max_reference, metacommunity_size, speciation_rate,
                                                              option, external_reference);
        metacomm_parameters.emplace_back(tmp_param);
        return max_reference;
    }

    unsigned long MetacommunitiesArray::addNew(const MetacommunityParameters &metacomm_in)
    {
        return addNew(metacomm_in.metacommunity_size, metacomm_in.speciation_rate, metacomm_in.option,
                      metacomm_in.external_reference);
    }

    bool MetacommunitiesArray::hasOption(const unsigned long &metacommunity_size, const long double &speciation_rate,
                                         const string &option, const unsigned long &external_reference)
    {
        for(auto &i : metacomm_parameters)
        {
            if(i->compare(metacommunity_size, speciation_rate, option, external_reference))
            {
                return true;
            }
        }
        return false;
    }

    bool MetacommunitiesArray::hasOption(unsigned long reference)
    {
        for(auto &i : metacomm_parameters)
        {
            if(i->compare(reference))
            {
                return true;
            }
        }
        return false;
    }

    bool MetacommunitiesArray::hasOption(const MetacommunityParameters &metacomm_in)
    {
        return hasOption(metacomm_in.metacommunity_size, metacomm_in.speciation_rate, metacomm_in.option,
                         metacomm_in.external_reference);
    }

    unsigned long MetacommunitiesArray::getReference(const unsigned long &metacommunity_size,
                                                     const long double &speciation_rate, const string &option,
                                                     const unsigned long &external_reference)
    {
        if(metacommunity_size == 0)
        {
            if(option == "simulated" || option == "analytical" || option == "none")
            {
                return 0;
            }
            else
            {
                if(external_reference == 0)
                {
                    return 0;
                }
            }
        }
        for(auto &i : metacomm_parameters)
        {
            if(i->compare(metacommunity_size, speciation_rate, option, external_reference))
            {
                return i->reference;
            }
        }
        return 0;
    }

    unsigned long MetacommunitiesArray::getReference(const MetacommunityParameters &metacomm_parameters)
    {
        return getReference(metacomm_parameters.metacommunity_size, metacomm_parameters.speciation_rate,
                            metacomm_parameters.option, metacomm_parameters.external_reference);
    }

    void MetacommunitiesArray::addNull()
    {
        MetacommunityParameters null_parameters;
        addNew(null_parameters);
    }

    bool MetacommunitiesArray::hasMetacommunityOption()
    {
        MetacommunityParameters null_parameters;
        for(const auto &item: metacomm_parameters)
        {
            if(*item != null_parameters)
            {
                return true;
            }
        }
        return false;
    }

}