Program Listing for File Metacommunity.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 SPECIATIONCOUNTER_METACOMMUNITY_H
#define SPECIATIONCOUNTER_METACOMMUNITY_H

#include <string>
#include <sqlite3.h>
#include <set>
#include <memory>
#include "Community.h"
#include "Tree.h"
#include "RNGController.h"
#include "SpecSimParameters.h"
#include "SpeciesAbundancesHandler.h"

using namespace std;
namespace necsim
{
    class Metacommunity : public virtual Community
    {
    protected:
        // Simulation seed and job_type (read from the output database or set to 1)
        unsigned long seed;
        unsigned long job_type;
        bool parameters_checked;
        unique_ptr<SpeciesAbundancesHandler> species_abundances_handler;
        shared_ptr<RNGController> random;
        unique_ptr<Tree> metacommunity_tree;
    public:

        Metacommunity();

        ~Metacommunity() override = default;

        void setCommunityParameters(shared_ptr<MetacommunityParameters> metacommunity_parameters);

        void checkSimulationParameters();

        void addSpecies(unsigned long &species_count, TreeNode* tree_node, set<unsigned long> &species_list) override;

        void createMetacommunityNSENeutralModel();

        void applyNoOutput(shared_ptr<SpecSimParameters> sp, shared_ptr<vector<TreeNode>> tree_data) override;

        void approximateSAD();

        void readSAD();

        void printMetacommunityParameters();

    };
}
#endif //SPECIATIONCOUNTER_METACOMMUNITY_H