flock-bones.hpp

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#ifndef GEESE_FLOCK_BONES_HPP
#define GEESE_FLOCK_BONES_HPP 1
 
class Geese;
 
class Flock {
public:
 
    std::vector< Geese > dat;
    size_t nfunctions  = 0u;
    bool initialized = false;
    
    // Common components
    std::mt19937 rengine;
    PhyloModel model = PhyloModel();
 
    Flock() {};
    ~Flock() {};
 
    size_t add_data(
        std::vector< std::vector<size_t> > & annotations,
        std::vector< size_t > &              geneid,
        std::vector< int > &                 parent,
        std::vector< bool > &                duplication
    );
 
    void set_seed(const size_t & s);
 
    void init(size_t bar_width = BARRY_PROGRESS_BAR_WIDTH);
    
    // void add_geese(Geese x);
    PhyloCounters * get_counters();
    PhyloSupport *  get_support_fun();
    std::vector< double > * get_stats_support();
    std::vector< std::vector< double > > * get_stats_target();
    PhyloModel *  get_model();
 
    double likelihood_joint(
        const std::vector< double > & par,
        bool as_log = false,
        bool use_reduced_sequence = true,
        size_t ncores = 1u
    );
 
    size_t nfuns() const noexcept;
    size_t ntrees() const noexcept;
    std::vector< size_t > nnodes() const noexcept;
    std::vector< size_t > nleafs() const noexcept;
    size_t nterms() const;
    size_t support_size() const noexcept;
    std::vector< std::string > colnames() const;
    size_t parse_polytomies(
        bool verb = true,
        std::vector< size_t > * dist = nullptr
        ) const noexcept;  
    void print() const;
 
    Geese * operator()(size_t i, bool check_bounds = true);
 
};
 
#endif