fourtaxon.h

#include <vector>
#include <string>
#include "libhmsbeagle/beagle.h"

typedef std::vector<int> CodedSequence;
typedef std::vector<double> PartialVector;

/*-----------------------------------------------------------------------------
|       FourTaxonExample reads in DNA sequence data for four taxa and simply 
|       recomputes the likelihood of the following unrooted tree numerous times:
|       
|       (1:0.01, 2:0.02, (3:0.03, 4:0.04):0.05)
|       
|       Future improvements:
|       - estimate something
*/
class FourTaxonExample
        {
        public:
                FourTaxonExample();
                void interpretCommandLineParameters(int argc, char* argv[]);
                void run();
                
        private:
                void helpMessage();
                void abort(std::string msg);
                void initBeagleLib();
                void readData();
                void writeData();
                void updateBrlen(unsigned brlen_index);
                void defineOperations();
                double calcLnL(int return_value);
                
        private:
                bool                                            quiet;
                unsigned                                        niters;
                unsigned                                        like_root_node;
                unsigned                                        like_parent_index;
                unsigned                                        like_child_index;
                unsigned                                        transmat_index;
                std::string                                     data_file_name;
        bool                        scaling;
        bool                        single;
        bool                        require_double;
                const unsigned                          ntaxa;
                unsigned                                        nsites;
        unsigned                    nrates;
                double                                          delta;
                double                                          mu;
                unsigned                                        seed;
                std::vector<std::string>        taxon_name;
                std::vector<CodedSequence>      data;
                std::vector<PartialVector>      partial;
                std::vector<int>                        transition_matrix_index;
                std::vector<double>                     brlens;
                std::vector<int>                        operations;
        std::vector<int>            scaleIndices;
                int                                                     instance_handle;
                int                                                     rsrc_number;
                bool                                            use_tip_partials;
        bool                        accumulate_on_the_fly;
        bool                        dynamic_scaling;
        bool                        do_rescaling;
        bool                        auto_scaling;
                int                         calculate_derivatives;
        bool                        empirical_derivatives;
        bool                        sse_vectorization;
        };