probabilities.h

#ifndef _SPEL_COMPUTATIONS_PROBABILITIES_H_
#define _SPEL_COMPUTATIONS_PROBABILITIES_H_

#ifndef _SPEL_COMPUTATIONS_BASE_H_
#include "base.h"
#endif

#ifndef _SPEL_COMPUTATIONS_BASIC_DATA_H_
#include "basic_data.h"
#endif

/*locus_probabilities_type*/
/*locus_probabilities(qtl_chromosome_value, population_value,*/
                    /*const multi_generation_observations&,*/
                    /*const selected_qtls_on_chromosome_type&);*/

MatrixXd permutation_matrix(size_t n_parents, size_t n_loci, size_t order);

locus_probabilities_type
locus_probabilities(const context_key&, const locus_key&,
                    const multi_generation_observations&,
                    const std::vector<double>&);

state_to_parental_origin_matrix_type
state_to_parental_origin_matrix(generation_value, int);

parental_origin_type
parental_origin(const locus_probabilities_type&, generation_value, const selected_qtls_on_chromosome_type&);

parental_origin_per_locus_type
joint_parental_origin_at_locus(const context_key& ck, const locus_key& lk);

collection<parental_origin_per_locus_type>
parental_origin_per_locus(const collection<parental_origin_type>&);

/*
collection<parental_origin_per_locus_type>
compute_parental_origins(const value<population_value>& pop,
                         const value<chromosome_value>& chr,
                         const value<std::vector<double>>& loci);
*/

#endif