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/* Spell-QTL  Software suite for the QTL analysis of modern datasets.
 * Copyright (C) 2016,2017  Damien Leroux <damien.leroux@inra.fr>, Sylvain Jasson <sylvain.jasson@inra.fr>
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

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#ifndef _SPEL_MODEL_MODEL_H_
#define _SPEL_MODEL_MODEL_H_

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#include <stdexcept>

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/*#include <Eigen/SVD>*/
/*#include <Eigen/QR>*/
#include "eigen.h"
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#include "beta_gamma.h"
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#include <cmath>

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#include "labelled_matrix.h"
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#include "settings.h"
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#include "print.h"
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#include "data/chromosome.h"
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/*#define COMPONENT_EPSILON (1.e-10)*/
#define COMPONENT_EPSILON (active_settings->tolerance)
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typedef labelled_matrix<Eigen::Matrix<double, -1, -1>, int, std::vector<char>> model_block_type;

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struct model_block_key_struc;
typedef std::shared_ptr<model_block_key_struc> model_block_key;


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struct model;

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static inline
void f_test(const model& model_current, const model& model_new, int col_num, MatrixXd* pvalue, MatrixXd* lod);

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struct key_already_exists : public std::exception {
    std::string m_what;
    key_already_exists(const model&, const model_block_key&);
    const char* what() const throw()
    {
        return m_what.c_str();
    }
};

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typedef enum { mbk_Covar, mbk_CI, mbk_POP, mbk_Dominance, mbk_Interaction } key_type;
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inline
collection<model_block_type>
disassemble_block_multipop(const model_block_type& block, const collection<const qtl_pop_type*>& all_pops)
{
    VectorXi keep = VectorXi::Zero(block.cols());
    int r0 = 0;
    collection<model_block_type> ret;
    ret.reserve(all_pops.size());
    for (const auto& vpop: all_pops) {
        const qtl_pop_type* pop = *vpop;
        auto sub_block = block.data.middleRows(r0, pop->size());
        size_t ncols = 0;
        for (int col = 0; col < sub_block.cols(); ++col) {
            keep(col) = !sub_block.col(col).isZero(active_settings->tolerance);
            ncols += keep(col);
        }
        /*MSG_DEBUG("disasm block keep = " << keep.transpose());*/
        /*MSG_QUEUE_FLUSH();*/
        ret.emplace_back(model_block_type{});
        auto& pop_block = *ret.back();
        pop_block.column_labels.reserve(ncols);
        pop_block.data.resize(pop->size(), ncols);
        int pcol = 0;
        for (int col = 0; col < sub_block.cols(); ++col) {
            if (keep(col)) {
                pop_block.data.col(pcol++) = sub_block.col(col);
                pop_block.column_labels.push_back(block.column_labels[col]);
            }
        }
        r0 += pop->size();
    }
    return ret;
}

inline
value<model_block_type>
assemble_block_multipop(const collection<model_block_type>& pop_blocks)
{
    std::map<std::vector<char>, int> col_indices;
    for (const auto& pb: pop_blocks) {
        for (const auto& v: pb->column_labels) {
            col_indices[v] = 0;
        }
    }

    int index = 0;
    for (auto& kv: col_indices) {
        kv.second = index++;
    }

    int r0 = 0;

    for (const auto& vpb: pop_blocks) {
        r0 += vpb->rows();
    }

    value<model_block_type> ret = model_block_type{};
    ret->data = MatrixXd::Zero(r0, col_indices.size());
    ret->column_labels.reserve(col_indices.size());
    for (const auto& kv: col_indices) {
        ret->column_labels.push_back(kv.first);
    }

    r0 = 0;

    for (const auto& vpb: pop_blocks) {
        const auto& pb = *vpb;
        for (int i = 0; i < pb.cols(); ++i) {
            int col = col_indices[pb.column_labels[i]];
            ret->data.block(r0, col, pb.rows(), 1) = pb.data.col(i);
        }
        r0 += pb.rows();
    }

    return ret;
}


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struct model_block_key_struc {
    key_type type;

    const chromosome* chr;
    locus_key loci;
    model_block_key left, right;

    model_block_key_struc(key_type kt, const chromosome* c, const locus_key& lk, const model_block_key& c1, const model_block_key& c2)
        : type(kt), chr(c), loci(lk), left(c1), right(c2)
    {}

    size_t
        order() const
        {
            switch (type) {
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                case mbk_Covar:
                case mbk_CI:
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                case mbk_POP: return 1; // loci->depth();
                case mbk_Dominance: return 2; // 2 * loci->depth();
                case mbk_Interaction: return left->order() + right->order();
            };
            return 0;
        }

    static
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    model_block_key
    cross_indicator()
    {
        model_block_key void_;
        locus_key void_lk;
        return std::make_shared<model_block_key_struc>(mbk_CI, (const chromosome*) NULL, void_lk, void_, void_);
    }

    static
    model_block_key
    covariables()
    {
        model_block_key void_;
        locus_key void_lk;
        return std::make_shared<model_block_key_struc>(mbk_Covar, (const chromosome*) NULL, void_lk, void_, void_);
    }
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    static
        model_block_key
        pop(const chromosome* c, locus_key loci)
        {
            model_block_key void_;
            return std::make_shared<model_block_key_struc>(mbk_POP, c, loci, void_, void_);
        }

    static
        model_block_key
        dominance(const model_block_key& haplo)
        {
            model_block_key void_;
            locus_key void_lk;
            return std::make_shared<model_block_key_struc>(mbk_Dominance, (const chromosome*) NULL, void_lk, haplo, void_);
        }

    static
        model_block_key
        interaction(const model_block_key& l, const model_block_key& r)
        {
            locus_key void_lk;
            if (l < r) {
                return std::make_shared<model_block_key_struc>(mbk_Interaction, (const chromosome*) NULL, void_lk, l, r);
            } else {
                return std::make_shared<model_block_key_struc>(mbk_Interaction, (const chromosome*) NULL, void_lk, r, l);
            }
        }

    friend
        std::ostream&
        operator << (std::ostream& os, const model_block_key_struc& mbk)
        {
            switch (mbk.type) {
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                case mbk_Covar:
                    os << "Covar";
                    break;
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                case mbk_CI:
                    os << "Cross";
                    break;
                case mbk_POP:
                    os << mbk.chr->name << ':' << mbk.loci;
                    break;
                case mbk_Dominance:
                    os << "Dom(" << mbk.left << ')';
                    break;
                case mbk_Interaction:
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                    os << '(' << mbk.left << ":" << mbk.right << ')';
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                    break;
            };
            return os;
        }
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    friend
        std::ostream&
        operator << (std::ostream& os, const model_block_key& mbk)
        {
            return os << (*mbk);
        }

    bool
        can_interact_with(const model_block_key& mbk) const
        {
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            if (type == mbk_CI || mbk->type == mbk_CI) {
                return active_settings->cross_indicator_can_interact;
            }
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            auto v1 = flatten();
            auto v2 = mbk->flatten();
            decltype(v1) inter(std::min(v1.size(), v2.size()));
            auto e = std::set_intersection(v1.begin(), v1.end(), v2.begin(), v2.end(), inter.begin());
            return e == inter.begin();
        }

    bool
        has_chromosome(const chromosome* c) const
        {
            switch (type) {
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                case mbk_Covar:
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                case mbk_CI:
                    return false;
                case mbk_POP:
                    return chr == c;
                case mbk_Dominance:
                    return left->has_chromosome(c);
                case mbk_Interaction:
                    return left->has_chromosome(c) || right->has_chromosome(c);
            };
            return false;
        }

    bool
        has_locus(const chromosome* c, double l) const
        {
            switch (type) {
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                case mbk_Covar:
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                case mbk_CI:
                    return false;
                case mbk_POP:
                    return chr == c && loci->has(l);
                case mbk_Dominance:
                    return left->has_locus(c, l);
                case mbk_Interaction:
                    return left->has_locus(c, l) || right->has_locus(c, l);
            };
            return false;
        }

    bool
        has(const model_block_key& mbk) const
        {
            return *this == *mbk
                || (left && left->has(mbk))
                || (right && right->has(mbk));
        }

    bool
        operator < (const model_block_key_struc& other) const
        {
            /* CI < POP < Dom < Inter
             * then sort on haplotypes
             * for interactions, sort on left&right children
             */
            switch (type) {
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                case mbk_Covar:
                    return other.type != mbk_Covar;
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                case mbk_CI:
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                    return other.type != mbk_CI && other.type != mbk_Covar;
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                case mbk_POP:
                    switch (other.type) {
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                        case mbk_Covar:
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                        case mbk_CI:
                            return false;
                        case mbk_POP:
                            return chr < other.chr || (chr == other.chr && loci < other.loci);
                        default:
                            return true;
                    };
                case mbk_Dominance:
                    switch (other.type) {
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                        case mbk_Covar:
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                        case mbk_CI:
                        case mbk_POP:
                            return false;
                        case mbk_Dominance:
                            return (*left) < (*other.left);
                        case mbk_Interaction:
                            return true;
                    };
                case mbk_Interaction:
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                    {
                        auto o1 = order();
                        auto o2 = other.order();
                        if (o1 < o2) {
                            return true;
                        }
                        if (o1 > o2) {
                            return false;
                        }
                    }
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                    switch (other.type) {
                        case mbk_Interaction:
                            return (*left) < (*other.left) || ((*left) == (*other.left) && (*right) < (*other.right));
                        default:
                            return false;
                    };
            };
            return false;
        }

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    bool remove_position(const chromosome* chr, double locus)
    {
        switch (type) {
            case mbk_Covar:
            case mbk_CI:
                return true;
            case mbk_POP:
                if (has_locus(chr, locus)) {
                    loci = loci - locus;
                }
                return !loci->is_empty();
            case mbk_Dominance:
                return left->remove_position(chr, locus);
            case mbk_Interaction:
                bool a = left->remove_position(chr, locus);
                bool b = right->remove_position(chr, locus);
                return a && b;
        };
        return false;
    }

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    friend
        inline
        bool
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        operator < (const model_block_key& k1, const model_block_key& k2)
        {
            if (!k1) {
                return !!k2;
            }
            if (!k2) {
                return false;
            }
            return (*k1) < (*k2);
        }
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    bool
        operator == (const model_block_key_struc& other) const
        {
            if (type != other.type) {
                return false;
            }
            switch (type) {
                case mbk_Interaction:
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                    if (!((*right) == (*other.right))) {
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                        return false;
                    }
                case mbk_Dominance:
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                    if (!((*left) == (*other.left))) {
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                        return false;
                    }
                    break;
                case mbk_POP:
                    return chr == other.chr && loci == other.loci;
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                case mbk_Covar:
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                case mbk_CI:
                    return true;
            };
            return false;
        }

    friend
        inline
        bool
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        operator == (const model_block_key& k1, const model_block_key& k2)
        {
            return k1 && k2 && (*k1) == (*k2);
        }
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    operator std::string () const { std::stringstream ret; ret << (*this); return ret.str(); }

private:
    typedef std::pair<const chromosome*, locus_key> item;

    std::vector<item>
        flatten() const
        {
            std::vector<item> ret;
            flatten(ret);
            std::sort(ret.begin(), ret.end(), [](const item& a, const item& b) { return a.first < b.first || (a.first == b.first && a.second < b.second); });
            return ret;
        }

    void
        flatten(std::vector<item>& ret) const
        {
            switch (type) {
                case mbk_Interaction:
                    right->flatten(ret);
                case mbk_Dominance:
                    left->flatten(ret);
                    break;
                case mbk_POP:
                    ret.emplace_back(chr, loci);
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                case mbk_Covar:
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                case mbk_CI:
                    ;
            };
        }

};


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struct mbk_comp {
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    bool
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        operator () (const model_block_key& k1, const model_block_key& k2) const
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        {
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            return (*k1) < (*k2);
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        }
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};

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typedef std::map<model_block_key, value<model_block_type>, mbk_comp> model_block_collection;
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namespace std {
    template <>
        struct hash<model_block_key> {
            size_t operator () (const model_block_key& mbk) const
            {
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                std::hash<const chromosome*> hc;
                std::hash<locus_key> hlk;
                size_t accum;
#if 0
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                /* WARNING FIXME this MUST NOT be used to hash a function parameter
                 * in a disk-cached task, because a POINTER is HASHED and the order
                 * is not guaranteed to be the same in every run.
                 */
                for (const auto& kv: mbk.selection) {
                    accum = impl::ROTATE<7>(impl::ROTATE<7>(accum * hc(kv.first)) ^ hlk(kv.second));
                }
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#endif
                accum = 0xbadc0def;
                switch (mbk->type) {
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                    case mbk_Covar:
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                    case mbk_CI:
                        return 0;
                    case mbk_POP:
                        accum = 0xdeadbe3f;
                        accum = impl::ROTATE<7>(impl::ROTATE<7>(accum * hc(mbk->chr)) ^ hlk(mbk->loci));
                        break;
                    case mbk_Dominance:
                        accum = impl::ROTATE<7>(accum * operator () (mbk->left));
                        break;
                    case mbk_Interaction:
                        accum = impl::ROTATE<7>(accum * operator () (mbk->left)) ^ impl::ROTATE<13>(accum * operator () (mbk->right));
                };
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                return accum;
            }
        };
} // namespace std



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static inline
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bool
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around_zero(double o)
{
    return o < COMPONENT_EPSILON && o > -COMPONENT_EPSILON;
}

static inline
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bool
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much_smaller_than(double a, double b)
{
    return a < (COMPONENT_EPSILON * b);
}

static inline
void
set_if_much_smaller_than(double& a, double b)
{
    double tmp = COMPONENT_EPSILON * b;
    if (a < tmp) {
        a = tmp;
    }
}

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using namespace Eigen;

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static inline
MatrixXd concat_right(const std::vector<MatrixXd>& mat_vec)
{
    size_t full_size = 0;
    MatrixXd ret;
    for (auto& m: mat_vec) {
        full_size += m.outerSize();
        /*MSG_DEBUG("preparing concat_right with matrix(" << m->innerSize() << ',' << m->outerSize() << ')');*/
    }
    ret.resize(mat_vec.front().innerSize(), full_size);
    full_size = 0;
    for (auto& m: mat_vec) {
        /*MSG_DEBUG("concat_right in M(" << ret.innerSize() << ',' << ret.outerSize() << ") at col " << full_size << "matrix(" << m->innerSize() << ',' << m->outerSize() << ')');*/
        /*ret.block(0, full_size, ret.innerSize(), m->outerSize()) = *m;*/
        ret.middleCols(full_size, m.outerSize()) = m;
        full_size += m.outerSize();
    }
    return ret;
}

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static inline
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MatrixXd concat_right(const collection<model_block_type>& mat_vec)
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{
    size_t full_size = 0;
    MatrixXd ret;
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    for (auto m: mat_vec) {
        full_size += m->outerSize();
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        /*MSG_DEBUG("preparing concat_right with matrix(" << m->innerSize() << ',' << m->outerSize() << ')');*/
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    }
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    ret.resize(mat_vec.front()->innerSize(), full_size);
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    full_size = 0;
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    for (auto m: mat_vec) {
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        /*MSG_DEBUG("concat_right in M(" << ret.innerSize() << ',' << ret.outerSize() << ") at col " << full_size << "matrix(" << m->innerSize() << ',' << m->outerSize() << ')');*/
        /*ret.block(0, full_size, ret.innerSize(), m->outerSize()) = *m;*/
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        ret.middleCols(full_size, m->outerSize()) = m->data;
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        full_size += m->outerSize();
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    }
    return ret;
}

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static inline
MatrixXd concat_right(const model_block_collection& mat_map)
{
    size_t full_size = 0;
    MatrixXd ret;
    for (auto m: mat_map) {
        full_size += m.second->outerSize();
        /*MSG_DEBUG("preparing concat_right with matrix(" << m->innerSize() << ',' << m->outerSize() << ')');*/
    }
    ret.resize(mat_map.begin()->second->innerSize(), full_size);
    full_size = 0;
    for (auto m: mat_map) {
        /*MSG_DEBUG("concat_right in M(" << ret.innerSize() << ',' << ret.outerSize() << ") at col " << full_size << "matrix(" << m->innerSize() << ',' << m->outerSize() << ')');*/
        /*ret.block(0, full_size, ret.innerSize(), m->outerSize()) = *m;*/
        ret.middleCols(full_size, m.second->outerSize()) = m.second->data;
        full_size += m.second->outerSize();
    }
    return ret;
}

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static inline
MatrixXd concat_down(const std::vector<MatrixXd>& mat_vec)
{
    size_t full_size = 0;
    MatrixXd ret;
    for (auto& m: mat_vec) {
        full_size += m.innerSize();
    }
    ret.resize(full_size, mat_vec.front().outerSize());
    full_size = 0;
    for (auto& m: mat_vec) {
        ret.middleRows(full_size, m.innerSize()) = m;
        full_size += m.innerSize();
    }
    return ret;
}

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static inline
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MatrixXd concat_down(const std::vector<const MatrixXd*>& mat_vec)
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{
    size_t full_size = 0;
    MatrixXd ret;
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    for (auto m: mat_vec) {
        full_size += m->innerSize();
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    }
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    ret.resize(full_size, mat_vec.front()->outerSize());
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    full_size = 0;
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    for (auto m: mat_vec) {
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        /*ret.block(full_size, 0, m->innerSize(), ret.outerSize()) = *m;*/
        ret.middleRows(full_size, m->innerSize()) = *m;
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        full_size += m->innerSize();
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    }
    return ret;
}


static inline
std::pair<int, MatrixXd>
rank_and_components(const MatrixXd& M)
{
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    JacobiSVD<MatrixXd> svd(M, ComputeThinU);
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    std::cout << "Singular values " << svd.singularValues().transpose() << std::endl;
    int nzsv = svd.nonzeroSingularValues();

    return {nzsv, svd.matrixU().leftCols(nzsv)};
}


static inline
MatrixXd components(const MatrixXd& M, const MatrixXd& P)
{
    MatrixXd pnorm(P.innerSize(), P.outerSize());
    for (int i = 0; i < P.outerSize(); ++i) {
        pnorm.col(i) = P.col(i).normalized();
    }
    MatrixXd orth = M - pnorm * pnorm.transpose() * M; /* feu ! */
    return rank_and_components(orth).second;
}


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enum class SolverType { QR };
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typedef std::vector<std::map<model_block_key, MatrixXd>> constraint_list;

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inline
std::ostream& operator << (std::ostream& os, const constraint_list& cl)
{
    for (const auto& map: cl) {
        for (const auto& kv: map) {
            os << kv.first << std::endl << kv.second << std::endl;
        }
        os << "---" << std::endl;
    }
    return os;
}

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MatrixXd
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contrast_groups(const collection<const qtl_pop_type*>& all_pops, const locus_key& lk);
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struct filename_stream {
    struct filtering_streambuf : public std::streambuf {
        std::streambuf* original;
        filtering_streambuf(std::streambuf* _) : original(_) {}
    protected:
        int overflow(int ch) override
        {
            switch (ch) {
                case ',':
                case '}':
                    return ch;
                case '{':
                    ch = '-';
                    break;
                case ' ':
                    ch = '_';
                default:;
            };
            return original->sputc(ch);
        }
    };

    std::ostringstream sstream;
    filtering_streambuf rdbuf;
    std::ostream ostream;

    filename_stream()
        : sstream(), rdbuf(sstream.rdbuf()), ostream(&rdbuf)
    {}

    template <typename T>
        friend
        filename_stream& operator << (filename_stream& fs, T x)
        {
            fs.ostream << x;
            return fs;
        }

    operator
        std::string () const
        {
            return sstream.str();
        }
};


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/*#define ULTRA_MEGA_PARANOID*/
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static inline
MatrixXd matrix_inverse(const MatrixXd& m)
{
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    /*return m.fullPivHouseholderQr().inverse();*/
    /*return m.inverse();*/
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    /* FIXME Should NOT use SVD (see note in compute() */
    JacobiSVD<MatrixXd> inverter(m, ComputeFullV);
    auto& V = inverter.matrixV();
    VectorXd inv_sv(inverter.singularValues());
    for (int i = 0; i < inv_sv.innerSize(); ++i) {
        if (!around_zero(inv_sv(i))) {
            inv_sv(i) = 1. / inv_sv(i);
        } else {
            inv_sv(i) = 0.;
        }
    }
#ifdef ULTRA_MEGA_PARANOID
    /* CHECK THAT THIS IS STABLE BY THE BEN ISRAEL SEQUENCE */
    MatrixXd svd_ret = V * inv_sv.asDiagonal() * V.transpose();
    MatrixXd ret = svd_ret;
    MatrixXd test = 2 * ret - ret * m * ret;
    if (!test.isApprox(ret, .00001)) {
        MSG_DEBUG("ret" << std::endl << ret << std::endl << "test" << std::endl << test);
    } else {
        MSG_DEBUG("m^-1 IS GOOD! Yeah man.");
    }
    return ret;
#else
    return V * inv_sv.asDiagonal() * V.transpose();
#endif
}


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struct gauss_elimination {
    MatrixXd block;
    std::vector<int> leading;

    gauss_elimination(const MatrixXd& mat)
        : block(mat)
        , leading(mat.rows())
    {
        for (int i = 0; i < block.rows(); ++i) {
            find_leading_coef(i);
        }

        sort_rows(0);
        for (int ref = 0; ref < block.rows(); ++ref) {
            if (is_null(ref)) {
                break;
            }
            anihilate_coef(ref, leading[ref]);
            sort_rows(ref);
        }
    }

    bool is_null(int row) const { return leading[row] == block.cols(); }
    int not_null(int row) const { return (int) (leading[row] != block.cols()); }

    int
        rank() const
        {
            /*MSG_DEBUG("echelon form" << std::endl << block);*/
            int count = 0;
            for (int i = 0; i < block.rows(); ++i) {
                count += not_null(i);
            }
            return count;
        }

    void
        sort_rows(int start)
        {
            std::vector<int> indices(block.rows() - start);
            int i = start;
            std::generate(indices.begin(), indices.end(), [&] () { return i++; });
            std::sort(indices.begin(), indices.end(), [&](int a, int b) { return leading[a] < leading[b]; });
            int sz = (int) indices.size();
            for (i = 0; i < sz; ++i) {
                if (i > indices[i]) {
                    swap_rows(i, indices[i]);
                }
            }
        }

    void
        swap_rows(int r1, int r2)
        {
            VectorXd tmp = block.row(r1);
            block.row(r1) = block.row(r2);
            block.row(r2) = tmp;
            std::swap(leading[r1], leading[r2]);
        }

    void
        anihilate_coef(int ref, int j)
        {
            for (int i = ref + 1; i < block.rows(); ++i) {
                if (leading[i] == j) {
                    anihilate_coef_in_row(ref, i, j);
                }
            }
        }

    void
        anihilate_coef_in_row(int ref, int r, int j)
        {
            block.row(r) *= 1. / block(r, j);
            block.row(r) -= block.row(ref);
            block(r, j) = 0;
            find_leading_coef(r);
            if (not_null(r)) {
                block.row(r) *= 1. / block(r, leading[r]);
            }
        }

    void
        find_leading_coef(int r)
        {
            int j;
            for (j = 0; j < block.cols() && block(r, j) == 0; ++j);
            leading[r] = j;
        }
};

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struct model {
    model()
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        : m_Y(), m_blocks(), m_X(), m_rank(), m_rss(), m_coefficients(), m_solver_type(), m_computed(false), m_with_constraints(false), m_ghost_constraint(), m_all_pops(), m_ancestor_names(), m_max_order(1), m_threshold(0)
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    {}

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    model(const value<MatrixXd>& y, double threshold, const collection<const qtl_pop_type*>& pops, const std::map<char, std::string>& anam, size_t mo=1, SolverType st=SolverType::QR)
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        : m_Y(y)
        , m_blocks(), m_X()
		, m_rank(), m_rss(), m_coefficients(), m_residuals()
		, m_solver_type(st)
        , m_computed(false)
        , m_with_constraints(false)
        , m_ghost_constraint()
        , m_all_pops(pops)
        , m_ancestor_names(anam)
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        , m_max_order(mo)
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        , m_threshold(threshold)
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    /*{ MSG_DEBUG("new model " << __LINE__ << " with Y(" << y.innerSize() << ',' << y.outerSize() << ')'); }*/
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    {}

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    model(const value<MatrixXd>& y, double threshold, const collection<const qtl_pop_type*>& pops, size_t mo=1, SolverType st=SolverType::QR)
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        : m_Y(y)
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        , m_blocks(), m_X()
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		, m_rank(), m_rss(), m_coefficients(), m_residuals()
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		, m_solver_type(st)
        , m_computed(false)
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        , m_with_constraints(false)
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        , m_ghost_constraint()
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        , m_all_pops(pops)
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        , m_ancestor_names((*pops.front())->ancestor_names)
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        , m_max_order(mo)
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        , m_threshold(threshold)
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    /*{ MSG_DEBUG("new model " << __LINE__ << " with Y(" << y.innerSize() << ',' << y.outerSize() << ')'); }*/
    {}

    model(const model& mo)
        : m_Y(mo.m_Y)
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        , m_blocks(mo.m_blocks), m_X(mo.m_X)
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		, m_rank(mo.m_rank), m_rss(mo.m_rss), m_coefficients(mo.m_coefficients)
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        , m_residuals(mo.m_residuals)
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		, m_solver_type(mo.m_solver_type)
        , m_computed(mo.m_computed)
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        , m_with_constraints(mo.m_with_constraints)
        , m_ghost_constraint()
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        , m_all_pops(mo.m_all_pops)
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        , m_ancestor_names(mo.m_ancestor_names)
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        , m_max_order(mo.m_max_order)
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        , m_threshold(mo.m_threshold)
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    /*{ MSG_DEBUG("new model " << __LINE__ << " with Y(" << m_Y->innerSize() << ',' << m_Y->outerSize() << ')'); }*/
    {}

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    model(const value<MatrixXd>& y, const model& mo)
        : m_Y(y)
        , m_blocks(mo.m_blocks), m_X(mo.m_X)
		, m_rank(), m_rss(), m_coefficients()
        , m_residuals()
		, m_solver_type(mo.m_solver_type)
        , m_computed(false)
        , m_with_constraints(mo.m_with_constraints)
        , m_ghost_constraint()
        , m_all_pops(mo.m_all_pops)
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        , m_ancestor_names(mo.m_ancestor_names)
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        , m_max_order(mo.m_max_order)
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        , m_threshold(mo.m_threshold)
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    /*{ MSG_DEBUG("new model " << __LINE__ << " with Y(" << m_Y->innerSize() << ',' << m_Y->outerSize() << ')'); }*/
    {}

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# if 0
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    model&
        operator = (const model& mo)
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        = delete;
#else
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    model&
        operator = (const model& mo)
        {
            m_Y = mo.m_Y;
            m_blocks = mo.m_blocks;
            m_computed = mo.m_computed;
            m_with_constraints = mo.m_with_constraints;
            m_ghost_constraint = mo.m_ghost_constraint;
            m_X = mo.m_X;
            m_rss = mo.m_rss;
            m_coefficients = mo.m_coefficients;
            m_residuals = mo.m_residuals;
            m_rank = mo.m_rank;
            m_all_pops = mo.m_all_pops;
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            m_ancestor_names = mo.m_ancestor_names;
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            m_max_order = mo.m_max_order;
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            m_threshold = mo.m_threshold;
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            return *this;
        }
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    model&
        operator = (model&& mo)
        {
            m_Y = mo.m_Y;
            m_blocks.clear();
            m_blocks.swap(mo.m_blocks);
            m_computed = mo.m_computed;
            m_with_constraints = mo.m_with_constraints;
            m_ghost_constraint = mo.m_ghost_constraint;
            m_X = mo.m_X;
            m_rss = mo.m_rss;
            m_coefficients = mo.m_coefficients;
            m_residuals = mo.m_residuals;
            m_rank = mo.m_rank;
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            m_ancestor_names.swap(mo.m_ancestor_names);
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            m_max_order = mo.m_max_order;
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            m_threshold = mo.m_threshold;
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            return *this;
        }
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#endif
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    constraint_list
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        compute_constraint(const model_block_key& mbk, const model_block_type& mb)
        {
            constraint_list ret;
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            if (mbk->type == mbk_CI) {
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                return ret;
            /*} else if (mbk.selection.size() == 1) {*/
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            } else if (mbk->type == mbk_POP) {
                size_t n_qtl = mb.column_labels.front().size();
                if (n_qtl == 1) {
                    /* only one chromosome: do the contrast groups trick */
                    ret = {{{mbk, contrast_groups(m_all_pops, mbk->loci)}}};
                } else {
                    std::vector<std::set<char>> uniq_letters_per_qtl(mb.column_labels.front().size());
                    /* need the epistasis magic here */
                    for (const auto& vec: mb.column_labels) {
                        auto i = uniq_letters_per_qtl.begin();
                        for (char c: vec) { i->insert(c); ++i; }
                    }
                    std::vector<size_t> letter_counts(uniq_letters_per_qtl.size());
                    for (size_t i = 0; i < letter_counts.size(); ++i) { letter_counts[i] = uniq_letters_per_qtl[i].size(); }
                    size_t start = 1;
                    size_t finish = (1 << letter_counts.size()) - 1;
                    for (size_t variant = start; variant < finish; ++variant) {
                        MatrixXd constraint = MatrixXd::Identity(1, 1);
                        for (size_t i = 0; i < letter_counts.size(); ++i) {
                            bool flat = (variant >> i) & 1;
                            MatrixXd tmp;
                            if (flat) {
                                tmp = kroneckerProduct(constraint, MatrixXd::Identity(letter_counts[i], letter_counts[i]));
                            } else {
                                tmp = kroneckerProduct(constraint, MatrixXd::Identity(letter_counts[i], letter_counts[i]));
                            }
                            constraint = tmp;
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                        }
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                        ret.emplace_back();
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                        /*MSG_DEBUG("Created constraint");*/
                        /*MSG_DEBUG("" << constraint);*/
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                        ret.back().insert({{mbk, constraint}});
                    }
                }