debug_matrix.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2019, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2019, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------

#pragma once

#include <iomanip>

#include <seqan3/alignment/matrix/matrix_concept.hpp>
#include <seqan3/alignment/matrix/row_wise_matrix.hpp>
#include <seqan3/alignment/matrix/trace_directions.hpp>
#include <seqan3/core/debug_stream.hpp>

namespace seqan3::detail
{

template <Matrix matrix_t, typename first_sequence_t = std::nullopt_t, typename second_sequence_t = std::nullopt_t>
class debug_matrix
{
protected:
    static constexpr bool has_first_sequence = !std::is_same_v<std::decay_t<first_sequence_t>, std::nullopt_t>;
    static constexpr bool has_second_sequence = !std::is_same_v<std::decay_t<second_sequence_t>, std::nullopt_t>;
    using entry_t = typename std::remove_reference_t<matrix_t>::entry_type;
    static constexpr bool is_traceback_matrix = std::is_same_v<std::decay_t<entry_t>, trace_directions>;
    static constexpr bool is_optional_score = is_type_specialisation_of_v<entry_t, std::optional>;
public:
    using entry_type = std::conditional_t<is_traceback_matrix || is_optional_score,
                                          entry_t,
                                          std::optional<entry_t>>;

    debug_matrix() = default; 
    debug_matrix(debug_matrix const &) = default; 
    debug_matrix(debug_matrix &&) = default; 
    debug_matrix & operator=(debug_matrix const &) = default; 
    debug_matrix & operator=(debug_matrix &&) = default; 
    ~debug_matrix() = default;  

    debug_matrix(matrix_t matrix)
        : debug_matrix(std::forward<matrix_t>(matrix), std::nullopt, std::nullopt)
    {}

    debug_matrix(matrix_t matrix, first_sequence_t first_sequence, second_sequence_t second_sequence)
        : _matrix{std::forward<matrix_t>(matrix)},
          _first_sequence{std::forward<first_sequence_t>(first_sequence)},
          _second_sequence{std::forward<second_sequence_t>(second_sequence)}
    {
        if constexpr(has_first_sequence)
        {
            assert(_matrix.cols() <= _first_sequence.size() + 1u);
        }

        if constexpr(has_second_sequence)
        {
            assert(_matrix.rows() <= _second_sequence.size() + 1u);
        }
    }

    size_t rows() const noexcept
    {
        if (!_transpose)
            return _rows.value_or(_matrix.rows());
        else
            return _cols.value_or(_matrix.cols());
    }

    size_t cols() const noexcept
    {
        if (!_transpose)
            return _cols.value_or(_matrix.cols());
        else
            return _rows.value_or(_matrix.rows());
    }

    first_sequence_t const & first_sequence() const noexcept
    {
        if (!_transpose)
            return _first_sequence;
        else
            return _second_sequence;
    }

    second_sequence_t const & second_sequence() const noexcept
    {
        if (!_transpose)
            return _second_sequence;
        else
            return _first_sequence;
    }

    entry_type at(size_t const row, size_t const col) const noexcept
    {
        assert(row < rows() && col < cols());

        size_t const _row = !_transpose ? row : col;
        size_t const _col = !_transpose ? col : row;

        if (!_masking_matrix.has_value() || _masking_matrix.value().at(_row, _col))
        {
            entry_t const & entry = _matrix.at(_row, _col);

            if (!is_traceback_matrix || !_transpose)
                return entry;

            if constexpr(is_traceback_matrix)
            {
                trace_directions reverse{};
                if ((entry & trace_directions::left) == trace_directions::left)
                    reverse |= trace_directions::up;
                if ((entry & trace_directions::up) == trace_directions::up)
                    reverse |= trace_directions::left;
                if ((entry & trace_directions::diagonal) == trace_directions::diagonal)
                    reverse |= trace_directions::diagonal;
                return reverse;
            }
        }

        if constexpr(is_traceback_matrix)
            return trace_directions::none;
        else
            return std::nullopt;
    }

    debug_matrix & mask_matrix(row_wise_matrix<bool> masking_matrix) noexcept
    {
        _masking_matrix = masking_matrix;
        return *this;
    }

    debug_matrix & mask_matrix(std::vector<bool> masking_vector) noexcept
    {
        return mask_matrix(row_wise_matrix<bool>{masking_vector, rows(), cols()});
    }

    debug_matrix & sub_matrix(size_t const new_rows, size_t const new_cols) noexcept
    {
        assert(new_rows <= _matrix.rows());
        assert(new_cols <= _matrix.cols());
        _rows = new_rows;
        _cols = new_cols;
        return *this;
    }

    debug_matrix & transpose_matrix() noexcept
    {
        _transpose = !_transpose;
        return *this;
    }

protected:
    struct format_type; // forward declaration

public:
    template <typename ostream_t>
    void print(ostream_t & cout, fmtflags2 const flags) const noexcept
    {
        format_type const & symbols = (flags & fmtflags2::utf8) == fmtflags2::utf8 ? unicode : csv;
        size_t const column_width = this->column_width.has_value() ?
                                    this->column_width.value() : auto_column_width(flags);

        auto char_first_sequence = [&]([[maybe_unused]] size_t const i) -> std::string
        {
            if constexpr(!has_first_sequence)
                return " ";
            else
                return as_string(first_sequence()[i], flags);
        };

        auto char_second_sequence = [&]([[maybe_unused]] size_t const i) -> std::string
        {
            if constexpr(!has_second_sequence)
                return " ";
            else
                return as_string(second_sequence()[i], flags);
        };

        auto print_cell = [&](std::string const & symbol)
        {
            // deal with unicode chars that mess up std::setw
            size_t const length_bytes = symbol.size();
            size_t const length = unicode_str_length(symbol);
            size_t const offset = length_bytes - length;

            cout << std::left
                 << std::setw(column_width + offset)
                 << symbol
                 << symbols.col_sep;
        };

        auto print_first_cell = [&](std::string const & symbol)
        {
            cout << symbol << symbols.col_sep;
        };

        // |_|d|a|t|a|b|a|s|e|
        auto print_first_row = [&]
        {
            print_first_cell(" ");
            print_cell(symbols.epsilon);

            for (size_t col = 0; col < cols() - 1; ++col)
                print_cell(char_first_sequence(col));

            cout << "\n";
        };

        // |-|-|-|-|-|-|-|-|-|
        auto print_divider = [&]
        {
            cout << " " << symbols.row_col_sep;
            for (size_t col = 0; col < cols(); ++col)
            {
                for (size_t i = 0; i < column_width; ++i)
                    cout << symbols.row_sep;

                cout << symbols.row_col_sep;
            }
            cout << "\n";
        };

        print_first_row();
        for (size_t row = 0; row < rows(); ++row)
        {
            if (symbols.row_sep[0] != '\0')
                print_divider();

            // one query letter + one row of scores / traces
            if (row == 0)
                print_first_cell(symbols.epsilon);
            else
                print_first_cell(char_second_sequence(row - 1));

            for (size_t col = 0; col < cols(); ++col)
                print_cell(entry_at(row, col, flags));

            cout << "\n";
        }
    }

    size_t auto_column_width(fmtflags2 const flags) const noexcept
    {
        size_t col_width = 1;
        for (size_t row = 0; row < rows(); ++row)
            for (size_t col = 0; col < cols(); ++col)
                col_width = std::max(col_width, unicode_str_length(entry_at(row, col, flags)));

        return col_width;
    }

protected:
    std::string entry_at(size_t const row, size_t const col, fmtflags2 flags) const noexcept
    {
        format_type const & symbols = (flags & fmtflags2::utf8) == fmtflags2::utf8 ? unicode : csv;

        entry_type const & entry = at(row, col);
        if (!is_traceback_matrix && entry == matrix_inf<entry_type>)
            return symbols.inf;

        return as_string(entry, flags);
    }

    template <typename entry_type>
    static std::string as_string(entry_type && entry, fmtflags2 const flags) noexcept
    {
        std::stringstream strstream;
        debug_stream_type stream{strstream};
        stream << flags << entry;
        return strstream.str();
    }

    static size_t unicode_str_length(std::string const & str) noexcept
    {
        size_t length = 0u;
        for (auto it = str.cbegin(); it < str.cend(); ++it, ++length)
        {
            uint8_t v = *it;
            if ((v & 0b11100000) == 0b11000000)
                ++it;
            else if ((v & 0b11110000) == 0b11100000)
                it += 2;
            else if ((v & 0b11111000) == 0b11110000)
                it += 3;
        }
        return length;
    }

    struct format_type
    {
        char const * epsilon{};
        char const * col_sep{};
        char const * row_sep{};
        char const * row_col_sep{};
        char const * inf{};
    };

    static constexpr format_type csv{" ", ";", "", "", ""};
    static constexpr format_type unicode{"ε", "║", "═", "╬", "∞"};

public:
    std::optional<size_t> column_width{std::nullopt};

protected:
    matrix_t _matrix;
    first_sequence_t _first_sequence;
    second_sequence_t _second_sequence;
    std::optional<size_t> _rows{};
    std::optional<size_t> _cols{};
    std::optional<row_wise_matrix<bool>> _masking_matrix{};
    bool _transpose{};
};

template <Matrix matrix_t>
debug_matrix(matrix_t &&)
   -> debug_matrix<matrix_t>;

template <Matrix matrix_t, typename first_sequence_t, typename second_sequence_t>
debug_matrix(matrix_t &&, first_sequence_t &&, second_sequence_t &&)
   -> debug_matrix<matrix_t, first_sequence_t, second_sequence_t>;

} // namespace seqan3::detail

namespace seqan3
{
template <detail::Matrix alignment_matrix_t>
inline debug_stream_type & operator<<(debug_stream_type & s, alignment_matrix_t && matrix)
{
    detail::debug_matrix debug{std::forward<alignment_matrix_t>(matrix)};

    std::stringstream sstream{};
    debug.print(sstream, s.flags2());
    s << sstream.str();
    return s;
}

} // namespace seqan3