musaline.hpp

#ifndef MUSALIGNA7GDNETYQI385MDKWOWOO
#define MUSALIGNA7GDNETYQI385MDKWOWOO

// Author: Geert-Jan Giezeman <geert@cs.uu.nl>
// Copyright: Utrecht University, 2012

#include <vector>
#include <limits>
#include "csuu_matrix.hpp"

namespace musaline {

    namespace detail {
        using Geert_cs_uu_nl::Matrix;
        const double mininf= -std::numeric_limits<double>::infinity();

        struct NwCell {
            double asb; 
            int from; 
            // 0: from topleft; 1: from top; 2: from left; 3: stop
        };

        struct NwgCell {
            double asb[3]; 
            int from; 
            bool ext_1;
            bool ext_2;
        };

    }

    struct Match {
        int n[2];
        double score;
    };

    struct Alignment {
        double score;
        size_t start[2];
        size_t  end[2];
        std::vector< Match > matches;
    };


#if 0

    enum AlignKind {FirstSeqWithGap=0, SecondSeqWithGap=1, BothSeqs, FirstWithMany, SecondWithMany};

    struct Alignment {
        double score;
        size_t start[2];
        size_t  end[2];
        std::vector< AlignKind > a;
    };
#endif

    template <class CostCalc>
    class LinearAligner {
    public:
        typedef CostCalc CostCalculator;
    private:
        mutable CostCalculator m_ccal;
        template <class Iter1, class Iter2>
        void fill_matrix_std(Geert_cs_uu_nl::Matrix<detail::NwCell> &matrix,
                Iter1 s1cur, Iter2 s2begin) const;
        template <class Iter1, class Iter2>
        void fill_matrix_partial(Geert_cs_uu_nl::Matrix<detail::NwCell> &matrix,
                Iter1 s1cur, Iter2 s2begin) const;
    public:
        LinearAligner(
                CostCalculator ccal = CostCalculator())
        :
        m_ccal(ccal) {}
        void set_cost_calculator(CostCalculator ccal) { m_ccal = ccal;}
        CostCalculator const &get_cost_calculator() const { return m_ccal;}
        template <class Sequence0, class Sequence1>
        Alignment global_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment cut_one_end_off_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment cut_one_begin_off_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment initial_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment end_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment inside_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment semi_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment partial_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
    };




    template <class CostCalc>
    class AffineAligner {
    public:
        typedef CostCalc CostCalculator;
    private:
        mutable CostCalculator m_ccal;

        template <class Iter1, class Iter2>
        void fill_matrix_std(Geert_cs_uu_nl::Matrix<detail::NwgCell> &matrix,
                Iter1 s1cur, Iter2 s2begin) const;
        template <class Iter1, class Iter2>
        void fill_matrix_partial(Geert_cs_uu_nl::Matrix<detail::NwgCell> &matrix,
                Iter1 s1cur, Iter2 s2begin) const;
    public:
        AffineAligner( CostCalculator ccal = CostCalculator())
        : m_ccal(ccal)
        {}
        void set_cost_calculator(CostCalculator ccal) { m_ccal = ccal;}
        CostCalculator const &get_cost_calculator() const { return m_ccal;}
        template <class Sequence0, class Sequence1>
        Alignment global_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment cut_one_end_off_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment cut_one_begin_off_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment inside_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment initial_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment end_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment semi_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment partial_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
    };

#if 0

    struct AlignType2 {
        AlignKind ak;
        double score;
        int n;
    };

    struct Alignment2 {
        double score;
        size_t start[2];
        size_t  end[2];
        std::vector<AlignType2> a;
    };
#endif

    namespace detail {
        struct FrCell {
            double asb; 
            int from; 
            int fragments;
        };
    }

    template <class CostCalc>
    class ConsolidatingAligner {
    public:
        typedef CostCalc CostCalculator;
    private:
        mutable CostCalculator m_ccal;
        template <class Iter1, class Iter2>
        void fill_matrix(Geert_cs_uu_nl::Matrix<detail::FrCell> &matrix,
                Iter1 s1begin, Iter2 s2begin, double initial_value) const;
        template <class Iter1, class Iter2>
        void fill_matrix_std(Geert_cs_uu_nl::Matrix<detail::FrCell> &matrix,
                Iter1 s1begin, Iter2 s2begin) const
        {
            fill_matrix(matrix, s1begin, s2begin, detail::mininf);
        }
        template <class Iter1, class Iter2>
        void fill_matrix_partial(Geert_cs_uu_nl::Matrix<detail::FrCell> &matrix,
                Iter1 s1begin, Iter2 s2begin) const
        {
            fill_matrix(matrix, s1begin, s2begin, 0.0);
        }

        template <class Sequence1>
        void gap_init_first_column(
                Geert_cs_uu_nl::Matrix<detail::FrCell> &matrix,
                Sequence1 const &seq1) const;
        template <class Sequence0>
        void gap_init_first_row(Geert_cs_uu_nl::Matrix<detail::FrCell> &matrix,
            Sequence0 const &seq0) const;

        template <class Sequence0, class Sequence1>
        void gap_init(Geert_cs_uu_nl::Matrix<detail::FrCell> &matrix,
            Sequence0 const &seq0, Sequence1 const &seq1) const;

    public:
        ConsolidatingAligner(
                CostCalculator ccal = CostCalculator())
        : m_ccal(ccal) {}
        void set_cost_calculator(CostCalculator ccal) { m_ccal = ccal;}
        CostCalculator const &get_cost_calculator() const { return m_ccal;}
        template <class Sequence0, class Sequence1>
        Alignment global_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment cut_one_end_off_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment cut_one_begin_off_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment initial_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment end_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment inside_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment semi_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
        template <class Sequence0, class Sequence1>
        Alignment partial_align(Sequence0 const &seq0, Sequence1 const &seq1) const;
    };

}

#include "musaline_impl.hpp"
#include "musaline_fragment.hpp"

// vim:set shiftwidth=4 softtabstop=4 expandtab cindent:

#endif // MUSALIGNA7GDNETYQI385MDKWOWOO