src/LocARNA/aligner.hh

#ifndef LOCARNA_ALIGNER_HH
#define LOCARNA_ALIGNER_HH

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "aux.hh"
#include "scoring_fwd.hh"
#include "rna_structure.hh"

#include "params.hh"

namespace LocARNA {

    class AlignerImpl;

    class Sequence;
    class AlignerParams;
    class ArcMatches;
    class Alignment;

    class AlignerRestriction;

    template <class T>
    class greater_second {
    public:
        bool
        operator()(const T &a, const T &b) {
            return a.second < b.second;
        }
    };

    class Aligner {
        AlignerImpl *pimpl_;

    public:
        Aligner(const Aligner &aligner);

        Aligner &
        operator=(const Aligner &aligner);

        Aligner(const AlignerParams &ap);

        static AlignerParams
        create() {
            return AlignerParams();
        }

        ~Aligner();

        Alignment const &
        get_alignment() const;

        void
        set_alignment(const Alignment &alignment);

        infty_score_t
        align();

        void
        trace();

        void
        set_restriction(const AlignerRestriction &r);

        const AlignerRestriction &
        get_restriction() const;

        void
        suboptimal(int k,
                   score_t threshold,
                   bool normalized,
                   score_t normalized_L,
                   size_t output_width,
                   bool verbose,
                   bool opt_local_out,
                   bool opt_pos_output,
                   bool opt_write_structure);

        infty_score_t
        normalized_align(score_t L, bool verbose);

        infty_score_t
        penalized_align(score_t position_penalty);

        score_t
        evaluate();

        RnaStructure
        optimize_consensus_structure();
    };

} // end namespace LocARNA

#endif // LOCARNA_ALIGNER_HH