aligner.hh

#ifndef LOCARNA_ALIGNER_HH
#define LOCARNA_ALIGNER_HH
 
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
 
#include <memory>
#include "aux.hh"
#include "scoring_fwd.hh"
#include "rna_structure.hh"
 
#include "aligner_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 {
        std::unique_ptr<AlignerImpl> pimpl_;
 
    public:
        Aligner(const Aligner &aligner);
 
        Aligner &
        operator=(const Aligner &aligner);
 
        Aligner(const AlignerParams &ap);
 
        ~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