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 opt_normalized,
                   score_t normalized_L,
                   size_t output_width,
                   bool opt_verbose,
                   bool opt_local_out,
                   bool opt_pos_output,
                   bool opt_write_structure
                   );
    
    
        infty_score_t
        normalized_align(score_t L, bool opt_verbose);

        infty_score_t
    penalized_align(score_t position_penalty);

        score_t
        evaluate();

        RnaStructure
        optimize_consensus_structure();
        

    };

} //end namespace LocARNA

#endif // LOCARNA_ALIGNER_HH