PredictorMfe.h

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#ifndef INTARNA_PREDICTORMFE_H_
#define INTARNA_PREDICTORMFE_H_
 
 
#include "IntaRNA/Predictor.h"
 
#include "IntaRNA/IndexRangeList.h"
 
#include <list>
#include <utility>
 
#include <boost/unordered_map.hpp>
 
namespace IntaRNA {
 
class PredictorMfe : public Predictor {
 
protected:
 
    template < class ValueType >
    class BestInteraction {
    public:
 
        BestInteraction( const ValueType val=(std::numeric_limits<ValueType>::has_infinity ? std::numeric_limits<ValueType>::infinity() : std::numeric_limits<ValueType>::max())
                , const size_t j1=RnaSequence::lastPos, const size_t j2=RnaSequence::lastPos )
            : val(val), j1(j1), j2(j2)
        {}
 
    public:
        ValueType val;
        size_t j1;
        size_t j2;
    };
 
    typedef BestInteraction<E_type> BestInteractionE;
    typedef BestInteraction<Z_type> BestInteractionZ;
 
 
 
public:
 
    PredictorMfe( const InteractionEnergy & energy
                , OutputHandler & output
                , PredictionTracker * predTracker );
 
    virtual ~PredictorMfe();
 
protected:
 
 
    using Predictor::energy;
 
    using Predictor::output;
 
    using Predictor::predTracker;
 
    typedef std::list<Interaction> InteractionList;
 
    InteractionList mfeInteractions;
 
    typedef boost::unordered_map< Interaction::BasePair, BestInteractionE, Interaction::BasePair::Hash > HashIdx2E;
 
    HashIdx2E mfe4leftEnd;
 
    std::pair< IndexRangeList, IndexRangeList > reportedInteractions;
 
    virtual
    void
    initOptima();
 
    bool
    isValidOutputSite( const size_t i1, const size_t j1,
            const size_t i2, const size_t j2 ) const;
 
    virtual
    void
    updateOptima( const size_t i1, const size_t j1
                , const size_t i2, const size_t j2
                , const E_type energy
                , const bool isHybridE
                , const bool incrementZall );
 
 
    virtual
    void
    traceBack( Interaction & interaction ) = 0;
 
 
    virtual
    void
    getNextBest( Interaction & curBest );
 
 
    virtual
    void
    updateMfe4leftEnd(const size_t i1, const size_t j1
                    , const size_t i2, const size_t j2
                    , const Interaction & curInteraction );
 
    virtual
    void
    reportOptima();
 
};
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFE_H_ */