PredictorMfeEns2dHeuristic.h

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#ifndef INTARNA_PREDICTORMFEENS2DHEURISTIC_H_
#define INTARNA_PREDICTORMFEENS2DHEURISTIC_H_
 
#include "IntaRNA/PredictorMfeEns2d.h"
#include "IntaRNA/Interaction.h"
 
#include "IntaRNA/Matrix.h"
 
namespace IntaRNA {
 
class PredictorMfeEns2dHeuristic: public PredictorMfeEns2d {
 
protected:
 
    typedef Matrix<BestInteractionZ> Z2dMatrix;
 
public:
 
    PredictorMfeEns2dHeuristic( const InteractionEnergy & energy
                            , OutputHandler & output
                            , PredictionTracker * predTracker
                            , BasePairProbabilities * pairProbabilities = nullptr );
 
    virtual ~PredictorMfeEns2dHeuristic() override;
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override;
 
protected:
 
    using PredictorMfeEns2d::energy;
 
    using PredictorMfeEns2d::output;
 
    using PredictorMfeEns2d::reportedInteractions;
 
    Z2dMatrix hybridZ;
 
    struct ProbabilityContinuation {
        size_t next1 = RnaSequence::lastPos, next2 = RnaSequence::lastPos;
        bool extraPair = false;
    };
    Matrix<ProbabilityContinuation> probabilityContinuation;
    Matrix<Z_type> probabilityFlow;
    Matrix<Z_type> probabilityMass;
    Z_type probabilityDenominator = 0;
 
protected:
 
    void predictRegionHeuristic(const IndexRange & r1,const IndexRange & r2);
 
    void recordProbabilityCandidate(size_t i1,size_t j1,size_t i2,size_t j2,
            Z_type hybrid,const ProbabilityContinuation & continuation);
 
    void commitProbabilityRegion();
 
    virtual
    void
    fillHybridZ();
 
    // Restricted output uses PredictorMfe's best finalized site per left boundary.
    // Intermediate hybridZ cells do not contain complete site ensemble energies.
 
};
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFEENS2DHEURISTIC_H_ */