PredictorSeedExtensionKinetic.h

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#ifndef INTARNA_PREDICTORSEEDEXTENSIONKINETIC_H_
#define INTARNA_PREDICTORSEEDEXTENSIONKINETIC_H_
 
#include "IntaRNA/PredictorMfe.h"
#include "IntaRNA/SeedHandlerIdxOffset.h"
 
#include <array>
#include <cstdint>
#include <map>
#include <vector>
 
namespace IntaRNA {
 
class PredictorSeedExtensionKinetic : public PredictorMfe {
public:
 
    PredictorSeedExtensionKinetic(const InteractionEnergy & energy,
            OutputHandler & output, PredictionTracker * predTracker,
            SeedHandler * seedHandler, const char score = 'A');
 
    virtual ~PredictorSeedExtensionKinetic();
 
    void predict(const IndexRange & r1 = IndexRange(0, RnaSequence::lastPos),
            const IndexRange & r2 = IndexRange(0, RnaSequence::lastPos)) override;
 
protected:
    void traceBack(Interaction & interaction) override;
 
    void getNextBest(Interaction & interaction) override;
 
private:
    using Boundary = std::array<size_t, 4>;
    using InteractionCache = std::map<Boundary, Interaction>;
 
    struct Candidate {
        Boundary bounds = {};
        size_t close1 = 0;
        size_t close2 = 0;
        size_t s1 = 0;
        size_t s2 = 0;
        bool left = true;
        bool macro = false;
        bool topologyKnown = false;
        bool topologyAllowed = false;
        bool active = false;
        bool localKnown = false;
        E_type local = E_INF;
        E_type hybrid = E_INF;
        E_type total = E_INF;
        std::int64_t delta = 0;
    };
 
    struct SideCandidates {
        std::vector<Candidate> moves;
        std::vector<signed char> complementary;
        size_t columns = 0;
    };
 
    SeedHandlerIdxOffset seedHandler;
    const char score;
    InteractionCache interactions;
    Boundary getBoundary(const Interaction & interaction) const;
 
    void extendSeed(Interaction & interaction, E_type hybrid,
            size_t last1, size_t last2);
 
    void buildCandidates(SideCandidates & side, const Boundary & bounds,
            bool left, size_t last1, size_t last2) const;
 
    const Candidate * updateCandidates(SideCandidates & side, const Boundary & bounds,
            E_type hybrid, E_type total) const;
 
    bool isBetter(const Candidate & candidate, const Candidate & best) const;
 
    void retain(const Interaction & interaction);
};
 
} // namespace IntaRNA
 
#endif /* INTARNA_PREDICTORSEEDEXTENSIONKINETIC_H_ */