SeededPartitionFunction.h

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#ifndef INTARNA_SEEDEDPARTITIONFUNCTION_H_
#define INTARNA_SEEDEDPARTITIONFUNCTION_H_
#include "IntaRNA/Interaction.h"
#include "IntaRNA/Matrix.h"
#include "IntaRNA/StackSeedDomain.h"
#include <functional>
 
namespace IntaRNA {
class SeededPartitionFunction {
public:
    using Pair = Interaction::BasePair;
    struct Domain { size_t n,m,span1,span2,loop1,loop2; bool noLP; };
    struct Weights {
        std::function<bool(Pair)> valid;
        std::function<Z_type(Pair)> initiation;
        std::function<Z_type(Pair,Pair)> transition, boundary;
        std::function<void(Pair,Pair,Z_type,Z_type)> complete;
        std::function<Pair(Pair,Pair)> selectRight;
        std::function<void(Pair,Pair,Pair,Z_type)> anchorComplete;
    };
    struct Result { Z_type z=0; Matrix<Z_type> mass; };
    static Result compute(const Domain & domain, const StackSeedDomain & seeds,
            const Weights & weights, bool pairs);
};
}
#endif