BasePairProbabilities.h

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#ifndef INTARNA_BASEPAIRPROBABILITIES_H_
#define INTARNA_BASEPAIRPROBABILITIES_H_
#include "IntaRNA/general.h"
#include "IntaRNA/IndexRange.h"
#include "IntaRNA/Matrix.h"
#include <utility>
#include <vector>
 
namespace IntaRNA {
class BasePairProbabilities {
public:
    enum class Status { pending, nonempty, empty, failed };
    BasePairProbabilities(size_t targetLength,size_t queryLength,bool collectSeedPairs=false);
    void addRegion(const IndexRange & target,const IndexRange & query,
            Z_type denominator,const Matrix<Z_type> & masses,const Matrix<unsigned char> * seedPairs=nullptr);
    void finalize();
    void fail() noexcept;
    Status status() const;
    Z_type getZ() const;
    const Matrix<Z_type> & rawMasses() const;
    bool collectsSeedPairs() const;
    void markApproximate();
    bool isApproximate() const;
    const Matrix<unsigned char> & seedPairs() const;
    Matrix<Z_type> probabilities() const;
private:
    Status state=Status::pending;
    bool approximate=false;
    Z_type z=0;
    Matrix<Z_type> mass;
    const bool collectSeeds;
    Matrix<unsigned char> seeds;
    std::vector<std::pair<IndexRange,IndexRange>> regions;
};
inline BasePairProbabilities::Status BasePairProbabilities::status() const { return state; }
inline Z_type BasePairProbabilities::getZ() const { return z; }
inline const Matrix<Z_type> & BasePairProbabilities::rawMasses() const { return mass; }
inline bool BasePairProbabilities::collectsSeedPairs() const { return collectSeeds; }
inline bool BasePairProbabilities::isApproximate() const { return approximate; }
inline const Matrix<unsigned char> & BasePairProbabilities::seedPairs() const { return seeds; }
inline void BasePairProbabilities::fail() noexcept { state=Status::failed; }
}
#endif