src/LocARNA/confusion_matrix.hh

#ifndef LOCARNA_CONFUSION_MATRIX
#define LOCARNA_CONFUSION_MATRIX

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <cstddef>
#include <cassert>
#include <string>

#include "base_pair_filter.hh"

namespace LocARNA {
    class RnaStructure;

    class ConfusionMatrix {
    public:
        ConfusionMatrix(const std::string &ref,
                        const std::string &pred,
                        const bool slide,
                        const bool conflict,
                        const BasePairFilter::Filter &filter =
                            BasePairFilter::BPMinLoopSize(3));

        ConfusionMatrix(const RnaStructure &ref,
                        const RnaStructure &pred,
                        const bool slide,
                        const bool conflict,
                        const BasePairFilter::Filter &filter =
                            BasePairFilter::BPMinLoopSize(3));

        size_t
        tp() const {
            return tp_;
        }

        size_t
        tn() const {
            return tn_;
        }

        size_t
        fp() const {
            return fp_;
        }

        size_t
        fn() const {
            return fn_;
        }

        double
        ppv() const;

        double
        sens() const;

        double
        spec() const;

        double
        f1_score() const;

        double
        mcc() const;

    protected:
        size_t
        count_common_bps(const RnaStructure &s1, const RnaStructure &s2);

        size_t
        count_tps(const RnaStructure &pred, const RnaStructure &ref);

        size_t
        count_conflicting_base_pairs(const RnaStructure &s1,
                                     const RnaStructure &s2);
        size_t
        count_potential_base_pairs(size_t length);

        size_t
        count_base_pairs(const RnaStructure &s);

    private:
        void
        compute_confusion_matrix(const RnaStructure &ref,
                                 const RnaStructure &pred);

        bool slide_;
        bool conflict_;
        const BasePairFilter::Filter &filter_;

        size_t tp_; 
        size_t tn_; 
        size_t fp_; 
        size_t fn_; 
    };

} // end namespace LocARNA

#endif // LOCARNA_CONFUSION_MATRIX