PredictionTrackerSpotProb.h

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#ifndef INTARNA_PREDICTIONTRACKERSPOTPROB_H_
#define INTARNA_PREDICTIONTRACKERSPOTPROB_H_
 
#include "IntaRNA/PredictionTracker.h"
#include "IntaRNA/InteractionEnergy.h"
 
#include <iostream>
 
#include <boost/algorithm/string.hpp>
 
namespace IntaRNA {
 
class PredictionTrackerSpotProb: public PredictionTracker
{
 
public:
 
    static const std::string str_spot;
    static const boost::regex regexSpotString;
 
public:
 
    PredictionTrackerSpotProb(
                const InteractionEnergy & energy
                , const std::string & spots
                , const std::string & outStreamName
                , const std::string & sep = ";"
            );
 
    PredictionTrackerSpotProb(
                const InteractionEnergy & energy
                , const std::string & spots
                , std::ostream & outStream
                , const std::string & sep = ";"
            );
 
 
    virtual ~PredictionTrackerSpotProb();
 
 
    virtual
    void
    updateOptimumCalled( const size_t i1, const size_t j1
                        , const size_t i2, const size_t j2
                        , const E_type energy
                        );
 
protected:
 
    class Spot {
    public:
        size_t idx1;
        size_t idx2;
        Z_type Z;
 
        /* default construction
         */
        Spot()
         : idx1(std::string::npos), idx2(std::string::npos), Z(0.0)
        {}
 
        /* construction from data
         * @param idx1 index in seq1
         * @param idx2 index in seq2
         */
        Spot(size_t idx1, size_t idx2)
         : idx1(idx1), idx2(idx2), Z(0.0)
        {}
 
    };
 
 
protected:
 
    const InteractionEnergy & energy;
 
    std::ostream * outStream;
 
    const bool deleteOutStream;
 
    std::vector<Spot> spots;
 
    const std::string sep;
 
    Z_type noSpotZ;
 
    Z_type overallZ;
 
protected:
 
 
    Spot fromString( std::string && spotString );
 
};
 
 
} // namespace
 
#endif /* PREDICTIONTRACKERSPOTPROB_H_ */