PredictorMfe2dSeedExtensionRIblast.h

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#ifndef INTARNA_PREDICTORMFE2DSEEDEXTENSIONRIBLAST_H_
#define INTARNA_PREDICTORMFE2DSEEDEXTENSIONRIBLAST_H_
 
#include "IntaRNA/PredictorMfe2d.h"
#include "IntaRNA/SeedHandlerIdxOffset.h"
 
namespace IntaRNA {
 
class PredictorMfe2dSeedExtensionRIblast: public PredictorMfe2d {
 
protected:
 
    typedef PredictorMfe2d::E2dMatrix E2dMatrix;
 
public:
 
    struct ExtendedSeed {
        size_t i1;
        size_t j1;
        size_t i2;
        size_t j2;
        E_type energy;
    };
 
    const int parallelDropOutLength = 5;
    const int thoroughDropOutLength = 16;
 
    PredictorMfe2dSeedExtensionRIblast(
            const InteractionEnergy & energy
            , OutputHandler & output
            , PredictionTracker * predTracker
            , SeedHandler * seedHandler );
 
 
    virtual ~PredictorMfe2dSeedExtensionRIblast();
 
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) );
 
 
protected:
 
 
    using PredictorMfe2d::energy;
 
    using PredictorMfe2d::output;
 
    SeedHandlerIdxOffset seedHandler;
 
    E2dMatrix hybridE_left;
 
    E2dMatrix hybridE_right;
 
protected:
 
    virtual
    void
    parallelExtension( ExtendedSeed & seed, const size_t max_extension1, size_t max_extension2 );
 
    void
    fillHybridE_left( const size_t j1, const size_t j2 );
 
    void
    fillHybridE_right( const size_t i1, const size_t i2 );
 
    virtual
    void
    traceBack( Interaction & interaction );
 
    void
    printMatrix( const E2dMatrix & matrix );
 
};
 
 
inline
void
PredictorMfe2dSeedExtensionRIblast::
printMatrix( const E2dMatrix & matrix )
{
    for (int i = 0; i < matrix.size1(); i++) {
        std::cout << "| ";
        for (int j = 0; j < matrix.size2(); j++) {
            std::cout << matrix(i, j) << " | ";
        }
        std::cout << std::endl;
    }
}
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFE2DSEEDEXTENSIONRIBLAST_H_ */