SeedHandlerExplicit.h

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#ifndef INTARNA_SEEDHANDLEREXPLICIT_H_
#define INTARNA_SEEDHANDLEREXPLICIT_H_
 
 
#include "IntaRNA/SeedHandler.h"
 
#include <boost/unordered_map.hpp>
 
namespace IntaRNA
{
 
class SeedHandlerExplicit : public SeedHandler
{
public:
 
    SeedHandlerExplicit(
            const InteractionEnergy & energy
            , const SeedConstraint & seedConstraint
            );
 
    virtual ~SeedHandlerExplicit();
 
 
    virtual
    size_t
    fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2);
 
    virtual
    void
    traceBackSeed( Interaction & interaction, const size_t i1, const size_t i2) const;
 
 
    virtual
    E_type
    getSeedE( const size_t i1, const size_t i2 ) const;
 
    virtual
    bool
    isSeedBound( const size_t i1, const size_t i2 ) const;
 
    virtual
    size_t
    getSeedLength1( const size_t i1, const size_t i2 ) const;
 
    virtual
    size_t
    getSeedLength2( const size_t i1, const size_t i2 ) const;
 
 
 
    static
    std::string
    checkSeedEncoding( const std::string & seed );
 
    static
    size_t
    getSeedMinBP( const std::string & seedEncoding );
 
    virtual
    bool
    updateToNextSeed( size_t & i1, size_t & i2
            , const size_t i1min = 0, const size_t i1max = RnaSequence::lastPos
            , const size_t i2min = 0, const size_t i2max = RnaSequence::lastPos
            ) const;
 
public:
 
    class SeedData {
    public:
 
        SeedData();
 
        SeedData( const std::string & seedEncoding, const InteractionEnergy & energyFunction );
 
        size_t start1;
        size_t start2;
        std::string dotBar1;
        std::string dotBar2;
        // flag about bp complementarity
        bool allBpCompl;
        E_type energy;
 
        bool
        isValid() const;
 
    };
 
protected:
 
    boost::unordered_map< Interaction::BasePair, SeedData, Interaction::BasePair::Hash > seedForLeftEnd;
 
};
 
} /* namespace IntaRNA */
 
#endif /* INTARNA_SEEDHANDLEREXPLICIT_H_ */