HelixHandler.h

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#ifndef INTARNA_HELIXHANDLER_H_
#define INTARNA_HELIXHANDLER_H_
 
#include "IntaRNA/InteractionEnergy.h"
#include "IntaRNA/HelixConstraint.h"
#include "IntaRNA/SeedHandler.h"
 
namespace IntaRNA {
 
class HelixHandler
{
 
public:
 
    HelixHandler();
 
    static
    HelixHandler* getHelixHandler( const InteractionEnergy & energy
            , const HelixConstraint & helixConstraint
            , SeedHandler * const seedHandler = NULL
    );
 
    virtual ~HelixHandler();
 
    virtual
    const HelixConstraint&
    getConstraint() const = 0;
 
    virtual
    const InteractionEnergy&
    getInteractionEnergy() const = 0;
 
 
    virtual
    size_t
    fillHelix(const size_t i1, const size_t j1, const size_t i2, const size_t j2) = 0;
 
    virtual
    size_t
    fillHelixSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2) = 0;
 
    virtual
    void
    traceBackHelix( Interaction & interaction, const size_t i1, const size_t i2) = 0;
 
    virtual
    void
    traceBackHelixSeed( Interaction & interaction, const size_t i1, const size_t i2) = 0;
 
    virtual
    E_type
    getHelixE( const size_t i1, const size_t i2 ) const = 0;
 
    virtual
    E_type
    getHelixSeedE( const size_t i1, const size_t i2 ) const = 0;
 
    virtual
    size_t
    getHelixLength1( const size_t i1, const size_t i2 ) const = 0;
 
    virtual
    size_t
    getHelixLength2( const size_t i1, const size_t i2 ) const = 0;
 
    virtual
    size_t
    getHelixSeedLength1( const size_t i1, const size_t i2 ) const = 0;
 
    virtual
    size_t
    getHelixSeedLength2( const size_t i1, const size_t i2 ) const = 0;
 
    virtual
    void
    setSeedHandler( SeedHandler & seedHandler ) = 0;
 
};
 
 
 
 
inline
HelixHandler::HelixHandler()
{
}
 
 
inline
HelixHandler::~HelixHandler()
{
}
 
 
} // namespace
#endif //INTARNA_HELIXHANDLER_H_