RegulatoryModulesStringKernel.h

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/*
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * Written (W) 2009 Sebastian J. Schultheiss and Soeren Sonnenburg
 * Copyright (C) 2009 Max-Planck-Society
 */

#ifndef _REGULATORYMODULESSTRINGKERNEL_H___
#define _REGULATORYMODULESSTRINGKERNEL_H___

#include <shogun/lib/common.h>
#include <shogun/kernel/string/StringKernel.h>
#include <shogun/features/DenseFeatures.h>

namespace shogun
{
class CRegulatoryModulesStringKernel: public CStringKernel<char>
{
    public:
        CRegulatoryModulesStringKernel();

        CRegulatoryModulesStringKernel(int32_t size, float64_t width, int32_t degree, int32_t shift, int32_t window);

        CRegulatoryModulesStringKernel(CStringFeatures<char>* lstr, CStringFeatures<char>* rstr,
            CDenseFeatures<uint16_t>* lpos, CDenseFeatures<uint16_t>* rpos,
            float64_t width, int32_t degree, int32_t shift, int32_t window, int32_t size=10);

        virtual ~CRegulatoryModulesStringKernel();

        virtual bool init(CFeatures* l, CFeatures* r);

        virtual EKernelType get_kernel_type() { return K_REGULATORYMODULES; }

        inline virtual const char* get_name() const { return "RegulatoryModulesStringKernel"; }

        void set_motif_positions(
            CDenseFeatures<uint16_t>* positions_lhs, CDenseFeatures<uint16_t>* positions_rhs);
        /* register the parameters
         */
        virtual void register_params();

    protected:
        virtual float64_t compute(int32_t idx_a, int32_t idx_b);

        float64_t compute_wds(char* avec, char* bvec, int32_t len);


        void set_wd_weights();

    protected:
        float64_t width;

        int32_t degree;
        int32_t shift;

        int32_t window;

        CDenseFeatures<uint16_t>* motif_positions_lhs;

        CDenseFeatures<uint16_t>* motif_positions_rhs;

        int32_t alen;
        int32_t blen;

        float64_t* position_weights;

        float64_t* weights;
};
}
#endif /* _REGULATORYMODULESSTRINGKERNEL_H__ */