SNPStringKernel.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) 2009-2010 Soeren Sonnenburg
 * Copyright (C) 2009-2010 Berlin Institute of Technology
 */

#ifndef _SNPSTRINGKERNEL_H___
#define _SNPSTRINGKERNEL_H___

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

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

        CSNPStringKernel(int32_t size, int32_t degree, int32_t win_len, bool inhomogene);

        CSNPStringKernel(
            CStringFeatures<char>* l, CStringFeatures<char>* r,
            int32_t degree, int32_t win_len, bool inhomogene);

        virtual ~CSNPStringKernel();

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

        virtual void cleanup();

        virtual EKernelType get_kernel_type()
        {
            return K_POLYMATCH;
        }

        void set_minor_base_string(const char* str)
        {
            m_str_min=strdup(str);
        }

        void set_major_base_string(const char* str)
        {
            m_str_maj=strdup(str);
        }

        char* get_minor_base_string()
        {
            return m_str_min;
        }

        char* get_major_base_string()
        {
            return m_str_maj;
        }

        void obtain_base_strings();

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

        /* register the parameters
         */
        virtual void register_params();

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

    protected:
        int32_t m_degree;
        int32_t m_win_len;

        bool m_inhomogene;

        int32_t m_str_len;

        char* m_str_min;
        char* m_str_maj;

    private:
        void init();
};
}
#endif /* _SNPSTRINGKERNEL_H___ */