LocalAlignmentStringKernel.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) 1999-2009 Soeren Sonnenburg
 * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
 */

#ifndef _LOCALALIGNMENTSTRINGKERNEL_H___
#define _LOCALALIGNMENTSTRINGKERNEL_H___

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

namespace shogun
{
#define LOGSUM_TBL 10000      /* span of the logsum table */

class CLocalAlignmentStringKernel: public CStringKernel<char>
{
    public:
        CLocalAlignmentStringKernel(int32_t size=0);

        CLocalAlignmentStringKernel(
            CStringFeatures<char>* l, CStringFeatures<char>* r,
            float64_t opening=12, float64_t extension=2);

        virtual ~CLocalAlignmentStringKernel();

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

        virtual void cleanup();

        virtual EKernelType get_kernel_type()
        {
            return K_LOCALALIGNMENT;
        }

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

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


    private:
        void init_logsum();

        int32_t LogSum(int32_t p1, int32_t p2);

        float32_t LogSum2(float32_t p1, float32_t p2);

        float64_t LAkernelcompute(
            int32_t* aaX, int32_t* aaY, int32_t nX, int32_t nY);

        void init_static_variables();

        void init();

    protected:
        bool initialized;

        int32_t *isAA;
        int32_t *aaIndex;

        int32_t m_opening;
        int32_t m_extension;

        static int32_t logsum_lookup[LOGSUM_TBL];
        static const int32_t blosum[];
        int32_t* scaled_blosum;
        static const char* aaList;
};
}
#endif /* _LOCALALIGNMENTSTRINGKERNEL_H__ */