SpectrumMismatchRBFKernel.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
 * Written (W) 1999-2008 Gunnar Raetsch
 * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
 */

#ifndef _SPECTRUMMISMATCHRBFKERNEL_H___
#define _SPECTRUMMISMATCHRBFKERNEL_H___

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

#include <shogun/lib/DynamicArray.h>
#include <string>
#include <vector>

namespace shogun
{

#ifndef DOXYGEN_SHOULD_SKIP_THIS

struct joint_list_struct
{
    unsigned int ex_index;
    unsigned int index;
    unsigned int mismatch;
};
#endif

class CSpectrumMismatchRBFKernel: public CStringKernel<char>
{
public:
    CSpectrumMismatchRBFKernel();

    CSpectrumMismatchRBFKernel(int32_t size, float64_t* AA_matrix_, int32_t nr_,
            int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width);

    CSpectrumMismatchRBFKernel(CStringFeatures<char>* l,
            CStringFeatures<char>* r, int32_t size, float64_t* AA_matrix_,
            int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch,
            float64_t width);

    virtual ~CSpectrumMismatchRBFKernel();

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

    virtual void cleanup();

    virtual EKernelType get_kernel_type()
    {
        return K_SPECTRUMMISMATCHRBF;
    }

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

    bool set_max_mismatch(int32_t max);

    inline int32_t get_max_mismatch() const
    {
        return max_mismatch;
    }

    inline bool set_degree(int32_t deg)
    {
        degree=deg;
        return true;
    }

    inline int32_t get_degree() const
    {
        return degree;
    }

    bool set_AA_matrix(float64_t* AA_matrix_=NULL, int32_t nr=128, int32_t nc=
            128);

protected:

    float64_t AA_helper(std::string &path, const char* joint_seq,
            unsigned int index);

    float64_t compute_helper(const char* joint_seq,
            std::vector<unsigned int> joint_index,
            std::vector<unsigned int> joint_mismatch, std::string path,
            unsigned int d, const int & alen);

    void compute_helper_all(const char* joint_seq,
            std::vector<struct joint_list_struct> & joint_list,
            std::string path, unsigned int d);

    void compute_all();

    float64_t compute(int32_t idx_a, int32_t idx_b);

    virtual void register_params();
    void register_alphabet();

protected:
    CAlphabet* alphabet;
    int32_t degree;
    int32_t max_mismatch;
    SGMatrix<float64_t> AA_matrix;
    float64_t width;

    bool initialized;

    CDynamicArray<float64_t>* kernel_matrix; // 2d
    int32_t kernel_matrix_length;
    int32_t target_letter_0;

private:
    void init();
};

}

#endif /* _SPECTRUMMISMATCHRBFKERNEL_H__ */