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/StringKernel.h>
#include <shogun/features/StringFeatures.h>


#include <shogun/lib/Array.h>
#include <shogun/lib/Array2.h>
#include <string>

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 remove_lhs();
        virtual void register_params();
        void register_alphabet();


    protected:
        CAlphabet* alphabet;
        int32_t degree;
        int32_t max_mismatch;
        float64_t* AA_matrix;
        int32_t AA_matrix_length;
        float64_t width;

        bool initialized;

        CArray2<float64_t> kernel_matrix ;
        int32_t kernel_matrix_length;
        int32_t target_letter_0;
    
    private:
        void init();
};

}

#endif /* _SPECTRUMMISMATCHRBFKERNEL_H__ */