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SpectrumMismatchRBFKernel.h
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00001 /*
00002  * This program is free software; you can redistribute it and/or modify
00003  * it under the terms of the GNU General Public License as published by
00004  * the Free Software Foundation; either version 3 of the License, or
00005  * (at your option) any later version.
00006  *
00007  * Written (W) 1999-2009 Soeren Sonnenburg
00008  * Written (W) 1999-2008 Gunnar Raetsch
00009  * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
00010  */
00011 
00012 #ifndef _SPECTRUMMISMATCHRBFKERNEL_H___
00013 #define _SPECTRUMMISMATCHRBFKERNEL_H___
00014 
00015 #include <shogun/lib/common.h>
00016 #include <shogun/lib/Trie.h>
00017 #include <shogun/kernel/string/StringKernel.h>
00018 #include <shogun/features/StringFeatures.h>
00019 
00020 #include <shogun/lib/DynamicArray.h>
00021 #include <string>
00022 #include <vector>
00023 
00024 namespace shogun
00025 {
00026 
00027 #ifndef DOXYGEN_SHOULD_SKIP_THIS
00028 
00029 struct joint_list_struct
00030 {
00032     unsigned int ex_index;
00034     unsigned int index;
00036     unsigned int mismatch;
00037 };
00038 #endif
00039 
00041 class CSpectrumMismatchRBFKernel: public CStringKernel<char>
00042 {
00043 public:
00045     CSpectrumMismatchRBFKernel();
00046 
00057     CSpectrumMismatchRBFKernel(int32_t size, float64_t* AA_matrix_, int32_t nr_,
00058             int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width);
00059 
00072     CSpectrumMismatchRBFKernel(CStringFeatures<char>* l,
00073             CStringFeatures<char>* r, int32_t size, float64_t* AA_matrix_,
00074             int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch,
00075             float64_t width);
00076 
00078     virtual ~CSpectrumMismatchRBFKernel();
00079 
00086     virtual bool init(CFeatures* l, CFeatures* r);
00087 
00089     virtual void cleanup();
00090 
00095     virtual EKernelType get_kernel_type()
00096     {
00097         return K_SPECTRUMMISMATCHRBF;
00098     }
00099 
00104     virtual const char* get_name() const
00105     {
00106         return "SpectrumMismatchRBFKernel";
00107     }
00108 
00114     bool set_max_mismatch(int32_t max);
00115 
00120     inline int32_t get_max_mismatch() const
00121     {
00122         return max_mismatch;
00123     }
00124 
00130     inline bool set_degree(int32_t deg)
00131     {
00132         degree=deg;
00133         return true;
00134     }
00135 
00140     inline int32_t get_degree() const
00141     {
00142         return degree;
00143     }
00144 
00151     bool set_AA_matrix(float64_t* AA_matrix_=NULL, int32_t nr=128, int32_t nc=
00152             128);
00153 
00154 protected:
00155 
00162     float64_t AA_helper(std::string &path, const char* joint_seq,
00163             unsigned int index);
00164 
00174     float64_t compute_helper(const char* joint_seq,
00175             std::vector<unsigned int> joint_index,
00176             std::vector<unsigned int> joint_mismatch, std::string path,
00177             unsigned int d, const int & alen);
00178 
00186     void compute_helper_all(const char* joint_seq,
00187             std::vector<struct joint_list_struct> & joint_list,
00188             std::string path, unsigned int d);
00189 
00191     void compute_all();
00192 
00201     float64_t compute(int32_t idx_a, int32_t idx_b);
00202 
00205     virtual void register_params();
00208     void register_alphabet();
00209 
00210 protected:
00212     CAlphabet* alphabet;
00214     int32_t degree;
00216     int32_t max_mismatch;
00218     SGMatrix<float64_t> AA_matrix;
00220     float64_t width;
00221 
00223     bool initialized;
00224 
00226     CDynamicArray<float64_t>* kernel_matrix; // 2d
00228     int32_t kernel_matrix_length;
00230     int32_t target_letter_0;
00231 
00232 private:
00233     void init();
00234 };
00235 
00236 }
00237 
00238 #endif /* _SPECTRUMMISMATCHRBFKERNEL_H__ */
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