SHOGUN v0.9.0
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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 _SPECTRUMRBFKERNEL_H___ 00013 #define _SPECTRUMRBFKERNEL_H___ 00014 00015 #include "lib/common.h" 00016 #include "lib/Trie.h" 00017 #include "kernel/StringKernel.h" 00018 #include "features/StringFeatures.h" 00019 00020 00021 #include "lib/Array.h" 00022 #include "lib/Array2.h" 00023 00024 #include <vector> // profile 00025 #include <string> // profile 00026 00027 namespace shogun 00028 { 00029 00030 class CSpectrumRBFKernel: public CStringKernel<char> 00031 { 00032 public: 00034 CSpectrumRBFKernel(void); 00035 00041 CSpectrumRBFKernel(int32_t size, float64_t* AA_matrix, int32_t degree, float64_t width); 00042 00049 CSpectrumRBFKernel( 00050 CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t size, float64_t* AA_matrix, int32_t degree, float64_t width); 00051 00052 virtual ~CSpectrumRBFKernel(); 00053 00060 virtual bool init(CFeatures* l, CFeatures* r); 00061 00063 virtual void cleanup(); 00064 00069 int32_t get_degree() const 00070 { 00071 return degree; 00072 } 00073 00078 virtual EKernelType get_kernel_type() { return K_SPECTRUMMISMATCHRBF; } 00079 00084 virtual const char* get_name() const { return "SpectrumMismatchRBF"; } 00085 00091 inline bool set_degree(int32_t deg) { degree=deg; return true; } 00092 00097 inline int32_t get_degree() { return degree; } 00098 00099 00100 bool set_AA_matrix(float64_t* AA_matrix_); 00101 00102 protected: 00103 00104 float64_t AA_helper(const char* path, const int degree, const char* joint_seq, unsigned int index); 00105 00106 void read_profiles_and_sequences(); // profile 00107 00108 00117 float64_t compute(int32_t idx_a, int32_t idx_b); 00118 00120 virtual void remove_lhs(); 00121 00122 00123 protected: 00125 CAlphabet* alphabet; 00127 int32_t degree; 00130 float64_t* AA_matrix ; 00132 float64_t width; 00133 00134 //int32_t* aa_to_index; // profile 00135 00136 //double background[20]; // profile 00137 std::vector< std::vector<float64_t> > profiles; //profile 00138 std::vector<std::string> sequence_labels; // profile 00139 TString<char>* sequences; // profile 00140 CStringFeatures<char>* string_features; 00141 int32_t nof_sequences; 00142 int32_t max_sequence_length; 00143 00145 bool initialized; 00146 00147 int32_t max_mismatch; 00148 00149 CArray2<float64_t> kernel_matrix ; 00150 int32_t target_letter_0 ; 00151 }; 00152 00153 } 00154 00155 00156 00157 #endif /* _SPECTRUMMISMATCHRBFKERNEL_H__ */