/usr/include/shogun/kernel/SpectrumRBFKernel.h is in libshogun-dev 1.1.0-4ubuntu2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 | /*
* 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 _SPECTRUMRBFKERNEL_H___
#define _SPECTRUMRBFKERNEL_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 <vector> // profile
#include <string> // profile
namespace shogun
{
/** @brief spectrum rbf kernel */
class CSpectrumRBFKernel: public CStringKernel<char>
{
public:
/** default constructor */
CSpectrumRBFKernel();
/** constructor
* @param size
* @param AA_matrix
* @param degree
* @param width
*/
CSpectrumRBFKernel(int32_t size, float64_t* AA_matrix, int32_t degree, float64_t width);
/** constructor
*
* @param l features of left-hand side
* @param r features of right-hand side
* @param size
* @param AA_matrix
* @param degree
* @param width
*/
CSpectrumRBFKernel(
CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t size, float64_t* AA_matrix, int32_t degree, float64_t width);
/** destructor */
virtual ~CSpectrumRBFKernel();
/** initialize kernel
*
* @param l features of left-hand side
* @param r features of right-hand side
* @return if initializing was successful
*/
virtual bool init(CFeatures* l, CFeatures* r);
/** clean up kernel */
virtual void cleanup();
/** get degree
*
* @return degree of the kernel
*/
int32_t get_degree() const
{
return degree;
}
/** return what type of kernel we are
*
* @return kernel type
*/
virtual EKernelType get_kernel_type() { return K_SPECTRUMRBF; }
/** return the kernel's name
*
* @return name
*/
virtual const char* get_name() const { return "SpectrumRBFKernel"; }
/** set degree
*
* @param deg new degree
* @return if setting was successful
*/
inline bool set_degree(int32_t deg) { degree=deg; return true; }
/** get degree
*
* @return degree
*/
inline int32_t get_degree() { return degree; }
/** set AA matrix
* @param AA_matrix_
*/
bool set_AA_matrix(float64_t* AA_matrix_);
protected:
/** AA helper
* @param path
* @param degree
* @param joint_seq
* @param index
*/
float64_t AA_helper(const char* path, const int degree, const char* joint_seq, unsigned int index);
/** read profiles and sequences */
void read_profiles_and_sequences();
/** compute kernel function for features a and b
* idx_{a,b} denote the index of the feature vectors
* in the corresponding feature object
*
* @param idx_a index a
* @param idx_b index b
* @return computed kernel function at indices a,b
*/
float64_t compute(int32_t idx_a, int32_t idx_b);
/** remove lhs from kernel */
virtual void remove_lhs();
/** register the parameters */
virtual void register_param();
/** register the alphabet */
void register_alphabet();
protected:
/** alphabet of features */
CAlphabet* alphabet;
/** degree */
int32_t degree;
/** maximum mismatch */
int32_t max_mismatch;
/** 128x128 scalar product matrix */
float64_t* AA_matrix ;
/** length of the AA_matrix -- for registration*/
int32_t AA_matrix_length;
/** width of Gaussian*/
float64_t width;
//int32_t* aa_to_index; // profile
//double background[20]; // profile
/** profiles */
std::vector< std::vector<float64_t> > profiles; //profile
/** sequence labels */
std::vector<std::string> sequence_labels; // profile
/** sequences */
SGString<char>* sequences; // profile
/** string features */
CStringFeatures<char>* string_features;
/** nof sequences */
int32_t nof_sequences;
/** max sequence length */
int32_t max_sequence_length;
/** if kernel is initialized */
bool initialized;
/** kernel matrix */
CArray2<float64_t> kernel_matrix;
/** target letter 0 */
int32_t target_letter_0;
private:
void init();
};
}
#endif /* _SPECTRUMMISMATCHRBFKERNEL_H__ */
|