/usr/include/shogun/kernel/LocalAlignmentStringKernel.h is in libshogun-dev 1.1.0-4ubuntu2.
This file is owned by root:root, with mode 0o644.
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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 | /*
* 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
* Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
*/
#ifndef _LOCALALIGNMENTSTRINGKERNEL_H___
#define _LOCALALIGNMENTSTRINGKERNEL_H___
#include <shogun/lib/common.h>
#include <shogun/kernel/StringKernel.h>
namespace shogun
{
#define LOGSUM_TBL 10000 /* span of the logsum table */
/** @brief The LocalAlignmentString kernel compares two sequences through all
* possible local alignments between the two sequences.
*
* The implementation is taken from http://www.mloss.org/software/view/40/ and
* only adjusted to work with shogun.
*/
class CLocalAlignmentStringKernel: public CStringKernel<char>
{
public:
/** constructor
* @param size cache size
*/
CLocalAlignmentStringKernel(int32_t size=0);
/** constructor
*
* @param l features of left-hand side
* @param r features of right-hand side
* @param opening gap opening penalty
* @param extension gap extension penalty
*/
CLocalAlignmentStringKernel(
CStringFeatures<char>* l, CStringFeatures<char>* r,
float64_t opening=12, float64_t extension=2);
virtual ~CLocalAlignmentStringKernel();
/** 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();
/** return what type of kernel we are
*
* @return kernel type LOCALALIGNMENT
*/
virtual EKernelType get_kernel_type()
{
return K_LOCALALIGNMENT;
}
/** return the kernel's name
*
* @return name LocalAlignment
*/
virtual const char* get_name() const
{
return "LocalAlignmentStringKernel";
}
protected:
/** 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
*/
virtual float64_t compute(int32_t idx_a, int32_t idx_b);
private:
/** initialize logarithmic sum */
void init_logsum();
/** logarithmic sum
*
* @param p1 parameter1
* @param p2 parameter2
* @return logarithmic sum as integer
*/
int32_t LogSum(int32_t p1, int32_t p2);
/** logarithmic sum 2
*
* @param p1 parameter 1
* @param p2 parameter 2
* @return logarithmic sum as floating point
*/
float32_t LogSum2(float32_t p1, float32_t p2);
/** LAkernel compute
*
* @param aaX aaX
* @param aaY aaY
* @param nX nX
* @param nY nY
* @return computed value
*/
float64_t LAkernelcompute(
int32_t* aaX, int32_t* aaY, int32_t nX, int32_t nY);
/** Initialize all static variables. This function should be called once
* before computing the first pair HMM score */
void init_static_variables();
void init();
protected:
/** if kernel is initialized */
bool initialized;
/** indicates whether a char is an amino-acid */
int32_t *isAA;
/** correspondance between amino-acid letter and index */
int32_t *aaIndex;
/** gap penalty opening */
int32_t m_opening;
/** gap penalty extension */
int32_t m_extension;
/** static logsum lookup */
static int32_t logsum_lookup[LOGSUM_TBL];
/** static blosum */
static const int32_t blosum[];
/** scaled blosum */
int32_t* scaled_blosum;
/** List of amino acids */
static const char* aaList;
};
}
#endif /* _LOCALALIGNMENTSTRINGKERNEL_H__ */
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