/usr/include/shogun/kernel/RegulatoryModulesStringKernel.h is in libshogun-dev 1.1.0-4ubuntu2.
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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 | /*
* 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) 2009 Sebastian J. Schultheiss and Soeren Sonnenburg
* Copyright (C) 2009 Max-Planck-Society
*/
#ifndef _REGULATORYMODULESSTRINGKERNEL_H___
#define _REGULATORYMODULESSTRINGKERNEL_H___
#include <shogun/lib/common.h>
#include <shogun/kernel/StringKernel.h>
#include <shogun/features/SimpleFeatures.h>
namespace shogun
{
/** @brief The Regulaty Modules kernel, based on the WD kernel,
* as published in Schultheiss et al., Bioinformatics (2009)
* on regulatory sequences.
*
*/
class CRegulatoryModulesStringKernel: public CStringKernel<char>
{
public:
/** default constructor */
CRegulatoryModulesStringKernel();
/** constructor
*
* @param size cache size
* @param width width of gaussian kernel
* @param degree degree of wds kernel
* @param shift shift of wds kernel
* @param window size of window around motifs to compute wds kernels on
*/
CRegulatoryModulesStringKernel(int32_t size, float64_t width, int32_t degree, int32_t shift, int32_t window);
/** constructor
*
* @param lstr string features of left-hand side
* @param rstr string features of right-hand side
* @param lpos motif positions on lhs
* @param rpos motif positions on rhs
* @param width width of gaussian kernel
* @param degree degree of wds kernel
* @param shift shift of wds kernel
* @param window size of window around motifs to compute wds kernels on
* @param size cache size
*/
CRegulatoryModulesStringKernel(CStringFeatures<char>* lstr, CStringFeatures<char>* rstr,
CSimpleFeatures<uint16_t>* lpos, CSimpleFeatures<uint16_t>* rpos,
float64_t width, int32_t degree, int32_t shift, int32_t window, int32_t size=10);
/** default destructor */
virtual ~CRegulatoryModulesStringKernel();
/** 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);
/** return what type of kernel we are
*
* @return kernel type
*/
virtual EKernelType get_kernel_type() { return K_REGULATORYMODULES; }
/** return the kernel's name
*
* @return name Regulatory Modules
*/
inline virtual const char* get_name() const { return "RegulatoryModulesStringKernel"; }
/** set motif positions
*
* @param positions_lhs motif positions on lhs
* @param positions_rhs motif positions on rhs
*/
void set_motif_positions(
CSimpleFeatures<uint16_t>* positions_lhs, CSimpleFeatures<uint16_t>* positions_rhs);
/* register the parameters
*/
virtual void register_params();
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);
/** compute WDS kernel for features a and b
*
* @param avec vector a
* @param bvec vector b
* @param len length of string
* @return computed kernel function
*/
float64_t compute_wds(char* avec, char* bvec, int32_t len);
/** set standard weighted degree kernel weighting */
void set_wd_weights();
protected:
/** width of Gaussian kernel part */
float64_t width;
/** degree of Weighted Degree kernel part */
int32_t degree;
/** shift of Weighted Degree with Shifts kernel part */
int32_t shift;
/** size of window around motifs */
int32_t window;
/** Matrix of motif positions from sequences left-hand side */
CSimpleFeatures<uint16_t>* motif_positions_lhs;
/** Matrix of motif positions from sequences right-hand side */
CSimpleFeatures<uint16_t>* motif_positions_rhs;
/** the length of matrix of motif positions -- for serialization purposes*/
int32_t alen;
/** the length of matrix of motif positions -- for serialization purposes*/
int32_t blen;
/** scaling weights in window */
float64_t* position_weights;
/** weights of WD kernel */
float64_t* weights;
};
}
#endif /* _REGULATORYMODULESSTRINGKERNEL_H__ */
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