/usr/include/shogun/kernel/SNPStringKernel.h is in libshogun-dev 1.1.0-4ubuntu2.
This file is owned by root:root, with mode 0o644.
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* 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) 2009-2010 Soeren Sonnenburg
* Copyright (C) 2009-2010 Berlin Institute of Technology
*/
#ifndef _SNPSTRINGKERNEL_H___
#define _SNPSTRINGKERNEL_H___
#include <shogun/lib/common.h>
#include <shogun/kernel/StringKernel.h>
namespace shogun
{
/** @brief The class SNPStringKernel computes a variant of the polynomial
* kernel on strings of same length.
*
* It is computed as FIXME
*
* \f[
* k({\bf x},{\bf x'})= (\sum_{i=0}^{L-1} I(x_i=x'_i)+c)^d
* \f]
*
* where I is the indicator function which evaluates to 1 if its argument is
* true and to 0 otherwise.
*
* Note that additional normalisation is applied, i.e.
* \f[
* k'({\bf x}, {\bf x'})=\frac{k({\bf x}, {\bf x'})}{\sqrt{k({\bf x}, {\bf x})k({\bf x'}, {\bf x'})}}
* \f]
*/
class CSNPStringKernel: public CStringKernel<char>
{
public:
/** default constructor */
CSNPStringKernel();
/** constructor
*
* @param size cache size
* @param degree degree
* @param win_len length of local window
* @param inhomogene whether inhomogeneous poly
*/
CSNPStringKernel(int32_t size, int32_t degree, int32_t win_len, bool inhomogene);
/** constructor
*
* @param l features of left-hand side
* @param r features of right-hand side
* @param degree degree
* @param win_len length of local window
* @param inhomogene whether inhomogeneous poly
*/
CSNPStringKernel(
CStringFeatures<char>* l, CStringFeatures<char>* r,
int32_t degree, int32_t win_len, bool inhomogene);
virtual ~CSNPStringKernel();
/** 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 POLYMATCH
*/
virtual EKernelType get_kernel_type()
{
return K_POLYMATCH;
}
/** set the base string for minor aleles
*
* @param str minor freq. string
*/
void set_minor_base_string(const char* str)
{
m_str_min=strdup(str);
}
/** set the base string for major aleles
*
* @param str major freq. string
*/
void set_major_base_string(const char* str)
{
m_str_maj=strdup(str);
}
/** get the base string for minor aleles
*
* @return minor freq. string
*/
char* get_minor_base_string()
{
return m_str_min;
}
/** get the base string for major aleles
*
* @return major freq. string
*/
char* get_major_base_string()
{
return m_str_maj;
}
/** compute the minor / major alele base strings */
void obtain_base_strings();
/** return the kernel's name
*
* @return name PolyMatchString
*/
virtual const char* get_name() const { return "SNPStringKernel"; }
/* 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);
protected:
/** degree */
int32_t m_degree;
/** window length */
int32_t m_win_len;
/** inhomogeneous poly kernel ? */
bool m_inhomogene;
/** total string length / must match length of min/maj strings and
* string length of each vector */
int32_t m_str_len;
/** allele A */
char* m_str_min;
/** allele B */
char* m_str_maj;
private:
void init();
};
}
#endif /* _SNPSTRINGKERNEL_H___ */
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