12 #ifndef _SPECTRUMMISMATCHRBFKERNEL_H___ 13 #define _SPECTRUMMISMATCHRBFKERNEL_H___ 15 #include <shogun/lib/config.h> 29 #ifndef DOXYGEN_SHOULD_SKIP_THIS 31 struct joint_list_struct
34 unsigned int ex_index;
38 unsigned int mismatch;
108 return "SpectrumMismatchRBFKernel";
177 std::vector<unsigned int> joint_index,
178 std::vector<unsigned int> joint_mismatch, std::string path,
179 unsigned int d,
const int & alen);
189 std::vector<struct joint_list_struct> & joint_list,
190 std::string path,
unsigned int d);
bool set_degree(int32_t deg)
float64_t AA_helper(std::string &path, const char *joint_seq, unsigned int index)
spectrum mismatch rbf kernel
bool set_max_mismatch(int32_t max)
void compute_helper_all(const char *joint_seq, std::vector< struct joint_list_struct > &joint_list, std::string path, unsigned int d)
virtual void register_params()
float64_t compute_helper(const char *joint_seq, std::vector< unsigned int > joint_index, std::vector< unsigned int > joint_mismatch, std::string path, unsigned int d, const int &alen)
The class Alphabet implements an alphabet and alphabet utility functions.
CDynamicArray< float64_t > * kernel_matrix
virtual ~CSpectrumMismatchRBFKernel()
virtual bool init(CFeatures *l, CFeatures *r)
int32_t get_degree() const
int32_t get_max_mismatch() const
bool set_AA_matrix(float64_t *AA_matrix_=NULL, int32_t nr=128, int32_t nc=128)
float64_t compute(int32_t idx_a, int32_t idx_b)
SGMatrix< float64_t > AA_matrix
virtual const char * get_name() const
virtual EKernelType get_kernel_type()
all of classes and functions are contained in the shogun namespace
The class Features is the base class of all feature objects.
CSpectrumMismatchRBFKernel()
int32_t kernel_matrix_length
T max(const Container< T > &a)
Template class StringKernel, is the base class of all String Kernels.