SHOGUN v0.9.0
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在文件SpectrumMismatchRBFKernel.h第35行定义。
公有成员 | |
CSpectrumMismatchRBFKernel (void) | |
CSpectrumMismatchRBFKernel (int32_t size, float64_t *AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width) | |
CSpectrumMismatchRBFKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t size, float64_t *AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width) | |
virtual | ~CSpectrumMismatchRBFKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual void | cleanup () |
int32_t | get_degree () const |
int32_t | get_max_mismatch () const |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
bool | set_max_mismatch (int32_t max) |
int32_t | get_max_mismatch () |
bool | set_degree (int32_t deg) |
int32_t | get_degree () |
bool | set_AA_matrix (float64_t *AA_matrix_=NULL, int32_t nr=128, int32_t nc=128) |
保护成员 | |
float64_t | AA_helper (std::string &path, const char *joint_seq, unsigned int index) |
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) |
void | compute_helper_all (const char *joint_seq, std::vector< struct joint_list_struct > &joint_list, std::string path, unsigned int d) |
void | compute_all () |
float64_t | compute (int32_t idx_a, int32_t idx_b) |
virtual void | remove_lhs () |
保护属性 | |
CAlphabet * | alphabet |
int32_t | degree |
int32_t | max_mismatch |
float64_t * | AA_matrix |
float64_t | width |
bool | initialized |
CArray2< float64_t > | kernel_matrix |
int32_t | target_letter_0 |
CSpectrumMismatchRBFKernel | ( | void | ) |
default constructor
在文件SpectrumMismatchRBFKernel.cpp第36行定义。
CSpectrumMismatchRBFKernel | ( | int32_t | size, |
float64_t * | AA_matrix_, | ||
int32_t | nr_, | ||
int32_t | nc_, | ||
int32_t | degree, | ||
int32_t | max_mismatch, | ||
float64_t | width | ||
) |
CSpectrumMismatchRBFKernel | ( | CStringFeatures< char > * | l, |
CStringFeatures< char > * | r, | ||
int32_t | size, | ||
float64_t * | AA_matrix_, | ||
int32_t | nr_, | ||
int32_t | nc_, | ||
int32_t | degree, | ||
int32_t | max_mismatch, | ||
float64_t | width | ||
) |
constructor
l | features of left-hand side |
r | features of right-hand side |
degree | degree |
在文件SpectrumMismatchRBFKernel.cpp第66行定义。
~CSpectrumMismatchRBFKernel | ( | ) | [virtual] |
在文件SpectrumMismatchRBFKernel.cpp第77行定义。
float64_t AA_helper | ( | std::string & | path, |
const char * | joint_seq, | ||
unsigned int | index | ||
) | [protected] |
在文件SpectrumMismatchRBFKernel.cpp第127行定义。
void cleanup | ( | ) | [virtual] |
float64_t compute | ( | int32_t | idx_a, |
int32_t | idx_b | ||
) | [protected, virtual] |
compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object
idx_a | index a |
idx_b | index b |
实现了CKernel。
在文件SpectrumMismatchRBFKernel.cpp第366行定义。
void compute_all | ( | ) | [protected] |
在文件SpectrumMismatchRBFKernel.cpp第331行定义。
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 | ||
) | [protected] |
void compute_helper_all | ( | const char * | joint_seq, |
std::vector< struct joint_list_struct > & | joint_list, | ||
std::string | path, | ||
unsigned int | d | ||
) | [protected] |
在文件SpectrumMismatchRBFKernel.cpp第234行定义。
int32_t get_degree | ( | ) |
int32_t get_degree | ( | ) | const |
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
int32_t get_max_mismatch | ( | ) |
int32_t get_max_mismatch | ( | ) | const |
get the number of mismatches that are allowed
在文件SpectrumMismatchRBFKernel.h第83行定义。
virtual const char* get_name | ( | void | ) | const [virtual] |
initialize kernel
l | features of left-hand side |
r | features of right-hand side |
在文件SpectrumMismatchRBFKernel.cpp第90行定义。
void remove_lhs | ( | ) | [protected, virtual] |
bool set_AA_matrix | ( | float64_t * | AA_matrix_ = NULL , |
int32_t | nr = 128 , |
||
int32_t | nc = 128 |
||
) |
在文件SpectrumMismatchRBFKernel.cpp第420行定义。
bool set_degree | ( | int32_t | deg | ) |
bool set_max_mismatch | ( | int32_t | max | ) |
set maximum mismatch
max | new maximum mismatch |
在文件SpectrumMismatchRBFKernel.cpp第437行定义。
128x128 scalar product matrix
在文件SpectrumMismatchRBFKernel.h第166行定义。
alphabet of features
在文件SpectrumMismatchRBFKernel.h第160行定义。
int32_t degree [protected] |
degree
在文件SpectrumMismatchRBFKernel.h第162行定义。
bool initialized [protected] |
if kernel is initialized
在文件SpectrumMismatchRBFKernel.h第171行定义。
CArray2<float64_t> kernel_matrix [protected] |
this *COULD* store the whole kernel matrix usually not applicable / necessary to compute the whole matrix
重载CKernel。
在文件SpectrumMismatchRBFKernel.h第174行定义。
int32_t max_mismatch [protected] |
maximum mismatch
在文件SpectrumMismatchRBFKernel.h第164行定义。
int32_t target_letter_0 [protected] |
在文件SpectrumMismatchRBFKernel.h第175行定义。
width of Gaussian
在文件SpectrumMismatchRBFKernel.h第168行定义。