Definition at line 35 of file SpectrumMismatchRBFKernel.h.
Public Member Functions | |
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) |
Protected Member Functions | |
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 () |
Protected Attributes | |
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
Definition at line 36 of file SpectrumMismatchRBFKernel.cpp.
CSpectrumMismatchRBFKernel | ( | int32_t | size, | |
float64_t * | AA_matrix_, | |||
int32_t | nr_, | |||
int32_t | nc_, | |||
int32_t | degree, | |||
int32_t | max_mismatch, | |||
float64_t | width | |||
) |
constructor
@param | degree degree |
Definition at line 52 of file SpectrumMismatchRBFKernel.cpp.
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 |
Definition at line 66 of file SpectrumMismatchRBFKernel.cpp.
~CSpectrumMismatchRBFKernel | ( | ) | [virtual] |
Definition at line 77 of file SpectrumMismatchRBFKernel.cpp.
float64_t AA_helper | ( | std::string & | path, | |
const char * | joint_seq, | |||
unsigned int | index | |||
) | [protected] |
Definition at line 127 of file SpectrumMismatchRBFKernel.cpp.
void cleanup | ( | ) | [virtual] |
clean up kernel
Reimplemented from CKernel.
Definition at line 118 of file SpectrumMismatchRBFKernel.cpp.
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 |
Implements CKernel.
Definition at line 366 of file SpectrumMismatchRBFKernel.cpp.
void compute_all | ( | ) | [protected] |
Definition at line 331 of file SpectrumMismatchRBFKernel.cpp.
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] |
Definition at line 234 of file SpectrumMismatchRBFKernel.cpp.
int32_t get_degree | ( | ) |
int32_t get_degree | ( | ) | const |
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 92 of file SpectrumMismatchRBFKernel.h.
int32_t get_max_mismatch | ( | ) |
get maximum mismatch
Definition at line 111 of file SpectrumMismatchRBFKernel.h.
int32_t get_max_mismatch | ( | ) | const |
get the number of mismatches that are allowed
Definition at line 83 of file SpectrumMismatchRBFKernel.h.
virtual const char* get_name | ( | void | ) | const [virtual] |
return the kernel's name
Reimplemented from CStringKernel< char >.
Definition at line 98 of file SpectrumMismatchRBFKernel.h.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 90 of file SpectrumMismatchRBFKernel.cpp.
void remove_lhs | ( | ) | [protected, virtual] |
remove lhs from kernel
Reimplemented from CKernel.
Definition at line 84 of file SpectrumMismatchRBFKernel.cpp.
bool set_AA_matrix | ( | float64_t * | AA_matrix_ = NULL , |
|
int32_t | nr = 128 , |
|||
int32_t | nc = 128 | |||
) |
Definition at line 420 of file SpectrumMismatchRBFKernel.cpp.
bool set_degree | ( | int32_t | deg | ) |
set degree
deg | new degree |
Definition at line 118 of file SpectrumMismatchRBFKernel.h.
bool set_max_mismatch | ( | int32_t | max | ) |
set maximum mismatch
max | new maximum mismatch |
Definition at line 437 of file SpectrumMismatchRBFKernel.cpp.
128x128 scalar product matrix
Definition at line 166 of file SpectrumMismatchRBFKernel.h.
alphabet of features
Definition at line 160 of file SpectrumMismatchRBFKernel.h.
int32_t degree [protected] |
degree
Definition at line 162 of file SpectrumMismatchRBFKernel.h.
bool initialized [protected] |
if kernel is initialized
Definition at line 171 of file SpectrumMismatchRBFKernel.h.
CArray2<float64_t> kernel_matrix [protected] |
this *COULD* store the whole kernel matrix usually not applicable / necessary to compute the whole matrix
Reimplemented from CKernel.
Definition at line 174 of file SpectrumMismatchRBFKernel.h.
int32_t max_mismatch [protected] |
maximum mismatch
Definition at line 164 of file SpectrumMismatchRBFKernel.h.
int32_t target_letter_0 [protected] |
Definition at line 175 of file SpectrumMismatchRBFKernel.h.
width of Gaussian
Definition at line 168 of file SpectrumMismatchRBFKernel.h.