SHOGUN  v1.1.0
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines
Public Member Functions | Protected Member Functions | Protected Attributes
CSpectrumMismatchRBFKernel Class Reference

Detailed Description

spectrum mismatch rbf kernel

Definition at line 42 of file SpectrumMismatchRBFKernel.h.

Inheritance diagram for CSpectrumMismatchRBFKernel:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 CSpectrumMismatchRBFKernel ()
 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 ()
virtual EKernelType get_kernel_type ()
virtual const char * get_name () const
bool set_max_mismatch (int32_t max)
int32_t get_max_mismatch () const
bool set_degree (int32_t deg)
int32_t get_degree () const
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 ()
virtual void register_params ()
void register_alphabet ()

Protected Attributes

CAlphabetalphabet
int32_t degree
int32_t max_mismatch
float64_tAA_matrix
int32_t AA_matrix_length
float64_t width
bool initialized
CArray2< float64_tkernel_matrix
int32_t kernel_matrix_length
int32_t target_letter_0

Constructor & Destructor Documentation

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

Parameters:
size
AA_matrix_
nr_
nc_
degree
max_mismatch
width

Definition at line 43 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

Parameters:
lfeatures of left-hand side
rfeatures of right-hand side
size
AA_matrix_
nr_
nc_
degree
max_mismatch
width

Definition at line 58 of file SpectrumMismatchRBFKernel.cpp.

destructor

Definition at line 70 of file SpectrumMismatchRBFKernel.cpp.


Member Function Documentation

float64_t AA_helper ( std::string &  path,
const char *  joint_seq,
unsigned int  index 
) [protected]

AA helper

Parameters:
path
joint_seq
index
Returns:
AA helper

Definition at line 120 of file SpectrumMismatchRBFKernel.cpp.

void cleanup ( ) [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 111 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

Parameters:
idx_aindex a
idx_bindex b
Returns:
computed kernel function at indices a,b

Implements CKernel.

Definition at line 360 of file SpectrumMismatchRBFKernel.cpp.

void compute_all ( ) [protected]

computer all

Definition at line 324 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]

compute helper

Parameters:
joint_seq
joint_index
joint_mismatch
path
d
alen
Returns:
helper
void compute_helper_all ( const char *  joint_seq,
std::vector< struct joint_list_struct > &  joint_list,
std::string  path,
unsigned int  d 
) [protected]

compute helper all

Parameters:
joint_seq
joint_list
path
d
Returns:
helper

Definition at line 227 of file SpectrumMismatchRBFKernel.cpp.

int32_t get_degree ( ) const

get degree

Returns:
degree

Definition at line 127 of file SpectrumMismatchRBFKernel.h.

virtual EKernelType get_kernel_type ( ) [virtual]

return what type of kernel we are

Returns:
kernel type

Implements CStringKernel< char >.

Definition at line 95 of file SpectrumMismatchRBFKernel.h.

int32_t get_max_mismatch ( ) const

get maximum mismatch

Returns:
maximum mismatch

Definition at line 114 of file SpectrumMismatchRBFKernel.h.

virtual const char* get_name ( ) const [virtual]

return the kernel's name

Returns:
name

Reimplemented from CStringKernel< char >.

Definition at line 101 of file SpectrumMismatchRBFKernel.h.

bool init ( CFeatures l,
CFeatures r 
) [virtual]

initialize kernel

Parameters:
lfeatures of left-hand side
rfeatures of right-hand side
Returns:
if initializing was successful

Reimplemented from CStringKernel< char >.

Definition at line 83 of file SpectrumMismatchRBFKernel.cpp.

void register_alphabet ( ) [protected]

register the alphabet

Definition at line 452 of file SpectrumMismatchRBFKernel.cpp.

void register_params ( ) [protected, virtual]

register the parameters

Reimplemented from CKernel.

Definition at line 441 of file SpectrumMismatchRBFKernel.cpp.

void remove_lhs ( ) [protected, virtual]

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 77 of file SpectrumMismatchRBFKernel.cpp.

bool set_AA_matrix ( float64_t AA_matrix_ = NULL,
int32_t  nr = 128,
int32_t  nc = 128 
)

set AA matrix

Parameters:
AA_matrix_
nr
nc
Returns:
true if set

Definition at line 414 of file SpectrumMismatchRBFKernel.cpp.

bool set_degree ( int32_t  deg)

set degree

Parameters:
degnew degree
Returns:
if setting was successful

Definition at line 121 of file SpectrumMismatchRBFKernel.h.

bool set_max_mismatch ( int32_t  max)

set maximum mismatch

Parameters:
maxnew maximum mismatch
Returns:
if setting was successful

Definition at line 431 of file SpectrumMismatchRBFKernel.cpp.


Member Data Documentation

float64_t* AA_matrix [protected]

128x128 scalar product matrix

Definition at line 203 of file SpectrumMismatchRBFKernel.h.

int32_t AA_matrix_length [protected]

length of the AA_matrix -- for registration

Definition at line 205 of file SpectrumMismatchRBFKernel.h.

CAlphabet* alphabet [protected]

alphabet of features

Definition at line 197 of file SpectrumMismatchRBFKernel.h.

int32_t degree [protected]

degree

Definition at line 199 of file SpectrumMismatchRBFKernel.h.

bool initialized [protected]

if kernel is initialized

Definition at line 210 of file SpectrumMismatchRBFKernel.h.

kernel matrix

Reimplemented from CKernel.

Definition at line 213 of file SpectrumMismatchRBFKernel.h.

int32_t kernel_matrix_length [protected]

kernel matrix length

Definition at line 215 of file SpectrumMismatchRBFKernel.h.

int32_t max_mismatch [protected]

maximum mismatch

Definition at line 201 of file SpectrumMismatchRBFKernel.h.

int32_t target_letter_0 [protected]

target letter 0

Definition at line 217 of file SpectrumMismatchRBFKernel.h.

float64_t width [protected]

width of Gaussian

Definition at line 207 of file SpectrumMismatchRBFKernel.h.


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines

SHOGUN Machine Learning Toolbox - Documentation