Public Member Functions | Protected Member Functions | Protected Attributes

CSpectrumRBFKernel Class Reference


Detailed Description

spectrum rbf kernel

Definition at line 31 of file SpectrumRBFKernel.h.

Inheritance diagram for CSpectrumRBFKernel:
Inheritance graph
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List of all members.

Public Member Functions

 CSpectrumRBFKernel ()
 CSpectrumRBFKernel (int32_t size, float64_t *AA_matrix, int32_t degree, float64_t width)
 CSpectrumRBFKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t size, float64_t *AA_matrix, int32_t degree, float64_t width)
virtual ~CSpectrumRBFKernel ()
virtual bool init (CFeatures *l, CFeatures *r)
virtual void cleanup ()
int32_t get_degree () const
virtual EKernelType get_kernel_type ()
virtual const char * get_name () const
bool set_degree (int32_t deg)
int32_t get_degree ()
bool set_AA_matrix (float64_t *AA_matrix_)

Protected Member Functions

float64_t AA_helper (const char *path, const int degree, const char *joint_seq, unsigned int index)
void read_profiles_and_sequences ()
float64_t compute (int32_t idx_a, int32_t idx_b)
virtual void remove_lhs ()
virtual void register_param ()
void register_alphabet ()

Protected Attributes

CAlphabetalphabet
int32_t degree
int32_t max_mismatch
float64_tAA_matrix
int32_t AA_matrix_length
float64_t width
std::vector< std::vector
< float64_t > > 
profiles
std::vector< std::string > sequence_labels
SGString< char > * sequences
CStringFeatures< char > * string_features
int32_t nof_sequences
int32_t max_sequence_length
bool initialized
CArray2< float64_tkernel_matrix
int32_t target_letter_0

Constructor & Destructor Documentation

default constructor

Definition at line 39 of file SpectrumRBFKernel.cpp.

CSpectrumRBFKernel ( int32_t  size,
float64_t AA_matrix,
int32_t  degree,
float64_t  width 
)

constructor

Parameters:
size 
AA_matrix 
degree 
width 

Definition at line 46 of file SpectrumRBFKernel.cpp.

CSpectrumRBFKernel ( CStringFeatures< char > *  l,
CStringFeatures< char > *  r,
int32_t  size,
float64_t AA_matrix,
int32_t  degree,
float64_t  width 
)

constructor

Parameters:
l features of left-hand side
r features of right-hand side
size 
AA_matrix 
degree 
width 

Definition at line 71 of file SpectrumRBFKernel.cpp.

~CSpectrumRBFKernel (  )  [virtual]

destructor

Definition at line 84 of file SpectrumRBFKernel.cpp.


Member Function Documentation

float64_t AA_helper ( const char *  path,
const int  degree,
const char *  joint_seq,
unsigned int  index 
) [protected]

AA helper

Parameters:
path 
degree 
joint_seq 
index 

Definition at line 336 of file SpectrumRBFKernel.cpp.

void cleanup (  )  [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 320 of file SpectrumRBFKernel.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_a index a
idx_b index b
Returns:
computed kernel function at indices a,b

Implements CKernel.

Definition at line 358 of file SpectrumRBFKernel.cpp.

int32_t get_degree (  )  const

get degree

Returns:
degree of the kernel

Definition at line 75 of file SpectrumRBFKernel.h.

int32_t get_degree (  ) 

get degree

Returns:
degree

Definition at line 103 of file SpectrumRBFKernel.h.

virtual EKernelType get_kernel_type (  )  [virtual]

return what type of kernel we are

Returns:
kernel type

Implements CStringKernel< char >.

Definition at line 84 of file SpectrumRBFKernel.h.

virtual const char* get_name (  )  const [virtual]

return the kernel's name

Returns:
name

Reimplemented from CStringKernel< char >.

Definition at line 90 of file SpectrumRBFKernel.h.

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

initialize kernel

Parameters:
l features of left-hand side
r features of right-hand side
Returns:
if initializing was successful

Reimplemented from CStringKernel< char >.

Definition at line 285 of file SpectrumRBFKernel.cpp.

void read_profiles_and_sequences (  )  [protected]

read profiles and sequences

Definition at line 97 of file SpectrumRBFKernel.cpp.

void register_alphabet (  )  [protected]

register the alphabet

Definition at line 406 of file SpectrumRBFKernel.cpp.

void register_param (  )  [protected, virtual]

register the parameters

Definition at line 395 of file SpectrumRBFKernel.cpp.

void remove_lhs (  )  [protected, virtual]

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 91 of file SpectrumRBFKernel.cpp.

bool set_AA_matrix ( float64_t AA_matrix_  ) 

set AA matrix

Parameters:
AA_matrix_ 

Definition at line 381 of file SpectrumRBFKernel.cpp.

bool set_degree ( int32_t  deg  ) 

set degree

Parameters:
deg new degree
Returns:
if setting was successful

Definition at line 97 of file SpectrumRBFKernel.h.


Member Data Documentation

float64_t* AA_matrix [protected]

128x128 scalar product matrix

Definition at line 149 of file SpectrumRBFKernel.h.

int32_t AA_matrix_length [protected]

length of the AA_matrix -- for registration

Definition at line 151 of file SpectrumRBFKernel.h.

CAlphabet* alphabet [protected]

alphabet of features

Definition at line 143 of file SpectrumRBFKernel.h.

int32_t degree [protected]

degree

Definition at line 145 of file SpectrumRBFKernel.h.

bool initialized [protected]

if kernel is initialized

Definition at line 172 of file SpectrumRBFKernel.h.

kernel matrix

Reimplemented from CKernel.

Definition at line 174 of file SpectrumRBFKernel.h.

int32_t max_mismatch [protected]

maximum mismatch

Definition at line 147 of file SpectrumRBFKernel.h.

int32_t max_sequence_length [protected]

max sequence length

Definition at line 169 of file SpectrumRBFKernel.h.

int32_t nof_sequences [protected]

nof sequences

Definition at line 167 of file SpectrumRBFKernel.h.

std::vector< std::vector<float64_t> > profiles [protected]

profiles

Definition at line 159 of file SpectrumRBFKernel.h.

std::vector<std::string> sequence_labels [protected]

sequence labels

Definition at line 161 of file SpectrumRBFKernel.h.

SGString<char>* sequences [protected]

sequences

Definition at line 163 of file SpectrumRBFKernel.h.

CStringFeatures<char>* string_features [protected]

string features

Definition at line 165 of file SpectrumRBFKernel.h.

int32_t target_letter_0 [protected]

target letter 0

Definition at line 176 of file SpectrumRBFKernel.h.

float64_t width [protected]

width of Gaussian

Definition at line 153 of file SpectrumRBFKernel.h.


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