CExplicitSpecFeatures Class Reference


Detailed Description

Features that compute the Spectrum Kernel feature space explicitly.

See also:
CCommWordStringKernel

Definition at line 25 of file ExplicitSpecFeatures.h.

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

Public Member Functions

 CExplicitSpecFeatures (CStringFeatures< uint16_t > *str, bool normalize=true)
 CExplicitSpecFeatures (const CExplicitSpecFeatures &orig)
virtual ~CExplicitSpecFeatures ()
virtual CFeaturesduplicate () const
virtual int32_t get_dim_feature_space ()
virtual float64_t dot (int32_t vec_idx1, int32_t vec_idx2)
virtual float64_t dense_dot (int32_t vec_idx1, const float64_t *vec2, int32_t vec2_len)
virtual void add_to_dense_vec (float64_t alpha, int32_t vec_idx1, float64_t *vec2, int32_t vec2_len, bool abs_val=false)
virtual int32_t get_nnz_features_for_vector (int32_t num)
virtual EFeatureType get_feature_type ()
virtual EFeatureClass get_feature_class ()
virtual int32_t get_num_vectors ()
virtual int32_t get_size ()
virtual const char * get_name () const

Protected Member Functions

void obtain_kmer_spectrum (CStringFeatures< uint16_t > *str)
void delete_kmer_spectrum ()

Protected Attributes

bool use_normalization
int32_t num_strings
int32_t alphabet_size
int32_t spec_size
float64_t ** k_spectrum

Constructor & Destructor Documentation

CExplicitSpecFeatures::CExplicitSpecFeatures ( CStringFeatures< uint16_t > *  str,
bool  normalize = true 
)

constructor

Parameters:
str stringfeatures (of words)
normalize whether to use sqrtdiag normalization

Definition at line 14 of file ExplicitSpecFeatures.cpp.

CExplicitSpecFeatures::CExplicitSpecFeatures ( const CExplicitSpecFeatures orig  ) 

copy constructor

Definition at line 27 of file ExplicitSpecFeatures.cpp.

CExplicitSpecFeatures::~CExplicitSpecFeatures (  )  [virtual]

destructor

Definition at line 35 of file ExplicitSpecFeatures.cpp.


Member Function Documentation

void CExplicitSpecFeatures::add_to_dense_vec ( float64_t  alpha,
int32_t  vec_idx1,
float64_t vec2,
int32_t  vec2_len,
bool  abs_val = false 
) [virtual]

add vector 1 multiplied with alpha to dense vector2

Parameters:
alpha scalar alpha
vec_idx1 index of first vector
vec2 pointer to real valued vector
vec2_len length of real valued vector
abs_val if true add the absolute value

Implements CDotFeatures.

Definition at line 63 of file ExplicitSpecFeatures.cpp.

void CExplicitSpecFeatures::delete_kmer_spectrum (  )  [protected]

free kmer spectrum

Definition at line 110 of file ExplicitSpecFeatures.cpp.

float64_t CExplicitSpecFeatures::dense_dot ( int32_t  vec_idx1,
const float64_t vec2,
int32_t  vec2_len 
) [virtual]

compute dot product between vector1 and a dense vector

Parameters:
vec_idx1 index of first vector
vec2 pointer to real valued vector
vec2_len length of real valued vector

Implements CDotFeatures.

Definition at line 50 of file ExplicitSpecFeatures.cpp.

float64_t CExplicitSpecFeatures::dot ( int32_t  vec_idx1,
int32_t  vec_idx2 
) [virtual]

compute dot product between vector1 and vector2, appointed by their indices

Parameters:
vec_idx1 index of first vector
vec_idx2 index of second vector

Implements CDotFeatures.

Definition at line 40 of file ExplicitSpecFeatures.cpp.

CFeatures * CExplicitSpecFeatures::duplicate (  )  const [virtual]

duplicate feature object

Returns:
feature object

Implements CFeatures.

Definition at line 119 of file ExplicitSpecFeatures.cpp.

virtual int32_t CExplicitSpecFeatures::get_dim_feature_space (  )  [virtual]

obtain the dimensionality of the feature space

(not mix this up with the dimensionality of the input space, usually obtained via get_num_features())

Returns:
dimensionality

Implements CDotFeatures.

Definition at line 55 of file ExplicitSpecFeatures.h.

virtual EFeatureClass CExplicitSpecFeatures::get_feature_class (  )  [virtual]

get feature class

Returns:
feature class

Implements CFeatures.

Definition at line 110 of file ExplicitSpecFeatures.h.

virtual EFeatureType CExplicitSpecFeatures::get_feature_type (  )  [virtual]

get feature type

Returns:
templated feature type

Implements CFeatures.

Definition at line 101 of file ExplicitSpecFeatures.h.

virtual const char* CExplicitSpecFeatures::get_name (  )  const [virtual]
Returns:
object name

Implements CSGObject.

Definition at line 134 of file ExplicitSpecFeatures.h.

virtual int32_t CExplicitSpecFeatures::get_nnz_features_for_vector ( int32_t  num  )  [virtual]

get number of non-zero features in vector

Parameters:
num which vector
Returns:
number of non-zero features in vector

Implements CDotFeatures.

Definition at line 91 of file ExplicitSpecFeatures.h.

virtual int32_t CExplicitSpecFeatures::get_num_vectors (  )  [virtual]

get number of strings

Returns:
number of strings

Implements CFeatures.

Definition at line 119 of file ExplicitSpecFeatures.h.

virtual int32_t CExplicitSpecFeatures::get_size (  )  [virtual]

get size of one element

Returns:
size of one element

Implements CFeatures.

Definition at line 128 of file ExplicitSpecFeatures.h.

void CExplicitSpecFeatures::obtain_kmer_spectrum ( CStringFeatures< uint16_t > *  str  )  [protected]

obtain the k-spectrum from a list of strings

Parameters:
str the string feature object already in k-mer format

Definition at line 81 of file ExplicitSpecFeatures.cpp.


Member Data Documentation

size of alphabet

Definition at line 152 of file ExplicitSpecFeatures.h.

k-mer counts for all strings

Definition at line 157 of file ExplicitSpecFeatures.h.

number of strings

Definition at line 150 of file ExplicitSpecFeatures.h.

int32_t CExplicitSpecFeatures::spec_size [protected]

size of k-mer spectrum

Definition at line 155 of file ExplicitSpecFeatures.h.

use sqrtdiag normalization

Definition at line 148 of file ExplicitSpecFeatures.h.


The documentation for this class was generated from the following files:

SHOGUN Machine Learning Toolbox - Documentation