Public Member Functions | Protected Attributes

CSNPFeatures Class Reference


Detailed Description

Features that compute the Weighted Degreee Kernel feature space explicitly.

See also:
CWeightedDegreeStringKernel

Definition at line 27 of file SNPFeatures.h.

Inheritance diagram for CSNPFeatures:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 CSNPFeatures (CStringFeatures< uint8_t > *str)
 CSNPFeatures (const CSNPFeatures &orig)
virtual ~CSNPFeatures ()
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 void * get_feature_iterator (int32_t vector_index)
virtual bool get_next_feature (int32_t &index, float64_t &value, void *iterator)
virtual void free_feature_iterator (void *iterator)
virtual CFeaturesduplicate () const
virtual EFeatureType get_feature_type ()
virtual EFeatureClass get_feature_class ()
virtual int32_t get_num_vectors ()
virtual int32_t get_size ()
void set_normalization_const (float64_t n=0)
float64_t get_normalization_const ()
void set_minor_base_string (const char *str)
void set_major_base_string (const char *str)
char * get_minor_base_string ()
char * get_major_base_string ()
void obtain_base_strings ()
virtual const char * get_name () const

Protected Attributes

CStringFeatures< uint8_t > * strings
int32_t string_length
int32_t num_strings
int32_t w_dim
float64_t normalization_const
uint8_t * m_str_min
uint8_t * m_str_maj

Constructor & Destructor Documentation

CSNPFeatures ( CStringFeatures< uint8_t > *  str )

constructor

Parameters:
strstringfeatures (of bytes)

Definition at line 17 of file SNPFeatures.cpp.

CSNPFeatures ( const CSNPFeatures orig )

copy constructor

Definition at line 38 of file SNPFeatures.cpp.

~CSNPFeatures (  ) [virtual]

destructor

Definition at line 54 of file SNPFeatures.cpp.


Member Function Documentation

void 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:
alphascalar alpha
vec_idx1index of first vector
vec2pointer to real valued vector
vec2_lenlength of real valued vector
abs_valif true add the absolute value

Implements CDotFeatures.

Definition at line 151 of file SNPFeatures.cpp.

float64_t 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_idx1index of first vector
vec2pointer to real valued vector
vec2_lenlength of real valued vector

Implements CDotFeatures.

Definition at line 112 of file SNPFeatures.cpp.

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

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

Parameters:
vec_idx1index of first vector
vec_idx2index of second vector

Implements CDotFeatures.

Definition at line 59 of file SNPFeatures.cpp.

CFeatures * duplicate (  ) const [virtual]

duplicate feature object

Returns:
feature object

Implements CFeatures.

Definition at line 263 of file SNPFeatures.cpp.

void free_feature_iterator ( void *  iterator ) [virtual]

clean up iterator call this function with the iterator returned by get_first_feature

Parameters:
iteratoras returned by get_first_feature

Implements CDotFeatures.

Definition at line 259 of file SNPFeatures.cpp.

virtual int32_t 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 50 of file SNPFeatures.h.

virtual EFeatureClass get_feature_class (  ) [virtual]

get feature class

Returns:
feature class

Implements CFeatures.

Definition at line 140 of file SNPFeatures.h.

void * get_feature_iterator ( int32_t  vector_index ) [virtual]

iterate over the non-zero features

call get_feature_iterator first, followed by get_next_feature and free_feature_iterator to cleanup

Parameters:
vector_indexthe index of the vector over whose components to iterate over
Returns:
feature iterator (to be passed to get_next_feature)

Implements CDotFeatures.

Definition at line 249 of file SNPFeatures.cpp.

virtual EFeatureType get_feature_type (  ) [virtual]

get feature type

Returns:
templated feature type

Implements CFeatures.

Definition at line 131 of file SNPFeatures.h.

char* get_major_base_string (  )

return the major base string

Returns:
major base string

Definition at line 207 of file SNPFeatures.h.

char* get_minor_base_string (  )

get the minor base string

Returns:
the minor base string

Definition at line 197 of file SNPFeatures.h.

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

Implements CSGObject.

Definition at line 217 of file SNPFeatures.h.

bool get_next_feature ( int32_t &  index,
float64_t value,
void *  iterator 
) [virtual]

iterate over the non-zero features

call this function with the iterator returned by get_first_feature and call free_feature_iterator to cleanup

Parameters:
indexis returned by reference (-1 when not available)
valueis returned by reference
iteratoras returned by get_first_feature
Returns:
true if a new non-zero feature got returned

Implements CDotFeatures.

Definition at line 254 of file SNPFeatures.cpp.

virtual int32_t get_nnz_features_for_vector ( int32_t  num ) [virtual]

get number of non-zero features in vector

Parameters:
numwhich vector
Returns:
number of non-zero features in vector

Implements CDotFeatures.

Definition at line 86 of file SNPFeatures.h.

float64_t get_normalization_const (  )

get normalization constant

Definition at line 168 of file SNPFeatures.h.

virtual int32_t get_num_vectors (  ) [virtual]

get number of vectors

Returns:
number of vectors

Implements CFeatures.

Definition at line 149 of file SNPFeatures.h.

virtual int32_t get_size (  ) [virtual]

get memory footprint of one feature

Returns:
memory footprint of one feature

Implements CFeatures.

Definition at line 158 of file SNPFeatures.h.

void obtain_base_strings (  )

compute the basee strings from current strings

Definition at line 190 of file SNPFeatures.cpp.

void set_major_base_string ( const char *  str )

set the major base string

Parameters:
strbase string

Definition at line 187 of file SNPFeatures.h.

void set_minor_base_string ( const char *  str )

set the minor base string

Parameters:
strbase string

Definition at line 177 of file SNPFeatures.h.

void set_normalization_const ( float64_t  n = 0 )

set normalization constant

Parameters:
nn=0 means automagic

Definition at line 236 of file SNPFeatures.cpp.


Member Data Documentation

uint8_t* m_str_maj [protected]

allele B

Definition at line 236 of file SNPFeatures.h.

uint8_t* m_str_min [protected]

allele A

Definition at line 234 of file SNPFeatures.h.

normalization const

Definition at line 231 of file SNPFeatures.h.

int32_t num_strings [protected]

number of strings

Definition at line 226 of file SNPFeatures.h.

int32_t string_length [protected]

length of string in vector

Definition at line 224 of file SNPFeatures.h.

CStringFeatures<uint8_t>* strings [protected]

stringfeatures the wdfeatures are based on

Definition at line 221 of file SNPFeatures.h.

int32_t w_dim [protected]

dim of feature space

Definition at line 228 of file SNPFeatures.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