Public Member Functions | Static 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
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List of all members.

Public Member Functions

 CSNPFeatures ()
 CSNPFeatures (CStringFeatures< uint8_t > *str)
 CSNPFeatures (const CSNPFeatures &orig)
virtual ~CSNPFeatures ()
virtual int32_t get_dim_feature_space () const
virtual float64_t dot (int32_t vec_idx1, CDotFeatures *df, 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 () const
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 (CSNPFeatures *snp=NULL)
virtual const char * get_name () const
virtual SGMatrix< float64_tget_histogram (bool normalize=true)

Static Public Member Functions

static SGMatrix< float64_tget_2x3_table (CSNPFeatures *pos, CSNPFeatures *neg)

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 (  ) 

default constructor

Definition at line 17 of file SNPFeatures.cpp.

CSNPFeatures ( CStringFeatures< uint8_t > *  str  ) 

constructor

Parameters:
str stringfeatures (of bytes)

Definition at line 33 of file SNPFeatures.cpp.

CSNPFeatures ( const CSNPFeatures orig  ) 

copy constructor

Definition at line 54 of file SNPFeatures.cpp.

~CSNPFeatures (  )  [virtual]

destructor

Definition at line 70 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:
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 172 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_idx1 index of first vector
vec2 pointer to real valued vector
vec2_len length of real valued vector

Implements CDotFeatures.

Definition at line 133 of file SNPFeatures.cpp.

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

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

Parameters:
vec_idx1 index of first vector
df DotFeatures (of same kind) to compute dot product with
vec_idx2 index of second vector

Implements CDotFeatures.

Definition at line 75 of file SNPFeatures.cpp.

CFeatures * duplicate (  )  const [virtual]

duplicate feature object

Returns:
feature object

Implements CFeatures.

Definition at line 290 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:
iterator as returned by get_first_feature

Implements CDotFeatures.

Definition at line 286 of file SNPFeatures.cpp.

SGMatrix< float64_t > get_2x3_table ( CSNPFeatures pos,
CSNPFeatures neg 
) [static]

compute 2x3 histogram table

Definition at line 352 of file SNPFeatures.cpp.

virtual int32_t get_dim_feature_space (  )  const [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 52 of file SNPFeatures.h.

virtual EFeatureClass get_feature_class (  )  [virtual]

get feature class

Returns:
feature class

Implements CFeatures.

Definition at line 143 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_index the 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 276 of file SNPFeatures.cpp.

virtual EFeatureType get_feature_type (  )  [virtual]

get feature type

Returns:
templated feature type

Implements CFeatures.

Definition at line 134 of file SNPFeatures.h.

SGMatrix< float64_t > get_histogram ( bool  normalize = true  )  [virtual]

compute histogram over strings

Definition at line 295 of file SNPFeatures.cpp.

char* get_major_base_string (  ) 

return the major base string

Returns:
major base string

Definition at line 210 of file SNPFeatures.h.

char* get_minor_base_string (  ) 

get the minor base string

Returns:
the minor base string

Definition at line 200 of file SNPFeatures.h.

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

Implements CSGObject.

Definition at line 223 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:
index is returned by reference (-1 when not available)
value is returned by reference
iterator as returned by get_first_feature
Returns:
true if a new non-zero feature got returned

Implements CDotFeatures.

Definition at line 281 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:
num which vector
Returns:
number of non-zero features in vector

Implements CDotFeatures.

Definition at line 89 of file SNPFeatures.h.

float64_t get_normalization_const (  ) 

get normalization constant

Definition at line 171 of file SNPFeatures.h.

virtual int32_t get_num_vectors (  )  const [virtual]

get number of vectors

Returns:
number of vectors

Implements CFeatures.

Definition at line 152 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 161 of file SNPFeatures.h.

void obtain_base_strings ( CSNPFeatures snp = NULL  ) 

compute the base strings from current strings optionally taking into account snp

Parameters:
snp optionally compute base string for snp too

Definition at line 236 of file SNPFeatures.cpp.

void set_major_base_string ( const char *  str  ) 

set the major base string

Parameters:
str base string

Definition at line 190 of file SNPFeatures.h.

void set_minor_base_string ( const char *  str  ) 

set the minor base string

Parameters:
str base string

Definition at line 180 of file SNPFeatures.h.

void set_normalization_const ( float64_t  n = 0  ) 

set normalization constant

Parameters:
n n=0 means automagic

Definition at line 263 of file SNPFeatures.cpp.


Member Data Documentation

uint8_t* m_str_maj [protected]

allele B

Definition at line 260 of file SNPFeatures.h.

uint8_t* m_str_min [protected]

allele A

Definition at line 258 of file SNPFeatures.h.

normalization const

Definition at line 255 of file SNPFeatures.h.

int32_t num_strings [protected]

number of strings

Definition at line 250 of file SNPFeatures.h.

int32_t string_length [protected]

length of string in vector

Definition at line 248 of file SNPFeatures.h.

CStringFeatures<uint8_t>* strings [protected]

stringfeatures the wdfeatures are based on

Definition at line 245 of file SNPFeatures.h.

int32_t w_dim [protected]

dim of feature space

Definition at line 252 of file SNPFeatures.h.


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