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:

Public Member Functions
	CSNPFeatures (void)
	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, 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 CFeatures *	duplicate () 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 ( void )

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 284 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 280 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 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 270 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.

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 220 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 275 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 ( ) [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 ( )

compute the basee strings from current strings

Definition at line 211 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 257 of file SNPFeatures.cpp.

Member Data Documentation

uint8_t* m_str_maj [protected]

allele B

Definition at line 239 of file SNPFeatures.h.

uint8_t* m_str_min [protected]

allele A

Definition at line 237 of file SNPFeatures.h.

float64_t normalization_const [protected]

normalization const

Definition at line 234 of file SNPFeatures.h.

int32_t num_strings [protected]

number of strings

Definition at line 229 of file SNPFeatures.h.

int32_t string_length [protected]

length of string in vector

Definition at line 227 of file SNPFeatures.h.

CStringFeatures<uint8_t>* strings [protected]

stringfeatures the wdfeatures are based on

Definition at line 224 of file SNPFeatures.h.

int32_t w_dim [protected]

dim of feature space

Definition at line 231 of file SNPFeatures.h.

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

CSNPFeatures Class Reference

Detailed Description

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation