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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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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)
- Public Member Functions inherited from CDotFeatures
 CDotFeatures (int32_t size=0)
 CDotFeatures (const CDotFeatures &orig)
 CDotFeatures (CFile *loader)
virtual ~CDotFeatures ()
virtual void dense_dot_range (float64_t *output, int32_t start, int32_t stop, float64_t *alphas, float64_t *vec, int32_t dim, float64_t b)
virtual void dense_dot_range_subset (int32_t *sub_index, int32_t num, float64_t *output, float64_t *alphas, float64_t *vec, int32_t dim, float64_t b)
float64_t get_combined_feature_weight ()
void set_combined_feature_weight (float64_t nw)
SGMatrix< float64_tget_computed_dot_feature_matrix ()
SGVector< float64_tget_computed_dot_feature_vector (int32_t num)
void benchmark_add_to_dense_vector (int32_t repeats=5)
void benchmark_dense_dot_range (int32_t repeats=5)
virtual SGVector< float64_tget_mean ()
virtual SGMatrix< float64_tget_cov ()
- Public Member Functions inherited from CFeatures
 CFeatures (int32_t size=0)
 CFeatures (const CFeatures &orig)
 CFeatures (CFile *loader)
virtual ~CFeatures ()
virtual int32_t add_preprocessor (CPreprocessor *p)
 set preprocessor
virtual CPreprocessordel_preprocessor (int32_t num)
 del current preprocessor
CPreprocessorget_preprocessor (int32_t num)
 get current preprocessor
void set_preprocessed (int32_t num)
bool is_preprocessed (int32_t num)
int32_t get_num_preprocessed ()
 get whether specified preprocessor (or all if num=1) was/were already applied
int32_t get_num_preprocessors () const
void clean_preprocessors ()
int32_t get_cache_size ()
virtual bool reshape (int32_t num_features, int32_t num_vectors)
void list_feature_obj ()
virtual void load (CFile *loader)
virtual void save (CFile *writer)
bool check_feature_compatibility (CFeatures *f)
bool has_property (EFeatureProperty p)
void set_property (EFeatureProperty p)
void unset_property (EFeatureProperty p)
virtual void set_subset (CSubset *subset)
virtual void remove_subset ()
virtual void subset_changed_post ()
index_t subset_idx_conversion (index_t idx) const
bool has_subset () const
virtual CFeaturescopy_subset (SGVector< index_t > indices)
- Public Member Functions inherited from CSGObject
 CSGObject ()
 CSGObject (const CSGObject &orig)
virtual ~CSGObject ()
virtual bool is_generic (EPrimitiveType *generic) const
template<class T >
void set_generic ()
void unset_generic ()
virtual void print_serializable (const char *prefix="")
virtual bool save_serializable (CSerializableFile *file, const char *prefix="")
virtual bool load_serializable (CSerializableFile *file, const char *prefix="")
void set_global_io (SGIO *io)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_global_version ()
SGVector< char * > get_modelsel_names ()
char * get_modsel_param_descr (const char *param_name)
index_t get_modsel_param_index (const char *param_name)

Static Public Member Functions

static SGMatrix< float64_tget_2x3_table (CSNPFeatures *pos, CSNPFeatures *neg)
- Static Public Member Functions inherited from CDotFeatures
static void * dense_dot_range_helper (void *p)

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
- Protected Attributes inherited from CDotFeatures
float64_t combined_weight
 feature weighting in combined dot features
- Protected Attributes inherited from CFeatures
CSubsetm_subset

Additional Inherited Members

- Public Attributes inherited from CSGObject
SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
- Protected Member Functions inherited from CDotFeatures
void display_progress (int32_t start, int32_t stop, int32_t v)

Constructor & Destructor Documentation

default constructor

Definition at line 17 of file SNPFeatures.cpp.

CSNPFeatures ( CStringFeatures< uint8_t > *  str)

constructor

Parameters
strstringfeatures (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
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 227 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 188 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_idx1index of first vector
dfDotFeatures (of same kind) to compute dot product with
vec_idx2index of second vector

Implements CDotFeatures.

Definition at line 130 of file SNPFeatures.cpp.

CFeatures * duplicate ( ) const
virtual

duplicate feature object

Returns
feature object

Implements CFeatures.

Definition at line 345 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 341 of file SNPFeatures.cpp.

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

compute 2x3 histogram table

Definition at line 407 of file SNPFeatures.cpp.

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 75 of file SNPFeatures.cpp.

EFeatureClass get_feature_class ( )
virtual

get feature class

Returns
feature class

Implements CFeatures.

Definition at line 90 of file SNPFeatures.cpp.

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 331 of file SNPFeatures.cpp.

EFeatureType get_feature_type ( )
virtual

get feature type

Returns
templated feature type

Implements CFeatures.

Definition at line 85 of file SNPFeatures.cpp.

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

compute histogram over strings

Definition at line 350 of file SNPFeatures.cpp.

char * get_major_base_string ( )

return the major base string

Returns
major base string

Definition at line 125 of file SNPFeatures.cpp.

char * get_minor_base_string ( )

get the minor base string

Returns
the minor base string

Definition at line 120 of file SNPFeatures.cpp.

virtual const char* get_name ( ) const
virtual
Returns
object name

Implements CSGObject.

Definition at line 188 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 336 of file SNPFeatures.cpp.

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 80 of file SNPFeatures.cpp.

float64_t get_normalization_const ( )

get normalization constant

Definition at line 105 of file SNPFeatures.cpp.

int32_t get_num_vectors ( ) const
virtual

get number of vectors

Returns
number of vectors

Implements CFeatures.

Definition at line 95 of file SNPFeatures.cpp.

int32_t get_size ( )
virtual

get memory footprint of one feature

Returns
memory footprint of one feature

Implements CFeatures.

Definition at line 100 of file SNPFeatures.cpp.

void obtain_base_strings ( CSNPFeatures snp = NULL)

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

Parameters
snpoptionally compute base string for snp too

Definition at line 291 of file SNPFeatures.cpp.

void set_major_base_string ( const char *  str)

set the major base string

Parameters
strbase string

Definition at line 115 of file SNPFeatures.cpp.

void set_minor_base_string ( const char *  str)

set the minor base string

Parameters
strbase string

Definition at line 110 of file SNPFeatures.cpp.

void set_normalization_const ( float64_t  n = 0)

set normalization constant

Parameters
nn=0 means automagic

Definition at line 318 of file SNPFeatures.cpp.

Member Data Documentation

uint8_t* m_str_maj
protected

allele B

Definition at line 225 of file SNPFeatures.h.

uint8_t* m_str_min
protected

allele A

Definition at line 223 of file SNPFeatures.h.

float64_t normalization_const
protected

normalization const

Definition at line 220 of file SNPFeatures.h.

int32_t num_strings
protected

number of strings

Definition at line 215 of file SNPFeatures.h.

int32_t string_length
protected

length of string in vector

Definition at line 213 of file SNPFeatures.h.

CStringFeatures<uint8_t>* strings
protected

stringfeatures the wdfeatures are based on

Definition at line 210 of file SNPFeatures.h.

int32_t w_dim
protected

dim of feature space

Definition at line 217 of file SNPFeatures.h.


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

SHOGUN Machine Learning Toolbox - Documentation