Features that compute the Weighted Degreee Kernel feature space explicitly.
Definition at line 27 of file SNPFeatures.h.
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 CFeatures * | duplicate () 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_t > | get_histogram (bool normalize=true) |
Static Public Member Functions | |
| static SGMatrix< float64_t > | get_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 |
| CSNPFeatures | ( | ) |
default constructor
Definition at line 17 of file SNPFeatures.cpp.
| CSNPFeatures | ( | CStringFeatures< uint8_t > * | str | ) |
constructor
| 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.
| 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
| 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 227 of file SNPFeatures.cpp.
compute dot product between vector1 and a dense vector
| vec_idx1 | index of first vector | |
| vec2 | pointer to real valued vector | |
| vec2_len | length 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
| 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 130 of file SNPFeatures.cpp.
| CFeatures * duplicate | ( | ) | const [virtual] |
duplicate 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
| iterator | as 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())
Implements CDotFeatures.
Definition at line 75 of file SNPFeatures.cpp.
| EFeatureClass get_feature_class | ( | ) | [virtual] |
get 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
| vector_index | the index of the vector over whose components to iterate over |
Implements CDotFeatures.
Definition at line 331 of file SNPFeatures.cpp.
| EFeatureType get_feature_type | ( | ) | [virtual] |
get feature type
Implements CFeatures.
Definition at line 85 of file SNPFeatures.cpp.
compute histogram over strings
Definition at line 350 of file SNPFeatures.cpp.
| char * get_major_base_string | ( | ) |
return the major base string
Definition at line 125 of file SNPFeatures.cpp.
| char * get_minor_base_string | ( | ) |
get the minor base string
Definition at line 120 of file SNPFeatures.cpp.
| virtual const char* get_name | ( | ) | const [virtual] |
| 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
| index | is returned by reference (-1 when not available) | |
| value | is returned by reference | |
| iterator | as returned by get_first_feature |
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
| num | which 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
Implements CFeatures.
Definition at line 95 of file SNPFeatures.cpp.
| int32_t get_size | ( | ) | [virtual] |
get 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
| snp | optionally 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
| str | base string |
Definition at line 115 of file SNPFeatures.cpp.
| void set_minor_base_string | ( | const char * | str | ) |
set the minor base string
| str | base string |
Definition at line 110 of file SNPFeatures.cpp.
| void set_normalization_const | ( | float64_t | n = 0 |
) |
set normalization constant
| n | n=0 means automagic |
Definition at line 318 of file SNPFeatures.cpp.
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.
