Features that compute the Spectrum Kernel feature space explicitly.
Definition at line 27 of file ExplicitSpecFeatures.h.
Classes | |
struct | explicit_spec_feature_iterator |
Public Member Functions | |
CExplicitSpecFeatures (void) | |
CExplicitSpecFeatures (CStringFeatures< uint16_t > *str, bool normalize=true) | |
CExplicitSpecFeatures (const CExplicitSpecFeatures &orig) | |
virtual | ~CExplicitSpecFeatures () |
virtual CFeatures * | duplicate () const |
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 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 int32_t | get_nnz_features_for_vector (int32_t num) |
virtual EFeatureType | get_feature_type () |
virtual EFeatureClass | get_feature_class () |
virtual int32_t | get_num_vectors () |
virtual int32_t | get_size () |
virtual const char * | get_name () const |
Protected Member Functions | |
void | obtain_kmer_spectrum (CStringFeatures< uint16_t > *str) |
void | delete_kmer_spectrum () |
Protected Attributes | |
bool | use_normalization |
int32_t | num_strings |
int32_t | alphabet_size |
int32_t | spec_size |
float64_t ** | k_spectrum |
CExplicitSpecFeatures | ( | void | ) |
default constructor
Definition at line 16 of file ExplicitSpecFeatures.cpp.
CExplicitSpecFeatures | ( | CStringFeatures< uint16_t > * | str, | |
bool | normalize = true | |||
) |
constructor
str | stringfeatures (of words) | |
normalize | whether to use sqrtdiag normalization |
Definition at line 30 of file ExplicitSpecFeatures.cpp.
CExplicitSpecFeatures | ( | const CExplicitSpecFeatures & | orig | ) |
copy constructor
Definition at line 43 of file ExplicitSpecFeatures.cpp.
~CExplicitSpecFeatures | ( | ) | [virtual] |
destructor
Definition at line 51 of file ExplicitSpecFeatures.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 84 of file ExplicitSpecFeatures.cpp.
void delete_kmer_spectrum | ( | ) | [protected] |
free kmer spectrum
Definition at line 134 of file ExplicitSpecFeatures.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 71 of file ExplicitSpecFeatures.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 56 of file ExplicitSpecFeatures.cpp.
CFeatures * duplicate | ( | ) | const [virtual] |
duplicate feature object
Implements CFeatures.
Definition at line 143 of file ExplicitSpecFeatures.cpp.
virtual 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 144 of file ExplicitSpecFeatures.h.
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())
Implements CDotFeatures.
Definition at line 59 of file ExplicitSpecFeatures.h.
virtual EFeatureClass get_feature_class | ( | ) | [virtual] |
get feature class
Implements CFeatures.
Definition at line 173 of file ExplicitSpecFeatures.h.
virtual 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 117 of file ExplicitSpecFeatures.h.
virtual EFeatureType get_feature_type | ( | ) | [virtual] |
get feature type
Implements CFeatures.
Definition at line 164 of file ExplicitSpecFeatures.h.
virtual const char* get_name | ( | void | ) | const [virtual] |
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 133 of file ExplicitSpecFeatures.h.
virtual 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 154 of file ExplicitSpecFeatures.h.
virtual int32_t get_num_vectors | ( | ) | [virtual] |
get number of strings
Implements CFeatures.
Definition at line 182 of file ExplicitSpecFeatures.h.
virtual int32_t get_size | ( | ) | [virtual] |
get size of one element
Implements CFeatures.
Definition at line 191 of file ExplicitSpecFeatures.h.
void obtain_kmer_spectrum | ( | CStringFeatures< uint16_t > * | str | ) | [protected] |
obtain the k-spectrum from a list of strings
str | the string feature object already in k-mer format |
Definition at line 102 of file ExplicitSpecFeatures.cpp.
int32_t alphabet_size [protected] |
size of alphabet
Definition at line 215 of file ExplicitSpecFeatures.h.
float64_t** k_spectrum [protected] |
k-mer counts for all strings
Definition at line 220 of file ExplicitSpecFeatures.h.
int32_t num_strings [protected] |
number of strings
Definition at line 213 of file ExplicitSpecFeatures.h.
int32_t spec_size [protected] |
size of k-mer spectrum
Definition at line 218 of file ExplicitSpecFeatures.h.
bool use_normalization [protected] |
use sqrtdiag normalization
Definition at line 211 of file ExplicitSpecFeatures.h.