, including all inherited members.
add_preproc(CPreProc *p) | CFeatures | [virtual] |
alphabet | CStringFeatures< ST > | [protected] |
append_features(CStringFeatures< ST > *sf) | CStringFeatures< ST > | |
append_features(TString< ST > *p_features, int32_t p_num_vectors, int32_t p_max_string_length) | CStringFeatures< ST > | |
apply_preproc(bool force_preprocessing=false) | CStringFeatures< ST > | [virtual] |
CFeatures(int32_t size=0) | CFeatures | |
CFeatures(const CFeatures &orig) | CFeatures | |
CFeatures(CFile *loader) | CFeatures | |
check_feature_compatibility(CFeatures *f) | CFeatures | |
clean_preprocs() | CFeatures | |
cleanup() | CStringFileFeatures< ST > | [protected, virtual] |
cleanup_feature_vector(int32_t num) | CStringFileFeatures< ST > | [protected, virtual] |
compute_feature_vector(int32_t num, int32_t &len) | CStringFeatures< ST > | [protected, virtual] |
compute_symbol_mask_table(int64_t max_val) | CStringFeatures< ST > | |
copy_features(int32_t &num_str, int32_t &max_str_len) | CStringFeatures< ST > | [virtual] |
create_random(float64_t *hist, int32_t rows, int32_t cols, int32_t num_vec) | CStringFeatures< ST > | [virtual] |
CSGObject() | CSGObject | |
CSGObject(const CSGObject &orig) | CSGObject | |
CStringFeatures() | CStringFeatures< ST > | |
CStringFeatures(EAlphabet alpha) | CStringFeatures< ST > | |
CStringFeatures(TString< ST > *p_features, int32_t p_num_vectors, int32_t p_max_string_length, EAlphabet alpha) | CStringFeatures< ST > | |
CStringFeatures(TString< ST > *p_features, int32_t p_num_vectors, int32_t p_max_string_length, CAlphabet *alpha) | CStringFeatures< ST > | |
CStringFeatures(CAlphabet *alpha) | CStringFeatures< ST > | |
CStringFeatures(const CStringFeatures &orig) | CStringFeatures< ST > | |
CStringFeatures(CFile *loader, EAlphabet alpha=DNA) | CStringFeatures< ST > | |
CStringFileFeatures() | CStringFileFeatures< ST > | |
CStringFileFeatures(const char *fname, EAlphabet alpha) | CStringFileFeatures< ST > | |
del_preproc(int32_t num) | CFeatures | [virtual] |
determine_maximum_string_length() | CStringFeatures< ST > | |
disable_on_the_fly_preprocessing() | CStringFeatures< ST > | |
duplicate() const | CStringFeatures< ST > | [virtual] |
embed_features(int32_t p_order) | CStringFeatures< ST > | |
embed_word(ST *seq, int32_t len) | CStringFeatures< ST > | |
enable_on_the_fly_preprocessing() | CStringFeatures< ST > | |
feature_cache | CStringFeatures< ST > | [protected] |
features | CStringFeatures< ST > | [protected] |
fetch_meta_info_from_file(int32_t granularity=1048576) | CStringFileFeatures< ST > | [protected] |
file | CStringFileFeatures< ST > | [protected] |
free_feature_vector(ST *feat_vec, int32_t num, bool dofree) | CStringFeatures< ST > | |
get_alphabet() | CStringFeatures< ST > | |
get_cache_size() | CFeatures | |
get_feature(int32_t vec_num, int32_t feat_num) | CStringFeatures< ST > | [virtual] |
get_feature_class() | CStringFeatures< ST > | [virtual] |
get_feature_type() | CStringFeatures< ST > | [virtual] |
get_feature_vector(ST **dst, int32_t *len, int32_t num) | CStringFeatures< ST > | |
get_feature_vector(int32_t num, int32_t &len, bool &dofree) | CStringFeatures< ST > | |
get_features(int32_t &num_str, int32_t &max_str_len) | CStringFeatures< ST > | [virtual] |
get_features(TString< ST > **dst, int32_t *num_str) | CStringFeatures< ST > | [virtual] |
get_histogram(float64_t **hist, int32_t *rows, int32_t *cols, bool normalize=true) | CStringFeatures< ST > | [virtual] |
get_io() | CSGObject | |
get_line(uint64_t &len, uint64_t &offs, int32_t &line_nr, uint64_t file_length) | CStringFileFeatures< ST > | [protected] |
get_masked_symbols(ST symbol, uint8_t mask) | CStringFeatures< ST > | |
get_max_num_symbols() | CStringFeatures< ST > | |
get_max_vector_length() | CStringFeatures< ST > | [virtual] |
get_name() const | CStringFeatures< ST > | [virtual] |
get_num_preproc() | CFeatures | |
get_num_preprocessed() | CFeatures | |
get_num_symbols() | CStringFeatures< ST > | |
get_num_vectors() | CStringFeatures< ST > | [virtual] |
get_order() | CStringFeatures< ST > | |
get_original_num_symbols() | CStringFeatures< ST > | |
get_parallel() | CSGObject | |
get_preproc(int32_t num) | CFeatures | |
get_size() | CStringFeatures< ST > | [virtual] |
get_transposed() | CStringFeatures< ST > | |
get_transposed(int32_t &num_feat, int32_t &num_vec) | CStringFeatures< ST > | |
get_vector_length(int32_t vec_num) | CStringFeatures< ST > | [virtual] |
get_version() | CSGObject | |
get_zero_terminated_string_copy(TString< ST > str) | CStringFeatures< ST > | [static] |
has_property(EFeatureProperty p) | CFeatures | |
have_same_length(int32_t len=-1) | CStringFeatures< ST > | |
io | CSGObject | |
is_generic(EPrimitiveType *generic) const | CSGObject | [virtual] |
is_preprocessed(int32_t num) | CFeatures | |
length_of_single_string | CStringFeatures< ST > | [protected] |
list_feature_obj() | CFeatures | |
load(CFile *loader) | CStringFeatures< ST > | [virtual] |
load_ascii_file(char *fname, bool remap_to_bin=true, EAlphabet ascii_alphabet=DNA, EAlphabet binary_alphabet=RAWDNA) | CStringFeatures< ST > | |
load_compressed(char *src, bool decompress) | CStringFeatures< ST > | [virtual] |
load_fasta_file(const char *fname, bool ignore_invalid=false) | CStringFeatures< ST > | |
load_fastq_file(const char *fname, bool ignore_invalid=false, bool bitremap_in_single_string=false) | CStringFeatures< ST > | |
load_from_directory(char *dirname) | CStringFeatures< ST > | |
load_serializable(CSerializableFile *file, const char *prefix="") | CSGObject | [virtual] |
load_serializable_post() | CSGObject | [protected, virtual] |
load_serializable_pre() | CSGObject | [protected, virtual] |
m_parameters | CSGObject | [protected] |
max_string_length | CStringFeatures< ST > | [protected] |
num_symbols | CStringFeatures< ST > | [protected] |
num_vectors | CStringFeatures< ST > | [protected] |
obtain_by_position_list(int32_t window_size, CDynamicArray< int32_t > *positions, int32_t skip=0) | CStringFeatures< ST > | |
obtain_by_sliding_window(int32_t window_size, int32_t step_size, int32_t skip=0) | CStringFeatures< ST > | |
obtain_from_char(CStringFeatures< char > *sf, int32_t start, int32_t p_order, int32_t gap, bool rev) | CStringFeatures< ST > | |
obtain_from_char_features(CStringFeatures< CT > *sf, int32_t start, int32_t p_order, int32_t gap, bool rev) | CStringFeatures< ST > | |
order | CStringFeatures< ST > | [protected] |
original_num_symbols | CStringFeatures< ST > | [protected] |
parallel | CSGObject | |
preprocess_on_get | CStringFeatures< ST > | [protected] |
print_serializable(const char *prefix="") | CSGObject | [virtual] |
reshape(int32_t num_features, int32_t num_vectors) | CFeatures | [virtual] |
save(CFile *writer) | CStringFeatures< ST > | [virtual] |
save_compressed(char *dest, E_COMPRESSION_TYPE compression, int level) | CStringFeatures< ST > | [virtual] |
save_serializable(CSerializableFile *file, const char *prefix="") | CSGObject | [virtual] |
save_serializable_post() | CSGObject | [protected, virtual] |
save_serializable_pre() | CSGObject | [protected, virtual] |
set_feature_vector(ST *src, int32_t len, int32_t num) | CStringFeatures< ST > | |
set_feature_vector(int32_t num, ST *string, int32_t len) | CStringFeatures< ST > | [virtual] |
set_features(TString< ST > *p_features, int32_t p_num_vectors, int32_t p_max_string_length) | CStringFeatures< ST > | |
set_generic() | CSGObject | |
set_io(IO *io) | CSGObject | |
set_parallel(Parallel *parallel) | CSGObject | |
set_preprocessed(int32_t num) | CFeatures | |
set_property(EFeatureProperty p) | CFeatures | |
set_version(Version *version) | CSGObject | |
shift_offset(ST offset, int32_t amount) | CStringFeatures< ST > | |
shift_symbol(ST symbol, int32_t amount) | CStringFeatures< ST > | |
single_string | CStringFeatures< ST > | [protected] |
symbol_mask_table | CStringFeatures< ST > | [protected] |
unembed_word(ST word, uint8_t *seq, int32_t len) | CStringFeatures< ST > | |
unset_generic() | CSGObject | |
unset_property(EFeatureProperty p) | CFeatures | |
version | CSGObject | |
~CFeatures() | CFeatures | [virtual] |
~CSGObject() | CSGObject | [virtual] |
~CStringFeatures() | CStringFeatures< ST > | [virtual] |
~CStringFileFeatures() | CStringFileFeatures< ST > | [virtual] |