, including all inherited members.
add_states(int32_t num_states, float64_t default_val=0) | CHMM | |
all_pat_prob | CHMM | [protected] |
all_path_prob_updated | CHMM | [protected] |
alloc_state_dependend_arrays() | CHMM | |
alpha_cache | CHMM | [protected] |
append_model(CHMM *append_model, float64_t *cur_out, float64_t *app_out) | CHMM | |
append_model(CHMM *append_model) | CHMM | |
arrayN1 | CHMM | [protected] |
arrayN2 | CHMM | [protected] |
backward(int32_t time, int32_t state, int32_t dimension) | CHMM | [protected] |
backward_comp(int32_t time, int32_t state, int32_t dimension) | CHMM | |
backward_comp_old(int32_t time, int32_t state, int32_t dimension) | CHMM | |
baum_welch_viterbi_train(BaumWelchViterbiType type) | CHMM | |
best_path(int32_t dimension) | CHMM | |
beta_cache | CHMM | [protected] |
build_parameter_dictionary(CMap< TParameter *, CSGObject * > &dict) | CSGObject | |
CDistribution() | CDistribution | |
check_model_derivatives() | CHMM | |
check_model_derivatives_combined() | CHMM | |
CHMM() | CHMM | |
CHMM(int32_t N, int32_t M, Model *model, float64_t PSEUDO) | CHMM | |
CHMM(CStringFeatures< uint16_t > *obs, int32_t N, int32_t M, float64_t PSEUDO) | CHMM | |
CHMM(int32_t N, float64_t *p, float64_t *q, float64_t *a) | CHMM | |
CHMM(int32_t N, float64_t *p, float64_t *q, int32_t num_trans, float64_t *a_trans) | CHMM | |
CHMM(FILE *model_file, float64_t PSEUDO) | CHMM | |
CHMM(CHMM *h) | CHMM | |
chop(float64_t value) | CHMM | |
clear_model() | CHMM | |
clear_model_defined() | CHMM | |
close_bracket(FILE *file) | CHMM | [protected] |
comma_or_space(FILE *file) | CHMM | [protected] |
conv_it | CHMM | [protected] |
convert_to_log() | CHMM | |
copy_model(CHMM *l) | CHMM | |
CSGObject() | CSGObject | |
CSGObject(const CSGObject &orig) | CSGObject | |
deep_copy() const | CSGObject | [virtual] |
end_state_distribution_q | CHMM | [protected] |
epsilon | CHMM | [protected] |
error(int32_t p_line, const char *str) | CHMM | [protected] |
estimate_model_baum_welch(CHMM *train) | CHMM | |
estimate_model_baum_welch_defined(CHMM *train) | CHMM | |
estimate_model_baum_welch_old(CHMM *train) | CHMM | |
estimate_model_baum_welch_trans(CHMM *train) | CHMM | |
estimate_model_viterbi(CHMM *train) | CHMM | |
estimate_model_viterbi_defined(CHMM *train) | CHMM | |
features | CDistribution | [protected] |
forward(int32_t time, int32_t state, int32_t dimension) | CHMM | [protected] |
forward_comp(int32_t time, int32_t state, int32_t dimension) | CHMM | |
forward_comp_old(int32_t time, int32_t state, int32_t dimension) | CHMM | |
free_state_dependend_arrays() | CHMM | |
get_A(T_STATES line_, T_STATES column) const | CHMM | |
get_a(T_STATES line_, T_STATES column) const | CHMM | |
get_B(T_STATES line_, uint16_t column) const | CHMM | |
get_b(T_STATES line_, uint16_t column) const | CHMM | |
get_best_path_state(int32_t dim, int32_t t) | CHMM | |
get_derivative(int32_t num_param, int32_t num_example) | CDistribution | [virtual] |
get_epsilon() | CHMM | |
get_features() | CDistribution | [virtual] |
get_global_io() | CSGObject | |
get_global_parallel() | CSGObject | |
get_global_version() | CSGObject | |
get_iterations() | CHMM | |
get_likelihood_example(int32_t num_example) | CDistribution | [virtual] |
get_log_derivative(int32_t num_param, int32_t num_example) | CHMM | [virtual] |
get_log_likelihood() | CDistribution | [virtual] |
get_log_likelihood_example(int32_t num_example) | CHMM | [virtual] |
get_log_likelihood_sample() | CDistribution | [virtual] |
get_log_model_parameter(int32_t num_param) | CHMM | [virtual] |
get_M() const | CHMM | |
get_model_parameter(int32_t num_param) | CDistribution | [virtual] |
get_modelsel_names() | CSGObject | |
get_modsel_param_descr(const char *param_name) | CSGObject | |
get_modsel_param_index(const char *param_name) | CSGObject | |
get_N() const | CHMM | |
get_name() const | CHMM | [virtual] |
get_num_model_parameters() | CHMM | [virtual] |
get_num_relevant_model_parameters() | CDistribution | [virtual] |
get_numbuffer(FILE *file, char *buffer, int32_t length) | CHMM | [protected] |
get_observations() | CHMM | |
get_p(T_STATES offset) const | CHMM | |
get_path(int32_t dim, float64_t &prob) | CHMM | |
get_pseudo() const | CHMM | |
get_pseudo_count() | CDistribution | [virtual] |
get_psi(int32_t time, T_STATES state, int32_t dimension) const | CHMM | |
get_q(T_STATES offset) const | CHMM | |
get_status() const | CHMM | |
GOTa | CHMM | [protected, static] |
GOTb | CHMM | [protected, static] |
GOTconst_a | CHMM | [protected, static] |
GOTconst_b | CHMM | [protected, static] |
GOTconst_p | CHMM | [protected, static] |
GOTconst_q | CHMM | [protected, static] |
GOTlearn_a | CHMM | [protected, static] |
GOTlearn_b | CHMM | [protected, static] |
GOTlearn_p | CHMM | [protected, static] |
GOTlearn_q | CHMM | [protected, static] |
GOTM | CHMM | [protected, static] |
GOTN | CHMM | [protected, static] |
GOTO | CHMM | [protected, static] |
GOTp | CHMM | [protected, static] |
GOTq | CHMM | [protected, static] |
init_model_defined() | CHMM | |
init_model_random() | CHMM | |
initial_state_distribution_p | CHMM | [protected] |
initialize(Model *model, float64_t PSEUDO, FILE *model_file=NULL) | CHMM | |
invalidate_model() | CHMM | |
io | CSGObject | |
is_generic(EPrimitiveType *generic) const | CSGObject | [virtual] |
iteration_count | CHMM | [protected] |
iterations | CHMM | [protected] |
line | CHMM | [protected] |
linear_model_derivative(T_STATES i, uint16_t j, int32_t dimension) | CHMM | |
linear_model_probability(int32_t dimension) | CHMM | |
linear_train(bool right_align=false) | CHMM | |
load_all_file_parameters(int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="") | CSGObject | |
load_definitions(FILE *file, bool verbose, bool initialize=true) | CHMM | |
load_file_parameters(const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="") | CSGObject | |
load_model(FILE *file) | CHMM | |
load_serializable(CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER) | CSGObject | [virtual] |
load_serializable_post() | CSGObject | [protected, virtual] |
load_serializable_pre() | CSGObject | [protected, virtual] |
loglikelihood | CHMM | [protected] |
M | CHMM | [protected] |
m_hash | CSGObject | |
m_model_selection_parameters | CSGObject | |
m_parameter_map | CSGObject | |
m_parameters | CSGObject | |
map_parameters(DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos) | CSGObject | |
migrate(DynArray< TParameter * > *param_base, const SGParamInfo *target) | CSGObject | [protected, virtual] |
mod_prob | CHMM | [protected] |
mod_prob_updated | CHMM | [protected] |
model | CHMM | [protected] |
model_derivative_a(T_STATES i, T_STATES j, int32_t dimension) | CHMM | |
model_derivative_b(T_STATES i, uint16_t j, int32_t dimension) | CHMM | |
model_derivative_p(T_STATES i, int32_t dimension) | CHMM | |
model_derivative_q(T_STATES i, int32_t dimension) | CHMM | |
model_probability(int32_t dimension=-1) | CHMM | |
model_probability_comp() | CHMM | |
N | CHMM | [protected] |
normalize(bool keep_dead_states=false) | CHMM | |
observation_matrix_b | CHMM | [protected] |
observation_matrix_B | CHMM | [protected] |
one_to_one_migration_prepare(DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL) | CSGObject | [protected, virtual] |
open_bracket(FILE *file) | CHMM | [protected] |
output_model(bool verbose=false) | CHMM | |
output_model_defined(bool verbose=false) | CHMM | |
p_observations | CHMM | [protected] |
parallel | CSGObject | |
pat_prob | CHMM | [protected] |
path | CHMM | [protected] |
path_deriv_dimension | CHMM | [protected] |
path_deriv_updated | CHMM | [protected] |
path_derivative_a(T_STATES i, T_STATES j, int32_t dimension) | CHMM | |
path_derivative_b(T_STATES i, uint16_t j, int32_t dimension) | CHMM | |
path_derivative_p(T_STATES i, int32_t dimension) | CHMM | |
path_derivative_q(T_STATES i, int32_t dimension) | CHMM | |
path_prob_dimension | CHMM | [protected] |
path_prob_updated | CHMM | [protected] |
permutation_entropy(int32_t window_width, int32_t sequence_number) | CHMM | |
prepare_path_derivative(int32_t dim) | CHMM | [protected] |
print_modsel_params() | CSGObject | |
print_serializable(const char *prefix="") | CSGObject | [virtual] |
PSEUDO | CHMM | [protected] |
pseudo_count | CDistribution | [protected] |
reused_caches | CHMM | [protected] |
save_likelihood(FILE *file) | CHMM | |
save_likelihood_bin(FILE *file) | CHMM | |
save_model(FILE *file) | CHMM | |
save_model_bin(FILE *file) | CHMM | |
save_model_derivatives(FILE *file) | CHMM | |
save_model_derivatives_bin(FILE *file) | CHMM | |
save_path(FILE *file) | CHMM | |
save_path_derivatives(FILE *file) | CHMM | |
save_path_derivatives_bin(FILE *file) | CHMM | |
save_serializable(CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER) | CSGObject | [virtual] |
save_serializable_post() | CSGObject | [protected, virtual] |
save_serializable_pre() | CSGObject | [protected, virtual] |
set_A(T_STATES line_, T_STATES column, float64_t value) | CHMM | |
set_a(T_STATES line_, T_STATES column, float64_t value) | CHMM | |
set_B(T_STATES line_, uint16_t column, float64_t value) | CHMM | |
set_b(T_STATES line_, uint16_t column, float64_t value) | CHMM | |
set_epsilon(float64_t eps) | CHMM | |
set_features(CFeatures *f) | CDistribution | [virtual] |
set_generic() | CSGObject | |
set_global_io(SGIO *io) | CSGObject | |
set_global_parallel(Parallel *parallel) | CSGObject | |
set_global_version(Version *version) | CSGObject | |
set_iterations(int32_t num) | CHMM | |
set_observation_nocache(CStringFeatures< uint16_t > *obs) | CHMM | |
set_observations(CStringFeatures< uint16_t > *obs, CHMM *hmm=NULL) | CHMM | |
set_p(T_STATES offset, float64_t value) | CHMM | |
set_pseudo(float64_t pseudo) | CHMM | |
set_pseudo_count(float64_t pseudo) | CDistribution | [virtual] |
set_psi(int32_t time, T_STATES state, T_STATES value, int32_t dimension) | CHMM | |
set_q(T_STATES offset, float64_t value) | CHMM | |
shallow_copy() const | CSGObject | [virtual] |
state_probability(int32_t time, int32_t state, int32_t dimension) | CHMM | |
states_per_observation_psi | CHMM | [protected] |
status | CHMM | [protected] |
train(CFeatures *data=NULL) | CHMM | [virtual] |
transition_matrix_A | CHMM | [protected] |
transition_matrix_a | CHMM | [protected] |
transition_probability(int32_t time, int32_t state_i, int32_t state_j, int32_t dimension) | CHMM | |
unset_generic() | CSGObject | |
update_parameter_hash() | CSGObject | [protected, virtual] |
version | CSGObject | |
~CDistribution() | CDistribution | [virtual] |
~CHMM() | CHMM | [virtual] |
~CSGObject() | CSGObject | [virtual] |