, including all inherited members.
best_path_set_segment_ids_mask(int32_t *segment_ids, float64_t *segment_mask, int32_t m) | CDynProg | |
best_path_set_segment_loss(SGMatrix< float64_t > segment_loss) | CDynProg | |
best_path_trans_deriv(int32_t *my_state_seq, int32_t *my_pos_seq, int32_t my_seq_len, const float64_t *seq_array, int32_t max_num_signals) | CDynProg | |
build_parameter_dictionary(CMap< TParameter *, CSGObject * > &dict) | CSGObject | |
CDynProg(int32_t p_num_svms=8) | CDynProg | |
check_svm_arrays() | CDynProg | |
compute_nbest_paths(int32_t max_num_signals, bool use_orf, int16_t nbest, bool with_loss, bool with_multiple_sequences) | CDynProg | |
create_word_string() | CDynProg | |
CSGObject() | CSGObject | |
CSGObject(const CSGObject &orig) | CSGObject | |
cum_num_words_default | CDynProg | [protected, static] |
deep_copy() const | CSGObject | [virtual] |
extend_orf(int32_t orf_from, int32_t orf_to, int32_t start, int32_t &last_pos, int32_t to) | CDynProg | [protected] |
find_frame(const int32_t from_state) | CDynProg | [protected] |
frame_plifs | CDynProg | [protected, static] |
get_a(T_STATES line_, T_STATES column) const | CDynProg | |
get_a_deriv(T_STATES line_, T_STATES column) const | CDynProg | |
get_global_io() | CSGObject | |
get_global_parallel() | CSGObject | |
get_global_version() | CSGObject | |
get_lin_feat(int32_t &dim1, int32_t &dim2) | CDynProg | |
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 | CDynProg | |
get_name() const | CDynProg | [protected, virtual] |
get_num_positions() | CDynProg | |
get_num_states() | CDynProg | |
get_num_svms() | CDynProg | |
get_p(T_STATES offset) const | CDynProg | |
get_p_deriv(T_STATES offset) const | CDynProg | |
get_path_losses(float64_t **my_losses, int32_t *seq_len) | CDynProg | |
get_path_scores(float64_t **my_scores, int32_t *seq_len) | CDynProg | |
get_positions() | CDynProg | |
get_q(T_STATES offset) const | CDynProg | |
get_q_deriv(T_STATES offset) const | CDynProg | |
get_scores() | CDynProg | |
get_segment_loss_object() | CDynProg | |
get_states() | CDynProg | |
init_content_svm_value_array(const int32_t p_num_svms) | CDynProg | |
init_mod_words_array(SGMatrix< int32_t > p_mod_words_array) | CDynProg | |
init_tiling_data(int32_t *probe_pos, float64_t *intensities, const int32_t num_probes) | CDynProg | |
io | CSGObject | |
is_generic(EPrimitiveType *generic) const | CSGObject | [virtual] |
load_all_file_parameters(int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="") | CSGObject | |
load_file_parameters(const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="") | CSGObject | |
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] |
long_transition_settings(bool use_long_transitions, int32_t threshold, int32_t max_len) | CDynProg | |
lookup_content_svm_values(const int32_t from_state, const int32_t to_state, const int32_t from_pos, const int32_t to_pos, float64_t *svm_values, int32_t frame) | CDynProg | [protected] |
lookup_tiling_plif_values(const int32_t from_state, const int32_t to_state, const int32_t len, float64_t *svm_values) | CDynProg | [protected] |
m_cum_num_words | CDynProg | [protected] |
m_cum_num_words_array | CDynProg | [protected] |
m_dict_weights | CDynProg | [protected] |
m_end_state_distribution_q | CDynProg | [protected] |
m_end_state_distribution_q_deriv | CDynProg | [protected] |
m_genestr | CDynProg | [protected] |
m_genestr_stop | CDynProg | [protected] |
m_hash | CSGObject | |
m_initial_state_distribution_p | CDynProg | [protected] |
m_initial_state_distribution_p_deriv | CDynProg | [protected] |
m_intron_list | CDynProg | [protected] |
m_lin_feat | CDynProg | [protected] |
m_long_transition_threshold | CDynProg | [protected] |
m_long_transitions | CDynProg | [protected] |
m_max_a_id | CDynProg | [protected] |
m_mod_words | CDynProg | [protected] |
m_mod_words_array | CDynProg | [protected] |
m_model_selection_parameters | CSGObject | |
m_my_losses | CDynProg | [protected] |
m_my_pos_seq | CDynProg | [protected] |
m_my_scores | CDynProg | [protected] |
m_my_state_seq | CDynProg | [protected] |
m_N | CDynProg | [protected] |
m_num_degrees | CDynProg | [protected] |
m_num_intron_plifs | CDynProg | [protected] |
m_num_lin_feat_plifs_cum | CDynProg | [protected] |
m_num_probes_cum | CDynProg | [protected] |
m_num_raw_data | CDynProg | [protected] |
m_num_svms | CDynProg | [protected] |
m_num_unique_words | CDynProg | [protected] |
m_num_words | CDynProg | [protected] |
m_num_words_array | CDynProg | [protected] |
m_observation_matrix | CDynProg | [protected] |
m_orf_info | CDynProg | [protected] |
m_parameter_map | CSGObject | |
m_parameters | CSGObject | |
m_PEN | CDynProg | [protected] |
m_PEN_state_signals | CDynProg | [protected] |
m_plif_list | CDynProg | [protected] |
m_plif_matrices | CDynProg | [protected] |
m_pos | CDynProg | [protected] |
m_positions | CDynProg | [protected] |
m_probe_pos | CDynProg | [protected] |
m_raw_intensities | CDynProg | [protected] |
m_scores | CDynProg | [protected] |
m_seg_loss_obj | CDynProg | [protected] |
m_segment_ids | CDynProg | [protected] |
m_segment_loss | CDynProg | [protected] |
m_segment_mask | CDynProg | [protected] |
m_segment_sum_weights | CDynProg | [protected] |
m_seq_len | CDynProg | [protected] |
m_seq_sparse1 | CDynProg | [protected] |
m_seq_sparse2 | CDynProg | [protected] |
m_sign_words | CDynProg | [protected] |
m_sign_words_array | CDynProg | [protected] |
m_states | CDynProg | [protected] |
m_string_words | CDynProg | [protected] |
m_string_words_array | CDynProg | [protected] |
m_svm_arrays_clean | CDynProg | [protected] |
m_transition_matrix_a | CDynProg | [protected] |
m_transition_matrix_a_deriv | CDynProg | [protected] |
m_transition_matrix_a_id | CDynProg | [protected] |
m_word_degree | CDynProg | [protected] |
m_wordstr | CDynProg | [protected] |
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_words_default | CDynProg | [protected, static] |
num_words_default | CDynProg | [protected, static] |
one_to_one_migration_prepare(DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL) | CSGObject | [protected, virtual] |
parallel | CSGObject | |
precompute_content_values() | CDynProg | |
precompute_stop_codons() | CDynProg | |
precompute_tiling_plifs(CPlif **PEN, const int32_t *tiling_plif_ids, const int32_t num_tiling_plifs) | CDynProg | |
print_modsel_params() | CSGObject | |
print_serializable(const char *prefix="") | CSGObject | [virtual] |
raw_intensities_interval_query(const int32_t from_pos, const int32_t to_pos, float64_t *intensities, int32_t type) | CDynProg | [protected] |
resize_lin_feat(int32_t num_new_feat) | CDynProg | |
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(SGMatrix< float64_t > a) | CDynProg | |
set_a(T_STATES line_, T_STATES column, float64_t value) | CDynProg | |
set_a_id(SGMatrix< int32_t > a) | CDynProg | |
set_a_trans_matrix(SGMatrix< float64_t > a_trans) | CDynProg | |
set_content_type_array(SGMatrix< float64_t > seg_path) | CDynProg | |
set_dict_weights(SGMatrix< float64_t > dictionary_weights) | CDynProg | |
set_gene_string(SGVector< char > genestr) | CDynProg | |
set_generic() | CSGObject | |
set_global_io(SGIO *io) | CSGObject | |
set_global_parallel(Parallel *parallel) | CSGObject | |
set_global_version(Version *version) | CSGObject | |
set_intron_list(CIntronList *intron_list, int32_t num_plifs) | CDynProg | |
set_lin_feat(float64_t *p_lin_feat, int32_t p_num_svms, int32_t p_seq_len) | CDynProg | |
set_my_pos_seq(int32_t *my_pos_seq) | CDynProg | |
set_my_state_seq(int32_t *my_state_seq) | CDynProg | |
set_num_states(int32_t N) | CDynProg | |
set_observation_matrix(SGNDArray< float64_t > seq) | CDynProg | |
set_orf_info(SGMatrix< int32_t > orf_info) | CDynProg | |
set_p(T_STATES offset, float64_t value) | CDynProg | |
set_p_vector(SGVector< float64_t > p) | CDynProg | |
set_plif_matrices(CPlifMatrix *pm) | CDynProg | |
set_pos(SGVector< int32_t > pos) | CDynProg | |
set_q(T_STATES offset, float64_t value) | CDynProg | |
set_q_vector(SGVector< float64_t > q) | CDynProg | |
set_sparse_features(CSparseFeatures< float64_t > *seq_sparse1, CSparseFeatures< float64_t > *seq_sparse2) | CDynProg | |
shallow_copy() const | CSGObject | [virtual] |
sign_words_default | CDynProg | [protected, static] |
string_words_default | CDynProg | [protected, static] |
unset_generic() | CSGObject | |
update_parameter_hash() | CSGObject | [protected, virtual] |
version | CSGObject | |
word_degree_default | CDynProg | [protected, static] |
~CDynProg() | CDynProg | [virtual] |
~CSGObject() | CSGObject | [virtual] |