| 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_gradient_parameter_dictionary(CMap< TParameter *, CSGObject * > *dict) | CSGObject | |
| CDynProg(int32_t p_num_svms=8) | CDynProg | |
| check_svm_arrays() | CDynProg | |
| clone() | CSGObject | virtual |
| 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 | protectedstatic |
| deep_copy() const | CSGObject | virtual |
| equals(CSGObject *other, float64_t accuracy=0.0, bool tolerant=false) | 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 | protectedstatic |
| 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 | protectedvirtual |
| 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_serializable(CSerializableFile *file, const char *prefix="") | CSGObject | virtual |
| load_serializable_post() | CSGObject | protectedvirtual |
| load_serializable_pre() | CSGObject | protectedvirtual |
| 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_gradient_parameters | CSGObject | |
| 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_parameters | CSGObject | |
| 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 |
| mod_words_default | CDynProg | protectedstatic |
| num_words_default | CDynProg | protectedstatic |
| parallel | CSGObject | |
| parameter_hash_changed() | CSGObject | virtual |
| 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="") | CSGObject | virtual |
| save_serializable_post() | CSGObject | protectedvirtual |
| save_serializable_pre() | CSGObject | protectedvirtual |
| 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_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| 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 | protectedstatic |
| string_words_default | CDynProg | protectedstatic |
| unset_generic() | CSGObject | |
| update_parameter_hash() | CSGObject | virtual |
| version | CSGObject | |
| word_degree_default | CDynProg | protectedstatic |
| ~CDynProg() | CDynProg | virtual |
| ~CSGObject() | CSGObject | virtual |
