, including all inherited members.
best_path_2struct(const float64_t *seq, int32_t seq_len, const int32_t *pos, CPlifBase **Plif_matrix, const char *genestr, int32_t genestr_len, int16_t nbest, float64_t *prob_nbest, int32_t *my_state_seq, int32_t *my_pos_seq, float64_t *dictionary_weights, int32_t dict_len, float64_t *segment_sum_weights) | CDynProg | |
best_path_2struct_call(int32_t nbest) | CDynProg | |
best_path_call(int32_t nbest, bool use_orf) | CDynProg | |
best_path_deriv_call() | CDynProg | |
best_path_deriv_call(int32_t nbest) | CDynProg | |
best_path_get_losses(float64_t **my_losses, int32_t *seq_len) | CDynProg | |
best_path_get_positions(int32_t **positions, int32_t *m, int32_t *n) | CDynProg | |
best_path_get_scores(float64_t **scores, int32_t *n) | CDynProg | |
best_path_get_states(int32_t **states, int32_t *m, int32_t *n) | CDynProg | |
best_path_no_b(int32_t max_iter, int32_t &best_iter, int32_t *my_path) | CDynProg | |
best_path_no_b_trans(int32_t max_iter, int32_t &max_best_iter, int16_t nbest, float64_t *prob_nbest, int32_t *my_paths) | CDynProg | |
best_path_set_dict_weights(float64_t *dictionary_weights, int32_t dict_len, int32_t n) | CDynProg | |
best_path_set_genestr(char *genestr, int32_t genestr_len, int32_t genestr_num) | CDynProg | |
best_path_set_my_pos_seq(int32_t *my_pos_seq, int32_t seq_len) | CDynProg | |
best_path_set_my_state_seq(int32_t *my_state_seq, int32_t seq_len) | CDynProg | |
best_path_set_orf_info(int32_t *orf_info, int32_t m, int32_t n) | CDynProg | |
best_path_set_plif_id_matrix(int32_t *plif_id_matrix, int32_t m, int32_t n) | CDynProg | |
best_path_set_plif_list(CDynamicArray< CPlifBase * > *plifs) | CDynProg | |
best_path_set_plif_state_signal_matrix(int32_t *plif_id_matrix, int32_t m, int32_t n) | CDynProg | |
best_path_set_pos(int32_t *pos, int32_t seq_len) | CDynProg | |
best_path_set_segment_ids_mask(int32_t *segment_ids, float64_t *segment_mask, int32_t m) | CDynProg | |
best_path_set_segment_loss(float64_t *segment_loss, int32_t num_segment_id1, int32_t num_segment_id2) | CDynProg | |
best_path_set_segment_sum_weights(float64_t *segment_sum_weights, int32_t num_states, int32_t seq_len) | CDynProg | |
best_path_set_seq(float64_t *seq, int32_t N, int32_t seq_len) | CDynProg | |
best_path_set_seq3d(float64_t *seq, int32_t p_N, int32_t seq_len, int32_t max_num_signals) | CDynProg | |
best_path_set_single_genestr(char *genestr, int32_t genestr_len) | CDynProg | |
best_path_simple_call(int32_t nbest) | CDynProg | |
best_path_trans(const float64_t *seq, int32_t seq_len, const int32_t *pos, const int32_t *orf_info, CPlifBase **PLif_matrix, CPlifBase **Plif_state_signals, int32_t max_num_signals, int32_t genestr_num, float64_t *prob_nbest, int32_t *my_state_seq, int32_t *my_pos_seq, bool use_orf) | CDynProg | |
best_path_trans_deriv(int32_t *my_state_seq, int32_t *my_pos_seq, float64_t *my_scores, float64_t *my_losses, int32_t my_seq_len, const float64_t *seq_array, int32_t seq_len, const int32_t *pos, CPlifBase **Plif_matrix, CPlifBase **Plif_state_signals, int32_t max_num_signals, int32_t genestr_num) | CDynProg | |
best_path_trans_simple(const float64_t *seq, int32_t seq_len, int16_t nbest, float64_t *prob_nbest, int32_t *my_state_seq) | CDynProg | |
CDynProg(int32_t p_num_svms=8) | CDynProg | |
check_svm_arrays() | CDynProg | |
clear_segment_loss(struct segment_loss_struct &loss) | CDynProg | [protected] |
clear_svm_values(struct svm_values_struct &svs) | CDynProg | [protected] |
create_word_string(const char *genestr, int32_t genestr_num, int32_t genestr_len, uint16_t ***wordstr) | CDynProg | |
CSGObject() | CSGObject | |
CSGObject(const CSGObject &orig) | CSGObject | |
cum_num_words | CDynProg | [protected] |
cum_num_words_array | CDynProg | [protected] |
cum_num_words_single | CDynProg | [protected] |
dict_weights | CDynProg | [protected] |
dict_weights_array | CDynProg | [protected] |
end_state_distribution_q | CDynProg | [protected] |
end_state_distribution_q_deriv | CDynProg | [protected] |
extend_orf(int32_t orf_from, int32_t orf_to, int32_t start, int32_t &last_pos, int32_t to) | CDynProg | [protected] |
extend_segment_loss(struct segment_loss_struct &loss, const int32_t *pos_array, int32_t segment_id, int32_t pos, int32_t &last_pos, float64_t &last_value) | CDynProg | [protected] |
extend_segment_sum_value(float64_t *segment_sum_weights, int32_t seqlen, int32_t num_states, int32_t pos, int32_t &last_segment_sum_pos, float64_t *segment_sum_value) | CDynProg | [protected] |
extend_svm_value(uint16_t *wordstr, int32_t pos, int32_t &last_svm_pos, float64_t *svm_value) | CDynProg | [protected] |
find_frame(const int32_t from_state) | CDynProg | [protected] |
find_segment_loss_till_pos(const int32_t *pos, int32_t t_end, CArray< int32_t > &segment_ids, CArray< float64_t > &segment_mask, struct segment_loss_struct &loss) | CDynProg | [protected] |
find_svm_values_till_pos(uint16_t ***wordstr, const int32_t *pos, int32_t t_end, struct svm_values_struct &svs) | CDynProg | [protected] |
find_svm_values_till_pos(uint16_t **wordstr, const int32_t *pos, int32_t t_end, struct svm_values_struct &svs) | CDynProg | [protected] |
get_a(T_STATES line_, T_STATES column) const | CDynProg | |
get_a_deriv(T_STATES line_, T_STATES column) const | CDynProg | |
get_lin_feat(int32_t &dim1, int32_t &dim2) | CDynProg | |
get_N() const | CDynProg | |
get_name() const | CDynProg | [protected, virtual] |
get_num_states() | CDynProg | |
get_num_svms() | CDynProg | |
get_p(T_STATES offset) const | CDynProg | |
get_p_deriv(T_STATES offset) const | CDynProg | |
get_q(T_STATES offset) const | CDynProg | |
get_q_deriv(T_STATES offset) const | CDynProg | |
init_content_svm_value_array(const int32_t p_num_svms, const int32_t seq_len) | CDynProg | |
init_cum_num_words_array(int32_t *p_cum_num_words_array, int32_t num_elem) | CDynProg | |
init_mod_words_array(int32_t *p_mod_words_array, int32_t num_elem, int32_t num_columns) | CDynProg | |
init_num_words_array(int32_t *p_num_words_array, int32_t num_elem) | CDynProg | |
init_segment_loss(struct segment_loss_struct &loss, int32_t seqlen, int32_t howmuchlookback) | CDynProg | [protected] |
init_sign_words_array(bool *p_sign_words_array, int32_t num_elem) | CDynProg | |
init_string_words_array(int32_t *p_string_words_array, int32_t num_elem) | CDynProg | |
init_svm_arrays(int32_t p_num_degrees, int32_t p_num_svms) | CDynProg | |
init_svm_values(struct svm_values_struct &svs, int32_t start_pos, int32_t seqlen, int32_t howmuchlookback) | CDynProg | [protected] |
init_tiling_data(int32_t *probe_pos, float64_t *intensities, const int32_t num_probes, const int32_t seq_len) | CDynProg | |
init_word_degree_array(int32_t *p_word_degree_array, int32_t num_elem) | CDynProg | |
initial_state_distribution_p | CDynProg | [protected] |
initial_state_distribution_p_deriv | CDynProg | [protected] |
io | CSGObject | |
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_call | CDynProg | [protected] |
m_dict_weights | CDynProg | [protected] |
m_genestr | CDynProg | [protected] |
m_genestr_len | CDynProg | [protected] |
m_genestr_stop | CDynProg | [protected] |
m_lin_feat | CDynProg | [protected] |
m_my_losses | CDynProg | [protected] |
m_my_pos_seq | CDynProg | [protected] |
m_my_scores | CDynProg | [protected] |
m_my_state_seq | CDynProg | [protected] |
m_num_lin_feat_plifs_cum | CDynProg | [protected] |
m_num_probes_cum | CDynProg | [protected] |
m_num_raw_data | CDynProg | [protected] |
m_orf_info | CDynProg | [protected] |
m_PEN | CDynProg | [protected] |
m_PEN_state_signals | CDynProg | [protected] |
m_plif_list | 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_segment_ids | CDynProg | [protected] |
m_segment_loss | CDynProg | [protected] |
m_segment_mask | CDynProg | [protected] |
m_segment_sum_weights | CDynProg | [protected] |
m_seq | CDynProg | [protected] |
m_states | CDynProg | [protected] |
m_step | CDynProg | [protected] |
max_a_id | CDynProg | [protected] |
mod_words | CDynProg | [protected] |
mod_words_array | CDynProg | [protected] |
N | CDynProg | [protected] |
num_degrees | CDynProg | [protected] |
num_strings | CDynProg | [protected] |
num_svms | CDynProg | [protected] |
num_svms_single | CDynProg | [protected] |
num_unique_words | CDynProg | [protected] |
num_unique_words_single | CDynProg | [protected] |
num_words | CDynProg | [protected] |
num_words_array | CDynProg | [protected] |
num_words_single | CDynProg | [protected] |
parallel | CSGObject | |
precompute_content_values(uint16_t ***wordstr, const int32_t *pos, const int32_t num_cand_pos, const int32_t genestr_len, float64_t *dictionary_weights, int32_t dict_len) | CDynProg | |
precompute_stop_codons(const char *genestr, int32_t genestr_len) | CDynProg | |
precompute_tiling_plifs(CPlif **PEN, const int32_t *tiling_plif_ids, const int32_t num_tiling_plifs, const int32_t seq_len, const int32_t *pos) | CDynProg | |
raw_intensities_interval_query(const int32_t from_pos, const int32_t to_pos, float64_t *intensities, int32_t type) | CDynProg | [protected] |
ref() | CSGObject | |
ref_count() const | CSGObject | |
reset_segment_sum_value(int32_t num_states, int32_t pos, int32_t &last_segment_sum_pos, float64_t *segment_sum_value) | CDynProg | [protected] |
reset_svm_value(int32_t pos, int32_t &last_svm_pos, float64_t *svm_value) | CDynProg | [protected] |
resize_lin_feat(int32_t num_new_feat, int32_t seq_len) | CDynProg | |
set_a(float64_t *a, int32_t M, int32_t N) | CDynProg | |
set_a(T_STATES line_, T_STATES column, float64_t value) | CDynProg | |
set_a_id(int32_t *a, int32_t M, int32_t N) | CDynProg | |
set_a_trans_matrix(float64_t *a_trans, int32_t num_trans, int32_t N) | CDynProg | |
set_genestr_len(int32_t genestr_len) | CDynProg | |
set_lin_feat(float64_t *p_lin_feat, int32_t p_num_svms, int32_t p_seq_len) | CDynProg | |
set_num_states(int32_t p_N) | CDynProg | |
set_p(T_STATES offset, float64_t value) | CDynProg | |
set_p_vector(float64_t *p, int32_t N) | CDynProg | |
set_q(T_STATES offset, float64_t value) | CDynProg | |
set_q_vector(float64_t *q, int32_t N) | CDynProg | |
sign_words | CDynProg | [protected] |
sign_words_array | CDynProg | [protected] |
string_words | CDynProg | [protected] |
string_words_array | CDynProg | [protected] |
svm_arrays_clean | CDynProg | [protected] |
svm_pos_start | CDynProg | [protected] |
svm_value_unnormalized_single | CDynProg | [protected] |
transition_matrix_a | CDynProg | [protected] |
transition_matrix_a_deriv | CDynProg | [protected] |
transition_matrix_a_id | CDynProg | [protected] |
translate_from_single_order(uint16_t *obs, int32_t sequence_length, int32_t start, int32_t order, int32_t max_val=2) | CDynProg | [protected] |
unref() | CSGObject | |
update_svm_values_till_pos(uint16_t ***wordstr, const int32_t *pos, int32_t t_end, int32_t prev_t_end, struct svm_values_struct &svs) | CDynProg | [protected] |
version | CSGObject | |
word_degree | CDynProg | [protected] |
word_degree_single | CDynProg | [protected] |
word_used_single | CDynProg | [protected] |
~CDynProg() | CDynProg | [virtual] |
~CSGObject() | CSGObject | [virtual] |