, including all inherited members.
best_path_2struct(const DREAL *seq, INT seq_len, const INT *pos, CPlifBase **Plif_matrix, const char *genestr, INT genestr_len, SHORT nbest, DREAL *prob_nbest, INT *my_state_seq, INT *my_pos_seq, DREAL *dictionary_weights, INT dict_len, DREAL *segment_sum_weights) | CDynProg | |
best_path_2struct_call(INT nbest) | CDynProg | |
best_path_call(INT nbest, bool use_orf) | CDynProg | |
best_path_deriv_call() | CDynProg | |
best_path_deriv_call(INT nbest) | CDynProg | |
best_path_get_losses(DREAL **my_losses, INT *seq_len) | CDynProg | |
best_path_get_positions(INT **positions, INT *m, INT *n) | CDynProg | |
best_path_get_scores(DREAL **scores, INT *n) | CDynProg | |
best_path_get_states(INT **states, INT *m, INT *n) | CDynProg | |
best_path_no_b(INT max_iter, INT &best_iter, INT *my_path) | CDynProg | |
best_path_no_b_trans(INT max_iter, INT &max_best_iter, SHORT nbest, DREAL *prob_nbest, INT *my_paths) | CDynProg | |
best_path_set_dict_weights(DREAL *dictionary_weights, INT dict_len, INT n) | CDynProg | |
best_path_set_genestr(CHAR *genestr, INT genestr_len, INT genestr_num) | CDynProg | |
best_path_set_my_pos_seq(INT *my_pos_seq, INT seq_len) | CDynProg | |
best_path_set_my_state_seq(INT *my_state_seq, INT seq_len) | CDynProg | |
best_path_set_orf_info(INT *orf_info, INT m, INT n) | CDynProg | |
best_path_set_plif_id_matrix(INT *plif_id_matrix, INT m, INT n) | CDynProg | |
best_path_set_plif_list(CDynamicArray< CPlifBase * > *plifs) | CDynProg | |
best_path_set_plif_state_signal_matrix(INT *plif_id_matrix, INT m, INT n) | CDynProg | |
best_path_set_pos(INT *pos, INT seq_len) | CDynProg | |
best_path_set_segment_ids_mask(INT *segment_ids, DREAL *segment_mask, INT m) | CDynProg | |
best_path_set_segment_loss(DREAL *segment_loss, INT num_segment_id1, INT num_segment_id2) | CDynProg | |
best_path_set_segment_sum_weights(DREAL *segment_sum_weights, INT num_states, INT seq_len) | CDynProg | |
best_path_set_seq(DREAL *seq, INT N, INT seq_len) | CDynProg | |
best_path_set_seq3d(DREAL *seq, INT p_N, INT seq_len, INT max_num_signals) | CDynProg | |
best_path_set_single_genestr(CHAR *genestr, INT genestr_len) | CDynProg | |
best_path_simple_call(INT nbest) | CDynProg | |
best_path_trans(const DREAL *seq, INT seq_len, const INT *pos, const INT *orf_info, CPlifBase **PLif_matrix, CPlifBase **Plif_state_signals, INT max_num_signals, INT genestr_num, DREAL *prob_nbest, INT *my_state_seq, INT *my_pos_seq, bool use_orf) | CDynProg | |
best_path_trans_deriv(INT *my_state_seq, INT *my_pos_seq, DREAL *my_scores, DREAL *my_losses, INT my_seq_len, const DREAL *seq_array, INT seq_len, const INT *pos, CPlifBase **Plif_matrix, CPlifBase **Plif_state_signals, INT max_num_signals, INT genestr_num) | CDynProg | |
best_path_trans_simple(const DREAL *seq, INT seq_len, SHORT nbest, DREAL *prob_nbest, INT *my_state_seq) | CDynProg | |
CDynProg(INT 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, INT genestr_num, INT genestr_len, WORD ***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(INT orf_from, INT orf_to, INT start, INT &last_pos, INT to) | CDynProg | [protected] |
extend_segment_loss(struct segment_loss_struct &loss, const INT *pos_array, INT segment_id, INT pos, INT &last_pos, DREAL &last_value) | CDynProg | [protected] |
extend_segment_sum_value(DREAL *segment_sum_weights, INT seqlen, INT num_states, INT pos, INT &last_segment_sum_pos, DREAL *segment_sum_value) | CDynProg | [protected] |
extend_svm_value(WORD *wordstr, INT pos, INT &last_svm_pos, DREAL *svm_value) | CDynProg | [protected] |
find_frame(const INT from_state) | CDynProg | [protected] |
find_segment_loss_till_pos(const INT *pos, INT t_end, CArray< INT > &segment_ids, CArray< DREAL > &segment_mask, struct segment_loss_struct &loss) | CDynProg | [protected] |
find_svm_values_till_pos(WORD ***wordstr, const INT *pos, INT t_end, struct svm_values_struct &svs) | CDynProg | [protected] |
find_svm_values_till_pos(WORD **wordstr, const INT *pos, INT 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_N() const | 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_q(T_STATES offset) const | CDynProg | |
get_q_deriv(T_STATES offset) const | CDynProg | |
init_content_svm_value_array(const INT seq_len) | CDynProg | |
init_cum_num_words_array(INT *p_cum_num_words_array, INT num_elem) | CDynProg | |
init_mod_words_array(INT *p_mod_words_array, INT num_elem, INT num_columns) | CDynProg | |
init_num_words_array(INT *p_num_words_array, INT num_elem) | CDynProg | |
init_segment_loss(struct segment_loss_struct &loss, INT seqlen, INT howmuchlookback) | CDynProg | [protected] |
init_sign_words_array(bool *p_sign_words_array, INT num_elem) | CDynProg | |
init_string_words_array(INT *p_string_words_array, INT num_elem) | CDynProg | |
init_svm_arrays(INT p_num_degrees, INT p_num_svms) | CDynProg | |
init_svm_values(struct svm_values_struct &svs, INT start_pos, INT seqlen, INT howmuchlookback) | CDynProg | [protected] |
init_tiling_data(DREAL *probe_pos, DREAL *intensities, const INT num_probes, const INT seq_len) | CDynProg | |
init_word_degree_array(INT *p_word_degree_array, INT num_elem) | CDynProg | |
initial_state_distribution_p | CDynProg | [protected] |
initial_state_distribution_p_deriv | CDynProg | [protected] |
io | CSGObject | [static] |
lookup_content_svm_values(const INT from_state, const INT to_state, const INT from_pos, const INT to_pos, DREAL *svm_values, INT frame) | CDynProg | [protected] |
lookup_tiling_plif_values(const INT from_state, const INT to_state, const INT len, DREAL *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_my_losses | CDynProg | [protected] |
m_my_pos_seq | CDynProg | [protected] |
m_my_scores | CDynProg | [protected] |
m_my_state_seq | CDynProg | [protected] |
m_num_probes | 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_precomputed_svm_values | CDynProg | [protected] |
m_precomputed_tiling_values | 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] |
m_use_tiling | 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 | [static] |
precompute_content_values(WORD ***wordstr, const INT *pos, const INT num_cand_pos, const INT genestr_len, DREAL *dictionary_weights, INT dict_len) | CDynProg | |
precompute_stop_codons(const CHAR *genestr, INT genestr_len) | CDynProg | |
precompute_tiling_plifs(CPlif **PEN, const INT num_penalties, const INT seq_len, const INT *pos) | CDynProg | |
raw_intensities_interval_query(const INT from_pos, const INT to_pos, DREAL *intensities) | CDynProg | [protected] |
reset_segment_sum_value(INT num_states, INT pos, INT &last_segment_sum_pos, DREAL *segment_sum_value) | CDynProg | [protected] |
reset_svm_value(INT pos, INT &last_svm_pos, DREAL *svm_value) | CDynProg | [protected] |
set_a(DREAL *a, INT M, INT N) | CDynProg | |
set_a(T_STATES line_, T_STATES column, DREAL value) | CDynProg | |
set_a_id(INT *a, INT M, INT N) | CDynProg | |
set_a_trans_matrix(DREAL *a_trans, INT num_trans, INT N) | CDynProg | |
set_genestr_len(INT genestr_len) | CDynProg | |
set_num_states(INT p_N) | CDynProg | |
set_p(T_STATES offset, DREAL value) | CDynProg | |
set_p_vector(DREAL *p, INT N) | CDynProg | |
set_q(T_STATES offset, DREAL value) | CDynProg | |
set_q_vector(DREAL *q, INT 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(WORD *obs, INT sequence_length, INT start, INT order, INT max_val=2) | CDynProg | [protected] |
update_svm_values_till_pos(WORD ***wordstr, const INT *pos, INT t_end, INT prev_t_end, struct svm_values_struct &svs) | CDynProg | [protected] |
version | CSGObject | [static] |
word_degree | CDynProg | [protected] |
word_degree_single | CDynProg | [protected] |
word_used_single | CDynProg | [protected] |
~CDynProg() | CDynProg | |
~CSGObject() | CSGObject | [virtual] |