CDynProg Member List

This is the complete list of members for CDynProg, 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_wordsCDynProg [protected]
cum_num_words_arrayCDynProg [protected]
cum_num_words_singleCDynProg [protected]
dict_weightsCDynProg [protected]
dict_weights_arrayCDynProg [protected]
end_state_distribution_qCDynProg [protected]
end_state_distribution_q_derivCDynProg [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_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 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_pCDynProg [protected]
initial_state_distribution_p_derivCDynProg [protected]
ioCSGObject
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_callCDynProg [protected]
m_dict_weightsCDynProg [protected]
m_genestrCDynProg [protected]
m_genestr_lenCDynProg [protected]
m_genestr_stopCDynProg [protected]
m_my_lossesCDynProg [protected]
m_my_pos_seqCDynProg [protected]
m_my_scoresCDynProg [protected]
m_my_state_seqCDynProg [protected]
m_num_probesCDynProg [protected]
m_orf_infoCDynProg [protected]
m_PENCDynProg [protected]
m_PEN_state_signalsCDynProg [protected]
m_plif_listCDynProg [protected]
m_posCDynProg [protected]
m_positionsCDynProg [protected]
m_precomputed_svm_valuesCDynProg [protected]
m_precomputed_tiling_valuesCDynProg [protected]
m_probe_posCDynProg [protected]
m_raw_intensitiesCDynProg [protected]
m_scoresCDynProg [protected]
m_segment_idsCDynProg [protected]
m_segment_lossCDynProg [protected]
m_segment_maskCDynProg [protected]
m_segment_sum_weightsCDynProg [protected]
m_seqCDynProg [protected]
m_statesCDynProg [protected]
m_stepCDynProg [protected]
m_use_tilingCDynProg [protected]
max_a_idCDynProg [protected]
mod_wordsCDynProg [protected]
mod_words_arrayCDynProg [protected]
NCDynProg [protected]
num_degreesCDynProg [protected]
num_stringsCDynProg [protected]
num_svmsCDynProg [protected]
num_svms_singleCDynProg [protected]
num_unique_wordsCDynProg [protected]
num_unique_words_singleCDynProg [protected]
num_wordsCDynProg [protected]
num_words_arrayCDynProg [protected]
num_words_singleCDynProg [protected]
parallelCSGObject
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)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]
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_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_wordsCDynProg [protected]
sign_words_arrayCDynProg [protected]
string_wordsCDynProg [protected]
string_words_arrayCDynProg [protected]
svm_arrays_cleanCDynProg [protected]
svm_pos_startCDynProg [protected]
svm_value_unnormalized_singleCDynProg [protected]
transition_matrix_aCDynProg [protected]
transition_matrix_a_derivCDynProg [protected]
transition_matrix_a_idCDynProg [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]
versionCSGObject
word_degreeCDynProg [protected]
word_degree_singleCDynProg [protected]
word_used_singleCDynProg [protected]
~CDynProg()CDynProg
~CSGObject()CSGObject [virtual]


SHOGUN Machine Learning Toolbox - Documentation