CDynProg Member List

This is the complete list of members for CDynProg, 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_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(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_pCDynProg [protected]
initial_state_distribution_p_derivCDynProg [protected]
ioCSGObject [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_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 [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_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(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]
versionCSGObject [static]
word_degreeCDynProg [protected]
word_degree_singleCDynProg [protected]
word_used_singleCDynProg [protected]
~CDynProg()CDynProg
~CSGObject()CSGObject [virtual]


SHOGUN Machine Learning Toolbox - Documentation