CDynProg Member List

This is the complete list of members for CDynProg, including all inherited members.
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_parameter_dictionary(CMap< TParameter *, CSGObject * > &dict)CSGObject
CDynProg(int32_t p_num_svms=8)CDynProg
check_svm_arrays()CDynProg
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_defaultCDynProg [protected, static]
deep_copy() const 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_plifsCDynProg [protected, static]
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 [protected, virtual]
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
ioCSGObject
is_generic(EPrimitiveType *generic) const CSGObject [virtual]
load_all_file_parameters(int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="")CSGObject
load_file_parameters(const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="")CSGObject
load_serializable(CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER)CSGObject [virtual]
load_serializable_post()CSGObject [protected, virtual]
load_serializable_pre()CSGObject [protected, virtual]
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_wordsCDynProg [protected]
m_cum_num_words_arrayCDynProg [protected]
m_dict_weightsCDynProg [protected]
m_end_state_distribution_qCDynProg [protected]
m_end_state_distribution_q_derivCDynProg [protected]
m_genestrCDynProg [protected]
m_genestr_stopCDynProg [protected]
m_hashCSGObject
m_initial_state_distribution_pCDynProg [protected]
m_initial_state_distribution_p_derivCDynProg [protected]
m_intron_listCDynProg [protected]
m_lin_featCDynProg [protected]
m_long_transition_thresholdCDynProg [protected]
m_long_transitionsCDynProg [protected]
m_max_a_idCDynProg [protected]
m_mod_wordsCDynProg [protected]
m_mod_words_arrayCDynProg [protected]
m_model_selection_parametersCSGObject
m_my_lossesCDynProg [protected]
m_my_pos_seqCDynProg [protected]
m_my_scoresCDynProg [protected]
m_my_state_seqCDynProg [protected]
m_NCDynProg [protected]
m_num_degreesCDynProg [protected]
m_num_intron_plifsCDynProg [protected]
m_num_lin_feat_plifs_cumCDynProg [protected]
m_num_probes_cumCDynProg [protected]
m_num_raw_dataCDynProg [protected]
m_num_svmsCDynProg [protected]
m_num_unique_wordsCDynProg [protected]
m_num_wordsCDynProg [protected]
m_num_words_arrayCDynProg [protected]
m_observation_matrixCDynProg [protected]
m_orf_infoCDynProg [protected]
m_parameter_mapCSGObject
m_parametersCSGObject
m_PENCDynProg [protected]
m_PEN_state_signalsCDynProg [protected]
m_plif_listCDynProg [protected]
m_plif_matricesCDynProg [protected]
m_posCDynProg [protected]
m_positionsCDynProg [protected]
m_probe_posCDynProg [protected]
m_raw_intensitiesCDynProg [protected]
m_scoresCDynProg [protected]
m_seg_loss_objCDynProg [protected]
m_segment_idsCDynProg [protected]
m_segment_lossCDynProg [protected]
m_segment_maskCDynProg [protected]
m_segment_sum_weightsCDynProg [protected]
m_seq_lenCDynProg [protected]
m_seq_sparse1CDynProg [protected]
m_seq_sparse2CDynProg [protected]
m_sign_wordsCDynProg [protected]
m_sign_words_arrayCDynProg [protected]
m_statesCDynProg [protected]
m_string_wordsCDynProg [protected]
m_string_words_arrayCDynProg [protected]
m_svm_arrays_cleanCDynProg [protected]
m_transition_matrix_aCDynProg [protected]
m_transition_matrix_a_derivCDynProg [protected]
m_transition_matrix_a_idCDynProg [protected]
m_word_degreeCDynProg [protected]
m_wordstrCDynProg [protected]
map_parameters(DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos)CSGObject
migrate(DynArray< TParameter * > *param_base, const SGParamInfo *target)CSGObject [protected, virtual]
mod_words_defaultCDynProg [protected, static]
num_words_defaultCDynProg [protected, static]
one_to_one_migration_prepare(DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL)CSGObject [protected, virtual]
parallelCSGObject
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="", int32_t param_version=VERSION_PARAMETER)CSGObject [virtual]
save_serializable_post()CSGObject [protected, virtual]
save_serializable_pre()CSGObject [protected, virtual]
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_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_defaultCDynProg [protected, static]
string_words_defaultCDynProg [protected, static]
unset_generic()CSGObject
update_parameter_hash()CSGObject [protected, virtual]
versionCSGObject
word_degree_defaultCDynProg [protected, static]
~CDynProg()CDynProg [virtual]
~CSGObject()CSGObject [virtual]
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