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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_gradient_parameter_dictionary(CMap< TParameter *, CSGObject * > *dict)CSGObject
CDynProg(int32_t p_num_svms=8)CDynProg
check_svm_arrays()CDynProg
clone()CSGObjectvirtual
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_defaultCDynProgprotectedstatic
deep_copy() const CSGObjectvirtual
equals(CSGObject *other, float64_t accuracy=0.0, bool tolerant=false)CSGObjectvirtual
extend_orf(int32_t orf_from, int32_t orf_to, int32_t start, int32_t &last_pos, int32_t to)CDynProgprotected
find_frame(const int32_t from_state)CDynProgprotected
frame_plifsCDynProgprotectedstatic
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 CDynProgprotectedvirtual
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 CSGObjectvirtual
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::get_version_parameter())CSGObjectvirtual
load_serializable_post()CSGObjectprotectedvirtual
load_serializable_pre()CSGObjectprotectedvirtual
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)CDynProgprotected
lookup_tiling_plif_values(const int32_t from_state, const int32_t to_state, const int32_t len, float64_t *svm_values)CDynProgprotected
m_cum_num_wordsCDynProgprotected
m_cum_num_words_arrayCDynProgprotected
m_dict_weightsCDynProgprotected
m_end_state_distribution_qCDynProgprotected
m_end_state_distribution_q_derivCDynProgprotected
m_genestrCDynProgprotected
m_genestr_stopCDynProgprotected
m_gradient_parametersCSGObject
m_hashCSGObject
m_initial_state_distribution_pCDynProgprotected
m_initial_state_distribution_p_derivCDynProgprotected
m_intron_listCDynProgprotected
m_lin_featCDynProgprotected
m_long_transition_thresholdCDynProgprotected
m_long_transitionsCDynProgprotected
m_max_a_idCDynProgprotected
m_mod_wordsCDynProgprotected
m_mod_words_arrayCDynProgprotected
m_model_selection_parametersCSGObject
m_my_lossesCDynProgprotected
m_my_pos_seqCDynProgprotected
m_my_scoresCDynProgprotected
m_my_state_seqCDynProgprotected
m_NCDynProgprotected
m_num_degreesCDynProgprotected
m_num_intron_plifsCDynProgprotected
m_num_lin_feat_plifs_cumCDynProgprotected
m_num_probes_cumCDynProgprotected
m_num_raw_dataCDynProgprotected
m_num_svmsCDynProgprotected
m_num_unique_wordsCDynProgprotected
m_num_wordsCDynProgprotected
m_num_words_arrayCDynProgprotected
m_observation_matrixCDynProgprotected
m_orf_infoCDynProgprotected
m_parameter_mapCSGObject
m_parametersCSGObject
m_plif_listCDynProgprotected
m_plif_matricesCDynProgprotected
m_posCDynProgprotected
m_positionsCDynProgprotected
m_probe_posCDynProgprotected
m_raw_intensitiesCDynProgprotected
m_scoresCDynProgprotected
m_seg_loss_objCDynProgprotected
m_segment_idsCDynProgprotected
m_segment_lossCDynProgprotected
m_segment_maskCDynProgprotected
m_segment_sum_weightsCDynProgprotected
m_seq_lenCDynProgprotected
m_seq_sparse1CDynProgprotected
m_seq_sparse2CDynProgprotected
m_sign_wordsCDynProgprotected
m_sign_words_arrayCDynProgprotected
m_statesCDynProgprotected
m_string_wordsCDynProgprotected
m_string_words_arrayCDynProgprotected
m_svm_arrays_cleanCDynProgprotected
m_transition_matrix_aCDynProgprotected
m_transition_matrix_a_derivCDynProgprotected
m_transition_matrix_a_idCDynProgprotected
m_word_degreeCDynProgprotected
m_wordstrCDynProgprotected
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)CSGObjectprotectedvirtual
mod_words_defaultCDynProgprotectedstatic
num_words_defaultCDynProgprotectedstatic
one_to_one_migration_prepare(DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL)CSGObjectprotectedvirtual
parallelCSGObject
parameter_hash_changed()CSGObjectvirtual
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="")CSGObjectvirtual
raw_intensities_interval_query(const int32_t from_pos, const int32_t to_pos, float64_t *intensities, int32_t type)CDynProgprotected
resize_lin_feat(int32_t num_new_feat)CDynProg
save_serializable(CSerializableFile *file, const char *prefix="", int32_t param_version=Version::get_version_parameter())CSGObjectvirtual
save_serializable_post()CSGObjectprotectedvirtual
save_serializable_pre()CSGObjectprotectedvirtual
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 CSGObjectvirtual
sign_words_defaultCDynProgprotectedstatic
string_words_defaultCDynProgprotectedstatic
unset_generic()CSGObject
update_parameter_hash()CSGObjectvirtual
versionCSGObject
word_degree_defaultCDynProgprotectedstatic
~CDynProg()CDynProgvirtual
~CSGObject()CSGObjectvirtual

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