Index A | B | C | D | E | F | G | I | L | M | N | O | P | Q | R | S | T | U | V | Z A accumulation_times (full_dia.alphatims.bruker.TimsTOF property) acquisition_mode (full_dia.alphatims.bruker.TimsTOF property) add_intensity_to_bin() (in module full_dia.alphatims.bruker) adjust_rubbish_q() (in module full_dia.fdr) as_dataframe() (full_dia.alphatims.bruker.TimsTOF method) assemble_pep_to_pg() (in module full_dia.assemble) assemble_pep_to_pg_core() (in module full_dia.assemble) assign_fg_mz() (full_dia.library.Library method) assign_proteins() (full_dia.library.Library method) B bin_intensities() (full_dia.alphatims.bruker.TimsTOF method) bootstrap() (in module full_dia.main) C cal_acc_recall() (in module full_dia.utils) cal_coelution_by_gaussion() (in module full_dia.fxic) cal_fg_mz_iso() (in module full_dia.decoy) cal_group_rank() (in module full_dia.utils) cal_im_recall() (in module full_dia.calib) cal_measure_im() (in module full_dia.fxic) cal_q_pg() (in module full_dia.fdr) cal_q_pr_batch() (in module full_dia.fdr) cal_q_pr_combined() (in module full_dia.fdr) cal_q_pr_core() (in module full_dia.fdr) cal_recall_seek_locus() (in module full_dia.search) cal_recall_seek_seed() (in module full_dia.search) cal_rt_im_recall() (in module full_dia.calib) cal_rt_recall() (in module full_dia.calib) cal_sa_by_np() (in module full_dia.utils) cal_turning_point() (in module full_dia.calib) calculate_dia_cycle_mask() (in module full_dia.alphatims.bruker) calculate_global_calibrated_mz_values() (full_dia.alphatims.bruker.TimsTOF method) calib_im() (in module full_dia.calib) calib_mz() (in module full_dia.calib) calib_rt() (in module full_dia.calib) calibrated_mz_max_value (full_dia.alphatims.bruker.TimsTOF property) calibrated_mz_min_value (full_dia.alphatims.bruker.TimsTOF property) calibrated_mz_values (full_dia.alphatims.bruker.TimsTOF property) centroid_spectra() (in module full_dia.alphatims.bruker) check_github_version() (in module full_dia.alphatims.utils) check_lib() (full_dia.library.Library method) check_run_info() (in module full_dia.utils) class_njit() (in module full_dia.alphatims.utils) clean_and_save() (in module full_dia.utils) concat_nonzero_locus() (in module full_dia.fxic) construct_data_by_quadrupole() (full_dia.tims.Tims method) construct_dfs() (full_dia.library.Library method) construct_train_data() (in module full_dia.refine) convert_cols_to_diann() (in module full_dia.utils) convert_from_indices() (full_dia.alphatims.bruker.TimsTOF method) convert_numba_to_tensor() (in module full_dia.utils) convert_seq_to_mass() (in module full_dia.decoy) convert_slice_key_to_float_array() (in module full_dia.alphatims.bruker) convert_slice_key_to_int_array() (in module full_dia.alphatims.bruker) convert_to_indices() (full_dia.alphatims.bruker.TimsTOF method) copy_map_to_gpu() (full_dia.tims.Tims method) create_cuda_zeros() (in module full_dia.utils) create_dict_from_hdf_group() (in module full_dia.alphatims.utils) create_hdf_group_from_dict() (in module full_dia.alphatims.utils) cross_cos() (in module full_dia.utils) current_value (full_dia.alphatims.utils.Option_Stack property) current_values (full_dia.alphatims.utils.Global_Stack property) cycle (full_dia.alphatims.bruker.TimsTOF property) D DeepMall (class in full_dia.models) DeepMap (class in full_dia.models) DeepQuant (class in full_dia.models) dia_mz_cycle (full_dia.alphatims.bruker.TimsTOF property) dia_precursor_cycle (full_dia.alphatims.bruker.TimsTOF property) directory (full_dia.alphatims.bruker.TimsTOF property) drop_batches_mismatch() (in module full_dia.cross) drop_runs_mismatch() (in module full_dia.cross) E estimate_strike_count() (full_dia.alphatims.bruker.TimsTOF method) estimate_xic_boundary() (in module full_dia.fxic) eval_one_epoch() (in module full_dia.refine) extract_mall() (in module full_dia.deepmall) extract_maps() (in module full_dia.deepmap) extract_scoring_big() (in module full_dia.deepmap) extract_xics() (in module full_dia.fxic) F filter_indices() (in module full_dia.alphatims.bruker) filter_spectra_by_abundant_peaks() (in module full_dia.alphatims.bruker) filter_tof_to_csr() (in module full_dia.alphatims.bruker) find_first_index() (in module full_dia.deepmap) find_maximum() (in module full_dia.fxic) fit_by_lowess() (in module full_dia.calib) flatten_yaml() (in module full_dia.cfg) format() (full_dia.log.MyFormatter method) forward() (full_dia.models.DeepMall method) (full_dia.models.DeepMap method) (full_dia.models.DeepQuant method) fragment_frames (full_dia.alphatims.bruker.TimsTOF property) frame_max_index (full_dia.alphatims.bruker.TimsTOF property) frame_nums (full_dia.tims.Tims property) frames (full_dia.alphatims.bruker.TimsTOF property) full_dia module full_dia.alphatims module full_dia.alphatims.bruker module full_dia.alphatims.utils module full_dia.assemble module full_dia.calib module full_dia.cfg module full_dia.cross module full_dia.dataloader module full_dia.decoy module full_dia.deepmall module full_dia.deepmap module full_dia.fdr module full_dia.fxic module full_dia.library module full_dia.log module full_dia.main module full_dia.models module full_dia.polish module full_dia.quant module full_dia.refine module full_dia.scoring module full_dia.search module full_dia.tims module full_dia.utils module G get_args() (in module full_dia.utils) get_centroid_tol_push() (full_dia.tims.Tims method) get_cycle_time() (full_dia.tims.Tims method) get_device_name() (full_dia.tims.Tims method) get_dia_push_indices() (in module full_dia.alphatims.bruker) get_dia_quadrupole() (full_dia.tims.Tims method) get_dia_windows() (full_dia.tims.Tims method) get_diann_info() (in module full_dia.utils) get_im_gap() (full_dia.tims.Tims method) get_logger() (full_dia.log.Logger class method) get_rt_range() (full_dia.tims.Tims method) get_scan_rts() (full_dia.tims.Tims method) Global_Stack (class in full_dia.alphatims.utils) gpu_bin_map() (in module full_dia.deepmap) gpu_bin_maps() (in module full_dia.deepmap) gpu_cal_fg_mz() (in module full_dia.decoy) gpu_cal_sa() (in module full_dia.fxic) gpu_extract_xics() (in module full_dia.fxic) gpu_sa_gausion_core() (in module full_dia.fxic) gpu_simple_smooth() (in module full_dia.fxic) gpu_simple_smooth_core() (in module full_dia.fxic) grid_xic_best() (in module full_dia.fxic) (in module full_dia.quant) group_by_species() (in module full_dia.cross) I index_precursors() (full_dia.alphatims.bruker.TimsTOF method) indptr_lookup() (in module full_dia.alphatims.bruker) init_bruker_dll() (in module full_dia.alphatims.bruker) init_gpu_params() (in module full_dia.utils) init_multi_ws() (in module full_dia.utils) init_single_ws() (in module full_dia.utils) intensity_corrections (full_dia.alphatims.bruker.TimsTOF property) intensity_max_value (full_dia.alphatims.bruker.TimsTOF property) intensity_min_value (full_dia.alphatims.bruker.TimsTOF property) intensity_values (full_dia.alphatims.bruker.TimsTOF property) interference_correction() (in module full_dia.quant) interp_xics() (in module full_dia.quant) (in module full_dia.utils) is_compressed (full_dia.alphatims.bruker.TimsTOF property) is_fg_share() (in module full_dia.polish) is_locked (full_dia.alphatims.utils.Global_Stack property) L Library (class in full_dia.library) load_default() (in module full_dia.cfg) load_model_big() (in module full_dia.deepmap) load_model_center() (in module full_dia.deepmap) load_models() (in module full_dia.deepmap) load_ms() (in module full_dia.tims) load_parameters() (in module full_dia.alphatims.utils) lock() (full_dia.alphatims.utils.Global_Stack method) Logger (class in full_dia.log) logger (full_dia.log.Logger attribute) M main() (in module full_dia.main) make_dataset_mall() (in module full_dia.refine) make_dataset_maps() (in module full_dia.refine) make_decoys() (in module full_dia.decoy) make_interference_areas_zero() (in module full_dia.polish) make_interference_areas_zero_core() (in module full_dia.polish) MallDataset (class in full_dia.dataloader) MapDataset (class in full_dia.dataloader) mask_tensor() (in module full_dia.quant) max_accumulation_time (full_dia.alphatims.bruker.TimsTOF property) meta_data (full_dia.alphatims.bruker.TimsTOF property) mobility_max_value (full_dia.alphatims.bruker.TimsTOF property) mobility_min_value (full_dia.alphatims.bruker.TimsTOF property) mobility_values (full_dia.alphatims.bruker.TimsTOF property) module full_dia full_dia.alphatims full_dia.alphatims.bruker full_dia.alphatims.utils full_dia.assemble full_dia.calib full_dia.cfg full_dia.cross full_dia.dataloader full_dia.decoy full_dia.deepmall full_dia.deepmap full_dia.fdr full_dia.fxic full_dia.library full_dia.log full_dia.main full_dia.models full_dia.polish full_dia.quant full_dia.refine full_dia.scoring full_dia.search full_dia.tims full_dia.utils move_all_zeros_end() (in module full_dia.utils) my_collate() (in module full_dia.refine) MyFormatter (class in full_dia.log) mz_max_value (full_dia.alphatims.bruker.TimsTOF property) mz_min_value (full_dia.alphatims.bruker.TimsTOF property) mz_values (full_dia.alphatims.bruker.TimsTOF property) N njit() (in module full_dia.alphatims.utils) numba_index_by_bool() (in module full_dia.tims) numba_paral_centroid() (in module full_dia.tims) numba_paral_repeat() (in module full_dia.tims) numba_paral_sort() (in module full_dia.tims) numba_paral_sum() (in module full_dia.tims) numba_scoring_putatives() (in module full_dia.scoring) O open_bruker_d_folder() (in module full_dia.alphatims.bruker) option_name (full_dia.alphatims.utils.Option_Stack property) Option_Stack (class in full_dia.alphatims.utils) P parse_decompressed_bruker_binary_type1() (in module full_dia.alphatims.bruker) parse_decompressed_bruker_binary_type2() (in module full_dia.alphatims.bruker) parse_keys() (in module full_dia.alphatims.bruker) perform_global() (in module full_dia.cross) pjit() (in module full_dia.alphatims.utils) plot_dia_windows() (full_dia.tims.Tims method) plot_fit_im() (in module full_dia.calib) plot_fit_mz() (in module full_dia.calib) plot_fit_rt() (in module full_dia.calib) polish_ends() (in module full_dia.calib) polish_lib_by_swath() (full_dia.library.Library method) polish_prs() (in module full_dia.polish) polish_prs_core() (in module full_dia.polish) precursor_indices (full_dia.alphatims.bruker.TimsTOF property) precursor_max_index (full_dia.alphatims.bruker.TimsTOF property) PrecursorFloatError precursors (full_dia.alphatims.bruker.TimsTOF property) print_ids() (in module full_dia.utils) process_frame() (in module full_dia.alphatims.bruker) profile() (in module full_dia.assemble) (in module full_dia.calib) (in module full_dia.cross) (in module full_dia.dataloader) (in module full_dia.decoy) (in module full_dia.deepmall) (in module full_dia.deepmap) (in module full_dia.fdr) (in module full_dia.fxic) (in module full_dia.library) (in module full_dia.main) (in module full_dia.models) (in module full_dia.polish) (in module full_dia.quant) (in module full_dia.refine) (in module full_dia.scoring) (in module full_dia.search) (in module full_dia.tims) (in module full_dia.utils) progress_callback() (in module full_dia.alphatims.utils) push_indptr (full_dia.alphatims.bruker.TimsTOF property) Q quad_indptr (full_dia.alphatims.bruker.TimsTOF property) quad_mz_max_value (full_dia.alphatims.bruker.TimsTOF property) quad_mz_min_value (full_dia.alphatims.bruker.TimsTOF property) quad_mz_values (full_dia.alphatims.bruker.TimsTOF property) quant_center_ions() (in module full_dia.quant) quant_pr_autoencoder() (in module full_dia.cross) R raw_quad_indptr (full_dia.alphatims.bruker.TimsTOF property) read_bruker_binary() (in module full_dia.alphatims.bruker) read_bruker_sql() (in module full_dia.alphatims.bruker) read_from_pq() (in module full_dia.utils) redo() (full_dia.alphatims.utils.Global_Stack method) (full_dia.alphatims.utils.Option_Stack method) refine_models() (in module full_dia.refine) release_gpu_scans() (in module full_dia.utils) reserve_sa_maximum() (in module full_dia.fxic) retrain_model_map() (in module full_dia.refine) rt_max_value (full_dia.alphatims.bruker.TimsTOF property) rt_values (full_dia.alphatims.bruker.TimsTOF property) S sample_name (full_dia.alphatims.bruker.TimsTOF property) save_as_hdf() (full_dia.alphatims.bruker.TimsTOF method) save_as_mgf() (in module full_dia.alphatims.bruker) save_as_pkl() (in module full_dia.utils) save_as_spectra() (full_dia.alphatims.bruker.TimsTOF method) (in module full_dia.alphatims.bruker) save_parameters() (in module full_dia.alphatims.utils) save_report_result() (in module full_dia.cross) scan_max_index (full_dia.alphatims.bruker.TimsTOF property) score_locus() (in module full_dia.scoring) scoring_by_cross() (in module full_dia.scoring) scoring_by_deep_layer() (in module full_dia.scoring) scoring_by_deep_prob() (in module full_dia.scoring) scoring_center_im() (in module full_dia.scoring) scoring_center_mz() (in module full_dia.scoring) scoring_center_snr() (in module full_dia.scoring) scoring_main_elution() (in module full_dia.scoring) scoring_mall() (in module full_dia.deepmall) scoring_maps() (in module full_dia.deepmap) scoring_meta() (in module full_dia.scoring) scoring_other_elution() (in module full_dia.scoring) scoring_putatives() (in module full_dia.scoring) scoring_rt() (in module full_dia.scoring) scoring_xic_intensity() (in module full_dia.scoring) screen_by_graph() (in module full_dia.calib) screen_by_hist() (in module full_dia.calib) screen_locus_by_deep() (in module full_dia.fxic) screen_locus_by_sa() (in module full_dia.fxic) search_core() (in module full_dia.search) seek_locus() (in module full_dia.search) seek_seed() (in module full_dia.search) select_best_profile() (in module full_dia.quant) select_other_profiles() (in module full_dia.quant) select_required_and_all_targets() (in module full_dia.search) set_cycle() (full_dia.alphatims.bruker.TimsTOF method) set_logger() (full_dia.log.Logger class method) (in module full_dia.alphatims.utils) set_precursor() (in module full_dia.alphatims.bruker) set_progress_callback() (in module full_dia.alphatims.utils) set_threads() (in module full_dia.alphatims.utils) show_python_info() (in module full_dia.alphatims.utils) size (full_dia.alphatims.utils.Global_Stack property) (full_dia.alphatims.utils.Option_Stack property) split_ms1_to_chunks() (full_dia.tims.Tims method) sum_gpu() (in module full_dia.decoy) T threadpool() (in module full_dia.alphatims.utils) Tims (class in full_dia.tims) TimsTOF (class in full_dia.alphatims.bruker) tof_indices (full_dia.alphatims.bruker.TimsTOF property) tof_max_index (full_dia.alphatims.bruker.TimsTOF property) train_model_mall() (in module full_dia.refine) train_one_epoch() (in module full_dia.refine) trim() (full_dia.alphatims.utils.Global_Stack method) (full_dia.alphatims.utils.Option_Stack method) trim_spectra() (in module full_dia.alphatims.bruker) U undo() (full_dia.alphatims.utils.Global_Stack method) (full_dia.alphatims.utils.Option_Stack method) update() (full_dia.alphatims.utils.Global_Stack method) (full_dia.alphatims.utils.Option_Stack method) update_from_yaml() (in module full_dia.cfg) update_sa_by_grid() (in module full_dia.fxic) update_scores() (in module full_dia.scoring) update_tolerance() (in module full_dia.search) use_calibrated_mz_values_as_default() (full_dia.alphatims.bruker.TimsTOF method) V valid_precursor_index() (in module full_dia.alphatims.bruker) valid_quad_mz_values() (in module full_dia.alphatims.bruker) version (full_dia.alphatims.bruker.TimsTOF property) Z zeroth_frame (full_dia.alphatims.bruker.TimsTOF property)