Index A | C | D | F | G | I | L | M | P | R | S | T | W A aa_idx_column (casanovoutils.constants.Constants attribute), [1] aa_scores_column (casanovoutils.constants.Constants attribute), [1] add_series() (casanovoutils.preccov.GraphPrecCov method), [1] align_and_explode() (in module casanovoutils.preccov), [1] align_scores() (in module casanovoutils.align), [1] align_tokens_with_gaps() (in module casanovoutils.align), [1] ax_title (casanovoutils.preccov.GraphPrecCov attribute), [1] ax_x_label (casanovoutils.preccov.GraphPrecCov attribute), [1] ax_y_label (casanovoutils.preccov.GraphPrecCov attribute), [1] C calc_precision_coverage() (in module casanovoutils.preccov), [1] casanovoutils module casanovoutils.align module, [1] casanovoutils.constants module, [1] casanovoutils.datasets module casanovoutils.denovoutils module, [1] casanovoutils.graphloss module casanovoutils.main module, [1] casanovoutils.mgfutils module, [1] casanovoutils.mzmlutils module, [1] casanovoutils.preccov module, [1] casanovoutils.residues module, [1] casanovoutils.summarize_mgf module casanovoutils.types module, [1] charge_distribution() (in module casanovoutils.summarize_mgf) clear() (casanovoutils.preccov.GraphPrecCov method), [1] COMMANDS (in module casanovoutils.datasets) (in module casanovoutils.denovoutils) (in module casanovoutils.graphloss) (in module casanovoutils.mgfutils) (in module casanovoutils.mzmlutils) (in module casanovoutils.preccov) (in module casanovoutils.residues) (in module casanovoutils.summarize_mgf) Commands (in module casanovoutils.types) COMMANDS() (in module casanovoutils.mzmlutils) (in module casanovoutils.residues) configure_logging() (in module casanovoutils) Constants (class in casanovoutils.constants), [1] count_charge_states() (in module casanovoutils.summarize_mgf) count_peaks() (in module casanovoutils.summarize_mgf) coverage_column (casanovoutils.constants.Constants attribute), [1] create_datasets() (in module casanovoutils.datasets) D detect_input_format() (in module casanovoutils.graphloss) DfPath (in module casanovoutils.denovoutils) downsample() (in module casanovoutils.mgfutils), [1] downsample_spectra() (in module casanovoutils.mgfutils), [1] dump_residues() (in module casanovoutils.residues), [1] F fig_dpi (casanovoutils.preccov.GraphPrecCov attribute), [1] fig_height (casanovoutils.preccov.GraphPrecCov attribute), [1] fig_width (casanovoutils.preccov.GraphPrecCov attribute), [1] fill_null_columns() (in module casanovoutils.preccov), [1] fragment_coverage() (in module casanovoutils.summarize_mgf) G get_aligned_dp_array() (in module casanovoutils.align), [1] get_ground_truth_df() (in module casanovoutils.denovoutils), [1] get_mgf_psms_df() (in module casanovoutils.denovoutils), [1] get_mztab_df() (in module casanovoutils.denovoutils), [1] get_pep_dict_mgf() (in module casanovoutils.mgfutils), [1] get_prec_cov_df() (in module casanovoutils.preccov), [1] get_pred_sequence_column() (casanovoutils.constants.Constants static method), [1] get_residues() (in module casanovoutils.residues), [1] graph_prec_cov() (in module casanovoutils.preccov), [1] GraphPrecCov (class in casanovoutils.preccov), [1] ground_truth_sequence_column (casanovoutils.constants.Constants attribute), [1] ground_truth_tokens (casanovoutils.constants.Constants attribute), [1] I iter_spectra() (in module casanovoutils.mgfutils), [1] L legend_border (casanovoutils.preccov.GraphPrecCov attribute), [1] legend_location (casanovoutils.preccov.GraphPrecCov attribute), [1] load_ground_truth_df() (in module casanovoutils.preccov), [1] LossSeries (in module casanovoutils.graphloss) M main() (in module casanovoutils.datasets) (in module casanovoutils.denovoutils), [1] (in module casanovoutils.graphloss) (in module casanovoutils.main), [1] (in module casanovoutils.mgfutils), [1] (in module casanovoutils.mzmlutils), [1] (in module casanovoutils.preccov), [1] (in module casanovoutils.residues), [1] (in module casanovoutils.summarize_mgf) measure_peptide_lengths() (in module casanovoutils.summarize_mgf) min_score (casanovoutils.constants.Constants attribute), [1] module casanovoutils casanovoutils.align, [1] casanovoutils.constants, [1] casanovoutils.datasets casanovoutils.denovoutils, [1] casanovoutils.graphloss casanovoutils.main, [1] casanovoutils.mgfutils, [1] casanovoutils.mzmlutils, [1] casanovoutils.preccov, [1] casanovoutils.residues, [1] casanovoutils.summarize_mgf casanovoutils.types, [1] mutate_row_as_dict() (in module casanovoutils.preccov), [1] P peak_counts() (in module casanovoutils.summarize_mgf) pep_score_column (casanovoutils.constants.Constants attribute), [1] peptide_lengths() (in module casanovoutils.summarize_mgf) pipeline() (in module casanovoutils.mgfutils), [1] plot() (in module casanovoutils.graphloss) plot_losses() (in module casanovoutils.graphloss) precision_column (casanovoutils.constants.Constants attribute), [1] predicted_tokens (casanovoutils.constants.Constants attribute), [1] process_spectrum() (in module casanovoutils.denovoutils), [1] purge_redundant() (in module casanovoutils.mgfutils), [1] PyteomicsSpectrum (in module casanovoutils.types) R read_dataframe() (in module casanovoutils.denovoutils), [1] read_from_csvfile() (in module casanovoutils.graphloss) read_from_file() (in module casanovoutils.graphloss) read_from_logfile() (in module casanovoutils.graphloss) recover_solution() (in module casanovoutils.align), [1] remove_redundant_peaks() (in module casanovoutils.mgfutils), [1] S sample_mzml() (in module casanovoutils.mzmlutils), [1] sample_spectra() (in module casanovoutils.mzmlutils), [1] save() (casanovoutils.preccov.GraphPrecCov method), [1] show() (casanovoutils.preccov.GraphPrecCov method), [1] shuffle() (in module casanovoutils.mgfutils), [1] spectra_per_peptide() (in module casanovoutils.mgfutils), [1] SpectraInput (in module casanovoutils.mgfutils) summarize_mgf() (in module casanovoutils.summarize_mgf) T tokenize_and_parse_scores() (in module casanovoutils.preccov), [1] tokenize_helper() (in module casanovoutils.denovoutils), [1] tokenize_sequences() (in module casanovoutils.denovoutils), [1] W write_dataframe() (in module casanovoutils.denovoutils), [1] write_spectra() (in module casanovoutils.mgfutils), [1]