Index

A

acetyl_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) add_meta() (msproteomicstoolslib.format.speclib_db_lib.SequenceHandler method) (msproteomicstoolslib.format.speclib_db_lib.Spectra method) add_peakgroup() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) add_peakgroup_data() (openswathgui.models.SqlSwathRun.SqlSwathRun method) add_peakgroup_tpl() (msproteomicstoolslib.data_structures.Precursor.Precursor method) add_spectra() (msproteomicstoolslib.format.speclib_db_lib.Library method) (msproteomicstoolslib.format.speclib_db_lib.SequenceHandler method) add_spectra_no_duplicates() (msproteomicstoolslib.format.speclib_db_lib.SequenceHandler method) addAminoacid() (msproteomicstoolslib.data_structures.aminoacides.Aminoacides method) addPrecursor() (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) (msproteomicstoolslib.data_structures.Run.Run method)

addSpectrum() (msproteomicstoolslib.data_structures.peptide.Peptide method) all_above_cutoff() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) all_ions() (msproteomicstoolslib.data_structures.peptide.Peptide method) all_selected() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) all_spectra() (msproteomicstoolslib.format.speclib_db_lib.Library method) Aminoacid (class in msproteomicstoolslib.data_structures.aminoacides) Aminoacides (class in msproteomicstoolslib.data_structures.aminoacides) analyse_mod() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) annotate_with_libkey() (msproteomicstoolslib.format.speclib_db_lib.Library method) append() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) appendModification() (msproteomicstoolslib.data_structures.modifications.Modifications method)

C

cal_UIS() (msproteomicstoolslib.data_structures.peptide.Peptide method) calIsoforms() (msproteomicstoolslib.data_structures.peptide.Peptide method) carbamido_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) ChromatogramTransition (class in openswathgui.models.ChromatogramTransition) cluster_id_ (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase attribute) cluster_ids_ (msproteomicstoolslib.data_structures.Precursor.Precursor attribute)

code (msproteomicstoolslib.data_structures.aminoacides.Aminoacid attribute) code3 (msproteomicstoolslib.data_structures.aminoacides.Aminoacid attribute) codes (msproteomicstoolslib.data_structures.modifications.Modification attribute) comparePeptideFragments() (msproteomicstoolslib.data_structures.peptide.Peptide method) composition (msproteomicstoolslib.data_structures.aminoacides.Aminoacid attribute) count_modifications() (msproteomicstoolslib.format.speclib_db_lib.Library method)

D

delete_library_from_DB() (msproteomicstoolslib.format.speclib_db_lib.Library method)

delete_reverse_spectra() (msproteomicstoolslib.format.speclib_db_lib.Library method) doBFS() (in module msproteomicstoolslib.algorithms.graphs.graphs)

E

elementsLib (msproteomicstoolslib.data_structures.aminoacides.Aminoacid attribute)

empty() (msproteomicstoolslib.format.speclib_db_lib.SequenceHandler method) escape_string() (msproteomicstoolslib.format.speclib_db_lib.Spectra method)

F

fdr_score (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase attribute) find() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) find_best_peptide_pg() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) find_by_sequence() (msproteomicstoolslib.format.speclib_db_lib.Library method) find_by_sql() (msproteomicstoolslib.format.speclib_db_lib.Library method) find_by_sql_fast() (msproteomicstoolslib.format.speclib_db_lib.Library method)

find_closest_in_iRT() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method) findShortestMSTPath() (in module msproteomicstoolslib.algorithms.graphs.graphs) fragmentSequence() (msproteomicstoolslib.data_structures.peptide.Peptide method) function() (msproteomicstoolslib.math.LinearRegression.SimpleLinearRegression method)

G

GeneralPeakGroup (class in msproteomicstoolslib.data_structures.PeakGroup) GeneralPrecursor (class in msproteomicstoolslib.data_structures.Precursor) get_aligned_filename() (msproteomicstoolslib.data_structures.Run.Run method) get_all_peakgroups() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method) get_all_peptide_sequences() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_all_precursor_ids() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_all_proteins() (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_all_spectra() (msproteomicstoolslib.format.speclib_db_lib.Library method) get_assay_data() (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_best_peakgroup() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method) get_best_peaks() (msproteomicstoolslib.data_structures.Run.Run method) get_best_peaks_with_cutoff() (msproteomicstoolslib.data_structures.Run.Run method) get_cluster_id() (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) get_data_for_precursor() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_data_for_transition() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_decoy() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method) (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) get_decoy_Q3() (msproteomicstoolslib.data_structures.peptide.Peptide method) get_dscore() (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) get_fdr_score() (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) get_feature_id() (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) get_fileheader() (msproteomicstoolslib.format.speclib_db_lib.Library method) get_first_offset() (msproteomicstoolslib.format.speclib_db_lib.Library method) get_id() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method) (msproteomicstoolslib.data_structures.Run.Run method) (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_intensity() (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) get_intensity_data() (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_known_modifications() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) get_meta_headers() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) get_normalized_retentiontime() (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) get_nr_runs() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) get_openswath_filename() (msproteomicstoolslib.data_structures.Run.Run method) get_original_filename() (msproteomicstoolslib.data_structures.Run.Run method) get_peaks() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) get_peptide() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) get_peptides() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) get_precursors_for_sequence() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_range_data() (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_rawspectrum_with_offset() (msproteomicstoolslib.format.speclib_db_lib.Library method) get_run_id() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) get_score_data() (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_selected_peakgroup() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method)

get_selected_peakgroups() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) get_sequence_for_protein() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_spectra_by_sequence() (msproteomicstoolslib.format.speclib_db_lib.Library method) get_spectra_headers() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) get_transitions_for_precursor() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_transitions_for_precursor_display() (openswathgui.models.SqlSwathRun.SqlSwathRun method) get_transitions_with_mass_for_precursor() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) get_value() (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.GuiPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) getAdjacencyList() (in module msproteomicstoolslib.algorithms.graphs.graphs) getAllPeakgroups() (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) getAllPeptides() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) getAllPrecursors() (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) getAminoacid() (msproteomicstoolslib.data_structures.aminoacides.Aminoacides method) getAssayRT() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getCharge() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getClusteredPeakgroups() (msproteomicstoolslib.data_structures.Precursor.Precursor method) getcode() (msproteomicstoolslib.data_structures.modifications.Modification method) getData() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getDataForChromatogram() (openswathgui.models.SqlDataAccess.SqlDataAccess method) getDataForChromatogramFromNativeId() (openswathgui.models.SqlDataAccess.SqlDataAccess method) getDataForChromatograms() (openswathgui.models.SqlDataAccess.SqlDataAccess method) getDeltaMassFromSequence() (msproteomicstoolslib.data_structures.peptide.Peptide method) getIntensity() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getLabel() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getMZ() (msproteomicstoolslib.data_structures.peptide.Peptide method) getMZfragment() (msproteomicstoolslib.data_structures.peptide.Peptide method) getName() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getOverallBestPeakgroup() (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) getPeptide() (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) getPeptideGroupLabel() (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) getPeptideSequence() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getPrecursor() (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) (msproteomicstoolslib.data_structures.Run.Run method) getPrecursorGroup() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.Run.Run method) getPrecursorGroups() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) getProbScore() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getProteinName() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) getRange() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getRun() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) getRunId() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) getSequence() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) getSequenceWithMods() (msproteomicstoolslib.data_structures.peptide.Peptide method) getSubelements() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getTransitionCount() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) getType() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) GuiPeakGroup (class in msproteomicstoolslib.data_structures.PeakGroup)

H

has_null_peptides() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) has_peptide() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method)

hasPrecursor() (msproteomicstoolslib.data_structures.Run.Run method) hasPrecursorGroup() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method)

I

icat_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) id (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor attribute) (msproteomicstoolslib.data_structures.Precursor.Precursor attribute) id_ (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase attribute) inferMapping() (in module msproteomicstoolslib.format.SWATHScoringReader) init_with_self() (msproteomicstoolslib.data_structures.peak.Peak method) (msproteomicstoolslib.format.speclib_db_lib.Library method) (msproteomicstoolslib.format.speclib_db_lib.SequenceHandler method)

initAminoacides() (msproteomicstoolslib.data_structures.aminoacides.Aminoacides method) initialize() (msproteomicstoolslib.data_structures.peak.Peak method) (msproteomicstoolslib.format.speclib_db_lib.Spectra method) insert() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) intensity_ (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase attribute) is_bool() (msproteomicstoolslib.data_structures.modifications.Modifications method) is_selected() (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) is_tryptic() (msproteomicstoolslib.format.speclib_db_lib.Spectra method)

L

Library (class in msproteomicstoolslib.format.speclib_db_lib)

M

measure_nr_spectra() (msproteomicstoolslib.format.speclib_db_lib.Library method) methyl_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) MinimalPeakGroup (class in msproteomicstoolslib.data_structures.PeakGroup) Modification (class in msproteomicstoolslib.data_structures.modifications)

Modifications (class in msproteomicstoolslib.data_structures.modifications) more_than_fraction_selected() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) mProphet_SWATHScoringReader (class in msproteomicstoolslib.format.SWATHScoringReader) msproteomicstoolslib (module) Multipeptide (class in msproteomicstoolslib.algorithms.alignment.Multipeptide)

N

name (msproteomicstoolslib.data_structures.aminoacides.Aminoacid attribute) newReader() (msproteomicstoolslib.format.SWATHScoringReader.SWATHScoringReader static method)

normalized_retentiontime (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase attribute) nr_unique_peptides() (msproteomicstoolslib.format.speclib_db_lib.Library method)

O

OpenSWATH_SWATHScoringReader (class in msproteomicstoolslib.format.SWATHScoringReader) other_known_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method)

other_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) oxidations_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method)

P

parse_comments() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) parse_files() (msproteomicstoolslib.format.SWATHScoringReader.SWATHScoringReader method) parse_row() (msproteomicstoolslib.format.SWATHScoringReader.mProphet_SWATHScoringReader method) (msproteomicstoolslib.format.SWATHScoringReader.OpenSWATH_SWATHScoringReader method) (msproteomicstoolslib.format.SWATHScoringReader.Peakview_SWATHScoringReader method) (msproteomicstoolslib.format.SWATHScoringReader.SWATHScoringReader method) parse_SearchEngineInfo() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) parse_sptxt() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) parse_str() (msproteomicstoolslib.data_structures.peak.Peak method) Peak (class in msproteomicstoolslib.data_structures.peak) PeakGroupBase (class in msproteomicstoolslib.data_structures.PeakGroup) peakgroups (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor attribute) peakgroups_ (msproteomicstoolslib.data_structures.Precursor.Precursor attribute) Peakview_SWATHScoringReader (class in msproteomicstoolslib.format.SWATHScoringReader) Peptide (class in msproteomicstoolslib.data_structures.peptide)

peptide (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup attribute) peptide_group_label_ (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup attribute) phospho_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) phosphos_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) Precursor (class in msproteomicstoolslib.data_structures.Precursor) precursor_group (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor attribute) (msproteomicstoolslib.data_structures.Precursor.Precursor attribute) PrecursorBase (class in msproteomicstoolslib.data_structures.Precursor) PrecursorGroup (class in msproteomicstoolslib.data_structures.PrecursorGroup) precursors_ (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup attribute) print_out() (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) printModifications() (msproteomicstoolslib.data_structures.modifications.Modifications method) protein_name (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor attribute) (msproteomicstoolslib.data_structures.Precursor.Precursor attribute) pseudoreverse() (msproteomicstoolslib.data_structures.peptide.Peptide method)

R

read_from_db_to_file() (msproteomicstoolslib.format.speclib_db_lib.Library static method) read_fromDB() (msproteomicstoolslib.format.speclib_db_lib.Library method) read_library_to_db() (msproteomicstoolslib.format.speclib_db_lib.Library static method) read_pepidx() (msproteomicstoolslib.format.speclib_db_lib.Library method) read_spectrum_sptxt_idx() (msproteomicstoolslib.format.speclib_db_lib.Library method) read_sptxt() (msproteomicstoolslib.format.speclib_db_lib.Library method) read_sptxt_pepidx() (msproteomicstoolslib.format.speclib_db_lib.Library method) read_sptxt_with_offset() (msproteomicstoolslib.format.speclib_db_lib.Library method) ReadFilter (class in msproteomicstoolslib.format.SWATHScoringReader) readModificationsFile() (msproteomicstoolslib.data_structures.modifications.Modifications method) remove() (msproteomicstoolslib.format.speclib_db_lib.SequenceHandler method) remove_duplicate_entries() (msproteomicstoolslib.format.speclib_db_lib.Library method) (msproteomicstoolslib.format.speclib_db_lib.SequenceHandler method)

remove_precursors() (openswathgui.models.SqlSwathRun.SqlSwathRun method) Residues (class in msproteomicstoolslib.data_structures.Residues) row (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup attribute) Run (class in msproteomicstoolslib.data_structures.Run) run (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup attribute) (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor attribute) (msproteomicstoolslib.data_structures.Precursor.Precursor attribute) run() (msproteomicstoolslib.math.LinearRegression.SimpleLinearRegression method) run_ (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup attribute) runid (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile attribute) (openswathgui.models.SqlSwathRun.SqlSwathRun attribute)

S

save() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) select_pg() (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method) select_this_peakgroup() (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) sequence (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor attribute) (msproteomicstoolslib.data_structures.Precursor.Precursor attribute) SequenceHandler (class in msproteomicstoolslib.format.speclib_db_lib) set_decoy() (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method) set_fdr_score() (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) set_feature_id() (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) set_intensity() (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) set_library_key() (msproteomicstoolslib.format.speclib_db_lib.Library method) set_normalized_retentiontime() (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method)

set_nr_runs() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) set_precursor_group() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) set_value() (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) setClusterID() (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) setProteinName() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) setSequence() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) shuffle_sequence() (msproteomicstoolslib.data_structures.peptide.Peptide method) SimpleLinearRegression (class in msproteomicstoolslib.math.LinearRegression) SingleChromatogramFile (class in openswathgui.models.SingleChromatogramFile) Spectra (class in msproteomicstoolslib.format.speclib_db_lib) SqlDataAccess (class in openswathgui.models.SqlDataAccess) SqlSwathRun (class in openswathgui.models.SqlSwathRun) SWATHScoringReader (class in msproteomicstoolslib.format.SWATHScoringReader)

T

to_pepidx_str() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) to_splib_str() (msproteomicstoolslib.format.speclib_db_lib.Spectra method)

to_write_string() (msproteomicstoolslib.data_structures.peak.Peak method) translateModificationsFromSequence() (msproteomicstoolslib.data_structures.modifications.Modifications method)

U

unselect_all() (msproteomicstoolslib.data_structures.Precursor.Precursor method)

unselect_pg() (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method)

V

validate() (msproteomicstoolslib.format.speclib_db_lib.Spectra method)

W

write() (msproteomicstoolslib.format.speclib_db_lib.Library method)

write_sorted() (msproteomicstoolslib.format.speclib_db_lib.Library method) write_toDB() (msproteomicstoolslib.format.speclib_db_lib.Library method)