Index

_

__init__() (msproteomicstoolslib.algorithms.alignment.AlignmentMST.TreeConsensusAlignment method)

__module__ (msproteomicstoolslib.algorithms.alignment.AlignmentMST.TreeConsensusAlignment attribute)

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) (openswathgui.models.SwathRun.SwathRun method) add_peakgroup_tpl() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) add_range_to_plot() (openswathgui.views.Plot.GuiQwtMultiLinePlot 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) addData() (msproteomicstoolslib.cython._optimized.CyLightTransformationData method) (msproteomicstoolslib.format.TransformationCollection.LightTransformationData method) addDataToTrafo() (in module msproteomicstoolslib.algorithms.alignment.AlignmentHelper) addPlots() (TAPIR.ApplicationView method) (TAPIR.GraphArea method) addPlotsDummy() (TAPIR.GraphArea method) addPrecursor() (msproteomicstoolslib.cython._optimized.CyPrecursorGroup method) (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) (msproteomicstoolslib.data_structures.Run.Run method) addSpectrum() (msproteomicstoolslib.data_structures.peptide.Peptide method) addTrafo() (msproteomicstoolslib.cython._optimized.CyLightTransformationData method) (msproteomicstoolslib.format.TransformationCollection.LightTransformationData method) addTransformationData() (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method) addTransformedData() (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method) align_features() (msproteomicstoolslib.algorithms.alignment.AlignmentAlgorithm.AlignmentAlgorithm method) alignAllCluster() (msproteomicstoolslib.algorithms.alignment.AlignmentMST.TreeConsensusAlignment method)

alignBestCluster() (msproteomicstoolslib.algorithms.alignment.AlignmentMST.TreeConsensusAlignment method) alignBestCluster_legacy() (msproteomicstoolslib.algorithms.alignment.AlignmentMST.TreeConsensusAlignment method) AlignmentAlgorithm (class in msproteomicstoolslib.algorithms.alignment.AlignmentAlgorithm) AlignmentStatistics (class in feature_alignment) 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) analyze_multipeptide_cluster() (in module requantAlignedValues) analyze_multipeptides() (in module requantAlignedValues) annotate_with_libkey() (msproteomicstoolslib.format.speclib_db_lib.Library method) append() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) appendModification() (msproteomicstoolslib.data_structures.modifications.Modifications method) appendValuesForPeptide() (msproteomicstoolslib.algorithms.alignment.DataCacher.CyDataCacher method) application (MainWindow.self attribute) ApplicationView (class in TAPIR)

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) changedText() (TAPIR.PeptideTreeWidget method) changePlotEngine() (TAPIR.GraphArea method) changeReturnPressedSlot() (TAPIR.PeptideTreeWidget method) chauvenet() (in module msproteomicstoolslib.math.chauvenet) ChromatogramTransition (class in openswathgui.models.ChromatogramTransition) clearZoomStack() (openswathgui.views.Plot.QwtMultiLinePlot method) closeAndSave() (TAPIR.ConfigDialog method) Cluster (class in msproteomicstoolslib.algorithms.alignment.AlignmentAlgorithm) 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) columnCount() (openswathgui.models.PeptideTree.PeptideTree method)

comparePeptideFragments() (msproteomicstoolslib.data_structures.peptide.Peptide method) composition (msproteomicstoolslib.data_structures.aminoacides.Aminoacid attribute) compute_decoy_frac() (msproteomicstoolslib.algorithms.alignment.FDRParameterEstimation.ParamEst method) ConfigDialog (class in TAPIR) count() (feature_alignment.AlignmentStatistics method) count_modifications() (msproteomicstoolslib.format.speclib_db_lib.Library method) create_curves() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) (openswathgui.views.Plot.QwtMultiLinePlot method) createRunCache() (requantAlignedValues.SwathChromatogramCollection method) CsvWriter (class in msproteomicstoolslib.format.MatrixWriters) CurveItemModel (class in openswathgui.views.Plot) CyDataCacher (class in msproteomicstoolslib.algorithms.alignment.DataCacher) CyLightTransformationData (class in msproteomicstoolslib.cython._optimized) CyLinearInterpolateWrapper (class in msproteomicstoolslib.cython._optimized) CyPeakgroupWrapperOnly (class in msproteomicstoolslib.cython._optimized) CyPrecursorGroup (class in msproteomicstoolslib.cython._optimized) CyPrecursorWrapperOnly (class in msproteomicstoolslib.cython._optimized)

D

data() (openswathgui.models.PeptideTree.PeptideTree method) data_model (MainWindow.self attribute) DataModel (class in openswathgui.models.MSData) de_duplicate_array() (msproteomicstoolslib.math.Smoothing.SmoothingPy method) 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)

doMSTAlignment() (in module feature_alignment) doParameterEstimation() (in module feature_alignment) doReferenceAlignment() (in module feature_alignment) draw_range() (openswathgui.views.Plot.QwtMultiLinePlot method) draw_transitions_ (DataModel.self attribute) drawCanvas() (openswathgui.views.Plot.QwtMultiLinePlot method)

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) estimate_aligned_fdr_cutoff() (in module feature_alignment)

estimate_real_fdr() (feature_alignment.Experiment method) expandLevel() (TAPIR.PeptideTreeWidget method) expandMultiElementItems() (openswathgui.views.PeptideTree.PeptidesTreeView method) Experiment (class in feature_alignment)

F

fdr_cutoff (DataModel.self attribute) 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) find_iterate_fdr() (msproteomicstoolslib.algorithms.alignment.FDRParameterEstimation.ParamEst 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_multipeptides() (msproteomicstoolslib.algorithms.alignment.MRExperiment.MRExperiment method) get_all_peakgroups() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (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) (openswathgui.models.SwathRun.SwathRun method) get_all_precursor_ids() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) (openswathgui.models.SwathRun.SwathRun method) get_all_proteins() (openswathgui.models.SqlSwathRun.SqlSwathRun method) (openswathgui.models.SwathRun.SwathRun method) get_all_spectra() (msproteomicstoolslib.format.speclib_db_lib.Library method) get_assay_data() (openswathgui.models.SqlSwathRun.SqlSwathRun method) (openswathgui.models.SwathRun.SwathRun method) get_best_peakgroup() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (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.cython._optimized.CyPeakgroupWrapperOnly method) (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) (openswathgui.models.SwathRun.SwathRun method) get_data_for_transition() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) (openswathgui.models.SwathRun.SwathRun method) get_decoy() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) (msproteomicstoolslib.cython._optimized.CyPrecursorGroup method) (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly 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.cython._optimized.CyPeakgroupWrapperOnly method) (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) get_fdr_score() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) get_feature_id() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (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.cython._optimized.CyPrecursorWrapperOnly 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) (openswathgui.models.SwathRun.SwathRun method) get_intensity() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) get_intensity_data() (openswathgui.models.SqlSwathRun.SqlSwathRun method) (openswathgui.models.SwathRun.SwathRun 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.cython._optimized.CyPeakgroupWrapperOnly method) (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_precursor_model() (TAPIR.ApplicationView method) (TAPIR.PeptideTreeWidget method) get_precursor_tree() (openswathgui.models.MSData.DataModel method) get_precursors_for_sequence() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) (openswathgui.models.SwathRun.SwathRun method) get_range_data() (openswathgui.models.SqlSwathRun.SqlSwathRun method) (openswathgui.models.SwathRun.SwathRun 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_runs() (openswathgui.models.MSData.DataModel method) get_score_data() (openswathgui.models.SqlSwathRun.SqlSwathRun method) (openswathgui.models.SwathRun.SwathRun method) get_selected_peakgroup() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (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) (openswathgui.models.SwathRun.SwathRun 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) (openswathgui.models.SwathRun.SwathRun method) get_transitions_for_precursor_display() (openswathgui.models.SqlSwathRun.SqlSwathRun method) (openswathgui.models.SwathRun.SwathRun method) get_transitions_with_mass_for_precursor() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) get_value() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (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.cython._optimized.CyPrecursorGroup method) (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) getAllPeptides() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) getAllPrecursors() (msproteomicstoolslib.cython._optimized.CyPrecursorGroup method) (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (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) getChromatogram() (requantAlignedValues.SwathChromatogramCollection method) (requantAlignedValues.SwathChromatogramRun method) getClusteredPeakgroups() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) getcode() (msproteomicstoolslib.data_structures.modifications.Modification method) getData() (msproteomicstoolslib.cython._optimized.CyLightTransformationData method) (msproteomicstoolslib.format.TransformationCollection.LightTransformationData method) (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) getDistanceMatrix() (in module msproteomicstoolslib.algorithms.alignment.AlignmentMST) getDrawTransitions() (openswathgui.models.MSData.DataModel method) getIntensity() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getLabel() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getLWP() (msproteomicstoolslib.math.Smoothing.SmoothingInterpolation method) getMedianRT() (msproteomicstoolslib.algorithms.alignment.AlignmentAlgorithm.Cluster method) getMZ() (msproteomicstoolslib.data_structures.peptide.Peptide method) getMZfragment() (msproteomicstoolslib.data_structures.peptide.Peptide method) getName() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getOverallBestPeakgroup() (msproteomicstoolslib.cython._optimized.CyPrecursorGroup method) (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) getPeptide() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) getPeptideGroupLabel() (msproteomicstoolslib.cython._optimized.CyPrecursorGroup method) (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method) getPeptideSequence() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getPrecursor() (msproteomicstoolslib.cython._optimized.CyPrecursorGroup method) (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.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) getRange() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getReferenceRunID() (msproteomicstoolslib.cython._optimized.CyLightTransformationData method) (msproteomicstoolslib.format.TransformationCollection.LightTransformationData method) (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method) getRTstd() (msproteomicstoolslib.algorithms.alignment.AlignmentAlgorithm.Cluster method) getRun() (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) getRunId() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) getRunIds() (openswathgui.models.SwathRunCollection.SwathRunCollection method) getRunIDs() (requantAlignedValues.SwathChromatogramCollection method) getSequence() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) getSequenceWithMods() (msproteomicstoolslib.data_structures.peptide.Peptide method) getStatus() (openswathgui.models.MSData.DataModel method) getStdev() (msproteomicstoolslib.algorithms.alignment.SplineAligner.TransformationError method) (msproteomicstoolslib.cython._optimized.CyLightTransformationData method) (msproteomicstoolslib.format.TransformationCollection.LightTransformationData method) getSubelements() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getSwathFile() (openswathgui.models.SwathRunCollection.SwathRunCollection method) getSwathFiles() (openswathgui.models.SwathRunCollection.SwathRunCollection method) getTotalScore() (msproteomicstoolslib.algorithms.alignment.AlignmentAlgorithm.Cluster method) getTrafo() (msproteomicstoolslib.cython._optimized.CyLightTransformationData method) (msproteomicstoolslib.format.TransformationCollection.LightTransformationData method) getTransformation() (msproteomicstoolslib.cython._optimized.CyLightTransformationData method) (msproteomicstoolslib.format.TransformationCollection.LightTransformationData method) (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method) getTransformationData() (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method) getTransformationError() (msproteomicstoolslib.algorithms.alignment.SplineAligner.SplineAligner method) getTransformedData() (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method) getTransitionCount() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method) (openswathgui.models.SqlSwathRun.SqlSwathRun method) (openswathgui.models.SwathRun.SwathRun method) getType() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method) getwriter() (in module msproteomicstoolslib.format.MatrixWriters) GraphArea (class in TAPIR) GuiPeakGroup (class in msproteomicstoolslib.data_structures.PeakGroup) GuiQwtMultiLinePlot (class in openswathgui.views.Plot)

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) headerData() (openswathgui.models.PeptideTree.PeptideTree 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) ImputeValuesHelper (class in requantAlignedValues) 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) (msproteomicstoolslib.math.Smoothing.LocalKernel method) (msproteomicstoolslib.math.Smoothing.SmoothingEarth method) (msproteomicstoolslib.math.Smoothing.SmoothingInterpolation method) (msproteomicstoolslib.math.Smoothing.SmoothingLinear method) (msproteomicstoolslib.math.Smoothing.SmoothingNull method) (msproteomicstoolslib.math.Smoothing.SmoothingPy method) (msproteomicstoolslib.math.Smoothing.SmoothingR method) (msproteomicstoolslib.math.Smoothing.SmoothingRExtern method) (msproteomicstoolslib.math.Smoothing.UnivarSplineCV method) (msproteomicstoolslib.math.Smoothing.UnivarSplineNoCV method) (openswathgui.views.Plot.GuiQwtMultiLinePlot method) (openswathgui.views.Plot.QwtMultiLinePlot method) initialize_from_chromatograms() (openswathgui.models.SwathRunCollection.SwathRunCollection method) initialize_from_data() (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method) initialize_from_directories() (openswathgui.models.SwathRunCollection.SwathRunCollection method) initialize_from_files() (openswathgui.models.SwathRunCollection.SwathRunCollection method) initialize_from_sql() (openswathgui.models.SwathRunCollection.SwathRunCollection method) initialize_from_sql_map() (openswathgui.models.SwathRunCollection.SwathRunCollection method)

initUI() (TAPIR.PeptideTreeWidget method) insert() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method) integrate_chromatogram() (in module requantAlignedValues) integrationBorderReference() (in module msproteomicstoolslib.algorithms.alignment.BorderIntegration) integrationBorderShortestDistance() (in module msproteomicstoolslib.algorithms.alignment.BorderIntegration) integrationBorderShortestPath() (in module msproteomicstoolslib.algorithms.alignment.BorderIntegration) 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) iterAllLevelElements() (openswathgui.views.PeptideTree.PeptidesTreeView method) iterTopLevelElements() (openswathgui.views.PeptideTree.PeptidesTreeView method) IWriter (class in msproteomicstoolslib.format.MatrixWriters)

L

Library (class in msproteomicstoolslib.format.speclib_db_lib) LightTransformationData (class in msproteomicstoolslib.format.TransformationCollection) load_from_yaml() (openswathgui.models.MSData.DataModel method) loadFiles() (openswathgui.models.MSData.DataModel method) (TAPIR.MainWindow method) loadMixedFiles() (openswathgui.models.MSData.DataModel method)

loadSqMassFiles() (openswathgui.models.MSData.DataModel method) LocalKernel (class in msproteomicstoolslib.math.Smoothing) LowessSmoothingBiostats (class in msproteomicstoolslib.math.Smoothing) LowessSmoothingCyLowess (class in msproteomicstoolslib.math.Smoothing) LowessSmoothingStatsmodels (class in msproteomicstoolslib.math.Smoothing)

M

main() (in module feature_alignment) (in module requantAlignedValues) MainWindow (class in TAPIR) 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) mousePressEvent() (openswathgui.views.Plot.QwtMultiLinePlot method) mouseReleaseEvent() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) (openswathgui.views.Plot.QwtMultiLinePlot method) mProphet_SWATHScoringReader (class in msproteomicstoolslib.format.SWATHScoringReader) MRExperiment (class in msproteomicstoolslib.algorithms.alignment.MRExperiment) msproteomicstoolslib (module) Multipeptide (class in msproteomicstoolslib.algorithms.alignment.Multipeptide)

N

name (msproteomicstoolslib.data_structures.aminoacides.Aminoacid attribute) newline() (msproteomicstoolslib.format.MatrixWriters.CsvWriter method) (msproteomicstoolslib.format.MatrixWriters.IWriter method) (msproteomicstoolslib.format.MatrixWriters.XlsWriter method) (msproteomicstoolslib.format.MatrixWriters.XlsxWriter method) 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

only_show_quantified (DataModel.self attribute) 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

ParamEst (class in msproteomicstoolslib.algorithms.alignment.FDRParameterEstimation) parse() (requantAlignedValues.SwathChromatogramRun method) 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) parseFromMzML() (requantAlignedValues.SwathChromatogramCollection method) parseFromSqMass() (requantAlignedValues.SwathChromatogramCollection method) parseFromTrafoFiles() (requantAlignedValues.SwathChromatogramCollection 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) PeptidesTreeView (class in openswathgui.views.PeptideTree) PeptideTree (class in openswathgui.models.PeptideTree) PeptideTreeNode (class in openswathgui.models.PeptideTree)

PeptideTreeWidget (class in TAPIR) phospho_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) phosphos_len() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) plots (GraphArea.self attribute) plotsUpdated (TAPIR.ApplicationView attribute) plotsUpdated() (TAPIR.MainWindow method) plotZoomChanged() (TAPIR.GraphArea 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) predict() (msproteomicstoolslib.cython._optimized.CyLinearInterpolateWrapper method) (msproteomicstoolslib.math.Smoothing.SmoothLLDMedian method) (msproteomicstoolslib.math.Smoothing.SmoothingEarth method) (msproteomicstoolslib.math.Smoothing.SmoothingInterpolation method) (msproteomicstoolslib.math.Smoothing.SmoothingLinear method) (msproteomicstoolslib.math.Smoothing.SmoothingNull method) (msproteomicstoolslib.math.Smoothing.SmoothingPy method) (msproteomicstoolslib.math.Smoothing.SmoothingR method) (msproteomicstoolslib.math.Smoothing.SmoothingRExtern method) (msproteomicstoolslib.math.Smoothing.UnivarSplineCV method) (msproteomicstoolslib.math.Smoothing.UnivarSplineNoCV method) (msproteomicstoolslib.math.Smoothing.WeightedNearestNeighbour method) predict_R_() (msproteomicstoolslib.math.Smoothing.SmoothingRExtern method) print_out() (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) print_stats() (feature_alignment.Experiment method) printAddresses() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) printModifications() (msproteomicstoolslib.data_structures.modifications.Modifications method) printTransformationData() (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method) protein_name (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor attribute) (msproteomicstoolslib.data_structures.Precursor.Precursor attribute) pseudoreverse() (msproteomicstoolslib.data_structures.peptide.Peptide method)

Q

QwtMultiLinePlot (class in openswathgui.views.Plot)

R

rangeChanged() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) re_duplicate_array() (msproteomicstoolslib.math.Smoothing.SmoothingPy method) 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) readTransformationData() (msproteomicstoolslib.format.TransformationCollection.TransformationCollection 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) (openswathgui.models.SwathRun.SwathRun method) replot() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) Residues (class in msproteomicstoolslib.data_structures.Residues) retrieveValues() (msproteomicstoolslib.algorithms.alignment.DataCacher.CyDataCacher method) row (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup attribute) rt_align_all_runs() (msproteomicstoolslib.algorithms.alignment.SplineAligner.SplineAligner method) 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 (SingleChromatogramFile attribute) (SqlSwathRun attribute) (SwathRun attribute) runImputeValues() (in module requantAlignedValues) runs (DataModel.self attribute) runSingleFileImputation() (in module requantAlignedValues)

S

save() (msproteomicstoolslib.format.speclib_db_lib.Spectra method) select_correct_swath() (requantAlignedValues.ImputeValuesHelper static method) select_one_per_run() (msproteomicstoolslib.algorithms.alignment.AlignmentAlgorithm.Cluster method) select_pg() (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method) select_this_peakgroup() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) selectAndScrollTo() (openswathgui.views.PeptideTree.PeptidesTreeView method) selectionChanged (TAPIR.PeptideTreeWidget attribute) sequence (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor attribute) (msproteomicstoolslib.data_structures.Precursor.Precursor attribute) SequenceHandler (class in msproteomicstoolslib.format.speclib_db_lib) set_communicate() (TAPIR.GraphArea method) set_communication() (TAPIR.ApplicationView method) set_decoy() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method) set_fdr_score() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) set_feature_id() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) set_intensity() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (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.cython._optimized.CyPeakgroupWrapperOnly method) (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.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) set_precursor_tree_structure() (openswathgui.models.PeptideTree.PeptideTree method) set_runs() (msproteomicstoolslib.algorithms.alignment.MRExperiment.MRExperiment method) set_value() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method) set_x_limits() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) (openswathgui.views.Plot.QwtMultiLinePlot method) set_y_limits() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) (openswathgui.views.Plot.QwtMultiLinePlot method) set_y_limits_auto() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) (openswathgui.views.Plot.QwtMultiLinePlot method) setAxisFontSize() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) (openswathgui.views.Plot.QwtMultiLinePlot method) setClusterID() (msproteomicstoolslib.cython._optimized.CyPeakgroupWrapperOnly method) (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup method) (msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) setDataModel() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) (openswathgui.views.Plot.QwtMultiLinePlot method) setDrawTransitions() (openswathgui.models.MSData.DataModel method)

setProteinName() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) setReferenceRunID() (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method) setSequence() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) Settings (class in TAPIR) setTitleFontSize() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) (openswathgui.views.Plot.QwtMultiLinePlot method) showFileLoadDialog() (TAPIR.MainWindow method) shuffle_sequence() (msproteomicstoolslib.data_structures.peptide.Peptide method) SimpleLinearRegression (class in msproteomicstoolslib.math.LinearRegression) SingleChromatogramFile (class in openswathgui.models.SingleChromatogramFile) SmoothingEarth (class in msproteomicstoolslib.math.Smoothing) SmoothingInterpolation (class in msproteomicstoolslib.math.Smoothing) SmoothingLinear (class in msproteomicstoolslib.math.Smoothing) SmoothingNull (class in msproteomicstoolslib.math.Smoothing) SmoothingPy (class in msproteomicstoolslib.math.Smoothing) SmoothingR (class in msproteomicstoolslib.math.Smoothing) SmoothingRExtern (class in msproteomicstoolslib.math.Smoothing) SmoothLLDMedian (class in msproteomicstoolslib.math.Smoothing) Spectra (class in msproteomicstoolslib.format.speclib_db_lib) SplineAligner (class in msproteomicstoolslib.algorithms.alignment.SplineAligner) SqlDataAccess (class in openswathgui.models.SqlDataAccess) SqlSwathRun (class in openswathgui.models.SqlSwathRun) static_cy_alignBestCluster() (in module msproteomicstoolslib.cython._optimized) swath_chromatograms (SwathRunCollection.self attribute) SwathChromatogramCollection (class in requantAlignedValues) SwathChromatogramRun (class in requantAlignedValues) SwathRun (class in openswathgui.models.SwathRun) SwathRunCollection (class in openswathgui.models.SwathRunCollection) 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) to_yaml() (feature_alignment.AlignmentStatistics method) TransformationCollection (class in msproteomicstoolslib.format.TransformationCollection) TransformationError (class in msproteomicstoolslib.algorithms.alignment.SplineAligner)

translateModificationsFromSequence() (msproteomicstoolslib.data_structures.modifications.Modifications method) TreeConsensusAlignment (class in msproteomicstoolslib.algorithms.alignment.AlignmentMST) TreeModel (class in openswathgui.models.TreeModels) TreeNode (class in openswathgui.models.TreeModels) treeSelectionChanged() (TAPIR.ApplicationView method) treeViewSelectionChangedSlot() (TAPIR.PeptideTreeWidget method)

U

UnivarSplineCV (class in msproteomicstoolslib.math.Smoothing) UnivarSplineNoCV (class in msproteomicstoolslib.math.Smoothing) unselect_all() (msproteomicstoolslib.cython._optimized.CyPrecursorWrapperOnly method) (msproteomicstoolslib.data_structures.Precursor.Precursor method) unselect_pg() (msproteomicstoolslib.data_structures.Precursor.Precursor method) (msproteomicstoolslib.data_structures.Precursor.PrecursorBase method)

update_all_curves() (openswathgui.views.Plot.GuiQwtMultiLinePlot method) (openswathgui.views.Plot.QwtMultiLinePlot method) update_all_plots() (TAPIR.GraphArea method) updateSettings() (TAPIR.MainWindow method)

V

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

W

WeightedNearestNeighbour (class in msproteomicstoolslib.math.Smoothing) write() (msproteomicstoolslib.format.MatrixWriters.CsvWriter method) (msproteomicstoolslib.format.MatrixWriters.IWriter method) (msproteomicstoolslib.format.MatrixWriters.XlsWriter method) (msproteomicstoolslib.format.MatrixWriters.XlsxWriter method) (msproteomicstoolslib.format.speclib_db_lib.Library method) write_out() (in module requantAlignedValues) write_out_matrix_file() (in module msproteomicstoolslib.algorithms.alignment.AlignmentHelper)

write_sorted() (msproteomicstoolslib.format.speclib_db_lib.Library method) write_to_file() (feature_alignment.Experiment method) write_toDB() (msproteomicstoolslib.format.speclib_db_lib.Library method) writeTransformationData() (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method)

X

XlsWriter (class in msproteomicstoolslib.format.MatrixWriters)

XlsxWriter (class in msproteomicstoolslib.format.MatrixWriters)

Z

zoomChanged (openswathgui.views.Plot.GuiQwtMultiLinePlot attribute) (openswathgui.views.Plot.QwtMultiLinePlot attribute)