Index

_ | A | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z

_

__iter__() (msproteomicstoolslib.data_structures.Run.Run method)
__repr__() (msproteomicstoolslib.math.LinearRegression.SimpleLinearRegression method)

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_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)
addData() (msproteomicstoolslib.format.TransformationCollection.LightTransformationData method)
addDataToTrafo() (in module msproteomicstoolslib.algorithms.alignment.AlignmentHelper)
addPrecursor() (msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup method)
(msproteomicstoolslib.data_structures.Run.Run method)
addSpectrum() (msproteomicstoolslib.data_structures.peptide.Peptide method)
addTrafo() (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)
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)

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)
chauvenet() (in module msproteomicstoolslib.math.chauvenet)
ChromatogramTransition (class in openswathgui.models.ChromatogramTransition)
clearZoomStack() (openswathgui.views.Plot.QwtMultiLinePlot 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)
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)

D

data() (openswathgui.models.PeptideTree.PeptideTree method)
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)
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)
expandMultiElementItems() (openswathgui.views.PeptideTree.PeptidesTreeView method)
Experiment (class in feature_alignment)

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)
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.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.SwathRun.SwathRun method)
get_all_precursor_ids() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method)
(openswathgui.models.SwathRun.SwathRun method)
get_all_spectra() (msproteomicstoolslib.format.speclib_db_lib.Library 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.SwathRun.SwathRun method)
get_decoy() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method)
(msproteomicstoolslib.data_structures.Precursor.PrecursorBase 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.SwathRun.SwathRun method)
get_intensity() (msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method)
get_intensity_data() (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.data_structures.PeakGroup.PeakGroupBase method)
get_nr_runs() (msproteomicstoolslib.algorithms.alignment.Multipeptide.Multipeptide method)
get_openswath_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_tree() (openswathgui.models.MSData.DataModel method)
get_precursors_for_sequence() (openswathgui.models.SingleChromatogramFile.SingleChromatogramFile method)
(openswathgui.models.SwathRun.SwathRun method)
get_range_data() (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.SwathRun.SwathRun 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_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.SwathRun.SwathRun method)
get_transitions_for_precursor_display() (openswathgui.models.SwathRun.SwathRun 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)
getCharge() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method)
(openswathgui.models.MSData.PrecursorModel method)
getChromatogram() (requantAlignedValues.SwathChromatogramCollection method)
(requantAlignedValues.SwathChromatogramRun method)
getClusteredPeakgroups() (msproteomicstoolslib.data_structures.Precursor.Precursor method)
getcode() (msproteomicstoolslib.data_structures.modifications.Modification method)
getData() (msproteomicstoolslib.format.TransformationCollection.LightTransformationData method)
(openswathgui.models.ChromatogramTransition.ChromatogramTransition method)
getDeltaMassFromSequence() (msproteomicstoolslib.data_structures.peptide.Peptide method)
getDistanceMatrix() (in module msproteomicstoolslib.algorithms.alignment.AlignmentMST)
getFullSequence() (openswathgui.models.MSData.PrecursorModel method)
getIntensity() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method)
getLabel() (openswathgui.models.ChromatogramTransition.ChromatogramTransition 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.data_structures.PrecursorGroup.PrecursorGroup 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)
getRange() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method)
getReferenceRunID() (msproteomicstoolslib.format.TransformationCollection.LightTransformationData method)
(msproteomicstoolslib.format.TransformationCollection.TransformationCollection method)
getRTstd() (msproteomicstoolslib.algorithms.alignment.AlignmentAlgorithm.Cluster method)
getRunIds() (openswathgui.models.SwathRunCollection.SwathRunCollection method)
getRunIDs() (requantAlignedValues.SwathChromatogramCollection method)
getSequenceWithMods() (msproteomicstoolslib.data_structures.peptide.Peptide method)
getStatus() (openswathgui.models.MSData.DataModel method)
getStdev() (msproteomicstoolslib.algorithms.alignment.SplineAligner.TransformationError 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.format.TransformationCollection.LightTransformationData method)
getTransformation() (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.SwathRun.SwathRun method)
getType() (openswathgui.models.ChromatogramTransition.ChromatogramTransition method)
getwriter() (in module msproteomicstoolslib.format.MatrixWriters)
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)
index() (openswathgui.models.TreeModels.TreeModel method)
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.LowessSmoothingPy 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.models.TreeModels.TreeModel 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)
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)
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)
loadMixedFiles() (openswathgui.models.MSData.DataModel method)
LocalKernel (class in msproteomicstoolslib.math.Smoothing)
LowessSmoothingPy (class in msproteomicstoolslib.math.Smoothing)

M

main() (in module feature_alignment)
(in module requantAlignedValues)
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

OpenSWATH_SWATHScoringReader (class in msproteomicstoolslib.format.SWATHScoringReader)
openswathgui (module)
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)
parent() (openswathgui.models.TreeModels.TreeModel method)
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)
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)
PeptidesTreeView (class in openswathgui.views.PeptideTree)
PeptideTree (class in openswathgui.models.PeptideTree)
PeptideTreeNode (class in openswathgui.models.PeptideTree)
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)
PrecursorModel (class in openswathgui.models.MSData)
predict() (msproteomicstoolslib.math.Smoothing.LowessSmoothingPy method)
(msproteomicstoolslib.math.Smoothing.SmoothLLDMedian 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)
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.SwathRun.SwathRun method)
replot() (openswathgui.views.Plot.GuiQwtMultiLinePlot method)
reset() (openswathgui.models.TreeModels.TreeModel method)
Residues (class in msproteomicstoolslib.data_structures.Residues)
row (msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup attribute)
rowCount() (openswathgui.models.TreeModels.TreeModel method)
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)
runid (SingleChromatogramFile attribute)
(SwathRun attribute)
runImputeValues() (in module requantAlignedValues)
runs (DataModel 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.data_structures.PeakGroup.MinimalPeakGroup method)
(msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase method)
selectAndScrollTo() (openswathgui.views.PeptideTree.PeptidesTreeView 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_tree_structure() (openswathgui.models.PeptideTree.PeptideTree method)
set_runs() (msproteomicstoolslib.algorithms.alignment.MRExperiment.MRExperiment method)
set_value() (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.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)
setReferenceRunID() (msproteomicstoolslib.format.TransformationCollection.TransformationCollection method)
setTitleFontSize() (openswathgui.views.Plot.GuiQwtMultiLinePlot method)
(openswathgui.views.Plot.QwtMultiLinePlot method)
shuffle_sequence() (msproteomicstoolslib.data_structures.peptide.Peptide method)
SimpleLinearRegression (class in msproteomicstoolslib.math.LinearRegression)
SingleChromatogramFile (class in openswathgui.models.SingleChromatogramFile)
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)
swath_chromatograms (SwathRunCollection 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)
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)

U

UnivarSplineCV (class in msproteomicstoolslib.math.Smoothing)
UnivarSplineNoCV (class in msproteomicstoolslib.math.Smoothing)
unselect_all() (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)

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)