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• paint() : AxisPainter , AxisWidget , Spectrum1DCanvas , TOPPASEdge , TOPPASInputFileListVertex , TOPPASMergerVertex , TOPPASOutputFileListVertex , TOPPASSplitterVertex , TOPPASToolVertex , TOPPASVertex
• paintAllIntensities_() : Spectrum2DCanvas
• paintConsensusElement_() : Spectrum2DCanvas
• paintConsensusElements_() : Spectrum2DCanvas
• paintConvexHulls_() : Spectrum2DCanvas
• paintDots_() : Spectrum2DCanvas
• paintEvent() : AxisWidget , ColorSelector , HistogramWidget , MultiGradientSelector , Spectrum1DCanvas , Spectrum2DCanvas
• paintFeatureConvexHulls_() : Spectrum2DCanvas
• paintFeatureData_() : Spectrum2DCanvas
• paintGL() : Spectrum3DOpenGLCanvas
• paintGridLines_() : Spectrum1DCanvas , SpectrumCanvas
• paintIcon_() : Spectrum2DCanvas
• paintIdentifications_() : Spectrum2DCanvas
• paintMaximumIntensities_() : Spectrum2DCanvas
• paintPrecursorPeaks_() : Spectrum2DCanvas
• paintTraceConvexHulls_() : Spectrum2DCanvas
• Param() : Param
• ParamEditor() : ParamEditor
• ParamEditorDelegate() : ParamEditorDelegate
• ParamEntry() : Param::ParamEntry
• paramEntryToParameterInformation_() : TOPPBase
• parameterChanged() : TOPPASVertex
• ParameterInformation() : ParameterInformation
• ParamIterator() : Param::ParamIterator
• ParamNode() : Param::ParamNode
• paramToParameterInformation_() : TOPPBase
• ParamTree() : ParamTree
• ParamXMLFile() : ParamXMLFile
• ParamXMLHandler() : ParamXMLHandler
• ParentPeakMower() : ParentPeakMower
• parse() : IMSAlphabetParser< AlphabetElementType, Container, InputSource > , IMSAlphabetTextParser , LogConfigHandler
• parse_() : XMLFile
• parse_nan() : StringUtils::real_policies_NANfixed_< T >
• parseAdductsFile_() : AccurateMassSearchEngine
• parseAdductString() : AdductInfo
• parseAnalysisSoftwareList_() : MzIdentMLDOMHandler
• parseBuffer_() : XMLFile
• parseCommandLine() : Param
• parseCommandLine_() : TOPPBase
• parseCvParam_() : MzIdentMLDOMHandler
• parseDBSequenceElements_() : MzIdentMLDOMHandler
• parseEnzyme_() : DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
• ParseError() : ParseError
• parseFooter_() : IndexedMzMLHandler
• parseFormula_() : EmpiricalFormula
• parseFragmentAnnotation_() : IdXMLFile
• parseHeader_() : ExperimentalDesignFile , MSPFile
• parseInputElements_() : MzIdentMLDOMHandler
• parseIsotopeDistribution_() : ElementDB
• parseLine_() : AbsoluteQuantitationMethodFile
• parseMappingFile_() : AccurateMassSearchEngine
• parseModRoundBrackets_() : AASequence
• parseModSquareBrackets_() : AASequence
• parseMzXMLData() : FTPeakDetectController
• parseOffsets() : IndexedMzMLDecoder
• parseParamGroup_() : MzIdentMLDOMHandler
• parsePeptideElements_() : MzIdentMLDOMHandler
• parsePeptideEvidenceElements_() : MzIdentMLDOMHandler
• parsePeptideSiblings_() : MzIdentMLDOMHandler
• parseProteinAmbiguityGroupElement_() : MzIdentMLDOMHandler
• parseProteinDetectionHypothesisElement_() : MzIdentMLDOMHandler
• parseProteinDetectionListElements_() : MzIdentMLDOMHandler
• parseRange_() : TOPPBase
• parseResidue_() : ResidueDB
• parseSpectrumIdentificationElements_() : MzIdentMLDOMHandler
• parseSpectrumIdentificationItemElement_() : MzIdentMLDOMHandler
• parseSpectrumIdentificationItemSetXLMS() : MzIdentMLDOMHandler
• parseSpectrumIdentificationListElements_() : MzIdentMLDOMHandler
• parseSpectrumIdentificationProtocolElements_() : MzIdentMLDOMHandler
• parseString_() : AASequence
• parseStructMappingFile_() : AccurateMassSearchEngine
• parseUserParam_() : MzIdentMLDOMHandler
• partitionIntoRuns_() : MzTabFile
• passes() : DataFilters
• passesFilters_() : ConsensusMapNormalizerAlgorithmMedian
• paste() : TOPPASScene
• path() : File
• pathLabelMapper_() : ExperimentalDesign
• Pattern() : Pattern< TNeedle, FuzzyAC >
• PatternAuxData() : PatternAuxData< TNeedle >
• Peak() : IMSIsotopeDistribution::Peak
• Peak1D() : Peak1D
• Peak2D() : Peak2D
• PeakAlignment() : PeakAlignment
• PeakFileOptions() : PeakFileOptions
• PeakIndex() : PeakIndex
• PeakIntegrator() : PeakIntegrator
• PeakIntensityPredictor() : PeakIntensityPredictor
• PeakMarker() : PeakMarker
• peakPairScore_() : PeakAlignment
• PeakPickerCWT() : PeakPickerCWT
• PeakPickerHiRes() : PeakPickerHiRes
• PeakPickerIterative() : PeakPickerIterative
• PeakPickerMaxima() : PeakPickerMaxima
• PeakPickerMRM() : PeakPickerMRM
• PeakPickerSH() : PeakPickerSH
• peakPickingPerWindowsInSpectrum_() : AScore
• peakselectionIsAllowed_() : MRMFragmentSelection
• PeakShape() : PeakShape
• PeakSpectrumCompareFunctor() : PeakSpectrumCompareFunctor
• PeakWidthEstimator() : PeakWidthEstimator
• PenaltyFactors() : PenaltyFactors
• PenaltyFactorsIntensity() : PenaltyFactorsIntensity
• PepNovoInfile() : PepNovoInfile
• PepNovoOutfile() : PepNovoOutfile
• Peptide() : Peptide
• PeptideAndProteinQuant() : PeptideAndProteinQuant
• PeptideCompound() : PeptideCompound
• peptideCount() : EnzymaticDigestionLogModel , ProteaseDigestion
• PeptideData() : PeptideAndProteinQuant::PeptideData
• PeptideDigestionFilter() : IDFilter::PeptideDigestionFilter
• PeptideEvidence() : PeptideEvidence
• PeptideHit() : PeptideHit
• PeptideHitVisualizer() : PeptideHitVisualizer
• PeptideIdentification() : PeptideIdentification
• PeptideIdentificationVisualizer() : PeptideIdentificationVisualizer
• PeptideIndexing() : PeptideIndexing
• peptideMassRule_() : IsotopeWaveletTransform< PeakType >
• PeptideProteinResolution() : PeptideProteinResolution
• peptideScore_() : AScore
• PepXMLFile() : PepXMLFile
• PepXMLFileMascot() : PepXMLFileMascot
• PercolatorOutfile() : PercolatorOutfile
• performAlignment() : Spectrum1DCanvas , Spectrum1DWidget
• performCrossValidation() : SVMWrapper
• performExtraction() : OpenSwathWorkflow
• performExtractionSonar() : OpenSwathWorkflowSonar
• performRTNormalization() : OpenSwathRetentionTimeNormalization
• performSonarExtraction_() : OpenSwathWorkflowSonar
• Permut() : CompNovoIdentificationBase::Permut
• permute_() : CompNovoIdentificationBase
• pick() : PeakPickerCWT , PeakPickerHiRes , PeakPickerIterative , PeakPickerMaxima , PeakPickerSH
• pickAndCalibrate() : TOFCalibration
• pickChromatogram() : PeakPickerMRM
• pickChromatogram_() : PeakPickerMRM
• pickChromatogramCrawdad_() : PeakPickerMRM
• pickExperiment() : MRMFeatureFinderScoring , PeakPickerCWT , PeakPickerHiRes , PeakPickerIterative , PeakPickerSH
• pickRecenterPeaks_() : PeakPickerIterative
• pickSpectrum() : TargetedSpectraExtractor
• pickTransitionGroup() : MRMTransitionGroupPicker
• pipelineDroppedOnWidget() : TOPPASWidget
• pipelineErrorSlot() : TOPPASScene
• pipelineExecutionFailed() : TOPPASScene
• PlainMSDataWritingConsumer() : PlainMSDataWritingConsumer
• plotCombinedSpectra() : ClusteredMS2ConsensusSpectrum
• plotFilteredSpectra() : MetaProSIPReporting
• plotHeatMap() : MetaProSIPReporting
• plotScoresAndWeights() : MetaProSIPReporting
• plotTargetDecoyEstimation() : PosteriorErrorProbabilityModel
• PointerComparator() : PointerComparator< Cmp >
• pointerComparator() : PointerComparator< Cmp >
• polar() : AAIndex
• pop_back() : ConstRefVector< ContainerT >
• populate_raster_() : LinearResamplerAlign
• populateChromatogramsWithData_() : MzMLHandler , MzMLSqliteHandler
• populateMetaData_() : SwathFile
• populatePeptideRTMap_() : ChromatogramExtractor
• populateSpectraWithData_() : MzMLHandler , MzMLSqliteHandler , MzXMLHandler
• PosBegin() : MSChromatogram , MSSpectrum
• PoseClusteringAffineSuperimposer() : PoseClusteringAffineSuperimposer
• PoseClusteringShiftSuperimposer() : PoseClusteringShiftSuperimposer
• PosEnd() : MSChromatogram , MSSpectrum
• position() : FASTAFile , MultiGradient
• positionScore_() : FeatureFinderAlgorithmPicked
• Postcondition() : Postcondition
• postDetectabilityHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
• postDigestHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
• PosteriorErrorProbabilityModel() : PosteriorErrorProbabilityModel
• postIonizationHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
• postProcess_() : FeatureFinderIdentificationAlgorithm
• postProcessHits_() : RNPxlSearch , SimpleSearchEngine
• postRawMSHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
• postRawTandemMSHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
• postRTHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
• postScoreHits_() : RNPxlSearch
• precalculatedColorAt() : MultiGradient
• precalculatedColorByIndex() : MultiGradient
• precalculatedColorIndex() : MultiGradient
• precalculatedColorIndex_() : Spectrum2DCanvas
• precalculatedSize() : MultiGradient
• preCheck() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
• PrecisionWrapper() : PrecisionWrapper< FloatingPointType >
• preComputeExpensiveFunctions_() : IsotopeWavelet
• Precondition() : Precondition
• Precursor() : Precursor
• PrecursorIonSelection() : PrecursorIonSelection
• PrecursorIonSelectionPreprocessing() : PrecursorIonSelectionPreprocessing
• PrecursorVisualizer() : PrecursorVisualizer
• predict() : MZTrafoModel , PeakIntensityPredictor , SimpleSVM , SVMWrapper
• predictContaminantsRT() : RTSimulation
• predictDetectabilities() : DetectabilitySimulation
• Prediction() : Prediction
• predictRT() : RTSimulation
• preferencesChange() : SpectrumCanvas
• preferencesDialog() : TOPPASBase , TOPPViewBase
• prefix() : String , StringUtils
• PrefixInfo_() : FuzzyStringComparator::PrefixInfo_
• prepare_coordinates() : ChromatogramExtractor
• prepareAlign_() : MapAlignmentAlgorithmSpectrumAlignment
• prepareChroms_() : MzMLSqliteHandler
• prepareExtractionCoordinates_() : OpenSwathWorkflowBase
• prepareFit_() : EmgScoring
• prepareLine() : OpenSwathOSWWriter , OpenSwathTSVWriter
• prepareMasterContainer_() : MRMTransitionGroupPicker
• prepareProteinPeptideMaps_() : MRMFeatureFinderScoring
• prepareResize() : TOPPASEdge
• prepareSpectra_() : ChromatogramExtractor , MzMLSqliteHandler
• preprocess() : SpectraSTSimilarityScore
• preprocess_() : ConsensusIDAlgorithmIdentity , ConsensusIDAlgorithmRanks
• preprocessDataPoints_() : TransformationModelInterpolated
• PreprocessedPairSpectra() : OPXLDataStructs::PreprocessedPairSpectra
• preprocessPairs_() : TOPPOpenPepXL
• preprocessSpectra() : OPXLSpectrumProcessingAlgorithms
• preprocessSpectra_() : RNPxlSearch , SimpleSearchEngine
• preScore() : XQuestScores
• primaryProteins_() : ProteinResolver
• print_profile() : LCElutionPeak
• printDeltaMassesList() : MultiplexDeltaMassesGenerator
• printEdgesOfConnectedFeatures_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• printNull_() : SimpleSVM
• printSamplesLabelsList() : MultiplexDeltaMassesGenerator
• printSummary() : TransformationDescription
• printToVoid_() : SVMWrapper
• printUsage_() : TOPPBase
• process_MS1_level_data_structure() : FTPeakDetectController
• process_MS2_level_data_structure() : FTPeakDetectController
• processChromatogram_() : MSDataWritingConsumer , NoopMSDataWritingConsumer , PlainMSDataWritingConsumer
• ProcessData() : ProcessData
• processFinished() : TOPPASScene
• processIntensities() : BackgroundIntensityBin
• processIntensityMaps() : BackgroundControl
• processMSPeaks() : ProcessData
• processMZFeatureVector() : MS1FeatureMerger
• processSpectrum_() : MSDataWritingConsumer , NoopMSDataWritingConsumer , PlainMSDataWritingConsumer
• Product() : Product
• ProductModel() : ProductModel< 2 >
• ProductVisualizer() : ProductVisualizer
• ProgressLogger() : ProgressLogger
• project_() : Spectrum3DOpenGLCanvas
• projectionInfo() : Spectrum2DWidget
• projectionsVisible() : Spectrum2DWidget
• proportionsActivated() : SaveImageDialog
• ProteaseDB() : ProteaseDB
• Protein() : Protein
• ProteinData() : PeptideAndProteinQuant::ProteinData
• ProteinGroup() : ProteinIdentification::ProteinGroup
• ProteinHit() : ProteinHit
• ProteinHitVisualizer() : ProteinHitVisualizer
• ProteinIdentification() : ProteinIdentification
• ProteinIdentificationVisualizer() : ProteinIdentificationVisualizer
• ProteinInference() : ProteinInference
• ProteinResolver() : ProteinResolver
• ProtonDistributionModel() : ProtonDistributionModel
• ProtXMLFile() : ProtXMLFile
• pseudoreversePeptide_() : MRMDecoy
• PSLPFormulation() : PSLPFormulation
• PSProteinInference() : PSProteinInference
• PTMXMLFile() : PTMXMLFile
• PTMXMLHandler() : PTMXMLHandler
• Publication() : Publication
• PuritySate_() : IsobaricChannelExtractor::PuritySate_
• push2Box_() : IsotopeWaveletTransform< PeakType >
• push2TmpBox_() : IsotopeWaveletTransform< PeakType >
• push_back() : ConstRefVector< ContainerT > , IMSAlphabet , TOPPASVertex::TOPPASFilenames
• pushValuesFromLine_() : MRMFeatureQCFile
• PValue_() : LabeledPairFinder