| OpenMS 2.5.0

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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
- ParentMolecule() : ParentMolecule
- ParentPeakMower() : ParentPeakMower
- parse() : IMSAlphabetParser< AlphabetElementType, Container, InputSource > , IMSAlphabetTextParser , LogConfigHandler
- parse_() : XMLFile
- parse_nan() : StringUtils::real_policies_NANfixed_< T >
- parseAdduct_() : NucleicAcidSearchEngine
- 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
- parseMod_() : NASequence
- parseModRoundBrackets_() : AASequence
- parseModSquareBrackets_() : AASequence
- parseMzXMLData() : FTPeakDetectController
- parseOffsets() : IndexedMzMLDecoder
- parseOneTableFile_() : ExperimentalDesignFile
- parseParamGroup_() : MzIdentMLDOMHandler
- parsePeptideElements_() : MzIdentMLDOMHandler
- parsePeptideEvidenceElements_() : MzIdentMLDOMHandler
- parsePeptideSiblings_() : MzIdentMLDOMHandler
- parseProteinAmbiguityGroupElement_() : MzIdentMLDOMHandler
- parseProteinDetectionHypothesisElement_() : MzIdentMLDOMHandler
- parseProteinDetectionListElements_() : MzIdentMLDOMHandler
- parseRange_() : TOPPBase
- parseResidue_() : ResidueDB
- parseRow_() : RibonucleotideDB
- parseSpectrumIdentificationElements_() : MzIdentMLDOMHandler
- parseSpectrumIdentificationItemElement_() : MzIdentMLDOMHandler
- parseSpectrumIdentificationItemSetXLMS() : MzIdentMLDOMHandler
- parseSpectrumIdentificationListElements_() : MzIdentMLDOMHandler
- parseSpectrumIdentificationProtocolElements_() : MzIdentMLDOMHandler
- parseString_() : AASequence , NASequence
- parseStructMappingFile_() : AccurateMassSearchEngine
- parseTwoTableFile_() : ExperimentalDesignFile
- 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
- peptideIDsMergeable() : ProteinIdentification
- PeptideIndexing() : PeptideIndexing
- peptideMassRule_() : IsotopeWaveletTransform< PeakType >
- PeptideProteinResolution() : PeptideProteinResolution
- peptideScore_() : AScore
- PepXMLFile() : PepXMLFile
- PepXMLFileMascot() : PepXMLFileMascot
- PercolatorOutfile() : PercolatorOutfile
- performAlignment() : Spectrum1DCanvas , Spectrum1DWidget
- performCalibration() : TOPPOpenSwathBase
- performCrossValidation() : SVMWrapper
- performExtraction() : OpenSwathWorkflow
- performExtractionSonar() : OpenSwathWorkflowSonar
- performRTNormalization() : OpenSwathCalibrationWorkflow
- performSonarExtraction_() : OpenSwathWorkflowSonar
- Permut() : CompNovoIdentificationBase::Permut
- permute_() : CompNovoIdentificationBase
- pick() : PeakPickerCWT , PeakPickerHiRes , PeakPickerIterative , PeakPickerMaxima , PeakPickerSH
- pick_() : PeakPickerHiRes
- pickAndCalibrate() : TOFCalibration
- pickApex() : MRMTransitionGroupPicker
- pickChromatogram() : PeakPickerMRM
- pickChromatogram_() : PeakPickerMRM
- pickChromatogramCrawdad_() : PeakPickerMRM
- pickExperiment() : MRMFeatureFinderScoring , PeakPickerCWT , PeakPickerHiRes , PeakPickerIterative , PeakPickerSH
- pickFragmentChromatograms() : MRMTransitionGroupPicker
- pickPrecursorChromatograms() : MRMTransitionGroupPicker
- 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
- pos_neg_mean_weighted_posteriors() : PosteriorErrorProbabilityModel
- pos_neg_sigma_weighted_posteriors() : PosteriorErrorProbabilityModel
- 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
- postprocess_() : FeatureGroupingAlgorithm
- postProcessHits_() : NucleicAcidSearchEngine , SimpleSearchEngineAlgorithm
- postRawMSHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
- postRawTandemMSHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
- postRTHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
- precalculatedColorAt() : MultiGradient
- precalculatedColorByIndex() : MultiGradient
- precalculatedColorIndex() : MultiGradient
- precalculatedColorIndex_() : Spectrum2DCanvas
- precalculatedSize() : MultiGradient
- preCheck() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
- precision() : BK_PrecPolicy< T >
- PrecisionWrapper() : PrecisionWrapper< FloatingPointType >
- preComputeExpensiveFunctions_() : IsotopeWavelet
- Precondition() : Precondition
- Precursor() : Precursor
- precursor_charge() : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_
- PrecursorInfo() : NucleicAcidSearchEngine::PrecursorInfo
- PrecursorIonSelection() : PrecursorIonSelection
- PrecursorIonSelectionPreprocessing() : PrecursorIonSelectionPreprocessing
- PrecursorVisualizer() : PrecursorVisualizer
- predict() : MZTrafoModel , PeakIntensityPredictor , SimpleSVM , SVMWrapper
- predictContaminantsRT() : RTSimulation
- predictDetectabilities() : DetectabilitySimulation
- Prediction() : Prediction
- predictPeptideRT() : LibSVMEncoder
- predictRT() : RTSimulation
- preferencesChange() : SpectrumCanvas
- preferencesDialog() : TOPPASBase , TOPPViewBase
- prefix() : String , StringUtils
- PrefixInfo_() : FuzzyStringComparator::PrefixInfo_
- prepare_coordinates() : ChromatogramExtractor
- prepareAlign_() : MapAlignmentAlgorithmSpectrumAlignment
- prepareChromOutput() : TOPPOpenSwathBase
- prepareChroms_() : MzMLSqliteHandler
- prepareExtractionCoordinates_() : OpenSwathWorkflowBase
- prepareFeatureOutput_() : MRMFeatureFinderScoring
- prepareFit_() : EmgScoring
- prepareLine() : OpenSwathOSWWriter , OpenSwathTSVWriter
- prepareMasterContainer_() : MRMTransitionGroupPicker
- prepareProteinPeptideMaps_() : MRMFeatureFinderScoring
- prepareResize() : TOPPASEdge
- prepareSpectra_() : ChromatogramExtractor , MzMLSqliteHandler
- prepareStatement() : SqliteConnector
- preprocess() : SpectraSTSimilarityScore
- preprocess_() : ConsensusIDAlgorithmIdentity , ConsensusIDAlgorithmRanks
- preprocessDataPoints_() : TransformationModelInterpolated
- PreprocessedPairSpectra() : OPXLDataStructs::PreprocessedPairSpectra
- preprocessingSirius() : SiriusAdapterAlgorithm
- preprocessPairs_() : OpenPepXLAlgorithm
- preprocessSpectra() : OPXLSpectrumProcessingAlgorithms
- preprocessSpectra_() : NucleicAcidSearchEngine , SimpleSearchEngineAlgorithm
- preScore() : XQuestScores
- primaryProteins_() : ProteinResolver
- print_profile() : LCElutionPeak
- PrintAddressVisitor() : IDBoostGraph::PrintAddressVisitor< CharT >
- printDeltaMassesList() : MultiplexDeltaMassesGenerator
- printEdgesOfConnectedFeatures_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
- printGraph() : IDBoostGraph
- 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
- processOutliers_() : PosteriorErrorProbabilityModel
- processRun_() : BasicProteinInferenceAlgorithm
- 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