|
OpenMS
2.5.0
|
- p -
- 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
- 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