Here is a list of all class members with links to the classes they belong to:
- p -
- p
: GammaDistributionFitter::GammaDistributionFitResult
- P
: SVMWrapper
- p_
: ToolDescriptionHandler
, PILISIdentification
- p_cleave
: EnzymaticDigestion::CleavageModel
- p_miss
: EnzymaticDigestion::CleavageModel
- P_PRECURSORS
: LayerData
- P_PROJECTIONS
: LayerData
- p_pv_map_
: MzIdentMLDOMHandler
- packages_
: SplineSpectrum::Navigator
, SplineSpectrum
- paint()
: AxisPainter
, AxisWidget
, Spectrum1DCanvas
, TOPPASEdge
, TOPPASInputFileListVertex
, TOPPASMergerVertex
, TOPPASOutputFileListVertex
, 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
- pair_min_quality_
: SimplePairFinder
- PairDistances
: QTClusterFinder
- pairfinder_
: MapAlignmentAlgorithmPoseClustering
- pairfinder_input_
: FeatureGroupingAlgorithmUnlabeled
- PairsIndex
: ILPDCWrapper
- PairsType
: FeatureDeconvolution
, ILPDCWrapper
- param
: ToolExternalDetails
, LayerData
- Param()
: Param
- param
: TOPPViewBase
- param_
: DefaultParamHandler
, FeatureXMLFile
, IdXMLFile
, INIFileEditorWindow
, ParamXMLHandler
, LocalLinearMap
, ParamEditor
, SVMWrapper
, TOPPASToolConfigDialog
, TOPPASToolVertex
, TOPPBase
- param_cmdline_
: TOPPBase
- param_common_
: TOPPBase
- param_common_tool_
: TOPPBase
- param_groups_
: MzMLValidator
, MzQuantMLValidator
- param_inifile_
: TOPPBase
- param_instance_
: TOPPBase
- PARAM_NAME
: LogConfigHandler
- param_name
: TOPPASToolVertex::IOInfo
- ParamEditor()
: ParamEditor
- ParamEditorDelegate()
: ParamEditorDelegate
- ParamEntry()
: Param::ParamEntry
- paramEntryToParameterInformation_()
: TOPPBase
- parameter_cvs
: MzIdentMLDOMHandler::SpectrumIdentificationProtocol
- parameter_ups
: MzIdentMLDOMHandler::SpectrumIdentificationProtocol
- parameterChanged()
: TOPPASVertex
- ParameterInformation()
: ParameterInformation
- parameters_
: IdXMLFile
, ModelDescription< D >
, MzTabParameterList
, TOPPBase
- ParameterTypes
: ParameterInformation
- ParamGroupList
: MSQuantifications
- ParamIterator()
: Param::ParamIterator
- ParamNode()
: Param::ParamNode
- params_
: AcqusHandler
, PepXMLFile
, TransformationModel
, TransformationXMLFile
- params_intensity_
: FeatureDistance
- params_mz_
: FeatureDistance
- params_rt_
: FeatureDistance
- paramToParameterInformation_()
: TOPPBase
- ParamTree()
: ParamTree
- ParamXMLFile()
: ParamXMLFile
- ParamXMLHandler()
: ParamXMLHandler
- PARENT
: CompNovoIonScoringBase
- parent_
: TOPPASInputFileDialog
- ParentPeakMower()
: ParentPeakMower
- parents
: ControlledVocabulary::CVTerm
- parse()
: IMSAlphabetParser< AlphabetElementType, Container, InputSource >
, IMSAlphabetTextParser
, LogConfigHandler
- parse_()
: XMLFile
- PARSE_ERROR
: TOPPBase
- parseAdductsFile_()
: AccurateMassSearchEngine
- parseAdductString()
: AdductInfo
- parseAnalysisSoftwareList_()
: MzIdentMLDOMHandler
- parseCommandLine()
: Param
- parseCommandLine_()
: TOPPBase
- parseCvParam_()
: MzIdentMLDOMHandler
- parseDBSequenceElements_()
: MzIdentMLDOMHandler
- ParseError()
: ParseError
- parseFooter_()
: IndexedMzMLFile
- parseFormula_()
: EmpiricalFormula
- parseHeader_()
: MSPFile
- parseHMMModel_()
: PILISModel
- parseInputElements_()
: MzIdentMLDOMHandler
- parseIsotopeDistribution_()
: ElementDB
- 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
- parseSpectrumIdentificationListElements_()
: MzIdentMLDOMHandler
- parseSpectrumIdentificationProtocolElements_()
: MzIdentMLDOMHandler
- parseString_()
: AASequence
- parseStructMappingFile_()
: AccurateMassSearchEngine
- parseTree_()
: SuffixArraySeqan
, SuffixArrayTrypticCompressed
- parseUserParam_()
: MzIdentMLDOMHandler
- parsing_success_
: IndexedMzMLFile
- partial_sequence_
: SequestInfile
- PARTICLEBEAM
: IonSource
- partition_()
: PILISCrossValidation
- partitionIntoRuns_()
: MzTabFile
- pass_threshold_
: IdentificationHit
- passes()
: DataFilters
- paste()
: TOPPASScene
- path()
: File
, ToolExternalDetails
- path_
: ParamXMLHandler
- path_to_file_
: SourceFile
, SourceFileVisualizer
- pattern_tolerance_
: FeatureFinderAlgorithmPicked
- patterns_
: MultiplexFiltering
- PAULIONTRAP
: MassAnalyzer
- pbuf_
: LogStreamBuf
- PD
: IonSource
, Precursor
- pe_ev_map_
: MzIdentMLDOMHandler
- peak
: FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern
, FeatureFinderAlgorithmPickedHelperStructs::Seed
- Peak()
: IMSIsotopeDistribution::Peak
- peak
: PeakIndex
- Peak1D()
: Peak1D
- Peak2D()
: Peak2D
- peak_apex_intensity
: PeakCandidate
- peak_before_mono_max_ppm_diff_
: DIAScoring
- peak_bound_
: PeakPickerCWT
- peak_bound_ms2_level_
: PeakPickerCWT
- peak_corr_bound_
: PeakPickerCWT
- peak_count_
: MzDataHandler< MapType >
, MzXMLHandler< MapType >::SpectrumData
- peak_depth
: ProbablePhosphoSites
- peak_map_
: MSSim
, SpectrumCheapDPCorr
- peak_mass_tolerance
: ProteinIdentification::SearchParameters
- peak_mass_tolerance_
: InspectInfile
, SequestInfile
- peak_penstyle_
: Spectrum1DCanvas
- PEAK_PICKING
: DataProcessing
- peak_position_
: Annotation1DPeakItem
- PEAK_SCORE
: SHFeature
- peak_tolerance_
: ProteinIdentificationVisualizer
- peak_type
: IMSIsotopeDistribution
- peak_width_
: PeakPickerIterative
, PeakPickerMRM
- PeakAlignment()
: PeakAlignment
- PeakConstIterator
: ContinuousWaveletTransform
, ContinuousWaveletTransformNumIntegration
- peakcount_
: NLargest
, WindowMower
- PeakFileOptions()
: PeakFileOptions
- PeakIndex()
: PeakIndex
- PeakIntensityPredictor()
: PeakIntensityPredictor
- PeakIterator
: Fitter1D
, OptimizePeakDeconvolution
, OptimizePick
, PeakPickerCWT::PeakArea_
, PeakPickerCWT
, PeakShape
, SignalToNoiseEstimator< Container >
, SignalToNoiseEstimatorMeanIterative< Container >
, SignalToNoiseEstimatorMedian< Container >
- PeakIterator_
: LayerStatisticsDialog
- PeakIteratorType
: AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
- PeakMarker()
: PeakMarker
- PeakMassType
: ProteinIdentification
- peakPairScore_()
: PeakAlignment
- PeakPickerCWT()
: PeakPickerCWT
- PeakPickerHiRes()
: PeakPickerHiRes
- PeakPickerIterative()
: PeakPickerIterative
- PeakPickerMaxima()
: PeakPickerMaxima
- PeakPickerMRM()
: PeakPickerMRM
- PeakPickerSH()
: PeakPickerSH
- peaks
: FeatureFinderAlgorithmPickedHelperStructs::MassTrace
, IsotopeCluster
, LayerData
, OptimizePeakDeconvolution::Data
, OptimizePick::Data
- PEAKS
: SpectrumSettings
- peaks_
: IMSIsotopeDistribution
, PILISModel
- peaks_container
: IMSIsotopeDistribution
- peaks_iterator
: IMSIsotopeDistribution
- peaks_per_peptide_
: MultiplexPeakPattern
- peaks_per_peptide_max_
: MultiplexFiltering
- peaks_per_peptide_min_
: MultiplexFiltering
- peakselectionIsAllowed_()
: MRMFragmentSelection
- PeakShape()
: PeakShape
- PeakSpectrumCompareFunctor()
: PeakSpectrumCompareFunctor
- PeakType
: BaseModel< D >
, EGHFitter1D::Data
, EmgFitter1D::Data
, FeatureFinderAlgorithmIsotopeWavelet
, FeatureFinderAlgorithmPicked
, FeatureFinderAlgorithmSH
, Fitter1D
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, MzDataHandler< MapType >
, MzMLHandler< MapType >
, MzXMLHandler< MapType >
, MRMTransitionGroup< SpectrumType, TransitionType >
, MSChromatogram< PeakT >
, MSExperiment< PeakT, ChromatogramPeakT >
, MSSpectrum< PeakT >
, SignalToNoiseEstimator< Container >
, SignalToNoiseEstimatorMeanIterative< Container >
, SignalToNoiseEstimatorMedian< Container >
, SpectrumCanvas
- PeakWidthEstimator()
: PeakWidthEstimator
- PEI
: IonSource
- pen_
: Annotations1DContainer
- pen_color_
: TOPPASVertex
- pen_size_max_
: Spectrum2DCanvas
- pen_size_min_
: Spectrum2DCanvas
- penalties
: OptimizePeakDeconvolution::Data
, OptimizePick::Data
, TwoDOptimization::Data
- penalties_
: OptimizePeakDeconvolution
, OptimizePick
, TwoDOptimization
- PenaltyFactors()
: PenaltyFactors
- PenaltyFactorsIntensity()
: PenaltyFactorsIntensity
- pep_hit_
: ConsensusXMLFile
, FeatureXMLFile
, IdXMLFile
, ProtXMLFile
- pep_id_
: ConsensusXMLFile
, FeatureXMLFile
, IdXMLFile
, MzIdentMLDOMHandler
, MzIdentMLHandler
, ProtXMLFile
- pep_ids_
: IdXMLFile
- pep_map_
: MzIdentMLDOMHandler
- PEP_PROB
: MS2Info
- pep_quant_
: PeptideAndProteinQuant
- pep_sequences_
: MzIdentMLHandler
- pep_to_prot
: FoundProteinFunctor
- PepIterator()
: PepIterator
- PEPLIST
: FileTypes
- PepNovoInfile()
: PepNovoInfile
- PepNovoOutfile()
: PepNovoOutfile
- PEPSIN_A
: ProteinIdentification
- Peptide()
: PILISCrossValidation::Peptide
, TargetedExperiment
, Peptide
, LightTargetedExperiment
- peptide
: RNPxlReportRow
- peptide_
: AASequence
- peptide_abundance_assay
: MzTabPeptideSectionRow
- peptide_abundance_std_error_study_variable
: MzTabPeptideSectionRow
- peptide_abundance_stdev_study_variable
: MzTabPeptideSectionRow
- peptide_abundance_study_variable
: MzTabPeptideSectionRow
- peptide_data_
: MzTab
- peptide_entries
: ProteinResolver::ResolverResult
- peptide_evidences_
: ConsensusXMLFile
, IdXMLFile
, PeptideHit
- peptide_group_label
: TransitionTSVReader::TSVTransition
, LightPeptide
- peptide_group_label_
: Peptide
- peptide_hit
: ProteinResolver::PeptideEntry
- peptide_hit_
: PepXMLFile
- peptide_hits_
: XTandemXMLFile
- peptide_identification
: ProteinResolver::PeptideEntry
, ProteinResolver::ResolverResult
- peptide_identification_index_
: MascotXMLHandler
- peptide_identifications_
: OMSSAXMLFile
- peptide_intensities_
: IsobaricNormalizer
- peptide_mass_unit_
: SequestInfile
- peptide_quantification_unit
: MzTabMetaData
- peptide_ratios_
: IsobaricNormalizer
- peptide_ref
: LightTransition
- peptide_ref_
: IncludeExcludeTarget
, ReactionMonitoringTransition
- peptide_reference_map_
: TargetedExperiment
, LightTargetedExperiment
- peptide_reference_map_dirty_
: TargetedExperiment
, LightTargetedExperiment
- peptide_search_engine_score
: MzTabMetaData
- peptide_similarity_
: MultiplexFiltering
- peptide_weight
: RNPxlReportRow
- PeptideAndProteinQuant()
: PeptideAndProteinQuant
- peptideCount()
: EnzymaticDigestion
- PeptideData()
: PeptideAndProteinQuant::PeptideData
- PeptideEvidence()
: PeptideEvidence
- PeptideHit()
: PeptideHit
- peptidehit_charge_
: PeptideHitVisualizer
- peptidehit_rank_
: PeptideHitVisualizer
- peptidehit_score_
: PeptideHitVisualizer
- peptidehit_sequence_
: PeptideHitVisualizer
- PeptideHitVisualizer()
: PeptideHitVisualizer
- PeptideIdent
: ProteinResolver::ResolverResult
- PeptideIdentification()
: PeptideIdentification
- PeptideIdentificationVisualizer
: MetaDataBrowser
, PeptideIdentificationVisualizer
- peptideMassRule_()
: IsotopeWaveletTransform< PeakType >
- peptideProbabilityThreshold_
: SuperHirnParameters
- PeptideQuant
: PeptideAndProteinQuant
- PeptideReferenceMapType
: TargetedExperiment
- PeptideRefMap_
: MRMFeatureFinderScoring
- PeptideRTMap_
: ChromatogramExtractor
- peptides
: LayerData
, ProteinResolver::ISDGroup
, ProteinResolver::MSDGroup
, ProteinResolver::ProteinEntry
, LightTargetedExperiment
, Protein
- peptides_
: BaseFeature
, PepXMLFile
, PepXMLFileMascot
, TargetedExperiment
- peptideScore()
: AScore
- PeptideSequence
: TransitionTSVReader::TSVTransition
- peptideSimilarityFilter()
: MultiplexFiltering
- PeptideTransitionMapType
: MRMDecoy
- PeptideType
: DIAScoring
, MRMFeatureFinderScoring
, OpenSwathScoring
, MRMScoring
- PeptideVectorType
: MRMAssay
, MRMDecoy
, TransitionTSVReader
- PEPXML
: FileTypes
- PepXMLFile()
: PepXMLFile
- PepXMLFileMascot()
: PepXMLFileMascot
- percentage_
: GradientVisualizer
- percentage_factor_
: SpectrumCanvas
- percentageIntensityElutionBorderVariation_
: SuperHirnParameters
- percentages_
: Gradient
- performAlignment()
: Spectrum1DCanvas
, Spectrum1DWidget
- performCrossValidation()
: SVMWrapper
- performExtraction()
: OpenSwathWorkflow
- performRTNormalization()
: OpenSwathWorkflow
- Permut
: CompNovoIdentification
, CompNovoIdentificationBase::Permut
, CompNovoIdentificationCID
- permut_
: CompNovoIdentificationBase::Permut
- permute_()
: CompNovoIdentificationBase
- permute_cache_
: CompNovoIdentificationBase
- pg_scores_
: MRMFeature
- PGScoresType
: MRMFeature
- ph_
: Digestion
- PHD
: Precursor
- PHOTODIODEARRAYDETECTOR
: IonDetector
- PHOTOMULTIPLIER
: IonDetector
- PI
: IonSource
, SHFeature
- PIC
: MSNumpressCoder
- pick()
: PeakPickerCWT
, PeakPickerHiRes
, PeakPickerIterative
, PeakPickerMaxima
, PeakPickerSH
- pickAndCalibrate()
: TOFCalibration
- pickChromatogram()
: PeakPickerMRM
- pickChromatogram_()
: PeakPickerMRM
- pickChromatogramCrawdad_()
: PeakPickerMRM
- picked_peaks
: TwoDOptimization::Data
- pickExperiment()
: MRMFeatureFinderScoring
, PeakPickerCWT
, PeakPickerHiRes
, PeakPickerIterative
, PeakPickerSH
- pickRecenterPeaks_()
: PeakPickerIterative
- pickTransitionGroup()
: MRMTransitionGroupPicker
- pidv_caller_
: PeptideIdentificationVisualizer
, ProteinIdentificationVisualizer
- PILISCrossValidation()
: PILISCrossValidation
- PILISIdentification()
: PILISIdentification
- PILISModel()
: PILISModel
- PILISModelGenerator()
: PILISModelGenerator
- PILISNeutralLossModel()
: PILISNeutralLossModel
- PILISNeutralLossModelGenerator
: PILISNeutralLossModel
- PILISScoring()
: PILISScoring
- pipelineDroppedOnWidget()
: TOPPASWidget
- pipelineErrorSlot()
: TOPPASScene
- pipelineExecutionFailed()
: TOPPASScene
- pka_
: Residue
- pkb_
: Residue
- pkc_
: Residue
- PlainMSDataWritingConsumer()
: PlainMSDataWritingConsumer
- plotCombinedSpectra()
: ClusteredMS2ConsensusSpectrum
- plotTargetDecoyEstimation()
: PosteriorErrorProbabilityModel
- pMZ_LIST
: ProcessData
- PNG
: FileTypes
- Point
: ClusteringGrid
, GridBasedCluster
, GridBasedClustering< Metric >
, MultiplexClustering
- point_indices_
: GridBasedCluster
- PointArrayType
: ConvexHull2D
- PointArrayTypeConstIterator
: ConvexHull2D
- POINTCOLLECTOR
: IonDetector
- pointer
: AASequence::ConstIterator
, AASequence::Iterator
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, ConstRefVector< ContainerT >
, DPosition< D, TCoordinateType >
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, IntensityIteratorWrapper< IteratorT >
, Matrix< Value >
- Pointer
: Matrix< Value >
- pointer
: SparseVector< Value >
- pointerComparator()
: PointerComparator< Cmp >
- PointerComparator()
: PointerComparator< Cmp >
- PointerType
: Map< Key, T >
- PointType
: Annotation1DCaret
, Annotation1DItem
, Annotations1DContainer
, ConvexHull2D
, SpectrumCanvas
- polar()
: AAIndex
- Polarity
: IonSource
- polarity_
: HasScanPolarity< SpectrumType >
, InstrumentSettings
, IonSource
, IonSourceVisualizer
- POLNULL
: IonSource
- pool_file_
: DocumentIDTagger
- pop_back()
: ConstRefVector< ContainerT >
- populateChromatogramsWithData()
: MzMLHandler< MapType >
- populateChromatogramsWithData_()
: MzMLHandler< MapType >
- populateMetaData_()
: SwathFile
- populatePeptideRTMap_()
: ChromatogramExtractor
- populateSpectraWithData()
: MzMLHandler< MapType >
- populateSpectraWithData_()
: MzMLHandler< MapType >
, MzXMLHandler< MapType >
- pos
: PenaltyFactors
, PeakPickerMaxima::PeakCandidate
- pos_
: ConsensusXMLFile
, ROCCurve
- pos_adducts_
: AccurateMassSearchEngine
- pos_adducts_fname_
: AccurateMassSearchEngine
- pos_charges_
: Compomer
- pos_col_
: MultiGradient
- pos_param_pairs_
: MzTabModification
- pos_range_
: RangeManager< D >
- PoseClusteringAffineSuperimposer()
: PoseClusteringAffineSuperimposer
- PoseClusteringShiftSuperimposer()
: PoseClusteringShiftSuperimposer
- position
: CompNovoIonScoringBase::IonScore
, DeNovoIonScoring::IonScore
, EnzymaticDigestion::BindingSite
, MultiGradient
, MzTabModificationMetaData
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, PeptideProteinMatchInformation
- position_
: AASequence::ConstIterator
, AASequence::Iterator
, Annotation1DCaret
, Annotation1DPeakItem
, Annotation1DTextItem
, ChromatogramPeak
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, AveragePosition< D >
, Peak1D
, Peak2D
, SparseVector< Value >::SparseVectorConstIterator
, SparseVector< Value >::SparseVectorConstReverseIterator
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
- position_weighted_sum_
: AveragePosition< D >
- PositionRangeType
: RangeManager< D >
- positions
: OptimizePeakDeconvolution::Data
, OptimizePick::Data
, TwoDOptimization::Data
- positionsAndBlacklistFilter()
: MultiplexFiltering
- positionScore_()
: FeatureFinderAlgorithmPicked
- PositionsType
: Annotation1DCaret
- PositionType
: BaseModel< D >
, ChromatogramPeak
, DBoundingBox< D >
, DRange< D >
, DIntervalBase< D >
, InterpolationModel
, AveragePosition< D >
, Peak1D
, Peak2D
, ProductModel< 2 >
, RangeManager< D >
- POSITIVE
: IonSource
- possible_charge_states_
: Precursor
- post
: MzIdentMLDOMHandler::PeptideEvidence
, MzTabPSMSectionRow
- post_moves
: MappingParam
- POSTACCELERATIONDETECTOR
: IonDetector
- 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
- postProcessHits_()
: SimpleSearchEngine
- postRawMSHook()
: BaseLabeler
, ICPLLabeler
, ITRAQLabeler
, LabelFreeLabeler
, O18Labeler
, SILACLabeler
- postRawTandemMSHook()
: BaseLabeler
, ICPLLabeler
, ITRAQLabeler
, LabelFreeLabeler
, O18Labeler
, SILACLabeler
- postRTHook()
: BaseLabeler
, ICPLLabeler
, ITRAQLabeler
, LabelFreeLabeler
, O18Labeler
, SILACLabeler
- POSTTRANSLATIONAL
: ResidueModification
- potential_adducts_
: FeatureDeconvolution
- potential_target_
: TOPPASScene
- ppm
: OpenSwathWorkflow::ChromExtractParams
- PPM
: XTandemInfile
- ppm_tolerance_
: GaussFilterAlgorithm
- ppmToleranceForMZClustering_
: SuperHirnParameters
- PQD
: Precursor
- pre
: MzIdentMLDOMHandler::PeptideEvidence
, MzTabPSMSectionRow
- pre_
: MultiGradient
- PRE_32
: MzMLHandlerHelper::BinaryData
- PRE_64
: MzMLHandlerHelper::BinaryData
- pre_min_
: MultiGradient
- pre_mod_name_
: Residue
- pre_moves
: MappingParam
- PRE_NONE
: MzMLHandlerHelper::BinaryData
- pre_scorer_
: PILISIdentification
- pre_size_
: MultiGradient
- pre_states_
: HMMState
- pre_steps_
: MultiGradient
- precalculatedColorAt()
: MultiGradient
- precalculatedColorByIndex()
: MultiGradient
- precalculatedColorIndex()
: MultiGradient
- precalculatedColorIndex_()
: Spectrum2DCanvas
- precalculatedSize()
: MultiGradient
- preCheck()
: BaseLabeler
, ICPLLabeler
, ITRAQLabeler
, LabelFreeLabeler
, O18Labeler
, SILACLabeler
- precision
: MzMLHandlerHelper::BinaryData
- precision_
: RealMassDecomposer
, Weights
, MzXMLHandler< MapType >::SpectrumData
- precisions_
: MzDataHandler< MapType >
- PrecisionWrapper()
: PrecisionWrapper< FloatingPointType >
- preComputeExpensiveFunctions_()
: IsotopeWavelet
- Precondition()
: Precondition
- PRECURSOR
: InstrumentSettings
- Precursor()
: Precursor
- precursor
: TransitionTSVReader::TSVTransition
- precursor_
: ChromatogramSettings
- precursor_adduct_
: SpectralMatch
- precursor_charge
: TransitionTSVReader::TSVTransition
- precursor_charge_
: SvmTheoreticalSpectrumGenerator
- precursor_chromatogram_map_
: MRMTransitionGroup< SpectrumType, TransitionType >
- precursor_chromatograms_
: MRMTransitionGroup< SpectrumType, TransitionType >
- precursor_cv_terms_
: IncludeExcludeTarget
, ReactionMonitoringTransition
- precursor_feature_map_
: MRMFeature
- precursor_features_
: MRMFeature
, MRMFeatureOpenMS
- precursor_isolation_target
: ChromatogramMeta
- precursor_lower_mz_
: XTandemInfile
- precursor_mass_error_unit_
: XTandemInfile
- precursor_mass_tolerance_
: BinnedSharedPeakCount
, BinnedSpectralContrastAngle
, BinnedSumAgreeingIntensities
, CompNovoIdentificationCID
, InspectInfile
, MascotInfile
, SequestInfile
- precursor_mass_tolerance_minus_
: XTandemInfile
- precursor_mass_tolerance_plus_
: XTandemInfile
- precursor_mass_type_
: XTandemInfile
- precursor_model_cd_
: PILISModel
- precursor_model_cr_
: PILISModel
- precursor_mz
: LightTransition
- precursor_mz_
: IncludeExcludeTarget
, ReactionMonitoringTransition
- precursor_mz_error_
: MetaboliteSpectralMatching
- PRECURSOR_RECALCULATION
: DataProcessing
- precursor_tolerance
: MzIdentMLDOMHandler::SpectrumIdentificationProtocol
, ProteinIdentification::SearchParameters
- precursor_tolerance_
: ProteinIdentificationVisualizer
- precursorCHRG
: MS2Fragment
- PrecursorIonSelection()
: PrecursorIonSelection
- PrecursorIonSelectionPreprocessing()
: PrecursorIonSelectionPreprocessing
- precursorMass
: MSPeak
- precursorMZ
: MS2ConsensusSpectrum
, MS2Fragment
, MSPeak
- precursors_
: SpectrumSettings
- precursorScan
: IsobaricChannelExtractor::PuritySate_
- PrecursorVisualizer()
: PrecursorVisualizer
- predict()
: PeakIntensityPredictor
, SVMWrapper
- predictContaminantsRT()
: RTSimulation
- predictDetectabilities()
: DetectabilitySimulation
- Prediction
: ReactionMonitoringTransition
, TargetedExperiment
, Prediction
- prediction_
: IncludeExcludeTarget
, ReactionMonitoringTransition
- predictRT()
: RTSimulation
- preferencesChange()
: SpectrumCanvas
- preferencesDialog()
: TOPPASBase
, TOPPViewBase
- prefix
: FuzzyStringComparator::PrefixInfo_
, LogStreamBuf::StreamStruct
, String
, StringUtils
- prefix_whitespaces
: FuzzyStringComparator::PrefixInfo_
- PrefixInfo_()
: FuzzyStringComparator::PrefixInfo_
- prepare_coordinates()
: ChromatogramExtractor
, OpenSwathWorkflow
- prepare_coordinates_wrap()
: OpenSwathWorkflow
- prepareAlign_()
: MapAlignmentAlgorithmSpectrumAlignment
- prepareFit_()
: EmgScoring
- prepareLine()
: OpenSwathTSVWriter
- prepareMasterContainer_()
: MRMTransitionGroupPicker
- prepareProteinPeptideMaps_()
: MRMFeatureFinderScoring
- prepareResize()
: TOPPASEdge
- prepareSpectra_()
: ChromatogramExtractor
- preprocess()
: SpectraSTSimilarityScore
- preprocess_()
: ConsensusIDAlgorithmIdentity
, ConsensusIDAlgorithmRanks
- preprocessDataPoints_()
: TransformationModelInterpolated
- preprocessing_tech
: LPWrapper::SolverParam
- preprocessSpectra_()
: SimpleSearchEngine
- pressure_
: HPLC
- PRETRANSLATIONAL
: ResidueModification
- PREV_AA
: MS2Info
- primary
: ProteinResolver::ProteinEntry
- primary_id_
: SpectralMatch
- primary_indistinguishable
: ProteinResolver::ProteinEntry
- primary_scan_regex
: MascotXMLHandler
- primaryProteins_()
: ProteinResolver
- print()
: SparseVector< Value >
- print_duplicate_references_
: SequestInfile
- print_profile()
: LCElutionPeak
- printEdgesOfConnectedFeatures_()
: FeatureDeconvolution
- printStatistic()
: SuffixArray
, SuffixArraySeqan
, SuffixArrayTrypticCompressed
- printToVoid_()
: SVMWrapper
- printUsage_()
: TOPPBase
- privvec
: ConsensusMap
, FeatureFinderAlgorithmPickedHelperStructs::MassTraces
, FeatureMap
- pro_id_
: MzIdentMLDOMHandler
, MzIdentMLHandler
- probabilities_
: PSProteinInference
- probability
: ProteinIdentification::ProteinGroup
- PROBABILITY
: SVMWrapper
- probability_container
: BasicStatistics< RealT >
- proc
: TOPPASScene::TOPPProcess
- process
: TOPPViewBase
- process_MS1_level_data_structure()
: FTPeakDetectController
- process_MS2_level_data_structure()
: FTPeakDetectController
- processChromatogram_()
: MSDataWritingConsumer
, NoopMSDataWritingConsumer
, PlainMSDataWritingConsumer
- ProcessData()
: ProcessData
- processFinished()
: TOPPASScene
- processing_
: MzMLHandler< MapType >
- processing_actions_
: DataProcessing
- ProcessingAction
: DataProcessing
- processIntensities()
: BackgroundIntensityBin
- processIntensityMaps()
: BackgroundControl
- processMSPeaks()
: ProcessData
- processMZFeatureVector()
: MS1FeatureMerger
- processSpectrum_()
: MSDataWritingConsumer
, NoopMSDataWritingConsumer
, PlainMSDataWritingConsumer
- prod_
: IsotopeWaveletTransform< PeakType >
- Product()
: Product
, ReactionMonitoringTransition
- product
: TransitionTSVReader::TSVTransition
- product_
: ChromatogramSettings
, ReactionMonitoringTransition
- product_cv_terms_
: IncludeExcludeTarget
- product_isolation_target
: ChromatogramMeta
- product_mz
: LightTransition
- product_mz_
: IncludeExcludeTarget
, ProductVisualizer
- product_window_low_
: ProductVisualizer
- product_window_up_
: ProductVisualizer
- ProductListType
: TraMLHandler
- ProductModel()
: ProductModel< 2 >
- products_
: SpectrumSettings
- ProductVisualizer()
: ProductVisualizer
- profileIntensities_
: RawData
- profileMasses_
: RawData
- PROFILESHAPE
: RawMSSignalSimulation
- progress_
: ConsensusXMLFile
, QcMLFile
, SuffixArrayTrypticCompressed
- progress_counter_
: FeatureFinderAlgorithmIsotopeWavelet
- ProgressLogger()
: ProgressLogger
- projection_box_
: Spectrum2DWidget
- projection_horz_
: Spectrum2DWidget
- projection_max_
: Spectrum2DWidget
- projection_mz_
: Spectrum2DCanvas
- projection_peaks_
: Spectrum2DWidget
- projection_rt_
: Spectrum2DCanvas
- projection_sum_
: Spectrum2DWidget
- projection_vert_
: Spectrum2DWidget
- projectionInfo()
: Spectrum2DWidget
- projections_2d_
: TOPPViewBase
- projections_auto_
: Spectrum2DWidget
- projections_timer_
: Spectrum2DWidget
- projectionsVisible()
: Spectrum2DWidget
- properties_B_
: GridBasedCluster
- property_A_
: GridBasedCluster
- PROPORTIONAL
: MassAnalyzer
- proportionsActivated()
: SaveImageDialog
- prot_acc
: PSLPFormulation::IndexTriple
- prot_dist_
: PILISModel
- prot_hit_
: ConsensusXMLFile
, FeatureXMLFile
, IdXMLFile
- prot_id_
: ConsensusXMLFile
, FeatureXMLFile
, IdXMLFile
, PepXMLFile
, ProtXMLFile
- prot_id_counter_
: PrecursorIonSelection
- prot_id_in_run_
: IdXMLFile
- prot_ids_
: IdXMLFile
- prot_masses_
: PrecursorIonSelectionPreprocessing
- prot_peptide_seq_map_
: PrecursorIonSelectionPreprocessing
- prot_quant_
: PeptideAndProteinQuant
- PROTEASE_K
: ProteinIdentification
- Protein
: TargetedExperiment
, Protein
, LightTargetedExperiment
- protein_abundance_assay
: MzTabProteinSectionRow
- protein_abundance_std_error_study_variable
: MzTabProteinSectionRow
- protein_abundance_stdev_study_variable
: MzTabProteinSectionRow
- protein_abundance_study_variable
: MzTabProteinSectionRow
- PROTEIN_C_TERM
: ResidueModification
- protein_coverage
: MzTabProteinSectionRow
- protein_data_
: MzTab
, ProteinResolver
- protein_entries
: ProteinResolver::ResolverResult
- protein_group_
: ProtXMLFile
- protein_groups_
: ProteinIdentification
- protein_hits_
: ProteinIdentification
, XTandemXMLFile
- protein_identification_
: MascotXMLHandler
, XTandemXMLFile
- protein_identifications_
: ConsensusMap
, ExperimentalSettings
, FeatureMap
- protein_index
: PeptideProteinMatchInformation
- protein_mass_filter_
: SequestInfile
- PROTEIN_N_TERM
: ResidueModification
- protein_name_length_
: InspectOutfile
- protein_open_
: XTandemXMLFile
- protein_quantification_unit
: MzTabMetaData
- protein_reference_map_
: TargetedExperiment
- protein_reference_map_dirty_
: TargetedExperiment
- protein_refs
: Peptide
, LightPeptide
- protein_score_type_
: ProteinIdentification
- protein_search_engine_score
: MzTabMetaData
- protein_significance_threshold_
: ProteinIdentification
- protein_type
: ProteinResolver::ProteinEntry
- ProteinData()
: PeptideAndProteinQuant::ProteinData
- ProteinGroup()
: ProteinIdentification::ProteinGroup
, ProtXMLFile
- ProteinHit()
: ProteinHit
- proteinhit_accession_
: ProteinHitVisualizer
- proteinhit_rank_
: ProteinHitVisualizer
- proteinhit_score_
: ProteinHitVisualizer
- proteinhit_sequence_
: ProteinHitVisualizer
- ProteinHitVisualizer()
: ProteinHitVisualizer
- proteinid_to_accession_
: ConsensusXMLFile
, FeatureXMLFile
, IdXMLFile
- ProteinIdentification()
: ProteinIdentification
- ProteinIdentificationVisualizer
: MetaDataBrowser
, ProteinIdentificationVisualizer
- ProteinInference()
: ProteinInference
- ProteinName
: TransitionTSVReader::TSVTransition
- ProteinQuant
: PeptideAndProteinQuant
- ProteinReferenceMapType
: TargetedExperiment
- ProteinResolver()
: ProteinResolver
- proteins
: ProteinResolver::ISDGroup
, ProteinResolver::MSDGroup
, ProteinResolver::PeptideEntry
, LightTargetedExperiment
, TargetedExperiment
- proteins_
: PepXMLFile
, TargetedExperiment
- ProteinType
: DIAScoring
, MRMFeatureFinderScoring
, MRMScoring
- ProteinVectorType
: MRMAssay
, MRMDecoy
, TransitionTSVReader
- ProtonDistributionModel()
: ProtonDistributionModel
- PROTXML
: FileTypes
- ProtXMLFile()
: ProtXMLFile
- pscf_
: PILISCrossValidation
- PSD
: Precursor
- pseudo_counts_
: HiddenMarkovModel
- pseudoreversePeptide()
: MRMDecoy
- psi_
: IsotopeWaveletTransform< PeakType >
- psi_mod_accession_
: ResidueModification
- PSLPFormulation()
: PSLPFormulation
- psm_data_
: MzTab
- PSM_ID
: MzTabPSMSectionRow
- psm_search_engine_score
: MzTabMetaData
- PSProteinInference()
: PSProteinInference
- PSQ
: FileTypes
- pt_prot_map_
: PrecursorIonSelectionPreprocessing
- ptm_file_
: PepNovoInfile
- ptm_informations_
: PTMXMLHandler
- PTMname_residues_mass_type_
: InspectInfile
, SequestInfile
- PTMXMLFile()
: PTMXMLFile
- PTMXMLHandler()
: PTMXMLHandler
- ptr_
: BaseVisualizer< ObjectType >
- publication
: MzTabMetaData
- Publication
: TargetedExperiment
, Publication
- publications_
: TargetedExperiment
- PULSECOUNTING
: IonDetector
- PuritySate_()
: IsobaricChannelExtractor::PuritySate_
- push2Box_()
: IsotopeWaveletTransform< PeakType >
- push2TmpBox_()
: IsotopeWaveletTransform< PeakType >
- push_back()
: ConstRefVector< ContainerT >
, IMSAlphabet
, SparseVector< Value >
- pv_db_map_
: MzIdentMLDOMHandler
- PValue_()
: LabeledPairFinder
- pw_filtering_
: ElutionPeakDetection
- PYMS
: IonSource