Here is a list of all class members with links to the classes they belong to:
- p -
- p
: GammaDistributionFitter::GammaDistributionFitResult
- P
: SVMWrapper
- p_
: TheoreticalSpectrumGenerator
, ToolDescriptionHandler
, PILISIdentification
- p_cleave
: EnzymaticDigestion::CleavageModel
- p_miss
: EnzymaticDigestion::CleavageModel
- P_PRECURSORS
: LayerData
- P_PROJECTIONS
: LayerData
- paint()
: TOPPASOutputFileListVertex
, TOPPASToolVertex
, TOPPASVertex
, AxisPainter
, AxisWidget
, Spectrum1DCanvas
, TOPPASEdge
, TOPPASInputFileListVertex
, TOPPASMergerVertex
- 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()
: Param
- param
: ToolExternalDetails
, TOPPViewBase
, LayerData
- param_
: LocalLinearMap
, SVMWrapper
, TOPPBase
, DefaultParamHandler
, FeatureXMLFile
, ParamXMLHandler
, IdXMLFile
, INIFileEditorWindow
, TOPPASToolConfigDialog
, ParamEditor
, TOPPASToolVertex
- 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
- parameterChanged()
: TOPPASVertex
- ParameterInformation()
: ParameterInformation
- parameters_
: TOPPBase
, IdXMLFile
, MzTabParameterList
, ModelDescription< D >
- ParameterTypes
: ParameterInformation
- ParamGroupList
: MSQuantifications
- ParamIterator()
: Param::ParamIterator
- ParamNode()
: Param::ParamNode
- params_
: TransformationModel
, AcqusHandler
, PepXMLFile
, 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_()
: AccurateMassSearchEngine
- parseCommandLine()
: Param
- parseCommandLine_()
: TOPPBase
- ParseError()
: ParseError
- parseFormula_()
: EmpiricalFormula
- parseHeader_()
: MSPFile
- parseHMMModel_()
: PILISModel
- parseIsotopeDistribution_()
: ElementDB
- parseMappingFile_()
: AccurateMassSearchEngine
- parseMzXMLData()
: FTPeakDetectController
- parseRange_()
: TOPPBase
- parseResidue_()
: ResidueDB
- parseString_()
: AASequence
- parseStructMappingFile_()
: AccurateMassSearchEngine
- parseTree_()
: SuffixArraySeqan
, SuffixArrayTrypticCompressed
- partial_sequence_
: SequestInfile
- PARTICLEBEAM
: IonSource
- partition_()
: PILISCrossValidation
- partitionIntoRuns_()
: MzTabFile
- pass_threshold_
: IdentificationHit
- passes()
: DataFilters
- paste()
: TOPPASScene
- path
: ToolExternalDetails
, File
- path_
: ParamXMLHandler
- path_to_file_
: SourceFile
, SourceFileVisualizer
- pattern_tolerance_
: FeatureFinderAlgorithmPicked< PeakType, FeatureType >
- PAULIONTRAP
: MassAnalyzer
- pbuf_
: LogStreamBuf
- PD
: IonSource
, Precursor
- peak
: PeakIndex
, FeatureFinderAlgorithmPickedHelperStructs::Seed
, FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern
- Peak()
: IMSIsotopeDistribution::Peak
- Peak1D()
: Peak1D
- Peak2D()
: Peak2D
- peak_bound_
: PeakPickerCWT
- peak_bound_ms2_level_
: PeakPickerCWT
- peak_corr_bound_
: PeakPickerCWT
- peak_count_
: MzDataHandler< MapType >
, MzXMLHandler< MapType >
- peak_depth
: ProbablePhosphoSites
- peak_map_
: SpectrumCheapDPCorr
, MSSim
- peak_mass_tolerance
: ProteinIdentification::SearchParameters
- peak_mass_tolerance_
: InspectInfile
, SequestInfile
- peak_penstyle_
: Spectrum1DCanvas
- PEAK_PICKING
: DataProcessing
- peak_position_
: Annotation1DPeakItem
- peak_positions_
: SILACFilter
- PEAK_SCORE
: SHFeature
- peak_tolerance_
: ProteinIdentificationVisualizer
- peak_type
: IMSIsotopeDistribution
- peak_width
: SILACFiltering
- peak_width_
: MRMTransitionGroupPicker
- PeakAlignment()
: PeakAlignment
- PeakConstIterator
: ContinuousWaveletTransform
, ContinuousWaveletTransformNumIntegration
- peakcount_
: NLargest
, WindowMower
- PeakFileOptions()
: PeakFileOptions
- PeakIndex()
: PeakIndex
- PeakIntensityPredictor()
: PeakIntensityPredictor
- PeakIterator
: SignalToNoiseEstimator< Container >
, SignalToNoiseEstimatorMeanIterative< Container >
, SignalToNoiseEstimatorMedian< Container >
, MzXMLHandler< MapType >
, Fitter1D
, OptimizePeakDeconvolution
, OptimizePick
, PeakPickerCWT
, PeakPickerCWT::PeakArea_
, PeakShape
- PeakIterator_
: LayerStatisticsDialog
- PeakIteratorType
: AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
- PeakMarker()
: PeakMarker
- PeakMassType
: ProteinIdentification
- peakPairScore_()
: PeakAlignment
- PeakPickerCWT()
: PeakPickerCWT
- PeakPickerHiRes()
: PeakPickerHiRes
- PeakPickerSH()
: PeakPickerSH
- PEAKS
: SpectrumSettings
- peaks
: IsotopeCluster
, FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >
, OptimizePeakDeconvolution::Data
, OptimizePick::Data
, LayerData
- peaks_
: PILISModel
, IMSIsotopeDistribution
- peaks_container
: IMSIsotopeDistribution
- peaks_iterator
: IMSIsotopeDistribution
- peakselectionIsAllowed_()
: MRMFragmentSelection
- PeakShape()
: PeakShape
- PeakSpectrumCompareFunctor()
: PeakSpectrumCompareFunctor
- PeakType
: SignalToNoiseEstimator< Container >
, SignalToNoiseEstimatorMeanIterative< Container >
, SignalToNoiseEstimatorMedian< Container >
, MzDataHandler< MapType >
, MzMLHandler< MapType >
, MzXMLHandler< MapType >
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, MRMTransitionGroup< SpectrumType, TransitionType >
, MSChromatogram< PeakT >
, MSExperiment< PeakT, ChromatogramPeakT >
, MSSpectrum< PeakT >
, EGHFitter1D::Data
, BaseModel< D >
, EmgFitter1D::Data
, Fitter1D
, LmaGaussFitter1D::Data
, LmaIsotopeFitter1D::Data
, SpectrumCanvas
- PEI
: IonSource
- pen_
: Annotations1DContainer
- pen_color_
: TOPPASVertex
- penalties
: OptimizePeakDeconvolution::Data
, OptimizePick::Data
, TwoDOptimization::Data
- penalties_
: TwoDOptimization
, OptimizePeakDeconvolution
, OptimizePick
- PenaltyFactors()
: PenaltyFactors
- PenaltyFactorsIntensity()
: PenaltyFactorsIntensity
- pep_hit_
: ConsensusXMLFile
, FeatureXMLFile
, IdXMLFile
, ProtXMLFile
- pep_id_
: ConsensusXMLFile
, FeatureXMLFile
, MzIdentMLHandler
, IdXMLFile
, ProtXMLFile
- pep_ids_
: IdXMLFile
- PEP_PROB
: MS2Info
- pep_quant_
: PeptideAndProteinQuant
- pep_sequences_
: MzIdentMLHandler
- pep_to_prot
: FoundProteinFunctor
- PEPIons_()
: ConsensusID
- PepIterator()
: PepIterator
- PEPLIST
: FileTypes
- PEPMatrix_()
: ConsensusID
- PepNovoInfile()
: PepNovoInfile
- PepNovoOutfile()
: PepNovoOutfile
- PEPSIN_A
: ProteinIdentification
- Peptide
: TargetedExperiment
, PILISCrossValidation::Peptide
, Peptide
- peptide
: RNPxlReportRow
- peptide_
: AASequence
- peptide_abundance_std_error_sub
: MzTabPeptideSectionRow
- peptide_abundance_stdev_sub
: MzTabPeptideSectionRow
- peptide_abundance_sub
: MzTabPeptideSectionRow
- peptide_entries
: ProteinResolver::ResolverResult
- peptide_group_label_
: Peptide
- peptide_group_labels_
: 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
: MzTabUnitIdMetaData
- peptide_ratios_
: IsobaricNormalizer
- peptide_ref
: LightTransition
- peptide_ref_
: ReactionMonitoringTransition
, IncludeExcludeTarget
- peptide_reference_map_
: TargetedExperiment
- peptide_reference_map_dirty_
: TargetedExperiment
- 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
, MRMFeatureFinderScoring
- peptides
: LightTargetedExperiment
, Protein
, ProteinResolver::ProteinEntry
, ProteinResolver::MSDGroup
, ProteinResolver::ISDGroup
, LayerData
- peptides_
: TargetedExperiment
, PepXMLFile
, PepXMLFileMascot
, BaseFeature
- peptideScore_()
: AScore
- PeptideSequence
: TransitionTSVReader::TSVTransition
- PeptideTransitionMapType
: MRMDecoy
- PeptideType
: DIAScoring
, MRMFeatureFinderScoring
, MRMScoring
- PeptideVectorType
: MRMDecoy
, TransitionTSVReader
- PEPXML
: FileTypes
- PepXMLFile()
: PepXMLFile
- PepXMLFileMascot()
: PepXMLFileMascot
- percentage_
: GradientVisualizer
- percentage_factor_
: SpectrumCanvas
- percentageIntensityElutionBorderVariation_
: SuperHirnParameters
- percentages_
: Gradient
- performAlignment()
: Spectrum1DCanvas
, Spectrum1DWidget
- performCrossValidation()
: SVMWrapper
- Permut
: CompNovoIdentification
, CompNovoIdentificationCID
, CompNovoIdentificationBase::Permut
- permut_
: CompNovoIdentificationBase::Permut
- permute_()
: CompNovoIdentificationBase
- permute_cache_
: CompNovoIdentificationBase
- persistence_id_
: PersistentObject
- PersistentObject()
: PersistentObject
- pg_scores_
: MRMFeature
- PGScoresType
: MRMFeature
- ph_
: Digestion
- PHD
: Precursor
- PHOTODIODEARRAYDETECTOR
: IonDetector
- PHOTOMULTIPLIER
: IonDetector
- PI
: IonSource
, SHFeature
- pick()
: PeakPickerCWT
, PeakPickerHiRes
, PeakPickerSH
- pickAndCalibrate()
: TOFCalibration
- pickChromatogram()
: MRMTransitionGroupPicker
- picked_chroms_
: MRMTransitionGroupPicker
- picked_exp_
: SILACFiltering
- picked_exp_seeds_
: SILACFiltering
- picked_peaks
: TwoDOptimization::Data
- pickExperiment()
: MRMFeatureFinderScoring
, PeakPickerCWT
, PeakPickerHiRes
, PeakPickerSH
- pickSeeds_()
: SILACFiltering
- 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
- plotCombinedSpectra()
: ClusteredMS2ConsensusSpectrum
- plotTargetDecoyEstimation()
: PosteriorErrorProbabilityModel
- pMZ_LIST
: ProcessData
- PNG
: FileTypes
- PointArrayType
: ConvexHull2D
- PointArrayTypeConstIterator
: ConvexHull2D
- POINTCOLLECTOR
: IonDetector
- PointCoordinate
: HierarchicalClustering< PointRef >
- Pointer
: Matrix< Value >
- pointer
: AASequence::ConstIterator
, AASequence::Iterator
, AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
, ConstRefVector< ContainerT >
, DPosition< D, TCoordinateType >
, Matrix< Value >
, SparseVector< Value >
, IntensityIteratorWrapper< IteratorT >
- pointerComparator()
: PointerComparator< Cmp >
- PointerComparator()
: PointerComparator< Cmp >
- PointerType
: Map< Key, T >
- points
: HierarchicalClustering< PointRef >::TreeNode
, SILACPattern
- PointType
: ConvexHull2D
, Annotation1DItem
, Annotations1DContainer
, SpectrumCanvas
- polar()
: AAIndex
- Polarity
: IonSource
- polarity_
: InstrumentSettings
, IonSource
, IonSourceVisualizer
- POLNULL
: IonSource
- pool_file_
: DocumentIDTagger
- pop_back()
: ConstRefVector< ContainerT >
- pos
: PenaltyFactors
- 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()
: SparseVector< Value >::SparseVectorConstReverseIterator
, EnzymaticDigestion::BindingSite
, CompNovoIonScoringBase::IonScore
, DeNovoIonScoring::IonScore
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::SparseVectorConstIterator
, MultiGradient
- position_
: AveragePosition< D >
, SparseVector< Value >::SparseVectorConstReverseIterator
, AASequence::ConstIterator
, AASequence::Iterator
, ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
, SparseVector< Value >::SparseVectorIterator
, SparseVector< Value >::SparseVectorReverseIterator
, SparseVector< Value >::SparseVectorConstIterator
, ChromatogramPeak
, Peak1D
, Peak2D
, Annotation1DPeakItem
, Annotation1DTextItem
- position_weighted_sum_
: AveragePosition< D >
- PositionRangeType
: RangeManager< D >
- positions
: OptimizePeakDeconvolution::Data
, OptimizePick::Data
, TwoDOptimization::Data
- positionScore_()
: FeatureFinderAlgorithmPicked< PeakType, FeatureType >
- PositionType
: AveragePosition< D >
, ChromatogramPeak
, DBoundingBox< D >
, DIntervalBase< D >
, DRange< D >
, Peak1D
, Peak2D
, RangeManager< D >
, BaseModel< D >
, InterpolationModel
, ProductModel< 2 >
- POSITIVE
: IonSource
- possible_charge_states_
: Precursor
- post_
: PeptideEvidence
- post_moves
: MappingParam
- POSTACCELERATIONDETECTOR
: IonDetector
- Postcondition()
: Postcondition
- postDetectabilityHook()
: BaseLabeler
, ICPLLabeler
, LabelFreeLabeler
, O18Labeler
, SILACLabeler
, ITRAQLabeler
- postDigestHook()
: ICPLLabeler
, ITRAQLabeler
, LabelFreeLabeler
, SILACLabeler
, O18Labeler
, BaseLabeler
- PosteriorErrorProbabilityModel()
: PosteriorErrorProbabilityModel
- postIonizationHook()
: BaseLabeler
, ICPLLabeler
, ITRAQLabeler
, LabelFreeLabeler
, SILACLabeler
, O18Labeler
- postRawMSHook()
: BaseLabeler
, ICPLLabeler
, LabelFreeLabeler
, O18Labeler
, SILACLabeler
, ITRAQLabeler
- postRawTandemMSHook()
: ICPLLabeler
, ITRAQLabeler
, LabelFreeLabeler
, O18Labeler
, SILACLabeler
, BaseLabeler
- postRTHook()
: BaseLabeler
, ICPLLabeler
, LabelFreeLabeler
, O18Labeler
, SILACLabeler
, ITRAQLabeler
- POSTTRANSLATIONAL
: ResidueModification
- potential_adducts_
: FeatureDeconvolution
- potential_target_
: TOPPASScene
- PPM
: XTandemInfile
- ppm_tolerance_
: GaussFilterAlgorithm
- ppmToleranceForMZClustering_
: SuperHirnParameters
- PQD
: Precursor
- pre_
: PeptideEvidence
, MultiGradient
- PRE_32
: MzMLHandler< MapType >::BinaryData
- PRE_64
: MzMLHandler< MapType >::BinaryData
- pre_min_
: MultiGradient
- pre_mod_name_
: Residue
- pre_moves
: MappingParam
- PRE_NONE
: MzMLHandler< MapType >::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
, SILACLabeler
, O18Labeler
- precision
: MzMLHandler< MapType >::BinaryData
- precision_
: RealMassDecomposer
, MzXMLHandler< MapType >
, Weights
- precisions_
: MzDataHandler< MapType >
- PrecisionWrapper()
: PrecisionWrapper< FloatingPointType >
- preComputeExpensiveFunctions_()
: IsotopeWavelet
- Precondition()
: Precondition
- PRECURSOR
: InstrumentSettings
- Precursor()
: Precursor
- precursor
: TransitionTSVReader::TSVTransition
- Precursor()
: Precursor
- precursor_
: ChromatogramSettings
- precursor_charge
: TransitionTSVReader::TSVTransition
- precursor_charge_
: SvmTheoreticalSpectrumGenerator
- precursor_cv_terms_
: ReactionMonitoringTransition
, IncludeExcludeTarget
- precursor_isolation_target
: ChromatogramMeta
- precursor_lower_mz_
: XTandemInfile
- precursor_mass_error_unit_
: XTandemInfile
- precursor_mass_tolerance_
: SequestInfile
, InspectInfile
, MascotInfile
, CompNovoIdentificationCID
- 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_
: ReactionMonitoringTransition
, IncludeExcludeTarget
- PRECURSOR_RECALCULATION
: DataProcessing
- precursor_tolerance
: ProteinIdentification::SearchParameters
- precursor_tolerance_
: ProteinIdentificationVisualizer
- precursorCHRG
: MS2Fragment
- PrecursorIonSelection()
: PrecursorIonSelection
- PrecursorIonSelectionPreprocessing()
: PrecursorIonSelectionPreprocessing
- precursorMass
: MSPeak
- precursorMZ
: MS2ConsensusSpectrum
, MS2Fragment
, MSPeak
- precursors_
: SpectrumSettings
- PrecursorVisualizer()
: PrecursorVisualizer
- predict()
: PeakIntensityPredictor
, SVMWrapper
, PeakIntensityPredictor
, SVMWrapper
- predictContaminantsRT()
: RTSimulation
- predictDetectabilities()
: DetectabilitySimulation
- Prediction
: ReactionMonitoringTransition
, Prediction
, TargetedExperiment
- prediction_
: IncludeExcludeTarget
, ReactionMonitoringTransition
- predictRT()
: RTSimulation
- preferencesChange()
: SpectrumCanvas
- preferencesDialog()
: TOPPViewBase
, TOPPASBase
- prefix
: LogStreamBuf::StreamStruct
, String
, FuzzyStringComparator::PrefixInfo_
, String
- prefix_whitespaces
: FuzzyStringComparator::PrefixInfo_
- PrefixInfo_()
: FuzzyStringComparator::PrefixInfo_
- prepareAlign_()
: MapAlignmentAlgorithmSpectrumAlignment
- prepareFit_()
: EmgScoring
- prepareHRDataCuda()
: FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >
- prepareMasterContainer_()
: MRMTransitionGroupPicker
- prepareResize()
: TOPPASEdge
- prepareSpectra_()
: ChromatogramExtractor
- preprocess()
: SpectraSTSimilarityScore
- preprocessing_tech
: LPWrapper::SolverParam
- pressure_
: HPLC
- PRETRANSLATIONAL
: ResidueModification
- PREV_AA
: MS2Info
- primary
: ProteinResolver::ProteinEntry
- primary_indistinguishable
: ProteinResolver::ProteinEntry
- primary_scan_regex
: MascotXMLHandler
- primaryProteins_()
: ProteinResolver
- print()
: SparseVector< Value >
- print_duplicate_references_
: SequestInfile
- print_profile()
: LCElutionPeak
- printEdgesOfConnectedFeatures_()
: FeatureDeconvolution
- printState_()
: GaussFitter
, EGHFitter1D
, EmgFitter1D
, LevMarqFitter1D
, GaussTraceFitter< PeakType >
, TraceFitter< PeakType >
, LmaGaussFitter1D
, LmaIsotopeFitter1D
, EGHTraceFitter< PeakType >
, GumbelDistributionFitter
, GammaDistributionFitter
- printStatistic()
: SuffixArrayTrypticCompressed
, SuffixArray
, SuffixArraySeqan
- printToVoid_()
: SVMWrapper
- printUsage_()
: TOPPBase
- priorities_
: SimpleExtender< PeakType, FeatureType >
- priority
: SimpleExtender< PeakType, FeatureType >::IndexWithPriority
- priority_threshold_
: SimpleExtender< PeakType, FeatureType >
- privvec
: ConsensusMap
, FeatureMap< FeatureT >
- pro_id_
: MzIdentMLHandler
- probabilities_
: PSProteinInference
- probability
: ProteinIdentification::ProteinGroup
- PROBABILITY
: SVMWrapper
- probability_container
: BasicStatistics< RealT >
- ProbabilityType
: SimpleExtender< PeakType, FeatureType >
- proc
: TOPPASScene::TOPPProcess
- process
: TOPPViewBase
- process_MS1_level_data_structure()
: FTPeakDetectController
- process_MS2_level_data_structure()
: FTPeakDetectController
- ProcessData()
: ProcessData
- processFinished()
: TOPPASScene
- processing_
: MzMLHandler< MapType >
- processing_actions_
: DataProcessing
- ProcessingAction
: DataProcessing
- processIntensities()
: BackgroundIntensityBin
- processIntensityMaps()
: BackgroundControl
- processMSPeaks()
: ProcessData
- processMZFeatureVector()
: MS1FeatureMerger
- prod_
: IsotopeWaveletTransform< PeakType >
- Product()
: Product
, ReactionMonitoringTransition
, Product
- product
: TransitionTSVReader::TSVTransition
- product_
: ReactionMonitoringTransition
, ChromatogramSettings
- product_cv_terms_
: IncludeExcludeTarget
- product_isolation_target
: ChromatogramMeta
- product_mz
: LightTransition
- product_mz_
: ProductVisualizer
, IncludeExcludeTarget
- product_window_low_
: ProductVisualizer
- product_window_up_
: ProductVisualizer
- ProductListType
: TraMLHandler
- ProductModel()
: ProductModel< 2 >
- products_
: SpectrumSettings
- ProductVisualizer()
: ProductVisualizer
- profileIntensities_
: RawData
- profileMasses_
: RawData
- PROFILESHAPE
: RawMSSignalSimulation
- progress_
: QcMLFile
, ConsensusXMLFile
, SuffixArrayTrypticCompressed
- progress_counter_
: FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >
- 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
- PROPORTIONAL
: MassAnalyzer
- proportionsActivated()
: SaveImageDialog
- prot_acc
: PSLPFormulation::IndexTriple
- prot_dist_
: PILISModel
- prot_hit_
: IdXMLFile
, ConsensusXMLFile
, FeatureXMLFile
- prot_id_
: PepXMLFile
, FeatureXMLFile
, ConsensusXMLFile
, IdXMLFile
, 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()
: Protein
, TargetedExperiment
- protein_abundance_std_error_sub
: MzTabProteinSectionRow
- protein_abundance_stdev_sub
: MzTabProteinSectionRow
- protein_abundance_sub
: MzTabProteinSectionRow
- protein_coverage
: MzTabProteinSectionRow
- protein_data_
: ProteinResolver
- protein_entries
: ProteinResolver::ResolverResult
- protein_group_
: ProtXMLFile
- protein_groups_
: ProteinIdentification
- protein_hits_
: XTandemXMLFile
, ProteinIdentification
- protein_identification_
: XTandemXMLFile
, MascotXMLHandler
- protein_identifications_
: ConsensusMap
, ExperimentalSettings
, FeatureMap< FeatureT >
- protein_mass_filter_
: SequestInfile
- protein_name_length_
: InspectOutfile
- protein_open_
: XTandemXMLFile
- protein_quantification_unit
: MzTabUnitIdMetaData
- protein_ref
: LightPeptide
- protein_reference_map_
: TargetedExperiment
- protein_reference_map_dirty_
: TargetedExperiment
- protein_refs
: Peptide
- protein_score_type_
: ProteinIdentification
- 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
, IdXMLFile
, FeatureXMLFile
- ProteinIdentification()
: ProteinIdentification
- ProteinIdentificationVisualizer
: MetaDataBrowser
, ProteinIdentificationVisualizer
- ProteinInference()
: ProteinInference
- ProteinName
: TransitionTSVReader::TSVTransition
- ProteinQuant
: PeptideAndProteinQuant
- ProteinReferenceMapType
: TargetedExperiment
- ProteinRefMap_
: MRMFeatureFinderScoring
- ProteinResolver()
: ProteinResolver
- proteins
: TargetedExperiment
, ProteinResolver::ISDGroup
, LightTargetedExperiment
, ProteinResolver::MSDGroup
, ProteinResolver::PeptideEntry
- proteins_
: TargetedExperiment
, PepXMLFile
- ProteinType
: DIAScoring
, MRMFeatureFinderScoring
, MRMScoring
- ProteinVectorType
: TransitionTSVReader
, MRMDecoy
- ProtonDistributionModel()
: ProtonDistributionModel
- PROTXML
: FileTypes
- ProtXMLFile()
: ProtXMLFile
- pscf_
: PILISCrossValidation
- PSD
: Precursor
- pseudo_counts_
: HiddenMarkovModel
- pseudoreversePeptide()
: MRMDecoy
- psi_
: IsotopeWaveletTransform< PeakType >
- psi_mod_accession_
: ResidueModification
- PSLPFormulation()
: PSLPFormulation
- 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
: TargetedExperiment
- publication
: MzTabUnitIdMetaData
- Publication()
: Publication
- publications_
: TargetedExperiment
- PULSECOUNTING
: IonDetector
- push2Box_()
: IsotopeWaveletTransform< PeakType >
- push2TmpBox_()
: IsotopeWaveletTransform< PeakType >
- push_back()
: IMSAlphabet
, ConstRefVector< ContainerT >
, SparseVector< Value >
- PValue_()
: LabeledPairFinder
- pw_filtering_
: ElutionPeakDetection
- PYMS
: IonSource