| OpenMS 2.5.0

Here is a list of all class members with links to the classes they belong to:

### - p -

- p : GammaDistributionFitter::GammaDistributionFitResult
- P : SVMWrapper
- p_ : MessagePasserFactory< Label > , ToolDescriptionHandler
- p_cleave : EnzymaticDigestionLogModel::CleavageModel_
- p_miss : EnzymaticDigestionLogModel::CleavageModel_
- P_PRECURSORS : LayerData
- P_PROJECTIONS : LayerData
- p_pv_map_ : MzIdentMLDOMHandler
- packages_ : SplineInterpolatedPeaks::Navigator , SplineInterpolatedPeaks
- paint() : AxisPainter , AxisWidget , Spectrum1DCanvas , TOPPASEdge , TOPPASInputFileListVertex , TOPPASMergerVertex , TOPPASOutputFileListVertex , TOPPASSplitterVertex , TOPPASToolVertex , TOPPASVertex
- paintAllIntensities_() : Spectrum2DCanvas
- paintConsensusElement_() : Spectrum2DCanvas
- paintConsensusElements_() : Spectrum2DCanvas
- paintConvexHulls_() : Spectrum2DCanvas
- paintDots_() : Spectrum2DCanvas
- painter_ : Spectrum3DOpenGLCanvas
- 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 , MetaboliteFeatureDeconvolution
- param : ToolExternalDetails , LayerData
- Param() : Param
- param_ : DefaultParamHandler , FeatureXMLFile , IdXMLFile , INIFileEditorWindow , ParamXMLHandler , LocalLinearMap , MapAlignmentAlgorithmKD , ParamEditor , SVMWrapper , TOPPASToolConfigDialog , TOPPASToolVertex , TOPPBase
- param_binsize_ : XFDRAlgorithm
- param_cmdline_ : TOPPBase
- param_common_ : TOPPBase
- param_common_tool_ : TOPPBase
- param_decoy_string_ : XFDRAlgorithm
- param_groups_ : MzMLValidator , MzQuantMLValidator
- param_inifile_ : TOPPBase
- param_instance_ : TOPPBase
- param_maxborder_ : XFDRAlgorithm
- param_minborder_ : XFDRAlgorithm
- param_mindeltas_ : XFDRAlgorithm
- param_minionsmatched_ : XFDRAlgorithm
- param_minscore_ : XFDRAlgorithm
- PARAM_NAME : LogConfigHandler
- param_name : TOPPASToolVertex::IOInfo
- param_no_qvalues_ : XFDRAlgorithm
- param_uniquexl_ : XFDRAlgorithm
- 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 : MRMFeaturePicker::ComponentGroupParams , MRMFeaturePicker::ComponentParams
- params_ : AcqusHandler , PepXMLFile , TransformationModel , TransformationXMLFile
- params_intensity_ : FeatureDistance
- params_mz_ : FeatureDistance
- params_rt_ : FeatureDistance
- paramToParameterInformation_() : TOPPBase
- ParamTree() : ParamTree
- PARAMXML : FileTypes
- ParamXMLFile() : ParamXMLFile
- ParamXMLHandler() : ParamXMLHandler
- PARENT : CompNovoIonScoringBase
- parent_ : TOPPASInputFileDialog
- parent_matches : IdentifiedSequence< SeqType >
- parent_molecule_groupings_ : IdentificationData
- parent_molecule_lookup_ : IdentificationData
- parent_molecule_refs : ParentMoleculeGroup
- parent_molecules_ : IdentificationData
- ParentGroupRef : IdentificationData
- parentMap : Pattern< TNeedle, FuzzyAC >
- ParentMatches : IdentificationData
- ParentMolecule : IdentificationData , ParentMolecule
- ParentMoleculeGroup : IdentificationData
- ParentMoleculeGrouping : IdentificationData
- ParentMoleculeGroupings : IdentificationData
- ParentMoleculeGroups : IdentificationData
- ParentMoleculeRef : IdentificationData
- ParentMolecules : IdentificationData
- ParentPeakMower() : ParentPeakMower
- parents : ControlledVocabulary::CVTerm
- parse() : IMSAlphabetParser< AlphabetElementType, Container, InputSource > , IMSAlphabetTextParser , LogConfigHandler
- parse_() : XMLFile
- parse_double_ : StringUtils
- PARSE_ERROR : TOPPBase
- parse_float_ : StringUtils
- 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
- parsing_success_ : IndexedMzMLHandler
- partial_sequence_ : SequestInfile
- PARTICLEBEAM : IonSource
- partitionIntoRuns_() : MzTabFile
- pass_threshold_ : IdentificationHit
- passes() : DataFilters
- passesFilters_() : ConsensusMapNormalizerAlgorithmMedian
- paste() : TOPPASScene
- path : ExperimentalDesign::MSFileSectionEntry , File , ToolExternalDetails
- path_ : ParamXMLHandler
- path_to_file_ : SourceFile , SourceFileVisualizer
- pathLabelMapper_() : ExperimentalDesign
- Pattern() : Pattern< TNeedle, FuzzyAC >
- pattern_tolerance_ : FeatureFinderAlgorithmPicked
- PatternAuxData() : PatternAuxData< TNeedle >
- patterns : SIPPeptide
- 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_annotations : MoleculeQueryMatch
- peak_apex_intensity : PeakCandidate
- peak_before_mono_max_ppm_diff_ : DIAScoring
- peak_bound_ : PeakPickerCWT
- peak_bound_ms2_level_ : PeakPickerCWT
- peak_colors_1d : LayerData
- peak_corr_bound_ : PeakPickerCWT
- peak_count_ : MzDataHandler , MzXMLHandler::SpectrumData
- peak_depth : ProbablePhosphoSites
- peak_height_max_ : TargetedSpectraExtractor
- peak_height_min_ : TargetedSpectraExtractor
- peak_integration_ : MRMTransitionGroupPicker
- peak_map_ : MSSim , SpectrumCheapDPCorr
- peak_mass_tolerance_ : InspectInfile , SequestInfile
- peak_meta_ : MSDataSqlConsumer
- peak_penstyle_ : Spectrum1DCanvas
- PEAK_PICKING : DataProcessing
- peak_position_ : Annotation1DPeakItem
- PEAK_SCORE : SHFeature
- peak_spread_ : TargetedSpectraExtractor::BinnedSpectrumComparator
- peak_tolerance_ : ProteinIdentificationVisualizer
- peak_type : IMSIsotopeDistribution
- peak_width_ : FeatureFinderIdentificationAlgorithm , PeakPickerIterative , PeakPickerMRM
- PeakAlignment() : PeakAlignment
- PeakAnnotations : IdentificationData
- PeakConstIterator : ContinuousWaveletTransform , ContinuousWaveletTransformNumIntegration
- peakcount_ : NLargest , WindowMower
- PeakFileOptions() : PeakFileOptions
- PeakIndex() : PeakIndex
- PeakIntegrator() : PeakIntegrator
- 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
- peakPickingPerWindowsInSpectrum_() : AScore
- peaks : FeatureFinderAlgorithmPickedHelperStructs::MassTrace , IsotopeCluster , LayerData , OptimizePeakDeconvolution::Data , OptimizePick::Data
- peaks_ : IMSIsotopeDistribution
- peaks_container : IMSIsotopeDistribution
- peaks_iterator : IMSIsotopeDistribution
- peaks_per_peptide_ : MultiplexIsotopicPeakPattern
- peakselectionIsAllowed_() : MRMFragmentSelection
- PeakShape() : PeakShape
- PeakSpectrumCompareFunctor() : PeakSpectrumCompareFunctor
- PeakT : MSExperiment , OnDiscMSExperiment
- PeakType : BaseModel< D > , EGHFitter1D::Data , EmgFitter1D::Data , FeatureFinderAlgorithmIsotopeWavelet , FeatureFinderAlgorithmPicked , FeatureFinderAlgorithmSH , Fitter1D , AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > , MzDataHandler , MzMLHandler , MzXMLHandler , MRMTransitionGroup< ChromatogramType, TransitionType > , MSChromatogram , MSExperiment , MSSpectrum , 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 , XQuestResultXMLHandler
- pep_indices : ConnectedComponent
- pep_map_ : MzIdentMLDOMHandler
- PEP_PROB : MS2Info
- pep_quant_ : PeptideAndProteinQuant
- pep_result_ : IDMergerAlgorithm
- pep_sequences_ : MzIdentMLHandler
- pep_to_indist_prot_grp_ : PeptideProteinResolution
- pep_to_prot : PeptideIndexing::FoundProteinFunctor
- pepHitVtx_to_run_ : IDBoostGraph
- PEPLIST : FileTypes
- PepNovoInfile() : PepNovoInfile
- PepNovoOutfile() : PepNovoOutfile
- pepPrior_ : MessagePasserFactory< Label >
- peptide : RNPxlReportRow
- Peptide : TargetedExperiment , Peptide , LightTargetedExperiment
- 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_compare_ : FeatureFinderIdentificationAlgorithm
- peptide_data_ : MzTab
- peptide_entries : ProteinResolver::ResolverResult
- peptide_evidences_ : ConsensusXMLFile , IdXMLFile , PeptideHit
- peptide_group_label : TransitionTSVFile::TSVTransition , LightCompound
- peptide_group_label_ : Peptide
- peptide_hit : ProteinResolver::PeptideEntry
- peptide_hit_ : PepXMLFile
- peptide_hit_index : LayerData
- peptide_hits_ : XTandemXMLFile
- peptide_id_index : LayerData , OPXLDataStructs::CrossLinkSpectrumMatch
- peptide_id_meta_values_ : XQuestResultXMLHandler
- peptide_identification : ProteinResolver::PeptideEntry , ProteinResolver::ResolverResult
- peptide_identification_index_ : MascotXMLHandler
- peptide_identifications_ : OMSSAXMLFile
- PEPTIDE_IDS_EMPTY : PeptideIndexing
- peptide_intensities_ : IsobaricNormalizer
- peptide_map_ : FeatureFinderIdentificationAlgorithm
- peptide_mass : OPXLDataStructs::AASeqWithMass
- peptide_mass_unit_ : SequestInfile
- peptide_max_size_ : SimpleSearchEngineAlgorithm
- peptide_min_size_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , SimpleSearchEngineAlgorithm
- peptide_missed_cleavages_ : SimpleSearchEngineAlgorithm
- peptide_mod_index : SimpleSearchEngineAlgorithm::AnnotatedHit_
- peptide_motif_ : SimpleSearchEngineAlgorithm
- peptide_quantification_unit : MzTabMetaData
- peptide_ratios_ : IsobaricNormalizer
- peptide_ref : LightTransition
- peptide_ref_ : IncludeExcludeTarget , ReactionMonitoringTransition
- peptide_reference_map_ : TargetedExperiment
- peptide_reference_map_dirty_ : TargetedExperiment
- peptide_search_engine_score : MzTabMetaData
- peptide_seq : OPXLDataStructs::AASeqWithMass
- peptide_similarity_ : MultiplexFiltering
- peptide_weight : RNPxlReportRow
- PeptideAndProteinQuant() : PeptideAndProteinQuant
- PeptideCompound() : PeptideCompound
- peptideCount() : EnzymaticDigestionLogModel , ProteaseDigestion
- PeptideData() : PeptideAndProteinQuant::PeptideData
- PeptideDB : AhoCorasickAmbiguous
- PeptideDigestionFilter() : IDFilter::PeptideDigestionFilter
- 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
- peptideIDsMergeable() : ProteinIdentification
- PeptideIndexing() : PeptideIndexing
- PeptideMap : FeatureFinderIdentificationAlgorithm
- PeptideMapT : MRMAssay
- peptideMassRule_() : IsotopeWaveletTransform< PeakType >
- PeptideNodeSet : IDBoostGraph
- PeptidePosition : OPXLDataStructs
- peptideProbabilityThreshold_ : SuperHirnParameters
- PeptideProteinResolution() : PeptideProteinResolution
- PeptideQuant : PeptideAndProteinQuant
- PeptideReferenceMapType : TargetedExperiment
- PeptideRefMap_ : MRMFeatureFinderScoring
- PeptideRefRTMap : FeatureFinderIdentificationAlgorithm
- PeptideRTMap_ : ChromatogramExtractor
- peptides : LayerData , ProteinResolver::ISDGroup , ProteinResolver::MSDGroup , ProteinResolver::ProteinEntry , Protein
- peptides_ : BaseFeature , PepXMLFile , PepXMLFileMascot , TargetedExperiment
- peptideScore_() : AScore
- PeptideSequence : TransitionTSVFile::TSVTransition
- PeptideTransitionMapType : MRMAssay , MRMDecoy
- PeptideType : MRMFeatureFinderScoring , MRMScoring
- PeptideVectorType : MRMAssay , MRMDecoy , TransitionTSVFile
- peptidoforms : TransitionTSVFile::TSVTransition
- PEPXML : FileTypes
- PepXMLFile() : PepXMLFile
- PepXMLFileMascot() : PepXMLFileMascot
- percentage_ : GradientVisualizer
- percentage_factor_ : SpectrumCanvas
- percentageIntensityElutionBorderVariation_ : SuperHirnParameters
- percentages_ : Gradient
- percentiles_after : TransformationDescription::TransformationStatistics
- percentiles_before : TransformationDescription::TransformationStatistics
- percents : TransformationDescription::TransformationStatistics
- PercolatorOutfile() : PercolatorOutfile
- percTIC : OPXLDataStructs::CrossLinkSpectrumMatch
- performAlignment() : Spectrum1DCanvas , Spectrum1DWidget
- performance_ : SimpleSVM
- performCalibration() : TOPPOpenSwathBase
- performCrossValidation() : SVMWrapper
- performExtraction() : OpenSwathWorkflow
- performExtractionSonar() : OpenSwathWorkflowSonar
- performRTNormalization() : OpenSwathCalibrationWorkflow
- performSonarExtraction_() : OpenSwathWorkflowSonar
- Permut : CompNovoIdentification , CompNovoIdentificationBase::Permut , CompNovoIdentificationCID
- permut_ : CompNovoIdentificationBase::Permut
- permute_() : CompNovoIdentificationBase
- permute_cache_ : CompNovoIdentificationBase
- pg_scores_ : MRMFeature
- ph_ : Digestion
- ph_2_sdat_ : MzIdentMLHandler
- PHD : Precursor
- PHOTODIODEARRAYDETECTOR : IonDetector
- PHOTOMULTIPLIER : IonDetector
- PI : EmgGradientDescent , IonSource , SHFeature
- pi_ : MRMTransitionGroupPicker
- PIC : MSNumpressCoder
- pick() : PeakPickerCWT , PeakPickerHiRes , PeakPickerIterative , PeakPickerMaxima , PeakPickerSH
- pick_() : PeakPickerHiRes
- pickAndCalibrate() : TOFCalibration
- pickApex() : MRMTransitionGroupPicker
- pickChromatogram() : PeakPickerMRM
- pickChromatogram_() : PeakPickerMRM
- pickChromatogramCrawdad_() : PeakPickerMRM
- picked_peaks : TwoDOptimization::Data
- picker_ : FIAMSDataProcessor , MRMTransitionGroupPicker
- pickExperiment() : MRMFeatureFinderScoring , PeakPickerCWT , PeakPickerHiRes , PeakPickerIterative , PeakPickerSH
- pickFragmentChromatograms() : MRMTransitionGroupPicker
- pickPrecursorChromatograms() : MRMTransitionGroupPicker
- pickRecenterPeaks_() : PeakPickerIterative
- pickSpectrum() : TargetedSpectraExtractor
- pickTransitionGroup() : MRMTransitionGroupPicker
- pidv_caller_ : PeptideIdentificationVisualizer , ProteinIdentificationVisualizer
- PIN : FileTypes
- pint_mono : SiriusMSFile::CompoundInfo
- pipelineDroppedOnWidget() : TOPPASWidget
- pipelineErrorSlot() : TOPPASScene
- pipelineExecutionFailed() : TOPPASScene
- pka_ : Residue
- pkb_ : Residue
- pkc_ : Residue
- PlainMSDataWritingConsumer() : PlainMSDataWritingConsumer
- plotCombinedSpectra() : ClusteredMS2ConsensusSpectrum
- plotFilteredSpectra() : MetaProSIPReporting
- plotHeatMap() : MetaProSIPReporting
- plotScoresAndWeights() : MetaProSIPReporting
- plotTargetDecoyEstimation() : PosteriorErrorProbabilityModel
- pmass : SiriusMSFile::CompoundInfo
- pMZ_LIST : ProcessData
- PNG : FileTypes
- Point : ClusteringGrid , GridBasedCluster , GridBasedClustering< Metric > , MultiplexClustering
- point_indices_ : GridBasedCluster
- PointArrayType : ConvexHull2D
- PointArrayTypeConstIterator : ConvexHull2D
- POINTCOLLECTOR : IonDetector
- pointer : _Iterator< _Val, _Ref, _Ptr > , KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , 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 > , MatchedIterator< CONT_T, TRAIT, CONST_T >
- Pointer : Matrix< Value >
- pointer : Matrix< Value > , NASequence::ConstIterator , NASequence::Iterator
- pointerComparator() : PointerComparator< Cmp >
- PointerComparator() : PointerComparator< Cmp >
- PointerType : Map< Key, T >
- points_across_baseline : PeakIntegrator::PeakShapeMetrics
- points_across_half_height : PeakIntegrator::PeakShapeMetrics
- 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 >
- populate_raster_() : LinearResamplerAlign
- populateChromatogramsWithData_() : MzMLHandler , MzMLSqliteHandler
- populateMetaData_() : SwathFile
- populatePeptideRTMap_() : ChromatogramExtractor
- populateSpectraWithData_() : MzMLHandler , MzMLSqliteHandler , MzXMLHandler
- pos : PenaltyFactors , PeakPickerMaxima::PeakCandidate
- pos_ : ConsensusXMLFile , ROCCurve
- pos_adducts_ : AccurateMassSearchEngine
- pos_adducts_fname_ : AccurateMassSearchEngine
- pos_charges_ : Compomer
- pos_col_ : MultiGradient
- pos_max_ : SplineInterpolatedPeaks::Navigator , SplineInterpolatedPeaks , SplinePackage
- pos_min_ : SplineInterpolatedPeaks::Navigator , SplineInterpolatedPeaks , SplinePackage
- pos_neg_mean_weighted_posteriors() : PosteriorErrorProbabilityModel
- pos_neg_sigma_weighted_posteriors() : PosteriorErrorProbabilityModel
- pos_param_pairs_ : MzTabModification
- pos_range_ : RangeManager< D >
- pos_step_width_ : SplinePackage
- pos_step_width_scaling_ : SplineInterpolatedPeaks::Navigator
- PosBegin() : MSChromatogram , MSSpectrum
- PoseClusteringAffineSuperimposer() : PoseClusteringAffineSuperimposer
- PoseClusteringShiftSuperimposer() : PoseClusteringShiftSuperimposer
- PosEnd() : MSChromatogram , MSSpectrum
- position : CompNovoIonScoringBase::IonScore , DeNovoIonScoring::IonScore , EnzymaticDigestionLogModel::BindingSite_ , FASTAFile , MultiGradient , MzTabModificationMetaData , OPXLDataStructs::AASeqWithMass , PeptideIndexing::PeptideProteinMatchInformation
- position_ : AASequence::ConstIterator , AASequence::Iterator , Annotation1DCaret , Annotation1DPeakItem , Annotation1DTextItem , ChromatogramPeak , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , AveragePosition< D > , NASequence::ConstIterator , NASequence::Iterator , Peak1D , Peak2D
- position_weighted_sum_ : AveragePosition< D >
- PositionRangeType : RangeManager< D >
- positions : OptimizePeakDeconvolution::Data , OptimizePick::Data , TwoDOptimization::Data
- 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 , MzTabOligonucleotideSectionRow , MzTabPSMSectionRow
- post_moves : MappingParam
- POSTACCELERATIONDETECTOR : IonDetector
- Postcondition() : Postcondition
- postDetectabilityHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
- postDigestHook() : BaseLabeler , ICPLLabeler , ITRAQLabeler , LabelFreeLabeler , O18Labeler , SILACLabeler
- PosteriorErrorProbabilityModel() : PosteriorErrorProbabilityModel
- POSTERRPROB : PercolatorOutfile
- 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
- POSTTRANSLATIONAL : ResidueModification
- potential_adducts_ : FeatureDeconvolution , MetaboliteFeatureDeconvolution
- potential_cmp : MetaboTargetedAssay
- potential_rmts : MetaboTargetedAssay
- potential_target_ : TOPPASScene
- pp_ : PeakPickerMRM
- pp_identifier_2_sil_ : MzIdentMLHandler
- ppm : ChromExtractParams
- PPM : XTandemInfile
- ppm_ : LinearResamplerAlign , SpectrumAccessQuadMZTransforming , Tagger
- ppm_error_abs_sum : OPXLDataStructs::CrossLinkSpectrumMatch
- ppm_error_abs_sum_alpha : OPXLDataStructs::CrossLinkSpectrumMatch
- ppm_error_abs_sum_beta : OPXLDataStructs::CrossLinkSpectrumMatch
- ppm_error_abs_sum_linear : OPXLDataStructs::CrossLinkSpectrumMatch
- ppm_error_abs_sum_linear_alpha : OPXLDataStructs::CrossLinkSpectrumMatch
- ppm_error_abs_sum_linear_beta : OPXLDataStructs::CrossLinkSpectrumMatch
- ppm_error_abs_sum_xlinks : OPXLDataStructs::CrossLinkSpectrumMatch
- ppm_error_abs_sum_xlinks_alpha : OPXLDataStructs::CrossLinkSpectrumMatch
- ppm_error_abs_sum_xlinks_beta : OPXLDataStructs::CrossLinkSpectrumMatch
- ppm_max_ : SiriusAdapterAlgorithm
- ppm_tolerance_ : GaussFilterAlgorithm
- ppmToleranceForMZClustering_ : SuperHirnParameters
- PQD : Precursor
- PQP : FileTypes
- pre : MzIdentMLDOMHandler::PeptideEvidence , MzTabOligonucleotideSectionRow , MzTabPSMSectionRow
- pre_ : MultiGradient
- PRE_32 : MzMLHandlerHelper::BinaryData
- PRE_64 : MzMLHandlerHelper::BinaryData
- pre_int_ : SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
- pre_int_H2O_ : SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
- pre_int_NH3_ : SimpleTSGXLMS , TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
- pre_min_ : MultiGradient
- pre_moves : MappingParam
- PRE_NONE : MzMLHandlerHelper::BinaryData
- pre_release_identifier : VersionInfo::VersionDetails
- pre_score : OPXLDataStructs::CrossLinkSpectrumMatch
- 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 , BK_PrecPolicy< T >
- precision_ : RealMassDecomposer , Weights , MzXMLHandler::SpectrumData
- precisions_ : MzDataHandler
- PrecisionWrapper() : PrecisionWrapper< FloatingPointType >
- preComputeExpensiveFunctions_() : IsotopeWavelet
- Precondition() : Precondition
- PRECURSOR : InstrumentSettings
- Precursor : NASequence , Precursor , Residue
- precursor : TransitionTSVFile::TSVTransition
- precursor_ : ChromatogramSettings
- precursor_adduct_ : SpectralMatch
- precursor_charge() : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , SpectrumMetaDataLookup::SpectrumMetaData , TransitionTSVFile::TSVTransition
- precursor_charge_ : MSstatsFile::MSstatsLine_ , MSstatsFile::MSstatsTMTLine_ , SvmTheoreticalSpectrumGenerator
- precursor_chromatogram_map_ : MRMTransitionGroup< ChromatogramType, TransitionType >
- precursor_chromatograms_ : MRMTransitionGroup< ChromatogramType, TransitionType >
- precursor_correction : OPXLDataStructs::CrossLinkSpectrumMatch , OPXLDataStructs::ProteinProteinCrossLink
- precursor_correction_steps_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
- precursor_cv_terms_ : IncludeExcludeTarget , ReactionMonitoringTransition
- precursor_error_ppm : NucleicAcidSearchEngine::AnnotatedHit , OPXLDataStructs::CrossLinkSpectrumMatch
- precursor_feature_map_ : MRMFeature
- precursor_features_ : MRMFeature , MRMFeatureOpenMS
- precursor_int : MetaboTargetedAssay
- precursor_intensity_ : NucleicAcidSpectrumGenerator
- precursor_isolation_target : ChromatogramMeta
- precursor_isotopes_ : SimpleSearchEngineAlgorithm
- precursor_lower_mz_ : XTandemInfile
- precursor_mass : OPXLDataStructs::XLPrecursor
- precursor_mass_error_unit_ : XTandemInfile
- precursor_mass_tolerance : DBSearchParam , ProteinIdentification::SearchParameters
- precursor_mass_tolerance_ : BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSumAgreeingIntensities , CompNovoIdentificationCID , InspectInfile , MascotInfile , OpenPepXLAlgorithm , OpenPepXLLFAlgorithm , SequestInfile , SimpleSearchEngineAlgorithm
- precursor_mass_tolerance_minus_ : XTandemInfile
- precursor_mass_tolerance_plus_ : XTandemInfile
- precursor_mass_tolerance_ppm : ProteinIdentification::SearchParameters
- precursor_mass_tolerance_unit_ : SimpleSearchEngineAlgorithm
- precursor_mass_tolerance_unit_ppm_ : OpenPepXLAlgorithm , OpenPepXLLFAlgorithm
- precursor_mass_type_ : XTandemInfile
- precursor_max_charge_ : SimpleSearchEngineAlgorithm
- precursor_min_charge_ : SimpleSearchEngineAlgorithm
- precursor_mz : SpectrumMetaDataLookup::SpectrumMetaData , LightTransition
- precursor_mz_ : IncludeExcludeTarget , ReactionMonitoringTransition
- precursor_mz_error_ : MetaboliteSpectralMatching
- precursor_mz_selected_ion_ : PeakFileOptions
- precursor_mz_tolerance_ : SiriusAdapterAlgorithm
- precursor_mz_tolerance_unit_ : SiriusAdapterAlgorithm
- PRECURSOR_RECALCULATION : DataProcessing
- precursor_ref : NucleicAcidSearchEngine::AnnotatedHit
- precursor_residual_peak_count : OPXLDataStructs::CrossLinkSpectrumMatch
- precursor_rt : SpectrumMetaDataLookup::SpectrumMetaData
- precursor_rt_tolerance_ : SiriusAdapterAlgorithm
- precursor_signal_proportion : OPXLDataStructs::CrossLinkSpectrumMatch
- precursor_statistics_ : SpectrumAnnotator
- precursor_target_intensity : OPXLDataStructs::CrossLinkSpectrumMatch
- precursor_target_peak_count : OPXLDataStructs::CrossLinkSpectrumMatch
- precursor_tol_ : MRMMapping
- precursor_tolerance : MzIdentMLDOMHandler::SpectrumIdentificationProtocol
- precursor_tolerance_ : ProteinIdentificationVisualizer
- precursor_tolerance_ppm : DBSearchParam
- precursor_total_intensity : OPXLDataStructs::CrossLinkSpectrumMatch
- precursorCHRG : MS2Fragment
- PrecursorInfo() : NucleicAcidSearchEngine::PrecursorInfo
- PrecursorIonSelection() : PrecursorIonSelection
- PrecursorIonSelectionPreprocessing() : PrecursorIonSelectionPreprocessing
- precursorMass : MSPeak
- precursorMZ : MS2ConsensusSpectrum , MS2Fragment , MSPeak
- precursors_ : BinnedSpectrum , SpectrumSettings
- precursorScan : IsobaricChannelExtractor::PuritySate_
- PrecursorVisualizer() : PrecursorVisualizer
- predict() : MZTrafoModel , PeakIntensityPredictor , SimpleSVM , SVMWrapper
- predictContaminantsRT() : RTSimulation
- predictDetectabilities() : DetectabilitySimulation
- Prediction : ReactionMonitoringTransition , TargetedExperiment , Prediction
- prediction_ : IncludeExcludeTarget , ReactionMonitoringTransition
- predictor_names_ : SimpleSVM
- PredictorMap : SimpleSVM
- predictPeptideRT() : LibSVMEncoder
- predictRT() : RTSimulation
- preferencesChange() : SpectrumCanvas
- preferencesDialog() : TOPPASBase , TOPPViewBase
- prefix : FuzzyStringComparator::PrefixInfo_ , LogStreamBuf::StreamStruct , String , StringUtils
- prefix_ : PeptideIndexing
- prefix_whitespaces : FuzzyStringComparator::PrefixInfo_
- 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
- preprocessing_tech : LPWrapper::SolverParam
- preprocessingSirius() : SiriusAdapterAlgorithm
- preprocessPairs_() : OpenPepXLAlgorithm
- preprocessSpectra() : OPXLSpectrumProcessingAlgorithms
- preprocessSpectra_() : NucleicAcidSearchEngine , SimpleSearchEngineAlgorithm
- preScore() : XQuestScores
- pressure_ : HPLC
- PRETRANSLATIONAL : ResidueModification
- PREV_AA : MS2Info
- previous_rt_ : MSDataAggregatingConsumer
- previous_seq_ : XTandemXMLFile
- primary : ProteinResolver::ProteinEntry
- primary_files : DataProcessingStep
- primary_id_ : SpectralMatch
- primary_indistinguishable : ProteinResolver::ProteinEntry
- primaryProteins_() : ProteinResolver
- print_debug_ : EmgGradientDescent
- print_duplicate_references_ : SequestInfile
- print_profile() : LCElutionPeak
- PrintAddressVisitor() : IDBoostGraph::PrintAddressVisitor< CharT >
- printDeltaMassesList() : MultiplexDeltaMassesGenerator
- printEdgesOfConnectedFeatures_() : FeatureDeconvolution , MetaboliteFeatureDeconvolution
- printGraph() : IDBoostGraph
- printNull_() : SimpleSVM
- printSamplesLabelsList() : MultiplexDeltaMassesGenerator
- printSummary() : TransformationDescription
- printToVoid_() : SVMWrapper
- printUsage_() : TOPPBase
- privvec : ConsensusMap , FeatureFinderAlgorithmPickedHelperStructs::MassTraces , FeatureMap
- prm_ : OpenSwathWorkflowBase
- pro_id_ : MzIdentMLDOMHandler , MzIdentMLHandler
- probabilities : SimpleSVM::Prediction
- probabilities_ : PSProteinInference
- probability : ProteinIdentification::ProteinGroup
- PROBABILITY : SVMWrapper
- probability_container : BasicStatistics< RealT >
- proc : TOPPASScene::TOPPProcess
- process_MS1_level_data_structure() : FTPeakDetectController
- process_MS2_level_data_structure() : FTPeakDetectController
- processChromatogram_() : MSDataWritingConsumer , NoopMSDataWritingConsumer , PlainMSDataWritingConsumer
- ProcessData() : ProcessData
- processFinished() : TOPPASScene
- processing_ : MzMLHandler
- processing_actions_ : DataProcessing
- processing_softwares_ : IdentificationData
- processing_step_opt : AppliedProcessingStep
- processing_steps_ : IdentificationData
- ProcessingAction : DataProcessing
- ProcessingSoftwareRef : IdentificationData
- ProcessingStepRef : IdentificationData
- processIntensities() : BackgroundIntensityBin
- processIntensityMaps() : BackgroundControl
- processMSPeaks() : ProcessData
- processMZFeatureVector() : MS1FeatureMerger
- processOutliers_() : PosteriorErrorProbabilityModel
- processRun_() : BasicProteinInferenceAlgorithm
- processSpectrum_() : MSDataWritingConsumer , NoopMSDataWritingConsumer , PlainMSDataWritingConsumer
- prod_ : IsotopeWaveletTransform< PeakType >
- Product() : Product , ReactionMonitoringTransition
- product : TransitionTSVFile::TSVTransition
- product_ : ChromatogramSettings , ReactionMonitoringTransition
- product_cv_terms_ : IncludeExcludeTarget
- product_isolation_target : ChromatogramMeta
- product_mz : LightTransition
- product_mz_ : IncludeExcludeTarget , ProductVisualizer
- product_tol_ : MRMMapping
- product_window_low_ : ProductVisualizer
- product_window_up_ : ProductVisualizer
- ProductListType : TraMLHandler
- ProductModel() : ProductModel< 2 >
- products_ : SpectrumSettings
- ProductVisualizer() : ProductVisualizer
- PROFILE : SpectrumSettings
- profile_ : SiriusAdapterAlgorithm
- profileIntensities_ : RawData
- profileMasses_ : RawData
- PROFILESHAPE : RawMSSignalSimulation
- prog_log_ : FeatureFinderIdentificationAlgorithm , FeatureFinderMultiplexAlgorithm
- progress_ : ConsensusXMLFile , FeatureFinderMultiplexAlgorithm , FeatureGroupingAlgorithmKD , QcMLFile
- progress_counter_ : FeatureFinderAlgorithmIsotopeWavelet
- ProgressLogger() : ProgressLogger
- project_() : Spectrum3DOpenGLCanvas
- 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_acc_to_indist_prot_grp_ : PeptideProteinResolution
- prot_grp_indices : ConnectedComponent
- prot_hit_ : ConsensusXMLFile , FeatureXMLFile , IdXMLFile
- prot_id_ : ConsensusXMLFile , FeatureXMLFile , IdXMLFile , PepXMLFile , ProtXMLFile
- prot_id_counter_ : PrecursorIonSelection
- prot_id_in_run_ : IdXMLFile
- prot_ids_ : IdXMLFile , XQuestResultXMLHandler
- prot_masses_ : PrecursorIonSelectionPreprocessing
- prot_peptide_seq_map_ : PrecursorIonSelectionPreprocessing
- prot_quant_ : PeptideAndProteinQuant
- prot_result_ : IDMergerAlgorithm
- ProteaseDB() : ProteaseDB
- Protein : TargetedExperiment , Protein , LightTargetedExperiment
- protein_ : AhoCorasickAmbiguous
- 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_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 : PeptideIndexing::PeptideProteinMatchInformation
- protein_mass_filter_ : SequestInfile
- PROTEIN_N_TERM : ResidueModification
- protein_name_length_ : InspectOutfile
- protein_quantification_unit : MzTabMetaData
- protein_reference_map_ : TargetedExperiment
- protein_reference_map_dirty_ : TargetedExperiment
- protein_refs : Peptide , LightCompound
- protein_score_type_ : ProteinIdentification
- protein_search_engine_score : MzTabMetaData
- protein_significance_threshold_ : ProteinIdentification
- protein_terminus : PepXMLFile::AminoAcidModification
- protein_type : ProteinResolver::ProteinEntry
- protein_uids_ : XTandemXMLFile
- 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 : TransitionTSVFile::TSVTransition
- ProteinNodeSet : IDBoostGraph
- ProteinProteinCrossLinkType : OPXLDataStructs
- ProteinQuant : PeptideAndProteinQuant
- ProteinReferenceMapType : TargetedExperiment
- ProteinResolver() : ProteinResolver
- proteins : ProteinResolver::ISDGroup , ProteinResolver::MSDGroup , ProteinResolver::PeptideEntry , LightTargetedExperiment , TargetedExperiment
- proteins_ : PepXMLFile , TargetedExperiment
- ProteinType : MRMFeatureFinderScoring , MRMScoring
- ProteinVectorType : MRMAssay , MRMDecoy , TransitionTSVFile
- protIDs_ : IDBoostGraph
- ProtonDistributionModel() : ProtonDistributionModel
- PROTXML : FileTypes
- ProtXMLFile() : ProtXMLFile
- PScore : AScore
- PSD : Precursor
- pseudo_counts_ : HiddenMarkovModel
- pseudoreversePeptide_() : MRMDecoy
- psi_ : IsotopeWaveletTransform< PeakType >
- psi_id_ : DigestionEnzymeProtein
- psi_mod_accession_ : ResidueModification
- PSLPFormulation() : PSLPFormulation
- psm_data_ : MzTab
- PSM_ID : MzTabPSMSectionRow
- psm_search_engine_score : MzTabMetaData
- PSMS : FileTypes
- 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 >
- pubchemids : CsiFingerIdMzTabWriter::CsiAdapterHit
- publication : MzTabMetaData
- Publication : TargetedExperiment , Publication
- publications_ : TargetedExperiment
- PULSECOUNTING : IonDetector
- PuritySate_() : IsobaricChannelExtractor::PuritySate_
- push2Box_() : IsotopeWaveletTransform< PeakType >
- push2TmpBox_() : IsotopeWaveletTransform< PeakType >
- push_back() : ConstRefVector< ContainerT > , IMSAlphabet , TOPPASVertex::TOPPASFilenames
- pushValuesFromLine_() : MRMFeatureQCFile
- pv_db_map_ : MzIdentMLDOMHandler
- PValue_() : LabeledPairFinder
- pw_filtering_ : ElutionPeakDetection
- PYMS : IonSource