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 , TOPPViewPrefDialog , 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_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
• passesFDR_() : DBSuitability
• passesFilters_() : ConsensusMapNormalizerAlgorithmMedian
• paste() : TOPPASScene
• path : ExperimentalDesign::MSFileSectionEntry , File , ToolExternalDetails
• path_ : ParamXMLHandler
• path_label_to_assay_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• path_to_file_ : SourceFile , SourceFileVisualizer
• pathLabelMapper_() : ExperimentalDesign
• Pattern() : Pattern< TNeedle, FuzzyAC >
• pattern_tolerance_ : FeatureFinderAlgorithmPicked
• PatternAuxData() : PatternAuxData< TNeedle >
• 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 , MzTab::CMMzTabStream , MzTab::IDMzTabStream , ProtXMLFile
• pep_ids_ : IdXMLFile , XQuestResultXMLHandler
• pep_indices : ConnectedComponent
• pep_map_ : MzIdentMLDOMHandler
• pep_optional_column_names_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• 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_count : TargetedExperiment::SummaryStatistics
• 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_hit_user_value_keys_ : MzTab::IDMzTabStream
• peptide_hits_ : XTandemXMLFile
• peptide_id_index : LayerData , OPXLDataStructs::CrossLinkSpectrumMatch
• peptide_id_meta_values_ : XQuestResultXMLHandler
• peptide_id_user_value_keys_ : MzTab::IDMzTabStream
• peptide_identification : ProteinResolver::PeptideEntry , ProteinResolver::ResolverResult
• peptide_identification_index_ : MascotXMLHandler
• peptide_identifications_ : OMSSAXMLFile
• peptide_ids_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• 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
• PeptideMass() : PeptideMass
• 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
• peptideSectionRowFromConsensusFeature_() : MzTab
• peptideSectionRowFromFeature_() : MzTab
• 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
• pg2prot_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• 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
• 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 >
• popIncompleteLayer_() : SpectrumCanvas
• 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() : InternalCalibration::CalibrantStats_
• 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
• processStdErr_() : ExternalProcess
• processStdOut_() : ExternalProcess
• 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 , MzTab::CMMzTabStream , MzTab::IDMzTabStream
• 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_count : TargetedExperiment::SummaryStatistics
• protein_data_ : MzTab , ProteinResolver
• protein_entries : ProteinResolver::ResolverResult
• protein_group_ : ProtXMLFile
• protein_groups_ : ProteinIdentification
• protein_hit_user_value_keys_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• 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_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
• proteinSectionRowFromProteinHit_() : MzTab
• ProteinType : MRMFeatureFinderScoring , MRMScoring
• ProteinVectorType : MRMAssay , MRMDecoy , TransitionTSVFile
• protIDs_ : IDBoostGraph
• ProtonDistributionModel() : ProtonDistributionModel
• PROTXML : FileTypes
• ProtXMLFile() : ProtXMLFile
• prt_group_id_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• prt_hit_id_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• prt_indistgroup_id_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• prt_optional_column_names_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• prt_run_id_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• PRT_STATE_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• PScore : AScore
• PSD : Precursor
• pseudo_counts_ : HiddenMarkovModel
• pseudoreversePeptide_() : MRMDecoy
• psi_ : IsotopeWaveletTransform< PeakType >
• psi_id_ : DigestionEnzymeProtein
• psi_mod_accession_ : ResidueModification
• PSLPFormulation() : PSLPFormulation
• psm_count : PeptideAndProteinQuant::PeptideData , PeptideAndProteinQuant::ProteinData
• psm_counts : PeptideAndProteinQuant::PeptideData , PeptideAndProteinQuant::ProteinData
• psm_data_ : MzTab
• PSM_ID : MzTabPSMSectionRow
• psm_id_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• psm_optional_column_names_ : MzTab::CMMzTabStream , MzTab::IDMzTabStream
• psm_search_engine_score : MzTabMetaData
• PSMS : FileTypes
• PSMSectionRowFromPeptideID_() : MzTab
• 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
• PythonModuleRequirement() : PythonModuleRequirement
• PythonSelector() : PythonSelector