- p -

• p : GammaDistributionFitter::GammaDistributionFitResult
• p_ : ToolDescriptionHandler
• p_cleave : EnzymaticDigestionLogModel::CleavageModel_
• p_miss : EnzymaticDigestionLogModel::CleavageModel_
• p_pv_map_ : MzIdentMLDOMHandler
• packages_ : SplineSpectrum::Navigator , SplineSpectrum
• pair_min_quality_ : SimplePairFinder
• pairfinder_ : MapAlignmentAlgorithmPoseClustering
• pairfinder_input_ : FeatureGroupingAlgorithmUnlabeled
• param : ToolExternalDetails , LayerData , TOPPViewBase
• param_ : DefaultParamHandler , FeatureXMLFile , IdXMLFile , INIFileEditorWindow , ParamXMLHandler , LocalLinearMap , MapAlignmentAlgorithmKD , ParamEditor , SVMWrapper , TOPPASToolConfigDialog , TOPPASToolVertex , TOPPBase
• param_cmdline_ : TOPPBase
• param_common_ : TOPPBase
• param_common_tool_ : TOPPBase
• param_groups_ : MzMLValidator , MzQuantMLValidator
• param_inifile_ : TOPPBase
• param_instance_ : TOPPBase
• PARAM_NAME : LogConfigHandler
• param_name : TOPPASToolVertex::IOInfo
• parameter_cvs : MzIdentMLDOMHandler::SpectrumIdentificationProtocol
• parameter_ups : MzIdentMLDOMHandler::SpectrumIdentificationProtocol
• parameters_ : IdXMLFile , ModelDescription< D > , MzTabParameterList , TOPPBase
• params_ : AcqusHandler , PepXMLFile , TransformationModel , TransformationXMLFile
• params_intensity_ : FeatureDistance
• params_mz_ : FeatureDistance
• params_rt_ : FeatureDistance
• parent_ : TOPPASInputFileDialog
• parents : ControlledVocabulary::CVTerm
• parse_double_ : StringUtils
• parse_float_ : StringUtils
• parsing_success_ : IndexedMzMLFile
• partial_sequence_ : SequestInfile
• pass_threshold_ : IdentificationHit
• path : ToolExternalDetails
• path_ : ParamXMLHandler
• path_to_file_ : SourceFile , SourceFileVisualizer
• pattern_tolerance_ : FeatureFinderAlgorithmPicked
• patterns : SIPPeptide
• patterns_ : MultiplexFiltering
• pbuf_ : LogStreamBuf
• pe_ev_map_ : MzIdentMLDOMHandler
• peak : FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern , FeatureFinderAlgorithmPickedHelperStructs::Seed , PeakIndex
• peak_apex_intensity : PeakCandidate
• peak_before_mono_max_ppm_diff_ : DIAScoring
• peak_bound_ : PeakPickerCWT
• peak_bound_ms2_level_ : PeakPickerCWT
• peak_corr_bound_ : PeakPickerCWT
• peak_count_ : MzDataHandler , MzXMLHandler::SpectrumData
• peak_depth : ProbablePhosphoSites
• peak_map_ : MSSim , SpectrumCheapDPCorr
• peak_mass_tolerance_ : InspectInfile , SequestInfile
• peak_penstyle_ : Spectrum1DCanvas
• peak_position_ : Annotation1DPeakItem
• PEAK_SCORE : SHFeature
• peak_tolerance_ : ProteinIdentificationVisualizer
• peak_width_ : PeakPickerIterative , PeakPickerMRM
• peakcount_ : NLargest , WindowMower
• peaks : FeatureFinderAlgorithmPickedHelperStructs::MassTrace , IsotopeCluster , LayerData , OptimizePeakDeconvolution::Data , OptimizePick::Data
• peaks_ : IMSIsotopeDistribution
• peaks_per_peptide_ : MultiplexIsotopicPeakPattern
• peaks_per_peptide_max_ : MultiplexFiltering
• peaks_per_peptide_min_ : MultiplexFiltering
• pen_ : Annotations1DContainer
• pen_color_ : TOPPASVertex
• pen_size_max_ : Spectrum2DCanvas
• pen_size_min_ : Spectrum2DCanvas
• penalties : OptimizePeakDeconvolution::Data , OptimizePick::Data , TwoDOptimization::Data
• penalties_ : OptimizePeakDeconvolution , OptimizePick , TwoDOptimization
• pep_hit_ : ConsensusXMLFile , FeatureXMLFile , IdXMLFile , ProtXMLFile
• pep_id_ : ConsensusXMLFile , FeatureXMLFile , IdXMLFile , MzIdentMLDOMHandler , MzIdentMLHandler , ProtXMLFile
• pep_ids_ : IdXMLFile
• pep_indices : ConnectedComponent
• pep_map_ : MzIdentMLDOMHandler
• PEP_PROB : MS2Info
• pep_quant_ : PeptideAndProteinQuant
• pep_sequences_ : MzIdentMLHandler
• pep_to_indist_prot_grp_ : PeptideProteinResolution
• peptide : RNPxlReportRow
• peptide_ : AASequence
• peptide_abundance_assay : MzTabPeptideSectionRow
• peptide_abundance_std_error_study_variable : MzTabPeptideSectionRow
• peptide_abundance_stdev_study_variable : MzTabPeptideSectionRow
• peptide_abundance_study_variable : MzTabPeptideSectionRow
• peptide_data_ : MzTab
• peptide_entries : ProteinResolver::ResolverResult
• peptide_evidences_ : ConsensusXMLFile , IdXMLFile , PeptideHit
• peptide_group_label : TransitionTSVReader::TSVTransition , 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_intensities_ : IsobaricNormalizer
• peptide_mass : OPXLDataStructs::AASeqWithMass
• peptide_mass_unit_ : SequestInfile
• peptide_mod_index : RNPxlSearch::AnnotatedHit
• 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
• peptidehit_charge_ : PeptideHitVisualizer
• peptidehit_rank_ : PeptideHitVisualizer
• peptidehit_score_ : PeptideHitVisualizer
• peptidehit_sequence_ : PeptideHitVisualizer
• peptideProbabilityThreshold_ : SuperHirnParameters
• PeptideRefMap_ : MRMFeatureFinderScoring
• PeptideRTMap_ : ChromatogramExtractor
• peptides : LayerData , ProteinResolver::ISDGroup , ProteinResolver::MSDGroup , ProteinResolver::ProteinEntry , Protein
• peptides_ : BaseFeature , PepXMLFile , PepXMLFileMascot , TargetedExperiment
• PeptideSequence : TransitionTSVReader::TSVTransition
• peptidoforms : TransitionTSVReader::TSVTransition
• percentage_ : GradientVisualizer
• percentage_factor_ : SpectrumCanvas
• percentageIntensityElutionBorderVariation_ : SuperHirnParameters
• percentages_ : Gradient
• percTIC : OPXLDataStructs::CrossLinkSpectrumMatch
• performance_ : SimpleSVM
• permut_ : CompNovoIdentificationBase::Permut
• permute_cache_ : CompNovoIdentificationBase
• pg_scores_ : MRMFeature
• ph_ : Digestion
• ph_2_sdat_ : MzIdentMLHandler
• PI : SHFeature
• picked_peaks : TwoDOptimization::Data
• pidv_caller_ : PeptideIdentificationVisualizer , ProteinIdentificationVisualizer
• pka_ : Residue
• pkb_ : Residue
• pkc_ : Residue
• pMZ_LIST : ProcessData
• point_indices_ : GridBasedCluster
• polarity_ : HasScanPolarity< SpectrumType > , InstrumentSettings , IonSource , IonSourceVisualizer
• pool_file_ : DocumentIDTagger
• pos : PenaltyFactors , PeakPickerMaxima::PeakCandidate
• pos_ : ConsensusXMLFile , ROCCurve
• pos_adducts_ : AccurateMassSearchEngine
• pos_adducts_fname_ : AccurateMassSearchEngine
• pos_charges_ : Compomer
• pos_col_ : MultiGradient
• pos_param_pairs_ : MzTabModification
• pos_range_ : RangeManager< D >
• position : CompNovoIonScoringBase::IonScore , DeNovoIonScoring::IonScore , EnzymaticDigestionLogModel::BindingSite_ , MzTabModificationMetaData , OPXLDataStructs::AASeqWithMass
• position_ : AASequence::ConstIterator , AASequence::Iterator , Annotation1DCaret , Annotation1DPeakItem , Annotation1DTextItem , ChromatogramPeak , ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > , AveragePosition< D > , Peak1D , Peak2D , SparseVector< Value >::SparseVectorConstIterator , SparseVector< Value >::SparseVectorConstReverseIterator , SparseVector< Value >::SparseVectorIterator , SparseVector< Value >::SparseVectorReverseIterator
• position_weighted_sum_ : AveragePosition< D >
• positions : OptimizePeakDeconvolution::Data , OptimizePick::Data , TwoDOptimization::Data
• possible_charge_states_ : Precursor
• post : MzIdentMLDOMHandler::PeptideEvidence , MzTabPSMSectionRow
• post_moves : MappingParam
• potential_adducts_ : FeatureDeconvolution , MetaboliteFeatureDeconvolution
• potential_target_ : TOPPASScene
• pp_identifier_2_sil_ : MzIdentMLHandler
• ppm : ChromExtractParams
• ppm_ : LinearResamplerAlign , SpectrumAccessQuadMZTransforming
• ppm_tolerance_ : GaussFilterAlgorithm
• ppmToleranceForMZClustering_ : SuperHirnParameters
• pre : MzIdentMLDOMHandler::PeptideEvidence , MzTabPSMSectionRow
• pre_ : MultiGradient
• pre_int_ : TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• pre_int_H2O_ : TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• pre_int_NH3_ : TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
• pre_min_ : MultiGradient
• pre_moves : MappingParam
• pre_score : OPXLDataStructs::CrossLinkSpectrumMatch
• pre_size_ : MultiGradient
• pre_states_ : HMMState
• pre_steps_ : MultiGradient
• precision : MzMLHandlerHelper::BinaryData
• precision_ : RealMassDecomposer , Weights , MzXMLHandler::SpectrumData
• precisions_ : MzDataHandler
• precursor : TransitionTSVReader::TSVTransition
• precursor_ : ChromatogramSettings
• precursor_adduct_ : SpectralMatch
• precursor_charge : SpectrumMetaDataLookup::SpectrumMetaData , TransitionTSVReader::TSVTransition
• precursor_charge_ : SvmTheoreticalSpectrumGenerator
• precursor_chromatogram_map_ : MRMTransitionGroup< ChromatogramType, TransitionType >
• precursor_chromatograms_ : MRMTransitionGroup< ChromatogramType, TransitionType >
• precursor_cv_terms_ : IncludeExcludeTarget , ReactionMonitoringTransition
• precursor_feature_map_ : MRMFeature
• precursor_features_ : MRMFeature , MRMFeatureOpenMS
• precursor_isolation_target : ChromatogramMeta
• precursor_lower_mz_ : XTandemInfile
• precursor_mass : OPXLDataStructs::XLPrecursor
• precursor_mass_error_unit_ : XTandemInfile
• precursor_mass_tolerance : ProteinIdentification::SearchParameters
• precursor_mass_tolerance_ : BinnedSharedPeakCount , BinnedSpectralContrastAngle , BinnedSumAgreeingIntensities , CompNovoIdentificationCID , InspectInfile , MascotInfile , SequestInfile
• precursor_mass_tolerance_minus_ : XTandemInfile
• precursor_mass_tolerance_plus_ : XTandemInfile
• precursor_mass_tolerance_ppm : ProteinIdentification::SearchParameters
• precursor_mass_type_ : XTandemInfile
• precursor_mz : SpectrumMetaDataLookup::SpectrumMetaData , LightTransition
• precursor_mz_ : IncludeExcludeTarget , ReactionMonitoringTransition
• precursor_mz_error_ : MetaboliteSpectralMatching
• precursor_rt : SpectrumMetaDataLookup::SpectrumMetaData
• precursor_statistics_ : SpectrumAnnotator
• precursor_tolerance : MzIdentMLDOMHandler::SpectrumIdentificationProtocol
• precursor_tolerance_ : ProteinIdentificationVisualizer
• precursorCHRG : MS2Fragment
• precursorMass : MSPeak
• precursorMZ : MS2ConsensusSpectrum , MS2Fragment , MSPeak
• precursors_ : SpectrumSettings
• precursorScan : IsobaricChannelExtractor::PuritySate_
• prediction_ : IncludeExcludeTarget , ReactionMonitoringTransition
• predictor_names_ : SimpleSVM
• prefix : FuzzyStringComparator::PrefixInfo_ , LogStreamBuf::StreamStruct
• prefix_ : PeptideIndexing
• prefix_whitespaces : FuzzyStringComparator::PrefixInfo_
• preprocessing_tech : LPWrapper::SolverParam
• pressure_ : HPLC
• PREV_AA : MS2Info
• previous_rt_ : MSDataAggregatingConsumer
• previous_seq_ : XTandemXMLFile
• primary_id_ : SpectralMatch
• print_duplicate_references_ : SequestInfile
• pro_id_ : MzIdentMLDOMHandler , MzIdentMLHandler
• probabilities : SimpleSVM::Prediction
• probabilities_ : PSProteinInference
• probability : ProteinIdentification::ProteinGroup
• proc : TOPPASScene::TOPPProcess
• process : TOPPViewBase
• processing_ : MzMLHandler
• processing_actions_ : DataProcessing
• prod_ : IsotopeWaveletTransform< PeakType >
• product : TransitionTSVReader::TSVTransition
• product_ : ChromatogramSettings , ReactionMonitoringTransition
• product_cv_terms_ : IncludeExcludeTarget
• product_isolation_target : ChromatogramMeta
• product_mz : LightTransition
• product_mz_ : IncludeExcludeTarget , ProductVisualizer
• product_window_low_ : ProductVisualizer
• product_window_up_ : ProductVisualizer
• products_ : SpectrumSettings
• profileIntensities_ : RawData
• profileMasses_ : RawData
• progress_ : ConsensusXMLFile , FeatureGroupingAlgorithmKD , QcMLFile
• progress_counter_ : FeatureFinderAlgorithmIsotopeWavelet
• projection_box_ : Spectrum2DWidget
• projection_horz_ : Spectrum2DWidget
• projection_max_ : Spectrum2DWidget
• projection_mz_ : Spectrum2DCanvas
• projection_peaks_ : Spectrum2DWidget
• projection_rt_ : Spectrum2DCanvas
• projection_sum_ : Spectrum2DWidget
• projection_vert_ : Spectrum2DWidget
• projections_2d_ : TOPPViewBase
• projections_auto_ : Spectrum2DWidget
• projections_timer_ : Spectrum2DWidget
• properties_B_ : GridBasedCluster
• property_A_ : GridBasedCluster
• 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
• protein_abundance_assay : MzTabProteinSectionRow
• protein_abundance_std_error_study_variable : MzTabProteinSectionRow
• protein_abundance_stdev_study_variable : MzTabProteinSectionRow
• protein_abundance_study_variable : MzTabProteinSectionRow
• protein_coverage : MzTabProteinSectionRow
• protein_data_ : MzTab , ProteinResolver
• protein_entries : ProteinResolver::ResolverResult
• protein_group_ : ProtXMLFile
• protein_groups_ : ProteinIdentification
• protein_hits_ : ProteinIdentification , XTandemXMLFile
• protein_identification_ : MascotXMLHandler , XTandemXMLFile
• protein_identifications_ : ConsensusMap , ExperimentalSettings , FeatureMap
• protein_mass_filter_ : SequestInfile
• 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
• proteinhit_accession_ : ProteinHitVisualizer
• proteinhit_rank_ : ProteinHitVisualizer
• proteinhit_score_ : ProteinHitVisualizer
• proteinhit_sequence_ : ProteinHitVisualizer
• proteinid_to_accession_ : ConsensusXMLFile , FeatureXMLFile , IdXMLFile
• ProteinName : TransitionTSVReader::TSVTransition
• proteins : ProteinResolver::ISDGroup , ProteinResolver::MSDGroup , ProteinResolver::PeptideEntry , LightTargetedExperiment , TargetedExperiment
• proteins_ : PepXMLFile , TargetedExperiment
• PScoreAlpha : OPXLDataStructs::CrossLinkSpectrumMatch
• PScoreBeta : OPXLDataStructs::CrossLinkSpectrumMatch
• PScoreBoth : OPXLDataStructs::CrossLinkSpectrumMatch
• PScoreCommon : OPXLDataStructs::CrossLinkSpectrumMatch
• PScoreXlink : OPXLDataStructs::CrossLinkSpectrumMatch
• pseudo_counts_ : HiddenMarkovModel
• psi_ : IsotopeWaveletTransform< PeakType >
• psi_id_ : Enzyme
• psi_mod_accession_ : ResidueModification
• psm_data_ : MzTab
• PSM_ID : MzTabPSMSectionRow
• psm_search_engine_score : MzTabMetaData
• pt_prot_map_ : PrecursorIonSelectionPreprocessing
• ptm_file_ : PepNovoInfile
• ptm_informations_ : PTMXMLHandler
• PTMname_residues_mass_type_ : InspectInfile , SequestInfile
• ptr_ : BaseVisualizer< ObjectType >
• pubchemids : CsiFingerIdMzTabWriter::CsiAdapterHit
• publication : MzTabMetaData
• publications_ : TargetedExperiment
• pv_db_map_ : MzIdentMLDOMHandler
• pw_filtering_ : ElutionPeakDetection