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p :
GammaDistributionFitter::GammaDistributionFitResult
p_ :
ToolDescriptionHandler
,
PILISIdentification
p_cleave :
EnzymaticDigestion::CleavageModel
p_miss :
EnzymaticDigestion::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
,
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
parsing_success_ :
IndexedMzMLFile
partial_sequence_ :
SequestInfile
pass_threshold_ :
IdentificationHit
path :
ToolExternalDetails
path_ :
ParamXMLHandler
path_to_file_ :
SourceFile
,
SourceFileVisualizer
pattern_tolerance_ :
FeatureFinderAlgorithmPicked
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< MapType >
,
MzXMLHandler< MapType >::SpectrumData
peak_depth :
ProbablePhosphoSites
peak_map_ :
MSSim
,
SpectrumCheapDPCorr
peak_mass_tolerance :
ProteinIdentification::SearchParameters
peak_mass_tolerance_ :
InspectInfile
,
SequestInfile
peak_penstyle_ :
Spectrum1DCanvas
peak_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
,
PILISModel
peaks_per_peptide_ :
MultiplexPeakPattern
peaks_per_peptide_max_ :
MultiplexFiltering
peaks_per_peptide_min_ :
MultiplexFiltering
pen_ :
Annotations1DContainer
pen_color_ :
TOPPASVertex
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_map_ :
MzIdentMLDOMHandler
PEP_PROB :
MS2Info
pep_quant_ :
PeptideAndProteinQuant
pep_sequences_ :
MzIdentMLHandler
pep_to_prot :
FoundProteinFunctor
peptide :
RNPxlReportRow
peptide_ :
AASequence
peptide_abundance_assay :
MzTabPeptideSectionRow
peptide_abundance_std_error_study_variable :
MzTabPeptideSectionRow
peptide_abundance_stdev_study_variable :
MzTabPeptideSectionRow
peptide_abundance_study_variable :
MzTabPeptideSectionRow
peptide_data_ :
MzTab
peptide_entries :
ProteinResolver::ResolverResult
peptide_evidences_ :
ConsensusXMLFile
,
IdXMLFile
,
PeptideHit
peptide_group_label :
TransitionTSVReader::TSVTransition
,
LightPeptide
peptide_group_label_ :
Peptide
peptide_hit :
ProteinResolver::PeptideEntry
peptide_hit_ :
PepXMLFile
peptide_hits_ :
XTandemXMLFile
peptide_identification :
ProteinResolver::PeptideEntry
,
ProteinResolver::ResolverResult
peptide_identification_index_ :
MascotXMLHandler
peptide_identifications_ :
OMSSAXMLFile
peptide_intensities_ :
IsobaricNormalizer
peptide_mass_unit_ :
SequestInfile
peptide_quantification_unit :
MzTabMetaData
peptide_ratios_ :
IsobaricNormalizer
peptide_ref :
LightTransition
peptide_ref_ :
IncludeExcludeTarget
,
ReactionMonitoringTransition
peptide_reference_map_ :
TargetedExperiment
,
LightTargetedExperiment
peptide_reference_map_dirty_ :
TargetedExperiment
,
LightTargetedExperiment
peptide_search_engine_score :
MzTabMetaData
peptide_similarity_ :
MultiplexFiltering
peptide_weight :
RNPxlReportRow
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
,
LightTargetedExperiment
,
Protein
peptides_ :
BaseFeature
,
PepXMLFile
,
PepXMLFileMascot
,
TargetedExperiment
PeptideSequence :
TransitionTSVReader::TSVTransition
percentage_ :
GradientVisualizer
percentage_factor_ :
SpectrumCanvas
percentageIntensityElutionBorderVariation_ :
SuperHirnParameters
percentages_ :
Gradient
permut_ :
CompNovoIdentificationBase::Permut
permute_cache_ :
CompNovoIdentificationBase
pg_scores_ :
MRMFeature
ph_ :
Digestion
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
,
EnzymaticDigestion::BindingSite
,
MzTabModificationMetaData
,
PeptideProteinMatchInformation
position_ :
AASequence::ConstIterator
,
AASequence::Iterator
,
Annotation1DCaret
,
Annotation1DPeakItem
,
Annotation1DTextItem
,
ChromatogramPeak
,
ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
,
AveragePosition< D >
,
Peak1D
,
Peak2D
,
SparseVector< Value >::SparseVectorConstIterator
,
SparseVector< Value >::SparseVectorConstReverseIterator
,
SparseVector< Value >::SparseVectorIterator
,
SparseVector< Value >::SparseVectorReverseIterator
position_weighted_sum_ :
AveragePosition< D >
positions :
OptimizePeakDeconvolution::Data
,
OptimizePick::Data
,
TwoDOptimization::Data
possible_charge_states_ :
Precursor
post :
MzIdentMLDOMHandler::PeptideEvidence
,
MzTabPSMSectionRow
post_moves :
MappingParam
potential_adducts_ :
FeatureDeconvolution
potential_target_ :
TOPPASScene
ppm :
OpenSwathWorkflow::ChromExtractParams
ppm_tolerance_ :
GaussFilterAlgorithm
ppmToleranceForMZClustering_ :
SuperHirnParameters
pre :
MzIdentMLDOMHandler::PeptideEvidence
,
MzTabPSMSectionRow
pre_ :
MultiGradient
pre_min_ :
MultiGradient
pre_mod_name_ :
Residue
pre_moves :
MappingParam
pre_scorer_ :
PILISIdentification
pre_size_ :
MultiGradient
pre_states_ :
HMMState
pre_steps_ :
MultiGradient
precision :
MzMLHandlerHelper::BinaryData
precision_ :
RealMassDecomposer
,
Weights
,
MzXMLHandler< MapType >::SpectrumData
precisions_ :
MzDataHandler< MapType >
precursor :
TransitionTSVReader::TSVTransition
precursor_ :
ChromatogramSettings
precursor_adduct_ :
SpectralMatch
precursor_charge :
TransitionTSVReader::TSVTransition
precursor_charge_ :
SvmTheoreticalSpectrumGenerator
precursor_chromatogram_map_ :
MRMTransitionGroup< SpectrumType, TransitionType >
precursor_chromatograms_ :
MRMTransitionGroup< SpectrumType, TransitionType >
precursor_cv_terms_ :
IncludeExcludeTarget
,
ReactionMonitoringTransition
precursor_feature_map_ :
MRMFeature
precursor_features_ :
MRMFeature
,
MRMFeatureOpenMS
precursor_isolation_target :
ChromatogramMeta
precursor_lower_mz_ :
XTandemInfile
precursor_mass_error_unit_ :
XTandemInfile
precursor_mass_tolerance_ :
BinnedSharedPeakCount
,
BinnedSpectralContrastAngle
,
BinnedSumAgreeingIntensities
,
CompNovoIdentificationCID
,
InspectInfile
,
MascotInfile
,
SequestInfile
precursor_mass_tolerance_minus_ :
XTandemInfile
precursor_mass_tolerance_plus_ :
XTandemInfile
precursor_mass_type_ :
XTandemInfile
precursor_model_cd_ :
PILISModel
precursor_model_cr_ :
PILISModel
precursor_mz :
LightTransition
precursor_mz_ :
IncludeExcludeTarget
,
ReactionMonitoringTransition
precursor_mz_error_ :
MetaboliteSpectralMatching
precursor_tolerance :
MzIdentMLDOMHandler::SpectrumIdentificationProtocol
,
ProteinIdentification::SearchParameters
precursor_tolerance_ :
ProteinIdentificationVisualizer
precursorCHRG :
MS2Fragment
precursorMass :
MSPeak
precursorMZ :
MS2ConsensusSpectrum
,
MS2Fragment
,
MSPeak
precursors_ :
SpectrumSettings
precursorScan :
IsobaricChannelExtractor::PuritySate_
prediction_ :
IncludeExcludeTarget
,
ReactionMonitoringTransition
prefix :
FuzzyStringComparator::PrefixInfo_
,
LogStreamBuf::StreamStruct
prefix_whitespaces :
FuzzyStringComparator::PrefixInfo_
preprocessing_tech :
LPWrapper::SolverParam
pressure_ :
HPLC
PREV_AA :
MS2Info
primary_id_ :
SpectralMatch
primary_scan_regex :
MascotXMLHandler
print_duplicate_references_ :
SequestInfile
pro_id_ :
MzIdentMLDOMHandler
,
MzIdentMLHandler
probabilities_ :
PSProteinInference
probability :
ProteinIdentification::ProteinGroup
proc :
TOPPASScene::TOPPProcess
process :
TOPPViewBase
processing_ :
MzMLHandler< MapType >
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
,
QcMLFile
,
SuffixArrayTrypticCompressed
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_dist_ :
PILISModel
prot_hit_ :
ConsensusXMLFile
,
FeatureXMLFile
,
IdXMLFile
prot_id_ :
ConsensusXMLFile
,
FeatureXMLFile
,
IdXMLFile
,
PepXMLFile
,
ProtXMLFile
prot_id_counter_ :
PrecursorIonSelection
prot_id_in_run_ :
IdXMLFile
prot_ids_ :
IdXMLFile
prot_masses_ :
PrecursorIonSelectionPreprocessing
prot_peptide_seq_map_ :
PrecursorIonSelectionPreprocessing
prot_quant_ :
PeptideAndProteinQuant
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_index :
PeptideProteinMatchInformation
protein_mass_filter_ :
SequestInfile
protein_name_length_ :
InspectOutfile
protein_open_ :
XTandemXMLFile
protein_quantification_unit :
MzTabMetaData
protein_reference_map_ :
TargetedExperiment
protein_reference_map_dirty_ :
TargetedExperiment
protein_refs :
Peptide
,
LightPeptide
protein_score_type_ :
ProteinIdentification
protein_search_engine_score :
MzTabMetaData
protein_significance_threshold_ :
ProteinIdentification
protein_type :
ProteinResolver::ProteinEntry
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
pscf_ :
PILISCrossValidation
pseudo_counts_ :
HiddenMarkovModel
psi_ :
IsotopeWaveletTransform< PeakType >
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 >
publication :
MzTabMetaData
publications_ :
TargetedExperiment
pv_db_map_ :
MzIdentMLDOMHandler
pw_filtering_ :
ElutionPeakDetection
OpenMS / TOPP release 2.0.0
Documentation generated on Sat May 16 2015 16:15:42 using doxygen 1.8.9.1