OpenMS Namespace Reference

Main OpenMS namespace. More...

Namespaces
	Constants
	Mathematical and physical constants namespace.
	DataArrays
	detail
	Detail
	DIAHelpers
	Exception
	Exception namespace
	FastLowessSmoothing
	LOWESS (locally weighted scatterplot smoothing).
	GUIHelpers
	Helpers
	IdentificationDataInternal
	ims
	Interfaces
	Internal
	Namespace used to hide implementation details from users.
	Logger
	Log streams.
	Math
	Math namespace.
	NNLS
	OptimizationFunctions
	SiriusVersion
	StringConversions
	StringUtils
	TargetedExperimentHelper
	This class stores helper structures that are used in multiple classes of the TargetedExperiment (e.g. ReactionMonitoringTransition and IncludeExcludeTarget).
	Test

Classes
class	FeatureDeconvolution
	An algorithm to decharge features (i.e. as found by FeatureFinder). More...
class	ILPDCWrapper
class	MetaboliteFeatureDeconvolution
	An algorithm to decharge small molecule features (i.e. as found by FeatureFinder). More...
class	AccurateMassSearchResult
class	AccurateMassSearchEngine
	An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB). More...
struct	Hit
struct	AA
class	Index
struct	ACNode
struct	ACSpawn
	a spin-off search path through the trie, which can deal with ambiguous AAs and mismatches More...
struct	ACTrieState
class	ACTrie
	An Aho Corasick trie (a set of nodes with suffix links mainly) More...
class	ProbablePhosphoSites
class	AScore
	Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the most probable phosphorylation-site(s). For each phosphorylation site a probability score is calculated. The algorithm is implemented according to Beausoleil et al. (Nat. Biotechnol. 2006). More...
class	BasicProteinInferenceAlgorithm
	Algorithm class that implements simple protein inference by aggregation of peptide scores. It has multiple parameter options like the aggregation method, when to distinguish peptidoforms, and if you want to use shared peptides ("use_shared_peptides"). First, the best PSM per spectrum is used, then only the best PSM per peptidoform is aggregated. Peptidoforms can optionally be distinguished via the treat_X_separate parameters: More...
class	BayesianProteinInferenceAlgorithm
	Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental). More...
class	ConsensusIDAlgorithm
	Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs). More...
class	ConsensusIDAlgorithmAverage
	Calculates a consensus from multiple ID runs by averaging the search scores. More...
class	ConsensusIDAlgorithmBest
	Calculates a consensus from multiple ID runs by taking the best search score. More...
class	ConsensusIDAlgorithmIdentity
	Abstract base class for ConsensusID algorithms that compare only identical sequences. More...
class	ConsensusIDAlgorithmPEPIons
	Calculates a consensus from multiple ID runs based on PEPs and shared ions. More...
class	ConsensusIDAlgorithmPEPMatrix
	Calculates a consensus from multiple ID runs based on PEPs and sequence similarities. More...
class	ConsensusIDAlgorithmRanks
	Calculates a consensus from multiple ID runs based on the ranks of the search hits. More...
class	ConsensusIDAlgorithmSimilarity
	Abstract base class for ConsensusID algorithms that take peptide similarity into account. More...
class	ConsensusIDAlgorithmWorst
	Calculates a consensus from multiple ID runs by taking the worst search score (conservative approach). More...
class	ConsensusMapMergerAlgorithm
	Merges identification data in ConsensusMaps. More...
class	FalseDiscoveryRate
	Calculates false discovery rates (FDR) from identifications. More...
class	FIAMSDataProcessor
	Data processing for FIA-MS data. More...
class	FIAMSScheduler
class	HMMState
	Hidden Markov Model State class for the Hidden Markov Model. More...
class	HiddenMarkovModel
	Hidden Markov Model implementation of PILIS. More...
class	IDConflictResolverAlgorithm
	Resolves ambiguous annotations of features with peptide identifications. More...
class	IDDecoyProbability
	IDDecoyProbability calculates probabilities using decoy approach. More...
class	IDMapper
	Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications. More...
class	IDMergerAlgorithm
	Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but concatenates PSMs. Checks search engine consistency of all inserted runs. It differs from the IDMerger tool, in that it is an algorithm class and it allows inserting multiple peptide hits per peptide sequence (not only the first occurrence). More...
class	IDRipper
	Ripping protein/peptide identification according their file origin. More...
struct	ScoreToTgtDecLabelPairs
class	IDScoreGetterSetter
	A class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps. More...
class	IDScoreSwitcherAlgorithm
class	IonIdentityMolecularNetworking
struct	PrecursorMassComparator
class	SpectralMatch
struct	SpectralMatchScoreComparator
class	MetaboliteSpectralMatching
class	PeptideIndexing
	Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds target/decoy information. More...
struct	ConnectedComponent
class	PeptideProteinResolution
	Resolves shared peptides based on protein scores. More...
class	PercolatorFeatureSetHelper
	Percolator feature set and integration helper. More...
class	PrecursorPurity
	Precursor purity or noise estimation. More...
class	ProtonDistributionModel
	A proton distribution model to calculate the proton distribution over charged peptides. More...
class	SimpleSearchEngineAlgorithm
class	SiriusAdapterAlgorithm
class	SiriusMSFile
class	BaseGroupFinder
	The base class of all element group finding algorithms. More...
class	BaseSuperimposer
	The base class of all superimposer algorithms. More...
class	ConsensusMapNormalizerAlgorithmMedian
	Algorithms of ConsensusMapNormalizer. More...
class	ConsensusMapNormalizerAlgorithmQuantile
	Algorithms of ConsensusMapNormalizer. More...
class	ConsensusMapNormalizerAlgorithmThreshold
	Algorithms of ConsensusMapNormalizer. More...
class	FeatureDistance
	A functor class for the calculation of distances between features or consensus features. More...
class	FeatureGroupingAlgorithm
	Base class for all feature grouping algorithms. More...
class	ClusterProxyKD
	Proxy for a (potential) cluster. More...
class	FeatureGroupingAlgorithmKD
	A feature grouping algorithm for unlabeled data. More...
class	FeatureGroupingAlgorithmLabeled
	A map feature grouping algorithm for labeling techniques with two labels. More...
class	FeatureGroupingAlgorithmQT
	A feature grouping algorithm for unlabeled data. More...
class	FeatureGroupingAlgorithmUnlabeled
	A map feature grouping algorithm for unlabeled data. More...
class	FeatureMapping
class	LabeledPairFinder
	The LabeledPairFinder allows the matching of labeled features (features with a fixed distance). More...
class	MapAlignmentAlgorithmIdentification
	A map alignment algorithm based on peptide identifications from MS2 spectra. More...
class	MapAlignmentAlgorithmKD
	An efficient reference-free feature map alignment algorithm for unlabeled data. More...
class	MapAlignmentAlgorithmPoseClustering
	A map alignment algorithm based on pose clustering. More...
class	MapAlignmentAlgorithmSpectrumAlignment
	A map alignment algorithm based on spectrum similarity (dynamic programming). More...
class	MapAlignmentAlgorithmTreeGuided
	A map alignment algorithm based on peptide identifications from MS2 spectra. More...
class	MapAlignmentEvaluationAlgorithm
	Base class for all Caap evaluation algorithms. More...
class	MapAlignmentEvaluationAlgorithmPrecision
	Caap evaluation algorithm to obtain a precision value. More...
class	MapAlignmentEvaluationAlgorithmRecall
	Caap evaluation algorithm to obtain a recall value. More...
class	MapAlignmentTransformer
	This class collects functions for applying retention time transformations to data structures. More...
class	PoseClusteringAffineSuperimposer
	A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation. More...
class	PoseClusteringShiftSuperimposer
	A superimposer that uses a voting scheme, also known as pose clustering, to find a good shift transformation. More...
class	QTClusterFinder
	A variant of QT clustering for the detection of feature groups. More...
class	SimplePairFinder
	This class implements a simple point pair finding algorithm. More...
class	StablePairFinder
	This class implements a pair finding algorithm for consensus features. More...
class	TransformationDescription
	Generic description of a coordinate transformation. More...
class	TransformationModel
	Base class for transformation models. More...
class	TransformationModelBSpline
	B-spline (non-linear) model for transformations. More...
class	TransformationModelInterpolated
	Interpolation model for transformations. More...
class	TransformationModelLinear
	Linear model for transformations. More...
class	TransformationModelLowess
	Lowess (non-linear) model for transformations. More...
class	MRMFragmentSelection
	This class can select appropriate fragment ions of an MS/MS spectrum of a peptide. More...
class	ReactionMonitoringTransition
	This class stores a SRM/MRM transition. More...
class	ChromatogramExtractor
	The ChromatogramExtractor extracts chromatograms from a spectra file. More...
class	ChromatogramExtractorAlgorithm
	The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data. More...
class	ConfidenceScoring
class	OpenSwathDataAccessHelper
	Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces. More...
class	FeatureOpenMS
	An implementation of the OpenSWATH Feature Access interface using OpenMS. More...
class	MRMFeatureOpenMS
	An implementation of the OpenSWATH MRM Feature Access interface using OpenMS. More...
class	TransitionGroupOpenMS
	An implementation of the OpenSWATH Transition Group Access interface using OpenMS. More...
class	SignalToNoiseOpenMS
	An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS. More...
class	SimpleOpenMSSpectraFactory
	A factory method that returns two ISpectrumAccess implementations. More...
class	SpectrumAccessOpenMS
	An implementation of the OpenSWATH Spectrum Access interface using OpenMS. More...
class	SpectrumAccessOpenMSCached
	An implementation of the Spectrum Access interface using on-disk caching. More...
class	SpectrumAccessOpenMSInMemory
	An implementation of the OpenSWATH Spectrum Access interface completely in memory. More...
class	SpectrumAccessQuadMZTransforming
	A transforming m/z wrapper around spectrum access using a quadratic equation. More...
class	SpectrumAccessSqMass
	An implementation of the Spectrum Access interface using SQL files. More...
class	SpectrumAccessTransforming
	An abstract base class implementing a transforming wrapper around spectrum access. More...
class	DiaPrescore
	Scoring of an spectrum given library intensities of a transition group. More...
class	DIAScoring
	Scoring of an spectrum at the peak apex of an chromatographic elution peak. More...
class	IonMobilityScoring
	A class that calls the ion mobility scoring routines. More...
class	MasstraceCorrelator
	Correlates individual masstraces found in mass spectrometric maps. More...
class	MRMAssay
	Generate assays from a TargetedExperiment. More...
class	MRMBatchFeatureSelector
class	MRMDecoy
	This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object. More...
class	MRMFeatureFilter
	The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria. More...
class	MRMFeatureFinderScoring
	The MRMFeatureFinder finds and scores peaks of transitions that co-elute. More...
class	MRMFeaturePicker
	_MRMFeaturePicker_ defines the structures containing parameters to be used in [MRMTransitionGroupPicker](MRMTransitionGroupPicker) for components and components groups. More...
class	MRMFeatureQC
	The MRMFeatureQC is a class to handle the parameters and options for MRMFeatureFilter. More...
class	MRMFeatureSelector
class	MRMFeatureSelectorQMIP
class	MRMFeatureSelectorScore
class	MRMFeatureSelector_test
class	MRMIonSeries
	Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy. More...
class	MRMRTNormalizer
	The MRMRTNormalizer will find retention time peptides in data. More...
class	MRMTransitionGroupPicker
	The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors. More...
class	OpenSwathHelper
	A helper class that is used by several OpenSWATH tools. More...
class	OpenSwathOSWWriter
	Class to write out an OpenSwath OSW SQLite output (PyProphet input). More...
struct	OpenSwath_Scores_Usage
	A structure to store which scores should be used by the OpenSWATH Algorithm. More...
struct	OpenSwath_Scores
	A structure to hold the different scores computed by OpenSWATH. More...
struct	OpenSwath_Ind_Scores
class	OpenSwathScoring
	A class that calls the scoring routines. More...
class	OpenSwathTSVWriter
	Class to write out an OpenSwath TSV output (mProphet input). More...
struct	ChromExtractParams
	ChromatogramExtractor parameters. More...
class	OpenSwathWorkflowBase
class	OpenSwathCalibrationWorkflow
	Execute all steps for retention time and m/z calibration of SWATH-MS data. More...
class	OpenSwathWorkflow
	Execute all steps in an OpenSwath analysis. More...
class	OpenSwathWorkflowSonar
	Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data) More...
class	PeakIntegrator
	Compute the area, background and shape metrics of a peak. More...
class	PeakPickerMRM
	The PeakPickerMRM finds peaks a single chromatogram. More...
class	SONARScoring
	Scoring of an spectrum using SONAR data. More...
class	SpectrumAddition
	The SpectrumAddition is used to add up individual spectra. More...
class	SwathMapMassCorrection
	A class containing correction functions for Swath MS maps. More...
class	SwathWindowLoader
	Class to read a file describing the Swath Windows. More...
class	TargetedSpectraExtractor
	This class filters, annotates, picks, and scores spectra (e.g., taken from a DDA experiment) based on a target list. More...
class	TransitionPQPFile
	This class supports reading and writing of PQP files. More...
class	TransitionTSVFile
	This class supports reading and writing of OpenSWATH transition lists. More...
class	AbsoluteQuantitation
	AbsoluteQuantitation is a class to support absolute or relative quantitation for targeted or untargeted quantitation workflows (e.g., Isotope Dilution Mass Spectrometry). More...
class	AbsoluteQuantitationMethod
	AbsoluteQuantitationMethod is a class to hold information about the quantitation method and for applying and/or generating the quantitation method. More...
class	IsobaricChannelExtractor
	Extracts individual channels from MS/MS spectra for isobaric labeling experiments. More...
class	IsobaricIsotopeCorrector
	Performs isotope impurity correction on the intensities extracted from an isobaric labeling experiment. More...
class	IsobaricNormalizer
	Performs median normalization on the extracted ratios of isobaric labeling experiment. More...
class	IsobaricQuantifier
	Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing. More...
class	IsobaricQuantifierStatistics
	Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion) More...
class	Matrix
	A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access. More...
class	IsobaricQuantitationMethod
	Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix. More...
class	IsotopeLabelingMDVs
	IsotopeLabelingMDVs is a class to support and analyze isotopic labeling experiments (i.e. MDVs : Mass Distribution Vectors, also known as Mass Isotopomer Distribution (MID)) More...
class	ItraqConstants
	Some constants used throughout iTRAQ classes. More...
class	ItraqEightPlexQuantitationMethod
	iTRAQ 8 plex quantitation to be used with the IsobaricQuantitation. More...
class	ItraqFourPlexQuantitationMethod
	iTRAQ 4 plex quantitation to be used with the IsobaricQuantitation. More...
class	KDTreeFeatureMaps
	Stores a set of features, together with a 2D tree for fast search. More...
class	KDTreeFeatureNode
	A node of the kD-tree with pointer to corresponding data and index. More...
class	PeptideAndProteinQuant
	Helper class for peptide and protein quantification based on feature data annotated with IDs. More...
class	ProteinInference
	[experimental class] given a peptide quantitation, infer corresponding protein quantities More...
class	ProteinResolver
	Helper class for peptide and protein quantification based on feature data annotated with IDs. More...
class	QuantitativeExperimentalDesign
	Merge files according to experimental design. More...
class	TMTEighteenPlexQuantitationMethod
	TMT 18plex quantitation to be used with the IsobaricQuantitation. More...
class	TMTElevenPlexQuantitationMethod
	TMT 11plex quantitation to be used with the IsobaricQuantitation. More...
class	TMTSixPlexQuantitationMethod
	TMT 6plex quantitation to be used with the IsobaricQuantitation. More...
class	TMTSixteenPlexQuantitationMethod
	TMT 16plex quantitation to be used with the IsobaricQuantitation. More...
class	TMTTenPlexQuantitationMethod
	TMT 10plex quantitation to be used with the IsobaricQuantitation. More...
struct	HyperScore
	An implementation of the X!Tandem HyperScore PSM scoring function. More...
struct	MorpheusScore
	An implementation of the Morpheus PSM scoring function Inspired by a C# implementation by C. Wenger released under MIT license. More...
struct	PScore
	Implementation of the PScore PSM scoring algorithm. More...
struct	RNPxlMarkerIonExtractor
struct	RNPxlModificationMassesResult
class	RNPxlModificationsGenerator
struct	RNPxlReportRow
	struct to hold a single report line More...
struct	RNPxlReportRowHeader
	create header line More...
struct	RNPxlReport
	create report More...
class	NeedlemanWunsch
	This class contains functions that are used to calculate the global alignment score of two amino acid sequences. This class uses the Needleman-Wunsch algorithm. For match and mismatch it uses a similarity scoring matrix. More...
class	SimpleSVM
	Simple interface to support vector machines for classification and regression (via LIBSVM). More...
class	IncludeExcludeTarget
	This class stores a SRM/MRM transition. More...
class	MetaboTargetedAssay
	This class provides methods for the extraction of targeted assays for metabolomics. More...
class	MetaboTargetedTargetDecoy
	Resolve overlapping fragments and missing decoys for experimental specific decoy generation in targeted/pseudo targeted metabolomics. More...
class	MRMMapping
	A class to map targeted assays to chromatograms. More...
class	OfflinePrecursorIonSelection
	Implements different algorithms for precursor ion selection. More...
class	PSProteinInference
	This class implements protein inference for the precursor ion selection strategies. More...
class	TargetedExperiment
	A description of a targeted experiment containing precursor and production ions. More...
class	DeconvolvedSpectrum
	A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroups representing masses. For MSn n>1, a PeakGroup representing the precursor mass is also added in this class. Properly assigning a precursor mass from the original precursor peak and its deconvolution result is very important in top down proteomics. This assignment is performed here for conventional datasets. But for FLASHIda acquired datasets, the assignment is already done by FLASHIda. So this class simply use the results from FLASHIda log file for assignment. The parsing of FLASHIda log file is done in FLASHDeconv tool class. More...
class	FLASHDeconvAlgorithm
	FLASHDeconv algorithm: ultrafast mass deconvolution algorithm for top down mass spectrometry dataset From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps: i) decharging and select candidate masses - speed up via binning ii) collecting isotopes from the candidate masses and deisotope - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups) More...
struct	FLASHDeconvHelperStructs
	Wrapper struct for all the structs needed by the FLASHDeconv Three structures are defined: PrecalculatedAveragine, TopPicItem, and LogMzPeak i) PrecalculatedAveragine - to match observed isotopic envelope against theoretical one, theoretical envelope from averagine model should be quickly calculated. To do so, precalculate averagines for different masses at the beginning of FLASHDeconv runs ii) TopPicItem - represent TopPic identification. Currently used for Qscore training. TopPic is the top-down proteomics identification tool (https://www.toppic.org/). iii) LogMzPeak - Log transformed peak from original peak. Contains information such as charge, isotope index, and uncharged mass. More...
class	MassFeatureTrace
	Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by FLASHDeconvAlgorithm In other words, per spectrum deconvolved masses are converted into deconvolved features Currently only works for MS1 spectra. (Top-down DIA is not yet used much). Every time an MS1 spectrum is deconvolved, the relevant information is stored in this class. Tracing is performed at the end of FLASHDeconv run. This class also comes with tsv, TopFD, ProMex format output functions. More...
class	PeakGroup
	Class describing a deconvolved mass. A mass contains multiple (LogMz) peaks of different charges and isotope indices. PeakGroup is the set of such peaks representing a single monoisotopic mass. PeakGroup also contains features that define the quality of it. It is used by Qscore calculation. DeconvolvedSpectrum consists of PeakGroups. More...
class	Qscore
	Qscore : quality score for PeakGroup. This class is being updated. For now, simply it calculate the Qscore using a fixed weight vector. The weight vector has been determined by logistic regression. But afterwards, the training part for the Qscore should be added in here. Or other technique such as deep learning would be used. This class also contains tsv output function. The tsv file contains features of PeakGroups which are used for training. More...
class	Qvalue
	Qvalue : contains functions to calculate Qvalues from deconvolution quality score. More...
class	OpenPepXLAlgorithm
	Search for peptide pairs linked with a labeled cross-linker. More...
class	OpenPepXLLFAlgorithm
	Search for cross-linked peptide pairs in tandem MS spectra. More...
class	OPXLDataStructs
class	OPXLHelper
	The OPXLHelper class contains functions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code. More...
class	OPXLSpectrumProcessingAlgorithms
class	XFDRAlgorithm
	Calculates false discovery rate estimates on crosslink identifications. More...
class	XQuestScores
	An implementation of the scores for cross-link identification from the xQuest algorithm (O. Rinner et al., 2008, "Identification of cross-linked peptides from large sequence databases") More...
class	ConsoleUtils
class	INIUpdater
class	TOPPOpenSwathBase
struct	ParameterInformation
	Struct that captures all information of a command line parameter. More...
class	SearchEngineBase
	Base class for Search Engine Adapters. More...
class	ToolHandler
struct	Citation
	Stores Citations for individual TOPP tools. More...
class	TOPPBase
	Base class for TOPP applications. More...
class	AAIndex
	Representation of selected AAIndex properties. More...
class	AASequence
	Representation of a peptide/protein sequence. More...
class	AdductInfo
class	CrossLinksDB
class	DecoyGenerator
	Methods to generate isobaric decoy sequences for DDA target-decoy searches. More...
class	DigestionEnzyme
	Base class for digestion enzymes. More...
class	DigestionEnzymeDB
	Digestion enzyme database (base class) More...
class	DigestionEnzymeProtein
	Representation of a digestion enzyme for proteins (protease) More...
class	DigestionEnzymeRNA
	Representation of a digestion enzyme for RNA (RNase) More...
class	Element
	Representation of an element. More...
class	ElementDB
	Singleton that stores elements and isotopes. More...
class	EmpiricalFormula
	Representation of an empirical formula. More...
class	EnzymaticDigestion
	Class for the enzymatic digestion of sequences. More...
class	CoarseIsotopePatternGenerator
	Isotope pattern generator for coarse isotope distributions. More...
class	FineIsotopePatternGenerator
	Isotope pattern generator for fine isotope distributions. More...
class	IsoSpecGeneratorWrapper
	Interface for the IsoSpec algorithm - a generator of infinitely-resolved theoretical spectra. More...
class	IsoSpecWrapper
	A convenience class for the IsoSpec algorithm - easier to use than the IsoSpecGeneratorWrapper classes. More...
class	IsoSpecTotalProbGeneratorWrapper
	Generate a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99). More...
class	IsoSpecThresholdGeneratorWrapper
	Provides a threshold-based generator of isotopologues: generates all isotopologues more probable than a given probability threshold. More...
class	IsoSpecOrderedGeneratorWrapper
	Generate the stream of configurations, ordered from most likely to least likely. More...
class	IsoSpecTotalProbWrapper
	Create a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99). More...
class	IsoSpecThresholdWrapper
	A non-generator version of IsoSpecThresholdGeneratorWrapper. More...
class	IsotopeDistribution
class	IsotopePatternGenerator
	Provides an interface for different isotope pattern generator methods. More...
class	MassDecomposition
	Class represents a decomposition of a mass into amino acids. More...
class	MassDecompositionAlgorithm
	Mass decomposition algorithm, given a mass it suggests possible compositions. More...
class	ModificationDefinition
	Representation of modification definition. More...
class	ModificationDefinitionsSet
	Representation of a set of modification definitions. More...
class	ModificationsDB
	database which holds all residue modifications from UniMod More...
class	ModifiedNASequenceGenerator
class	ModifiedPeptideGenerator
class	NASequence
	Representation of a nucleic acid sequence. More...
class	NucleicAcidSpectrumGenerator
	Generates theoretical spectra for nucleic acid sequences. More...
class	ProteaseDB
	Database for enzymes that digest proteins (proteases) More...
class	ProteaseDigestion
	Class for the enzymatic digestion of proteins represented as AASequence or String. More...
class	Residue
	Representation of an amino acid residue. More...
class	ResidueDB
	OpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called. More...
class	ResidueModification
	Representation of a modification on an amino acid residue. More...
class	Ribonucleotide
	Representation of a ribonucleotide (modified or unmodified) More...
class	RibonucleotideDB
	Database of ribonucleotides (modified and unmodified) More...
class	RNaseDB
	Database for enzymes that digest RNA (RNases) More...
class	RNaseDigestion
	Class for the enzymatic digestion of RNAs. More...
class	SimpleTSGXLMS
	Generates theoretical spectra for cross-linked peptides. More...
class	SpectrumAnnotator
	Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options. More...
class	Tagger
	Calculate sequence tags from m/z values. More...
class	TheoreticalSpectrumGenerator
	Generates theoretical spectra for peptides with various options. More...
class	TheoreticalSpectrumGeneratorXLMS
	Generates theoretical spectra for cross-linked peptides. More...
class	WeightWrapper
	Encapsulated weight queries to simplify mono vs average weight computation. More...
class	AverageLinkage
	AverageLinkage ClusterMethod. More...
class	ClusterAnalyzer
	Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's) More...
class	ClusterFunctor
	Base class for cluster functors. More...
class	ClusterHierarchical
	Hierarchical clustering with generic clustering functions. More...
class	UnnormalizedComparator
	Exception thrown if clustering is attempted without a normalized compare functor. More...
class	ClusteringGrid
	data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering More...
class	CompleteLinkage
	CompleteLinkage ClusterMethod. More...
class	EuclideanSimilarity
	CompareFunctor for 2Dpoints. More...
class	GridBasedCluster
	basic data structure for clustering More...
class	MinimumDistance
	basic data structure for distances between clusters More...
class	GridBasedClustering
	2D hierarchical clustering implementation optimized for large data sets containing many small clusters i.e. dimensions of clusters << dimension of entire dataset More...
class	HashGrid
	Container for (2-dimensional coordinate, value) pairs. More...
class	SingleLinkage
	SingleLinkage ClusterMethod. More...
class	BinnedSharedPeakCount
	Compare functor scoring the shared peaks for similarity measurement. More...
class	BinnedSpectralContrastAngle
	Compare functor scoring the spectral contrast angle for similarity measurement. More...
class	BinnedSpectrum
	This is a binned representation of a PeakSpectrum. More...
class	BinnedSpectrumCompareFunctor
	Base class for compare functors of BinnedSpectra. More...
class	BinnedSumAgreeingIntensities
	Sum of agreeing intensities for similarity measurement. More...
class	PeakAlignment
	make a PeakAlignment of two PeakSpectra More...
class	PeakSpectrumCompareFunctor
	Base class for compare functors of spectra, that return a similarity value for two spectra. More...
class	SpectraSTSimilarityScore
	Similarity score of SpectraST. More...
class	SpectrumAlignment
	Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) alignment if absolute tolerances are given. Scoring function is the m/z distance between peaks. Intensity does not play a role! More...
class	SpectrumAlignmentScore
	Similarity score via spectra alignment. More...
class	SpectrumCheapDPCorr
	SpectrumCheapDPCorr calculates an optimal alignment on stick spectra. More...
class	SpectrumPrecursorComparator
	SpectrumPrecursorComparator compares just the parent mass of two spectra. More...
class	SteinScottImproveScore
	Similarity score based of Stein & Scott. More...
class	ZhangSimilarityScore
	Similarity score of Zhang. More...
class	Colorizer
	Color and style the fonts shown on cout/cerr (or other streams) More...
class	Factory
	Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. More...
class	FactoryBase
	Base class for Factory<T> More...
class	FuzzyStringComparator
	Fuzzy comparison of strings, tolerates numeric differences. More...
class	LogConfigHandler
	The LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream. More...
struct	PrecisionWrapper
	Wrapper class to implement output with appropriate precision. See precisionWrapper(). More...
class	ProgressLogger
	Base class for all classes that want to report their progress. More...
class	RAIICleanup
	Exception-safe way of executing arbitrary code at the end of a scope. More...
class	SingletonRegistry
	Holds pointers to unique instance of a singleton factory. More...
class	StreamHandler
	Provides a central class to register globally used output streams. Currently supported streams are. More...
class	UniqueIdGenerator
	A generator for unique ids. More...
class	UniqueIdIndexer
	A base class for containers with elements derived from UniqueIdInterface. This adds functionality to convert a unique id into an index into the container. More...
class	UniqueIdInterface
	A base class defining a common interface for all classes having a unique id. More...
class	VersionInfo
	Version information class. More...
class	Adduct
class	BinaryTreeNode
	Elements of a binary tree used to represent a hierarchical clustering process. More...
class	CalibrationData
	A helper class, holding all calibration points. More...
class	ChargePair
	Representation of a (putative) link between two Features, which stem from the same compound but have different charge (including different adduct ions (H+, Na+, ..) More...
class	Compomer
	Holds information on an edge connecting two features from a (putative) charge ladder. More...
class	ConstRefVector
	This vector holds pointer to the elements of another container. More...
class	ConvexHull2D
	A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling. More...
class	CVMappingRule
	Representation of a CV Mapping rule used by CVMappings. More...
class	CVMappings
	Representation of controlled vocabulary mapping rules (for PSI formats) More...
class	CVMappingTerm
	Representation of controlled vocabulary term. More...
class	CVReference
	Controlled Vocabulary Reference. More...
class	DataValue
	Class to hold strings, numeric values, lists of strings and lists of numeric values. More...
class	Date
	Date Class. More...
class	DateTime
	DateTime Class. More...
class	DBoundingBox
	A D-dimensional bounding box. More...
class	DefaultParamHandler
	A base class for all classes handling default parameters. More...
class	DistanceMatrix
	A two-dimensional distance matrix, similar to OpenMS::Matrix. More...
class	DPosition
	Representation of a coordinate in D-dimensional space. More...
class	DRange
	A D-dimensional half-open interval. More...
class	ExposedVector
	Makes a vector<VectorElement> available in the derived class and exposed commonly used vector member functions at class level. More...
class	FASTAContainer
	template parameter for vector-based FASTA access More...
class	FASTAContainer< TFI_File >
	FASTAContainer<TFI_File> will make FASTA entries available chunk-wise from start to end by loading it from a FASTA file. This avoids having to load the full file into memory. While loading, the container will memorize the file offsets of each entry, allowing to read an arbitrary i'th entry again from disk. If possible, only entries from the currently cached chunk should be queried, otherwise access will be slow. More...
class	FASTAContainer< TFI_Vector >
	FASTAContainer<TFI_Vector> simply takes an existing vector of FASTAEntries and provides the same interface with a potentially huge speed benefit over FASTAContainer<TFI_File> since it does not need disk access, but at the cost of memory. More...
class	DecoyHelper
	Helper class for calculations on decoy proteins. More...
class	FlagSet
	Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64. More...
class	GridFeature
	Representation of a feature in a hash grid. More...
struct	IsotopeCluster
	Stores information about an isotopic cluster (i.e. potential peptide charge variants) More...
class	ListUtils
	Collection of utility functions for management of vectors. More...
struct	VecLowPrecision
class	LPWrapper
class	MassExplainer
	computes empirical formulas for given mass differences using a set of allowed elements More...
class	MatchedIterator
	For each element in the reference container the closest peak in the target will be searched. If no match is found within the tolerance window, the peak will be skipped over. More...
struct	ValueTrait
	Trait for MatchedIterator to find pairs with a certain distance, which is computed directly on the value_type of the container. More...
struct	PpmTrait
struct	DaTrait
struct	OSWHierarchy
	hierarchy levels of the OSWData tree More...
struct	OSWIndexTrace
struct	OSWTransition
	high-level meta data of a transition More...
class	OSWPeakGroup
class	OSWPeptidePrecursor
	A peptide with a charge state. More...
class	OSWProtein
	A Protein is the highest entity and contains one or more peptides which were found/traced. More...
class	OSWData
	Holds all or partial information from an OSW file. More...
class	Param
	Management and storage of parameters / INI files. More...
class	ParamValue
	Class to hold strings, numeric values, vectors of strings and vectors of numeric values using the stl types. More...
class	QTCluster
	A representation of a QT cluster used for feature grouping. More...
class	String
	A more convenient string class. More...
class	StringListUtils
	Utilities operating on lists of Strings. More...
class	StringUtilsHelper
class	StringView
	StringView provides a non-owning view on an existing string. More...
class	MapUtilities
	Utilities for Feature and ConsensusMap. More...
class	MorphologicalFilter
	This class implements baseline filtering operations using methods from mathematical morphology. More...
class	InternalCalibration
	A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference masses. More...
class	MZTrafoModel
	Create and apply models of a mass recalibration function. More...
class	PrecursorCorrection
	This class provides methods for precursor correction. More...
class	TOFCalibration
	This class implements an external calibration for TOF data using external calibrant spectra. More...
class	DataFilters
	DataFilter array providing some convenience functions. More...
class	Deisotoper
class	ElutionPeakDetection
	Extracts chromatographic peaks from a mass trace. More...
class	FeatureHypothesis
	Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis). More...
class	CmpMassTraceByMZ
class	CmpHypothesesByScore
struct	Range
	Internal structure to store a lower and upper bound of an m/z range. More...
class	FeatureFindingMetabo
	Method for the assembly of mass traces belonging to the same isotope pattern, i.e., that are compatible in retention times, mass-to-charge ratios, and isotope abundances. More...
class	FeatureOverlapFilter
class	IsotopeDistributionCache
	Pre-calculate isotope distributions for interesting mass ranges. More...
class	MassTraceDetection
	A mass trace extraction method that gathers peaks similar in m/z and moving along retention time. More...
class	SplineInterpolatedPeaks
	Data structure for spline interpolation of MS1 spectra and chromatograms. More...
class	SplinePackage
	fundamental data structure for SplineInterpolatedPeaks More...
class	IDFilter
	Collection of functions for filtering peptide and protein identifications. More...
class	SignalToNoiseEstimator
	This class represents the abstract base class of a signal to noise estimator. More...
class	SignalToNoiseEstimatorMeanIterative
	Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities. More...
class	SignalToNoiseEstimatorMedian
	Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) More...
class	SignalToNoiseEstimatorMedianRapid
	Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based) More...
class	GaussFilter
	This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data. More...
class	GaussFilterAlgorithm
	This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data. More...
class	LowessSmoothing
	LOWESS (locally weighted scatterplot smoothing). More...
class	SavitzkyGolayFilter
	Computes the Savitzky-Golay filter coefficients using QR decomposition. More...
class	BernNorm
	BernNorm scales the peaks by ranking them and then scaling them according to rank. More...
class	ComplementFilter
	total intensity of peak pairs that could result from complementing fragments of charge state 1 More...
class	ComplementMarker
	ComplementMarker marks peak pairs which could represent y - b ion pairs. More...
class	FilterFunctor
	A FilterFunctor extracts some spectrum characteristics for quality assessment. More...
class	GoodDiffFilter
	GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss. More...
class	IntensityBalanceFilter
	IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions. More...
class	IsotopeDiffFilter
	IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks. More...
class	IsotopeMarker
	IsotopeMarker marks peak pairs which could represent an ion and its isotope. More...
class	LinearResampler
	Linear Resampling of raw data. More...
class	LinearResamplerAlign
	Linear Resampling of raw data with alignment. More...
class	MarkerMower
	MarkerMower uses PeakMarker to find peaks, those that are not marked get removed. More...
class	NeutralLossDiffFilter
	NeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained by a neutral loss. More...
class	NeutralLossMarker
	NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water, ammonia) More...
class	NLargest
	NLargest removes all but the n largest peaks. More...
class	Normalizer
	Normalizes the peak intensities spectrum-wise. More...
class	ParentPeakMower
	ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions. More...
class	PeakMarker
	PeakMarker marks peaks that seem to fulfill some criterion. More...
class	Scaler
	Scaler scales the peak by ranking the peaks and assigning intensity according to rank. More...
class	SpectraMerger
	Merges blocks of MS or MS2 spectra. More...
class	SqrtMower
	Scales the intensity of peaks to the sqrt. More...
class	ThresholdMower
	ThresholdMower removes all peaks below a threshold. More...
class	TICFilter
	TICFilter calculates TIC. More...
class	WindowMower
	WindowMower augments the highest peaks in a sliding or jumping window. More...
class	AbsoluteQuantitationMethodFile
	File adapter for AbsoluteQuantitationMethod files. More...
class	AbsoluteQuantitationStandardsFile
	Load files containing runConcentration data. More...
class	Base64
	Class to encode and decode Base64. More...
class	Bzip2Ifstream
	Decompresses files which are compressed in the bzip2 format (*.bz2) More...
class	Bzip2InputStream
	Implements the BinInputStream class of the xerces-c library in order to read bzip2 compressed XML files. More...
class	CachedmzML
	An class that uses on-disk caching to read and write spectra and chromatograms. More...
class	ChromeleonFile
	Load Chromeleon HPLC text file and save it into a `MSExperiment`. More...
class	CompressedInputSource
	This class is based on xercesc::LocalFileInputSource. More...
class	ConsensusXMLFile
	This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation. More...
class	ControlledVocabulary
	Representation of a controlled vocabulary. More...
class	CsvFile
	This class handles csv files. Currently only loading is implemented. Does NOT support comment lines! More...
class	CVMappingFile
	Used to load CvMapping files. More...
class	CsiFingerIdMzTabWriter
class	MSDataAggregatingConsumer
	Aggregates spectra by retention time. More...
class	MSDataCachedConsumer
	Transforming and cached writing consumer of MS data. More...
class	MSDataChainingConsumer
	Consumer class that passes all consumed data through a set of operations. More...
class	MSDataSqlConsumer
	A data consumer that inserts MS data into a SQLite database. More...
class	MSDataStoringConsumer
	Consumer class that simply stores the data. More...
class	MSDataTransformingConsumer
	Transforming consumer of MS data. More...
class	MSDataWritingConsumer
	Consumer class that writes MS data to disk using the mzML format. More...
class	PlainMSDataWritingConsumer
	Consumer class that writes MS data to disk using the mzML format. More...
class	NoopMSDataWritingConsumer
	Consumer class that perform no operation. More...
class	NoopMSDataConsumer
	Consumer class that performs no operation. More...
class	SiriusFragmentAnnotation
class	SiriusMzTabWriter
class	FullSwathFileConsumer
	Abstract base class which can consume spectra coming from SWATH experiment stored in a single file. More...
class	RegularSwathFileConsumer
	In-memory implementation of FullSwathFileConsumer. More...
class	CachedSwathFileConsumer
	On-disk cached implementation of FullSwathFileConsumer. More...
class	MzMLSwathFileConsumer
	On-disk mzML implementation of FullSwathFileConsumer. More...
class	DTA2DFile
	DTA2D File adapter. More...
class	DTAFile
	File adapter for DTA files. More...
class	EDTAFile
	File adapter for Enhanced DTA files. More...
class	ExperimentalDesignFile
	Load an experimental design from a TSV file. (see ExperimentalDesign for details on the supported format) More...
class	FASTAFile
	This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusual symbols (such as translation end (*)), they will be kept! You can use aggregate methods load() and store() to read/write a set of protein sequences at the cost of memory. More...
class	FeatureXMLFile
	This class provides Input/Output functionality for feature maps. More...
class	FileHandler
	Facilitates file handling by file type recognition. More...
struct	FileTypes
	Centralizes the file types recognized by FileHandler. More...
class	FileTypeList
	holds a vector of known file types, e.g. as a way to specify supported input formats More...
class	FLASHDeconvFeatureFile
	FLASHDeconv feature level output *.tsv, *.ms1ft (for Promex), *.feature (for TopPIC) file formats. More...
class	FLASHDeconvSpectrumFile
	FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats. More...
class	GNPSMetaValueFile
class	GNPSMGFFile
class	GNPSQuantificationFile
class	GzipIfstream
	Decompresses files which are compressed in the gzip format (*.gzip) More...
class	GzipInputStream
	Implements the BinInputStream class of the xerces-c library in order to read gzip compressed XML files. More...
class	IndexedMzMLDecoder
	A class to analyze indexedmzML files and extract the offsets of individual tags. More...
class	MzMLSpectrumDecoder
	A class to decode input strings that contain an mzML chromatogram or spectrum tag. More...
class	HDF5Connector
	File adapter for HDF5 files. More...
class	IBSpectraFile
	Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results. More...
class	IdXMLFile
	Used to load and store idXML files. More...
class	IndentedStream
	Class for writing data which spans multiple lines with an indentation for each line (all except the first). More...
class	IndexedMzMLFileLoader
	A class to load an indexedmzML file. More...
class	InspectInfile
	Inspect input file adapter. More...
class	InspectOutfile
	Representation of an Inspect outfile. More...
class	KroenikFile
	File adapter for Kroenik (HardKloer sibling) files. More...
class	MascotGenericFile
	Read/write Mascot generic files (MGF). More...
class	MascotInfile
	Mascot input file adapter. More...
class	MascotRemoteQuery
	Class which handles the communication between OpenMS and the Mascot server. More...
class	MascotXMLFile
	Used to load Mascot XML files. More...
class	MRMFeaturePickerFile
	_MRMFeaturePickerFile_ loads components and components groups parameters from a .csv file. More...
class	MRMFeatureQCFile
	File adapter for MRMFeatureQC files. More...
class	MS2File
	MS2 input file adapter. More...
class	MsInspectFile
	File adapter for MsInspect files. More...
class	MSNumpressCoder
	Class to encode and decode data encoded with MSNumpress. More...
class	MSPFile
	File adapter for MSP files (NIST spectra library) More...
class	MSPGenericFile
	Load MSP text file and save it into an `MSExperiment`. More...
class	MSPGenericFile_friend
class	MSstatsFile
	File adapter for MSstats files. More...
class	MzDataFile
	File adapter for MzData files. More...
class	MzIdentMLFile
	File adapter for MzIdentML files. More...
class	MzMLFile
	File adapter for MzML files. More...
class	MzQCFile
	File adapter for mzQC files used to load and store mzQC files. More...
class	MzQuantMLFile
	File adapter for MzQuantML files. More...
class	MzTabModification
	Data model of MzTab files. More...
class	MzTabModificationList
struct	MzTabModificationMetaData
struct	MzTabAssayMetaData
struct	MzTabMSRunMetaData
struct	MzTabStudyVariableMetaData
class	MzTabMetaData
	all meta data of a mzTab file. Please refer to specification for documentation. More...
struct	MzTabProteinSectionRow
	PRT - Protein section (Table based) More...
struct	MzTabPeptideSectionRow
	PEP - Peptide section (Table based) More...
struct	MzTabPSMSectionRow
	PSM - PSM section (Table based) More...
struct	MzTabSmallMoleculeSectionRow
	SML Small molecule section (table based) More...
struct	MzTabNucleicAcidSectionRow
	NUC - Nucleic acid section (table-based) More...
struct	MzTabOligonucleotideSectionRow
	OLI - Oligonucleotide section (table-based) More...
struct	MzTabOSMSectionRow
	OSM - OSM (oligonucleotide-spectrum match) section (table-based) More...
class	MzTab
	Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...
class	MzTabDouble
class	MzTabDoubleList
class	MzTabInteger
class	MzTabIntegerList
class	MzTabBoolean
class	MzTabString
class	MzTabParameter
class	MzTabParameterList
class	MzTabStringList
class	MzTabSpectraRef
struct	MzTabSoftwareMetaData
struct	MzTabSampleMetaData
struct	MzTabCVMetaData
struct	MzTabInstrumentMetaData
struct	MzTabContactMetaData
class	MzTabBase
class	MzTabFile
	File adapter for MzTab files. More...
struct	CompareMzTabMMatchRef
	Data model of MzTabM files. Please see the official MzTabM specification at https://github.com/HUPO-PSI/mzTab/tree/master/specification_document-releases/2_0-Metabolomics-Release. More...
class	MzTabMAssayMetaData
	MztabM Assay Metadata. More...
class	MzTabMMSRunMetaData
	MztabM MSRun Metadata. More...
class	MzTabMStudyVariableMetaData
	MztabM StudyVariable Metadata. More...
class	MzTabMDatabaseMetaData
	MztabM Database Metadata. More...
class	MzTabMMetaData
	MztabM Metadata. More...
class	MzTabMSmallMoleculeSectionRow
	SML Small molecule section (mztab-m) More...
class	MzTabMSmallMoleculeFeatureSectionRow
	SMF Small molecule feature section (mztab-m) More...
class	MzTabMSmallMoleculeEvidenceSectionRow
	SME Small molecule evidence section (mztab-m) More...
class	MzTabM
	Data model of MzTab-M files Please see the MzTab-M specification at https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc#use-cases-for-mztab. More...
class	MzTabMFile
	File adapter for MzTab-M files. More...
class	MzXMLFile
	File adapter for MzXML 3.1 files. More...
class	OMSFile
	This class supports reading and writing of OMS files. More...
class	OMSSACSVFile
	File adapter for OMSSACSV files. More...
class	OMSSAXMLFile
	Used to load OMSSAXML files. More...
class	FeatureFileOptions
	Options for loading files containing features. More...
class	PeakFileOptions
	Options for loading files containing peak data. More...
class	OSWFile
	This class serves for reading in and writing OpenSWATH OSW files. More...
struct	ToolInfo
	A struct to pass information about the tool as one parameter. More...
class	ParamCTDFile
	Serializes a Param class in paramCTD file format. Note: only storing is currently possible. More...
class	ParamCWLFile
	Load from JSON (in a Common Workflow Language (CWL) compatible way) into the Param class. More...
class	ParamXMLFile
	The file pendant of the Param class used to load and store the param datastructure as paramXML. More...
class	PeakTypeEstimator
	Estimates if the data of a spectrum is raw data or peak data. More...
class	PepNovoInfile
	PepNovo input file adapter. More...
class	PepNovoOutfile
	Representation of a PepNovo output file. More...
class	PepXMLFile
	Used to load and store PepXML files. More...
class	PepXMLFileMascot
	Used to load Mascot PepXML files. More...
class	PercolatorInfile
	Class for storing Percolator tab-delimited input files. More...
class	PercolatorOutfile
	Class for reading Percolator tab-delimited output files. More...
class	ProtXMLFile
	Used to load (storing not supported, yet) ProtXML files. More...
class	PTMXMLFile
	Used to load and store PTMXML files. More...
class	QcMLFile
	File adapter for QcML files used to load and store QcML files. More...
class	SequestInfile
	Sequest input file adapter. More...
class	SequestOutfile
	Representation of a Sequest output file. More...
class	SpecArrayFile
	File adapter for SpecArray (.pepList) files. More...
class	SqliteConnector
	File adapter for Sqlite files. More...
class	SqMassFile
	An class that uses on-disk SQLite database to read and write spectra and chromatograms. More...
class	SVOutStream
	Stream class for writing to comma/tab/...-separated values files. More...
class	SwathFile
	File adapter for Swath files. More...
class	TextFile
	This class provides some basic file handling methods for text files. More...
class	ToolDescriptionFile
	File adapter for ToolDescriptor files. More...
class	TraMLFile
	File adapter for HUPO PSI TraML files. More...
class	TransformationXMLFile
	Used to load and store TransformationXML files. More...
class	TriqlerFile
	File adapter for Triqler files. More...
class	UnimodXMLFile
	Used to load XML files from unimod.org files. More...
class	XMLValidator
	Validator for XML files. More...
class	XMassFile
	File adapter for 'XMass Analysis (fid)' files. More...
class	XQuestResultXMLFile
	Used to load and store xQuest result files. More...
class	XTandemInfile
	XTandem input file. More...
class	XTandemXMLFile
	Used to load XTandemXML files. More...
class	ZlibCompression
	Compresses and uncompresses data using zlib. More...
class	FAIMSHelper
	Helper functions for FAIMS data. More...
class	IMDataConverter
	This class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models. More...
class	IMTypes
class	BaseFeature
	A basic LC-MS feature. More...
class	ChromatogramPeak
	A 1-dimensional raw data point or peak for chromatograms. More...
class	ChromatogramTools
	Conversion class to convert chromatograms. More...
class	ConsensusFeature
	A consensus feature spanning multiple LC-MS/MS experiments. More...
class	ConsensusMap
	A container for consensus elements. More...
class	MapConversion
class	DimBase
	A base class for a dimension which represents a certain unit (e.g. RT or m/z). Derived classes implement virtual functions, which receive a well-defined data type, e.g. a Feature, and return the appropriate value for their dimension (the DimRT class would return the RT of the feature). This makes it possible to extract dimensions using a runtime configuration of DimBase instances. Very useful when mapping units (RT, m/z) to axis when plotting etc. More...
class	DimRT
class	DimMZ
class	DimINT
class	DimIM
class	DimMapper
	Allows dynamical switching (at runtime) between a dimension (RT, m/z, int, IM, etc) and X,Y,Z coordinates. You can set either of them, and query the other. The Mapping is stored internally. The unit to which the X,Y,Z coordinates currently mapped onto can also be queried (useful for axis labels etc). More...
class	Area
struct	DPeak
	Metafunction to choose among Peak1D respectively Peak2D through a template argument. More...
class	Feature
	An LC-MS feature. More...
class	FeatureHandle
	Representation of a Peak2D, RichPeak2D or Feature . More...
struct	AnnotationStatistics
class	FeatureMap
	A container for features. More...
class	MassTrace
	A container type that gathers peaks similar in m/z and moving along retention time. More...
class	MobilityPeak1D
	A 1-dimensional raw data mobility point or peak. The unit (ms, 1/K_0, etc) is implicit. More...
class	MobilityPeak2D
	A 2-dimensional raw data point or peak. More...
class	Mobilogram
	The representation of a 1D ion mobilogram. More...
class	MRMFeature
	A multi-chromatogram MRM feature. More...
class	MRMTransitionGroup
	The representation of a group of transitions in a targeted proteomics experiment. More...
class	MSChromatogram
	The representation of a chromatogram. More...
class	MSExperiment
	In-Memory representation of a mass spectrometry run. More...
class	MSSpectrum
	The representation of a 1D spectrum. More...
class	OnDiscMSExperiment
	Representation of a mass spectrometry experiment on disk. More...
class	Peak1D
	A 1-dimensional raw data point or peak. More...
class	Peak2D
	A 2-dimensional raw data point or peak. More...
struct	PeakIndex
	Index of a peak or feature. More...
struct	RangeBase
	Base class for a simple range with minimum and maximum. More...
struct	RangeRT
struct	RangeMZ
struct	RangeIntensity
struct	RangeMobility
class	RangeManager
	Handles the management of a multidimensional range, e.g. RangeMZ and RangeIntensity for spectra. More...
class	RangeManagerContainer
class	HasMetaValue
	Predicate that determines if a class has a certain metavalue. More...
class	InRTRange
	Predicate that determines if a spectrum lies inside/outside a specific retention time range. More...
class	InMSLevelRange
	Predicate that determines if a spectrum lies inside/outside a specific MS level set. More...
class	HasScanMode
	Predicate that determines if a spectrum has a certain scan mode. More...
class	HasScanPolarity
	Predicate that determines if a spectrum has a certain scan polarity. More...
class	IsEmptySpectrum
	Predicate that determines if a spectrum is empty. More...
class	IsZoomSpectrum
	Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum. More...
class	HasActivationMethod
	Predicate that determines if a spectrum was generated using any activation method given in the constructor list. More...
class	InPrecursorMZRange
	Predicate that determines if a spectrum's precursor is within a certain m/z range. More...
class	HasPrecursorCharge
	Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list. More...
class	InMzRange
	Predicate that determines if a peak lies inside/outside a specific m/z range. More...
class	InIntensityRange
	Predicate that determines if a peak lies inside/outside a specific intensity range. More...
class	IsInCollisionEnergyRange
	Predicate that determines if an MSn spectrum was generated with a collision energy in the given range. More...
class	IsInIsolationWindowSizeRange
	Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range. More...
class	IsInIsolationWindow
	Predicate that determines if the isolation window covers ANY of the given m/z values. More...
class	RichPeak2D
	A 2-dimensional raw data point or peak with meta information. More...
class	BSpline2d
	b spline interpolation More...
class	CubicSpline2d
	cubic spline interpolation as described in R.L. Burden, J.D. Faires, Numerical Analysis, 4th ed. PWS-Kent, 1989, ISBN 0-53491-585-X, pp. 126-131. More...
class	EmgGradientDescent
	Compute the area, background and shape metrics of a peak. More...
class	EmgGradientDescent_friend
class	GridSearch
class	NonNegativeLeastSquaresSolver
	Wrapper for a non-negative least squares (NNLS) solver. More...
class	AbsoluteQuantitationStandards
	AbsoluteQuantitationStandards is a class to handle the relationship between runs, components, and their actual concentrations. More...
class	Acquisition
	Information about one raw data spectrum that was combined with several other raw data spectra. More...
class	AcquisitionInfo
	Description of the combination of raw data to a single spectrum. More...
class	ChromatogramSettings
	Representation of chromatogram settings, e.g. SRM/MRM chromatograms. More...
class	ContactPerson
	Contact person information. More...
class	CVTerm
	Representation of controlled vocabulary term. More...
class	CVTermList
	Representation of controlled vocabulary term list. More...
class	CVTermListInterface
	Interface to the controlled vocabulary term list. More...
class	DataProcessing
	Description of the applied preprocessing steps. More...
class	Digestion
	Meta information about digestion of a sample. More...
class	DocumentIdentifier
	Manage source document information. More...
class	ExperimentalDesign
	Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class. More...
class	ExperimentalSettings
	Description of the experimental settings. More...
class	Gradient
	Representation of a HPLC gradient. More...
class	HPLC
	Representation of a HPLC experiment. More...
class	IdentificationData
class	IdentificationDataConverter
class	Identification
	Represents a object which can store the information of an analysisXML instance. More...
class	IdentificationHit
	Represents a object which can store the information of an analysisXML instance. More...
class	Instrument
	Description of a MS instrument. More...
class	InstrumentSettings
	Description of the settings a MS Instrument was run with. More...
class	IonDetector
	Description of a ion detector (part of a MS Instrument) More...
class	IonSource
	Description of an ion source (part of a MS Instrument) More...
class	MassAnalyzer
	Description of a mass analyzer (part of a MS Instrument) More...
class	MetaInfo
	A Type-Name-Value tuple class. More...
class	MetaInfoDescription
	Description of the meta data arrays of MSSpectrum. More...
class	MetaInfoInterface
	Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). More...
class	MetaInfoInterfaceUtils
	Utilities operating on containers inheriting from MetaInfoInterface. More...
class	MetaInfoRegistry
	Registry which assigns unique integer indices to strings. More...
class	Modification
	Meta information about chemical modification of a sample. More...
class	MSQuantifications
class	PeptideEvidence
	Representation of a peptide evidence. More...
class	PeptideHit
	Representation of a peptide hit. More...
class	PeptideIdentification
	Represents the peptide hits for a spectrum. More...
class	Precursor
	Precursor meta information. More...
class	Product
	Product meta information. More...
class	ProteinHit
	Representation of a protein hit. More...
class	ProteinIdentification
	Representation of a protein identification run. More...
class	Sample
	Meta information about the sample. More...
class	SampleTreatment
	Base class for sample treatments (Digestion, Modification, Tagging, ...) More...
struct	ScanWindow
	Scan window description. More...
class	Software
	Description of the software used for processing. More...
class	SourceFile
	Description of a file location, used to store the origin of (meta) data. More...
class	SpectrumIdentification
	Represents a object which can store the information of an analysisXML instance. More...
class	SpectrumLookup
	Helper class for looking up spectra based on different attributes. More...
class	SpectrumMetaDataLookup
	Helper class for looking up spectrum meta data. More...
class	SpectrumSettings
	Representation of 1D spectrum settings. More...
class	Tagging
	Meta information about tagging of a sample e.g. ICAT labeling. More...
class	Contaminants
	This class is a metric for the QualityControl TOPP tool. More...
class	DBSuitability
	This class holds the functionality of calculating the database suitability. More...
class	DBSuitability_friend
class	FeatureSummary
class	FragmentMassError
class	FWHM
	QC metric calculating (un)calibrated m/z error. More...
class	IdentificationSummary
class	MissedCleavages
	This class is a metric for the QualityControl TOPP Tool. More...
class	Ms2IdentificationRate
	This class is a metric for the QualityControl-ToppTool. More...
class	Ms2SpectrumStats
	QC metric to determine the number of MS2 scans per MS1 scan over RT. More...
class	MzCalibration
	QC metric calculating (un)calibrated m/z error. More...
class	PeptideMass
	QC metric calculating theoretical mass of a peptide sequence. More...
class	PSMExplainedIonCurrent
class	QCBase
	This class serves as an abstract base class for all QC classes. More...
class	RTAlignment
	Take the original retention time before map alignment and use the alignment's trafoXML for calculation of the new alignment retention times. More...
class	SpectrumCount
class	TIC
class	ExternalProcess
	A wrapper around QProcess to conveniently start an external program and forward its outputs. More...
class	File
	Basic file handling operations. More...
class	FileWatcher
	Watcher that monitors file changes. More...
class	JavaInfo
	Detect Java and retrieve information. More...
class	NetworkGetRequest
class	PythonInfo
	Detect Python and retrieve information. More...
class	RWrapper
	R-Wrapper Class. More...
class	StopWatch
	This class is used to determine the current process' CPU (user and/or kernel) and wall time. More...
class	SysInfo
	Some functions to get system information. More...
class	UpdateCheck
	Helper Functions to perform an update query to the OpenMS REST server. More...
class	BaseModel
	Abstract base class for all D-dimensional models. More...
class	BiGaussFitter1D
	BiGaussian distribution fitter (1-dim.) approximated using linear interpolation. More...
class	BiGaussModel
	BiGaussian distribution approximated using linear interpolation. More...
class	EGHTraceFitter
	A RT Profile fitter using an Exponential Gaussian Hybrid background model. More...
class	ElutionModelFitter
	Helper class for fitting elution models to features. More...
class	EmgFitter1D
	Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization. More...
class	EmgModel
	Exponentially modified gaussian distribution model for elution profiles. More...
class	EmgScoring
	Scoring of an elution peak using an exponentially modified gaussian distribution model. More...
class	ExtendedIsotopeFitter1D
	Extended isotope distribution fitter (1-dim.) approximated using linear interpolation. More...
class	ExtendedIsotopeModel
	Extended isotope distribution approximated using linear interpolation. More...
class	FeatureFinder
	The main feature finder class. More...
struct	Summary
	Summary of fitting results. More...
class	FeatureFinderAlgorithm
	Abstract base class for FeatureFinder algorithms. More...
class	FeatureFinderAlgorithmIsotopeWavelet
	Implements the isotope wavelet feature finder. More...
class	FeatureFinderAlgorithmMetaboIdent
class	FeatureFinderAlgorithmMRM
	FeatureFinderAlgorithm for MRM experiments. More...
class	FeatureFinderAlgorithmPicked
	FeatureFinderAlgorithm for picked peaks. More...
struct	FeatureFinderAlgorithmPickedHelperStructs
	Wrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes. More...
struct	FeatureFinderDefs
	The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes. More...
class	FeatureFinderIdentificationAlgorithm
class	FeatureFinderMultiplexAlgorithm
class	Fitter1D
	Abstract base class for all 1D-dimensional model fitter. More...
class	GaussFitter1D
	Gaussian distribution fitter (1-dim.) approximated using linear interpolation. More...
class	GaussModel
	Normal distribution approximated using linear interpolation. More...
class	GaussTraceFitter
	Fitter for RT profiles using a Gaussian background model. More...
class	InterpolationModel
	Abstract class for 1D-models that are approximated using linear interpolation. More...
class	IsotopeFitter1D
	Isotope distribution fitter (1-dim.) approximated using linear interpolation. More...
class	IsotopeModel
	Isotope distribution approximated using linear interpolation. More...
class	IsotopeWavelet
	Implements the isotope wavelet function. More...
class	IsotopeWaveletTransform
	A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the FeatureFinderAlgorithmIsotopeWavelet class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform. More...
class	LevMarqFitter1D
	Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization. More...
class	MaxLikeliFitter1D
	Abstract base class for all 1D-model fitters using maximum likelihood optimization. More...
class	ModelDescription
	Stores the name and parameters of a model. More...
class	MultiplexClustering
	clusters results from multiplex filtering More...
class	MultiplexDeltaMasses
	data structure for mass shift pattern More...
class	MultiplexDeltaMassesGenerator
	generates complete list of all possible mass shifts due to isotopic labelling More...
class	MultiplexFilteredMSExperiment
	data structure storing all peaks (and optionally their raw data points) of an experiment corresponding to one specific peak pattern More...
class	MultiplexFilteredPeak
	data structure storing a single peak that passed all filters More...
class	MultiplexFiltering
	base class for filtering centroided and profile data for peak patterns More...
class	MultiplexFilteringCentroided
	filters centroided data for peak patterns More...
class	MultiplexFilteringProfile
	filters centroided and profile data for peak patterns More...
class	MultiplexIsotopicPeakPattern
	data structure for pattern of isotopic peaks More...
class	MultiplexSatelliteCentroided
	data structure storing a single satellite peak More...
class	MultiplexSatelliteProfile
	data structure storing a single satellite data point More...
class	PeakWidthEstimator
	Rough estimation of the peak width at m/z. More...
class	ProductModel
	Class for product models i.e. models with D independent dimensions. More...
class	ProductModel< 2 >
	The class template is only implemented for D=2 because we use Peak2D here. More...
class	SeedListGenerator
	Generate seed lists for feature detection. More...
class	TraceFitter
	Abstract fitter for RT profile fitting. More...
class	ContinuousWaveletTransform
	This class is the base class of the continuous wavelet transformation. More...
class	ContinuousWaveletTransformNumIntegration
	This class computes the continuous wavelet transformation using a marr wavelet. More...
class	OptimizePeakDeconvolution
	This class provides the deconvolution of peak regions using non-linear optimization. More...
class	OptimizePick
	This class provides the non-linear optimization of the peak parameters. More...
class	PeakPickerCWT
	This class implements a peak picking algorithm using wavelet techniques. More...
class	PeakPickerHiRes
	This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. More...
struct	PeakCandidate
	A small structure to hold peak candidates. More...
class	PeakPickerIterative
	This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data). More...
class	PeakPickerMaxima
	This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. More...
class	PeakPickerSH
class	PeakShape
	Internal representation of a peak shape (used by the PeakPickerCWT) More...
class	TwoDOptimization
	This class provides the two-dimensional optimization of the picked peak parameters. More...
class	Annotation1DCaret
	An annotation item which paints a set of carets on the canvas. More...
class	Annotation1DDistanceItem
	An annotation item which represents a measured distance between two peaks. More...
class	Annotation1DItem
	An abstract class acting as an interface for the different 1D annotation items. More...
class	Annotation1DPeakItem
	A peak annotation item. More...
class	Annotation1DTextItem
	An annotation item which represents an arbitrary text on the canvas. More...
class	Annotation1DVerticalLineItem
	An annotation item which represents a vertical line (or more precisely a line along the gravity axis, i.e. it could also be horizontal) and text label on top. More...
class	Annotations1DContainer
	Container for annotations to content of Plot1DCanvas. More...
class	FLASHDeconvWizardBase
	Main window of the FLASHDeconvWizard tool. More...
class	INIFileEditorWindow
	shows the ParamEditor widget in a QMainWindow with a toolbar More...
class	QApplicationTOPP
	Extension to the QApplication for running TOPPs GUI tools. More...
class	SwathWizardBase
	Main window of the SwathWizard tool. More...
class	TOPPASBase
	Main window of the TOPPAS tool. More...
class	TOPPViewBase
	Main window of TOPPView tool. More...
class	AxisPainter
	Draws a coordinate axis. It has only static methods, that's why the constructor is private. More...
class	AxisTickCalculator
	Calculates ticks for a given value range. More...
class	AxisWidget
	Widget that represents an axis of a graph. More...
class	ColorSelector
	A widget for selecting a color. More...
class	DataTabBase
	all tabs need to implement this interface More...
class	DataSelectionTabs
	A tabbed view, to browse lists of spectra or identifications. More...
class	DataFilterDialog
	Dialog for creating and changing a DataFilter. More...
class	FeatureEditDialog
	Dialog for editing a feature. More...
class	HistogramDialog
	Dialog that show a HistogramWidget. More...
class	LayerStatisticsDialog
	Dialog showing statistics about the data of the current layer. More...
class	ListFilterDialog
	Dialog for creating and changing a DataFilter. More...
class	Plot1DGoToDialog
	simple goto/set visible area dialog for exact placement of the viewing window More...
class	Plot2DGoToDialog
	GoTo dialog used to zoom to a m/z and retention time range or to a feature. More...
class	SaveImageDialog
	Dialog for saving an image. More...
class	SpectrumAlignmentDialog
	Lets the user select two spectra and set the parameters for the spectrum alignment. More...
class	TheoreticalSpectrumGenerationDialog
	Dialog which allows to enter an AA or NA sequence and generates a theoretical spectrum for it. More...
class	ToolsDialog
	TOPP tool selection dialog. More...
class	TOPPASInputFileDialog
	Dialog which allows to specify an input file. More...
class	TOPPASInputFilesDialog
	Dialog which allows to specify a list of input files. More...
class	TOPPASIOMappingDialog
	Dialog which allows to configure the input/output parameter mapping of an edge. More...
class	TOPPASOutputFilesDialog
	Dialog which allows to specify the directory for the output files. More...
class	TOPPASToolConfigDialog
	TOPP tool configuration dialog. More...
class	TOPPASVertexNameDialog
	Dialog which allows to change the name of an input/output vertex. More...
class	TOPPViewOpenDialog
	Dataset opening options for TOPPView. More...
class	DIATreeTab
	Hierarchical visualization and selection of spectra. More...
class	EnhancedTabBar
	Convenience tab bar implementation. More...
class	SignalProvider
	provides a signal mechanism (by deriving from QObject) for classes which are not allowed to have signals themselves. More...
class	EnhancedTabBarWidgetInterface
	Widgets that are placed into an EnhancedTabBar must implement this interface. More...
class	EnhancedWorkspace
class	GUIProgressLoggerImpl
	Implements a GUI version of the ProgressLoggerImpl. More...
class	HistogramWidget
	Widget which can visualize a histogram. More...
class	InputFile
	A simple widget with a line-edit and a browse button to choose filenames. More...
class	IPeptideIds
	Abstract base class which defines an interface for PeptideIdentifications. More...
class	LayerData1DBase
	Base class for all 1D layers, a special case of LayerData. More...
class	LayerData1DChrom
class	LayerData1DIonMobility
class	LayerData1DPeak
struct	LayerDataDefs
class	LayerDataBase
	Class that stores the data for one layer. More...
class	LayerAnnotatorBase
class	LayerAnnotatorPeptideID
class	LayerAnnotatorAMS
class	LayerAnnotatorOSW
class	LayerDataChrom
	Class that stores the data for one layer of type Chromatogram. More...
class	LayerDataConsensus
	Class that stores the data for one layer of type ConsensusMap. More...
class	LayerDataFeature
	Class that stores the data for one layer of type FeatureMap. More...
class	LayerDataIdent
	Class that stores the data for one layer of type PeptideIdentifications. More...
class	LayerDataIonMobility
	Class that stores the data for one layer of type IonMobility. More...
class	LayerDataPeak
	Class that stores the data for one layer of type PeakMap. More...
class	LayerListView
	Pimped QListView for Layers of a Canvas. More...
class	ListEditor
	Editor for editing int, double and string lists (including output and input file lists) More...
class	LogWindow
	A log window (QTextEdit) with convenience functions. More...
class	MetaDataBrowser
	A meta data visualization widget. More...
class	ExternalProcessMBox
	A wrapper around ExternalProcess to conveniently show a MessageBox when an error occurs. More...
class	MultiGradient
	A gradient of multiple colors and arbitrary distances between colors. More...
class	MultiGradientSelector
	A widget witch allows constructing gradients of multiple colors. More...
class	OutputDirectory
	A simple widget with a line-edit and a browse button to choose filenames. More...
class	Painter1DBase
	A base class for painting all items from a data layer (as supported by class derived from here) onto a 1D Canvas. More...
class	Painter1DPeak
	Painter1D for spectra. More...
class	Painter1DChrom
	Painter1D for chromatograms. More...
class	Painter1DIonMobility
	Painter1D for mobilograms. More...
class	Painter2DBase
	A base class for painting all items from a data layer (as supported by class derived from here) onto a 2D Canvas. More...
class	Painter2DPeak
	Painter2D for spectra. More...
class	Painter2DChrom
	Painter2D for chromatograms. More...
class	Painter2DIonMobility
	Painter2D for ion mobilograms. More...
class	Painter2DFeature
	Painter2D for Features. More...
class	Painter2DConsensus
	Painter2D for ConsensusFeatures. More...
class	Painter2DIdent
	Painter2D for Identifications. More...
class	PainterBase
	An empty base class with some static convenience functions. More...
class	ParamEditor
	A GUI for editing or viewing a Param object. More...
class	Gravitator
	Manipulates X or Y component of points in the X-Y plane, by assuming one axis (either X or Y axis) has gravity acting upon it. More...
class	Plot1DCanvas
	Canvas for visualization of one or several spectra. More...
class	Plot1DWidget
	Widget for visualization of several spectra. More...
class	Plot2DCanvas
	Canvas for 2D-visualization of peak map, feature map and consensus map data. More...
class	Plot2DWidget
	Widget for 2D-visualization of peak map and feature map data. More...
class	Plot3DCanvas
	Canvas for 3D-visualization of peak map data. More...
class	Plot3DOpenGLCanvas
	OpenGL Canvas for 3D-visualization of map data. More...
class	Plot3DWidget
	Widget for 3D-visualization of map data. More...
class	LayerStack
class	PlotCanvas
	Base class for visualization canvas classes. More...
class	PlotWidget
	Base class for spectrum widgets. More...
class	RecentFilesMenu
	Manages recent files opened by the user and provides a QMenu to go with it. More...
class	SpectraIDViewTab
	Tabular visualization / selection of identified spectra. More...
class	SpectraTreeTab
	Hierarchical visualization and selection of spectra. More...
class	SwathLibraryStats
	A multi-tabbed widget for the SwathWizard offering setting of parameters, input-file specification and running Swath and more. More...
class	TableView
	A better QTable for TOPPView, which supports exporting to TSV and conveniently adding data to cells and headers. More...
class	TOPPASEdge
	An edge representing a data flow in TOPPAS. More...
class	TOPPASInputFileListVertex
	A vertex representing an input file list. More...
class	TOPPASMergerVertex
	A special vertex that allows to merge several inputs. More...
class	TOPPASOutputFileListVertex
	A vertex representing an output file list. More...
class	TOPPASResource
	Represents a data resource for TOPPAS workflows. More...
class	TOPPASResources
	A dictionary mapping string keys to lists of TOPPASResource objects. More...
class	FakeProcess
	A FakeProcess class. More...
class	TOPPASScene
	A container for all visual items of a TOPPAS workflow. More...
class	TOPPASSplitterVertex
	A special vertex that allows to split a list of inputs. More...
class	TOPPASToolVertex
	A vertex representing a TOPP tool. More...
class	TOPPASTreeView
	Tree view implementation for the list of TOPP tools. More...
class	TOPPASVertex
	The base class of the different vertex classes. More...
class	TOPPASWidget
	Widget visualizing and allowing to edit TOPP pipelines. More...
class	TOPPViewMenu
	The file menu items for TOPPView. More...
class	TreeView
	A better QTreeWidget for TOPPView, which supports header context menu and conveniently adding/getting headers names. More...
class	TVControllerBase
	Base behavior for different visualizaton modules in TOPPView. More...
class	TVDIATreeTabController
	Behavior of TOPPView in spectra view mode. More...
class	TVIdentificationViewController
	Behavior of TOPPView in identification mode. More...
class	TVSpectraViewController
	Behavior of TOPPView in spectra view mode. More...
class	TVToolDiscovery
	Scans for tools and generates a param for each asynchronously. More...
struct	RangeStats
	Struct representing the statistics about a set of values. More...
struct	StatsCounter
	a simple counting struct, for non-numerical occurrences of meta-values More...
struct	RangeStatsType
	Origin and name of a statistic. More...
class	LayerStatistics
	Compute summary statistics (count/min/max/avg) about a container, e.g. intensity, charge, meta values, ... More...
class	LayerStatisticsPeakMap
	Computes statistics and distributions for a PeakMap. More...
class	LayerStatisticsFeatureMap
	Computes statistics and distributions for a PeakMap. More...
class	LayerStatisticsConsensusMap
	Computes statistics and distributions for a PeakMap. More...
class	LayerStatisticsIdent
	Computes statistics and distributions for a vector<PeptideIdentifications> More...
class	LayerStoreData
	Base class to store either the currently visible or all data of a canvas. More...
class	LayerStoreDataPeakMapVisible
	Visitor which can save a visible piece of data; subsequently the data can be stored to a file. More...
class	LayerStoreDataPeakMapAll
	Visitor which can save a full experiment; subsequently the data can be stored to a file. More...
class	LayerStoreDataFeatureMapVisible
	Visitor which can save a visible piece of data; subsequently the data can be stored to a file. More...
class	LayerStoreDataFeatureMapAll
	Visitor which can save a full FeatureMap; subsequently the data can be stored to a file. More...
class	LayerStoreDataConsensusMapVisible
	Visitor which can save a visible piece of data; subsequently the data can be stored to a file. More...
class	LayerStoreDataConsensusMapAll
	Visitor which can save a full ConsensusMap; subsequently the data can be stored to a file. More...
class	LayerStoreDataIdentVisible
	Visitor which can save a visible piece of data; subsequently the data can be stored to a file. More...
class	LayerStoreDataIdentAll
	Visitor which can save a full set of Identifications; subsequently the data can be stored to a file. More...
class	AcquisitionInfoVisualizer
	Class that displays all meta information for AcquisitionInfo objects. More...
class	AcquisitionVisualizer
	Class that displays all meta information for Acquisition objects. More...
class	BaseVisualizer
	A base class for all visualizer classes. More...
class	BaseVisualizerGUI
	A base class for all visualizer classes. More...
class	ContactPersonVisualizer
	Class that displays all meta information for ContactPerson objects. More...
class	DataProcessingVisualizer
	Class that displays all meta information for DataProcessing objects. More...
class	DigestionVisualizer
	Class that displays all meta information of digestion objects. More...
class	DocumentIdentifierVisualizer
	Class that displays all meta information for DocumentIdentifier objects. More...
class	ExperimentalSettingsVisualizer
	Class that displays all meta information for ExperimentalSettings objects. More...
class	GradientVisualizer
	GradientVisualizer is a visualizer class for objects of type gradient. More...
class	HPLCVisualizer
	Class that displays all meta information for HPLC objects. More...
class	InstrumentSettingsVisualizer
	Class that displays all meta information for InstrumentSettings objects. More...
class	InstrumentVisualizer
	Class that displays all meta information for an MS instrument. More...
class	IonDetectorVisualizer
	Class that displays all meta information for IonDetector objects. More...
class	IonSourceVisualizer
	Class that displays all meta information for IonSource objects. More...
class	MassAnalyzerVisualizer
	Class that displays all meta information for MassAnalyzer objects. More...
class	MetaInfoDescriptionVisualizer
	Class that displays all meta information for MetaInfoDescription objects. More...
class	MetaInfoVisualizer
	MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member. More...
class	ModificationVisualizer
	Class that displays all meta information of modification objects. More...
class	PeptideHitVisualizer
	Class that displays all meta information for PeptideHit objects. More...
class	PeptideIdentificationVisualizer
	Class that displays all meta information for PeptideIdentification objects. More...
class	PrecursorVisualizer
	Class that displays all meta information for Precursor objects. More...
class	ProductVisualizer
	Class that displays all meta information for Product objects. More...
class	ProteinHitVisualizer
	Class that displays all meta information for ProteinHit objects. More...
class	ProteinIdentificationVisualizer
	Class that displays all meta information for ProteinIdentification objects. More...
class	SampleVisualizer
	Class that displays all meta information of sample objects. More...
class	ScanWindowVisualizer
	Class that displays all meta information for ScanWindow objects. More...
class	SoftwareVisualizer
	Class that displays all meta information for Software objects. More...
class	SourceFileVisualizer
	Class that displays all meta information for SourceFile objects. More...
class	SpectrumSettingsVisualizer
	Class that displays all meta information for SpectrumSettings objects. More...
class	TaggingVisualizer
	Class that displays all meta information of tagging objects. More...

Typedefs
typedef std::pair< double, double >	ScoreToTgtDecLabelPair
typedef std::map< Internal::ToolDescriptionInternal, Internal::ToolDescriptionInternal >	ToolMapping
	Updates an INI. More...
typedef std::map< String, Internal::ToolDescription >	ToolListType
	Handles lists of TOPP tools and their categories (for TOPPAS) More...
typedef DigestionEnzymeProtein	Protease
typedef DigestionEnzymeRNA	RNase
using	RibonucleotideChainEnd = Ribonucleotide
	Dummy nucleotide used to represent 5' and 3' chain ends. Usually, just the phosphates. More...
typedef OPENMS_INT32_TYPE	Int32
	Signed integer type (32bit) More...
typedef OPENMS_UINT32_TYPE	UInt32
	Unsigned integer type (32bit) More...
typedef OPENMS_INT64_TYPE	Int64
	Signed integer type (64bit) More...
typedef OPENMS_UINT64_TYPE	UInt64
	Unsigned integer type (64bit) More...
typedef time_t	Time
	Time type. More...
typedef unsigned int	UInt
	Unsigned integer type. More...
typedef int	Int
	Signed integer type. More...
typedef OPENMS_BYTE_TYPE	Byte
	Byte type. More...
typedef OPENMS_UINT64_TYPE	UID
	A unique object ID (as unsigned 64bit type). More...
typedef size_t	Size
	Size type e.g. used as variable which can hold result of size() More...
typedef ptrdiff_t	SignedSize
	Signed Size type e.g. used as pointer difference. More...
typedef std::vector< Int >	IntList
	Vector of signed integers. More...
typedef std::vector< double >	DoubleList
	Vector of double precision real types. More...
typedef std::vector< String >	StringList
	Vector of String. More...
typedef boost::shared_ptr< const Eigen::MatrixXd >	EigenMatrixXdPtr
typedef boost::shared_ptr< Eigen::MatrixXd >	MutableEigenMatrixXdPtr
typedef OpenMS::OnDiscMSExperiment	OnDiscPeakMap
using	IndProtGrp = OpenMS::ProteinIdentification::ProteinGroup
using	IndProtGrps = std::vector< IndProtGrp >
typedef std::vector< MzTabProteinSectionRow >	MzTabProteinSectionRows
typedef std::vector< MzTabPeptideSectionRow >	MzTabPeptideSectionRows
typedef std::vector< MzTabPSMSectionRow >	MzTabPSMSectionRows
typedef std::vector< MzTabSmallMoleculeSectionRow >	MzTabSmallMoleculeSectionRows
typedef std::vector< MzTabNucleicAcidSectionRow >	MzTabNucleicAcidSectionRows
typedef std::vector< MzTabOligonucleotideSectionRow >	MzTabOligonucleotideSectionRows
typedef std::vector< MzTabOSMSectionRow >	MzTabOSMSectionRows
typedef std::pair< String, MzTabString >	MzTabOptionalColumnEntry
typedef std::vector< MzTabMSmallMoleculeSectionRow >	MzTabMSmallMoleculeSectionRows
typedef std::vector< MzTabMSmallMoleculeFeatureSectionRow >	MzTabMSmallMoleculeFeatureSectionRows
typedef std::vector< MzTabMSmallMoleculeEvidenceSectionRow >	MzTabMSmallMoleculeEvidenceSectionRows
typedef Peak2D	PeakType
using	RangeAllType = RangeManager< RangeRT, RangeMZ, RangeIntensity, RangeMobility >
	Range which contains all known dimensions. More...
typedef MSSpectrum	PeakSpectrum
	Spectrum consisting of raw data points or peaks. More...
typedef MSExperiment	PeakMap
	Two-dimensional map of raw data points or peaks. More...
typedef MSChromatogram	Chromatogram
	Chromatogram consisting of raw data points or peaks. More...
typedef boost::shared_ptr< DataProcessing >	DataProcessingPtr
typedef boost::shared_ptr< const DataProcessing >	ConstDataProcessingPtr
typedef boost::shared_ptr< OSWData >	OSWDataSharedPtrType
	SharedPtr on OSWData. More...
using	PointXYType = DPosition< 2U >
	Type of the Points in a 'flat' canvas (1D and 2D) More...
using	LayerDataBaseUPtr = std::unique_ptr< LayerDataBase >
using	LayerDataChromUPtr = std::unique_ptr< LayerDataChrom >
using	LayerDataPeakUPtr = std::unique_ptr< LayerDataPeak >
using	LayerDataFeatureUPtr = std::unique_ptr< LayerDataFeature >
using	LayerDataConsensusUPtr = std::unique_ptr< LayerDataConsensus >
using	FS_TV = FlagSet< TV_STATUS >
using	FS_LAYER = FlagSet< LayerDataBase::DataType >
using	RangeStatsInt = RangeStats< int >
using	RangeStatsDouble = RangeStats< double >
using	RangeStatsVariant = std::variant< RangeStatsInt, RangeStatsDouble >
using	StatsMap = std::map< RangeStatsType, RangeStatsVariant >
	collection of Min/Max/Avg statistics from different sources. Note: must be sorted, i.e. do not switch to unordered_map! More...
using	StatsCounterMap = std::map< std::string, StatsCounter >
	collection of MetaValues which are not numeric (counts only the number of occurrences per metavalue) More...

Enumerations
enum class	ConsoleColor {   RED , GREEN , YELLOW , BLUE ,   MAGENTA , CYAN , UNDERLINE , BRIGHT ,   INVERT }
	Text colors/styles supported by Colorizer. More...
enum class	DIM_UNIT {   RT = 0 , MZ , INT , IM_MS ,   IM_VSSC , FAIMS_CV , SIZE_OF_DIM_UNITS }
enum	ASCII {   ASCII__BACKSPACE = '\b' , ASCII__BELL = '\a' , ASCII__CARRIAGE_RETURN = '\r' , ASCII__HORIZONTAL_TAB = '\t' ,   ASCII__NEWLINE = '\n' , ASCII__RETURN = ASCII__NEWLINE , ASCII__SPACE = ' ' , ASCII__TAB = ASCII__HORIZONTAL_TAB ,   ASCII__VERTICAL_TAB = '\v' , ASCII__COLON = ':' , ASCII__COMMA = ',' , ASCII__EXCLAMATION_MARK = '!' ,   ASCII__POINT = '.' , ASCII__QUESTION_MARK = '?' , ASCII__SEMICOLON = ';' }
enum class	FilterLayout { COMPACT , ONE_BY_ONE , BOTH }
enum	MzTabCellStateType {   MZTAB_CELLSTATE_DEFAULT , MZTAB_CELLSTATE_NULL , MZTAB_CELLSTATE_NAN , MZTAB_CELLSTATE_INF ,   SIZE_OF_MZTAB_CELLTYPE }
	Base functionality to for MzTab data models. More...
enum	Newline { nl }
	custom newline indicator More...
enum class	DriftTimeUnit {   NONE , MILLISECOND , VSSC , FAIMS_COMPENSATION_VOLTAGE ,   SIZE_OF_DRIFTTIMEUNIT }
	Drift time unit for ion mobility. More...
enum class	IMFormat {   NONE , CONCATENATED , MULTIPLE_SPECTRA , MIXED ,   SIZE_OF_IMFORMAT }
	Different ways to represent ion mobility data in a spectrum. More...
enum class	DIM { X = 0 , Y = 1 , Z = 2 }
enum class	MSDim { RT , MZ , INT , IM }
	Dimensions of data acquisition for MS data. More...
enum class	HasRangeType { ALL , SOME , NONE }
	Enum listing state of dimensions (RangeBases) More...
enum class	IntensityAveragingMethod : int {   MEDIAN , MEAN , SUM , MIN ,   MAX }
	Possible methods for merging peak intensities. More...
enum class	CheckBoxState { HIDDEN , ENABLED , PRECHECKED }
	state of an ion (and its intensity) More...
enum class	WidgetHeader { VISIBLE_ONLY , WITH_INVISIBLE }
	Enum to decide which headers(=column) names should be get/set in a table/tree widget. More...
enum class	ShapeIcon { DIAMOND , SQUARE , CIRCLE , TRIANGLE }
enum class	TV_STATUS {   HAS_CANVAS , HAS_LAYER , HAS_MIRROR_MODE , IS_1D_VIEW ,   TOPP_IDLE }
enum class	RangeStatsSource { CORE , METAINFO , ARRAYINFO , SIZE_OF_STATSSOURCE }
	Where did a statistic come from? Useful for display to user, and for internal dispatch when user requests a more detailed value distribution. More...

Functions
std::ostream &	operator<< (std::ostream &os, const AccurateMassSearchResult &amsr)
AA	nextValidAA (const std::string::const_iterator end, std::string::const_iterator &it_q)
template<>
String	ChromatogramExtractor::extract_id_< OpenSwath::LightTargetedExperiment > (OpenSwath::LightTargetedExperiment &transition_exp_used, const String &id, int &prec_charge)
template<>
String	ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment > (OpenMS::TargetedExperiment &transition_exp_used, const String &id, int &prec_charge)
std::ostream &	operator<< (std::ostream &os, const TargetedExperiment::SummaryStatistics &s)
	prints out the summary statistics More...
std::ostream &	operator<< (std::ostream &os, const AASequence &peptide)
std::istream &	operator>> (std::istream &os, const AASequence &peptide)
std::ostream &	operator<< (std::ostream &os, const DigestionEnzyme &enzyme)
std::ostream &	operator<< (std::ostream &os, const DigestionEnzymeProtein &enzyme)
std::ostream &	operator<< (std::ostream &, const Element &)
std::ostream &	operator<< (std::ostream &os, const EmpiricalFormula &formula)
std::ostream &	operator<< (std::ostream &os, const Residue &residue)
std::ostream &	operator<< (std::ostream &os, const Ribonucleotide &ribo)
	Stream output operator. More...
bool	compareBinaryTreeNode (const BinaryTreeNode &x, const BinaryTreeNode &y)
	returns the value of (x.distance < y.distance) for use with sort More...
template<UInt N, typename T >
std::size_t	hash_value (const DPosition< N, T > &b)
std::ostream &	operator<< (std::ostream &o_stream, OpenMS::Colorizer &col)
std::ostream &	operator<< (std::ostream &os, const Exception::BaseException &e)
	Output operator for exceptions. More...
std::ostream &	operator<< (std::ostream &os, LogConfigHandler const &lch)
	Overload for the insertion operator (operator<<) to have a formatted output of the LogConfigHandler. More...
template<typename FloatingPointType >
const PrecisionWrapper< FloatingPointType >	precisionWrapper (const FloatingPointType rhs)
	Wrapper function that sets the appropriate precision for output temporarily. The original precision is restored afterwards so that no side effects remain. This is a "make"-function that deduces the typename FloatingPointType from its argument and returns a PrecisionWrapper<FloatingPointType>. More...
template<typename FloatingPointType >
std::ostream &	operator<< (std::ostream &os, const PrecisionWrapper< FloatingPointType > &rhs)
	Output operator for a PrecisionWrapper. Specializations are defined for float, double, long double. More...
std::ostream &	operator<< (std::ostream &os, StreamHandler const &stream_handler)
	Overload for the insertion operator (operator<<) to have a formatted output of the StreamHandler. More...
template<typename Type >
std::string	typeAsString (const Type &=Type())
	Returns the Type as as std::string. More...
std::ostream &	operator<< (std::ostream &os, const ChargePair &cons)
	Print the contents of a ChargePair to a stream. More...
template<UInt D>
std::ostream &	operator<< (std::ostream &os, const DBoundingBox< D > &bounding_box)
	Print the contents to a stream. More...
template<typename Value >
std::ostream &	operator<< (std::ostream &os, const DistanceMatrix< Value > &matrix)
	Print the contents to a stream. More...
template<UInt D, typename TCoordinateType >
DPosition< D, TCoordinateType >	operator* (DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
	Scalar multiplication (a bit inefficient) More...
template<UInt D, typename TCoordinateType >
DPosition< D, TCoordinateType >	operator* (typename DPosition< D, TCoordinateType >::CoordinateType scalar, DPosition< D, TCoordinateType > position)
	Scalar multiplication (a bit inefficient) More...
template<UInt D, typename TCoordinateType >
DPosition< D, TCoordinateType >	operator/ (DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
	Scalar multiplication (a bit inefficient) More...
template<UInt D, typename TCoordinateType >
std::ostream &	operator<< (std::ostream &os, const DPosition< D, TCoordinateType > &pos)
	Print the contents to a stream. More...
template<UInt D>
std::ostream &	operator<< (std::ostream &os, const DRange< D > &area)
	Print the contents to a stream. More...
template<typename T >
std::ostream &	operator<< (std::ostream &os, const std::vector< T > &v)
	Output stream operator for std::vectors. More...
template<typename T >
std::ostream &	operator<< (std::ostream &os, const VecLowPrecision< T > &val)
template<typename TString >
std::vector< String > &	operator<< (std::vector< String > &sl, const TString &string)
	Operator for appending entries with less code. More...
template<typename Value >
std::ostream &	operator<< (std::ostream &os, const Matrix< Value > &matrix)
	Print the contents to a stream. More...
std::ostream &	operator<< (std::ostream &os, const Param &param)
	Output of Param to a stream. More...
::size_t	hash_value (OpenMS::String const &s)
EigenMatrixXdPtr	convertOpenMSMatrix2EigenMatrixXd (const Matrix< double > &m)
bool	matrixIsIdentityMatrix (const Matrix< double > &channel_frequency)
float	estimateNoiseFromRandomScans (const MSExperiment &exp, const UInt ms_level, const UInt n_scans=10, const double percentile=80)
UInt32	endianize32 (const UInt32 &n)
	Endianizes a 32 bit type from big endian to little endian and vice versa. More...
UInt64	endianize64 (const UInt64 &n)
	Endianizes a 64 bit type from big endian to little endian and vice versa. More...
template<int type_size>
void	invertEndianess (void *byte_buffer, const size_t element_count)
template<>
void	invertEndianess< 4 > (void *byte_buffer, const size_t element_count)
template<>
void	invertEndianess< 8 > (void *byte_buffer, const size_t element_count)
std::ostream &	operator<< (std::ostream &os, const ControlledVocabulary &cv)
	Print the contents to a stream. More...
DriftTimeUnit	toDriftTimeUnit (const std::string &dtu_string)
const std::string &	toString (const DriftTimeUnit value)
IMFormat	toIMFormat (const std::string &IM_format)
const std::string &	toString (const IMFormat value)
std::ostream &	operator<< (std::ostream &os, const ChromatogramPeak &point)
	Print the contents to a stream. More...
std::ostream &	operator<< (std::ostream &os, const ConsensusFeature &cons)
	Print the contents of a ConsensusFeature to a stream. More...
std::ostream &	operator<< (std::ostream &os, const ConsensusMap &cons_map)
	Print the contents of a ConsensusMap to a stream. More...
std::ostream &	operator<< (std::ostream &os, const FeatureHandle &cons)
	Print the contents of a FeatureHandle to a stream. More...
std::ostream &	operator<< (std::ostream &os, const AnnotationStatistics &ann)
	Print content of an AnnotationStatistics object to a stream. More...
std::ostream &	operator<< (std::ostream &os, const FeatureMap &map)
std::ostream &	operator<< (std::ostream &os, const MobilityPeak1D &point)
	Print the contents to a stream. More...
std::ostream &	operator<< (std::ostream &os, const MobilityPeak2D &point)
	Print the contents to a stream. More...
std::ostream &	operator<< (std::ostream &os, const Mobilogram &mb)
std::ostream &	operator<< (std::ostream &os, const MSChromatogram &chrom)
	Print the contents to a stream. More...
std::ostream &	operator<< (std::ostream &os, const MSExperiment &exp)
	Print the contents to a stream. More...
std::ostream &	operator<< (std::ostream &os, const MSSpectrum &spec)
std::ostream &	operator<< (std::ostream &os, const Peak1D &point)
	Print the contents to a stream. More...
std::ostream &	operator<< (std::ostream &os, const Peak2D &point)
	Print the contents to a stream. More...
std::ostream &	operator<< (std::ostream &out, const RangeBase &b)
std::ostream &	operator<< (std::ostream &out, const RangeRT &range)
std::ostream &	operator<< (std::ostream &out, const RangeMZ &range)
std::ostream &	operator<< (std::ostream &out, const RangeIntensity &range)
std::ostream &	operator<< (std::ostream &out, const RangeMobility &range)
template<typename... Range>
std::ostream &	operator<< (std::ostream &out, const RangeManager< Range... > &me)
template<class DataArrayT >
DataArrayT::iterator	getDataArrayByName (DataArrayT &a, const String &name)
	Helper functions for MSSpectrum and MSChromatogram. More...
template<class DataArrayT >
DataArrayT::const_iterator	getDataArrayByName (const DataArrayT &a, const String &name)
template<typename PeakContainerT >
void	removePeaks (PeakContainerT &p, const double pos_start, const double pos_end, const bool ignore_data_arrays=false)
	remove all peaks EXCEPT in the given range More...
template<typename PeakContainerT >
void	subtractMinimumIntensity (PeakContainerT &p)
template<typename PeakContainerT >
void	makePeakPositionUnique (PeakContainerT &p, const IntensityAveragingMethod m=IntensityAveragingMethod::MEDIAN)
	Make peak positions unique. More...
void	copySpectrumMeta (const MSSpectrum &input, MSSpectrum &output, bool clear_spectrum=true)
	Copies only the meta data contained in the input spectrum to the output spectrum. More...
std::ostream &	operator<< (std::ostream &os, const ChromatogramSettings &spec)
	Print the contents to a stream. More...
std::ostream &	operator<< (std::ostream &os, const ExperimentalSettings &exp)
	Print the contents to a stream. More...
template<typename ContainerType , typename PredicateType >
static void	removeFromSetIf_ (ContainerType &container, PredicateType predicate)
	Representation of spectrum identification results and associated data. More...
std::ostream &	operator<< (std::ostream &stream, const PeptideHit &hit)
	Stream operator. More...
std::ostream &	operator<< (std::ostream &stream, const ProteinHit &hit)
	Stream operator. More...
std::ostream &	operator<< (std::ostream &os, const SpectrumSettings &spec)
	Print the contents to a stream. More...
std::string	bytesToHumanReadable (UInt64 bytes)
	convert bytes to a human readable unit (TiB, GiB, MiB, KiB), e.g. "45.34 MiB" More...
template<typename PeakType >
bool	intensityComparator (const PeakType &a, const PeakType &b)
template<typename PeakType >
bool	intensityAscendingComparator (const PeakType &a, const PeakType &b)
template<typename PeakType >
bool	intensityPointerComparator (PeakType *a, PeakType *b)
template<typename PeakType >
bool	positionComparator (const PeakType &a, const PeakType &b)
bool	operator< (const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
bool	sort_peaks_by_intensity (const PeakCandidate &a, const PeakCandidate &b)
std::ostream &	operator<< (std::ostream &os, const LayerDataBase &rhs)
	Print the contents to a stream. More...
FS_TV	operator+ (const TV_STATUS left, const TV_STATUS right)
	allow + operations on the enum, e.g. 'HAS_CANVAS + HAS_LAYER + IS_1D_VIEW' More...
FS_LAYER	operator+ (const LayerDataBase::DataType left, const LayerDataBase::DataType right)
	allow + operations on the enum, e.g. 'DT_PEAK + DT_FEATURE' More...
Numbers of digits used for writing floating point numbers (a.k.a. precision).
These functions are provided to unify the handling of this issue throughout OpenMS. (So please don't use ad-hoc numbers ;-) ) If you want to avoid side effects you can use precisionWrapper() to write a floating point number with appropriate precision; in this case the original state of the stream is automatically restored afterwards. See precisionWrapper() for details. In practice, the number of decimal digits that the type can represent without loss of precision are 6 digits for single precision and 15 digits for double precision. We have \(2^{24}/10^{6}=16.777216\) and \(2^{53}/10^{15}=9.007199254740992\), so rounding will remove the remaining difference. Example: #define NUMBER 12345.67890123456789012345678901 std::cout << NUMBER << '\n'; // default precision, writes: 12345.7 double d = NUMBER; std::cout.precision(writtenDigits<double>(0.0)); // explicit template instantiation std::cout << writtenDigits<double>(0.0) << ": " << d << '\n'; // writes: 15: 12345.6789012346 float r = NUMBER; std::cout.precision(writtenDigits(r)); // type deduced from argument std::cout << writtenDigits(r) << ": " << r << '\n'; // writes: 6: 12345.7 long double l = NUMBER; std::cout.precision(writtenDigits(1L)); // argument is not used, but L suffix indicates a long double std::cout << writtenDigits(1L) << ": " << l << '\n'; // writes: 18: 12345.6789012345671 double x = 88.99; std::cout.precision(15); std::cout << "15: " << x << '\n'; // writes: 15: 88.99 std::cout.precision(16); std::cout << "16: " << x << '\n'; // writes: 16: 88.98999999999999
template<typename FloatingPointType >
constexpr Int	writtenDigits (const FloatingPointType &=FloatingPointType())
	Number of digits commonly used for writing a floating point type (a.k.a. precision). Specializations are defined for float, double, long double. More...
template<>
constexpr Int	writtenDigits< float > (const float &)
	Number of digits commonly used for writing a float (a.k.a. precision). More...
template<>
constexpr Int	writtenDigits< double > (const double &)
	Number of digits commonly used for writing a double (a.k.a. precision). More...
template<>
constexpr Int	writtenDigits< int > (const int &)
	We do not want to bother people who unintentionally provide an int argument to this. More...
template<>
constexpr Int	writtenDigits< unsigned int > (const unsigned int &)
	We do not want to bother people who unintentionally provide an unsigned int argument to this. More...
template<>
constexpr Int	writtenDigits< long int > (const long int &)
	We do not want to bother people who unintentionally provide a long int argument to this. More...
template<>
constexpr Int	writtenDigits< unsigned long int > (const unsigned long int &)
	We do not want to bother people who unintentionally provide an unsigned long int argument to this. More...
template<>
constexpr Int	writtenDigits< DataValue > (const DataValue &)
	DataValue will be printed like double. More...
template<>
constexpr Int	writtenDigits< long double > (const long double &)
	Number of digits commonly used for writing a long double (a.k.a. precision). ... More...

Variables
constexpr char const	AAtoChar [28]
constexpr char const	CharToAA [128]
	Conversion table from 7-bit ASCII char to internal value representation for an amino acid (AA) More...
struct OpenMS::PrecursorMassComparator	PrecursorMZLess
struct OpenMS::SpectralMatchScoreComparator	SpectralMatchScoreGreater
Colorizer	red
Colorizer	green
Colorizer	yellow
Colorizer	blue
Colorizer	magenta
Colorizer	cyan
Colorizer	bright
Colorizer	underline
Colorizer	invert
std::string_view	DIM_NAMES [(int) DIM_UNIT::SIZE_OF_DIM_UNITS] = {"RT [s]", "m/z [Th]", "intensity", "IM [milliseconds]", "IM [vs / cm2]", "FAIMS CV"}
std::string_view	DIM_NAMES_SHORT [(int) DIM_UNIT::SIZE_OF_DIM_UNITS] = {"RT", "m/z", "int", "IM", "IM", "FCV"}
Logger::LogStream	OpenMS_Log_fatal
	Global static instance of a LogStream to capture messages classified as fatal errors. By default it is bound to cerr. More...
Logger::LogStream	OpenMS_Log_error
	Global static instance of a LogStream to capture messages classified as errors. By default it is bound to cerr. More...
Logger::LogStream	OpenMS_Log_warn
	Global static instance of a LogStream to capture messages classified as warnings. By default it is bound to cout. More...
Logger::LogStream	OpenMS_Log_info
	Global static instance of a LogStream to capture messages classified as information. By default it is bound to cout. More...
Logger::LogStream	OpenMS_Log_debug
	Global static instance of a LogStream to capture messages classified as debug output. By default it is not bound to any output stream. TOPP(AS)Base will connect cout, iff 0 < debug-level. More...
StreamHandler	STREAM_HANDLER
	Global StreamHandler instance. More...
const double	BinaryDataEncoder_default_numpressErrorTolerance = .0001
const std::string	NamesOfDriftTimeUnit [(size_t) DriftTimeUnit::SIZE_OF_DRIFTTIMEUNIT]
	Names of IM Units. Should be usable as axis annotation. More...
const std::string	NamesOfIMFormat [(size_t) IMFormat::SIZE_OF_IMFORMAT]
	Names of IMFormat. More...
static const std::array< const char *,(size_t) RangeStatsSource::SIZE_OF_STATSSOURCE >	StatsSourceNames = {"core statistics", "meta values", "data arrays"}
	Names corresponding to elements of enum RangeStatsSource. More...
const std::string	user_section = "preferences:user:"
const FileTypeList	supported_types ({ FileTypes::MZML, FileTypes::MZXML, FileTypes::MZDATA, FileTypes::SQMASS, FileTypes::FEATUREXML, FileTypes::CONSENSUSXML, FileTypes::IDXML, FileTypes::DTA, FileTypes::DTA2D, FileTypes::MGF, FileTypes::MS2, FileTypes::MSP, FileTypes::BZ2, FileTypes::GZ })
	supported types which can be opened with File–>Open More...

Detailed Description

Main OpenMS namespace.

Total Ion Count (TIC) as a QC metric.

Number of MS spectra per MS level (SpectrumCount) as a QC metric.

Detected Proteins/Peptides as a Proteomics QC metric.

Detected Compounds as a Metabolomics QC metric.

In this namespace all the main OpenMS classes are located.

Simple class to return a summary of detected compounds from a featureXML file.

Simple class to return a summary of detected proteins/peptides from a given idXML file.

Simple class to calculate the TIC of an MSExperiment. Allows for multiple usage, because each calculated TIC is stored internally. Those results can then be returned using getResults().

---

Class Documentation

OpenMS::ProbablePhosphoSites

class OpenMS::ProbablePhosphoSites

Collaboration diagram for ProbablePhosphoSites:

Class Members
Size	AScore
Size	first
Size	peak_depth	filtering level that gave rise to maximum discriminatory score
Size	second
Size	seq_1	index of best permutation with site in phosphorylated state
Size	seq_2	index of permutation with site in unphosphorylated state

OpenMS::OpenSwath_Scores_Usage

struct OpenMS::OpenSwath_Scores_Usage

A structure to store which scores should be used by the OpenSWATH Algorithm.

This can be used to turn on/off individual scores.

Collaboration diagram for OpenSwath_Scores_Usage:

Class Members
bool	use_coelution_score_
bool	use_dia_scores_
bool	use_elution_model_score_
bool	use_im_scores
bool	use_intensity_score_
bool	use_ionseries_scores
bool	use_library_score_
bool	use_mi_score_
bool	use_ms1_correlation
bool	use_ms1_fullscan
bool	use_ms1_mi
bool	use_ms2_isotope_scores
bool	use_nr_peaks_score_
bool	use_rt_score_
bool	use_shape_score_
bool	use_sn_score_
bool	use_sonar_scores
bool	use_total_mi_score_
bool	use_total_xic_score_
bool	use_uis_scores

OpenMS::ChromExtractParams

struct OpenMS::ChromExtractParams

ChromatogramExtractor parameters.

A small helper struct to pass the parameters for the chromatogram extraction through to the actual algorithm.

Collaboration diagram for ChromExtractParams:

Class Members
double	extra_rt_extract	Whether to extract some extra in the retention time (can be useful if one wants to look at the chromatogram outside the window)
String	extraction_function	The extraction function in mass space.
double	im_extraction_window	Extraction window in ion mobility.
double	min_upper_edge_dist	Whether to not extract anything closer than this (in Da) from the upper edge.
double	mz_extraction_window	Extraction window in Da or ppm (e.g. 50ppm means extraction +/- 25ppm)
bool	ppm	Whether the extraction window is given in ppm or Da.
double	rt_extraction_window	The retention time extraction window.

OpenMS::RNPxlModificationMassesResult

struct OpenMS::RNPxlModificationMassesResult

Collaboration diagram for RNPxlModificationMassesResult:

Class Members
map< String, set< String > >	mod_combinations	empirical formula -> nucleotide formula(s) (formulas if modifications lead to ambiguities)
map< String, double >	mod_masses	empirical formula -> mass

OpenMS::FASTAContainer

class OpenMS::FASTAContainer

template<typename TBackend>
class OpenMS::FASTAContainer< TBackend >

template parameter for vector-based FASTA access

This class allows for a chunk-wise single linear read over a (large) FASTA file, with spurious (since potentially slow) access to earlier entries which are currently not in the active chunk.

Internally uses FASTAFile class to read single sequences.

FASTAContainer supports two template specializations FASTAContainer<TFI_File> and FASTAContainer<TFI_Vector>.

FASTAContainer<TFI_File> will make FASTA entries available chunk-wise from start to end by loading it from a FASTA file. This avoids having to load the full file into memory. While loading, the container will memorize the file offsets of each entry, allowing to read an arbitrary i'th entry again from disk. If possible, only entries from the currently cached chunk should be queried, otherwise access will be slow.

FASTAContainer<TFI_Vector> simply takes an existing vector of FASTAEntries and provides the same interface (with a potentially huge speed benefit over FASTAContainer<TFI_File> since it does not need disk access, but at the cost of memory).

If an algorithm searches through a FASTA file linearly, you can use FASTAContainer<TFI_File> to pre-load a small chunk and start working, while loading the next chunk in a background thread and swap it in when the active chunk was processed.

OpenMS::Range

struct OpenMS::Range

Internal structure to store a lower and upper bound of an m/z range.

Collaboration diagram for Range:

Class Members
double	left_boundary
double	right_boundary

OpenMS::MzTabModificationMetaData

struct OpenMS::MzTabModificationMetaData

Collaboration diagram for MzTabModificationMetaData:

Class Members
MzTabParameter	modification
MzTabString	position
MzTabString	site

OpenMS::MzTabAssayMetaData

struct OpenMS::MzTabAssayMetaData

Collaboration diagram for MzTabAssayMetaData:

Class Members
vector< int >	ms_run_ref
map< Size, MzTabModificationMetaData >	quantification_mod
MzTabParameter	quantification_reagent
MzTabString	sample_ref

OpenMS::MzTabMSRunMetaData

struct OpenMS::MzTabMSRunMetaData

Collaboration diagram for MzTabMSRunMetaData:

Class Members
MzTabParameter	format
MzTabParameterList	fragmentation_method
MzTabParameter	id_format
MzTabString	location

OpenMS::MzTabStudyVariableMetaData

struct OpenMS::MzTabStudyVariableMetaData

Collaboration diagram for MzTabStudyVariableMetaData:

Class Members
vector< int >	assay_refs
MzTabString	description
vector< int >	sample_refs

OpenMS::MzTabPeptideSectionRow

struct OpenMS::MzTabPeptideSectionRow

PEP - Peptide section (Table based)

Collaboration diagram for MzTabPeptideSectionRow:

Class Members
MzTabString	accession	The protein’s accession.
map< Size, MzTabDouble >	best_search_engine_score	Search engine(s) score(s) for the peptide.
MzTabInteger	charge	Precursor ion’s charge.
MzTabString	database	Name of the sequence database.
MzTabString	database_version	Version (and optionally # of entries).
MzTabDouble	mass_to_charge	Precursor ion’s m/z.
MzTabModificationList	modifications	Modifications identified in the peptide.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
map< Size, MzTabDouble >	peptide_abundance_assay
map< Size, MzTabDouble >	peptide_abundance_std_error_study_variable
map< Size, MzTabDouble >	peptide_abundance_stdev_study_variable
map< Size, MzTabDouble >	peptide_abundance_study_variable
MzTabInteger	reliability	(1-3) 0=null Identification reliability for the peptide.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabDoubleList	retention_time_window
MzTabParameterList	search_engine	Search engine(s) that identified the peptide.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run
MzTabString	sequence	The peptide’s sequence.
MzTabSpectraRef	spectra_ref	Spectra identifying the peptide.
MzTabBoolean	unique	0=false, 1=true, null else: Peptide is unique for the protein.
MzTabString	uri	Location of the PSMs source entry.

OpenMS::MzTabSmallMoleculeSectionRow

struct OpenMS::MzTabSmallMoleculeSectionRow

SML Small molecule section (table based)

Collaboration diagram for MzTabSmallMoleculeSectionRow:

Class Members
map< Size, MzTabDouble >	best_search_engine_score	Search engine(s) identifications score(s).
MzTabDouble	calc_mass_to_charge	Precursor ion’s m/z.
MzTabInteger	charge	Precursor ion’s charge.
MzTabString	chemical_formula	Chemical formula of the identified compound.
MzTabString	database	Name of the used database.
MzTabString	database_version	String Version of the database (and optionally # of compounds).
MzTabString	description	Human readable description (i.e. the name)
MzTabDouble	exp_mass_to_charge	Precursor ion’s m/z.
MzTabStringList	identifier	The small molecule’s identifier.
MzTabString	inchi_key	InChi Key of the identified compound.
MzTabString	modifications	Modifications identified on the small molecule.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabInteger	reliability	(1-3) The identification reliability.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabParameterList	search_engine	Search engine(s) identifying the small molecule.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run
map< Size, MzTabDouble >	smallmolecule_abundance_assay
map< Size, MzTabDouble >	smallmolecule_abundance_std_error_study_variable
map< Size, MzTabDouble >	smallmolecule_abundance_stdev_study_variable
map< Size, MzTabDouble >	smallmolecule_abundance_study_variable
MzTabString	smiles	Molecular structure in SMILES format.
MzTabString	species	Human readable name of the species.
MzTabSpectraRef	spectra_ref	Spectra identifying the small molecule.
MzTabInteger	taxid	NEWT taxonomy for the species.
MzTabString	uri	The source entry’s location.

OpenMS::MzTabNucleicAcidSectionRow

struct OpenMS::MzTabNucleicAcidSectionRow

NUC - Nucleic acid section (table-based)

Collaboration diagram for MzTabNucleicAcidSectionRow:

Class Members
MzTabString	accession	The nucleic acid’s accession.
MzTabStringList	ambiguity_members	Alternative nucleic acid identifications.
map< Size, MzTabDouble >	best_search_engine_score	Best search engine(s) score(s) (over all MS runs)
MzTabDouble	coverage	(0-1) Fraction of nucleic acid sequence identified.
MzTabString	database	Name of the sequence database.
MzTabString	database_version	Version of the sequence database.
MzTabString	description	Human readable description (i.e. the name)
MzTabStringList	go_terms	List of GO terms for the nucleic acid.
MzTabModificationList	modifications	Modifications identified in the nucleic acid.
map< Size, MzTabInteger >	num_oligos_distinct_ms_run
map< Size, MzTabInteger >	num_oligos_unique_ms_run
map< Size, MzTabInteger >	num_osms_ms_run
vector< MzTabOptionalColumnEntry >	opt_	Optional Columns must start with “opt_”
MzTabInteger	reliability
MzTabParameterList	search_engine	Search engine(s) that identified the nucleic acid.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run
MzTabString	species	Human readable name of the species.
MzTabInteger	taxid	NEWT taxonomy for the species.
MzTabString	uri	Location of the nucleic acid’s source entry.

OpenMS::MzTabOligonucleotideSectionRow

struct OpenMS::MzTabOligonucleotideSectionRow

OLI - Oligonucleotide section (table-based)

Collaboration diagram for MzTabOligonucleotideSectionRow:

Class Members
MzTabString	accession	The nucleic acid’s accession.
map< Size, MzTabDouble >	best_search_engine_score	Search engine(s) score(s) for the match.
MzTabInteger	end
MzTabModificationList	modifications	Modifications identified in the oligonucleotide.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabString	post
MzTabString	pre
MzTabInteger	reliability	(1-3) 0=null Identification reliability for the match.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabDoubleList	retention_time_window
MzTabParameterList	search_engine	Search engine(s) that identified the match.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run	Search engine(s) score(s) per individual MS run.
MzTabString	sequence	The oligonucleotide’s sequence.
MzTabInteger	start
MzTabBoolean	unique	0=false, 1=true, null else: Oligonucleotide maps uniquely to the nucleic acid sequence.
MzTabString	uri	Location of the oligonucleotide's source entry.

OpenMS::MzTabOSMSectionRow

struct OpenMS::MzTabOSMSectionRow

OSM - OSM (oligonucleotide-spectrum match) section (table-based)

Collaboration diagram for MzTabOSMSectionRow:

Class Members
MzTabDouble	calc_mass_to_charge	The theoretical m/z ratio of the oligonucleotide.
MzTabInteger	charge	The charge of the experimental precursor ion.
MzTabDouble	exp_mass_to_charge	The m/z ratio of the experimental precursor ion.
MzTabModificationList	modifications	Modifications identified in the oligonucleotide.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabInteger	reliability	(1-3) 0=null Identification reliability for the match.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabParameterList	search_engine	Search engine(s) that identified the match.
map< Size, MzTabDouble >	search_engine_score	Search engine(s) score(s) for the match.
MzTabString	sequence	The oligonucleotide’s sequence.
MzTabSpectraRef	spectra_ref	Reference to the spectrum underlying the match.
MzTabString	uri	Location of the OSM’s source entry.

OpenMS::MzTabSoftwareMetaData

struct OpenMS::MzTabSoftwareMetaData

Collaboration diagram for MzTabSoftwareMetaData:

Class Members
map< Size, MzTabString >	setting
MzTabParameter	software

OpenMS::MzTabSampleMetaData

struct OpenMS::MzTabSampleMetaData

Collaboration diagram for MzTabSampleMetaData:

Class Members
map< Size, MzTabParameter >	cell_type
map< Size, MzTabParameter >	custom
MzTabString	description
map< Size, MzTabParameter >	disease
map< Size, MzTabParameter >	species
map< Size, MzTabParameter >	tissue

OpenMS::MzTabCVMetaData

struct OpenMS::MzTabCVMetaData

Collaboration diagram for MzTabCVMetaData:

Class Members
MzTabString	full_name
MzTabString	label
MzTabString	url
MzTabString	version

OpenMS::MzTabInstrumentMetaData

struct OpenMS::MzTabInstrumentMetaData

Collaboration diagram for MzTabInstrumentMetaData:

Class Members
map< Size, MzTabParameter >	analyzer
MzTabParameter	detector
MzTabParameter	name
MzTabParameter	source

OpenMS::MzTabContactMetaData

struct OpenMS::MzTabContactMetaData

Collaboration diagram for MzTabContactMetaData:

Class Members
MzTabString	affiliation
MzTabString	email
MzTabString	name

OpenMS::MzTabMAssayMetaData

class OpenMS::MzTabMAssayMetaData

MztabM Assay Metadata.

Collaboration diagram for MzTabMAssayMetaData:

Class Members
map< Size, MzTabParameter >	custom	Additional parameters or values for a given assay.
MzTabString	external_uri	A reference to further information about the assay.
MzTabInteger	ms_run_ref	An association from a given assay to the source MS run.
MzTabString	name	Name of the assay.
MzTabInteger	sample_ref	An association from a given assay to the sample analysed.

OpenMS::MzTabMMSRunMetaData

class OpenMS::MzTabMMSRunMetaData

MztabM MSRun Metadata.

Collaboration diagram for MzTabMMSRunMetaData:

Class Members
MzTabParameter	format	Parameter specifying the data format of the external MS data file.
map< Size, MzTabParameter >	fragmentation_method	The type of fragmentation used in a given ms run.
MzTabString	hash	Hash value of the corresponding external MS data file.
MzTabParameter	hash_method	Parameter specifying the hash methods.
MzTabParameter	id_format	Parameter specifying the id format used in the external data file.
MzTabInteger	instrument_ref	Link to a specific instrument.
MzTabString	location	Location of the external data file.
map< Size, MzTabParameter >	scan_polarity	The polarity mode of a given run.

OpenMS::MzTabMStudyVariableMetaData

class OpenMS::MzTabMStudyVariableMetaData

MztabM StudyVariable Metadata.

Collaboration diagram for MzTabMStudyVariableMetaData:

Class Members
vector< int >	assay_refs	References to the IDs of assays grouped in the study variable.
MzTabParameter	average_function	The function used to calculate the study variable quantification value.
MzTabString	description	A textual description of the study variable.
MzTabParameterList	factors	Additional parameters or factors.
MzTabString	name	Name of the study variable.
MzTabParameter	variation_function	The function used to calculate the study variable quantification variation value.

OpenMS::MzTabMDatabaseMetaData

class OpenMS::MzTabMDatabaseMetaData

MztabM Database Metadata.

Collaboration diagram for MzTabMDatabaseMetaData:

Class Members
MzTabParameter	database	The description of databases used.
MzTabString	prefix	The prefix used in the “identifier” column of data tables.
MzTabString	uri	The URI to the database.
MzTabString	version	The database version.

OpenMS::MzTabMSmallMoleculeSectionRow

class OpenMS::MzTabMSmallMoleculeSectionRow

SML Small molecule section (mztab-m)

Collaboration diagram for MzTabMSmallMoleculeSectionRow:

Class Members
MzTabStringList	adducts	Adducts.
MzTabParameter	best_id_confidence_measure	The identification approach with the highest confidence.
MzTabDouble	best_id_confidence_value	The best confidence measure.
MzTabStringList	chemical_formula	Potential chemical formula of the reported compound.
MzTabStringList	chemical_name	Possible chemical/common names or general description.
MzTabStringList	database_identifier	Names of the used databases.
MzTabStringList	inchi	InChi of the potential compound identifications.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabString	reliability	Reliability of the given small molecule identification.
map< Size, MzTabDouble >	small_molecule_abundance_assay	The small molecule’s abundance in every assay described in the metadata section.
map< Size, MzTabDouble >	small_molecule_abundance_study_variable	The small molecule’s abundance in all the study variables described in the metadata section.
map< Size, MzTabDouble >	small_molecule_abundance_variation_study_variable	A measure of the variability of the study variable abundance measurement.
MzTabStringList	smf_id_refs	References to all the features on which quantification has been based.
MzTabStringList	smiles	Molecular structure in SMILES format.
MzTabString	sml_identifier	The small molecule’s identifier.
MzTabDoubleList	theoretical_neutral_mass	Precursor theoretical neutral mass.
MzTabStringList	uri	The source entry’s location.

OpenMS::MzTabMSmallMoleculeFeatureSectionRow

class OpenMS::MzTabMSmallMoleculeFeatureSectionRow

SMF Small molecule feature section (mztab-m)

Collaboration diagram for MzTabMSmallMoleculeFeatureSectionRow:

Class Members
MzTabString	adduct	Adduct.
MzTabInteger	charge	Precursor ion’s charge.
MzTabDouble	exp_mass_to_charge	Precursor ion’s m/z.
MzTabParameter	isotopomer	If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabDouble	retention_time	Time point in seconds.
MzTabDouble	rt_end	The end time of the feature on the retention time axis.
MzTabDouble	rt_start	The start time of the feature on the retention time axis.
map< Size, MzTabDouble >	small_molecule_feature_abundance_assay	Feature abundance in every assay.
MzTabInteger	sme_id_ref_ambiguity_code	Ambiguity in identifications.
MzTabStringList	sme_id_refs	Reference to the identification evidence.
MzTabString	smf_identifier	Within file unique identifier for the small molecule feature.

OpenMS::MzTabMSmallMoleculeEvidenceSectionRow

class OpenMS::MzTabMSmallMoleculeEvidenceSectionRow

SME Small molecule evidence section (mztab-m)

Collaboration diagram for MzTabMSmallMoleculeEvidenceSectionRow:

Class Members
MzTabString	adduct	Adduct.
MzTabDouble	calc_mass_to_charge	Precursor ion’s m/z.
MzTabInteger	charge	Precursor ion’s charge.
MzTabString	chemical_formula	The putative molecular formula.
MzTabString	chemical_name	Possible chemical/common names or general description.
MzTabString	database_identifier	The putative identification for the small molecule sourced from an external database.
MzTabParameter	derivatized_form	derivatized form.
MzTabString	evidence_input_id	Within file unique identifier for the input data used to support this identification e.g. fragment spectrum, RT and m/z pair.
MzTabDouble	exp_mass_to_charge	Precursor ion’s m/z.
map< Size, MzTabDouble >	id_confidence_measure	Statistical value or score for the identification.
MzTabParameter	identification_method	Database search, search engine or process that was used to identify this small molecule.
MzTabString	inchi	InChi of the potential compound identifications.
MzTabParameter	ms_level	The highest MS level used to inform identification.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabInteger	rank	Rank of the identification (1 = best)
MzTabString	sme_identifier	Within file unique identifier for the small molecule evidence result.
MzTabString	smiles	Potential molecular structure as SMILES.
MzTabSpectraRef	spectra_ref	Reference to a spectrum.
MzTabString	uri	The source entry’s location.

OpenMS::ToolInfo

struct OpenMS::ToolInfo

A struct to pass information about the tool as one parameter.

Collaboration diagram for ToolInfo:

Class Members
string	category_
vector< string >	citations_
string	description_
string	docurl_
string	name_
string	version_

OpenMS::DPeak

struct OpenMS::DPeak

template<UInt dimensions>
struct OpenMS::DPeak< dimensions >

Metafunction to choose among Peak1D respectively Peak2D through a template argument.

The result is accessible via typedef Type:

• DPeak<1>::Type is Peak1D
• DPeak<2>::Type is Peak2D

Example:

template class BaseModel<UInt D>
{
    // BaseModel<D>::PeakType is either Peak1D or Peak2D, depending on D
    typedef typename DPeak<D>::Type PeakType;
};

OpenMS::FeatureFinderAlgorithmPickedHelperStructs

struct OpenMS::FeatureFinderAlgorithmPickedHelperStructs

Wrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes.

See also

FeatureFinderAlgorithmPicked

TraceFitter

OpenMS::PeakCandidate

struct OpenMS::PeakCandidate

A small structure to hold peak candidates.

Collaboration diagram for PeakCandidate:

Class Members
int	index
double	integrated_intensity
double	leftWidth
float	mz
double	peak_apex_intensity
double	rightWidth

OpenMS::StatsCounter

struct OpenMS::StatsCounter

a simple counting struct, for non-numerical occurrences of meta-values

Collaboration diagram for StatsCounter:

Class Members
size_t	counter

Typedef Documentation

ConstDataProcessingPtr

typedef boost::shared_ptr<const DataProcessing> ConstDataProcessingPtr

DataProcessingPtr

typedef boost::shared_ptr<DataProcessing> DataProcessingPtr

EigenMatrixXdPtr

typedef boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr

Matrix utility functions.

FS_LAYER

using FS_LAYER = FlagSet<LayerDataBase::DataType>

FS_TV

using FS_TV = FlagSet<TV_STATUS>

IndProtGrp

typedef OpenMS::ProteinIdentification::ProteinGroup IndProtGrp

IndProtGrps

typedef std::vector< IndProtGrp > IndProtGrps

LayerDataBaseUPtr

using LayerDataBaseUPtr = std::unique_ptr<LayerDataBase>

LayerDataChromUPtr

using LayerDataChromUPtr = std::unique_ptr<LayerDataChrom>

LayerDataConsensusUPtr

using LayerDataConsensusUPtr = std::unique_ptr<LayerDataConsensus>

LayerDataFeatureUPtr

using LayerDataFeatureUPtr = std::unique_ptr<LayerDataFeature>

LayerDataPeakUPtr

using LayerDataPeakUPtr = std::unique_ptr<LayerDataPeak>

MutableEigenMatrixXdPtr

typedef boost::shared_ptr< Eigen::MatrixXd > MutableEigenMatrixXdPtr

MzTabMSmallMoleculeEvidenceSectionRows

typedef std::vector<MzTabMSmallMoleculeEvidenceSectionRow> MzTabMSmallMoleculeEvidenceSectionRows

MzTabMSmallMoleculeFeatureSectionRows

typedef std::vector<MzTabMSmallMoleculeFeatureSectionRow> MzTabMSmallMoleculeFeatureSectionRows

MzTabMSmallMoleculeSectionRows

typedef std::vector<MzTabMSmallMoleculeSectionRow> MzTabMSmallMoleculeSectionRows

MzTabNucleicAcidSectionRows

typedef std::vector<MzTabNucleicAcidSectionRow> MzTabNucleicAcidSectionRows

MzTabOligonucleotideSectionRows

typedef std::vector<MzTabOligonucleotideSectionRow> MzTabOligonucleotideSectionRows

MzTabOptionalColumnEntry

typedef std::pair<String, MzTabString> MzTabOptionalColumnEntry

MzTabOSMSectionRows

typedef std::vector<MzTabOSMSectionRow> MzTabOSMSectionRows

MzTabPeptideSectionRows

typedef std::vector<MzTabPeptideSectionRow> MzTabPeptideSectionRows

MzTabProteinSectionRows

typedef std::vector<MzTabProteinSectionRow> MzTabProteinSectionRows

MzTabPSMSectionRows

typedef std::vector<MzTabPSMSectionRow> MzTabPSMSectionRows

MzTabSmallMoleculeSectionRows

typedef std::vector<MzTabSmallMoleculeSectionRow> MzTabSmallMoleculeSectionRows

OnDiscPeakMap

typedef OpenMS::OnDiscMSExperiment OnDiscPeakMap

OSWDataSharedPtrType

typedef boost::shared_ptr<OSWData> OSWDataSharedPtrType

SharedPtr on OSWData.

PeakType

typedef Peak2D PeakType

PointXYType

using PointXYType = DPosition<2U>

Type of the Points in a 'flat' canvas (1D and 2D)

Protease

typedef DigestionEnzymeProtein Protease

RangeAllType

using RangeAllType = RangeManager<RangeRT, RangeMZ, RangeIntensity, RangeMobility>

Range which contains all known dimensions.

RangeStatsDouble

using RangeStatsDouble = RangeStats<double>

RangeStatsInt

using RangeStatsInt = RangeStats<int>

RangeStatsVariant

using RangeStatsVariant = std::variant<RangeStatsInt, RangeStatsDouble>

RibonucleotideChainEnd

using RibonucleotideChainEnd = Ribonucleotide

Dummy nucleotide used to represent 5' and 3' chain ends. Usually, just the phosphates.

RNase

typedef DigestionEnzymeRNA RNase

ScoreToTgtDecLabelPair

typedef std::pair<double, double> ScoreToTgtDecLabelPair

Used to collect data from the ID structures with the original score as first and target decoy annotation as second member of the pair. Target = 1.0. Usually Target+decoy for peptides = target and protein groups with at least one target = target. But could also be proportional

StatsCounterMap

using StatsCounterMap = std::map<std::string, StatsCounter>

collection of MetaValues which are not numeric (counts only the number of occurrences per metavalue)

StatsMap

using StatsMap = std::map<RangeStatsType, RangeStatsVariant>

collection of Min/Max/Avg statistics from different sources. Note: must be sorted, i.e. do not switch to unordered_map!

ToolListType

typedef std::map<String, Internal::ToolDescription> ToolListType

Handles lists of TOPP tools and their categories (for TOPPAS)

Path's were *.ttd files are searched for:

Default: The OpenMS share directory ([OpenMS]/share/TOOLS/EXTERNAL) OS specific directories

• [OpenMS]/share/TOOLS/EXTERNAL/LINUX (for Mac and Linux)
• [OpenMS]/share/TOOLS/EXTERNAL/WINDOWS (for Windows) Environment: OPENMS_TTD_PATH (use only one path here!) map each tool to its ToolDescription

ToolMapping

typedef std::map<Internal::ToolDescriptionInternal, Internal::ToolDescriptionInternal> ToolMapping

Updates an INI.

map each old TOPP tool to its new Name

Enumeration Type Documentation

ASCII

enum ASCII

Enumerator
ASCII__BACKSPACE
ASCII__BELL
ASCII__CARRIAGE_RETURN
ASCII__HORIZONTAL_TAB
ASCII__NEWLINE
ASCII__RETURN
ASCII__SPACE
ASCII__TAB
ASCII__VERTICAL_TAB
ASCII__COLON
ASCII__COMMA
ASCII__EXCLAMATION_MARK
ASCII__POINT
ASCII__QUESTION_MARK
ASCII__SEMICOLON

CheckBoxState

enum CheckBoxState

strong

state of an ion (and its intensity)

Enumerator
HIDDEN	check box hidden (invisible)
ENABLED	check box enabled (visible, but not checked)
PRECHECKED	check box enabled and checked by default

ConsoleColor

enum ConsoleColor

strong

Text colors/styles supported by Colorizer.

Enumerator
RED
GREEN
YELLOW
BLUE
MAGENTA
CYAN
UNDERLINE
BRIGHT	keeps the foreground color, but makes it brighter
INVERT	invert foreground and background color (inverting twice stays inverted)

DIM

enum DIM

strong

Declare Dimensions for referencing dimensions in plotting etc e.g. Point[X], Point[Y] The order X,Y,Z,... is important here. Some classes rely upon it.

Enumerator
X
Y
Z

DIM_UNIT

enum DIM_UNIT

strong

Enum for different units which can be displayed on a plotting axis The order is arbitrary.

Enumerator
RT	RT in seconds.
MZ	m/z
INT	intensity
IM_MS	ion mobility milliseconds
IM_VSSC	volt-second per square centimeter (i.e. 1/K_0)
FAIMS_CV	FAIMS compensation voltage.
SIZE_OF_DIM_UNITS

DriftTimeUnit

enum DriftTimeUnit

strong

Drift time unit for ion mobility.

Enumerator
NONE	No unit.
MILLISECOND	milliseconds
VSSC	volt-second per square centimeter (i.e. 1/K_0)
FAIMS_COMPENSATION_VOLTAGE	compensation voltage
SIZE_OF_DRIFTTIMEUNIT

FilterLayout

enum FilterLayout

strong

Enumerator
COMPACT	make a single item, e.g. 'all readable files (*.mzML *.mzXML);;'
ONE_BY_ONE	list all types individually, e.g. 'mzML files (*.mzML);;mzXML files (*.mzXML);;'
BOTH	combine COMPACT and ONE_BY_ONE

HasRangeType

enum HasRangeType

strong

Enum listing state of dimensions (RangeBases)

Enumerator
ALL	all dimensions are filled
SOME	some dimensions are empty, some are filled
NONE	all dimensions are empty (=cleared)

IMFormat

enum IMFormat

strong

Different ways to represent ion mobility data in a spectrum.

Enumerator
NONE	no ion mobility
CONCATENATED	ion mobility frame is stacked in a single spectrum (i.e. has an IM float data array)
MULTIPLE_SPECTRA	ion mobility is recorded as multiple spectra per frame (i.e. has one IM annotation per spectrum)
MIXED	an MSExperiment contains both CONCATENATED and MULTIPLE_SPECTRA
SIZE_OF_IMFORMAT

IntensityAveragingMethod

enum IntensityAveragingMethod : int

strong

Possible methods for merging peak intensities.

See also

makePeakPositionUnique()

Enumerator
MEDIAN
MEAN
SUM
MIN
MAX

MSDim

enum MSDim

strong

Dimensions of data acquisition for MS data.

Enumerator
RT
MZ
INT
IM

Newline

enum Newline

custom newline indicator

Enumerator
nl

RangeStatsSource

enum RangeStatsSource

strong

Where did a statistic come from? Useful for display to user, and for internal dispatch when user requests a more detailed value distribution.

Enumerator
CORE	statistic was obtained from a core data structure of the container, e.g. intensity
METAINFO	statistic was obtained from MetaInfoInterface of container elements, e.g. "FWHM" for FeatureMaps
ARRAYINFO	statistic was obtained from Float/IntegerArrays of the container elements, e.g. "IonMobility" for PeakMap
SIZE_OF_STATSSOURCE

ShapeIcon

enum ShapeIcon

strong

Enumerator
DIAMOND
SQUARE
CIRCLE
TRIANGLE

TV_STATUS

enum TV_STATUS

strong

Enumerator
HAS_CANVAS
HAS_LAYER
HAS_MIRROR_MODE
IS_1D_VIEW
TOPP_IDLE

WidgetHeader

enum WidgetHeader

strong

Enum to decide which headers(=column) names should be get/set in a table/tree widget.

Enumerator
VISIBLE_ONLY
WITH_INVISIBLE

Function Documentation

bytesToHumanReadable()

std::string OpenMS::bytesToHumanReadable

(

UInt64

bytes

)

convert bytes to a human readable unit (TiB, GiB, MiB, KiB), e.g. "45.34 MiB"

ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment >()

String OpenMS::ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment > ( OpenMS::TargetedExperiment &  transition_exp_used, const String &  id, int &  prec_charge  )

inline

References OpenMS::Constants::c, PeptideCompound::getChargeState(), TargetedExperiment::getCompoundByRef(), TargetedExperiment::getPeptideByRef(), PeptideCompound::hasCharge(), TargetedExperiment::hasCompound(), TargetedExperiment::hasPeptide(), and Peptide::sequence.

ChromatogramExtractor::extract_id_< OpenSwath::LightTargetedExperiment >()

String OpenMS::ChromatogramExtractor::extract_id_< OpenSwath::LightTargetedExperiment > ( OpenSwath::LightTargetedExperiment &  transition_exp_used, const String &  id, int &  prec_charge  )

inline

References LightCompound::charge, LightCompound::compound_name, LightTargetedExperiment::getCompoundByRef(), and LightCompound::sequence.

compareBinaryTreeNode()

bool OpenMS::compareBinaryTreeNode	(	const BinaryTreeNode &	x,
		const BinaryTreeNode &	y
	)

returns the value of (x.distance < y.distance) for use with sort

convertOpenMSMatrix2EigenMatrixXd()

EigenMatrixXdPtr OpenMS::convertOpenMSMatrix2EigenMatrixXd ( const Matrix< double > &  m )

inline

References Matrix< Value >::cols(), and Matrix< Value >::rows().

copySpectrumMeta()

void OpenMS::copySpectrumMeta	(	const MSSpectrum &	input,
		MSSpectrum &	output,
		bool	clear_spectrum = true
	)

Copies only the meta data contained in the input spectrum to the output spectrum.

Note

Actual data is not copied.

Parameters

[in]	input	The input spectrum.
[out]	output	The output spectrum (will be cleared and will contain all metadata of the input spectrum).
	clear_spectrum	Whether the output spectrum should be cleared first (all raw data and data arrays will be deleted)

Referenced by PeakPickerIterative::pick().

endianize32()

UInt32 OpenMS::endianize32 ( const UInt32 &  n )

inline

Endianizes a 32 bit type from big endian to little endian and vice versa.

Referenced by Base64::decodeIntegersCompressed_(), Base64::encode(), Base64::encodeIntegers(), and invertEndianess< 4 >().

endianize64()

UInt64 OpenMS::endianize64 ( const UInt64 &  n )

inline

Endianizes a 64 bit type from big endian to little endian and vice versa.

Referenced by Base64::decodeIntegersCompressed_(), Base64::encode(), Base64::encodeIntegers(), and invertEndianess< 8 >().

estimateNoiseFromRandomScans()

float OpenMS::estimateNoiseFromRandomScans	(	const MSExperiment &	exp,
		const UInt	ms_level,
		const UInt	n_scans = 10,
		const double	percentile = 80
	)

Picks n_scans from the given ms_level randomly and returns either average intensity at a certain percentile. If no scans with the required level are present, 0.0 is returned

getDataArrayByName()

DataArrayT::const_iterator OpenMS::getDataArrayByName	(	const DataArrayT &	a,
		const String &	name
	)

hash_value() [1/2]

std::size_t OpenMS::hash_value

(

const DPosition< N, T > &

b

)

Hash value for OpenMS::DPosition.

References DPosition< D, TCoordinateType >::begin(), and DPosition< D, TCoordinateType >::end().

hash_value() [2/2]

::size_t OpenMS::hash_value

(

OpenMS::String const &

s

)

intensityAscendingComparator()

bool OpenMS::intensityAscendingComparator	(	const PeakType &	a,
		const PeakType &	b
	)

References Peak2D::getIntensity().

intensityComparator()

bool OpenMS::intensityComparator	(	const PeakType &	a,
		const PeakType &	b
	)

References Peak2D::getIntensity().

intensityPointerComparator()

bool OpenMS::intensityPointerComparator	(	PeakType *	a,
		PeakType *	b
	)

References Peak2D::getIntensity().

invertEndianess()

void OpenMS::invertEndianess ( void *  byte_buffer, const size_t  element_count  )

inline

invertEndianess< 4 >()

void OpenMS::invertEndianess< 4 > ( void *  byte_buffer, const size_t  element_count  )

inline

References endianize32().

invertEndianess< 8 >()

void OpenMS::invertEndianess< 8 > ( void *  byte_buffer, const size_t  element_count  )

inline

References endianize64().

makePeakPositionUnique()

void OpenMS::makePeakPositionUnique	(	PeakContainerT &	p,
		const IntensityAveragingMethod	m = IntensityAveragingMethod::MEDIAN
	)

Make peak positions unique.

A peak container may contain multiple peaks with the same position, i.e. either an MSSpectrum containing peaks with the same m/z position, or an MSChromatogram containing peaks with identical RT position. One scenario where this might happen is when multiple spectra are merged to a single one.

The method combines peaks with the same position to a single one with the intensity determined by method m.

Parameters

[in]	p	The peak container to be manipulated.
[in]	m	The method for determining peak intensity from peaks with same position (median, mean, sum, min, max).

References MAX, MEAN, OpenMS::Math::mean(), MEDIAN, OpenMS::Math::median(), MIN, OPENMS_LOG_WARN, SUM, and OpenMS::Math::sum().

matrixIsIdentityMatrix()

bool OpenMS::matrixIsIdentityMatrix ( const Matrix< double > &  channel_frequency )

inline

References Matrix< Value >::rows().

nextValidAA()

AA OpenMS::nextValidAA	(	const std::string::const_iterator	end,
		std::string::const_iterator &	it_q
	)

Return the first valid AA from current position of it_q in the string, or (if the string ends) an invalid AA On return, it_q points to AA after the returned AA.

operator*() [1/2]

DPosition<D, TCoordinateType> OpenMS::operator*	(	DPosition< D, TCoordinateType >	position,
		typename DPosition< D, TCoordinateType >::CoordinateType	scalar
	)

Scalar multiplication (a bit inefficient)

operator*() [2/2]

DPosition<D, TCoordinateType> OpenMS::operator*	(	typename DPosition< D, TCoordinateType >::CoordinateType	scalar,
		DPosition< D, TCoordinateType >	position
	)

Scalar multiplication (a bit inefficient)

operator+() [1/2]

FS_LAYER OpenMS::operator+	(	const LayerDataBase::DataType	left,
		const LayerDataBase::DataType	right
	)

allow + operations on the enum, e.g. 'DT_PEAK + DT_FEATURE'

operator+() [2/2]

FS_TV OpenMS::operator+	(	const TV_STATUS	left,
		const TV_STATUS	right
	)

allow + operations on the enum, e.g. 'HAS_CANVAS + HAS_LAYER + IS_1D_VIEW'

operator/()

DPosition<D, TCoordinateType> OpenMS::operator/	(	DPosition< D, TCoordinateType >	position,
		typename DPosition< D, TCoordinateType >::CoordinateType	scalar
	)

Scalar multiplication (a bit inefficient)

operator<()

bool OpenMS::operator<	(	const MultiplexDeltaMasses &	dm1,
		const MultiplexDeltaMasses &	dm2
	)

operator<<() [1/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	,
		const Element &
	)

operator<<() [2/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	o_stream,
		OpenMS::Colorizer &	col
	)

stream operator for Colorizers, which will (depending on the state of col) add color to the o_stream, and print some internal string, e.g. 'cout << red("this is red")' or 'cout << red() << "stream stays red until dooms day";' or reset the color e.g. 'cout << red.undo() << "not red anymore"'

operator<<() [3/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const AASequence &	peptide
	)

operator<<() [4/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const AccurateMassSearchResult &	amsr
	)

Referenced by SVOutStream::writeValueOrNan().

operator<<() [5/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const AnnotationStatistics &	ann
	)

Print content of an AnnotationStatistics object to a stream.

operator<<() [6/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const ChargePair &	cons
	)

Print the contents of a ChargePair to a stream.

operator<<() [7/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const ChromatogramPeak &	point
	)

Print the contents to a stream.

operator<<() [8/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const ChromatogramSettings &	spec
	)

Print the contents to a stream.

operator<<() [9/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const ConsensusFeature &	cons
	)

Print the contents of a ConsensusFeature to a stream.

operator<<() [10/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const ConsensusMap &	cons_map
	)

Print the contents of a ConsensusMap to a stream.

operator<<() [11/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const ControlledVocabulary &	cv
	)

Print the contents to a stream.

operator<<() [12/50]

std::ostream & operator<<	(	std::ostream &	os,
		const DBoundingBox< D > &	bounding_box
	)

Print the contents to a stream.

operator<<() [13/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const DigestionEnzyme &	enzyme
	)

operator<<() [14/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const DigestionEnzymeProtein &	enzyme
	)

operator<<() [15/50]

std::ostream & operator<<	(	std::ostream &	os,
		const DistanceMatrix< Value > &	matrix
	)

Print the contents to a stream.

operator<<() [16/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const DPosition< D, TCoordinateType > &	pos
	)

Print the contents to a stream.

References precisionWrapper().

operator<<() [17/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const DRange< D > &	area
	)

Print the contents to a stream.

References DRange< D >::max_, and DRange< D >::min_.

operator<<() [18/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const EmpiricalFormula &	formula
	)

operator<<() [19/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const ExperimentalSettings &	exp
	)

Print the contents to a stream.

operator<<() [20/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const FeatureHandle &	cons
	)

Print the contents of a FeatureHandle to a stream.

operator<<() [21/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const FeatureMap &	map
	)

operator<<() [22/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const LayerDataBase &	rhs
	)

Print the contents to a stream.

operator<<() [23/50]

std::ostream & operator<<	(	std::ostream &	os,
		const Matrix< Value > &	matrix
	)

Print the contents to a stream.

operator<<() [24/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const MobilityPeak1D &	point
	)

Print the contents to a stream.

operator<<() [25/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const MobilityPeak2D &	point
	)

Print the contents to a stream.

operator<<() [26/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const Mobilogram &	mb
	)

operator<<() [27/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const MSChromatogram &	chrom
	)

Print the contents to a stream.

operator<<() [28/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const MSExperiment &	exp
	)

Print the contents to a stream.

operator<<() [29/50]

std::ostream& OpenMS::operator<< ( std::ostream &  os, const MSSpectrum &  spec  )

inline

operator<<() [30/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const Param &	param
	)

Output of Param to a stream.

operator<<() [31/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const Peak1D &	point
	)

Print the contents to a stream.

operator<<() [32/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const Peak2D &	point
	)

Print the contents to a stream.

operator<<() [33/50]

std::ostream& OpenMS::operator<< ( std::ostream &  os, const PrecisionWrapper< FloatingPointType > &  rhs  )

inline

Output operator for a PrecisionWrapper. Specializations are defined for float, double, long double.

References PrecisionWrapper< FloatingPointType >::ref_.

operator<<() [34/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const Residue &	residue
	)

operator<<() [35/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const Ribonucleotide &	ribo
	)

Stream output operator.

ostream iterator to write the residue to a stream

operator<<() [36/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const SpectrumSettings &	spec
	)

Print the contents to a stream.

operator<<() [37/50]

std::ostream& OpenMS::operator<< ( std::ostream &  os, const std::vector< T > &  v  )

inline

Output stream operator for std::vectors.

Parameters

os	The target stream.
v	The vector to write to stream.

operator<<() [38/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		const TargetedExperiment::SummaryStatistics &	s
	)

prints out the summary statistics

operator<<() [39/50]

std::ostream& OpenMS::operator<< ( std::ostream &  os, const VecLowPrecision< T > &  val  )

inline

modified version of the stream operator (works for vectors of float, double, long double) which prints only three fractional digits; usage 'os << VecLowPrecision(my_vec);'

References VecLowPrecision< T >::value.

operator<<() [40/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		LogConfigHandler const &	lch
	)

Overload for the insertion operator (operator<<) to have a formatted output of the LogConfigHandler.

operator<<() [41/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	os,
		StreamHandler const &	stream_handler
	)

Overload for the insertion operator (operator<<) to have a formatted output of the StreamHandler.

operator<<() [42/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	out,
		const RangeBase &	b
	)

operator<<() [43/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	out,
		const RangeIntensity &	range
	)

operator<<() [44/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	out,
		const RangeManager< Range... > &	me
	)

References RangeManager< RangeBases >::printRange().

operator<<() [45/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	out,
		const RangeMobility &	range
	)

operator<<() [46/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	out,
		const RangeMZ &	range
	)

operator<<() [47/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	out,
		const RangeRT &	range
	)

operator<<() [48/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	stream,
		const PeptideHit &	hit
	)

Stream operator.

operator<<() [49/50]

std::ostream& OpenMS::operator<<	(	std::ostream &	stream,
		const ProteinHit &	hit
	)

Stream operator.

operator<<() [50/50]

std::vector<String>& OpenMS::operator<< ( std::vector< String > &  sl, const TString &  string  )

inline

Operator for appending entries with less code.

operator>>()

std::istream& OpenMS::operator>>	(	std::istream &	os,
		const AASequence &	peptide
	)

positionComparator()

bool OpenMS::positionComparator	(	const PeakType &	a,
		const PeakType &	b
	)

References Peak2D::getMZ().

precisionWrapper()

const PrecisionWrapper<FloatingPointType> OpenMS::precisionWrapper ( const FloatingPointType  rhs )

inline

Wrapper function that sets the appropriate precision for output temporarily. The original precision is restored afterwards so that no side effects remain. This is a "make"-function that deduces the typename FloatingPointType from its argument and returns a PrecisionWrapper<FloatingPointType>.

Example:

std::cout
<< 0.1234567890123456789f << ' ' << 0.1234567890123456789 << ' ' << 0.1234567890123456789l << '\n'
<< precisionWrapper(0.1234567890123456789f) << '\n' // float
<< 0.1234567890123456789f << ' ' << 0.1234567890123456789 << ' ' << 0.1234567890123456789l << '\n'
<< precisionWrapper(0.1234567890123456789) << '\n' // double
<< 0.1234567890123456789f << ' ' << 0.1234567890123456789 << ' ' << 0.1234567890123456789l << '\n'
<< precisionWrapper(0.1234567890123456789l) << '\n' // long double
<< 0.1234567890123456789f << ' ' << 0.1234567890123456789 << ' ' << 0.1234567890123456789l << '\n';

Result:

0.123457 0.123457 0.123457
0.123457
0.123457 0.123457 0.123457
0.123456789012346
0.123457 0.123457 0.123457
0.123456789012345679
0.123457 0.123457 0.123457

Note: Unfortunately we cannot return a const& - this will change when rvalue references become part of the new C++ standard. In the meantime, we need a copy constructor for PrecisionWrapper.

Referenced by operator<<(), DTA2DFile::store(), and DTA2DFile::storeTIC().

removePeaks()

void OpenMS::removePeaks	(	PeakContainerT &	p,
		const double	pos_start,
		const double	pos_end,
		const bool	ignore_data_arrays = false
	)

remove all peaks EXCEPT in the given range

sort_peaks_by_intensity()

bool sort_peaks_by_intensity	(	const PeakCandidate &	a,
		const PeakCandidate &	b
	)

References PeakCandidate::peak_apex_intensity.

Referenced by PeakPickerIterative::pick().

subtractMinimumIntensity()

void OpenMS::subtractMinimumIntensity

(

PeakContainerT &

p

)

toDriftTimeUnit()

DriftTimeUnit OpenMS::toDriftTimeUnit

(

const std::string &

dtu_string

)

convert an entry in NamesOfDriftTimeUnit[] to DriftTimeUnit enum

Exceptions

Exception::InvalidValue

if dtu_string is not contained in NamesOfDriftTimeUnit[]

toIMFormat()

IMFormat OpenMS::toIMFormat

(

const std::string &

IM_format

)

convert an entry in NamesOfIMFormat[] to IMFormat enum

Exceptions

Exception::InvalidValue

if IM_format is not contained in NamesOfIMFormat[]

toString() [1/2]

const std::string& OpenMS::toString

(

const DriftTimeUnit

value

)

convert a DriftTimeUnit enum to String

Exceptions

Exception::InvalidValue

if value is SIZE_OF_DRIFTTIMEUNIT

toString() [2/2]

const std::string& OpenMS::toString

(

const IMFormat

value

)

convert an IMFormat enum to String

Exceptions

Exception::InvalidValue

if value is SIZE_OF_IMFORMAT

typeAsString()

std::string OpenMS::typeAsString

(

const Type &

= Type()

)

Returns the Type as as std::string.

Have you ever spent a long time trying to find out what a typedef actually "points" to? Then this can help.

typeAsString is implemented as a function template. There are two ways to us this:

SomeType instance;
string what_type_1 = typeAsString(instance);
string what_type_2 = typeAsString< SomeType >();

The typeAsString< SomeType >() version seems to go a bit deeper. Sometimes the results depend on how the typeAsString() is instantiated in the first place. The argument given to the function is never used, it only serves to infer the type. You can even supply function pointers, etc.

Example (Tutorial_typeAsString.cpp):

// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/TypeAsString.h>
#include <OpenMS/KERNEL/DPeak.h>
#include <iostream>
 
double someFunc(int, int *)
{
  return 9.9;
}
 
template <typename, int = 5>
struct WOW
{
  static float staticMemberFunc(float &) {return 0; }
  double memberFunc(const double &) {return 0; }
};
 
template <typename X, int I, unsigned J = 666, template <class, int> class WauWau = WOW>
struct Oink {};
 
int main()
{
  using namespace OpenMS;
  using namespace std;
 
  cout << typeAsString(1) << endl;
  cout << typeAsString(2u) << endl;
  cout << typeAsString(3.) << endl;
  cout << typeAsString(4.f) << endl;
  cout << endl;
  cout << typeAsString<Int>() << endl;
  cout << typeAsString<PointerSizeUInt>() << endl;
  cout << endl;
  cout << typeAsString(Peak1D()) << endl;
  cout << typeAsString(DPeak<1>::Type()) << endl;
  cout << typeAsString(DPeak<1>::Type::PositionType()) << endl;
  cout << typeAsString<DPeak<1>::Type::CoordinateType>() << endl;
  cout << typeAsString<DPeak<1>::Type::IntensityType>() << endl;
  cout << endl;
  cout << typeAsString(&someFunc) << endl;
  cout << typeAsString<WOW<char const * const *** const &> >() << endl;
  cout << typeAsString<Oink<double, 55> >() << endl;
  cout << typeAsString(&WOW<string, 8>::staticMemberFunc) << endl;
  cout << typeAsString(&WOW<char, 8>::memberFunc) << endl;
 
  return 0;
} // end of Tutorial_typeAsString.cpp

On a 64 bit platform running GCC 4.3.1, this produced the following output:

int
unsigned int
double
float
 
int
long unsigned int
 
OpenMS::Peak1D
OpenMS::Peak1D
OpenMS::DPosition<1u>
double
float
 
double ()(int, int*)
WOW<const char* const*** const&, 5>
Oink<double, 55, 666u, WOW>
float ()(float&)
double (WOW<char, 8>::*)(const double&)

writtenDigits()

constexpr Int writtenDigits ( const FloatingPointType &  = FloatingPointType() )

inlineconstexpr

Number of digits commonly used for writing a floating point type (a.k.a. precision). Specializations are defined for float, double, long double.

The general template definition will return the default precision of 6 according to 27.4.4.1 basic_iosconstructors (C++ Standard).

Referenced by OpenMS::StringUtils::numberLength().

writtenDigits< DataValue >()

constexpr Int OpenMS::writtenDigits< DataValue > ( const DataValue &  )

inlineconstexpr

DataValue will be printed like double.

writtenDigits< double >()

constexpr Int OpenMS::writtenDigits< double > ( const double &  )

inlineconstexpr

Number of digits commonly used for writing a double (a.k.a. precision).

Referenced by DistanceMatrix< Value >::operator<<(), and DTAFile::store().

writtenDigits< float >()

constexpr Int OpenMS::writtenDigits< float > ( const float &  )

inlineconstexpr

Number of digits commonly used for writing a float (a.k.a. precision).

writtenDigits< int >()

constexpr Int OpenMS::writtenDigits< int > ( const int &  )

inlineconstexpr

We do not want to bother people who unintentionally provide an int argument to this.

writtenDigits< long double >()

constexpr Int OpenMS::writtenDigits< long double > ( const long double &  )

inlineconstexpr

Number of digits commonly used for writing a long double (a.k.a. precision). ...

Note: On Microsoft platforms, the I/O system seems to treat long double just like double. We observed that std::numeric_limits<long double>::digits10 == 18 with GCC 3.4 on MinGW, but this promise is not kept by the Microsoft I/O system libraries. Therefore we use the value of digits10 for double also for long double. See http://msdn.microsoft.com/ + search: "long double".

writtenDigits< long int >()

constexpr Int OpenMS::writtenDigits< long int > ( const long int &  )

inlineconstexpr

We do not want to bother people who unintentionally provide a long int argument to this.

writtenDigits< unsigned int >()

constexpr Int OpenMS::writtenDigits< unsigned int > ( const unsigned int &  )

inlineconstexpr

We do not want to bother people who unintentionally provide an unsigned int argument to this.

writtenDigits< unsigned long int >()

constexpr Int OpenMS::writtenDigits< unsigned long int > ( const unsigned long int &  )

inlineconstexpr

We do not want to bother people who unintentionally provide an unsigned long int argument to this.

Variable Documentation

AAtoChar

constexpr char const AAtoChar[28]

constexpr

representation of an AminoAcid (see AA class). Ambiguous AA's are consecutive (which saves effort during their enumeration)

BinaryDataEncoder_default_numpressErrorTolerance

const double BinaryDataEncoder_default_numpressErrorTolerance = .0001

blue

Colorizer blue

extern

bright

Colorizer bright

extern

CharToAA

constexpr char const CharToAA[128]

constexpr

Initial value:

= {
    
    27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 
    27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 
  
    27, 27, 27, 27, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 
    27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 
 
  
    27, 00, 22, 02, 03, 15, 05, 06, 07,  8, 23, 10,  9, 12, 04, 13, 
 
  
    14, 16, 17, 18, 19, 20, 21, 11, 25, 01, 24, 27, 27, 27, 27, 27, 
 
  
    27, 00, 22, 02, 03, 15, 05, 06, 07,  8, 23, 10,  9, 12, 04, 13,   
 
  
    14, 16, 17, 18, 19, 20, 21, 11, 25, 01, 24, 27, 27, 27, 27, 27, 
  }

Conversion table from 7-bit ASCII char to internal value representation for an amino acid (AA)

cyan

Colorizer cyan

extern

DIM_NAMES

std::string_view DIM_NAMES[(int) DIM_UNIT::SIZE_OF_DIM_UNITS] = {"RT [s]", "m/z [Th]", "intensity", "IM [milliseconds]", "IM [vs / cm2]", "FAIMS CV"}

inline

Referenced by DimBase::getDimName().

DIM_NAMES_SHORT

std::string_view DIM_NAMES_SHORT[(int) DIM_UNIT::SIZE_OF_DIM_UNITS] = {"RT", "m/z", "int", "IM", "IM", "FCV"}

inline

Referenced by DimBase::getDimNameShort().

green

Colorizer green

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invert

Colorizer invert

extern

magenta

Colorizer magenta

extern

NamesOfDriftTimeUnit

const std::string NamesOfDriftTimeUnit[(size_t) DriftTimeUnit::SIZE_OF_DRIFTTIMEUNIT]

extern

Names of IM Units. Should be usable as axis annotation.

NamesOfIMFormat

const std::string NamesOfIMFormat[(size_t) IMFormat::SIZE_OF_IMFORMAT]

extern

Names of IMFormat.

OpenMS_Log_debug

Logger::LogStream OpenMS_Log_debug

extern

Global static instance of a LogStream to capture messages classified as debug output. By default it is not bound to any output stream. TOPP(AS)Base will connect cout, iff 0 < debug-level.

Referenced by main().

OpenMS_Log_error

Logger::LogStream OpenMS_Log_error

extern

Global static instance of a LogStream to capture messages classified as errors. By default it is bound to cerr.

Referenced by main().

OpenMS_Log_fatal

Logger::LogStream OpenMS_Log_fatal

extern

Global static instance of a LogStream to capture messages classified as fatal errors. By default it is bound to cerr.

OpenMS_Log_info

Logger::LogStream OpenMS_Log_info

extern

Global static instance of a LogStream to capture messages classified as information. By default it is bound to cout.

OpenMS_Log_warn

Logger::LogStream OpenMS_Log_warn

extern

Global static instance of a LogStream to capture messages classified as warnings. By default it is bound to cout.

PrecursorMZLess

struct OpenMS::PrecursorMassComparator PrecursorMZLess

red

Colorizer red

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SpectralMatchScoreGreater

struct OpenMS::SpectralMatchScoreComparator SpectralMatchScoreGreater

StatsSourceNames

const std::array<const char*, (size_t)RangeStatsSource::SIZE_OF_STATSSOURCE> StatsSourceNames = {"core statistics", "meta values", "data arrays"}

static

Names corresponding to elements of enum RangeStatsSource.

STREAM_HANDLER

StreamHandler STREAM_HANDLER

extern

Global StreamHandler instance.

supported_types

const FileTypeList supported_types({ FileTypes::MZML, FileTypes::MZXML, FileTypes::MZDATA, FileTypes::SQMASS, FileTypes::FEATUREXML, FileTypes::CONSENSUSXML, FileTypes::IDXML, FileTypes::DTA, FileTypes::DTA2D, FileTypes::MGF, FileTypes::MS2, FileTypes::MSP, FileTypes::BZ2, FileTypes::GZ })

(

{ FileTypes::MZML, FileTypes::MZXML, FileTypes::MZDATA, FileTypes::SQMASS, FileTypes::FEATUREXML, FileTypes::CONSENSUSXML, FileTypes::IDXML, FileTypes::DTA, FileTypes::DTA2D, FileTypes::MGF, FileTypes::MS2, FileTypes::MSP, FileTypes::BZ2, FileTypes::GZ }

)

supported types which can be opened with File–>Open

Referenced by TOPPViewBase::addDataFile(), and TOPPViewBase::chooseFilesDialog_().

underline

Colorizer underline

extern

user_section

const std::string user_section = "preferences:user:"

Referenced by TOPPViewBase::addData(), TOPPViewBase::addDataFile(), TOPPViewBase::fileChanged_(), TOPPViewBase::getCanvasParameters(), TOPPViewBase::initializeDefaultParameters_(), TOPPViewBase::loadPreferences(), TOPPViewBase::preferencesDialog(), TOPPViewBase::savePreferences(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateCurrentPath().

yellow

Colorizer yellow

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