OpenMS
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
 
 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
 
struct  HyperScore
 An implementation of the X!Tandem HyperScore PSM scoring function. 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
 
struct  MorpheusScore
 An implementation of the Morpheus PSM scoring function Inspired by a C# implementation by C. Wenger released under MIT license. More...
 
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...
 
struct  PScore
 Implementation of the PScore PSM scoring algorithm. More...
 
class  SimpleSearchEngineAlgorithm
 
class  SiriusExportAlgorithm
 
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  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  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 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  PeakPickerChromatogram
 The PeakPickerChromatogram 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
 
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 class representing a thin wrapper around an Eigen matrix. 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  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  RNPxlMarkerIonExtractor
 
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  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  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
 
class  ModificationDefinitionsSet
 
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
 
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  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  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  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
 
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
 
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  BaseModel
 Abstract base class for 1-dimensional models. More...
 
class  BiGaussFitter1D
 BiGaussian distribution fitter (1-dim.) approximated using linear interpolation. More...
 
class  BiGaussModel
 
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
 
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
 
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  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
 
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  SeedListGenerator
 Generate seed lists for feature detection. More...
 
class  TraceFitter
 Abstract fitter for RT profile fitting. 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  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  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  LinearResampler
 Linear Resampling of raw data. More...
 
class  LinearResamplerAlign
 Linear Resampling of raw data with alignment. More...
 
class  NLargest
 NLargest removes all but the n largest peaks. More...
 
class  Normalizer
 Normalizes the peak intensities spectrum-wise. More...
 
class  Scaler
 Scales each peak by ranking the peaks per spectrum 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
 Removes all peaks below an intensity threshold. More...
 
class  WindowMower
 Retains 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
 
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  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  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
 
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
 
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
 
class  MsInspectFile
 
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  MzTabModification
 Data model of MzTab files. More...
 
class  MzTabModificationList
 
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
 
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  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
 
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
 Exports .cwl files. More...
 
class  ParamJSONFile
 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
 
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
 
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
 
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
 
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  BinnedSpectrum
 This is a binned representation of a PeakSpectrum. 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  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  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  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  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  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  GridSearch
 
class  NonNegativeLeastSquaresSolver
 Wrapper for a non-negative least squares (NNLS) solver. More...
 
class  SimpleSVM
 Simple interface to support vector machines for classification and regression (via LIBSVM). 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  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
 
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
 
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

using SpectrumSequence = std::vector< OpenSwath::SpectrumPtr >
 a vector of spectrum pointers that DIA scores can operate on, allows for clever integration of only the target regions More...
 
typedef std::pair< double, double > ScoreToTgtDecLabelPair
 
typedef std::map< Internal::ToolDescriptionInternal, Internal::ToolDescriptionInternalToolMapping
 Updates an INI. More...
 
typedef std::map< String, Internal::ToolDescriptionToolListType
 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 ProgressLogger::ProgressLoggerImpl *(* MakeGUIProgressLoggerFunc) ()
 
typedef int32_t Int32
 Signed integer type (32bit) More...
 
typedef uint32_t UInt32
 Unsigned integer type (32bit) More...
 
typedef int64_t Int64
 Signed integer type (64bit) More...
 
typedef uint64_t 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 uint8_t Byte
 Byte type. More...
 
typedef uint64_t 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< IntIntList
 Vector of signed integers. More...
 
typedef std::vector< double > DoubleList
 Vector of double precision real types. More...
 
typedef std::vector< StringStringList
 Vector of String. More...
 
typedef OpenMS::OnDiscMSExperiment OnDiscPeakMap
 
using IndProtGrp = OpenMS::ProteinIdentification::ProteinGroup
 
using IndProtGrps = std::vector< IndProtGrp >
 
typedef std::vector< MzTabProteinSectionRowMzTabProteinSectionRows
 
typedef std::vector< MzTabPeptideSectionRowMzTabPeptideSectionRows
 
typedef std::vector< MzTabPSMSectionRowMzTabPSMSectionRows
 
typedef std::vector< MzTabSmallMoleculeSectionRowMzTabSmallMoleculeSectionRows
 
typedef std::vector< MzTabNucleicAcidSectionRowMzTabNucleicAcidSectionRows
 
typedef std::vector< MzTabOligonucleotideSectionRowMzTabOligonucleotideSectionRows
 
typedef std::vector< MzTabOSMSectionRowMzTabOSMSectionRows
 
typedef std::pair< String, MzTabStringMzTabOptionalColumnEntry
 
typedef std::vector< MzTabMSmallMoleculeSectionRowMzTabMSmallMoleculeSectionRows
 
typedef std::vector< MzTabMSmallMoleculeFeatureSectionRowMzTabMSmallMoleculeFeatureSectionRows
 
typedef std::vector< MzTabMSmallMoleculeEvidenceSectionRowMzTabMSmallMoleculeEvidenceSectionRows
 
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< DataProcessingDataProcessingPtr
 
typedef boost::shared_ptr< const DataProcessingConstDataProcessingPtr
 
typedef boost::shared_ptr< OSWDataOSWDataSharedPtrType
 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 class  MZ_UNITS { DA = 0 , PPM , SIZE_OF_MZ_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...
 
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...
 
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 (and colors the diagonal, if the stream is cout/cerr) 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...
 
std::ostream & operator<< (std::ostream &os, const Param &param)
 Output of Param to a stream. More...
 
::size_t hash_value (OpenMS::String const &s)
 
bool operator< (const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
 
bool sort_peaks_by_intensity (const PeakCandidate &a, const PeakCandidate &b)
 
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...
 
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::string bytesToHumanReadable (UInt64 bytes)
 convert bytes to a human readable unit (TiB, GiB, MiB, KiB), e.g. "45.34 MiB" More...
 
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
constexpr Int writtenDigits< double >(const double &)
Number of digits commonly used for writing a double (a.k.a. precision).
Definition: Types.h:189
constexpr Int writtenDigits(const FloatingPointType &=FloatingPointType())
Number of digits commonly used for writing a floating point type (a.k.a. precision)....
Definition: Types.h:264
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"}
 
std::string_view MZ_UNIT_NAMES [(int) MZ_UNITS::SIZE_OF_MZ_UNITS] = {"Da", "ppm"}
 
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...
 
MakeGUIProgressLoggerFunc make_gui_progress_logger
 
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_STATSSOURCEStatsSourceNames = {"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:
[legend]
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:
[legend]
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:
[legend]
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::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::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:
[legend]
Class Members
int index
double integrated_intensity
double leftWidth
float mz
double peak_apex_intensity
double rightWidth

◆ OpenMS::Range

struct OpenMS::Range

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

Collaboration diagram for Range:
[legend]
Class Members
double left_boundary
double right_boundary

◆ OpenMS::MzTabModificationMetaData

struct OpenMS::MzTabModificationMetaData
Collaboration diagram for MzTabModificationMetaData:
[legend]
Class Members
MzTabParameter modification
MzTabString position
MzTabString site

◆ OpenMS::MzTabAssayMetaData

struct OpenMS::MzTabAssayMetaData
Collaboration diagram for MzTabAssayMetaData:
[legend]
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:
[legend]
Class Members
MzTabParameter format
MzTabParameterList fragmentation_method
MzTabParameter id_format
MzTabString location

◆ OpenMS::MzTabStudyVariableMetaData

struct OpenMS::MzTabStudyVariableMetaData
Collaboration diagram for MzTabStudyVariableMetaData:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
Class Members
map< Size, MzTabString > setting
MzTabParameter software

◆ OpenMS::MzTabSampleMetaData

struct OpenMS::MzTabSampleMetaData
Collaboration diagram for MzTabSampleMetaData:
[legend]
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:
[legend]
Class Members
MzTabString full_name
MzTabString label
MzTabString url
MzTabString version

◆ OpenMS::MzTabInstrumentMetaData

struct OpenMS::MzTabInstrumentMetaData
Collaboration diagram for MzTabInstrumentMetaData:
[legend]
Class Members
map< Size, MzTabParameter > analyzer
MzTabParameter detector
MzTabParameter name
MzTabParameter source

◆ OpenMS::MzTabContactMetaData

struct OpenMS::MzTabContactMetaData
Collaboration diagram for MzTabContactMetaData:
[legend]
Class Members
MzTabString affiliation
MzTabString email
MzTabString name

◆ OpenMS::MzTabMAssayMetaData

class OpenMS::MzTabMAssayMetaData

MztabM Assay Metadata.

Collaboration diagram for MzTabMAssayMetaData:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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:

◆ OpenMS::StatsCounter

struct OpenMS::StatsCounter

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

Collaboration diagram for StatsCounter:
[legend]
Class Members
size_t counter

Typedef Documentation

◆ ConstDataProcessingPtr

typedef boost::shared_ptr<const DataProcessing> ConstDataProcessingPtr

◆ DataProcessingPtr

typedef boost::shared_ptr<DataProcessing> DataProcessingPtr

◆ FS_LAYER

◆ FS_TV

◆ 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>

◆ MakeGUIProgressLoggerFunc

typedef ProgressLogger::ProgressLoggerImpl*(* MakeGUIProgressLoggerFunc) ()

◆ MzTabMSmallMoleculeEvidenceSectionRows

◆ MzTabMSmallMoleculeFeatureSectionRows

◆ MzTabMSmallMoleculeSectionRows

◆ MzTabNucleicAcidSectionRows

◆ MzTabOligonucleotideSectionRows

◆ MzTabOptionalColumnEntry

◆ MzTabOSMSectionRows

◆ MzTabPeptideSectionRows

◆ MzTabProteinSectionRows

◆ MzTabPSMSectionRows

◆ MzTabSmallMoleculeSectionRows

◆ 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

◆ RangeAllType

Range which contains all known dimensions.

◆ RangeStatsDouble

using RangeStatsDouble = RangeStats<double>

◆ RangeStatsInt

using RangeStatsInt = RangeStats<int>

◆ RangeStatsVariant

◆ RibonucleotideChainEnd

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

◆ 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

◆ SpectrumSequence

a vector of spectrum pointers that DIA scores can operate on, allows for clever integration of only the target regions

◆ StatsCounterMap

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

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

◆ StatsMap

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

◆ 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

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

◆ 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 

◆ MZ_UNITS

enum MZ_UNITS
strong
Enumerator
DA 

Dalton.

PPM 

parts-per-million

SIZE_OF_MZ_UNITS 

◆ 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 >()

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

◆ compareBinaryTreeNode()

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

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

◆ 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]inputThe input spectrum.
[out]outputThe output spectrum (will be cleared and will contain all metadata of the input spectrum).
clear_spectrumWhether 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() [2/2]

::size_t OpenMS::hash_value ( OpenMS::String const &  s)

◆ 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]pThe peak container to be manipulated.
[in]mThe 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().

◆ 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<<() [1/49]

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

◆ operator<<() [2/49]

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<<() [3/49]

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

◆ operator<<() [4/49]

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

◆ operator<<() [5/49]

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

Print content of an AnnotationStatistics object to a stream.

◆ operator<<() [6/49]

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

Print the contents of a ChargePair to a stream.

◆ operator<<() [7/49]

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

Print the contents to a stream.

◆ operator<<() [8/49]

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

Print the contents to a stream.

◆ operator<<() [9/49]

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

Print the contents of a ConsensusFeature to a stream.

◆ operator<<() [10/49]

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

Print the contents of a ConsensusMap to a stream.

◆ operator<<() [11/49]

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

Print the contents to a stream.

◆ operator<<() [12/49]

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

Print the contents to a stream.

◆ operator<<() [13/49]

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

◆ operator<<() [14/49]

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

◆ operator<<() [15/49]

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

Print the contents to a stream (and colors the diagonal, if the stream is cout/cerr)

◆ operator<<() [16/49]

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

Print the contents to a stream.

References precisionWrapper().

◆ operator<<() [17/49]

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<<() [18/49]

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

◆ operator<<() [19/49]

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

Print the contents to a stream.

◆ operator<<() [20/49]

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

Print the contents of a FeatureHandle to a stream.

◆ operator<<() [21/49]

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

◆ operator<<() [22/49]

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

Print the contents to a stream.

◆ operator<<() [23/49]

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

Print the contents to a stream.

◆ operator<<() [24/49]

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

Print the contents to a stream.

◆ operator<<() [25/49]

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

◆ operator<<() [26/49]

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

Print the contents to a stream.

◆ operator<<() [27/49]

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

Print the contents to a stream.

◆ operator<<() [28/49]

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

◆ operator<<() [29/49]

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

Output of Param to a stream.

◆ operator<<() [30/49]

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

Print the contents to a stream.

◆ operator<<() [31/49]

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

Print the contents to a stream.

◆ operator<<() [32/49]

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<<() [33/49]

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

◆ operator<<() [34/49]

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

Stream output operator.

ostream iterator to write the residue to a stream

◆ operator<<() [35/49]

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

Print the contents to a stream.

◆ operator<<() [36/49]

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

Output stream operator for std::vectors.

Parameters
osThe target stream.
vThe vector to write to stream.

◆ operator<<() [37/49]

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

prints out the summary statistics

◆ operator<<() [38/49]

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<<() [39/49]

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<<() [40/49]

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<<() [41/49]

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

◆ operator<<() [42/49]

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

◆ operator<<() [43/49]

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

◆ operator<<() [44/49]

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

◆ operator<<() [45/49]

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

◆ operator<<() [46/49]

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

◆ operator<<() [47/49]

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

Stream operator.

◆ operator<<() [48/49]

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

Stream operator.

◆ operator<<() [49/49]

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 
)

◆ 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';
const PrecisionWrapper< FloatingPointType > precisionWrapper(const FloatingPointType rhs)
Wrapper function that sets the appropriate precision for output temporarily. The original precision i...
Definition: PrecisionWrapper.h:69

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 
)

◆ 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::InvalidValueif 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::InvalidValueif 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::InvalidValueif value is SIZE_OF_DRIFTTIMEUNIT

◆ toString() [2/2]

const std::string& OpenMS::toString ( const IMFormat  value)

convert an IMFormat enum to String

Exceptions
Exception::InvalidValueif value is SIZE_OF_IMFORMAT

◆ 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 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

◆ green

Colorizer green
extern

◆ invert

Colorizer invert
extern

◆ magenta

Colorizer magenta
extern

◆ make_gui_progress_logger

MakeGUIProgressLoggerFunc make_gui_progress_logger
extern

◆ MZ_UNIT_NAMES

std::string_view MZ_UNIT_NAMES[(int) MZ_UNITS::SIZE_OF_MZ_UNITS] = {"Da", "ppm"}
inline

◆ 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

◆ 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

◆ underline

Colorizer underline
extern

◆ user_section

◆ yellow

Colorizer yellow
extern