 eol_bspline | |
  BSpline | |
 ms | |
  numpress | |
   MSNumpress | |
 OpenMS | Main OpenMS namespace |
  Constants | Mathematical and physical constants namespace |
  DIAHelpers | |
  Exception | Exception namespace |
   UnregisteredParameter | An unregistered parameter was accessed |
   WrongParameterType | A parameter was accessed with the wrong type |
   RequiredParameterNotGiven | A required parameter was not given |
   BaseException | Exception base class |
   Precondition | Precondition failed exception |
   Postcondition | Postcondition failed exception |
   MissingInformation | Not all required information provided |
   IndexUnderflow | Int underflow exception |
   SizeUnderflow | UInt underflow exception |
   IndexOverflow | Int overflow exception |
   FailedAPICall | A call to an external library (other than OpenMS) went wrong |
   InvalidRange | Invalid range exception |
   InvalidSize | Invalid UInt exception |
   OutOfRange | Out of range exception |
   InvalidValue | Invalid value exception |
   InvalidParameter | Exception indicating that an invalid parameter was handed over to an algorithm |
   ConversionError | Invalid conversion exception |
   IllegalSelfOperation | Illegal self operation exception |
   NullPointer | Null pointer argument is invalid exception |
   InvalidIterator | Invalid iterator exception |
   IncompatibleIterators | Incompatible iterator exception |
   NotImplemented | Not implemented exception |
   IllegalTreeOperation | Illegal tree operation exception |
   OutOfMemory | Out of memory exception |
   BufferOverflow | Buffer overflow exception |
   DivisionByZero | Division by zero error exception |
   OutOfGrid | Out of grid exception |
   FileNotFound | File not found exception |
   FileNotReadable | File not readable exception |
   FileNotWritable | File not writable exception |
   IOException | General IOException |
   FileEmpty | File is empty |
   IllegalPosition | Invalid 3-dimensional position exception |
   ParseError | Parse Error exception |
   UnableToCreateFile | Unable to create file exception |
   IllegalArgument | A method or algorithm argument contains illegal values |
   ElementNotFound | Element could not be found exception |
   UnableToFit | Exception used if an error occurred while fitting a model to a given dataset |
   UnableToCalibrate | Exception used if an error occurred while calibrating a dataset |
   DepletedIDPool | Exception used if no more unique document ID's can be drawn from ID pool |
   GlobalExceptionHandler | OpenMS global exception handler |
  ims | |
   IMSAlphabet | Holds an indexed list of bio-chemical elements |
    MassSortingCriteria_ | Private class-functor to sort out elements in mass ascending order |
   IMSAlphabetParser | An abstract templatized parser to load the data that is used to initialize Alphabet objects |
   IMSAlphabetTextParser | Implements abstract AlphabetParser to read data from the plain text format |
   IMSElement | Represents a chemical atom with name and isotope distribution |
   IMSIsotopeDistribution | Represents a distribution of isotopes restricted to the first K elements |
    Peak | Structure that represents an isotope peak - pair of mass and abundance |
   IntegerMassDecomposer | Implements MassDecomposer interface using algorithm and data structures described in paper "Efficient Mass Decomposition" S. Böcker, Z. Lipták, ACM SAC-BIO, 2004 doi:10.1145/1066677.1066715 |
   MassDecomposer | An interface to handle decomposing of integer values/masses over a set of integer weights (alphabet) |
   RealMassDecomposer | Handles decomposing of non-integer values/masses over a set of non-integer weights with an error allowed |
   Weights | Represents a set of weights (double values and scaled with a certain precision their integer counterparts) with a quick access |
  Interfaces | |
   BinaryDataArray | The datastructures used by the OpenSwath interfaces |
   ChromatogramMeta | Identifying information for a chromatogram |
   Chromatogram | A single chromatogram |
   SpectrumMeta | Identifying information for a spectrum |
   Spectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
   IMSDataConsumer | The interface of a consumer of spectra and chromatograms |
   ISpectraReader | The interface of read-access to a list of spectra |
   IChromatogramsReader | The interface of read-access to a list of chromatograms |
   ISpectraWriter | |
   IChromatogramsWriter | |
  Internal | Namespace used to hide implementation details from users |
   ClassTest | Namespace for class tests |
   DIntervalBase | A base class for D-dimensional interval |
   FileMapping | Maps input/output files to filenames for the external program |
   MappingParam | Filename mappings for all input/output files |
   ToolDescriptionInternal | ToolDescription Class |
   ToolExternalDetails | |
   ToolDescription | |
   IntensityIteratorWrapper | An iterator wrapper to access peak intensities instead of the peak itself |
   AcqusHandler | Read-only acqus File handler for XMass Analysis |
   FidHandler | Read-only fid File handler for XMass Analysis |
   MascotXMLHandler | Handler that is used for parsing MascotXML data |
   MzDataHandler | XML handler for MzDataFile |
   MzIdentMLDOMHandler | XML DOM handler for MzIdentMLFile |
    AnalysisSoftware | |
    DatabaseInput | |
    DBSequence | |
    ModificationParam | |
    PeptideEvidence | |
    SpectrumIdentification | |
    SpectrumIdentificationProtocol | |
   MzIdentMLHandler | XML STREAM handler for MzIdentMLFile |
   MzMLHandler | XML handler for MzMLFile |
    ChromatogramData | Data necessary to generate a single chromatogram |
    SpectrumData | Data necessary to generate a single spectrum |
   MzMLHandlerHelper | |
    BinaryData | Binary data representation |
   MzQuantMLHandler | XML handler for MzQuantMLFile |
   MzXMLHandler | XML handlers for MzXMLFile |
    SpectrumData | Data necessary to generate a single spectrum |
   ParamXMLHandler | XML Handler for Param files |
   PTMXMLHandler | Handler that is used for parsing PTMXML data |
   ToolDescriptionHandler | XML handler for ToolDescriptionFile |
   TraMLHandler | XML handler for TraMLFile |
   UnimodXMLHandler | Handler that is used for parsing XTandemXML data |
   StringManager | Helper class for XML parsing that handles the memory management for conversions of Xerces strings |
   XMLHandler | Base class for XML handlers |
    EndParsingSoftly | Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file is needed) |
   XTandemInfileNote | Note representation of bioml structure used by XTandem |
   XTandemInfileXMLHandler | Handler that is used for parsing XTandemXML data |
   MzDataValidator | Semantically validates MzXML files |
   MzIdentMLValidator | Semantically validates MzXML files |
   MzMLValidator | Semantically validates MzXML files |
   MzQuantMLValidator | Semantically validates MzQuantML files |
   SemanticValidator | Semantically validates XML files using CVMappings and a ControlledVocabulary |
    CVTerm | Representation of a parsed CV term |
   TraMLValidator | Semantically validates MzXML files |
   XMLFile | Base class for loading/storing XML files that have a handler derived from XMLHandler |
   AreaIterator | Forward iterator for an area of peaks in an experiment |
   IntensityLess | Comparator that allows to compare the indices of two peaks by their intensity |
   IntensityIterator | Intensity iterator for a FeatureFinderDefs::IndexSet |
   MzIterator | M/z iterator for a FeatureFinderDefs::IndexSet |
   RtIterator | Retention time iterator for a FeatureFinderDefs::IndexSet |
   Spectrum1DPrefDialog | Preferences dialog for Spectrum1DWidget |
   Spectrum2DPrefDialog | Preferences dialog for Spectrum2DWidget |
   Spectrum3DPrefDialog | Preferences dialog for Spectrum3DWidget |
   TOPPViewPrefDialog | Preferences dialog for TOPPView |
   ListTable | |
   ListEditorDelegate | Internal delegate class |
   OpenMSLineEdit | Custom QLineEdit which emits a signal when losing focus (such that we can commit its data) |
   ParamEditorDelegate | Internal delegate class for QTreeWidget |
   ParamTree | QTreeWidget that emits a signal whenever a new row is selected |
   OpenMSOSInfo | |
  Logger | Log streams |
   LogStreamBuf | Stream buffer used by LogStream |
    LogCacheStruct | Holds a counter of occurrences and an index for the occurrence sequence of the corresponding log message |
    StreamStruct | Holds a stream that is connected to the LogStream. It also includes the minimum and maximum level at which the LogStream redirects messages to this stream |
   LogStreamNotifier | |
   LogStream | Log Stream Class |
  Math | Math namespace |
   BilinearInterpolation | Provides access to bilinearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero |
   LinearInterpolation | Provides access to linearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero |
   AsymmetricStatistics | Internal class for asymmetric distributions |
   AveragePosition | Maintain an average position by summing up positions with weights |
   BasicStatistics | Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation |
   GammaDistributionFitter | Implements a fitter for the Gamma distribution |
    GammaDistributionFitResult | Struct to represent the parameters of a gamma distribution |
   GaussFitter | Implements a fitter for gaussian functions |
    GaussFitResult | Struct of parameters of a gaussian distribution |
   GumbelDistributionFitter | Implements a fitter for the Gumbel distribution |
    GumbelDistributionFitResult | Struct to represent the parameters of a gumbel distribution |
   Histogram | Representation of a histogram |
   LinearRegression | This class offers functions to perform least-squares fits to a straight line model, |
   PosteriorErrorProbabilityModel | Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture |
   QuadraticRegression | |
   ROCCurve | ROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cutoff values |
    simsortdec | Predicate for sort() |
  NNLS | |
  OpenMSBoost | |
  OptimizationFunctions | |
   PenaltyFactorsIntensity | Class for the penalty factors used during the optimization |
   PenaltyFactors | Class for the penalty factors used during the optimization |
  SimTypes | |
   SimProtein | Plain data object holding sequence and abundance information on a single protein |
   SimRandomNumberGenerator | Wrapper class for random number generators used by the simulation classes |
  StringConversions | |
  TargetedExperimentHelper | This class stores helper structures that are used in multiple classes of the TargetedExperiment (e.g. ReactionMonitoringTransition and IncludeExcludeTarget) |
   Configuration | |
   CV | |
   Protein | |
   RetentionTime | |
   Compound | |
   Peptide | |
    Modification | |
   Contact | |
   Publication | |
   Instrument | |
   Prediction | |
   TraMLProduct | |
  FeatureDeconvolution | An algorithm to decharge features (i.e. as found by FeatureFinder) |
  ILPDCWrapper | |
  CompNovoIdentification | Run with CompNovoIdentification |
  CompNovoIdentificationBase | Run with CompNovoIdentificationBase |
   Permut | Simple class to store permutations and a score |
  CompNovoIdentificationCID | Run with CompNovoIdentificationCID |
  CompNovoIonScoring | Run with CompNovoIonScoring |
  CompNovoIonScoringBase | Run with CompNovoIonScoringBase |
   IonScore | |
  CompNovoIonScoringCID | Run with CompNovoIonScoringCID |
  DeNovoAlgorithm | Base class for ion scoring implementation for de novo algorithms |
  DeNovoIdentification | Base class for de novo identification |
  DeNovoIonScoring | Base class for ion scoring implementation for de novo algorithms |
   IonScore | IonScore |
  DeNovoPostScoring | Base class for ion scoring implementation for de novo algorithms |
  AdductInfo | |
  AccurateMassSearchResult | |
  AccurateMassSearchEngine | An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB) |
   CompareEntryAndMass_ | |
   MappingEntry_ | |
  ProbablePhosphoSites | |
  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 |
  ConsensusID | Calculates a consensus ID from several ID runs |
  FalseDiscoveryRate | Calculates an FDR from identifications |
  HMMState | Hidden Markov Model State class for the Hidden Markov Model |
  HiddenMarkovModel | Hidden Markov Model implementation of PILIS |
  IDDecoyProbability | IDDecoyProbability calculates probabilities using decoy approach |
   Transformation_ | Struct to be used to store a transformation (used for fitting) |
  IDMapper | Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications |
  IDRipper | Ripping protein/peptide identification according their file origin |
  PrecursorMassComparator | |
  SpectralMatch | |
  SpectralMatchScoreComparator | |
  MetaboliteSpectralMatching | |
  PILISCrossValidation | Implementation of a cross validation training for the PILIS model |
   Option | This struct represents a cross validation option |
   Peptide | This struct represents a peptide spectrum pair |
  PILISIdentification | This class actually implements a complete ProteinIdentification run with PILIS |
  PILISModel | This class implements the simulation of the spectra from PILIS |
  PILISModelGenerator | This class implements the simulation of the spectra from PILIS |
  PILISNeutralLossModel | This class implements the simulation of the spectra from PILIS |
  PILISScoring | This class actually implements the E-value based scoring of PILIS |
  ProtonDistributionModel | A proton distribution model to calculate the proton distribution over charged peptides |
  BaseGroupFinder | The base class of all element group finding algorithms |
  BaseSuperimposer | The base class of all superimposer algorithms |
  ConsensusMapNormalizerAlgorithmMedian | Algorithms of ConsensusMapNormalizer |
  ConsensusMapNormalizerAlgorithmQuantile | Algorithms of ConsensusMapNormalizer |
  ConsensusMapNormalizerAlgorithmThreshold | Algorithms of ConsensusMapNormalizer |
  FeatureDistance | A functor class for the calculation of distances between features or consensus features |
   DistanceParams_ | Structure for storing distance parameters |
  FeatureGroupingAlgorithm | Base class for all feature grouping algorithms |
  FeatureGroupingAlgorithmIdentification | A map feature grouping algorithm for identified features |
  FeatureGroupingAlgorithmLabeled | A map feature grouping algorithm for labeling techniques with two labels |
  FeatureGroupingAlgorithmQT | A feature grouping algorithm for unlabeled data |
  FeatureGroupingAlgorithmUnlabeled | A map feature grouping algorithm for unlabeled data |
  LabeledPairFinder | The LabeledPairFinder allows the matching of labeled features (features with a fixed distance) |
  MapAlignmentAlgorithm | Base class for all map-alignment algorithms |
  MapAlignmentAlgorithmIdentification | A map alignment algorithm based on peptide identifications from MS2 spectra |
  MapAlignmentAlgorithmPoseClustering | A map alignment algorithm based on pose clustering |
  MapAlignmentAlgorithmSpectrumAlignment | A map alignment algorithm based on spectrum similarity (dynamic programming) |
   Compare | Innerclass necessary for using the sort algo |
  MapAlignmentEvaluationAlgorithm | Base class for all Caap evaluation algorithms |
  MapAlignmentEvaluationAlgorithmPrecision | Caap evaluation algorithm to obtain a precision value |
  MapAlignmentEvaluationAlgorithmRecall | Caap evaluation algorithm to obtain a recall value |
  MapAlignmentTransformer | The MapAlignmentTransformer class |
  PoseClusteringAffineSuperimposer | A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation |
  PoseClusteringShiftSuperimposer | A superimposer that uses a voting scheme, also known as pose clustering, to find a good shift transformation |
  QTClusterFinder | A variant of QT clustering for the detection of feature groups |
  SimplePairFinder | This class implements a simple point pair finding algorithm |
  StablePairFinder | This class implements a pair finding algorithm for consensus features |
  TransformationDescription | Generic description of a coordinate transformation |
  TransformationModel | Base class for transformation models |
  TransformationModelBSpline | B-spline (non-linear) model for transformations |
  TransformationModelInterpolated | Interpolation model for transformations |
   Interpolator | The class defines a generic interpolation technique used in the TransformationModelInterpolated |
  TransformationModelLinear | Linear model for transformations |
  MRMFragmentSelection | This class can select appropriate fragment ions of an MS/MS spectrum of a peptide |
  ReactionMonitoringTransition | This class stores a SRM/MRM transition |
   ProductMZLess | Comparator by Product ion MZ |
  ChromatogramExtractor | The ChromatogramExtractor extracts chromatograms from a spectra file |
  ChromatogramExtractorAlgorithm | The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data |
   ExtractionCoordinates | |
  ConfidenceScoring | |
  OpenSwathDataAccessHelper | Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces |
  FeatureOpenMS | An implementation of the OpenSWATH Feature Access interface using OpenMS |
  MRMFeatureOpenMS | An implementation of the OpenSWATH MRM Feature Access interface using OpenMS |
  TransitionGroupOpenMS | An implementation of the OpenSWATH Transition Group Access interface using OpenMS |
  SignalToNoiseOpenMS | An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS |
  SimpleOpenMSSpectraFactory | A factory method that returns two ISpectrumAccess implementations |
  SpectrumAccessOpenMS | An implementation of the OpenSWATH Spectrum Access interface using OpenMS |
  SpectrumAccessOpenMSCached | An implementation of the Spectrum Access interface using on-disk caching |
  DiaPrescore | Scoring of an spectrum given library intensities of a transition group |
  DIAScoring | Scoring of an spectrum at the peak apex of an chromatographic elution peak |
  MRMDecoy | This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object |
  MRMFeatureFinderScoring | The MRMFeatureFinder finds and scores peaks of transitions that co-elute |
  MRMRTNormalizer | The MRMRTNormalizer will find retention time peptides in data |
  MRMTransitionGroupPicker | The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors |
  OpenSwathHelper | A helper class that is used by several OpenSWATH tools |
  OpenSwath_Scores_Usage | A structure to store which scores should be used by the Algorithm |
  OpenSwath_Scores | A structure to hold the different scores computed by OpenSWATH |
  OpenSwathScoring | A class that calls the scoring routines |
  PeakPickerMRM | The PeakPickerMRM finds peaks a single chromatogram |
  SpectrumAddition | The SpectrumAddition is used to add up individual spectra |
  SwathWindowLoader | Class to read a file describing the Swath Windows |
  TransitionTSVReader | This class can convert TraML and TSV files into each other |
   TSVTransition | Internal structure to represent a transition |
  LocalLinearMap | Trained Local Linear Map (LLM) model for peak intensity prediction |
   LLMParam | Define parameters needed by the Local Linear Map (LLM) model |
  PeakIntensityPredictor | Predict peak heights of peptides based on Local Linear Map model |
  IsobaricChannelExtractor | Extracts individual channels from MS/MS spectra for isobaric labeling experiments |
   PuritySate_ | Small struct to capture the current state of the purity computation |
  IsobaricIsotopeCorrector | Performs isotope impurity correction on the intensities extracted from an isobaric labeling experiment |
  IsobaricNormalizer | Performs median normalization on the extracted ratios of isobaric labeling experiment |
  IsobaricQuantifier | Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing |
  IsobaricQuantifierStatistics | Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion) |
  Matrix | A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access |
  IsobaricQuantitationMethod | Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix |
   IsobaricChannelInformation | Summary of an isobaric quantitation channel |
  ItraqChannelExtractor | [experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map |
  ItraqConstants | Some constants used throughout iTRAQ classes |
   ChannelInfo | Stores information on an iTRAQ channel |
  ItraqEightPlexQuantitationMethod | ITRAQ 8 plex quantitation to be used with the IsobaricQuantitation |
  ItraqFourPlexQuantitationMethod | ITRAQ 4 plex quantitation to be used with the IsobaricQuantitation |
  ItraqQuantifier | Does post-processing on raw iTRAQ channel quantitation |
   ItraqQuantifierStats | Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion) |
  PeptideAndProteinQuant | Helper class for peptide and protein quantification based on feature data annotated with IDs |
   PeptideData | Quantitative and associated data for a peptide |
   ProteinData | Quantitative and associated data for a protein |
   Statistics | Statistics for processing summary |
  ProteinInference | [experimental class] given a peptide quantitation, infer corresponding protein quantities |
  ProteinResolver | Helper class for peptide and protein quantification based on feature data annotated with IDs |
   ISDGroup | |
   MSDGroup | Representation of an msd group. Contains peptides, proteins and a pointer to its ISD group |
   PeptideEntry | Peptide. First in silico. If experimental is set to true it is MS/MS derived |
   ProteinEntry | Protein from FASTA file |
   ResolverResult | |
  QuantitativeExperimentalDesign | Merge files according to experimental design |
  TMTSixPlexQuantitationMethod | TMT 6plex quantitation to be used with the IsobaricQuantitation |
  TMTTenPlexQuantitationMethod | TMT 10plex quantitation to be used with the IsobaricQuantitation |
  ModifiedPeptideGenerator | |
  RNPxlModificationMassesResult | |
  RNPxlModificationsGenerator | |
  SVMData | Data structure used in SVMWrapper |
  SVMWrapper | Serves as a wrapper for the libsvm |
  IncludeExcludeTarget | This class stores a SRM/MRM transition |
  InclusionExclusionList | Provides functionality for writing inclusion or exclusion lists |
   IEWindow | |
   WindowDistance_ | Determine distance between two spectra |
  OfflinePrecursorIonSelection | Implements different algorithms for precursor ion selection |
  PrecursorIonSelection | This class implements different precursor ion selection strategies |
   SeqTotalScoreMore | Compare by score |
   TotalScoreMore | Compare by score |
  PrecursorIonSelectionPreprocessing | This class implements the database preprocessing needing for precursor ion selection |
  PSLPFormulation | Implements ILP formulation of precursor selection problems |
   IndexLess | |
   IndexTriple | Struct that holds the indices of the precursors in the feature map and the ilp formulation |
   ScanLess | |
   VariableIndexLess | |
  PSProteinInference | This class implements protein inference for the precursor ion selection strategies |
  TargetedExperiment | This class stores an prediction of an SRM/MRM transition |
  ConsoleUtils | |
  INIUpdater | |
  ParameterInformation | Struct that captures all information of a command line parameter |
  ToolHandler | |
  TOPPBase | Base class for TOPP applications |
  AAIndex | Representation of selected AAIndex properties |
  AASequence | Representation of a peptide/protein sequence |
   ConstIterator | ConstIterator for AASequence |
   Iterator | Iterator class for AASequence |
  EdwardsLippertIterator | Finds all Peptide Candidates with given masses and given fasta file |
  EdwardsLippertIteratorTryptic | EdwardsLippertIterator that only retrieves tryptic sequences |
  Element | Representation of an element |
  ElementDB | Stores elements |
  EmpiricalFormula | Representation of an empirical formula |
  EnzymaticDigestion | Class for the enzymatic digestion of proteins |
   BindingSite | |
   CleavageModel | |
  IsotopeDistribution | Isotope distribution class |
  MassDecomposition | Class represents a decomposition of a mass into amino acids |
  MassDecompositionAlgorithm | Mass decomposition algorithm, given a mass it suggests possible compositions |
  ModificationDefinition | Representation of modification definition |
  ModificationDefinitionsSet | Representation of a set of modification definitions |
  ModificationsDB | Database which holds all residue modifications from UniMod |
  ModifierRep | Implements modification for suffix arrays |
  PepIterator | Abstract base class for different peptide iterators |
  Residue | Representation of a residue |
  ResidueDB | Residue data base which holds residues |
  ResidueModification | Representation of a modification |
  SvmTheoreticalSpectrumGenerator | Simulates MS2 spectra with support vector machines |
   DescriptorSet | A set of descriptors for a single training row |
   IonType | Nested class |
   SvmModelParameterSet | Simple container storing the model parameters required for simulation |
  SvmTheoreticalSpectrumGeneratorSet | Loads SvmTheoreticalSpectrumGenerator instances for different charges |
  SvmTheoreticalSpectrumGeneratorTrainer | Train SVM models that are used by SvmTheoreticalSpectrumGenerator |
  TheoreticalSpectrumGenerator | Generates theoretical spectra with various options |
  TrypticIterator | Finds all tryptic Peptides with every missed cleavage |
  WeightWrapper | Encapsulated weight queries to simplify mono vs average weight computation |
  AverageLinkage | AverageLinkage ClusterMethod |
  ClusterAnalyzer | Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's) |
  ClusterFunctor | Base class for cluster functors |
   InsufficientInput | Exception thrown if not enough data (<2) is used |
  ClusterHierarchical | Hierarchical clustering with generic clustering functions |
  UnnormalizedComparator | Exception thrown if clustering is attempted without a normalized compare functor |
  ClusteringGrid | Data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering |
  CompleteLinkage | CompleteLinkage ClusterMethod |
  EuclideanSimilarity | CompareFunctor for 2Dpoints |
  GridBasedCluster | Basic data structure for clustering |
  MinimumDistance | Basic data structure for distances between clusters |
  GridBasedClustering | 2D hierarchical clustering implementation optimized for large data sets containing many small clusters i.e. dimensions of clusters << dimension of entire dataset |
  HashGrid | Container for (2-dimensional coordinate, value) pairs |
   ConstIterator | Constant element iterator for the hash grid |
   Iterator | Element iterator for the hash grid |
  SingleLinkage | SingleLinkage ClusterMethod |
  BinnedSharedPeakCount | Compare functor scoring the shared peaks for similarity measurement |
  BinnedSpectralContrastAngle | Compare functor scoring the spectral contrast angle for similarity measurement |
  BinnedSpectrum | This is a binned representation of a PeakSpectrum |
   NoSpectrumIntegrated | Exception which is thrown if BinnedSpectrum bins are accessed and no PeakSpektrum has been integrated yet i.e. bins_ is empty |
  BinnedSpectrumCompareFunctor | Base class for compare functors of BinnedSpectra |
   IncompatibleBinning | Exception thrown if compared spectra are incompatible |
  BinnedSumAgreeingIntensities | Compare functor scoring the sum of agreeing intensities for similarity measurement |
  PeakAlignment | Make a PeakAlignment of two PeakSpectra |
  PeakSpectrumCompareFunctor | Base class for compare functors of spectra, that return a similarity value for two spectra |
  SpectraSTSimilarityScore | Similarity score of SpectraST |
  SpectrumAlignment | Aligns the peaks of two spectra |
  SpectrumAlignmentScore | Similarity score via spectra alignment |
  SpectrumCheapDPCorr | SpectrumCheapDPCorr calculates an optimal alignment on stick spectra |
  SpectrumPrecursorComparator | SpectrumPrecursorComparator compares just the parent mass of two spectra |
  SteinScottImproveScore | Similarity score based of Stein & Scott |
  ZhangSimilarityScore | Similarity score of Zhang |
  BinaryComposeFunctionAdapter | Represents the binary compose function object adapter |
  Factory | Returns FactoryProduct* based on the name of the desired concrete FactoryProduct |
  FactoryBase | Base class for Factory<T> |
  FuzzyStringComparator | Fuzzy comparison of strings, tolerates numeric differences |
   AbortComparison | Internal exception class |
   InputLine | Stores information about the current input line (i.e., stream for the line and the current position in the stream) |
   PrefixInfo_ | Wrapper for the prefix information computed for the failure report |
   StreamElement_ | Stores information about characters, numbers, and white spaces loaded from the InputStream |
  LogConfigHandler | The LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream |
  PrecisionWrapper | Wrapper class to implement output with appropriate precision. See precisionWrapper() |
  ProgressLogger | Base class for all classes that want to report their progress |
   ProgressLoggerImpl | This class represents an actual implementation of a logger |
  SingletonRegistry | Holds pointers to unique instance of a singleton factory |
  StreamHandler | Provides a central class to register globally used output streams. Currently supported streams are |
  UnaryComposeFunctionAdapter | Represents the function object unary adapter |
  UniqueIdGenerator | A generator for unique ids |
  UniqueIdIndexer | A base class for random access containers for classes derived from UniqueIdInterface that adds functionality to convert a unique id into an index into the container |
  UniqueIdInterface | A base class defining a common interface for all classes having a unique id |
  VersionInfo | Version information class |
   VersionDetails | |
  Adduct | |
  BigString | Concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $) |
  BinaryTreeNode | Elements of a binary tree used to represent a hierarchical clustering process |
  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+, ..) |
  Compomer | Holds information on an edge connecting two features from a (putative) charge ladder |
  ConstRefVector | This vector holds pointer to the elements of another container |
   ConstRefVectorConstIterator | ConstIterator for the ConstRefVector |
   ConstRefVectorIterator | Mutable iterator for the ConstRefVector |
  ConvexHull2D | A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling |
  CVMappingRule | Representation of a CV Mapping rule used by CVMappings |
  CVMappings | Representation of controlled vocabulary mapping rules (for PSI formats) |
  CVMappingTerm | Representation of controlled vocabulary term |
  CVReference | Controlled Vocabulary Reference |
  DataValue | Class to hold strings, numeric values, lists of strings and lists of numeric values |
  Date | Date Class |
  DateTime | DateTime Class |
  DBoundingBox | A D-dimensional bounding box |
  DefaultParamHandler | A base class for all classes handling default parameters |
  DistanceMatrix | A two-dimensional distance matrix, similar to OpenMS::Matrix |
  DPosition | Representation of a coordinate in D-dimensional space |
  DRange | A D-dimensional half-open interval |
  GridFeature | Representation of a feature in a hash grid |
  IsotopeCluster | Stores information about an isotopic cluster (i.e. potential peptide charge variants) |
   ChargedIndexSet | Index set with associated charge estimate |
  ListUtils | Collection of utility functions for management of vectors |
   DoubleTolerancePredicate_ | Predicate to check double equality with a given tolerance |
  LPWrapper | |
   SolverParam | Struct that holds the parameters of the LP solver |
  Map | Map class based on the STL map (containing several convenience functions) |
   IllegalKey | Map illegal key exception |
  MassExplainer | Computes empirical formulas for given mass differences using a set of allowed elements |
  Param | Management and storage of parameters / INI files |
   ParamEntry | Parameter entry used to store the actual information inside of a Param entry |
   ParamIterator | Forward const iterator for the Param class |
    TraceInfo | Struct that captures information on entered / left nodes for ParamIterator |
   ParamNode | Node inside a Param object which is used to build the internal tree |
  QTCluster | A representation of a QT cluster used for feature grouping |
  SparseVector | SparseVector implementation. The container will not actually store a specified type of element - the sparse element, e.g. zero (by default) |
   SparseVectorConstIterator | Const_iterator for SparseVector |
   SparseVectorConstReverseIterator | Const_reverse_iterator for SparseVector |
   SparseVectorIterator | Random access iterator for SparseVector including the hop() function to jump to the next non-sparse element |
   SparseVectorReverseIterator | Random access reverse iterator for SparseVector including the hop() function to jump to the next non-sparse element |
   ValueProxy | Class ValueProxy allows the SparseVector to differentiate between writing and reading, so zeros can be ignored See "more effective c++" section 30 |
  String | A more convenient string class |
  StringListUtils | Utilities operating on lists of Strings |
  StringUtils | |
  SuffixArray | Abstract class for suffix array |
  SuffixArrayPeptideFinder | Wrapper for easy use of sufArray |
  FloatsWithTolLess | Comparator for two doubles with a tolerance value |
  IntsInRangeLess | Comparator for two doubles with a tolerance value |
  SuffixArraySeqan | Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum |
  SuffixArrayTrypticCompressed | Class that implements a suffix array for a String. It can be used to find peptide Candidates for a MS spectrum |
  SuffixArrayTrypticSeqan | Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum |
  MorphologicalFilter | This class implements baseline filtering operations using methods from mathematical morphology |
  InternalCalibration | A simple calibration method using linear interpolation of given reference masses |
  TOFCalibration | This class implements an external calibration for TOF data using external calibrant spectra |
  DataFilters | DataFilter array providing some convenience functions |
   DataFilter | Representation of a peak/feature filter combining FilterType, FilterOperation and a value |
  ElutionPeakDetection | Extracts chromatographic peaks from a mass trace |
  CmpMassTraceByMZ | 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 |
  FeatureHypothesis | |
  CmpHypothesesByScore | |
  FeatureFindingMetabo | |
  IsotopeDistributionCache | Pre-calculate isotope distributions for interesting mass ranges |
  MassTraceDetection | A mass trace extraction method that gathers peaks similar in m/z and moving along retention time |
  SplinePackage | Fundamental data structure for SplineSpectrum |
  SplineSpectrum | Data structure for spline interpolation of MS1 spectra |
   Navigator | Iterator class for access of spline packages |
  IDFilter | Used to filter identifications by different criteria |
  SignalToNoiseEstimator | This class represents the abstract base class of a signal to noise estimator |
   GaussianEstimate | Protected struct to store parameters my, sigma for a Gaussian distribution |
  SignalToNoiseEstimatorMeanIterative | Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities |
  SignalToNoiseEstimatorMedian | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) |
  SignalToNoiseEstimatorMedianRapid | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based) |
   NoiseEstimator | Class to compute the noise value at a given position |
  GaussFilter | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data |
  GaussFilterAlgorithm | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data |
  LowessSmoothing | LOWESS (locally weighted scatterplot smoothing) |
  SavitzkyGolayFilter | Computes the Savitzky-Golay filter coefficients using QR decomposition |
  BernNorm | BernNorm scales the peaks by ranking them and then scaling them according to rank |
  ComplementFilter | Total intensity of peak pairs that could result from complementing fragments of charge state 1 |
  ComplementMarker | ComplementMarker marks peak pairs which could represent y - b ion pairs |
  FilterFunctor | A FilterFunctor extracts some spectrum characteristics for quality assessment |
  GoodDiffFilter | GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss |
  IntensityBalanceFilter | IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions |
  IsotopeDiffFilter | IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks |
  IsotopeMarker | IsotopeMarker marks peak pairs which could represent an ion and its isotope |
  LinearResampler | Linear Resampling of raw data |
  LinearResamplerAlign | Linear Resampling of raw data with alignment |
  MarkerMower | MarkerMower uses PeakMarker to find peaks, those that are not marked get removed |
  NeutralLossDiffFilter | NeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained by a neutral loss |
  NeutralLossMarker | NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water, ammonia) |
  NLargest | NLargest removes all but the n largest peaks |
  Normalizer | Normalizer normalizes the peak intensities |
  ParentPeakMower | ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions |
  PeakMarker | PeakMarker marks peaks that seem to fulfill some criterion |
  Scaler | Scaler scales the peak by ranking the peaks and assigning intensity according to rank |
  SpectraMerger | Merges blocks of MS or MS2 spectra |
   SpectraDistance_ | |
  SqrtMower | Scales the intensity of peaks to the sqrt |
  ThresholdMower | ThresholdMower removes all peaks below a threshold |
  TICFilter | TICFilter calculates TIC |
  WindowMower | WindowMower augments the highest peaks in a sliding or jumping window |
  Base64 | Class to encode and decode Base64 |
   Reinterpreter32_ | Internal class needed for type-punning |
   Reinterpreter64_ | Internal class needed for type-punning |
  Bzip2Ifstream | Decompresses files which are compressed in the bzip2 format (*.bz2) |
  Bzip2InputStream | Implements the BinInputStream class of the xerces-c library in order to read bzip2 compressed XML files |
  CachedmzML | An class that uses on-disk caching to read and write spectra and chromatograms |
  CompressedInputSource | This class is based on xercesc::LocalFileInputSource |
  ConsensusXMLFile | This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation |
  ControlledVocabulary | Representation of a controlled vocabulary |
   CVTerm | Representation of a CV term |
  CsvFile | This class handles csv files. Currently only loading is implemented |
  CVMappingFile | Used to load CvMapping files |
  MSDataCachedConsumer | Transforming and cached writing consumer of MS data |
  MSDataChainingConsumer | Consumer class that passes all operations on to a set of consumers |
  MSDataTransformingConsumer | Transforming consumer of MS data |
  MSDataWritingConsumer | Consumer class that writes MS data to disk using the mzML format |
  PlainMSDataWritingConsumer | Consumer class that writes MS data to disk using the mzML format |
  NoopMSDataWritingConsumer | Consumer class that perform no operation |
  NoopMSDataConsumer | Consumer class that perform no operation |
  FullSwathFileConsumer | Abstract base class which can consume spectra coming from SWATH experiment stored in a single file |
  RegularSwathFileConsumer | In-memory implementation of FullSwathFileConsumer |
  CachedSwathFileConsumer | On-disk cached implementation of FullSwathFileConsumer |
  DTA2DFile | DTA2D File adapter |
  DTAFile | File adapter for DTA files |
  EDTAFile | File adapter for Enhanced DTA files |
  FASTAFile | This class serves for reading in FASTA files |
   FASTAEntry | FASTA entry type (identifier, description and sequence) |
  FastaIterator | Iterator over FASTA file |
  FastaIteratorIntern | Iterator for a FASTA file |
  FeatureXMLFile | This class provides Input/Output functionality for feature maps |
  FileHandler | Facilitates file handling by file type recognition |
  FileTypes | Centralizes the file types recognized by FileHandler |
  GzipIfstream | Decompresses files which are compressed in the gzip format (*.gzip) |
  GzipInputStream | Implements the BinInputStream class of the xerces-c library in order to read gzip compressed XML files |
  IndexedMzMLDecoder | A class to analyze indexedmzML files and extract the offsets of individual tags |
  MzMLSpectrumDecoder | A class to decode input strings that contain an mzML chromatogram or spectrum tag |
  IBSpectraFile | Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results |
  IdXMLFile | Used to load and store idXML files |
  IndexedMzMLFile | A class to read an indexedmzML file |
  IndexedMzMLFileLoader | A class to load an indexedmzML file |
  InspectInfile | Inspect input file adapter |
  InspectOutfile | Representation of an Inspect outfile |
  KroenikFile | File adapter for Kroenik (HardKloer sibling) files |
  LibSVMEncoder | Serves for encoding sequences into feature vectors |
  MascotGenericFile | Mascot input file adapter |
  MascotInfile | Mascot input file adapter |
  MascotRemoteQuery | Class which handles the communication between OpenMS and the Mascot server |
  MascotXMLFile | Used to load MascotXML files |
  MS2File | MS2 input file adapter |
  MsInspectFile | File adapter for MsInspect files |
  MSNumpressCoder | Class to encode and decode data encoded with MSNumpress |
   NumpressConfig | Configuration class for MSNumpress |
  MSPFile | File adapter for MSP files (NIST spectra library) |
  MzDataFile | File adapter for MzData files |
  MzIdentMLFile | File adapter for MzIdentML files |
  MzMLFile | File adapter for MzML files |
  MzQuantMLFile | File adapter for MzQuantML files |
  MzTabNullAbleInterface | |
  MzTabNullNaNAndInfAbleInterface | |
  MzTabNullAbleBase | |
  MzTabNullNaNAndInfAbleBase | |
  MzTabDouble | |
  MzTabDoubleList | |
  MzTabInteger | |
  MzTabIntegerList | |
  MzTabBoolean | |
  MzTabString | |
  MzTabParameter | |
  MzTabParameterList | |
  MzTabStringList | |
  MzTabModification | |
  MzTabModificationList | |
  MzTabSpectraRef | |
  MzTabSampleMetaData | |
  MzTabSoftwareMetaData | |
  MzTabModificationMetaData | |
  MzTabAssayMetaData | |
  MzTabCVMetaData | |
  MzTabInstrumentMetaData | |
  MzTabContactMetaData | |
  MzTabMSRunMetaData | |
  MzTabStudyVariableMetaData | |
  MzTabMetaData | |
  MzTabProteinSectionRow | |
  MzTabPeptideSectionRow | |
  MzTabPSMSectionRow | |
  MzTabSmallMoleculeSectionRow | |
  MzTab | Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/ |
  MzTabFile | File adapter for MzTab files |
  MzXMLFile | File adapter for MzXML 2.1 files |
  OMSSACSVFile | File adapter for OMSSACSV files |
  OMSSAXMLFile | Used to load OMSSAXML files |
  FeatureFileOptions | Options for loading files containing features |
  PeakFileOptions | Options for loading files containing peak data |
  ParamXMLFile | The file pendant of the Param class used to load and store the param datastructure as paramXML |
  PeakTypeEstimator | Estimates if the data of a spectrum is raw data or peak data |
  PepNovoInfile | PepNovo input file adapter |
  PepNovoOutfile | Representation of a PepNovo output file |
  PepXMLFile | Used to load and store PepXML files |
   AminoAcidModification | |
  PepXMLFileMascot | Used to load Mascot PepXML files |
  ProtXMLFile | Used to load (storing not supported, yet) ProtXML files |
  PTMXMLFile | Used to load and store PTMXML files |
  QcMLFile | File adapter for QcML files |
   Attachment | Representation of an attachment |
   QualityParameter | Representation of a quality parameter |
  SequestInfile | Sequest input file adapter |
  SequestOutfile | Representation of a Sequest output file |
  SpecArrayFile | File adapter for SpecArray (.pepList) files |
  SVOutStream | Stream class for writing to comma/tab/...-separated values files |
  SwathFile | File adapter for Swath files |
  TextFile | This class provides some basic file handling methods for text files |
  ToolDescriptionFile | File adapter for ToolDescriptor files |
  TraMLFile | File adapter for HUPO PSI TraML files |
  TransformationXMLFile | Used to load and store TransformationXML files |
  UnimodXMLFile | Used to load XML files from unimod.org files |
  XMLValidator | Validator for XML files |
  XMassFile | File adapter for 'XMass Analysis (fid)' files |
  XTandemInfile | XTandem input file |
  XTandemXMLFile | Used to load XTandemXML files |
  BaseFeature | A basic LC-MS feature |
   QualityLess | Compare by quality |
  ChromatogramPeak | A 1-dimensional raw data point or peak for chromatograms |
   IntensityLess | Comparator by intensity |
   PositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for RTLess |
   RTLess | Comparator by RT position |
  ChromatogramTools | Conversion class to convert chromatograms |
  PointerComparator | Wrapper that takes a comparator for `something' and makes a comparator for pointers to `something' out of it. Normally you should use the make-function pointerComparator() because then you do not need to specify the template arguments |
  ReverseComparator | Wrapper that reverses (exchanges) the two arguments of a comparator. Normally you should use the make-function reverseComparator() because then you do not need to specify the template arguments |
  LexicographicComparator | A wrapper class that combines two comparators lexicographically. Normally you should use the make-function lexicographicComparator() because then you do not need to specify the template arguments |
  PairComparatorFirstElement | Class for comparison of std::pair using first ONLY e.g. for use with std::sort |
  PairComparatorSecondElement | Class for comparison of std::pair using second ONLY e.g. for use with std::sort |
  PairComparatorFirstElementMore | Class for comparison of std::pair using first ONLY e.g. for use with std::sort |
  PairComparatorSecondElementMore | Class for comparison of std::pair using second ONLY e.g. for use with std::sort |
  PairMatcherFirstElement | Class for comparison of std::pair using first ONLY e.g. for use with std::sort |
  PairMatcherSecondElement | Struct for comparison of std::pair using second ONLY e.g. for use with std::sort |
  EqualInTolerance | Struct for binary predicate to consider equality with a certain tolerance |
  ConsensusFeature | A 2-dimensional consensus feature |
   MapsLess | Compare by the sets of consensus elements (lexicographically) |
   Ratio | Slim struct to feed the need for systematically storing of ratios ( |
   SizeLess | Compare by size(), the number of consensus elements |
  ConsensusMap | A container for consensus elements |
   FileDescription | Source file description for input files |
  MapConversion | |
  DPeak | Metafunction to choose among Peak1D respectively Peak2D through a template argument |
  DRichPeak | Metafunction to choose among RichPeak1D respectively RichPeak2D through a template argument |
  Feature | An LC-MS feature |
  FeatureHandle | Representation of a Peak2D, RichPeak2D or Feature |
   FeatureHandleMutable_ | Helper class returned by FeatureHandle::asMutable(), which see |
   IndexLess | Comparator by map and unique id |
  AnnotationStatistics | |
  FeatureMap | A container for features |
  MassTrace | A container type that gathers peaks similar in m/z and moving along retention time |
  MRMFeature | A multi-chromatogram MRM feature |
  MRMTransitionGroup | The representation of a transition group that has information about the individual chromatograms as well as the transitions it refers to |
  MSChromatogram | The representation of a chromatogram |
   FloatDataArray | Float data array class |
   IntegerDataArray | Float data array class |
   MZLess | Comparator for the retention time |
   StringDataArray | String data array class |
  MSExperiment | In-Memory representation of a mass spectrometry experiment |
   ContainerAdd_ | Helper class to add either general data points in set2DData or use mass traces from meta values |
   ContainerAdd_< ContainerIterator, false > | |
   ContainerAdd_< ContainerIterator, true > | |
  MSSpectrum | The representation of a 1D spectrum |
   FloatDataArray | Float data array class |
   IntegerDataArray | Integer data array class |
   RTLess | Comparator for the retention time |
   StringDataArray | String data array class |
  OnDiscMSExperiment | Representation of a mass spectrometry experiment on disk |
  Peak1D | A 1-dimensional raw data point or peak |
   IntensityLess | |
   MZLess | Comparator by m/z position |
   PositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for MZLess |
  Peak2D | A 2-dimensional raw data point or peak |
   IntensityLess | |
   MZLess | Comparator by m/z position |
   PositionLess | Comparator by position. Lexicographical comparison (first RT then m/z) is done |
   RTLess | Comparator by RT position |
  PeakIndex | Index of a peak or feature |
  RangeManager | Handles the management of a position and intensity range |
  HasMetaValue | Predicate that determines if a class has a certain metavalue |
  InRTRange | Predicate that determines if a spectrum lies inside/outside a specific retention time range |
  InMSLevelRange | Predicate that determines if a spectrum lies inside/outside a specific MS level set |
  HasScanMode | Predicate that determines if a spectrum has a certain scan mode |
  HasScanPolarity | Predicate that determines if a spectrum has a certain scan polarity |
  IsEmptySpectrum | Predicate that determines if a spectrum is empty |
  IsZoomSpectrum | Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum |
  HasActivationMethod | Predicate that determines if a spectrum was generated using any activation method given in the constructor list |
  InPrecursorMZRange | Predicate that determines if a spectrum's precursor is within a certain m/z range |
  HasPrecursorCharge | Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list |
  InMzRange | Predicate that determines if a peak lies inside/outside a specific m/z range |
  InIntensityRange | Predicate that determines if a peak lies inside/outside a specific intensity range |
  IsInCollisionEnergyRange | Predicate that determines if an MSn spectrum was generated with a collision energy in the given range |
  IsInIsolationWindowSizeRange | Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range |
  RichPeak1D | A 1-dimensional raw data point or peak with meta information |
  RichPeak2D | A 2-dimensional raw data point or peak with meta information |
  BSpline2d | B spline interpolation |
  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 |
  NonNegativeLeastSquaresSolver | Wrapper for a non-negative least squares (NNLS) solver |
  Spline2d | Wrapper for Spline interpolation |
  Acquisition | Information about one raw data spectrum that was combined with several other raw data spectra |
  AcquisitionInfo | Description of the combination of raw data to a single spectrum |
  ChromatogramSettings | Representation of chromatogram settings, e.g. SRM/MRM chromatograms |
  ContactPerson | Contact person information |
  CVTerm | Representation of controlled vocabulary term |
   Unit | |
  CVTermList | Representation of controlled vocabulary term list |
  DataProcessing | Description of the applied preprocessing steps |
  Digestion | Meta information about digestion of a sample |
  DocumentIdentifier | Manage source document information |
  DocumentIDTagger | Tags OpenMS file containers with a DocumentID |
  ExperimentalSettings | Description of the experimental settings |
  Gradient | Representation of a HPLC gradient |
  HPLC | Representation of a HPLC experiment |
  Identification | Represents a object which can store the information of an analysisXML instance |
  IdentificationHit | Represents a object which can store the information of an analysisXML instance |
  Instrument | Description of a MS instrument |
  InstrumentSettings | Description of the settings a MS Instrument was run with |
  IonDetector | Description of a ion detector (part of a MS Instrument) |
  IonSource | Description of an ion source (part of a MS Instrument) |
  MassAnalyzer | Description of a mass analyzer (part of a MS Instrument) |
  MetaInfo | A Type-Name-Value tuple class |
  MetaInfoDescription | Description of the meta data arrays of MSSpectrum |
  MetaInfoInterface | Interface for classes that can store arbitrary meta information (Type-Name-Value tuples) |
  MetaInfoRegistry | Registry which assigns unique integer indices to strings |
  Modification | Meta information about chemical modification of a sample |
  MSQuantifications | |
   AnalysisSummary | |
   Assay | |
  PeptideEvidence | Representation of a peptide evidence |
  PeptideHit | Representation of a peptide hit |
   ScoreLess | Lesser predicate for scores of hits |
   ScoreMore | Greater predicate for scores of hits |
  PeptideIdentification | Represents the peptide hits for a spectrum |
  Precursor | Precursor meta information |
  Product | Product meta information |
  ProteinHit | Representation of a protein hit |
   ScoreLess | Lesser predicate for scores of hits |
   ScoreMore | Greater predicate for scores of hits |
  ProteinIdentification | Representation of a protein identification run |
   ProteinGroup | Bundles multiple (e.g. indistinguishable) proteins in a group |
   SearchParameters | Search parameters of the DB search |
  Sample | Meta information about the sample |
  SampleTreatment | Base class for sample treatments (Digestion, Modification, Tagging, ...) |
  ScanWindow | Scan window description |
  Software | Description of the software used for processing |
  SourceFile | Description of a file location, used to store the origin of (meta) data |
  SpectrumIdentification | Represents a object which can store the information of an analysisXML instance |
  SpectrumSettings | Representation of 1D spectrum settings |
  Tagging | Meta information about tagging of a sample e.g. ICAT labeling |
  DetectabilitySimulation | Simulates peptide detectability |
  DigestSimulation | Simulates protein digestion |
  EGHFitter1D | Exponential-Gaussian hybrid distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization |
   Data | Helper struct (contains the size of an area and a raw data container) |
   EGHFitterFunctor | |
  EGHModel | Exponential-Gaussian hybrid distribution model for elution profiles |
  IonizationSimulation | Simulates Protein ionization |
  BaseLabeler | Abstract base class for all kinds of labeling techniques |
  ICPLLabeler | Simulate ICPL experiments |
  ITRAQLabeler | Simulate iTRAQ experiments |
  LabelFreeLabeler | Abstract base class for all kinds of labeling techniques |
  O18Labeler | Simulate O-18 experiments |
  SILACLabeler | Simulate SILAC experiments |
  MSSim | Central class for simulation of mass spectrometry experiments |
  RawMSSignalSimulation | Simulates MS signals for a given set of peptides |
   ContaminantInfo | |
  RawTandemMSSignalSimulation | Simulates tandem MS signals for a given set of peptides |
  RTSimulation | Simulates/Predicts retention times for peptides or peptide separation |
  File | Basic file handling operations |
  FileWatcher | Watcher that monitors file changes |
  JavaInfo | Detect Java and retrieve information |
  StopWatch | StopWatch Class |
  SysInfo | Some static functions to get system information |
  BaseModel | Abstract base class for all D-dimensional models |
  BiGaussFitter1D | BiGaussian distribution fitter (1-dim.) approximated using linear interpolation |
  BiGaussModel | BiGaussian distribution approximated using linear interpolation |
  EGHTraceFitter | A RT Profile fitter using an Exponential Gaussian Hybrid background model |
   EGHTraceFunctor | |
  EmgFitter1D | Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization |
   Data | Helper struct (contains the size of an area and a raw data container) |
   EgmFitterFunctor | |
  EmgModel | Exponentially modified gaussian distribution model for elution profiles |
  EmgScoring | Scoring of an elution peak using an exponentially modified gaussian distribution model |
  ExtendedIsotopeFitter1D | Extended isotope distribution fitter (1-dim.) approximated using linear interpolation |
  ExtendedIsotopeModel | Extended isotope distribution approximated using linear interpolation |
  FeaFiModule | Implements a module of the FeatureFinder algorithm |
  FeatureFinder | The main feature finder class |
  Summary | Summary of fitting results |
  FeatureFinderAlgorithm | Abstract base class for FeatureFinder algorithms |
  FeatureFinderAlgorithmIsotopeWavelet | Implements the isotope wavelet feature finder |
   BoxElement | Internally used data structure for the sweep line algorithm |
  FeatureFinderAlgorithmMRM | FeatureFinderAlgorithm for MRM experiments |
  FeatureFinderAlgorithmPicked | FeatureFinderAlgorithm for picked peaks |
  FeatureFinderAlgorithmPickedHelperStructs | Wrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes |
   IsotopePattern | Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked |
   MassTrace | Helper struct for mass traces used in FeatureFinderAlgorithmPicked |
   MassTraces | Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked |
   Seed | Helper structure for seeds used in FeatureFinderAlgorithmPicked |
   TheoreticalIsotopePattern | Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked |
  FeatureFinderDefs | The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes |
   NoSuccessor | Exception that is thrown if a method an invalid IndexPair is given |
  Fitter1D | Abstract base class for all 1D-dimensional model fitter |
  GaussFitter1D | Gaussian distribution fitter (1-dim.) approximated using linear interpolation |
  GaussModel | Normal distribution approximated using linear interpolation |
  GaussTraceFitter | Fitter for RT profiles using a Gaussian background model |
   GaussTraceFunctor | |
  InterpolationModel | Abstract class for 1D-models that are approximated using linear interpolation |
  IsotopeFitter1D | Isotope distribution fitter (1-dim.) approximated using linear interpolation |
  IsotopeModel | Isotope distribution approximated using linear interpolation |
  IsotopeWavelet | Implements the isotope wavelet function |
   fi_ | Internal union for fast computation of the power function |
  IsotopeWaveletTransform | A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the FeatureFinderAlgorithmIsotopeWavelet class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform |
   BoxElement | Internally used data structure |
   TransSpectrum | Internally (only by GPUs) used data structure . It allows efficient data exchange between CPU and GPU and avoids unnecessary memory moves. The class is tailored on the isotope wavelet transform and is in general not applicable on similar - but different - situations |
  LevMarqFitter1D | Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization |
   GenericFunctor | |
  MaxLikeliFitter1D | Abstract base class for all 1D-model fitters using maximum likelihood optimization |
  ModelDescription | Stores the name and parameters of a model |
  MultiplexClustering | Clusters results from multiplex filtering |
   MultiplexDistance | Scaled Euclidean distance for clustering |
  MultiplexFiltering | Base class for filtering centroided and profile data for peak patterns |
   BlackListEntry | Structure for peak blacklisting |
   PeakReference | Structure for peak position in neighbouring spectra |
  MultiplexFilteringCentroided | Filters centroided data for peak patterns |
  MultiplexFilteringProfile | Filters centroided and profile data for peak patterns |
  MultiplexFilterResult | Data structure storing all peaks (and optionally their raw data points) corresponding to one specific peak pattern |
  MultiplexFilterResultPeak | Data structure storing a single peak that passed all filters |
  MultiplexFilterResultRaw | Data structure storing a single raw data point that passed all filters |
  MultiplexPeakPattern | Data structure for pattern of isotopic peaks |
  PeakWidthEstimator | Rough estimation of the peak width at m/z |
  ProductModel | Class for product models i.e. models with D independent dimensions |
  ProductModel< 2 > | The class template is only implemented for D=2 because we use Peak2D here |
  SeedListGenerator | Generate seed lists for feature detection |
  TraceFitter | Abstract fitter for RT profile fitting |
   GenericFunctor | |
   ModelData | |
  ContinuousWaveletTransform | This class is the base class of the continuous wavelet transformation |
  ContinuousWaveletTransformNumIntegration | This class computes the continuous wavelet transformation using a marr wavelet |
  OptimizePeakDeconvolution | This class provides the deconvolution of peak regions using non-linear optimization |
   Data | Class containing the data needed for optimization |
  OptimizePick | This class provides the non-linear optimization of the peak parameters |
   Data | |
   OptPeakFunctor | |
  PeakPickerCWT | This class implements a peak picking algorithm using wavelet techniques |
   PeakArea_ | Class for the internal peak representation |
  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 |
   PeakBoundary | Structure for peak boundaries |
  PeakCandidate | A small structure to hold peak candidates |
  PeakPickerIterative | This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data) |
  PeakPickerMaxima | This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width |
   PeakCandidate | The PeakCandidate describes the output of the peak picker |
  PeakPickerSH | |
  PeakShape | Internal representation of a peak shape (used by the PeakPickerCWT) |
   PositionLess | Comparison of mz_positions |
  TwoDOptimization | This class provides the two-dimensional optimization of the picked peak parameters |
   Data | Helper struct (contains the size of an area and a raw data container) |
   TwoDOptFunctor | |
  FeatureFinderAlgorithmSH | The Superhirn FeatureFinderAlgorithm |
  FeatureFinderAlgorithmSHCtrl | A facade for various Superhirn FeatureFinder classes. Use FeatureFinderAlgorithmSH instead |
  BackgroundControl | |
  BackgroundIntensityBin | |
  CentroidData | |
  CentroidPeak | |
  DeconvPeak | |
  ClusteredMS2ConsensusSpectrum | |
  ConsensusIsotopePattern | |
  Deisotoper | |
  MS1Signal | |
  FeatureLCProfile | |
  FTPeakDetectController | |
  IsotopicDist | |
  LCElutionPeak | |
  LCMS | |
   OPERATOR_FeatureCompare | |
   OPERATOR_MZ | |
  LCMSCData | |
  MS1FeatureMerger | |
   OPERATOR_FEATURE_TR | |
  MS2ConsensusSpectrum | |
  MS2Feature | |
  MS2Fragment | |
  MS2Info | |
  MSPeak | |
  ProcessData | |
  RawData | |
  SHFeature | |
  SuperHirnParameters | SuperHirn parameters singleton class containing all static configuration variables |
  SuperHirnUtil | |
  Annotation1DCaret | An annotation item which paints a set of carets on the canvas |
  Annotation1DDistanceItem | An annotation item which represents a measured distance between two peaks |
  Annotation1DItem | An abstract class acting as an interface for the different 1D annotation items |
  Annotation1DPeakItem | A peak annotation item |
  Annotation1DTextItem | An annotation item which represents an arbitrary text on the canvas |
  Annotations1DContainer | Container for annotations to content of Spectrum1DCanvas |
  IDEvaluationBase | Main window of the IDEvaluation tool |
  INIFileEditorWindow | Shows the ParamEditor widget in a QMainWindow with a toolbar |
  QApplicationTOPP | Extension to the QApplication for running TOPPs GUI tools |
  TOPPASBase | Main window of the TOPPAS tool |
  TOPPViewBase | Main window of TOPPView tool |
  AxisPainter | Draws a coordinate axis. It has only static methods, that's why the constructor is private |
  AxisTickCalculator | Calculates ticks for a given value range |
  AxisWidget | Widget that represents an axis of a graph |
  ColorSelector | A widget for selecting a color |
  DataFilterDialog | Dialog for creating and changing a DataFilter |
  FeatureEditDialog | Dialog for editing a feature |
  HistogramDialog | Dialog that show a HistogramWidget |
  LayerStatisticsDialog | Dialog showing statistics about the data of the current layer |
   MetaStatsValue_ | Struct representing the statistics about one meta information |
  SaveImageDialog | Dialog for saving an image |
  Spectrum1DGoToDialog | Simple goto/set visible area dialog for exact placement of the viewing window |
  Spectrum2DGoToDialog | GoTo dialog used to zoom to a m/z and retention time range or to a feature |
  SpectrumAlignmentDialog | Lets the user select two spectra and set the parameters for the spectrum alignment |
  TheoreticalSpectrumGenerationDialog | Dialog which allows to enter an AA sequence and generates a theoretical spectrum for it |
  ToolsDialog | TOPP tool selection dialog |
  TOPPASInputFileDialog | Dialog which allows to specify an input file |
  TOPPASInputFilesDialog | Dialog which allows to specify a list of input files |
  TOPPASIOMappingDialog | Dialog which allows to configure the input/output parameter mapping of an edge |
  TOPPASOutputFilesDialog | Dialog which allows to specify the directory for the output files |
  TOPPASToolConfigDialog | TOPP tool configuration dialog |
  TOPPASVertexNameDialog | Dialog which allows to change the name of an input vertex |
  TOPPViewOpenDialog | Dataset opening options for TOPPView |
  EnhancedTabBar | Convenience tab bar implementation |
  EnhancedTabBarWidgetInterface | Widgets that are placed into an EnhancedTabBar must implement this interface |
  EnhancedWorkspace | |
  GUIProgressLoggerImpl | Implements a GUI version of the ProgressLoggerImpl |
  HistogramWidget | Widget which can visualize a histogram |
  LayerData | Class that stores the data for one layer |
  ListEditor | Editor for editing int, double and string lists (including output and input file lists) |
  MetaDataBrowser | A meta data visualization widget |
  MultiGradient | A gradient of multiple colors and arbitrary distances between colors |
  MultiGradientSelector | A widget witch allows constructing gradients of multiple colors |
  ParamEditor | A GUI for editing or viewing a Param object |
  SpectraIdentificationViewWidget | Tabular visualization / selection of identified spectra |
  SpectraViewWidget | Hierarchical visualization and selection of spectra |
  Spectrum1DCanvas | Canvas for visualization of one or several spectra |
  Spectrum1DWidget | Widget for visualization of several spectra |
  Spectrum2DCanvas | Canvas for 2D-visualization of peak map, feature map and consensus map data |
  Spectrum2DWidget | Widget for 2D-visualization of peak map and feature map data |
  Spectrum3DCanvas | Canvas for 3D-visualization of peak map data |
  Spectrum3DOpenGLCanvas | OpenGL Canvas for 3D-visualization of map data |
  Spectrum3DWidget | Widget for 3D-visualization of map data |
  SpectrumCanvas | Base class for visualization canvas classes |
  SpectrumWidget | Base class for spectrum widgets |
  TOPPASEdge | An edge representing a data flow in TOPPAS |
  TOPPASInputFileListVertex | A vertex representing an input file list |
  TOPPASLogWindow | QTextEdit implementation with a "clear" button in the context menu |
  TOPPASMergerVertex | A special vertex that allows to merge several inputs |
  TOPPASOutputFileListVertex | A vertex representing an output file list |
  TOPPASResource | Represents a data resource for TOPPAS workflows |
  TOPPASResources | A dictionary mapping string keys to lists of TOPPASResource objects |
  FakeProcess | A FakeProcess class |
  TOPPASScene | A container for all visual items of a TOPPAS workflow |
   TOPPProcess | Stores the information for a TOPP process |
  TOPPASTabBar | Convenience tab bar implementation |
  TOPPASToolVertex | A vertex representing a TOPP tool |
   IOInfo | Stores the information for input/output files/lists |
  TOPPASTreeView | Tree view implementation for the list of TOPP tools |
  TOPPASVertex | The base class of the different vertex classes |
   VertexRoundPackage | Info for one edge and round, to be passed to next node |
  TOPPASWidget | Widget visualizing and allowing to edit TOPP pipelines |
  TOPPViewBehaviorInterface | Interface class to model different behaviors of TOPPView |
  TOPPViewIdentificationViewBehavior | Behavior of TOPPView in identification mode |
  TOPPViewSpectraViewBehavior | Behavior of TOPPView in spectra view mode |
  AcquisitionInfoVisualizer | Class that displays all meta information for AcquisitionInfo objects |
  AcquisitionVisualizer | Class that displays all meta information for Acquisition objects |
  BaseVisualizer | A base class for all visualizer classes |
  BaseVisualizerGUI | A base class for all visualizer classes |
  ContactPersonVisualizer | Class that displays all meta information for ContactPerson objects |
  DataProcessingVisualizer | Class that displays all meta information for DataProcessing objects |
  DigestionVisualizer | Class that displays all meta information of digestion objects |
  DocumentIdentifierVisualizer | Class that displays all meta information for DocumentIdentifier objects |
  ExperimentalSettingsVisualizer | Class that displays all meta information for ExperimentalSettings objects |
  GradientVisualizer | GradientVisualizer is a visualizer class for objects of type gradient |
  HPLCVisualizer | Class that displays all meta information for HPLC objects |
  InstrumentSettingsVisualizer | Class that displays all meta information for InstrumentSettings objects |
  InstrumentVisualizer | Class that displays all meta information for an MS instrument |
  IonDetectorVisualizer | Class that displays all meta information for IonDetector objects |
  IonSourceVisualizer | Class that displays all meta information for IonSource objects |
  MassAnalyzerVisualizer | Class that displays all meta information for MassAnalyzer objects |
  MetaInfoDescriptionVisualizer | Class that displays all meta information for MetaInfoDescription objects |
  MetaInfoVisualizer | MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member |
  ModificationVisualizer | Class that displays all meta information of modification objects |
  PeptideHitVisualizer | Class that displays all meta information for PeptideHit objects |
  PeptideIdentificationVisualizer | Class that displays all meta information for PeptideIdentification objects |
  PrecursorVisualizer | Class that displays all meta information for Precursor objects |
  ProductVisualizer | Class that displays all meta information for Product objects |
  ProteinHitVisualizer | Class that displays all meta information for ProteinHit objects |
  ProteinIdentificationVisualizer | Class that displays all meta information for ProteinIdentification objects |
  SampleVisualizer | Class that displays all meta information of sample objects |
  ScanWindowVisualizer | Class that displays all meta information for ScanWindow objects |
  SoftwareVisualizer | Class that displays all meta information for Software objects |
  SourceFileVisualizer | Class that displays all meta information for SourceFile objects |
  SpectrumSettingsVisualizer | Class that displays all meta information for SpectrumSettings objects |
  TaggingVisualizer | Class that displays all meta information of tagging objects |
  OpenSwathTSVWriter | Class to write out an OpenSwath TSV output (mProphet input) |
  OpenSwathWorkflow | Class to execute an OpenSwath Workflow |
   ChromExtractParams | ChromatogramExtractor parameters |
 OpenSwath | |
  Scoring | Scoring functions used by MRMScoring |
  MRMScoring | This class implements different scores for peaks found in SRM/MRM |
  mySqrt | |
  mean_and_stddev | Functor to compute the mean and stddev of sequence using the std::foreach algorithm |
  IDataFrameWriter | |
  DataMatrix | |
  CSVWriter | |
  OSBinaryDataArray | The datastructures used by the OpenSwath interfaces |
  OSChromatogramMeta | Identifying information for a chromatogram |
  OSChromatogram | A single chromatogram |
  OSSpectrumMeta | Identifying information for a spectrum |
  OSSpectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
  ISpectrumAccess | The interface of a mass spectrometry experiment |
  IFeature | |
  IMRMFeature | |
  ITransitionGroup | |
  ISignalToNoise | |
  MockFeature | Mock object implementing IFeature |
  MockMRMFeature | Mock object implementing IMRMFeature |
  MockTransitionGroup | Mock object implementing ITransitionGroup |
  MockSignalToNoise | Mock object implementing ISignalToNoise |
  SwathMap | Data structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2 |
  LightTransition | |
  LightModification | |
  LightPeptide | |
  LightProtein | |
  LightTargetedExperiment | |
  TransitionHelper | |
  Peptide | |
  Protein | |
  TargetedExperiment | |
 seqan | |
  FoundProteinFunctor | |
  SAValue< Index< StringSet< Peptide >, IndexWotd<> > > | |
  EquivalenceClassAA_ | |
 glp_prob | |
 MarkerIonExtractor | |
 PeptideProteinMatchInformation | |
 QApplication | |
 QDate | |
 QDateTime | |
 QDialog | |
 QFileSystemWatcher | |
 QGLWidget | |
 QGraphicsItem | |
 QGraphicsScene | |
 QGraphicsView | |
 QItemDelegate | |
 QLineEdit | |
 QListWidget | |
 QMainWindow | |
 QObject | |
 QProcess | |
 QTabBar | |
 QTextEdit | |
 QTreeWidget | |
 QWidget | |
 QWorkspace | |
 RNPxlReportRow | |
 RNPxlReportRowHeader | |
 SimpleSearchEngine | |
  HasInvalidPeptideLengthPredicate | |
 TOPPRNPxl | |