| AAIndex | Representation of selected AAIndex properties |
| AASequence | Representation of a peptide/protein sequence |
| FuzzyStringComparator::AbortComparison | Internal exception class |
| 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 |
| AcquisitionInfoVisualizer | Class that displays all meta information for AcquisitionInfo objects |
| AcquisitionVisualizer | Class that displays all meta information for Acquisition objects |
| AcqusHandler | Read-only acqus File handler for XMass Analysis |
| Adduct | |
| PepXMLFile::AminoAcidModification | |
| MSQuantifications::AnalysisSummary | |
| 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 |
| AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT > | Forward iterator for an area of peaks in an experiment |
| AScore | Implementation of the Ascore For a given Peptidesequence and its MS^2 spectrum it is tried to identify the most probable phosphorylation-site(s). For each phosphorylation site a score is calculated, which is an indicator for the probability that this site is phosphorylated. The algorithm is implemented according to Beausoleil et al |
| MSQuantifications::Assay | |
| AsymmetricStatistics< Real > | Internal class for asymmetric distributions |
| QcMLFile::Attachment | Representation of an attachment |
| AverageLinkage | AverageLinkage ClusterMethod |
| AveragePosition< D > | Maintain an average position by summing up positions with weights |
| 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 |
| BackgroundControl | |
| BackgroundIntensityBin | |
| Base64 | Class to encode and decode Base64 |
| BaseException | Exception base class |
| BaseFeature | A basic LC-MS feature |
| BaseGroupFinder | The base class of all element group finding algorithms |
| BaseLabeler | Abstract base class for all kinds of labeling techniques |
| BaseModel< D > | Abstract base class for all D-dimensional models |
| BaseSuperimposer | The base class of all superimposer algorithms |
| BaseVisualizer< ObjectType > | A base class for all visualizer classes |
| BaseVisualizerGUI | A base class for all visualizer classes |
| BasicStatistics< RealT > | Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation |
| BernNorm | BernNorm scales the peaks by ranking them and then scaling them according to rank |
| BiGaussFitter1D | Bigaussian distribution fitter (1-dim.) approximated using linear interpolation |
| BiGaussModel | Bigaussian distribution approximated using linear interpolation |
| BigString | Concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $) |
| BilinearInterpolation< Key, Value > | 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 |
| binary_function | |
| BinaryComposeFunctionAdapter< OP1, OP2, OP3 > | Represents the binary compose function object adapter |
| MzMLHandler< MapType >::BinaryData | Spectrum representation |
| BinaryDataArray | The datastructures used by the OpenSwath interfaces |
| BinaryTreeNode | Elements of a binary tree used to represent a hierarchical clustering process |
| EnzymaticDigestion::BindingSite | |
| BinInputStream | |
| 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 |
| BinnedSpectrumCompareFunctor | Base class for compare functors of BinnedSpectra |
| BinnedSumAgreeingIntensities | Compare functor scoring the sum of agreeing intensities for similarity measurement |
| SILACFiltering::BlacklistEntry | Structure for blacklist |
| HierarchicalClustering< PointRef >::BoundingBox | Bounding box of cluster |
| FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::BoxElement | Internally used data structure for the sweep line algorithm |
| IsotopeWaveletTransform< PeakType >::BoxElement | Internally used data structure |
| BufferOverflow | Buffer overflow exception |
| 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 |
| CentroidData | |
| CentroidPeak | |
| ItraqConstants::ChannelInfo | Stores information on an iTRAQ channel |
| IsotopeCluster::ChargedIndexSet | Index set with associated charge estimate |
| 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+, ..) |
| Chromatogram | A single chromatogram |
| ChromatogramExtractor | The ChromatogramExtractor extracts chromatograms from a mzML file |
| ChromatogramMeta | Identifying information for a chromatogram |
| ChromatogramPeak | A 1-dimensional raw data point or peak for chromatograms |
| ChromatogramSettings | Representation of chromatogram settings, e.g. SRM/MRM chromatograms |
| ChromatogramTools | Conversion class to interconvert chromatograms |
| EnzymaticDigestion::CleavageModel | |
| HierarchicalClustering< PointRef >::Cluster | Set of points. Describes a cluster on the grid. A point consists of a PointCoordinate and a PointRef |
| ClusterAnalyzer | Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's) |
| ClusteredMS2ConsensusSpectrum | |
| ClusterFunctor | Base class for cluster functors |
| ClusterHierarchical | Hierarchical clustering with generic clustering functions |
| CmpHypothesesByScore | |
| 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 |
| ColorSelector | A widget for selecting a color |
| MapAlignmentAlgorithmSpectrumAlignment::Compare | Innerclass necessary for using the sort algo |
| CompareFouriertransform | Compare Discrete Cosines value from a Fourier transformation, also known as Discrete Cosines Transformation |
| 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 |
| CompleteLinkage | CompleteLinkage ClusterMethod |
| CompNovoIdentification | Run with CompNovoIdentification |
| CompNovoIdentificationBase | Run with CompNovoIdentificationBase |
| CompNovoIdentificationCID | Run with CompNovoIdentificationCID |
| CompNovoIonScoring | Run with CompNovoIonScoring |
| CompNovoIonScoringBase | Run with CompNovoIonScoringBase |
| CompNovoIonScoringCID | Run with CompNovoIonScoringCID |
| Compomer | Holds information on an edge connecting two features from a (putative) charge ladder |
| Compound | |
| CompressedInputSource | This class is based on xercesc::LocalFileInputSource |
| Configuration | |
| ConsensusFeature | A 2-dimensional consensus feature |
| ConsensusID | Calculates a consensus ID from several ID runs |
| ConsensusIsotopePattern | |
| ConsensusMap | A container for consensus elements |
| ConsensusMapNormalizerAlgorithmMedian | Algorithms of ConsensusMapNormalizer |
| ConsensusMapNormalizerAlgorithmQuantile | Algorithms of ConsensusMapNormalizer |
| ConsensusMapNormalizerAlgorithmThreshold | Algorithms of ConsensusMapNormalizer |
| ConsensusXMLFile | This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation |
| AASequence::ConstIterator | ConstIterator for AASequence |
| HashGrid< Cluster >::ConstIterator | Constant element iterator for the hash grid |
| ConstRefVector< ContainerT > | This vector holds pointer to the elements of another container |
| ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT > | ConstIterator for the ConstRefVector |
| ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT > | Mutable iterator for the ConstRefVector |
| Contact | |
| ContactPerson | Contact person information |
| ContactPersonVisualizer | Class that displays all meta information for ContactPerson objects |
| RawMSSignalSimulation::ContaminantInfo | |
| ContinuousWaveletTransform | This class is the base class of the continuous wavelet transformation |
| ContinuousWaveletTransformNumIntegration | This class computes the continuous wavelet transformation using a marr wavelet |
| ControlledVocabulary | Representation of a controlled vocabulary |
| ConversionError | Invalid conversion exception |
| ConvexHull2D | A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling |
| CsvFile | This class handles csv files. Currently only loading is implemented |
| CSVWriter | |
| cudaHelp | An internally used class, subsuming several variables |
| CV | |
| CVMappingFile | Used to load CvMapping files |
| 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 |
| SemanticValidator::CVTerm | Representation of a parsed CV term |
| CVTerm | Representation of controlled vocabulary term |
| ControlledVocabulary::CVTerm | Representation of a CV term |
| CVTermList | Representation of controlled vocabulary term list |
| EGHFitter1D::Data | Helper struct (contains the size of an area and a raw data container) |
| EmgFitter1D::Data | Helper struct (contains the size of an area and a raw data container) |
| LmaGaussFitter1D::Data | Helper struct (contains the size of an area and a raw data container) |
| LmaIsotopeFitter1D::Data | Helper struct (contains the size of an area, a raw data container, the relative abundance of i-th isotopic peak and the distance between consecutive isotopic peaks) |
| OptimizePeakDeconvolution::Data | Class containing the data needed for optimization |
| OptimizePick::Data | |
| TwoDOptimization::Data | Helper struct (contains the size of an area and a raw data container) |
| DataFilters::DataFilter | Representation of a peak/feature filter combining FilterType, FilterOperation and a value |
| DataFilterDialog | Dialog for creating and changing a DataFilter |
| DataFilterDialogTemplate | |
| DataFilters | DataFilter array providing some convenience functions |
| DataMatrix | |
| DataProcessing | Descripton of the applied preprocessing steps |
| DataProcessingVisualizer | Class that displays all meta information for DataProcessing objects |
| DataValue | Class to hold strings, numeric values, lists of strings and lists of numeric values |
| Date | Date Class |
| DateTime | DateTime Class |
| DBAdapter | A class for accessing and storing data in a SQL database |
| DBConnection | A class for connecting to a SQL database |
| DBOpenDialog | Dialog that allow selecting a spectrum from a DB |
| DBoundingBox< D > | A D-dimensional bounding box |
| DeconvPeak | |
| DefaultHandler | |
| DefaultParamHandler | A base class for all classes handling default parameters |
| Deisotoper | |
| 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 |
| DeNovoPostScoring | Base class for ion scoring implementation for de novo algorithms |
| DepletedIDPool | Exception used if no more unique document ID's can be drawn from ID pool |
| SvmTheoreticalSpectrumGenerator::DescriptorSet | A set of descriptors for a single training row |
| DetectabilitySimulation | Simulates peptide detectability |
| 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 |
| Digestion | Meta information about digestion of a sample |
| DigestionVisualizer | Class that displays all meta information of digestion objects |
| DigestSimulation | Simulates protein digestion |
| DIntervalBase< D > | A base class for D-dimensional interval |
| DistanceMatrix< Value > | A two-dimensional distance matrix, similar to OpenMS::Matrix |
| FeatureDistance::DistanceParams_ | Structure for storing distance parameters |
| DivisionByZero | Division by zero error exception |
| DocumentIdentifier | Manage source document information |
| DocumentIdentifierVisualizer | Class that displays all meta information for DocumentIdentifier objects |
| DocumentIDTagger | Tags OpenMS file containers with a DocumentID |
| DoubleList | DoubleReal list |
| DPeak< dimensions > | Metafunction to choose among Peak1D respectively Peak2D through a template argument |
| DPosition< D, TCoordinateType > | Representation of a coordinate in D-dimensional space |
| DRange< D > | A D-dimensional half-open interval |
| DRichPeak< dimensions > | Metafunction to choose among RichPeak1D respectively RichPeak2D through a template argument |
| DTA2DFile | DTA2D File adapter |
| DTAFile | File adapter for DTA files |
| EDTAFile | File adapter for Enhanced DTA files |
| EdwardsLippertIterator | Finds all Peptide Candidates with given masses and given fasta file |
| EdwardsLippertIteratorTryptic | EdwardsLippertIterator that only retrieves tryptic seqences |
| EGHFitter1D | Exponential-Gaussian hybrid distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization |
| EGHModel | Exponential-Gaussian hybrid distribution model for elution profiles |
| EGHTraceFitter< PeakType > | A RT Profile fitter using an Exponential Gaussian Hybrid background model |
| Element | Representation of an element |
| ElementDB | Stores elements |
| ElementNotFound | Element could not be found exception |
| ElutionPeakDetection | Extracts chromatographic peaks from a mass trace |
| EmgFitter1D | Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization |
| EmgModel | Exponentially modified gaussian distribution model for elution profiles |
| EmgScoring | Scoring of an elution peak using an exponentially modified gaussian distribution model |
| EmpiricalFormula | Representation of an empirical formula |
| XMLHandler::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) |
| EnhancedTabBar | Convenience tab bar implementation |
| EnhancedTabBarWidgetInterface | Widgets that are placed into an EnhancedTabBar must implement this interface |
| EnhancedWorkspace | |
| EnzymaticDigestion | Class for the enzymatic digestion of proteins |
| EqualInTolerance< CompareType > | Struct for binary predicate to consider equality with a certain tolerance |
| EquivalenceClassAA_< T > | |
| ErrorHandler | |
| EuclideanSimilarity | CompareFunctor for 2Dpoints |
| ExperimentalSettings | Description of the experimental settings |
| ExperimentalSettingsVisualizer | Class that displays all meta information for ExperimentalSettings objects |
| ExtendedIsotopeFitter1D | Extended isotope distribution fitter (1-dim.) approximated using linear interpolation |
| ExtendedIsotopeModel | Extended isotope distribution approximated using linear interpolation |
| Factory< FactoryProduct > | Returns FactoryProduct* based on the name of the desired concrete FactoryProduct |
| FactoryBase | Base class for Factory<T> |
| FailedAPICall | A call to an external library (other than OpenMS) went wrong |
| FakeProcess | A FakeProcess class |
| FalseDiscoveryRate | Calculates an FDR from identifications |
| FASTAFile::FASTAEntry | FASTA entry type (identifier, description and sequence) |
| FASTAFile | This class serves for reading in FASTA files |
| FastaIterator | Iterator over FASTA file |
| FastaIteratorIntern | Iterator for a FASTA file |
| FeaFiModule< PeakType, FeatureType > | Implements a module of the FeatureFinder algorithm |
| Feature | An LC-MS feature |
| FeatureDeconvolution | An algorithm to decharge features (i.e. as found by FeatureFinder) |
| FeatureDistance | A functor class for the calculation of distances between features or consensus features |
| FeatureEditDialog | Dialog for editing a feature |
| FeatureEditDialogTemplate | |
| FeatureFileOptions | Options for loading files containing features |
| FeatureFinder | The main feature finder class |
| FeatureFinderAlgorithm< PeakType, FeatureType > | Abstract base class for FeatureFinder algorithms |
| FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType > | Implements the isotope wavelet feature finder |
| FeatureFinderAlgorithmMRM< PeakType, FeatureType > | FeatureFinderAlgorithm for MRM experiments |
| FeatureFinderAlgorithmPicked< PeakType, FeatureType > | FeatureFinderAlgorithm for picked peaks |
| FeatureFinderAlgorithmPickedHelperStructs | Wrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes |
| FeatureFinderAlgorithmSH< PeakType, FeatureType > | The Superhirn FeatureFinderAlgorithm |
| FeatureFinderAlgorithmSHCtrl | |
| FeatureFinderAlgorithmSimple< PeakType, FeatureType > | FeatureFinderAlgorithm implementation using the Simple* modules |
| FeatureFinderAlgorithmSimplest< PeakType, FeatureType > | FeatureFinderAlgorithm implementation using the Simple* modules |
| FeatureFinderDefs | The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes |
| FeatureFindingMetabo | |
| 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 |
| FeatureHandle | Representation of a Peak2D, RichPeak2D or Feature |
| FeatureHandle::FeatureHandleMutable_ | Helper class returned by FeatureHandle::asMutable(), which see |
| FeatureHypothesis | |
| FeatureLCProfile | |
| FeatureMap< FeatureT > | A container for features |
| FeatureOpenMS | An implementation of the OpenSWATH Feature Access interface using OpenMS |
| FeatureXMLFile | This class provides Input/Output functionality for feature maps |
| IsotopeWavelet::fi_ | Internal union for fast computation of the power function |
| FidHandler | Read-only fid File handler for XMass Analysis |
| File | Basic file handling operations |
| ConsensusMap::FileDescription | Source file description for input files |
| FileEmpty | File is empty |
| FileHandler | Facilitates file handling by file type recognition |
| FileMapping | Maps input/output files to filenames for the external program |
| FileNotFound | File not found exception |
| FileNotReadable | File not readable exception |
| FileNotWritable | File not writable exception |
| FileTypes | Centralizes the file types recognized by FileHandler |
| FileWatcher | Watcher that monitors file changes |
| FilterFunctor | A FilterFunctor extracts some spectrum characteristics for quality assessment |
| Fitter1D | Abstract base class for all 1D-dimensional model fitter |
| MSChromatogram< PeakT >::FloatDataArray | Float data array class |
| MSSpectrum< PeakT >::FloatDataArray | Float data array class |
| FoundProteinFunctor | |
| FTPeakDetectController | |
| FuzzyStringComparator | Fuzzy comparison of strings, tolerates numeric differences |
| GammaDistributionFitter::GammaDistributionFitResult | Struct to represent the parameters of a gamma distribution |
| GammaDistributionFitter | Implements a fitter for the Gamma distribution |
| GaussFilter | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data |
| GaussFitter::GaussFitResult | Struct of parameters of a gaussian distribution |
| GaussFitter | Implements a fitter for gaussian functions |
| GaussFitter1D | Gaussian distribution fitter (1-dim.) approximated using linear interpolation |
| SignalToNoiseEstimator< Container >::GaussianEstimate | Protected struct to store parameters my, sigma for a Gaussian distribution |
| GaussModel | Normal distribution approximated using linear interpolation |
| GaussTraceFitter< PeakType > | Fitter for RT profiles using a gaussian background model |
| GlobalExceptionHandler | OpenMS global exception handler |
| glp_prob | |
| GoodDiffFilter | GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss |
| Gradient | Representation of a HPLC gradient |
| GradientVisualizer | GradientVisualizer is a visualizer class for objects of type gradient |
| GridFeature | Representation of a feature in a hash grid |
| GumbelDistributionFitter::GumbelDistributionFitResult | Struct to represent the parameters of a gumbel distribution |
| GumbelDistributionFitter | Implements a fitter for the Gumbel distribution |
| 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 |
| HasActivationMethod< SpectrumType > | Predicate that determines if a spectrum was generated using any activation method given in the constructor list |
| HashGrid< Cluster > | Container for (2-dimensional coordinate, value) pairs |
| HasMetaValue< MetaContainer > | Predicate that determines if a class has a certain metavalue |
| HasPrecursorCharge< SpectrumType > | Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list |
| HasScanMode< SpectrumType > | Predicate that determines if a spectrum has a certain scan mode |
| HiddenMarkovModel | Hidden Markov Model implementation of PILIS |
| HierarchicalClustering< PointRef > | Generic 2-dimensional hierarchical clustering with geometric hashing |
| Histogram< ValueType, BinSizeType > | Representation of a histogram |
| HistogramDialog | Dialog that show a HistogramWidget |
| HistogramWidget | Widget which can visualize a histogram |
| HMMState | Hidden Markov Model State class for the Hidden Markov Model |
| HPLC | Representation of a HPLC experiment |
| HPLCVisualizer | Class that displays all meta information for HPLC objects |
| ICPLLabeler | Simulate ICPL experiments |
| IDataFrameWriter | |
| IDDecoyProbability | IDDecoyProbability calculates probabilities using decoy approach |
| 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 |
| IDEvaluationBase | Main window of the IDEvaluation tool |
| IDFilter | Used to filter identifications by different criteria |
| IDMapper | Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications |
| IDRipper | Ripping protein/peptide identification according their file origin |
| IdXMLFile | Used to load and store idXML files |
| InclusionExclusionList::IEWindow | |
| IFeature | |
| IllegalArgument | A method or algorithm argument contains illegal values |
| Map< Key, T >::IllegalKey | Map illegal key exception |
| IllegalPosition | Invalid 3-dimensional position exception |
| IllegalSelfOperation | Illegal self operation exception |
| IllegalTreeOperation | Illegal tree operation exception |
| ILPDCWrapper | |
| IMRMFeature | |
| IMSAlphabet | Holds an indexed list of bio-chemical elements |
| IMSAlphabetParser< AlphabetElementType, Container, InputSource > | 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 |
| IncludeExcludeTarget | This class stores a SRM/MRM transition |
| InclusionExclusionList | Provides functionalty for writing inclusion or exclusion lists |
| BinnedSpectrumCompareFunctor::IncompatibleBinning | Exception thrown if compared spectra are incompatible |
| IncompatibleIterators | Incompatible iterator exception |
| FeatureHandle::IndexLess | Comparator by map and unique id |
| PSLPFormulation::IndexLess | |
| IndexOverflow | Int overflow exception |
| PSLPFormulation::IndexTriple | Struct that holds the indices of the precursors in the feature map and the ilp formulation |
| IndexUnderflow | Int underflow exception |
| SimpleExtender< PeakType, FeatureType >::IndexWithPriority | A helper structure to sort indizes by their priority |
| INIFileEditorWindow | Shows the ParamEditor widget in a QMainWindow with a toolbar |
| InIntensityRange< PeakType > | Predicate that determines if a peak lies inside/outside a specific intensity range |
| INIUpdater | |
| InMSLevelRange< SpectrumType > | Predicate that determines if a spectrum lies inside/outside a specific MS level set |
| InMzRange< PeakType > | Predicate that determines if a peak lies inside/outside a specific m/z range |
| InPrecursorMZRange< SpectrumType > | Predicate that determines if a spectrum's precursor is within a certain m/z range |
| FuzzyStringComparator::InputLine | Stores information about the current input line (i.e., stream for the line and the current position in the stream) |
| InputSource | |
| InRTRange< SpectrumType > | Predicate that determines if a spectrum lies inside/outside a specific retention time range |
| InspectInfile | Inspect input file adapter |
| InspectOutfile | Representation of an Inspect outfile |
| Instrument | Description of a MS instrument |
| Instrument | |
| InstrumentSettings | Description of the settings a MS Instrument was run with |
| InstrumentSettingsVisualizer | Class that displays all meta information for InstrumentSettings objects |
| InstrumentVisualizer | Class that displays all meta information for an MS instrument |
| ClusterFunctor::InsufficientInput | Exception thrown if not enough data (<2) is used |
| MSChromatogram< PeakT >::IntegerDataArray | Float data array class |
| MSSpectrum< PeakT >::IntegerDataArray | Integer data array class |
| IntegerMassDecomposer< ValueType, DecompositionValueType > | Implements MassDecomposer interface using algorithm and data structures described in paper "Efficient Mass Decomposition" S. Bcker, Zs. Liptk, ACM SAC-BIO, 2004 |
| IntensityBalanceFilter | IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions |
| IntensityIterator< FeaFiModuleType > | Intensity iterator for a FeatureFinderDefs::IndexSet |
| IntensityIteratorWrapper< IteratorT > | An iterator wrapper to access peak intensities instead of the peak itself |
| ChromatogramPeak::IntensityLess | Comparator by intensity |
| Peak1D::IntensityLess | |
| Peak2D::IntensityLess | |
| IntensityLess< FeaFiModuleType > | Comparator that allows to compare the indices of two peaks by their intensity |
| InternalCalibration | A simple calibration method using linear interpolation of given reference masses |
| InterpolationModel | Abstract class for 1D-models that are approximated using linear interpolation |
| IntList | Int list |
| InvalidIterator | Invalid iterator exception |
| InvalidParameter | Exception indicating that an invalid parameter was handed over to an algorithm |
| DBConnection::InvalidQuery | Exception in case of an invalid Query |
| InvalidRange | Invalid range exception |
| InvalidSize | Invalid UInt exception |
| InvalidValue | Invalid value exception |
| IOException | General IOException |
| TOPPASToolVertex::IOInfo | Stores the information for input/output files/lists |
| IonDetector | Description of a ion detector (part of a MS Instrument) |
| IonDetectorVisualizer | Class that displays all meta information for IonDetector objects |
| IonizationSimulation | Simulates Protein ionization |
| CompNovoIonScoringBase::IonScore | |
| DeNovoIonScoring::IonScore | IonScore |
| IonSource | Description of a ion source (part of a MS Instrument) |
| IonSourceVisualizer | Class that displays all meta information for IonSource objects |
| SvmTheoreticalSpectrumGenerator::IonType | Nested class |
| ProteinResolver::ISDGroup | |
| IsEmptySpectrum< SpectrumType > | Predicate that determines if a spectrum is empty |
| ISignalToNoise | |
| IsotopeCluster | Stores information about an isotopic cluster (i.e. potential peptide charge variants) |
| IsotopeDiffFilter | IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks |
| IsotopeDistribution | Isotope distribution class |
| IsotopeDistributionCache | Prealculate isotope distributions for interesting mass ranges |
| IsotopeFitter1D | Isotope distribution fitter (1-dim.) approximated using linear interpolation |
| IsotopeMarker | IsotopeMarker marks peak pairs which could represent an ion and its isotope |
| IsotopeModel | Isotope distribution approximated using linear interpolation |
| FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern | Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked |
| IsotopeWavelet | Implements the isotope wavelet function |
| IsotopeWaveletParallelFor< PeakType, FeatureType > | A class for distributing the data over several GPUs using Intel Threading Building Blocks |
| IsotopeWaveletTransform< PeakType > | 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 |
| IsotopicDist | |
| ISpectrumAccess | The interface of a mass spectrometry experiment |
| IsZoomSpectrum< SpectrumType > | Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum |
| AASequence::Iterator | Iterator class for AASequence |
| iterator | |
| HashGrid< Cluster >::Iterator | Element iterator for the hash grid |
| ITransitionGroup | |
| 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 |
| ITRAQLabeler | Simulate iTRAQ experiments |
| ItraqQuantifier | Does post-processing on raw iTRAQ channel quantitation |
| ItraqQuantifier::ItraqQuantifierStats | Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion) |
| KroenikFile | File adapter for Kroenik (HardKloer sibling) files |
| LabeledPairFinder | The LabeledPairFinder allows the matching of labeled features (features with a fixed distance) |
| LabelFreeLabeler | Abstract base class for all kinds of labeling techniques |
| LayerData | Class that stores the data for one layer |
| LayerStatisticsDialog | Dialog showing statistics about the data of the current layer |
| LayerStatisticsDialogTemplate | |
| LCElutionPeak | |
| LCMS | |
| LCMSCData | |
| LevMarqFitter1D | Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization |
| LexicographicComparator< Cmp1, Cmp2 > | 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 |
| LibSVMEncoder | Serves for encoding sequences into feature vectors |
| LightModification | |
| LightPeptide | |
| LightProtein | |
| LightTargetedExperiment | |
| LightTransition | |
| LinearInterpolation< Key, Value > | 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 |
| LinearRegression | This class offers functions to perform least-squares fits to a straight line model,  |
| LinearResampler | Linear Resampling of raw data |
| LinearResamplerAlign | Linear Resampling of raw data with alignment |
| ListEditor | Editor for editing int, double and string lists (including output and input file lists) |
| ListEditorDelegate | Internal delegate class |
| ListTable | |
| LocalLinearMap::LLMParam | Define parameters needed by the Local Linear Map (LLM) model |
| LmaGaussFitter1D | Gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization |
| LmaGaussModel | Normal distribution model for elution profiles |
| LmaIsotopeFitter1D | Isotope distribution fitter (1-dim.) approximated using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization |
| LmaIsotopeModel | Isotope distribution approximated using linear interpolation |
| LocalLinearMap | Trained Local Linear Map (LLM) model for peak intensity prediction |
| LogStreamBuf::LogCacheStruct | Holds a counter of occurences and an index for the occurence sequence of the corresponding log message |
| LogConfigHandler | The LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream |
| LogStream | Log Stream Class |
| LogStreamBuf | Stream buffer used by LogStream |
| LogStreamNotifier | |
| LowessSmoothing | LOWESS (locally weighted scatterplot smoothing) |
| LPWrapper | |
| Map< Key, T > | Map class based on the STL map (containing serveral convenience functions) |
| 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) |
| 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 |
| MappingParam | Filename mappings for all input/output files |
| ConsensusFeature::MapsLess | Compare by the sets of consensus elements (lexicographically) |
| MarkerIonExtractor | |
| MarkerMower | MarkerMower uses PeakMarker to find peaks, those that are not marked get removed |
| 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 |
| MascotXMLHandler | Handler that is used for parsing MascotXML data |
| MassAnalyzer | Descripton of a mass analyzer (part of a MS Instrument) |
| MassAnalyzerVisualizer | Class that displays all meta information for MassAnalyzer objects |
| MassDecomposer< ValueType, DecompositionValueType > | An inteface to handle decomposing of integer values/masses over a set of integer weights (alphabet) |
| MassDecomposition | Class represents a decomposition of a mass into amino acids |
| MassDecompositionAlgorithm | Mass decomposition algorithm, given a mass it suggests possible compositions |
| MassExplainer | Computes empirical formulas for given mass differences using a set of allowed elements |
| IMSAlphabet::MassSortingCriteria_ | Private class-functor to sort out elements in mass ascending order |
| MassTrace | A container type that gathers peaks similar in m/z and moving along retention time |
| FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType > | Helper struct for mass traces used in FeatureFinderAlgorithmPicked |
| MassTraceDetection | A mass trace extraction method that gathers peaks similar in m/z and moving along retention time |
| FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType > | Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked |
| Matrix< Value > | A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access |
| MaxLikeliFitter1D | Abstract base class for all 1D-model fitters using maximum likelihood optimization |
| mean_and_stddev | Functor to compute the mean and stddev of sequence using the std::foreach algorithm |
| MetaDataBrowser | A meta data visualization widget |
| MetaInfo | A Type-Name-Value tuple class |
| MetaInfoDescription | Description of the meta data arrays of MSSpectrum |
| MetaInfoDescriptionVisualizer | Class that displays all meta information for MetaInfoDescription objects |
| MetaInfoInterface | Interface for classes that can store arbitrary meta information (Type-Name-Value tuples) |
| MetaInfoRegistry | Registry which assigns unique integer indices to strings |
| MetaInfoVisualizer | MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member |
| LayerStatisticsDialog::MetaStatsValue_ | Struct representing the statistics about one meta information |
| MissingInformation | Not all required information provided |
| MockFeature | Mock object implementing IFeature |
| MockMRMFeature | Mock object implementing IMRMFeature |
| MockSignalToNoise | Mock object implementing ISignalToNoise |
| MockTransitionGroup | Mock object implementing ITransitionGroup |
| ModelDescription< D > | Stores the name and parameters of a model |
| ModelFitter< PeakType, FeatureType > | Tests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model |
| Modification | Meta information about chemical modification of a sample |
| Peptide::Modification | |
| ModificationDefinition | Representation of modification definition |
| ModificationDefinitionsSet | Representation of a set of modification definitions |
| ModificationMassesResult | |
| ModificationsDB | Database which holds all residue modifications from UniMod |
| ModificationVisualizer | Class that displays all meta information of modification objects |
| ModifierRep | Implements modification for suffix arrays |
| MorphologicalFilter | This class implements baseline filtering operations using methods from mathematical morphology |
| MRMDecoy | This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object |
| MRMFeature | A multi-chromatogram MRM feature |
| MRMFeatureFinderScoring | The MRMFeatureFinder finds and scores peaks of transitions that coelute |
| MRMFeatureOpenMS | An implementation of the OpenSWATH MRM Feature Access interface using OpenMS |
| MRMFragmentSelection | This class can select appropriate fragment ions of an MS/MS spectrum of a peptide |
| MRMRTNormalizer | The MRMRTNormalizer will find retention time peptides in data |
| MRMScoring | This class implements different scores for peaks found in SRM/MRM |
| MRMTransitionGroup< SpectrumType, TransitionType > | The representation of a transition group that has information about the individual chromatograms as well as the transitions it refers to |
| MRMTransitionGroupPicker | The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors |
| MS1FeatureMerger | |
| MS1Signal | |
| MS2ConsensusSpectrum | |
| MS2Feature | |
| MS2File | MS2 input file adapter |
| MS2Fragment | |
| MS2Info | |
| MSChromatogram< PeakT > | The representation of a chromatogram |
| ProteinResolver::MSDGroup | |
| MSExperiment< PeakT, ChromatogramPeakT > | Representation of a mass spectrometry experiment |
| MsInspectFile | File adapter for MsInspect files |
| MSPeak | |
| MSPFile | File adapter for MSP files (NIST spectra library) |
| MSQuantifications | |
| MSSim | Central class for simulation of mass spectrometry experiments |
| MSSpectrum< PeakT > | The representation of a 1D spectrum |
| MultiGradient | A gradient of multiple colors and arbitrary distances between colors |
| MultiGradientSelector | A widget witch allows constructing gradients of multiple colors |
| mySqrt | |
| MzDataFile | File adapter for MzData files |
| MzDataHandler< MapType > | XML handler for MzDataFile |
| MzDataValidator | Semantically validates MzXML files |
| MzIdentMLFile | File adapter for MzIdentML files |
| MzIdentMLHandler | XML handler for MzIdentMLFile |
| MzIdentMLValidator | Semantically validates MzXML files |
| MzIterator< FeaFiModuleType > | M/z iterator for a FeatureFinderDefs::IndexSet |
| MSChromatogram< PeakT >::MZLess | Comparator for the retention time |
| Peak1D::MZLess | Comparator by m/z position |
| Peak2D::MZLess | Comparator by m/z position |
| MzMLFile | File adapter for MzML files |
| MzMLHandler< MapType > | XML handler for MzMLFile |
| MzMLValidator | Semantically validates MzXML files |
| MzQuantMLFile | File adapter for MzQuantML files |
| MzQuantMLHandler | XML handler for MzQuantMLFile |
| MzQuantMLValidator | Semantically validates MzQuantML files |
| MzTab | Data model of MzTab files. The format specification is in development and subject to change. Use at your own risk. Please see the official MzTab specification at https://code.google.com/p/mztab/ |
| MzTabBoolean | |
| MzTabDouble | |
| MzTabDoubleList | |
| MzTabFile | File adapter for MzTab files |
| MzTabInteger | |
| MzTabModification | |
| MzTabModificationList | |
| MzTabNAAbleBase | |
| MzTabNAAbleInterface | Data model of MzTab files. The format specification is in development and subject to change. Use at your own risk. Please see the official MzTab specification at https://code.google.com/p/mztab/ |
| MzTabParameter | |
| MzTabParameterList | |
| MzTabPeptideSectionRow | |
| MzTabProteinSectionRow | |
| MzTabSmallMoleculeSectionRow | |
| MzTabSpectraRef | |
| MzTabString | |
| MzTabStringList | |
| MzTabSubIdMetaData | |
| MzTabUnitIdMetaData | |
| MzXMLFile | File adapter for MzXML 2.1 files |
| MzXMLHandler< MapType > | XML handlers for MzXMLFile |
| 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 |
| NonNegativeLeastSquaresSolver | Wrapper for a non-negative least squares (NNLS) solver |
| Normalizer | Normalizer normalizes the peak intensities |
| BinnedSpectrum::NoSpectrumIntegrated | Exception which is thrown if BinnedSpectrum bins are accessed and no PeakSpektrum has been integrated yet i.e. bins_ is empty |
| FeatureFinderDefs::NoSuccessor | Exception that is thrown if a method an invalid IndexPair is given |
| DBConnection::NotConnected | Exception in case of trying to execute a query without having established a database connection |
| NotImplemented | Not implemented exception |
| NullPointer | Null pointer argument is invalid exception |
| O18Labeler | Simulate O-18 experiments |
| OfflinePrecursorIonSelection | Implements different algorithms for precursor ion selection |
| OMSSACSVFile | File adapter for OMSSACSV files |
| OMSSAXMLFile | Used to load OMSSAXML files |
| OpenMSOSInfo | |
| OpenMSXMLFormatTarget | |
| OpenSwath_Scores | A structure to hold the different scores computed by the FeatureFinder |
| OpenSwathDataAccessHelper | Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces |
| OpenSwathHelper | A helper class that is used by several OpenSWATH tools |
| MS1FeatureMerger::OPERATOR_FEATURE_TR | |
| LCMS::OPERATOR_FeatureCompare | |
| LCMS::OPERATOR_MZ | |
| OptimizePeakDeconvolution | This class provides the deconvolution of peak regions using non-linear optimization |
| OptimizePick | This class provides the non-linear optimization of the peak parameters |
| PILISCrossValidation::Option | This struct represents a cross validation option |
| OutOfGrid | Out of grid exception |
| OutOfMemory | Out of memory exception |
| OutOfRange | Out of range exception |
| pair | |
| PairComparatorFirstElement< PairType > | Class for comparison of std::pair using first ONLY e.g. for use with std::sort |
| PairComparatorFirstElementMore< PairType > | Class for comparison of std::pair using first ONLY e.g. for use with std::sort |
| PairComparatorSecondElement< PairType > | Class for comparison of std::pair using second ONLY e.g. for use with std::sort |
| PairComparatorSecondElementMore< PairType > | Class for comparison of std::pair using second ONLY e.g. for use with std::sort |
| PairMatcherFirstElement< PairType > | Class for comparison of std::pair using first ONLY e.g. for use with std::sort |
| PairMatcherSecondElement< PairType > | Struct for comparison of std::pair using second ONLY e.g. for use with std::sort |
| Param | Management and storage of parameters / INI files |
| ParamEditor | A GUI for editing or viewing a Param object |
| ParamEditorDelegate | Internal delegate class for QTreeWidget |
| ParamEditorTemplate | |
| Param::ParamEntry | Parameter entry used to store the actual information inside of a Param entry |
| ParameterInformation | Struct that captures all information of a command line parameter |
| Param::ParamIterator | Forward const iterator for the Param class |
| Param::ParamNode | Node inside a Param object which is used to build the internal tree |
| ParamTree | QTreeWidget that emits a signal whenever a new row is selected |
| ParamXMLFile | The file pendant of the Param class used to load and store the param datastructure as paramXML |
| ParamXMLHandler | XML Handler for Param files |
| ParentPeakMower | ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions |
| ParseError | Parse Error exception |
| IMSIsotopeDistribution::Peak | Structure that represents an isotope peak - pair of mass and abundance |
| Peak1D | A 1-dimensional raw data point or peak |
| Peak2D | A 2-dimensional raw data point or peak |
| PeakAlignment | Make a PeakAlignment of two PeakSpectra |
| PeakPickerCWT::PeakArea_ | Class for the internal peak representation |
| PeakFileOptions | Options for loading files containing peak data |
| PeakIndex | Index of a peak or feature |
| PeakIntensityPredictor | Predict peak heights of peptides based on Local Linear Map model |
| PeakMarker | PeakMarker marks peaks that seem to fulfill some criterion |
| PeakPickerCWT | This class implements a peak picking algorithm using wavelet techniques |
| 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 |
| PeakPickerSH | |
| PeakShape | Internal representation of a peak shape (used by the PeakPickerCWT) |
| PeakSpectrumCompareFunctor | Base class for compare functors of spectra, that return a similiarity value for two spectra |
| PeakTypeEstimator | Estimates if the data of a spectrum is raw data or peak data |
| PeakWidthEstimator | This class implements a peak width estimation algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). Peaks are detected and a spline is fitted to the raw data in a window around the peak. Then a search for to the half-maximum is performed on the spline to the left and right of the peak maximum. The Full Width at the Half Maximum is collected. Finally a linear regression is performed to determine FWHM(m/z) |
| PenaltyFactors | Class for the penalty factors used during the optimization |
| PenaltyFactorsIntensity | Class for the penalty factors used during the optimization |
| PepIterator | Abstract base class for different peptide iterators |
| PepNovoInfile | PepNovo input file adapter |
| PepNovoOutfile | Representation of a PepNovo output file |
| PILISCrossValidation::Peptide | This struct represents a peptide spectrum pair |
| Peptide | |
| Peptide | |
| PeptideAndProteinQuant | Helper class for peptide and protein quantification based on feature data annotated with IDs |
| PeptideAndProteinQuant::PeptideData | Quantitative and associated data for a peptide |
| ProteinResolver::PeptideEntry | |
| PeptideEvidence | Representation of a MzIdentML PeptideEvidence |
| PeptideHit | Representation of a peptide hit |
| PeptideHitVisualizer | Class that displays all meta information for PeptideHit objects |
| PeptideIdentification | Represents the peptide hits for a spectrum |
| PeptideIdentificationVisualizer | Class that displays all meta information for PeptideIdentification objects |
| PepXMLFile | Used to load and store PepXML files |
| PepXMLFileMascot | Used to load Mascot PepXML files |
| CompNovoIdentificationBase::Permut | Simple class to store permutations and a score |
| PersistentObject | Base class for all persistent objects |
| PILISCrossValidation | Implementation of a cross valdidation training for the PILIS model |
| 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 |
| PointerComparator< Cmp > | 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 |
| 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 |
| ChromatogramPeak::PositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for RTLess |
| Peak1D::PositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for MZLess |
| Peak2D::PositionLess | Comparator by position. Lexicographical comparison (first RT then m/z) is done |
| PeakShape::PositionLess | Comparison of mz_positions |
| Postcondition | Postcondition failed exception |
| PosteriorErrorProbabilityModel | Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture |
| PrecisionWrapper< FloatingPointType > | Wrapper class to implement output with appropriate precision. See precisionWrapper() |
| Precondition | Precondition failed exception |
| Precursor | Precursor meta information |
| PrecursorIonSelection | This class implements different precursor ion selection strategies |
| PrecursorIonSelectionPreprocessing | This class implements the database preprocessing needing for precursor ion selection |
| PrecursorVisualizer | Class that displays all meta information for Precursor objects |
| Prediction | |
| FuzzyStringComparator::PrefixInfo_ | Wrapper for the prefix information computed for the failure report |
| SimpleExtender< PeakType, FeatureType >::IndexWithPriority::PriorityLess | Compares two indizes by priority |
| ProbablePhosphoSites | |
| ProcessData | |
| Product | Product meta information |
| ProductModel< 2 > | The class template is only implemented for D=2 because we use Peak2D here |
| ReactionMonitoringTransition::ProductMZLess | Comparator by Product ion MZ |
| ProductVisualizer | Class that displays all meta information for Product objects |
| ProgressLogger | Base class for all classes that want to report their progess |
| Protein | |
| Protein | |
| PeptideAndProteinQuant::ProteinData | Quantitative and associated data for a protein |
| ProteinResolver::ProteinEntry | |
| ProteinIdentification::ProteinGroup | Bundles multiple (e.g. indistinguishable) proteins in a group |
| ProteinHit | Representation of a protein hit |
| ProteinHitVisualizer | Class that displays all meta information for ProteinHit objects |
| ProteinIdentification | Representation of a protein identification run |
| ProteinIdentificationVisualizer | Class that displays all meta information for ProteinIdentification objects |
| 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 |
| ProtonDistributionModel | A proton distribution model to calculate the proton distribution over charged peptides |
| ProtXMLFile | Used to load (storing not supported, yet) ProtXML files |
| PSLPFormulation | Implements ILP formulation of precursor selection problems |
| PSProteinInference | This class implements protein inference for the precursor ion selection strategies |
| PTMXMLFile | Used to load and store PTMXML files |
| PTMXMLHandler | Handler that is used for parsing PTMXML data |
| Publication | |
| QApplication | |
| QApplicationTOPP | Extension to the QApplication for running TOPPs GUI tools |
| QcMLFile | File adapter for QcML files |
| QDate | |
| QDateTime | |
| QDialog | |
| QFileSystemWatcher | |
| QGLWidget | |
| QGraphicsItem | |
| QGraphicsScene | |
| QGraphicsView | |
| QItemDelegate | |
| QListWidget | |
| QMainWindow | |
| QObject | |
| QProcess | |
| QTabBar | |
| QTCluster | A representation of a QT cluster used for feature grouping |
| QTClusterFinder | A variant of QT clustering for the detection of feature groups |
| QTextEdit | |
| QTreeWidget | |
| BaseFeature::QualityLess | Compare by quality |
| QcMLFile::QualityParameter | Representation of a quality parameter |
| QuantitativeExperimentalDesign | Merge files according to experimental design |
| QWidget | |
| QWorkspace | |
| RangeManager< D > | Handles the managment of a position and intensity range |
| ConsensusFeature::Ratio | Slim struct to feed the need for systematically storing of ratios ( |
| RawData | |
| RawMSSignalSimulation | Simulates MS signals for a given set of peptides |
| RawTandemMSSignalSimulation | Simulates tandem MS signales for a given set of peptides |
| ReactionMonitoringTransition | This class stores a SRM/MRM transition |
| RealMassDecomposer | Handles decomposing of non-integer values/masses over a set of non-integer weights with an error allowed |
| Base64::Reinterpreter32_ | Internal class needed for type-punning |
| Base64::Reinterpreter64_ | Internal class needed for type-punning |
| RequiredParameterNotGiven | A required parameter was not given |
| Residue | Representation of a residue |
| ResidueDB | Residue data base which holds residues |
| ResidueModification | Representation of a modification |
| ProteinResolver::ResolverResult | |
| PeakWidthEstimator::Result | |
| RetentionTime | |
| ReverseComparator< Cmp > | 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 |
| RichPeak1D | A 1-dimensional raw data point or peak mith meta information |
| RichPeak2D | A 2-dimensional raw data point or peak with meta information |
| RNPxlReportRow | |
| RNPxlReportRowHeader | |
| ROCCurve | ROCCurves show the tradeoff in sensitivity and specitivity for binary classifiers using different cutoff values |
| RtIterator< FeaFiModuleType > | Retention time iterator for a FeatureFinderDefs::IndexSet |
| ChromatogramPeak::RTLess | Comparator by RT position |
| Peak2D::RTLess | Comparator by RT position |
| MSSpectrum< PeakT >::RTLess | Comparator for the retention time |
| RTSimulation | Simulates/Predicts retention times for peptides or peptide separation |
| Sample | Meta information about the sample |
| SampleTreatment | Base class for sample treatments (Digestion, Modification, Tagging, ...) |
| SampleVisualizer | Class that displays all meta information of sample objects |
| SAValue< Index< StringSet< Peptide >, IndexWotd<> > > | |
| SaveImageDialog | Dialog for saving an image |
| SavitzkyGolayFilter | Computes the Savitzky-Golay filter coefficients using QR decomposition |
| Scaler | Scaler scales the peak by ranking the peaks and assigning intensity according to rank |
| PSLPFormulation::ScanLess | |
| ScanWindow | Scan window description |
| ScanWindowVisualizer | Class that displays all meta information for ScanWindow objects |
| ProteinHit::ScoreLess | Lesser predicate for scores of hits |
| PeptideHit::ScoreLess | Lesser predicate for scores of hits |
| ProteinHit::ScoreMore | Greater predicate for scores of hits |
| PeptideHit::ScoreMore | Greater predicate for scores of hits |
| ProteinIdentification::SearchParameters | Search parameters of the DB search |
| FeatureFinderAlgorithmPickedHelperStructs::Seed | Helper structure for seeds used in FeatureFinderAlgorithmPicked |
| SeedListGenerator | Generate seed lists for feature detection |
| SemanticValidator | Semantically validates XML files using CVMappings and a ControlledVocabulary |
| PrecursorIonSelection::SeqTotalScoreMore | Compare by score |
| SequestInfile | Sequest input file adapter |
| SequestOutfile | Representation of a Sequest output file |
| SHFeature | |
| SignalToNoiseEstimator< Container > | This class represents the abstract base class of a signal to noise estimator |
| SignalToNoiseEstimatorMeanIterative< Container > | Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities |
| SignalToNoiseEstimatorMedian< Container > | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) |
| SignalToNoiseOpenMS< PeakT > | An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS |
| SILACClustering | Clustering implementation for SILAC stuff |
| SILACFilter | Filter to use for SILACFiltering |
| SILACFiltering | Filtering for SILAC data |
| SILACLabeler | Simulate SILAC experiments |
| SILACPattern | A single SILAC pattern containing multiple found points |
| SILACPoint | A single SILAC point |
| SimpleExtender< PeakType, FeatureType > | Simple feature extension algorithm |
| SimpleOpenMSSpectraFactory | A factory method that returns two ISpectrumAccess implementations |
| SimplePairFinder | This class implements a simple point pair finding algorithm |
| SimpleSeeder< PeakType, FeatureType > | Simple seeding class that uses the strongest peak as next seed |
| SimRandomNumberGenerator | Wrapper class for random number generators used by the simulation classes |
| ROCCurve::simsortdec | Predicate for sort() |
| SingleLinkage | SingleLinkage ClusterMethod |
| SingletonRegistry | Holds pointers to unique instance of a singleton factory |
| ConsensusFeature::SizeLess | Compare by size(), the number of consensus elements |
| SizeUnderflow | UInt underflow exception |
| Software | Description of the software used for processing |
| SoftwareVisualizer | Class that displays all meta information for Software objects |
| LPWrapper::SolverParam | Struct that holds the parameters of the LP solver |
| SourceFile | Description of a file location, used to store the origin of (meta) data |
| SourceFileVisualizer | Class that displays all meta information for SourceFile objects |
| SparseVector< Value > | SparseVector implementation. The container will not actually store a specified type of element - the sparse element, e.g. zero (by default) |
| SparseVector< Value >::SparseVectorConstIterator | Const_iterator for SparseVector |
| SparseVector< Value >::SparseVectorConstReverseIterator | Const_reverse_iterator for SparseVector |
| SparseVector< Value >::SparseVectorIterator | Random access iterator for SparseVector including the hop() function to jump to the next non-sparse element |
| SparseVector< Value >::SparseVectorReverseIterator | Random access reverse iterator for SparseVector including the hop() function to jump to the next non-sparse element |
| SpecArrayFile | File adapter for SpecArray (.pepList) files |
| SpectraMerger::SpectraDistance_ | |
| SpectraIdentificationViewWidget | Tabular visualization/ selection of identified specra |
| SpectraMerger | Merges blocks of MS or MS2 spectra |
| SpectraSTSimilarityScore | Similarity score of SpectraST |
| SpectraViewWidget | Hierarchical visualization and selection of spectra |
| Spectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
| Spectrum1DCanvas | Canvas for visualization of one or several spectra |
| Spectrum1DGoToDialog | Simple goto/set visible area dialog for exact placement of the viewing window |
| Spectrum1DGoToDialogTemplate | |
| Spectrum1DPrefDialog | Preferences dialog for Spectrum1DWidget |
| Spectrum1DPrefDialogTemplate | |
| Spectrum1DWidget | Widget for visualization of several spectra |
| Spectrum2DCanvas | Canvas for 2D-visualization of peak map, feature map and consensus map data |
| Spectrum2DGoToDialog | GoTo dialog used to zoom to a m/z and retention time range or to a feature |
| Spectrum2DGoToDialogTemplate | |
| Spectrum2DPrefDialog | Preferences dialog for Spectrum2DWidget |
| Spectrum2DPrefDialogTemplate | |
| 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 |
| Spectrum3DPrefDialog | Preferences dialog for Spectrum3DWidget |
| Spectrum3DPrefDialogTemplate | |
| Spectrum3DWidget | Widget for 3D-visualization of map data |
| SpectrumAccessOpenMS | An implementation of the OpenSWATH Spectrum Access interface using OpenMS |
| SpectrumAccessOpenMSCached | An implementation of the OpenSWATH Spectrum Access interface using Disk caching |
| SpectrumAddition | The SpectrumAddition adds together a list of spectra |
| SpectrumAlignment | Aligns the peaks of two spectra |
| SpectrumAlignmentDialog | Lets the user select two spectra and set the parameters for the spectrum alignment |
| SpectrumAlignmentDialogTemplate | |
| SpectrumAlignmentScore | Similarity score via spectra alignment |
| SpectrumCanvas | Base class for visualization canvas classes |
| SpectrumCheapDPCorr | SpectrumCheapDPCorr calculates an optimal alignment on stick spectra |
| SpectrumIdentification | Represents a object which can store the information of an analysisXML instance |
| SILACFiltering::SpectrumInterpolation | Wrapper class for spectrum interpolation |
| SpectrumMeta | Identifying information for a spectrum |
| SpectrumPrecursorComparator | SpectrumPrecursorComparator compares just the parent mass of two spectra |
| SpectrumSettings | Representation of 1D spectrum settings |
| SpectrumSettingsVisualizer | Class that displays all meta information for SpectrumSettings objects |
| SpectrumWidget | Base class for spectrum widgets |
| SqrtMower | Scales the intensity of peaks to the sqrt |
| StablePairFinder | This class implements a pair finding algorithm for consensus features |
| PeptideAndProteinQuant::Statistics | Statistics for processing summary |
| SteinScottImproveScore | Similarity score based of Stein & Scott |
| StopWatch | StopWatch Class |
| streambuf | |
| FuzzyStringComparator::StreamElement_ | Stores information about characters, numbers, and whitesspaces loaded from the InputStream |
| StreamHandler | Provides a central class to register globally used output streams. Currently supported streams are |
| LogStreamBuf::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 |
| String | A more convenient string class |
| MSChromatogram< PeakT >::StringDataArray | String data array class |
| MSSpectrum< PeakT >::StringDataArray | String data array class |
| StringList | String list |
| StringManager | Helper class for XML parsing that handles the memory management for conversions of Xerces strings |
| SuffixArray | Abstract class for suffix array |
| SuffixArrayPeptideFinder | Wrapper for easy use of sufArray |
| 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 |
| Summary | Summary of fitting results |
| SuperHirnParameters | SuperHirn parameters singleton class containing all static configuration variables |
| SuperHirnUtil | |
| SVMData | Data structure used in SVMWrapper |
| SvmTheoreticalSpectrumGenerator::SvmModelParameterSet | Simple container storing the model parameters required for simulation |
| SvmTheoreticalSpectrumGenerator | Simulates ms2 spectra with support vector machines |
| SvmTheoreticalSpectrumGeneratorSet | Loads SvmTheoreticalSpectrumGenerator instances for different charges |
| SvmTheoreticalSpectrumGeneratorTrainer | Train SVM models that are used by SvmTheoreticalSpectrumGenerator |
| SVMWrapper | Serves as a wrapper for the libsvm |
| SVOutStream | Stream class for writing to comma/tab/...-separated values files |
| Tagging | Meta information about tagging of a sample e.g. ICAT labeling |
| TaggingVisualizer | Class that displays all meta information of tagging objects |
| TargetedExperiment | This class stores an prediction of an SRM/MRM transition |
| TargetedExperiment | |
| TextFile | This class provides some basic file handling methods for text files |
| FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern | Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked |
| TheoreticalSpectrumGenerationDialog | Dialog which allows to enter an AA sequence and generates a theoretical spectrum for it |
| TheoreticalSpectrumGenerationDialogTemplate | |
| TheoreticalSpectrumGenerator | Generates theoretical spectra with various options |
| ThresholdMower | ThresholdMower removes all peaks below a threshold |
| TICFilter | TICFilter calculates TIC |
| TOFCalibration | This class implements an external calibration for TOF data using external calibrant spectra |
| ToolDescription | |
| ToolDescriptionFile | File adapter for ToolDescriptor files |
| ToolDescriptionHandler | XML handler for ToolDescriptionFile |
| ToolDescriptionInternal | ToolDescription Class |
| ToolExternalDetails | |
| ToolHandler | |
| ToolsDialog | TOPP tool selection dialog |
| TOPPASBase | Main window of the TOPPAS tool |
| TOPPASEdge | An edge representing a data flow in TOPPAS |
| TOPPASInputFileDialog | Dialog which allows to specify an input file |
| TOPPASInputFileDialogTemplate | |
| TOPPASInputFileListVertex | A vertex representing an input file list |
| TOPPASInputFilesDialog | Dialog which allows to specify a list of input files |
| TOPPASInputFilesDialogTemplate | |
| TOPPASIOMappingDialog | Dialog which allows to configure the input/output parameter mapping of an edge |
| TOPPASIOMappingDialogTemplate | |
| 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 |
| TOPPASOutputFilesDialog | Dialog which allows to specify the directory for the output files |
| TOPPASOutputFilesDialogTemplate | |
| TOPPASResource | Represents a data resource for TOPPAS workflows |
| TOPPASResources | A dictionary mapping string keys to lists of TOPPASResource objects |
| TOPPASScene | A container for all visual items of a TOPPAS workflow |
| TOPPASTabBar | Convenience tab bar implementation |
| TOPPASToolConfigDialog | TOPP tool configuration dialog |
| TOPPASToolVertex | A vertex representing a TOPP tool |
| TOPPASTreeView | Tree view implementation for the list of TOPP tools |
| TOPPASVertex | The base class of the different vertex classes |
| TOPPASVertexNameDialog | Dialog which allows to change the name of an input vertex |
| TOPPASVertexNameDialogTemplate | |
| TOPPASWidget | Widget visualizing and allowing to edit TOPP pipelines |
| TOPPBase | Base class for TOPP applications |
| TOPPASScene::TOPPProcess | Stores the information for a TOPP process |
| TOPPRNPxl | |
| TOPPRNPxlXICFilter | |
| TOPPViewBase | Main window of TOPPView tool |
| TOPPViewBehaviorInterface | Interface class to model different behaviors of TOPPView |
| TOPPViewIdentificationViewBehavior | Behavior of TOPPView in identification mode |
| TOPPViewOpenDialog | Dataset opening options for TOPPView |
| TOPPViewOpenDialogTemplate | |
| TOPPViewPrefDialog | Preferences dialog for TOPPView |
| TOPPViewPrefDialogTemplate | |
| TOPPViewSpectraViewBehavior | Behavior of TOPPView in spectra view mode |
| PrecursorIonSelection::TotalScoreMore | Compare by score |
| TraceFitter< PeakType > | Abstract fitter for RT profile fitting |
| Param::ParamIterator::TraceInfo | Struct that captures information on entered / left nodes for ParamIterator |
| TraMLFile | File adapter for HUPO PSI TraML files |
| TraMLHandler | XML handler for TraMLFile |
| TraMLProduct | |
| TraMLValidator | Semantically validates MzXML files |
| IDDecoyProbability::Transformation_ | Struct to be used to store a transformation (used for fitting) |
| TransformationDescription | Generic description of a coordinate transformation |
| TransformationModel | Base class for transformation models |
| TransformationModelBSpline | B-spline model for transformations |
| TransformationModelInterpolated | Interpolation model for transformations |
| TransformationModelLinear | Linear model for transformations |
| TransformationXMLFile | Used to load and store TransformationXML files |
| TransitionGroupOpenMS< SpectrumT, TransitionT > | An implementation of the OpenSWATH Transition Group Access interface using OpenMS |
| TransitionHelper | |
| TransitionTSVReader | This class can convert TraML and TSV files into each other |
| IsotopeWaveletTransform< PeakType >::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 |
| HierarchicalClustering< PointRef >::TreeDistance | Wrapper class for two trees and the corresponding distance |
| HierarchicalClustering< PointRef >::TreeNode | Tree node used for clustering |
| TrypticIterator | Finds all tryptic Peptides with every missed cleavage |
| TransitionTSVReader::TSVTransition | |
| TwoDOptimization | This class provides the two-dimensional optimization of the picked peak parameters |
| UnableToCalibrate | Exception used if an error occurred while calibrating a dataset |
| UnableToCreateFile | Unable to create file exception |
| UnableToFit | Exception used if an error occurred while fitting a model to a given dataset |
| unary_function | |
| UnaryComposeFunctionAdapter< OP1, OP2 > | Represents the function object unary adapter |
| UnimodXMLFile | Used to load XML files from unimod.org files |
| UnimodXMLHandler | Handler that is used for parsing XTandemXML data |
| UniqueIdGenerator | A generator for unique ids |
| UniqueIdIndexer< RandomAccessContainer > | 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 |
| CVTerm::Unit | |
| UnnormalizedComparator | Exception thrown if clustering is attempted without a normalized compare functor |
| unordered_multimap | |
| UnregisteredParameter | An unregistered parameter was accessed |
| SparseVector< Value >::ValueProxy | Class ValueProxy allows the SparseVector to differentiate between writing and reading, so zeros can be ignored See "more effective c++" section 30 |
| PSLPFormulation::VariableIndexLess | |
| VersionInfo::VersionDetails | |
| VersionInfo | Version information class |
| TOPPASVertex::VertexRoundPackage | Info for one edge and round, to be passed to next node |
| Weights | Represents a set of weights (double values and scaled with a certain precision their integer counterparts) with a quick access |
| WeightWrapper | Encapsulated weight queries to simplify mono vs average weight computation |
| InclusionExclusionList::WindowDistance_ | Determine distance between two spectra |
| WindowMower | WindowMower augments the highest peaks in a sliding window |
| WrongParameterType | A parameter was accessed with the wrong type |
| XMassFile | File adapter for 'XMass Analysis (fid)' files |
| XMLFile | Base class for loading/storing XML files that have a handler derived from XMLHandler |
| XMLFormatTarget | |
| XMLHandler | Base class for XML handlers |
| XMLValidator | Validator for XML files |
| XTandemInfile | XTandem input file adapter |
| XTandemInfileNote | Note representation of bioml structure used by XTandem |
| XTandemInfileXMLHandler | Handler that is used for parsing XTandemXML data |
| XTandemXMLFile | Used to load XTandemXML files |
| ZhangSimilarityScore | Similarity score of Zhang |