| OpenMS 2.5.0

Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 1 2 3 4]

▶N eol_bspline |
C BSpline |
▶N KDTree |
▶C_Alloc_base |
C NoLeakAlloc |
C_Base_iterator |
C_Bracket_accessor |
C_Iterator |
C_Node |
C_Node_base |
C_Node_compare |
C_Region |
C always_true |
C KDTree |
C squared_difference |
C squared_difference_counted |
▶N ms |
▶N numpress |
▶N OpenMS | Main OpenMS namespace
▶N Constants | Mathematical and physical constants namespace
▶N DataArrays |
C FloatDataArray | Float data array class
C IntegerDataArray | Integer data array class
C StringDataArray | String data array class
▶N Exception | Exception namespace
C BaseException | Exception base class
C BufferOverflow | Buffer overflow exception
C ConversionError | Invalid conversion exception
C DepletedIDPool | Exception used if no more unique document ID's can be drawn from ID pool
C DivisionByZero | Division by zero error exception
C ElementNotFound | Element could not be found exception
C FailedAPICall | A call to an external library (other than OpenMS) went wrong
C FileEmpty | File is empty
C FileNameTooLong | Filename is too long to be writable/readable by the filesystem
C FileNotFound | File not found exception
C FileNotReadable | File not readable exception
C FileNotWritable | File not writable exception
C GlobalExceptionHandler | OpenMS global exception handler
C IllegalArgument | A method or algorithm argument contains illegal values
C IllegalPosition | Invalid 3-dimensional position exception
C IllegalSelfOperation | Illegal self operation exception
C IllegalTreeOperation | Illegal tree operation exception
C IncompatibleIterators | Incompatible iterator exception
C IndexOverflow | Int overflow exception
C IndexUnderflow | Int underflow exception
C InvalidIterator | Invalid iterator exception
C InvalidParameter | Exception indicating that an invalid parameter was handed over to an algorithm
C InvalidRange | Invalid range exception
C InvalidSize | Invalid UInt exception
C InvalidValue | Invalid value exception
C IOException | General IOException
C MissingInformation | Not all required information provided
C NotImplemented | Not implemented exception
C NullPointer | Null pointer argument is invalid exception
C OutOfGrid | Out of grid exception
C OutOfMemory | Out of memory exception
C OutOfRange | Out of range exception
C ParseError | Parse Error exception
C Postcondition | Postcondition failed exception
C Precondition | Precondition failed exception
C RequiredParameterNotGiven | A required parameter was not given
C SizeUnderflow | UInt underflow exception
C UnableToCalibrate | Exception used if an error occurred while calibrating a dataset
C UnableToCreateFile | Unable to create file exception
C UnableToFit | Exception used if an error occurred while fitting a model to a given dataset
C UnregisteredParameter | An unregistered parameter was accessed
C WrongParameterType | A parameter was accessed with the wrong type
▶N IdentificationDataInternal |
C AppliedProcessingStep | A processing step that was applied to a data item, possibly with associated scores
C DataProcessingSoftware | Information about software used for data processing
C DataProcessingStep | Data processing step that is applied to the data (e.g. database search, PEP calculation, filtering, ConsensusID)
C DataQuery | Search query, e.g. spectrum or feature
C DBSearchParam | Parameters specific to a database search step
C IdentifiedCompound |
C IdentifiedSequence | Identified sequence (peptide or oligonucleotide)
C IteratorWrapper | Wrapper that adds `operator<` to iterators, so they can be used as (part of) keys in maps/sets or `multi_index_containers`
C MoleculeParentMatch | Meta data for the association between an identified molecule (e.g. peptide) and a parent molecule (e.g. protein)
C MoleculeQueryMatch | Meta data for a search hit (e.g. peptide-spectrum match)
C ParentMolecule | Representation of a parent molecule that is identified only indirectly (e.g. a protein)
C ParentMoleculeGroup | : Group of ambiguously identified parent molecules (e.g. protein group)
C ParentMoleculeGrouping | Set of groups of ambiguously identified parent molecules (e.g. results of running a protein inference algorithm)
C QueryMatchGroup | : Group of related (co-identified) molecule-query matches
C ScoredProcessingResult | Base class for ID data with scores and processing steps (and meta info)
C ScoreType | Information about a score type
▶N ims |
▶C IMSAlphabet | Holds an indexed list of bio-chemical elements
C MassSortingCriteria_ | Private class-functor to sort out elements in mass ascending order
C IMSAlphabetParser | An abstract templatized parser to load the data that is used to initialize `Alphabet` objects
C IMSAlphabetTextParser | Implements abstract `AlphabetParser` to read data from the plain text format
C IMSElement | Represents a chemical atom with name and isotope distribution
▶C IMSIsotopeDistribution | Represents a distribution of isotopes restricted to the first K elements
C Peak | Structure that represents an isotope peak - pair of mass and abundance
C 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
C MassDecomposer | An interface to handle decomposing of integer values/masses over a set of integer weights (alphabet)
C RealMassDecomposer | Handles decomposing of non-integer values/masses over a set of non-integer weights with an error allowed
C Weights | Represents a set of weights (double values and scaled with a certain precision their integer counterparts) with a quick access
▶N Interfaces |
C BinaryDataArray | The datastructures used by the OpenSwath interfaces
C Chromatogram | A single chromatogram
C ChromatogramMeta | Identifying information for a chromatogram
C IChromatogramsReader | The interface of read-access to a list of chromatograms
C IChromatogramsWriter |
C IMSDataConsumer | The interface of a consumer of spectra and chromatograms
C ISpectraReader | The interface of read-access to a list of spectra
C ISpectraWriter |
C Spectrum | The structure that captures the generation of a peak list (including the underlying acquisitions)
C SpectrumMeta | Identifying information for a spectrum
▶N Internal | Namespace used to hide implementation details from users
C AcqusHandler | Read-only acqus File handler for XMass Analysis
C AreaIterator | Forward iterator for an area of peaks in an experiment
C CachedMzMLHandler | An class that uses on-disk caching to read and write spectra and chromatograms
C DIntervalBase | A base class for D-dimensional interval
C FidHandler | Read-only fid File handler for XMass Analysis
C FileMapping | Maps input/output files to filenames for the external program
▶C IDBoostGraph | Creates and maintains a boost graph based on the OpenMS ID datastructures
C dfs_ccsplit_visitor | A boost dfs visitor that copies connected components into a vector of graphs
C GetPosteriorVisitor |
C LabelVisitor | Visits nodes in the boost graph (ptrs to an ID Object) and depending on their type creates a label
C PrintAddressVisitor |
C SetPosteriorVisitor |
C IndexedMzMLHandler | A low-level class to read an indexedmzML file
C IntensityIteratorWrapper | An iterator wrapper to access peak intensities instead of the peak itself
C ListEditorDelegate | Internal delegate class
C ListTable |
C Looper |
C Looper< grid_size, grid_size, EvalResult, Tuple, TupleTypes... > |
C Looper< param_index, grid_size, EvalResult, Tuple, FirstTupleType, TupleTypes... > |
C MappingParam | Filename mappings for all input/output files
C MascotXMLHandler | Handler that is used for parsing MascotXML data
C MessagePasserFactory |
C MzDataHandler |
C MzDataValidator | Semantically validates MzXML files
▶C MzIdentMLDOMHandler | XML DOM handler for MzIdentMLFile
C AnalysisSoftware | Struct to hold the used analysis software for that file
C DatabaseInput | Struct to hold the information from the DatabaseInput xml tag
C DBSequence | Struct to hold the information from the DBSequence xml tag
C ModificationParam | Struct to hold the information from the ModificationParam xml tag
C PeptideEvidence | Struct to hold the PeptideEvidence information
C SpectrumIdentification | Struct to hold the information from the SpectrumIdentification xml tag
C SpectrumIdentificationProtocol | Struct to hold the information from the SpectrumIdentificationProtocol xml tag
C MzIdentMLHandler | XML STREAM handler for MzIdentMLFile
C MzIdentMLValidator | Semantically validates MzXML files
▶C MzMLHandler | Handler for mzML file format
C ChromatogramData | Data necessary to generate a single chromatogram
C SpectrumData | Data necessary to generate a single spectrum
▶C MzMLHandlerHelper | Helper for mzML file format
C BinaryData | Representation for binary data in mzML
C MzMLSqliteHandler | Sqlite handler for storing spectra and chromatograms in sqMass format
C MzMLSqliteSwathHandler | Sqlite handler for SWATH data sets
C MzMLValidator | Semantically validates MzXML files
C MzQuantMLHandler | XML handler for MzQuantMLFile
C MzQuantMLValidator | Semantically validates MzQuantML files
▶C MzXMLHandler |
C SpectrumData | Data necessary to generate a single spectrum
C OpenMSLineEdit | Custom QLineEdit which emits a signal when losing focus (such that we can commit its data)
C OpenMSOSInfo |
C ParamEditorDelegate | Internal delegate class for QTreeWidget
C ParamTree | QTreeWidget that emits a signal whenever a new row is selected
C ParamXMLHandler | XML Handler for Param files
C PTMXMLHandler | Handler that is used for parsing PTMXML data
▶C RNPxlFragmentAnnotationHelper | Convenience functions to construct appealing fragment annotation strings and store them as PeptideHit::PeakAnnotation
C FragmentAnnotationDetail_ | Single fragment annotation
▶C SemanticValidator | Semantically validates XML files using CVMappings and a ControlledVocabulary
C CVTerm | Representation of a parsed CV term
C Spectrum1DPrefDialog | Preferences dialog for Spectrum1DWidget
C Spectrum2DPrefDialog | Preferences dialog for Spectrum2DWidget
C Spectrum3DPrefDialog | Preferences dialog for Spectrum3DWidget
C StringManager |
C ToolDescription |
C ToolDescriptionHandler | XML handler for ToolDescriptionFile
C ToolDescriptionInternal | ToolDescription Class
C ToolExternalDetails |
C TOPPViewPrefDialog | Preferences dialog for TOPPView
C TraMLHandler | XML handler for TraMLFile
C TraMLValidator | Semantically validates MzXML files
C UnimodXMLHandler | Handler that is used for parsing XTandemXML data
C XMLFile | Base class for loading/storing XML files that have a handler derived from XMLHandler
▶C XMLHandler | Base class for XML handlers
C 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)
C XQuestResultXMLHandler | XMLHandler for the result files of XQuest
▶N Logger | Log streams
C LogStream | Log Stream Class
▶C LogStreamBuf | Stream buffer used by LogStream
C LogCacheStruct | Holds a counter of occurrences and an index for the occurrence sequence of the corresponding log message
C 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
C LogStreamNotifier |
▶N Math | Math namespace
C AsymmetricStatistics | Internal class for asymmetric distributions
C AveragePosition | Maintain an average position by summing up positions with weights
C BasicStatistics | Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation
C 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
▶C GammaDistributionFitter | Implements a fitter for the Gamma distribution
C GammaDistributionFitResult | Struct to represent the parameters of a gamma distribution
▶C GaussFitter | Implements a fitter for Gaussian functions
C GaussFitResult | Struct of parameters of a Gaussian distribution
▶C GumbelDistributionFitter | Implements a fitter for the Gumbel distribution
C GumbelDistributionFitResult | Struct to represent the parameters of a gumbel distribution
▶C GumbelMaxLikelihoodFitter | Implements a fitter for the Gumbel distribution
C Functor |
C GumbelDistributionFitResult | Struct to represent the parameters of a gumbel distribution
C GumbelDistributionFunctor |
C Histogram | Representation of a histogram
C 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
C LinearRegression | This class offers functions to perform least-squares fits to a straight line model,
C LinearRegressionWithoutIntercept | This class offers functions to perform least-squares fits to a straight line model,
C PosteriorErrorProbabilityModel | Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture
C QuadraticRegression |
C RANSAC | This class provides a generic implementation of the RANSAC outlier detection algorithm. Is implemented and tested after the SciPy reference: http://wiki.scipy.org/Cookbook/RANSAC
C RansacModel | Generic plug-in template base class using 'Curiously recurring template pattern' (CRTP) to allow for arbitrary RANSAC models (e.g. linear or quadratic fits)
C RansacModelLinear | Implementation of a linear RANSAC model fit
C RansacModelQuadratic | Implementation of a quadratic RANSAC model fit
C RANSACParam | A simple struct to carry all the parameters required for a RANSAC run
▶C ROCCurve | ROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cutoff values
C simsortdec | Predicate for sort()
C SummaryStatistics | Helper class to gather (and dump) some statistics from a e.g. vector<double>
▶N OptimizationFunctions |
C PenaltyFactors | Class for the penalty factors used during the optimization
C PenaltyFactorsIntensity | Class for the penalty factors used during the optimization
▶N SimTypes |
C SimProtein | Plain data object holding sequence and abundance information on a single protein
C SimRandomNumberGenerator | Wrapper class for random number generators used by the simulation classes
▶N StringConversions |
C BK_PrecPolicy |
▶N TargetedExperimentHelper | This class stores helper structures that are used in multiple classes of the TargetedExperiment (e.g. ReactionMonitoringTransition and IncludeExcludeTarget)
C Compound | Represents a compound (small molecule)
C Configuration |
C Contact |
C CV |
C Instrument |
C Interpretation | Product ion interpretation
▶C Peptide | Represents a peptide (amino acid sequence)
C Modification |
C PeptideCompound | Base class to represent either a peptide or a compound
C Prediction |
C Protein |
C Publication |
C RetentionTime | This class stores a retention time structure that is used in TargetedExperiment (representing a TraML file)
C TraMLProduct | Represents a product ion
C AAIndex | Representation of selected AAIndex properties
▶C AASequence | Representation of a peptide/protein sequence
C ConstIterator | ConstIterator for AASequence
C Iterator | Iterator class for AASequence
C AbsoluteQuantitation | AbsoluteQuantitation is a class to support absolute or relative quantitation for targeted or untargeted quantitation workflows (e.g., Isotope Dilution Mass Spectrometry)
C AbsoluteQuantitationMethod | AbsoluteQuantitationMethod is a class to hold information about the quantitation method and for applying and/or generating the quantitation method
C AbsoluteQuantitationMethodFile | File adapter for AbsoluteQuantitationMethod files
▶C AbsoluteQuantitationStandards | AbsoluteQuantitationStandards is a class to handle the relationship between runs, components, and their actual concentrations
C featureConcentration | Structure to hold a single component and its corresponding known concentration
C runConcentration | Structure to map runs to components to known concentrations
C AbsoluteQuantitationStandardsFile | Load files containing runConcentration data
▶C AccurateMassSearchEngine | An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB)
C CompareEntryAndMass_ |
C MappingEntry_ |
C AccurateMassSearchResult |
C Acquisition | Information about one raw data spectrum that was combined with several other raw data spectra
C AcquisitionInfo | Description of the combination of raw data to a single spectrum
C AcquisitionInfoVisualizer | Class that displays all meta information for AcquisitionInfo objects
C AcquisitionVisualizer | Class that displays all meta information for Acquisition objects
C Adduct |
C AdductInfo |
C AhoCorasickAmbiguous | Extended Aho-Corasick algorithm capable of matching ambiguous amino acids in the pattern (i.e. proteins)
C Annotation1DCaret | An annotation item which paints a set of carets on the canvas
C Annotation1DDistanceItem | An annotation item which represents a measured distance between two peaks
C Annotation1DItem | An abstract class acting as an interface for the different 1D annotation items
C Annotation1DPeakItem | A peak annotation item
C Annotation1DTextItem | An annotation item which represents an arbitrary text on the canvas
C Annotations1DContainer | Container for annotations to content of Spectrum1DCanvas
C AnnotationStatistics |
C AScore | Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the most probable phosphorylation-site(s). For each phosphorylation site a probability score is calculated. The algorithm is implemented according to Beausoleil et al. (Nat. Biotechnol. 2006)
C AverageLinkage | AverageLinkage ClusterMethod
C AxisPainter | Draws a coordinate axis. It has only static methods, that's why the constructor is private
C AxisTickCalculator | Calculates ticks for a given value range
C AxisWidget | Widget that represents an axis of a graph
C BackgroundControl |
C BackgroundIntensityBin |
▶C Base64 | Class to encode and decode Base64
C Reinterpreter32_ | Internal class needed for type-punning
C Reinterpreter64_ | Internal class needed for type-punning
▶C BaseFeature | A basic LC-MS feature
C QualityLess | Compare by quality
C BaseGroupFinder | The base class of all element group finding algorithms
C BaseLabeler | Abstract base class for all kinds of labeling techniques
C BaseModel | Abstract base class for all D-dimensional models
C BaseSuperimposer | The base class of all superimposer algorithms
C BaseVisualizer | A base class for all visualizer classes
C BaseVisualizerGUI | A base class for all visualizer classes
C BasicProteinInferenceAlgorithm | Algorithm class that implements simple protein inference by aggregation of peptide scores. It has multiple parameter options like the aggregation method, when to distinguish peptidoforms, and if you want to use shared peptides ("use_shared_peptides"). First, the best PSM per spectrum is used, then only the best PSM per peptidoform is aggregated. Peptidoforms can optionally be distinguished via the treat_X_separate parameters:
C BayesianProteinInferenceAlgorithm | Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental)
C BernNorm | BernNorm scales the peaks by ranking them and then scaling them according to rank
C BiGaussFitter1D | BiGaussian distribution fitter (1-dim.) approximated using linear interpolation
C BiGaussModel | BiGaussian distribution approximated using linear interpolation
C BinaryTreeNode | Elements of a binary tree used to represent a hierarchical clustering process
C BinnedSharedPeakCount | Compare functor scoring the shared peaks for similarity measurement
C BinnedSpectralContrastAngle | Compare functor scoring the spectral contrast angle for similarity measurement
C BinnedSpectrum | This is a binned representation of a PeakSpectrum
C BinnedSpectrumCompareFunctor | Base class for compare functors of BinnedSpectra
C BinnedSumAgreeingIntensities | Sum of agreeing intensities for similarity measurement
C BSpline2d | B spline interpolation
C Bzip2Ifstream | Decompresses files which are compressed in the bzip2 format (*.bz2)
C Bzip2InputStream | Implements the BinInputStream class of the xerces-c library in order to read bzip2 compressed XML files
C CachedmzML | An class that uses on-disk caching to read and write spectra and chromatograms
C CachedSwathFileConsumer | On-disk cached implementation of FullSwathFileConsumer
C CalibrationData | A helper class, holding all calibration points
C CentroidData |
C CentroidPeak |
C 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+, ..)
C ChromatogramExtractor | The ChromatogramExtractor extracts chromatograms from a spectra file
▶C ChromatogramExtractorAlgorithm | The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data
C ExtractionCoordinates |
▶C ChromatogramPeak | A 1-dimensional raw data point or peak for chromatograms
C IntensityLess | Comparator by intensity
C PositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for RTLess
C RTLess | Comparator by RT position
C ChromatogramSettings | Representation of chromatogram settings, e.g. SRM/MRM chromatograms
C ChromatogramTools | Conversion class to convert chromatograms
C ChromeleonFile | Load Chromeleon HPLC text file and save it into a `MSExperiment`
C ChromExtractParams | ChromatogramExtractor parameters
C Citation | Stores Citations for individual TOPP tools
C ClusterAnalyzer | Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's)
C ClusteredMS2ConsensusSpectrum |
▶C ClusterFunctor | Base class for cluster functors
C InsufficientInput | Exception thrown if not enough data (<2) is used
C ClusterHierarchical | Hierarchical clustering with generic clustering functions
C ClusteringGrid | Data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering
C ClusterProxyKD | Proxy for a (potential) cluster
C CmpHypothesesByScore |
C CmpMassTraceByMZ |
C CoarseIsotopePatternGenerator | Isotope pattern generator for coarse isotope distributions
C ColorSelector | A widget for selecting a color
C ComplementFilter | Total intensity of peak pairs that could result from complementing fragments of charge state 1
C ComplementMarker | ComplementMarker marks peak pairs which could represent y - b ion pairs
C CompleteLinkage | CompleteLinkage ClusterMethod
C CompNovoIdentification | Run with CompNovoIdentification
▶C CompNovoIdentificationBase | Run with CompNovoIdentificationBase
C Permut | Simple class to store permutations and a score
C CompNovoIdentificationCID | Run with CompNovoIdentificationCID
C CompNovoIonScoring | Run with CompNovoIonScoring
▶C CompNovoIonScoringBase | Run with CompNovoIonScoringBase
C IonScore |
C CompNovoIonScoringCID | Run with CompNovoIonScoringCID
C Compomer | Holds information on an edge connecting two features from a (putative) charge ladder
C CompressedInputSource | This class is based on xercesc::LocalFileInputSource
▶C ConfidenceScoring |
C GLM_ | Binomial GLM
C RTNorm_ | Helper for RT normalization (range 0-100)
C ConnectedComponent |
▶C ConsensusFeature | A consensus feature spanning multiple LC-MS/MS experiments
C MapsLess | Compare by the sets of consensus elements (lexicographically)
C Ratio | Slim struct to feed the need for systematically storing of ratios (
C SizeLess | Compare by size(), the number of consensus elements
C ConsensusIDAlgorithm | Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs)
C ConsensusIDAlgorithmAverage | Calculates a consensus from multiple ID runs by averaging the search scores
C ConsensusIDAlgorithmBest | Calculates a consensus from multiple ID runs by taking the best search score
C ConsensusIDAlgorithmIdentity | Abstract base class for ConsensusID algorithms that compare only identical sequences
C ConsensusIDAlgorithmPEPIons | Calculates a consensus from multiple ID runs based on PEPs and shared ions
C ConsensusIDAlgorithmPEPMatrix | Calculates a consensus from multiple ID runs based on PEPs and sequence similarities
C ConsensusIDAlgorithmRanks | Calculates a consensus from multiple ID runs based on the ranks of the search hits
C ConsensusIDAlgorithmSimilarity | Abstract base class for ConsensusID algorithms that take peptide similarity into account
C ConsensusIDAlgorithmWorst | Calculates a consensus from multiple ID runs by taking the worst search score (conservative approach)
C ConsensusIsotopePattern |
▶C ConsensusMap | A container for consensus elements
C ColumnHeader | Description of the columns in a consensus map
C ConsensusMapMergerAlgorithm | Merges identification data in ConsensusMaps
C ConsensusMapNormalizerAlgorithmMedian | Algorithms of ConsensusMapNormalizer
C ConsensusMapNormalizerAlgorithmQuantile | Algorithms of ConsensusMapNormalizer
C ConsensusMapNormalizerAlgorithmThreshold | Algorithms of ConsensusMapNormalizer
C ConsensusXMLFile | This class provides Input functionality for ConsensusMaps and Output functionality for alignments and quantitation
C ConsoleUtils |
▶C ConstRefVector | This vector holds pointer to the elements of another container
C ConstRefVectorConstIterator | ConstIterator for the ConstRefVector
C ConstRefVectorIterator | Mutable iterator for the ConstRefVector
C ContactPerson | Contact person information
C ContactPersonVisualizer | Class that displays all meta information for ContactPerson objects
▶C Contaminants | This class is a metric for the QualityControl TOPP tool
C ContaminantsSummary | Structure for storing results
C ContinuousWaveletTransform | This class is the base class of the continuous wavelet transformation
C ContinuousWaveletTransformNumIntegration | This class computes the continuous wavelet transformation using a marr wavelet
▶C ControlledVocabulary | Representation of a controlled vocabulary
C CVTerm | Representation of a CV term
C ConvexHull2D | A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling
C CrossLinksDB |
▶C CsiFingerIdMzTabWriter |
C CsiAdapterHit | Internal structure used in SiriusAdapter that is used for the conversion of the Csi:FingerID output to an mzTab
C CsiAdapterIdentification |
C CsiAdapterRun |
C CsvFile | This class handles csv files. Currently only loading is implemented
C 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
C CVMappingFile | Used to load CvMapping files
C CVMappingRule | Representation of a CV Mapping rule used by CVMappings
C CVMappings | Representation of controlled vocabulary mapping rules (for PSI formats)
C CVMappingTerm | Representation of controlled vocabulary term
C CVReference | Controlled Vocabulary Reference
▶C CVTerm | Representation of controlled vocabulary term
C Unit |
C CVTermList | Representation of controlled vocabulary term list
C CVTermListInterface | Interface to the controlled vocabulary term list
C DataFilterDialog | Dialog for creating and changing a DataFilter
▶C DataFilters | DataFilter array providing some convenience functions
C DataFilter | Representation of a peak/feature filter combining FilterType, FilterOperation and a value
C DataProcessing | Description of the applied preprocessing steps
C DataProcessingVisualizer | Class that displays all meta information for DataProcessing objects
C DataValue | Class to hold strings, numeric values, lists of strings and lists of numeric values
C Date | Date Class
C DateTime | DateTime Class
C DaTrait |
C DBoundingBox | A D-dimensional bounding box
C DeconvPeak |
▶C DecoyHelper | Helper class for calculcations on decoy proteins
C Result |
C DefaultParamHandler | A base class for all classes handling default parameters
C Deisotoper |
C DeNovoAlgorithm | Base class for ion scoring implementation for de novo algorithms
C DeNovoIdentification | Base class for de novo identification
▶C DeNovoIonScoring | Base class for ion scoring implementation for de novo algorithms
C IonScore | IonScore
C DeNovoPostScoring | Base class for ion scoring implementation for de novo algorithms
C DetectabilitySimulation | Simulates peptide detectability
C DiaPrescore | Scoring of an spectrum given library intensities of a transition group
C DIAScoring | Scoring of an spectrum at the peak apex of an chromatographic elution peak
C Digestion | Meta information about digestion of a sample
C DigestionEnzyme | Abstract base class for digestion enzymes
C DigestionEnzymeDB | Digestion enzyme database (base class)
C DigestionEnzymeProtein | Representation of a digestion enzyme for proteins (protease)
C DigestionEnzymeRNA | Representation of a digestion enzyme for RNA (RNase)
C DigestionVisualizer | Class that displays all meta information of digestion objects
C DigestSimulation | Simulates protein digestion
C DistanceMatrix | A two-dimensional distance matrix, similar to OpenMS::Matrix
C DocumentIdentifier | Manage source document information
C DocumentIdentifierVisualizer | Class that displays all meta information for DocumentIdentifier objects
C DocumentIDTagger | Tags OpenMS file containers with a DocumentID
C DPeak | Metafunction to choose among Peak1D respectively Peak2D through a template argument
C DPosition | Representation of a coordinate in D-dimensional space
C DRange | A D-dimensional half-open interval
C DTA2DFile | DTA2D File adapter
C DTAFile | File adapter for DTA files
C EDTAFile | File adapter for Enhanced DTA files
▶C EGHFitter1D | Exponential-Gaussian hybrid distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization
C Data | Helper struct (contains the size of an area and a raw data container)
C EGHFitterFunctor |
C EGHModel | Exponential-Gaussian hybrid distribution model for elution profiles
▶C EGHTraceFitter | A RT Profile fitter using an Exponential Gaussian Hybrid background model
C EGHTraceFunctor |
C Element | Representation of an element
C ElementDB | Stores elements
C ElutionModelFitter | Helper class for fitting elution models to features
C ElutionPeakDetection | Extracts chromatographic peaks from a mass trace
▶C EmgFitter1D | Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization
C Data | Helper struct (contains the size of an area and a raw data container)
C EgmFitterFunctor |
C EmgGradientDescent | Compute the area, background and shape metrics of a peak
C EmgGradientDescent_friend |
C EmgModel | Exponentially modified gaussian distribution model for elution profiles
C EmgScoring | Scoring of an elution peak using an exponentially modified gaussian distribution model
C EmpiricalFormula | Representation of an empirical formula
C EnhancedTabBar | Convenience tab bar implementation
C EnhancedTabBarWidgetInterface | Widgets that are placed into an EnhancedTabBar must implement this interface
C EnhancedWorkspace |
C EnzymaticDigestion | Class for the enzymatic digestion of sequences
▶C EnzymaticDigestionLogModel | Class for the Log L model of enzymatic digestion of proteins
C BindingSite_ |
C CleavageModel_ |
C EqualInTolerance | Struct for binary predicate to consider equality with a certain tolerance
C EuclideanSimilarity | CompareFunctor for 2Dpoints
▶C ExperimentalDesign | Representation of the Experimental Design in OpenMS. Instances can be loaded via the ExperimentalDesignFile class
C MSFileSectionEntry |
C SampleSection |
C ExperimentalDesignFile | Provides means to load an ExperimentalDesign from a TSV file
C ExperimentalSettings | Description of the experimental settings
C ExperimentalSettingsVisualizer | Class that displays all meta information for ExperimentalSettings objects
C ExtendedIsotopeFitter1D | Extended isotope distribution fitter (1-dim.) approximated using linear interpolation
C ExtendedIsotopeModel | Extended isotope distribution approximated using linear interpolation
C Factory | Returns FactoryProduct* based on the name of the desired concrete FactoryProduct
C FactoryBase | Base class for Factory<T>
C FakeProcess | A FakeProcess class
C FalseDiscoveryRate | Calculates false discovery rates (FDR) from identifications
C FASTAContainer | Template parameter for vector-based FASTA access
C FASTAContainer< TFI_File > | FASTAContainer<TFI_File> will make FASTA entries available chunk-wise from start to end by loading it from a FASTA file. This avoids having to load the full file into memory. While loading, the container will memorize the file offsets of each entry, allowing to read an arbitrary i'th entry again from disk. If possible, only entries from the currently cached chunk should be queried, otherwise access will be slow
C FASTAContainer< TFI_Vector > | FASTAContainer<TFI_Vector> simply takes an existing vector of FASTAEntries and provides the same interface with a potentially huge speed benefit over FASTAContainer<TFI_File> since it does not need disk access, but at the cost of memory
▶C FASTAFile | This class serves for reading in and writing FASTA files
C FASTAEntry | FASTA entry type (identifier, description and sequence)
C Feature | An LC-MS feature
C FeatureDeconvolution | An algorithm to decharge features (i.e. as found by FeatureFinder)
▶C FeatureDistance | A functor class for the calculation of distances between features or consensus features
C DistanceParams_ | Structure for storing distance parameters
C FeatureEditDialog | Dialog for editing a feature
C FeatureFileOptions | Options for loading files containing features
C FeatureFinder | The main feature finder class
C FeatureFinderAlgorithm | Abstract base class for FeatureFinder algorithms
▶C FeatureFinderAlgorithmIsotopeWavelet | Implements the isotope wavelet feature finder
C BoxElement | Internally used data structure for the sweep line algorithm
C FeatureFinderAlgorithmMRM | FeatureFinderAlgorithm for MRM experiments
C FeatureFinderAlgorithmPicked | FeatureFinderAlgorithm for picked peaks
▶C FeatureFinderAlgorithmPickedHelperStructs | Wrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes
C IsotopePattern | Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked
C MassTrace | Helper struct for mass traces used in FeatureFinderAlgorithmPicked
C MassTraces | Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked
C Seed | Helper structure for seeds used in FeatureFinderAlgorithmPicked
C TheoreticalIsotopePattern | Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked
C FeatureFinderAlgorithmSH | The Superhirn FeatureFinderAlgorithm
C FeatureFinderAlgorithmSHCtrl | A facade for various Superhirn FeatureFinder classes. Use FeatureFinderAlgorithmSH instead
▶C FeatureFinderDefs | The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes
C NoSuccessor | Exception that is thrown if a method an invalid IndexPair is given
▶C FeatureFinderIdentificationAlgorithm |
C FeatureCompare | Comparison functor for features
C FeatureFilterPeptides | Predicate for filtering features by assigned peptides:
C FeatureFilterQuality | Predicate for filtering features by overall quality:
C PeptideCompare | Comparison functor for (unassigned) peptide IDs
C RTRegion | Region in RT in which a peptide elutes:
C FeatureFinderMultiplexAlgorithm |
C FeatureFindingMetabo | Method for the assembly of mass traces belonging to the same isotope pattern, i.e., that are compatible in retention times, mass-to-charge ratios, and isotope abundances
C FeatureGroupingAlgorithm | Base class for all feature grouping algorithms
C FeatureGroupingAlgorithmKD | A feature grouping algorithm for unlabeled data
C FeatureGroupingAlgorithmLabeled | A map feature grouping algorithm for labeling techniques with two labels
C FeatureGroupingAlgorithmQT | A feature grouping algorithm for unlabeled data
C FeatureGroupingAlgorithmUnlabeled | A map feature grouping algorithm for unlabeled data
▶C FeatureHandle | Representation of a Peak2D, RichPeak2D or Feature
C FeatureHandleMutable_ | Helper class returned by FeatureHandle::asMutable(), which see
C IndexLess | Comparator by map and unique id
C FeatureHypothesis | Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis)
C FeatureLCProfile |
C FeatureMap | A container for features
▶C FeatureMapping |
C FeatureToMs2Indices |
C FeatureOpenMS | An implementation of the OpenSWATH Feature Access interface using OpenMS
C FeatureXMLFile | This class provides Input/Output functionality for feature maps
C FIAMSDataProcessor | Data processing for FIA-MS data
C FIAMSScheduler |
▶C File | Basic file handling operations
C TemporaryFiles_ | Internal helper class, which holds temporary filenames and deletes these files at program exit
C FileHandler | Facilitates file handling by file type recognition
C FileTypes | Centralizes the file types recognized by FileHandler
C FileWatcher | Watcher that monitors file changes
C FilterFunctor | A FilterFunctor extracts some spectrum characteristics for quality assessment
C FineIsotopePatternGenerator | Isotope pattern generator for fine isotope distributions
C Fitter1D | Abstract base class for all 1D-dimensional model fitter
▶C FragmentMassError |
C FMEStatistics | Structure for storing results: average and variance of all FragmentMassErrors in ppm
C FTPeakDetectController |
C FullSwathFileConsumer | Abstract base class which can consume spectra coming from SWATH experiment stored in a single file
▶C FuzzyStringComparator | Fuzzy comparison of strings, tolerates numeric differences
C AbortComparison | Internal exception class
C InputLine | Stores information about the current input line (i.e., stream for the line and the current position in the stream)
C PrefixInfo_ | Wrapper for the prefix information computed for the failure report
C StreamElement_ | Stores information about characters, numbers, and white spaces loaded from the InputStream
C GaussFilter | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data
C GaussFilterAlgorithm | This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data
C GaussFitter1D | Gaussian distribution fitter (1-dim.) approximated using linear interpolation
C GaussModel | Normal distribution approximated using linear interpolation
▶C GaussTraceFitter | Fitter for RT profiles using a Gaussian background model
C GaussTraceFunctor |
C GoodDiffFilter | GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss
C Gradient | Representation of a HPLC gradient
C GradientVisualizer | GradientVisualizer is a visualizer class for objects of type gradient
C GridBasedCluster | Basic data structure for clustering
C GridBasedClustering | 2D hierarchical clustering implementation optimized for large data sets containing many small clusters i.e. dimensions of clusters << dimension of entire dataset
C GridFeature | Representation of a feature in a hash grid
C GridSearch |
C GUIHelpers | Class which holds static GUI-related helper functions
C GUIProgressLoggerImpl | Implements a GUI version of the ProgressLoggerImpl
C GzipIfstream | Decompresses files which are compressed in the gzip format (*.gzip)
C GzipInputStream | Implements the BinInputStream class of the xerces-c library in order to read gzip compressed XML files
C HasActivationMethod | Predicate that determines if a spectrum was generated using any activation method given in the constructor list
▶C HashGrid | Container for (2-dimensional coordinate, value) pairs
C ConstIterator | Constant element iterator for the hash grid
C Iterator | Element iterator for the hash grid
C HasMetaValue | Predicate that determines if a class has a certain metavalue
C HasPrecursorCharge | Predicate that determines if a spectrum has a certain precursor charge as given in the constructor list
C HasScanMode | Predicate that determines if a spectrum has a certain scan mode
C HasScanPolarity | Predicate that determines if a spectrum has a certain scan polarity
C HDF5Connector | File adapter for HDF5 files
C HiddenMarkovModel | Hidden Markov Model implementation of PILIS
C HistogramDialog | Dialog that show a HistogramWidget
C HistogramWidget | Widget which can visualize a histogram
C HMMState | Hidden Markov Model State class for the Hidden Markov Model
C HPLC | Representation of a HPLC experiment
C HPLCVisualizer | Class that displays all meta information for HPLC objects
C HyperScore | An implementation of the X!Tandem HyperScore PSM scoring function
C IBSpectraFile | Implements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results
C ICPLLabeler | Simulate ICPL experiments
C IDConflictResolverAlgorithm | Resolves ambiguous annotations of features with peptide identifications
▶C IDDecoyProbability | IDDecoyProbability calculates probabilities using decoy approach
C Transformation_ | Struct to be used to store a transformation (used for fitting)
C Identification | Represents a object which can store the information of an analysisXML instance
▶C IdentificationData | Representation of spectrum identification results and associated data
C ModifyMultiIndexAddProcessingStep | Helper functor for adding processing steps to elements in a boost::multi_index_container structure
C ModifyMultiIndexAddScore | Helper functor for adding scores to elements in a boost::multi_index_container structure
C ModifyMultiIndexRemoveParentMatches | Helper functor for removing invalid parent matches from elements in a boost::multi_index_container structure
C IdentificationDataConverter |
C IdentificationHit | Represents a object which can store the information of an analysisXML instance
▶C IDFilter | Collection of functions for filtering peptide and protein identifications
C DigestionFilter | Is peptide evidence digestion product of some protein
C GetMatchingItems | Builds a map index of data that have a String index to find matches and return the objects
C HasDecoyAnnotation | Is this a decoy hit?
C HasGoodScore | Is the score of this hit at least as good as the given value?
C HasMatchingAccession | Given a list of protein accessions, do any occur in the annotation(s) of this hit?
C HasMatchingAccessionUnordered | Given a list of protein accessions, do any occur in the annotation(s) of this hit?
C HasMaxMetaValue | Does a meta value of this hit have at most the given value?
C HasMaxRank | Is the rank of this hit below or at the given cut-off?
C HasMetaValue | Is a meta value with given key and value set on this hit?
C HasNoHits | Is the list of hits of this peptide/protein ID empty?
C PeptideDigestionFilter | Filter Peptide Hit by its digestion product
▶C IDMapper | Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications
C SpectraIdentificationState | Result of a partitioning by identification state with mapPrecursorsToIdentifications()
C IDMergerAlgorithm | Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but concatenates PSMs. Checks search engine consistency of all inserted runs. It differs from the IDMerger tool, in that it is an algorithm class and it allows inserting multiple peptide hits per peptide sequence (not only the first occurrence)
C IDRipper | Ripping protein/peptide identification according their file origin
▶C IDScoreGetterSetter | A class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps
C IsHitType |
C IsIDType |
C IdXMLFile | Used to load and store idXML files
C ILPDCWrapper |
C IncludeExcludeTarget | This class stores a SRM/MRM transition
▶C InclusionExclusionList | Provides functionality for writing inclusion or exclusion lists
C IEWindow |
C WindowDistance_ | Determine distance between two spectra
C IndexedMzMLDecoder | A class to analyze indexedmzML files and extract the offsets of individual tags
C IndexedMzMLFileLoader | A class to load an indexedmzML file
C INIFileEditorWindow | Shows the ParamEditor widget in a QMainWindow with a toolbar
C InIntensityRange | Predicate that determines if a peak lies inside/outside a specific intensity range
C INIUpdater |
C InMSLevelRange | Predicate that determines if a spectrum lies inside/outside a specific MS level set
C InMzRange | Predicate that determines if a peak lies inside/outside a specific m/z range
C InPrecursorMZRange | Predicate that determines if a spectrum's precursor is within a certain m/z range
C InRTRange | Predicate that determines if a spectrum lies inside/outside a specific retention time range
C InspectInfile | Inspect input file adapter
C InspectOutfile | Representation of an Inspect outfile
C Instrument | Description of a MS instrument
C InstrumentSettings | Description of the settings a MS Instrument was run with
C InstrumentSettingsVisualizer | Class that displays all meta information for InstrumentSettings objects
C InstrumentVisualizer | Class that displays all meta information for an MS instrument
C IntensityBalanceFilter | IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions
▶C InternalCalibration | A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference masses
C LockMass | Helper class, describing a lock mass
C InterpolationModel | Abstract class for 1D-models that are approximated using linear interpolation
C IonDetector | Description of a ion detector (part of a MS Instrument)
C IonDetectorVisualizer | Class that displays all meta information for IonDetector objects
C IonizationSimulation | Simulates Protein ionization
C IonMobilityScoring | A class that calls the ion mobility scoring routines
C IonSource | Description of an ion source (part of a MS Instrument)
C IonSourceVisualizer | Class that displays all meta information for IonSource objects
C IsEmptySpectrum | Predicate that determines if a spectrum is empty
C IsInCollisionEnergyRange | Predicate that determines if an MSn spectrum was generated with a collision energy in the given range
C IsInIsolationWindow | Predicate that determines if the isolation window covers ANY of the given m/z values
C IsInIsolationWindowSizeRange | Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range
▶C IsobaricChannelExtractor | Extracts individual channels from MS/MS spectra for isobaric labeling experiments
C PuritySate_ | Small struct to capture the current state of the purity computation
C IsobaricIsotopeCorrector | Performs isotope impurity correction on the intensities extracted from an isobaric labeling experiment
C IsobaricNormalizer | Performs median normalization on the extracted ratios of isobaric labeling experiment
C IsobaricQuantifier | Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing
C IsobaricQuantifierStatistics | Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion)
▶C IsobaricQuantitationMethod | Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix
C IsobaricChannelInformation | Summary of an isobaric quantitation channel
C IsoSpecGeneratorWrapper | Interface for the IsoSpec algorithm - a generator of infinitely-resolved theoretical spectra
C IsoSpecOrderedGeneratorWrapper | Generate the stream of configurations, ordered from most likely to least likely
C IsoSpecThresholdGeneratorWrapper | Provides a threshold-based generator of isotopologues: generates all isotopologues more probable than a given probability threshold
C IsoSpecThresholdWrapper | A non-generator version of IsoSpecThresholdGeneratorWrapper
C IsoSpecTotalProbGeneratorWrapper | Generate a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99)
C IsoSpecTotalProbWrapper | Create a p-set of configurations for a given p (that is, a set of configurations such that their probabilities sum up to p). The p in normal usage will usually be close to 1 (e.g. 0.99)
C IsoSpecWrapper | A convenience class for the IsoSpec algorithm - easier to use than the IsoSpecGeneratorWrapper classes
▶C IsotopeCluster | Stores information about an isotopic cluster (i.e. potential peptide charge variants)
C ChargedIndexSet | Index set with associated charge estimate
C IsotopeDiffFilter | IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks
C IsotopeDistribution |
C IsotopeDistributionCache | Pre-calculate isotope distributions for interesting mass ranges
C IsotopeFitter1D | Isotope distribution fitter (1-dim.) approximated using linear interpolation
C IsotopeMarker | IsotopeMarker marks peak pairs which could represent an ion and its isotope
C IsotopeModel | Isotope distribution approximated using linear interpolation
C IsotopePatternGenerator | Provides an interface for different isotope pattern generator methods
▶C IsotopeWavelet | Implements the isotope wavelet function
C fi_ | Internal union for fast computation of the power function
▶C 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
C BoxElement | Internally used data structure
C 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
C IsotopicDist |
C IsZoomSpectrum | Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum
▶C ItraqConstants | Some constants used throughout iTRAQ classes
C ChannelInfo | Stores information on an iTRAQ channel
C ItraqEightPlexQuantitationMethod | ITRAQ 8 plex quantitation to be used with the IsobaricQuantitation
C ItraqFourPlexQuantitationMethod | ITRAQ 4 plex quantitation to be used with the IsobaricQuantitation
C ITRAQLabeler | Simulate iTRAQ experiments
C JavaInfo | Detect Java and retrieve information
C KDTreeFeatureMaps | Stores a set of features, together with a 2D tree for fast search
C KDTreeFeatureNode | A node of the kD-tree with pointer to corresponding data and index
C KroenikFile | File adapter for Kroenik (HardKloer sibling) files
C LabeledPairFinder | The LabeledPairFinder allows the matching of labeled features (features with a fixed distance)
C LabelFreeLabeler | Abstract base class for all kinds of labeling techniques
C LayerData | Class that stores the data for one layer
▶C LayerStatisticsDialog | Dialog showing statistics about the data of the current layer
C MetaStatsValue_ | Struct representing the statistics about one meta information
C LCElutionPeak |
▶C LCMS |
C OPERATOR_FeatureCompare |
C OPERATOR_MZ |
C LCMSCData |
▶C LevMarqFitter1D | Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization
C GenericFunctor |
C 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
C LibSVMEncoder | Serves for encoding sequences into feature vectors
C LinearResampler | Linear Resampling of raw data
C LinearResamplerAlign | Linear Resampling of raw data with alignment
C ListEditor | Editor for editing int, double and string lists (including output and input file lists)
▶C ListUtils | Collection of utility functions for management of vectors
C DoubleTolerancePredicate_ | Predicate to check double equality with a given tolerance
▶C LocalLinearMap | Trained Local Linear Map (LLM) model for peak intensity prediction
C LLMParam | Define parameters needed by the Local Linear Map (LLM) model
C LogConfigHandler | The LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream
C LowessSmoothing | LOWESS (locally weighted scatterplot smoothing)
▶C LPWrapper |
C SolverParam | Struct that holds the parameters of the LP solver
▶C Map | Map class based on the STL map (containing several convenience functions)
C IllegalKey | Map illegal key exception
C MapAlignmentAlgorithmIdentification | A map alignment algorithm based on peptide identifications from MS2 spectra
C MapAlignmentAlgorithmKD | An efficient reference-free feature map alignment algorithm for unlabeled data
C MapAlignmentAlgorithmPoseClustering | A map alignment algorithm based on pose clustering
▶C MapAlignmentAlgorithmSpectrumAlignment | A map alignment algorithm based on spectrum similarity (dynamic programming)
C Compare | Inner class necessary for using the sort algorithm
C MapAlignmentAlgorithmTreeGuided | A map alignment algorithm based on peptide identifications from MS2 spectra
C MapAlignmentEvaluationAlgorithm | Base class for all Caap evaluation algorithms
C MapAlignmentEvaluationAlgorithmPrecision | Caap evaluation algorithm to obtain a precision value
C MapAlignmentEvaluationAlgorithmRecall | Caap evaluation algorithm to obtain a recall value
C MapAlignmentTransformer | This class collects functions for applying retention time transformations to data structures
C MapConversion |
C MarkerMower | MarkerMower uses PeakMarker to find peaks, those that are not marked get removed
C MascotGenericFile | Read/write Mascot generic files (MGF)
C MascotInfile | Mascot input file adapter
C MascotRemoteQuery | Class which handles the communication between OpenMS and the Mascot server
C MascotXMLFile | Used to load Mascot XML files
C MassAnalyzer | Description of a mass analyzer (part of a MS Instrument)
C MassAnalyzerVisualizer | Class that displays all meta information for MassAnalyzer objects
C MassDecomposition | Class represents a decomposition of a mass into amino acids
C MassDecompositionAlgorithm | Mass decomposition algorithm, given a mass it suggests possible compositions
C MassExplainer | Computes empirical formulas for given mass differences using a set of allowed elements
C MassTrace | A container type that gathers peaks similar in m/z and moving along retention time
C MasstraceCorrelator | Correlates individual masstraces found in mass spectrometric maps
C MassTraceDetection | A mass trace extraction method that gathers peaks similar in m/z and moving along retention time
C MatchedIterator | For each element in the reference container the closest peak in the target will be searched. If no match is found within the tolerance window, the peak will be skipped over
C Matrix | A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access
C MaxLikeliFitter1D | Abstract base class for all 1D-model fitters using maximum likelihood optimization
C MetaboliteFeatureDeconvolution | An algorithm to decharge small molecule features (i.e. as found by FeatureFinder)
C MetaboliteSpectralMatching |
▶C MetaboTargetedAssay | This class provides methods for the extraction of targeted assays for metabolomics
C CompoundSpectrumPair | CompoundSpectrumPair stores a pair of CompoundInfo and MSSpectrum
C MetaDataBrowser | A meta data visualization widget
C MetaInfo | A Type-Name-Value tuple class
C MetaInfoDescription | Description of the meta data arrays of MSSpectrum
C MetaInfoDescriptionVisualizer | Class that displays all meta information for MetaInfoDescription objects
C MetaInfoInterface | Interface for classes that can store arbitrary meta information (Type-Name-Value tuples)
C MetaInfoInterfaceUtils | Utilities operating on containers inheriting from MetaInfoInterface
C MetaInfoRegistry | Registry which assigns unique integer indices to strings
C MetaInfoVisualizer | MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member
C MinimumDistance | Basic data structure for distances between clusters
C MissedCleavages | This class is a metric for the QualityControl TOPP Tool
C ModelDescription | Stores the name and parameters of a model
C Modification | Meta information about chemical modification of a sample
C ModificationDefinition | Representation of modification definition
C ModificationDefinitionsSet | Representation of a set of modification definitions
C ModificationsDB | Database which holds all residue modifications from UniMod
C ModificationVisualizer | Class that displays all meta information of modification objects
C ModifiedNASequenceGenerator |
▶C ModifiedPeptideGenerator |
C MapToResidueType |
▶C MorpheusScore | An implementation of the Morpheus PSM scoring function Inspired by a C# implementation by C. Wenger released under MIT license
C Result | Score and subscores
C MorphologicalFilter | This class implements baseline filtering operations using methods from mathematical morphology
C MRMAssay | Generate assays from a TargetedExperiment
C MRMBatchFeatureSelector |
C MRMDecoy | This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object
C MRMFeature | A multi-chromatogram MRM feature
C MRMFeatureFilter | The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria
C MRMFeatureFinderScoring | The MRMFeatureFinder finds and scores peaks of transitions that co-elute
C MRMFeatureOpenMS | An implementation of the OpenSWATH MRM Feature Access interface using OpenMS
▶C MRMFeaturePicker | _MRMFeaturePicker_ defines the structures containing parameters to be used in [MRMTransitionGroupPicker](MRMTransitionGroupPicker) for components and components groups
C ComponentGroupParams | Structure to contain information about a component group with its parameters
C ComponentParams | Structure to contain information about a single component with its parameters
C MRMFeaturePickerFile | _MRMFeaturePickerFile_ loads components and components groups parameters from a .csv file
▶C MRMFeatureQC | The MRMFeatureQC is a class to handle the parameters and options for MRMFeatureFilter
C ComponentGroupPairQCs | Quality Controls (QCs) for multiple components (between or within component_groups)
C ComponentGroupQCs | Quality Controls (QCs) within a component group
C ComponentQCs | Quality Controls (QCs) for individual components
C MRMFeatureQCFile | File adapter for MRMFeatureQC files
▶C MRMFeatureSelector |
C SelectorParameters |
C MRMFeatureSelector_test |
C MRMFeatureSelectorQMIP |
C MRMFeatureSelectorScore |
C MRMFragmentSelection | This class can select appropriate fragment ions of an MS/MS spectrum of a peptide
C MRMIonSeries | Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy
C MRMMapping | A class to map targeted assays to chromatograms
C MRMRTNormalizer | The MRMRTNormalizer will find retention time peptides in data
C MRMTransitionGroup | The representation of a group of transitions in a targeted proteomics experiment
C MRMTransitionGroupPicker | The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors
▶C MS1FeatureMerger |
C OPERATOR_FEATURE_TR |
C MS1Signal |
C MS2ConsensusSpectrum |
C MS2Feature |
C MS2File | MS2 input file adapter
C MS2Fragment |
▶C Ms2IdentificationRate | This class is a metric for the QualityControl-ToppTool
C IdentificationRateData | Structure for storing results
C MS2Info |
▶C Ms2SpectrumStats | QC metric to determine the number of MS2 scans per MS1 scan over RT
C ScanEvent |
▶C MSChromatogram | The representation of a chromatogram
C MZLess | Comparator for the retention time
C MSDataAggregatingConsumer | Aggregates spectra by retention time
C MSDataCachedConsumer | Transforming and cached writing consumer of MS data
C MSDataChainingConsumer | Consumer class that passes all consumed data through a set of operations
C MSDataSqlConsumer | A data consumer that inserts MS data into a SQLite database
C MSDataStoringConsumer | Consumer class that simply stores the data
C MSDataTransformingConsumer | Transforming consumer of MS data
C MSDataWritingConsumer | Consumer class that writes MS data to disk using the mzML format
▶C MSExperiment | In-Memory representation of a mass spectrometry experiment
C ContainerAdd_ | Helper class to add either general data points in set2DData or use mass traces from meta values
C ContainerAdd_< ContainerValueType, false > |
C ContainerAdd_< ContainerValueType, true > |
C MsInspectFile | File adapter for MsInspect files
▶C MSNumpressCoder | Class to encode and decode data encoded with MSNumpress
C NumpressConfig | Configuration class for MSNumpress
C MSPeak |
C MSPFile | File adapter for MSP files (NIST spectra library)
C MSPGenericFile | Load MSP text file and save it into an `MSExperiment`
C MSPGenericFile_friend |
▶C MSQuantifications |
C AnalysisSummary |
C Assay |
C MSSim | Central class for simulation of mass spectrometry experiments
▶C MSSpectrum | The representation of a 1D spectrum
C RTLess | Comparator for the retention time
▶C MSstatsFile | File adapter for MzTab files
C AggregatedConsensusInfo |
C MSstatsLine_ |
C MSstatsTMTLine_ |
C MultiGradient | A gradient of multiple colors and arbitrary distances between colors
C MultiGradientSelector | A widget witch allows constructing gradients of multiple colors
▶C MultiplexClustering | Clusters results from multiplex filtering
C MultiplexDistance | Scaled Euclidean distance for clustering
▶C MultiplexDeltaMasses | Data structure for mass shift pattern
C DeltaMass | Mass shift with corresponding label set
▶C MultiplexDeltaMassesGenerator | Generates complete list of all possible mass shifts due to isotopic labelling
C Label | Complete label information
C MultiplexFilteredMSExperiment | Data structure storing all peaks (and optionally their raw data points) of an experiment corresponding to one specific peak pattern
C MultiplexFilteredPeak | Data structure storing a single peak that passed all filters
C MultiplexFiltering | Base class for filtering centroided and profile data for peak patterns
C MultiplexFilteringCentroided | Filters centroided data for peak patterns
C MultiplexFilteringProfile | Filters centroided and profile data for peak patterns
C MultiplexIsotopicPeakPattern | Data structure for pattern of isotopic peaks
C MultiplexSatelliteCentroided | Data structure storing a single satellite peak
C MultiplexSatelliteProfile | Data structure storing a single satellite data point
C MzCalibration | QC metric calculating (un)calibrated m/z error
C MzDataFile | File adapter for MzData files
C MzIdentMLFile | File adapter for MzIdentML files
C MzMLFile | File adapter for MzML files
C MzMLSpectrumDecoder | A class to decode input strings that contain an mzML chromatogram or spectrum tag
C MzMLSwathFileConsumer | On-disk mzML implementation of FullSwathFileConsumer
C MzQuantMLFile | File adapter for MzQuantML files
C MzTab | Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/
C MzTabAssayMetaData |
C MzTabBoolean |
C MzTabContactMetaData |
C MzTabCVMetaData |
C MzTabDouble |
C MzTabDoubleList |
C MzTabFile | File adapter for MzTab files
C MzTabInstrumentMetaData |
C MzTabInteger |
C MzTabIntegerList |
C MzTabMetaData | All meta data of a mzTab file. Please refer to specification for documentation
C MzTabModification |
C MzTabModificationList |
C MzTabModificationMetaData |
C MzTabMSRunMetaData |
▶C MzTabNucleicAcidSectionRow | NUC - Nucleic acid section (table-based)
C RowCompare | Comparison operator for sorting rows
C MzTabNullAbleBase | Base class for atomic, non-container types (Double, Int)
C MzTabNullAbleInterface | Basic interface for all MzTab datatypes (can be null; are converted from and to cell string)
C MzTabNullNaNAndInfAbleBase | Base class for the atomic non-container like MzTab data types (Double, Int)
C MzTabNullNaNAndInfAbleInterface | Interface for NaN- and Inf- able datatypes (Double and Integer in MzTab). These are as well null-able
▶C MzTabOligonucleotideSectionRow | OLI - Oligonucleotide section (table-based)
C RowCompare | Comparison operator for sorting rows
▶C MzTabOSMSectionRow | OSM - OSM (oligonucleotide-spectrum match) section (table-based)
C RowCompare | Comparison operator for sorting rows
C MzTabParameter |
C MzTabParameterList |
▶C MzTabPeptideSectionRow | PEP - Peptide section (Table based)
C RowCompare | Comparison operator for sorting rows
▶C MzTabProteinSectionRow | PRT - Protein section (Table based)
C RowCompare | Comparison operator for sorting rows
▶C MzTabPSMSectionRow | PSM - PSM section (Table based)
C RowCompare | Comparison operator for sorting rows
C MzTabSampleMetaData |
C MzTabSmallMoleculeSectionRow | SML Small molecule section (table based)
C MzTabSoftwareMetaData |
C MzTabSpectraRef |
C MzTabString |
C MzTabStringList |
C MzTabStudyVariableMetaData |
▶C MZTrafoModel | Create and apply models of a mass recalibration function
C RTLess | Comparator by position. As this class has dimension 1, this is basically an alias for MZLess
C MzXMLFile | File adapter for MzXML 3.1 files
▶C NASequence | Representation of a nucleic acid sequence
C ConstIterator | ConstIterator of NASequence class
C Iterator | Iterator of NASequence class
C NetworkGetRequest |
C NeutralLossDiffFilter | NeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained by a neutral loss
C NeutralLossMarker | NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water, ammonia)
C NLargest | NLargest removes all but the n largest peaks
C NonNegativeLeastSquaresSolver | Wrapper for a non-negative least squares (NNLS) solver
C NoopMSDataConsumer | Consumer class that performs no operation
C NoopMSDataWritingConsumer | Consumer class that perform no operation
C Normalizer | Normalizes the peak intensities spectrum-wise
C NucleicAcidSpectrumGenerator | Generates theoretical spectra for nucleic acid sequences
C O18Labeler | Simulate O-18 experiments
C OfflinePrecursorIonSelection | Implements different algorithms for precursor ion selection
C OMSSACSVFile | File adapter for OMSSACSV files
C OMSSAXMLFile | Used to load OMSSAXML files
C OnDiscMSExperiment | Representation of a mass spectrometry experiment on disk
C OpenPepXLAlgorithm | Search for peptide pairs linked with a labeled cross-linker
C OpenPepXLLFAlgorithm | Search for cross-linked peptide pairs in tandem MS spectra
C OpenSwath_Ind_Scores |
C OpenSwath_Scores | A structure to hold the different scores computed by OpenSWATH
C OpenSwath_Scores_Usage | A structure to store which scores should be used by the OpenSWATH Algorithm
C OpenSwathCalibrationWorkflow | Execute all steps for retention time and m/z calibration of SWATH-MS data
C OpenSwathDataAccessHelper | Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces
C OpenSwathHelper | A helper class that is used by several OpenSWATH tools
C OpenSwathOSWWriter | Class to write out an OpenSwath OSW SQLite output (PyProphet input)
C OpenSwathScoring | A class that calls the scoring routines
C OpenSwathTSVWriter | Class to write out an OpenSwath TSV output (mProphet input)
C OpenSwathWorkflow | Execute all steps in an OpenSwath analysis
C OpenSwathWorkflowBase |
C OpenSwathWorkflowSonar | Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data)
▶C OptimizePeakDeconvolution | This class provides the deconvolution of peak regions using non-linear optimization
C Data | Class containing the data needed for optimization
▶C OptimizePick | This class provides the non-linear optimization of the peak parameters
C Data |
C OptPeakFunctor |
▶C OPXLDataStructs |
C AASeqWithMass | The AASeqWithMass struct represents a normal peptide with its precomputed mass
C AASeqWithMassComparator | The AASeqWithMassComparator is a comparator for AASeqWithMass objects
C CLSMScoreComparator | Comparator to sort CrossLinkSpectrumMatches by the main score
C CrossLinkSpectrumMatch | The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum in OpenPepXL
C PreprocessedPairSpectra | The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spectra to each other
C ProteinProteinCrossLink | The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL
C XLPrecursor | The XLPrecursor struct represents a cross-link candidate in the process of filtering candidates by precursor masses in OpenPepXL
C XLPrecursorComparator | The XLPrecursorComparator is a comparator for XLPrecursors, that allows direct comparison of the XLPrecursor precursor mass with double numbers
▶C OPXLHelper | Functions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code
C PeptideIDScoreComparator | A comparator for PeptideIdentifications that compares the scores in the first PeptideHit
C OPXLSpectrumProcessingAlgorithms |
C OSWFile | This class serves for reading in and writing OpenSWATH OSW files
C PairComparatorFirstElement | Class for comparison of std::pair using first ONLY e.g. for use with std::sort
C PairComparatorFirstElementMore | Class for comparison of std::pair using first ONLY e.g. for use with std::sort
C PairComparatorSecondElement | Class for comparison of std::pair using second ONLY e.g. for use with std::sort
C PairComparatorSecondElementMore | Class for comparison of std::pair using second ONLY e.g. for use with std::sort
C PairMatcherFirstElement | Class for comparison of std::pair using first ONLY e.g. for use with std::sort
C PairMatcherSecondElement | Struct for comparison of std::pair using second ONLY e.g. for use with std::sort
▶C Param | Management and storage of parameters / INI files
C ParamEntry | Parameter entry used to store the actual information inside of a Param entry
▶C ParamIterator | Forward const iterator for the Param class
C TraceInfo | Struct that captures information on entered / left nodes for ParamIterator
C ParamNode | Node inside a Param object which is used to build the internal tree
C ParamEditor | A GUI for editing or viewing a Param object
C ParameterInformation | Struct that captures all information of a command line parameter
C ParamXMLFile | The file pendant of the Param class used to load and store the param datastructure as paramXML
C ParentPeakMower | ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions
▶C Peak1D | A 1-dimensional raw data point or peak
C IntensityLess |
C MZLess | Comparator by m/z position
C PositionLess | Comparator by position. As this class has dimension 1, this is basically an alias for MZLess
▶C Peak2D | A 2-dimensional raw data point or peak
C IntensityLess |
C MZLess | Comparator by m/z position
C PositionLess | Comparator by position. Lexicographical comparison (first RT then m/z) is done
C RTLess | Comparator by RT position
C PeakAlignment | Make a PeakAlignment of two PeakSpectra
C PeakCandidate | A small structure to hold peak candidates
C PeakFileOptions | Options for loading files containing peak data
C PeakIndex | Index of a peak or feature
▶C PeakIntegrator | Compute the area, background and shape metrics of a peak
C PeakArea |
C PeakBackground |
C PeakShapeMetrics |
C PeakIntensityPredictor | Predict peak heights of peptides based on Local Linear Map model
C PeakMarker | PeakMarker marks peaks that seem to fulfill some criterion
▶C PeakPickerCWT | This class implements a peak picking algorithm using wavelet techniques
C PeakArea_ | Class for the internal peak representation
▶C 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
C PeakBoundary | Structure for peak boundaries
C PeakPickerIterative | This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data)
▶C 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
C PeakCandidate | The PeakCandidate describes the output of the peak picker
C PeakPickerMRM | The PeakPickerMRM finds peaks a single chromatogram
C PeakPickerSH |
▶C PeakShape | Internal representation of a peak shape (used by the PeakPickerCWT)
C PositionLess | Comparison of mz_positions
C PeakSpectrumCompareFunctor | Base class for compare functors of spectra, that return a similarity value for two spectra
C PeakTypeEstimator | Estimates if the data of a spectrum is raw data or peak data
C PeakWidthEstimator | Rough estimation of the peak width at m/z
C PepNovoInfile | PepNovo input file adapter
C PepNovoOutfile | Representation of a PepNovo output file
▶C PeptideAndProteinQuant | Helper class for peptide and protein quantification based on feature data annotated with IDs
C PeptideData | Quantitative and associated data for a peptide
C ProteinData | Quantitative and associated data for a protein
C Statistics | Statistics for processing summary
C PeptideEvidence | Representation of a peptide evidence
▶C PeptideHit | Representation of a peptide hit
C PeakAnnotation | Contains annotations of a peak
C PepXMLAnalysisResult | Analysis Result (containing search engine / prophet results)
C RankLess | Lesser predicate for scores of hits
C ScoreLess | Lesser predicate for scores of hits
C ScoreMore | Greater predicate for scores of hits
C SequenceLessComparator | Lesser predicate for (modified) sequence of hits
C PeptideHitVisualizer | Class that displays all meta information for PeptideHit objects
C PeptideIdentification | Represents the peptide hits for a spectrum
C PeptideIdentificationVisualizer | Class that displays all meta information for PeptideIdentification objects
▶C PeptideIndexing | Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds target/decoy information
C FoundProteinFunctor |
C PeptideProteinMatchInformation |
C PeptideProteinResolution | Resolves shared peptides based on protein scores
▶C PepXMLFile | Used to load and store PepXML files
C AminoAcidModification |
C PepXMLFileMascot | Used to load Mascot PepXML files
▶C PercolatorFeatureSetHelper | Percolator feature set and integration helper
C lq_PeptideEvidence | For accession dependent sorting of PeptideEvidences
C lq_ProteinHit | For accession dependent sorting of ProteinHits
C PercolatorOutfile | Class for reading Percolator tab-delimited output files
C PlainMSDataWritingConsumer | Consumer class that writes MS data to disk using the mzML format
C 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
C PoseClusteringAffineSuperimposer | A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation
C PoseClusteringShiftSuperimposer | A superimposer that uses a voting scheme, also known as pose clustering, to find a good shift transformation
C PpmTrait |
C PrecisionWrapper | Wrapper class to implement output with appropriate precision. See precisionWrapper()
C Precursor | Precursor meta information
C PrecursorCorrection | This class provides methods for precursor correction
▶C PrecursorIonSelection | This class implements different precursor ion selection strategies
C SeqTotalScoreMore | Compare by score
C TotalScoreMore | Compare by score
C PrecursorIonSelectionPreprocessing | This class implements the database preprocessing needing for precursor ion selection
C PrecursorMassComparator |
▶C PrecursorPurity | Precursor purity or noise estimation
C PurityScores |
C PrecursorVisualizer | Class that displays all meta information for Precursor objects
C ProbablePhosphoSites |
C ProcessData |
C Product | Product meta information
C ProductModel | Class for product models i.e. models with D independent dimensions
C ProductModel< 2 > | The class template is only implemented for D=2 because we use Peak2D here
C ProductVisualizer | Class that displays all meta information for Product objects
▶C ProgressLogger | Base class for all classes that want to report their progress
C ProgressLoggerImpl | This class represents an actual implementation of a logger
C ProteaseDB | Database for enzymes that digest proteins (proteases)
C ProteaseDigestion | Class for the enzymatic digestion of proteins
▶C ProteinHit | Representation of a protein hit
C ProteinHitAccessionHash | Hash of a ProteinHit based on its accession only!
C ProteinHitPtrAccessionHash |
C ScoreLess | Lesser predicate for scores of hits
C ScoreMore | Greater predicate for scores of hits
C ProteinHitVisualizer | Class that displays all meta information for ProteinHit objects
▶C ProteinIdentification | Representation of a protein identification run
C ProteinGroup | Bundles multiple (e.g. indistinguishable) proteins in a group
C SearchParameters | Search parameters of the DB search
C ProteinIdentificationVisualizer | Class that displays all meta information for ProteinIdentification objects
C ProteinInference | [experimental class] given a peptide quantitation, infer corresponding protein quantities
▶C ProteinResolver | Helper class for peptide and protein quantification based on feature data annotated with IDs
C ISDGroup |
C MSDGroup | Representation of an msd group. Contains peptides, proteins and a pointer to its ISD group
C PeptideEntry | Peptide. First in silico. If experimental is set to true it is MS/MS derived
C ProteinEntry | Protein from FASTA file
C ResolverResult |
C ProtonDistributionModel | A proton distribution model to calculate the proton distribution over charged peptides
C ProtXMLFile | Used to load (storing not supported, yet) ProtXML files
C PScore | Implementation of the PScore PSM scoring algorithm
▶C PSLPFormulation | Implements ILP formulation of precursor selection problems
C IndexLess |
C IndexTriple | Struct that holds the indices of the precursors in the feature map and the ilp formulation
C ScanLess |
C VariableIndexLess |
C PSProteinInference | This class implements protein inference for the precursor ion selection strategies
C PTMXMLFile | Used to load and store PTMXML files
C QApplicationTOPP | Extension to the QApplication for running TOPPs GUI tools
▶C QCBase | This class serves as an abstract base class for all QC classes
C SpectraMap | Map to find a spectrum via its NativeID
C Status | Storing a status of available/needed inputs (i.e. a set of Requires) as UInt64
▶C QcMLFile | File adapter for QcML files used to load and store QcML files
C Attachment | Representation of an attachment
C QualityParameter | Representation of a quality parameter
C QTCluster | A representation of a QT cluster used for feature grouping
C QTClusterFinder | A variant of QT clustering for the detection of feature groups
C QuantitativeExperimentalDesign | Merge files according to experimental design
C Range | Internal structure to store a lower and upper bound of an m/z range
C RangeManager | Handles the management of a position and intensity range
C RawData |
▶C RawMSSignalSimulation | Simulates MS signals for a given set of peptides
C ContaminantInfo |
C RawTandemMSSignalSimulation | Simulates tandem MS signals for a given set of peptides
▶C ReactionMonitoringTransition | This class stores a SRM/MRM transition
C ProductMZLess | Comparator by Product ion MZ
C RegularSwathFileConsumer | In-memory implementation of FullSwathFileConsumer
C Residue | Representation of a residue
C ResidueDB | Residue data base which holds residues
C ResidueModification | Representation of a modification
C 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
C Ribonucleotide | Representation of a ribonucleotide (modified or unmodified)
C RibonucleotideDB | Database of ribonucleotides (modified and unmodified)
C RichPeak2D | A 2-dimensional raw data point or peak with meta information
C RNaseDB | Database for enzymes that digest RNA (RNases)
C RNaseDigestion | Class for the enzymatic digestion of RNAs
C RNPxlMarkerIonExtractor |
C RNPxlModificationMassesResult |
C RNPxlModificationsGenerator |
C RNPxlReport | Create report
C RNPxlReportRow | Struct to hold a single report line
C RNPxlReportRowHeader | Create header line
C RTAlignment | Take the original retention time before map alignment and use the alignment's trafoXML for calculation of the new alignment retention times
C RTSimulation | Simulates/Predicts retention times for peptides or peptide separation
C RWrapper | R-Wrapper Class
C Sample | Meta information about the sample
C SampleTreatment | Base class for sample treatments (Digestion, Modification, Tagging, ...)
C SampleVisualizer | Class that displays all meta information of sample objects
C SaveImageDialog | Dialog for saving an image
C SavitzkyGolayFilter | Computes the Savitzky-Golay filter coefficients using QR decomposition
C Scaler | Scaler scales the peak by ranking the peaks and assigning intensity according to rank
C ScanWindow | Scan window description
C ScanWindowVisualizer | Class that displays all meta information for ScanWindow objects
C ScoreToTgtDecLabelPairs |
C SeedListGenerator | Generate seed lists for feature detection
C SequestInfile | Sequest input file adapter
C SequestOutfile | Representation of a Sequest output file
C SHFeature |
▶C SignalToNoiseEstimator | This class represents the abstract base class of a signal to noise estimator
C GaussianEstimate | Protected struct to store parameters my, sigma for a Gaussian distribution
C SignalToNoiseEstimatorMeanIterative | Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities
C SignalToNoiseEstimatorMedian | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based)
▶C SignalToNoiseEstimatorMedianRapid | Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based)
C NoiseEstimator | Class to compute the noise value at a given position
C SignalToNoiseOpenMS | An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS
C SILACLabeler | Simulate SILAC experiments
C SimpleOpenMSSpectraFactory | A factory method that returns two ISpectrumAccess implementations
C SimplePairFinder | This class implements a simple point pair finding algorithm
▶C SimpleSearchEngineAlgorithm |
C AnnotatedHit_ | Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space
▶C SimpleSVM | Simple interface to support vector machines for classification (via LIBSVM)
C Prediction | SVM prediction result
▶C SimpleTSGXLMS | Generates theoretical spectra for cross-linked peptides
C LossIndex |
C SimplePeak | A simple struct to represent peaks with mz and charge and sort them easily
C SimplePeakComparator | Comparator to sort SimplePeaks by mz
C SingleLinkage | SingleLinkage ClusterMethod
C SingletonRegistry | Holds pointers to unique instance of a singleton factory
▶C SiriusAdapterAlgorithm |
C SiriusTemporaryFileSystemObjects | Struct for temporary folder structure
C SiriusFragmentAnnotation |
▶C SiriusMSFile |
C AccessionInfo |
C CompoundInfo |
▶C SiriusMzTabWriter |
C SiriusAdapterHit | Internal structure used in SiriusAdapter that is used for the conversion of the sirius output to an mzTab.SiriusAdapterHit: formula (String) - Sumformula adduct (String) - Assigned adduct rank (int) - Rank of the possible sumformula for a compound (spectrum) calculated by Sirius score (double) - Overall score of the possible sumformula for a compound (spectrum) calculated by Sirius treescore (double) - Fragmentation pattern score isoscore (double) - Isotope pattern score explainedpeaks (int) - Number of explained peaks explainedintensity (double) - Relative amount of explained intensity
C SiriusAdapterIdentification |
C SiriusAdapterRun |
C Software | Description of the software used for processing
C SoftwareVisualizer | Class that displays all meta information for Software objects
C SONARScoring | Scoring of an spectrum using SONAR data
C SourceFile | Description of a file location, used to store the origin of (meta) data
C SourceFileVisualizer | Class that displays all meta information for SourceFile objects
C SpecArrayFile | File adapter for SpecArray (.pepList) files
C SpectraIdentificationViewWidget | Tabular visualization / selection of identified spectra
C SpectralMatch |
C SpectralMatchScoreComparator |
▶C SpectraMerger | Merges blocks of MS or MS2 spectra
C SpectraDistance_ |
C SpectraSTSimilarityScore | Similarity score of SpectraST
C SpectraViewWidget | Hierarchical visualization and selection of spectra
C Spectrum1DCanvas | Canvas for visualization of one or several spectra
C Spectrum1DGoToDialog | Simple goto/set visible area dialog for exact placement of the viewing window
C Spectrum1DWidget | Widget for visualization of several spectra
C Spectrum2DCanvas | Canvas for 2D-visualization of peak map, feature map and consensus map data
C Spectrum2DGoToDialog | GoTo dialog used to zoom to a m/z and retention time range or to a feature
C Spectrum2DWidget | Widget for 2D-visualization of peak map and feature map data
C Spectrum3DCanvas | Canvas for 3D-visualization of peak map data
C Spectrum3DOpenGLCanvas | OpenGL Canvas for 3D-visualization of map data
C Spectrum3DWidget | Widget for 3D-visualization of map data
C SpectrumAccessOpenMS | An implementation of the OpenSWATH Spectrum Access interface using OpenMS
C SpectrumAccessOpenMSCached | An implementation of the Spectrum Access interface using on-disk caching
C SpectrumAccessOpenMSInMemory | An implementation of the OpenSWATH Spectrum Access interface completely in memory
C SpectrumAccessQuadMZTransforming | A transforming m/z wrapper around spectrum access using a quadratic equation
C SpectrumAccessSqMass | An implementation of the Spectrum Access interface using SQL files
C SpectrumAccessTransforming | An abstract base class implementing a transforming wrapper around spectrum access
C SpectrumAddition | The SpectrumAddition is used to add up individual spectra
C SpectrumAlignment | Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) alignment if absolute tolerances are given. Scoring function is the m/z distance between peaks. Intensity does not play a role!
C SpectrumAlignmentDialog | Lets the user select two spectra and set the parameters for the spectrum alignment
C SpectrumAlignmentScore | Similarity score via spectra alignment
C SpectrumAnnotator | Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options
C SpectrumCanvas | Base class for visualization canvas classes
C SpectrumCheapDPCorr | SpectrumCheapDPCorr calculates an optimal alignment on stick spectra
C SpectrumIdentification | Represents a object which can store the information of an analysisXML instance
C SpectrumLookup | Helper class for looking up spectra based on different attributes
▶C SpectrumMetaDataLookup | Helper class for looking up spectrum meta data
C SpectrumMetaData | Meta data of a spectrum
C SpectrumPrecursorComparator | SpectrumPrecursorComparator compares just the parent mass of two spectra
C SpectrumSettings | Representation of 1D spectrum settings
C SpectrumSettingsVisualizer | Class that displays all meta information for SpectrumSettings objects
C SpectrumWidget | Base class for spectrum widgets
▶C SplineInterpolatedPeaks | Data structure for spline interpolation of MS1 spectra and chromatograms
C Navigator | Iterator class for access of spline packages
C SplinePackage | Fundamental data structure for SplineInterpolatedPeaks
C SqliteConnector | File adapter for Sqlite files
▶C SqMassFile | An class that uses on-disk SQLite database to read and write spectra and chromatograms
C SqMassConfig | Configuration class for SqMassFile
C SqrtMower | Scales the intensity of peaks to the sqrt
C StablePairFinder | This class implements a pair finding algorithm for consensus features
C SteinScottImproveScore | Similarity score based of Stein & Scott
C StopWatch | StopWatch Class
C StreamHandler | Provides a central class to register globally used output streams. Currently supported streams are
C String | A more convenient string class
C StringListUtils | Utilities operating on lists of Strings
▶C StringUtils |
C real_policies_NANfixed_ |
C StringView | StringView provides a non-owning view on an existing string
C Summary | Summary of fitting results
C SuperHirnParameters | SuperHirn parameters singleton class containing all static configuration variables
C SuperHirnUtil |
C SVMData | Data structure used in SVMWrapper
▶C SvmTheoreticalSpectrumGenerator | Simulates MS2 spectra with support vector machines
C DescriptorSet | A set of descriptors for a single training row
C IonType | Nested class
C SvmModelParameterSet | Simple container storing the model parameters required for simulation
C SvmTheoreticalSpectrumGeneratorSet | Loads SvmTheoreticalSpectrumGenerator instances for different charges
C SvmTheoreticalSpectrumGeneratorTrainer | Train SVM models that are used by SvmTheoreticalSpectrumGenerator
C SVMWrapper | Serves as a wrapper for the libsvm
C SVOutStream | Stream class for writing to comma/tab/...-separated values files
C SwathFile | File adapter for Swath files
C SwathMapMassCorrection | A class containing correction functions for Swath MS maps
C SwathWindowLoader | Class to read a file describing the Swath Windows
▶C SysInfo | Some functions to get system information
C MemUsage | A convenience class to report either absolute or delta (between two timepoints) RAM usage
C Tagger | Calculate sequence tags from m/z values
C Tagging | Meta information about tagging of a sample e.g. ICAT labeling
C TaggingVisualizer | Class that displays all meta information of tagging objects
C TargetedExperiment | A description of a targeted experiment containing precursor and production ions
▶C TargetedSpectraExtractor | This class filters, annotates, picks, and scores spectra (e.g., taken from a DDA experiment) based on a target list
C BinnedSpectrumComparator |
C Comparator |
C Match |
C TextFile | This class provides some basic file handling methods for text files
C TheoreticalSpectrumGenerationDialog | Dialog which allows to enter an AA sequence and generates a theoretical spectrum for it
C TheoreticalSpectrumGenerator | Generates theoretical spectra for peptides with various options
▶C TheoreticalSpectrumGeneratorXLMS | Generates theoretical spectra for cross-linked peptides
C LossIndex |
C ThresholdMower | ThresholdMower removes all peaks below a threshold
C TIC |
C TICFilter | TICFilter calculates TIC
C TMTElevenPlexQuantitationMethod | TMT 11plex quantitation to be used with the IsobaricQuantitation
C TMTSixPlexQuantitationMethod | TMT 6plex quantitation to be used with the IsobaricQuantitation
C TMTSixteenPlexQuantitationMethod | TMT 16plex quantitation to be used with the IsobaricQuantitation
C TMTTenPlexQuantitationMethod | TMT 10plex quantitation to be used with the IsobaricQuantitation
C TOFCalibration | This class implements an external calibration for TOF data using external calibrant spectra
C ToolDescriptionFile | File adapter for ToolDescriptor files
C ToolHandler |
C ToolsDialog | TOPP tool selection dialog
C TOPPASBase | Main window of the TOPPAS tool
C TOPPASEdge | An edge representing a data flow in TOPPAS
C TOPPASInputFileDialog | Dialog which allows to specify an input file
C TOPPASInputFileListVertex | A vertex representing an input file list
C TOPPASInputFilesDialog | Dialog which allows to specify a list of input files
C TOPPASIOMappingDialog | Dialog which allows to configure the input/output parameter mapping of an edge
C TOPPASLogWindow | QTextEdit implementation with a "clear" button in the context menu
C TOPPASMergerVertex | A special vertex that allows to merge several inputs
C TOPPASOutputFileListVertex | A vertex representing an output file list
C TOPPASOutputFilesDialog | Dialog which allows to specify the directory for the output files
C TOPPASResource | Represents a data resource for TOPPAS workflows
C TOPPASResources | A dictionary mapping string keys to lists of TOPPASResource objects
▶C TOPPASScene | A container for all visual items of a TOPPAS workflow
C TOPPProcess | Stores the information for a TOPP process
C TOPPASSplitterVertex | A special vertex that allows to split a list of inputs
C TOPPASTabBar | Convenience tab bar implementation
C TOPPASToolConfigDialog | TOPP tool configuration dialog
▶C TOPPASToolVertex | A vertex representing a TOPP tool
C IOInfo | Stores the information for input/output files/lists
C TOPPASTreeView | Tree view implementation for the list of TOPP tools
▶C TOPPASVertex | The base class of the different vertex classes
C TOPPASFilenames |
C VertexRoundPackage | Info for one edge and round, to be passed to next node
C TOPPASVertexNameDialog | Dialog which allows to change the name of an input/output vertex
C TOPPASWidget | Widget visualizing and allowing to edit TOPP pipelines
C TOPPBase | Base class for TOPP applications
C TOPPOpenSwathBase |
C TOPPViewBase | Main window of TOPPView tool
C TOPPViewIdentificationViewBehavior | Behavior of TOPPView in identification mode
C TOPPViewOpenDialog | Dataset opening options for TOPPView
C TOPPViewSpectraViewBehavior | Behavior of TOPPView in spectra view mode
▶C TraceFitter | Abstract fitter for RT profile fitting
C GenericFunctor |
C ModelData |
C TraMLFile | File adapter for HUPO PSI TraML files
▶C TransformationDescription | Generic description of a coordinate transformation
C TransformationStatistics | Summary statistics before/after applying the transformation. For deviations before/after transformation, the percentiles 100, 99, 95, 90, 75, 50, 25 are returned
▶C TransformationModel | Base class for transformation models
C DataPoint | Coordinate pair (with optional annotation)
C TransformationModelBSpline | B-spline (non-linear) model for transformations
▶C TransformationModelInterpolated | Interpolation model for transformations
C Interpolator | The class defines a generic interpolation technique used in the TransformationModelInterpolated
C TransformationModelLinear | Linear model for transformations
C TransformationModelLowess | Lowess (non-linear) model for transformations
C TransformationXMLFile | Used to load and store TransformationXML files
C TransitionGroupOpenMS | An implementation of the OpenSWATH Transition Group Access interface using OpenMS
C TransitionPQPFile | This class supports reading and writing of PQP files
▶C TransitionTSVFile | This class supports reading and writing of OpenSWATH transition lists
C TSVTransition | Internal structure to represent a transition
▶C TwoDOptimization | This class provides the two-dimensional optimization of the picked peak parameters
C Data | Helper struct (contains the size of an area and a raw data container)
C TwoDOptFunctor |
C UnimodXMLFile | Used to load XML files from unimod.org files
C UniqueIdGenerator | A generator for unique ids
C 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
C UniqueIdInterface | A base class defining a common interface for all classes having a unique id
C UnnormalizedComparator | Exception thrown if clustering is attempted without a normalized compare functor
C UpdateCheck | Helper Functions to perform an update query to the OpenMS REST server
C ValueTrait | Trait for MatchedIterator to find pairs with a certain distance, which is computed directly on the value_type of the container
C VecLowPrecision |
▶C VersionInfo | Version information class
C VersionDetails |
C WeightWrapper | Encapsulated weight queries to simplify mono vs average weight computation
C WindowMower | WindowMower augments the highest peaks in a sliding or jumping window
C XFDRAlgorithm | Calculates false discovery rate estimates on crosslink identifications
C XMassFile | File adapter for 'XMass Analysis (fid)' files
C XMLValidator | Validator for XML files
C XQuestResultXMLFile | Used to load and store xQuest result files
C XQuestScores | An implementation of the scores for cross-link identification from the xQuest algorithm (O. Rinner et al., 2008, "Identification of cross-linked peptides from large sequence databases")
C XTandemInfile | XTandem input file
C XTandemXMLFile | Used to load XTandemXML files
C ZhangSimilarityScore | Similarity score of Zhang
C ZlibCompression | Compresses and uncompresses data using zlib
▶N OpenSwath |
▶N Scoring | Scoring functions used by MRMScoring
C XCorrArrayType |
C CSVWriter |
C DataMatrix |
C IDataFrameWriter |
C IFeature |
C IMRMFeature |
C ISignalToNoise |
C ISpectrumAccess | The interface of a mass spectrometry experiment
C ITransitionGroup |
C LightCompound |
C LightModification |
C LightProtein |
C LightTargetedExperiment |
C LightTransition |
C mean_and_stddev | Functor to compute the mean and stddev of sequence using the std::foreach algorithm
C MockFeature | Mock object implementing IFeature
C MockMRMFeature | Mock object implementing IMRMFeature
C MockSignalToNoise | Mock object implementing ISignalToNoise
C MockTransitionGroup | Mock object implementing ITransitionGroup
C MRMScoring | This class implements different scores for peaks found in SRM/MRM
C mySqrt |
C OSBinaryDataArray | The datastructures used by the OpenSwath interfaces
C OSChromatogram | A single chromatogram
C OSChromatogramMeta | Identifying information for a chromatogram
C OSSpectrum | The structure that captures the generation of a peak list (including the underlying acquisitions)
▶C OSSpectrumMeta | Identifying information for a spectrum
C RTLess | Comparator for the retention time
C Peptide |
C Protein |
C SwathMap | Data structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2
C SwathQC | Quality Control function for OpenSwath
C TargetedExperiment |
C TransitionHelper |
▶N seqan |
C AAcid_ |
C AdaptedIdentity |
C BitsPerValue< AAcid > |
C CompareTypeImpl< AAcid, char > |
C CompareTypeImpl< AAcid, uint8_t > |
C Host< Pattern< TNeedle, FuzzyAC > > |
C Host< Pattern< TNeedle, FuzzyAC > const > |
C OMS_TranslateTableAAToChar_ |
C OMS_TranslateTableByteToAA_ |
C OMS_TranslateTableCharToAA_ |
C PAM30MS |
C Pattern< TNeedle, FuzzyAC > |
C PatternAuxData |
C ScoringMatrixData_< int, AminoAcid, AdaptedIdentity > |
C ScoringMatrixData_< int, AminoAcid, PAM30MS > |
C Spawn | State of an AC spawn, operating on a trie
C ValueSize< AAcid > |
▶N std | STL namespace
C hash< OpenMS::String > |
C Epifany |
C glp_prob |
C MetaProSIPClustering |
C MetaProSIPDecomposition |
C MetaProSIPInterpolation |
C MetaProSIPReporting |
C MetaProSIPXICExtraction |
▶C NucleicAcidSearchEngine |
C AnnotatedHit |
C HasInvalidLength |
C PrecursorInfo |
C QApplication |
C QDate |
C QDateTime |
C QDialog |
C QFileSystemWatcher |
C QGraphicsItem |
C QGraphicsScene |
C QGraphicsView |
C QItemDelegate |
C QLineEdit |
C QListWidget |
C QMainWindow |
C QMdiArea |
C QObject |
C QOpenGLFunctions_2_0 |
C QOpenGLWidget |
C QProcess |
C QTabBar |
C QTextEdit |
C QTreeWidget |
C QWidget |
C RateScorePair |
C RIALess |
C RIntegration |
C SequenceLess |
C SIPIncorporation | Datastructure for reporting an incorporation event
C SIPPeptide | Datastructure for reporting a peptide with one or more incorporation rates comparator for vectors of SIPPeptides based on their size. Used to sort by group size
C SizeLess |
C TOPPGNPSExport |
C UTILProteomicsLFQ |