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Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 123456]
oCAAIndexRepresentation of selected AAIndex properties
oCAASequenceRepresentation of a peptide/protein sequence
oCFuzzyStringComparator::AbortComparisonInternal exception class
oCAccurateMassSearchResult
oCAcqusHandlerRead-only acqus File handler for XMass Analysis
oCAdduct
oCAdductInfo
oCPepXMLFile::AminoAcidModification
oCMzIdentMLDOMHandler::AnalysisSoftware
oCMSQuantifications::AnalysisSummary
oCAnnotation1DItemAn abstract class acting as an interface for the different 1D annotation items
oCAnnotationStatistics
oCAScoreImplementation 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
oCMSQuantifications::Assay
oCQcMLFile::AttachmentRepresentation of an attachment
oCAveragePosition< D >Maintain an average position by summing up positions with weights
oCAxisPainterDraws a coordinate axis. It has only static methods, that's why the constructor is private
oCAxisTickCalculatorCalculates ticks for a given value range
oCBackgroundControl
oCBackgroundIntensityBin
oCBase64Class to encode and decode Base64
oCBaseVisualizer< ObjectType >A base class for all visualizer classes
oCBaseVisualizer< Acquisition >
oCBaseVisualizer< AcquisitionInfo >
oCBaseVisualizer< ContactPerson >
oCBaseVisualizer< DataProcessing >
oCBaseVisualizer< Digestion >
oCBaseVisualizer< DocumentIdentifier >
oCBaseVisualizer< ExperimentalSettings >
oCBaseVisualizer< Gradient >
oCBaseVisualizer< HPLC >
oCBaseVisualizer< Instrument >
oCBaseVisualizer< InstrumentSettings >
oCBaseVisualizer< IonDetector >
oCBaseVisualizer< IonSource >
oCBaseVisualizer< MassAnalyzer >
oCBaseVisualizer< MetaInfoDescription >
oCBaseVisualizer< MetaInfoInterface >
oCBaseVisualizer< Modification >
oCBaseVisualizer< PeptideHit >
oCBaseVisualizer< PeptideIdentification >
oCBaseVisualizer< Precursor >
oCBaseVisualizer< Product >
oCBaseVisualizer< ProteinHit >
oCBaseVisualizer< ProteinIdentification >
oCBaseVisualizer< Sample >
oCBaseVisualizer< ScanWindow >
oCBaseVisualizer< Software >
oCBaseVisualizer< SourceFile >
oCBaseVisualizer< SpectrumSettings >
oCBaseVisualizer< Tagging >
oCbasic_string< Char >STL class
oCBasicStatistics< RealT >Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation
oCBasicStatistics< CoordinateType >
oCBigStringConcatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $)
oCBilinearInterpolation< Key, Value >Provides access to bilinearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero
oCbinary_function
oCMzMLHandlerHelper::BinaryDataBinary data representation
oCBinaryDataArrayThe datastructures used by the OpenSwath interfaces
oCBinaryTreeNodeElements of a binary tree used to represent a hierarchical clustering process
oCEnzymaticDigestion::BindingSite
oCBinInputStream
oCBinnedSpectrumThis is a binned representation of a PeakSpectrum
oCMultiplexFiltering::BlackListEntryStructure for peak blacklisting
oCFeatureFinderAlgorithmIsotopeWavelet::BoxElementInternally used data structure for the sweep line algorithm
oCIsotopeWaveletTransform< PeakType >::BoxElementInternally used data structure
oCBSpline< T >
oCBSpline2dB spline interpolation
oCBSpline< double >
oCBzip2IfstreamDecompresses files which are compressed in the bzip2 format (*.bz2)
oCCentroidData
oCCentroidPeak
oCItraqConstants::ChannelInfoStores information on an iTRAQ channel
oCChargePairRepresentation of a (putative) link between two Features, which stem from the same compound but have different charge (including different adduct ions (H+, Na+, ..)
oCChromatogramA single chromatogram
oCMzMLHandler< MapType >::ChromatogramDataData necessary to generate a single chromatogram
oCChromatogramMetaIdentifying information for a chromatogram
oCChromatogramPeakA 1-dimensional raw data point or peak for chromatograms
oCChromatogramToolsConversion class to convert chromatograms
oCOpenSwathWorkflow::ChromExtractParamsChromatogramExtractor parameters
oCEnzymaticDigestion::CleavageModel
oCClusterAnalyzerBundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's)
oCClusterFunctorBase class for cluster functors
oCClusterHierarchicalHierarchical clustering with generic clustering functions
oCClusteringGridData structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering
oCCmpHypothesesByScore
oCCmpMassTraceByMZMethod 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
oCMapAlignmentAlgorithmSpectrumAlignment::CompareInnerclass necessary for using the sort algo
oCAccurateMassSearchEngine::CompareEntryAndMass_
oCCompomerHolds information on an edge connecting two features from a (putative) charge ladder
oCConsensusIsotopePattern
oCConsensusMapNormalizerAlgorithmMedianAlgorithms of ConsensusMapNormalizer
oCConsensusMapNormalizerAlgorithmQuantileAlgorithms of ConsensusMapNormalizer
oCConsensusMapNormalizerAlgorithmThresholdAlgorithms of ConsensusMapNormalizer
oCConsoleUtils
oCset< K >::const_iteratorSTL iterator class
oCAASequence::ConstIteratorConstIterator for AASequence
oCConstRefVector< ContainerT >This vector holds pointer to the elements of another container
oCConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >ConstIterator for the ConstRefVector
oCMSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, addMassTraces >Helper class to add either general data points in set2DData or use mass traces from meta values
oCMSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, false >
oCMSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, true >
oCRawMSSignalSimulation::ContaminantInfo
oCContinuousWaveletTransformThis class is the base class of the continuous wavelet transformation
oCControlledVocabularyRepresentation of a controlled vocabulary
oCConvexHull2DA 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling
oCCubicSpline2dCubic 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
oCCV
oCCVMappingRuleRepresentation of a CV Mapping rule used by CVMappings
oCCVMappingsRepresentation of controlled vocabulary mapping rules (for PSI formats)
oCCVMappingTermRepresentation of controlled vocabulary term
oCCVReferenceControlled Vocabulary Reference
oCControlledVocabulary::CVTermRepresentation of a CV term
oCSemanticValidator::CVTermRepresentation of a parsed CV term
oCCVTermRepresentation of controlled vocabulary term
oCTwoDOptimization::DataHelper struct (contains the size of an area and a raw data container)
oCEGHFitter1D::DataHelper struct (contains the size of an area and a raw data container)
oCEmgFitter1D::DataHelper struct (contains the size of an area and a raw data container)
oCOptimizePeakDeconvolution::DataClass containing the data needed for optimization
oCOptimizePick::Data
oCMzIdentMLDOMHandler::DatabaseInput
oCDataFilters::DataFilterRepresentation of a peak/feature filter combining FilterType, FilterOperation and a value
oCDataFilterDialogTemplate
oCDataFiltersDataFilter array providing some convenience functions
oCDataValueClass to hold strings, numeric values, lists of strings and lists of numeric values
oCMzIdentMLDOMHandler::DBSequence
oCDefaultHandler
oCDefaultParamHandlerA base class for all classes handling default parameters
oCDeisotoper
oCSvmTheoreticalSpectrumGenerator::DescriptorSetA set of descriptors for a single training row
oCDIntervalBase< D >A base class for D-dimensional interval
oCDistanceMatrix< Value >A two-dimensional distance matrix, similar to OpenMS::Matrix
oCFeatureDistance::DistanceParams_Structure for storing distance parameters
oCDocumentIdentifierManage source document information
oCDocumentIDTaggerTags OpenMS file containers with a DocumentID
oCListUtils::DoubleTolerancePredicate_Predicate to check double equality with a given tolerance
oCDPeak< dimensions >Metafunction to choose among Peak1D respectively Peak2D through a template argument
oCDPosition< D, TCoordinateType >Representation of a coordinate in D-dimensional space
oCDPosition< 1 >
oCDPosition< 2 >
oCDPosition< 2, Int64 >
oCDPosition< D >
oCDPosition< DIMENSION >
oCDRichPeak< dimensions >Metafunction to choose among RichPeak1D respectively RichPeak2D through a template argument
oCDTAFileFile adapter for DTA files
oCEDTAFileFile adapter for Enhanced DTA files
oCElementRepresentation of an element
oCElementDBStores elements
oCEmgScoringScoring of an elution peak using an exponentially modified gaussian distribution model
oCEmpiricalFormulaRepresentation of an empirical formula
oCEnhancedTabBarWidgetInterfaceWidgets that are placed into an EnhancedTabBar must implement this interface
oCEnzymaticDigestionClass for the enzymatic digestion of proteins
oCEquivalenceClassAA_< T >
oCErrorHandler
oCEuclideanSimilarityCompareFunctor for 2Dpoints
oCexceptionSTL class
oCChromatogramExtractorAlgorithm::ExtractionCoordinates
oCFactoryBaseBase class for Factory<T>
oCFASTAFile::FASTAEntryFASTA entry type (identifier, description and sequence)
oCFASTAFileThis class serves for reading in FASTA files
oCFeatureEditDialogTemplate
oCFeatureFileOptionsOptions for loading files containing features
oCFeatureFinderAlgorithmPickedHelperStructsWrapper struct for all the classes needed by the FeatureFinderAlgorithmPicked and the associated classes
oCFeatureFinderAlgorithmSHCtrlA facade for various Superhirn FeatureFinder classes. Use FeatureFinderAlgorithmSH instead
oCFeatureFinderDefsThe purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes
oCFeatureHypothesis
oCFeatureLCProfile
oCIsotopeWavelet::fi_Internal union for fast computation of the power function
oCFileBasic file handling operations
oCFileHandlerFacilitates file handling by file type recognition
oCFileMappingMaps input/output files to filenames for the external program
oCFileTypesCentralizes the file types recognized by FileHandler
oCFoundProteinFunctor
oCFTPeakDetectController
oCFuzzyStringComparatorFuzzy comparison of strings, tolerates numeric differences
oCGammaDistributionFitter::GammaDistributionFitResultStruct to represent the parameters of a gamma distribution
oCGammaDistributionFitterImplements a fitter for the Gamma distribution
oCGaussFilterAlgorithmThis class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform profile data
oCGaussFitter::GaussFitResultStruct of parameters of a gaussian distribution
oCGaussFitterImplements a fitter for gaussian functions
oCSignalToNoiseEstimator< Container >::GaussianEstimateProtected struct to store parameters my, sigma for a Gaussian distribution
oCLevMarqFitter1D::GenericFunctor
oCTraceFitter::GenericFunctor
oCGlobalExceptionHandlerOpenMS global exception handler
oCglp_prob
oCGradientRepresentation of a HPLC gradient
oCGridBasedClusterBasic data structure for clustering
oCGridFeatureRepresentation of a feature in a hash grid
oCGumbelDistributionFitter::GumbelDistributionFitResultStruct to represent the parameters of a gumbel distribution
oCGumbelDistributionFitterImplements a fitter for the Gumbel distribution
oCGzipIfstreamDecompresses files which are compressed in the gzip format (*.gzip)
oCHashGrid< Cluster >Container for (2-dimensional coordinate, value) pairs
oCSimpleSearchEngine::HasInvalidPeptideLengthPredicate
oCHiddenMarkovModelHidden Markov Model implementation of PILIS
oCHistogram< ValueType, BinSizeType >Representation of a histogram
oCHMMStateHidden Markov Model State class for the Hidden Markov Model
oCHPLCRepresentation of a HPLC experiment
oCIBSpectraFileImplements the export of consensusmaps into the IBSpectra format used by isobar to load quantification results
oCIChromatogramsReaderThe interface of read-access to a list of chromatograms
oCIChromatogramsWriter
oCIDataFrameWriter
oCIDFilterUsed to filter identifications by different criteria
oCInclusionExclusionList::IEWindow
oCIFeature
oCILPDCWrapper
oCIMRMFeature
oCIMSAlphabetHolds an indexed list of bio-chemical elements
oCIMSAlphabetParser< AlphabetElementType, Container, InputSource >An abstract templatized parser to load the data that is used to initialize Alphabet objects
oCIMSAlphabetParser<>
oCIMSDataConsumer< MapType >The interface of a consumer of spectra and chromatograms
oCIMSDataConsumer< MSExperiment<> >
oCIMSDataConsumer<>
oCIMSElementRepresents a chemical atom with name and isotope distribution
oCIMSIsotopeDistributionRepresents a distribution of isotopes restricted to the first K elements
oCIndexedMzMLDecoderA class to analyze indexedmzML files and extract the offsets of individual tags
oCIndexedMzMLFileA class to read an indexedmzML file
oCIndexedMzMLFileLoaderA class to load an indexedmzML file
oCPSLPFormulation::IndexTripleStruct that holds the indices of the precursors in the feature map and the ilp formulation
oCINIUpdater
oCFuzzyStringComparator::InputLineStores information about the current input line (i.e., stream for the line and the current position in the stream)
oCInputSource
oCInspectInfileInspect input file adapter
oCInspectOutfileRepresentation of an Inspect outfile
oCTransformationModelInterpolated::InterpolatorThe class defines a generic interpolation technique used in the TransformationModelInterpolated
oCTOPPASToolVertex::IOInfoStores the information for input/output files/lists
oCCompNovoIonScoringBase::IonScore
oCDeNovoIonScoring::IonScoreIonScore
oCSvmTheoreticalSpectrumGenerator::IonTypeNested class
oCios_baseSTL class
oCProteinResolver::ISDGroup
oCISignalToNoise
oCIsobaricQuantitationMethod::IsobaricChannelInformationSummary of an isobaric quantitation channel
oCIsobaricIsotopeCorrectorPerforms isotope impurity correction on the intensities extracted from an isobaric labeling experiment
oCIsobaricNormalizerPerforms median normalization on the extracted ratios of isobaric labeling experiment
oCIsobaricQuantifierStatisticsStatistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion)
oCIsotopeClusterStores information about an isotopic cluster (i.e. potential peptide charge variants)
oCIsotopeDistributionIsotope distribution class
oCIsotopeDistributionCachePre-calculate isotope distributions for interesting mass ranges
oCFeatureFinderAlgorithmPickedHelperStructs::IsotopePatternHelper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked
oCIsotopeWaveletImplements the isotope wavelet function
oCIsotopeWaveletTransform< PeakType >A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the FeatureFinderAlgorithmIsotopeWavelet class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform
oCIsotopicDist
oCISpectraReaderThe interface of read-access to a list of spectra
oCISpectraWriter
oCISpectrumAccessThe interface of a mass spectrometry experiment
oCiterator
oCAASequence::IteratorIterator class for AASequence
oCITransitionGroup
oCItraqConstantsSome constants used throughout iTRAQ classes
oCItraqQuantifier::ItraqQuantifierStatsStatistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion)
oCJavaInfoDetect Java and retrieve information
oCKroenikFileFile adapter for Kroenik (HardKloer sibling) files
oCLayerDataClass that stores the data for one layer
oCLayerStatisticsDialogTemplate
oCLCElutionPeak
oCLCMS
oCLCMSCData
oCLibSVMEncoderServes for encoding sequences into feature vectors
oCLightModification
oCLightPeptide
oCLightProtein
oCLightTargetedExperiment
oCLightTransition
oCLinearInterpolation< Key, Value >Provides access to linearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero
oCLinearInterpolation< double >
oCLinearRegressionThis class offers functions to perform least-squares fits to a straight line model, $ Y(c,x) = c_0 + c_1 x $
oClist< T >STL class
oCListUtilsCollection of utility functions for management of vectors
oCLocalLinearMap::LLMParamDefine parameters needed by the Local Linear Map (LLM) model
oCLocalLinearMapTrained Local Linear Map (LLM) model for peak intensity prediction
oCLogStreamBuf::LogCacheStructHolds a counter of occurrences and an index for the occurrence sequence of the corresponding log message
oCLogConfigHandlerThe LogConfigHandler provides the functionality to configure the internal logging of OpenMS algorithms that use the global instances of LogStream
oCLogStreamNotifier
oCLPWrapper
oCmap< K, T >STL class
oCMapAlignmentEvaluationAlgorithmBase class for all Caap evaluation algorithms
oCMapAlignmentTransformerThe MapAlignmentTransformer class
oCMapConversion
oCAccurateMassSearchEngine::MappingEntry_
oCMappingParamFilename mappings for all input/output files
oCMarkerIonExtractor
oCMassDecomposer< ValueType, DecompositionValueType >An interface to handle decomposing of integer values/masses over a set of integer weights (alphabet)
oCMassDecompositionClass represents a decomposition of a mass into amino acids
oCMassExplainerComputes empirical formulas for given mass differences using a set of allowed elements
oCIMSAlphabet::MassSortingCriteria_Private class-functor to sort out elements in mass ascending order
oCMassTraceA container type that gathers peaks similar in m/z and moving along retention time
oCFeatureFinderAlgorithmPickedHelperStructs::MassTraceHelper struct for mass traces used in FeatureFinderAlgorithmPicked
oCmean_and_stddevFunctor to compute the mean and stddev of sequence using the std::foreach algorithm
oCMetaInfoA Type-Name-Value tuple class
oCMetaInfoInterfaceInterface for classes that can store arbitrary meta information (Type-Name-Value tuples)
oCMetaInfoRegistryRegistry which assigns unique integer indices to strings
oCLayerStatisticsDialog::MetaStatsValue_Struct representing the statistics about one meta information
oCMinimumDistanceBasic data structure for distances between clusters
oCTraceFitter::ModelData
oCModelDescription< D >Stores the name and parameters of a model
oCModificationDefinitionRepresentation of modification definition
oCModificationDefinitionsSetRepresentation of a set of modification definitions
oCMzIdentMLDOMHandler::ModificationParam
oCModificationsDBDatabase which holds all residue modifications from UniMod
oCModifiedPeptideGenerator
oCModifierRepImplements modification for suffix arrays
oCMRMRTNormalizerThe MRMRTNormalizer will find retention time peptides in data
oCMRMScoringThis class implements different scores for peaks found in SRM/MRM
oCMRMTransitionGroup< SpectrumType, TransitionType >The representation of a transition group that has information about the individual chromatograms as well as the transitions it refers to
oCMRMTransitionGroup< SpectrumT, TransitionT >
oCMS1FeatureMerger
oCMS1Signal
oCMS2ConsensusSpectrum
oCMS2Fragment
oCMS2Info
oCProteinResolver::MSDGroupRepresentation of an msd group. Contains peptides, proteins and a pointer to its ISD group
oCMsInspectFileFile adapter for MsInspect files
oCMSNumpressCoderClass to encode and decode data encoded with MSNumpress
oCMSPeak
oCMultiGradientA gradient of multiple colors and arbitrary distances between colors
oCMultiplexClustering::MultiplexDistanceScaled Euclidean distance for clustering
oCMultiplexFilterResultData structure storing all peaks (and optionally their raw data points) corresponding to one specific peak pattern
oCMultiplexFilterResultPeakData structure storing a single peak that passed all filters
oCMultiplexFilterResultRawData structure storing a single raw data point that passed all filters
oCMultiplexPeakPatternData structure for pattern of isotopic peaks
oCMzIdentMLDOMHandlerXML DOM handler for MzIdentMLFile
oCMzMLHandlerHelper
oCMzMLSpectrumDecoderA class to decode input strings that contain an mzML chromatogram or spectrum tag
oCMzTabData model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/
oCMzTabAssayMetaData
oCMzTabContactMetaData
oCMzTabCVMetaData
oCMzTabFileFile adapter for MzTab files
oCMzTabInstrumentMetaData
oCMzTabMetaData
oCMzTabModificationMetaData
oCMzTabMSRunMetaData
oCMzTabNullAbleInterface
oCMzTabPeptideSectionRow
oCMzTabProteinSectionRow
oCMzTabPSMSectionRow
oCMzTabSampleMetaData
oCMzTabSmallMoleculeSectionRow
oCMzTabSoftwareMetaData
oCMzTabStudyVariableMetaData
oCSplineSpectrum::NavigatorIterator class for access of spline packages
oCSignalToNoiseEstimatorMedianRapid::NoiseEstimatorClass to compute the noise value at a given position
oCnoncopyable
oCNonNegativeLeastSquaresSolverWrapper for a non-negative least squares (NNLS) solver
oCMSNumpressCoder::NumpressConfigConfiguration class for MSNumpress
oCOMSSACSVFileFile adapter for OMSSACSV files
oCOnDiscMSExperiment< PeakT, ChromatogramPeakT >Representation of a mass spectrometry experiment on disk
oCOpenMSOSInfo
oCOpenSwath_ScoresA structure to hold the different scores computed by OpenSWATH
oCOpenSwath_Scores_UsageA structure to store which scores should be used by the Algorithm
oCOpenSwathDataAccessHelperSeveral helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces
oCOpenSwathHelperA helper class that is used by several OpenSWATH tools
oCOpenSwathScoringA class that calls the scoring routines
oCOpenSwathTSVWriterClass to write out an OpenSwath TSV output (mProphet input)
oCMS1FeatureMerger::OPERATOR_FEATURE_TR
oCLCMS::OPERATOR_FeatureCompare
oCLCMS::OPERATOR_MZ
oCOptimizePickThis class provides the non-linear optimization of the peak parameters
oCPILISCrossValidation::OptionThis struct represents a cross validation option
oCOptimizePick::OptPeakFunctor
oCOSBinaryDataArrayThe datastructures used by the OpenSwath interfaces
oCOSChromatogramA single chromatogram
oCOSChromatogramMetaIdentifying information for a chromatogram
oCOSSpectrumThe structure that captures the generation of a peak list (including the underlying acquisitions)
oCOSSpectrumMetaIdentifying information for a spectrum
oCParamManagement and storage of parameters / INI files
oCParamEditorTemplate
oCParam::ParamEntryParameter entry used to store the actual information inside of a Param entry
oCParameterInformationStruct that captures all information of a command line parameter
oCParam::ParamIteratorForward const iterator for the Param class
oCParam::ParamNodeNode inside a Param object which is used to build the internal tree
oCIMSIsotopeDistribution::PeakStructure that represents an isotope peak - pair of mass and abundance
oCPeak1DA 1-dimensional raw data point or peak
oCPeak2DA 2-dimensional raw data point or peak
oCPeakPickerCWT::PeakArea_Class for the internal peak representation
oCPeakPickerHiRes::PeakBoundaryStructure for peak boundaries
oCPeakCandidateA small structure to hold peak candidates
oCPeakPickerMaxima::PeakCandidateThe PeakCandidate describes the output of the peak picker
oCPeakFileOptionsOptions for loading files containing peak data
oCPeakIndexIndex of a peak or feature
oCPeakIntensityPredictorPredict peak heights of peptides based on Local Linear Map model
oCPeakPickerMaximaThis 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
oCMultiplexFiltering::PeakReferenceStructure for peak position in neighbouring spectra
oCPeakShapeInternal representation of a peak shape (used by the PeakPickerCWT)
oCPeakTypeEstimatorEstimates if the data of a spectrum is raw data or peak data
oCPeakWidthEstimatorRough estimation of the peak width at m/z
oCPenaltyFactorsClass for the penalty factors used during the optimization
oCPepIteratorAbstract base class for different peptide iterators
oCPepNovoInfilePepNovo input file adapter
oCPepNovoOutfileRepresentation of a PepNovo output file
oCPILISCrossValidation::PeptideThis struct represents a peptide spectrum pair
oCPeptide
oCPeptideAndProteinQuant::PeptideDataQuantitative and associated data for a peptide
oCProteinResolver::PeptideEntryPeptide. First in silico. If experimental is set to true it is MS/MS derived
oCMzIdentMLDOMHandler::PeptideEvidence
oCPeptideEvidenceRepresentation of a peptide evidence
oCPeptideProteinMatchInformation
oCCompNovoIdentificationBase::PermutSimple class to store permutations and a score
oCPeakShape::PositionLessComparison of mz_positions
oCPrecisionWrapper< FloatingPointType >Wrapper class to implement output with appropriate precision. See precisionWrapper()
oCPrecursorMassComparator
oCFuzzyStringComparator::PrefixInfo_Wrapper for the prefix information computed for the failure report
oCProbablePhosphoSites
oCProcessData
oCProductModel< D >Class for product models i.e. models with D independent dimensions
oCProgressLoggerBase class for all classes that want to report their progress
oCProgressLogger::ProgressLoggerImplThis class represents an actual implementation of a logger
oCProtein
oCPeptideAndProteinQuant::ProteinDataQuantitative and associated data for a protein
oCProteinResolver::ProteinEntryProtein from FASTA file
oCProteinIdentification::ProteinGroupBundles multiple (e.g. indistinguishable) proteins in a group
oCProteinInference[experimental class] given a peptide quantitation, infer corresponding protein quantities
oCPSProteinInferenceThis class implements protein inference for the precursor ion selection strategies
oCIsobaricChannelExtractor::PuritySate_Small struct to capture the current state of the purity computation
oCQApplication
oCQDate
oCQDateTime
oCQDialog
oCQFileSystemWatcher
oCQGLWidget
oCQGraphicsItem
oCQGraphicsScene
oCQGraphicsView
oCQItemDelegate
oCQLineEdit
oCQListWidget
oCQMainWindow
oCQObject
oCQProcess
oCQTabBar
oCQTClusterA representation of a QT cluster used for feature grouping
oCQTextEdit
oCQTreeWidget
oCQuadraticRegression
oCQcMLFile::QualityParameterRepresentation of a quality parameter
oCQWidget
oCQWorkspace
oCRangeManager< D >Handles the management of a position and intensity range
oCRangeManager< 1 >
oCRangeManager< 2 >
oCConsensusFeature::RatioSlim struct to feed the need for systematically storing of ratios (
oCRawData
oCRealMassDecomposerHandles decomposing of non-integer values/masses over a set of non-integer weights with an error allowed
oCBase64::Reinterpreter32_Internal class needed for type-punning
oCBase64::Reinterpreter64_Internal class needed for type-punning
oCResidueRepresentation of a residue
oCResidueDBResidue data base which holds residues
oCResidueModificationRepresentation of a modification
oCProteinResolver::ResolverResult
oCRNPxlModificationMassesResult
oCRNPxlModificationsGenerator
oCRNPxlReportRow
oCRNPxlReportRowHeader
oCROCCurveROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cutoff values
oCSAValue< Index< StringSet< Peptide >, IndexWotd<> > >
oCPeptideHit::ScoreLessLesser predicate for scores of hits
oCProteinHit::ScoreLessLesser predicate for scores of hits
oCProteinHit::ScoreMoreGreater predicate for scores of hits
oCPeptideHit::ScoreMoreGreater predicate for scores of hits
oCFeatureFinderAlgorithmPickedHelperStructs::SeedHelper structure for seeds used in FeatureFinderAlgorithmPicked
oCSeedListGeneratorGenerate seed lists for feature detection
oCSequestInfileSequest input file adapter
oCSequestOutfileRepresentation of a Sequest output file
oCset< K >STL class
oCSHFeature
oCSignalToNoiseEstimatorMedianRapidEstimates the signal/noise (S/N) ratio of each data point in a scan by using the median (window based)
oCSimpleOpenMSSpectraFactoryA factory method that returns two ISpectrumAccess implementations
oCSimProteinPlain data object holding sequence and abundance information on a single protein
oCSimRandomNumberGeneratorWrapper class for random number generators used by the simulation classes
oCROCCurve::simsortdecPredicate for sort()
oCSingletonRegistryHolds pointers to unique instance of a singleton factory
oCLPWrapper::SolverParamStruct that holds the parameters of the LP solver
oCSparseVector< Value >SparseVector implementation. The container will not actually store a specified type of element - the sparse element, e.g. zero (by default)
oCSparseVector< float >
oCSparseVector< Value >::SparseVectorConstIteratorConst_iterator for SparseVector
oCSparseVector< Value >::SparseVectorConstReverseIteratorConst_reverse_iterator for SparseVector
oCSparseVector< Value >::SparseVectorIteratorRandom access iterator for SparseVector including the hop() function to jump to the next non-sparse element
oCSparseVector< Value >::SparseVectorReverseIteratorRandom access reverse iterator for SparseVector including the hop() function to jump to the next non-sparse element
oCSpecArrayFileFile adapter for SpecArray (.pepList) files
oCSpectralMatch
oCSpectralMatchScoreComparator
oCSpectrumThe structure that captures the generation of a peak list (including the underlying acquisitions)
oCSpectrum1DGoToDialogTemplate
oCSpectrum1DPrefDialogTemplate
oCSpectrum2DGoToDialogTemplate
oCSpectrum2DPrefDialogTemplate
oCSpectrum3DPrefDialogTemplate
oCSpectrumAdditionThe SpectrumAddition is used to add up individual spectra
oCSpectrumAlignmentDialogTemplate
oCMzMLHandler< MapType >::SpectrumDataData necessary to generate a single spectrum
oCMzXMLHandler< MapType >::SpectrumDataData necessary to generate a single spectrum
oCMzIdentMLDOMHandler::SpectrumIdentification
oCMzIdentMLDOMHandler::SpectrumIdentificationProtocol
oCSpectrumMetaIdentifying information for a spectrum
oCSpline2d< ValType >Wrapper for Spline interpolation
oCSplinePackageFundamental data structure for SplineSpectrum
oCSplineSpectrumData structure for spline interpolation of MS1 spectra
oCPeptideAndProteinQuant::StatisticsStatistics for processing summary
oCStopWatchStopWatch Class
oCstreambuf
oCFuzzyStringComparator::StreamElement_Stores information about characters, numbers, and white spaces loaded from the InputStream
oCStreamHandlerProvides a central class to register globally used output streams. Currently supported streams are
oCLogStreamBuf::StreamStructHolds 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
oCStringListUtilsUtilities operating on lists of Strings
oCStringManagerHelper class for XML parsing that handles the memory management for conversions of Xerces strings
oCStringUtils
oCSuffixArrayAbstract class for suffix array
oCSummarySummary of fitting results
oCSuperHirnParametersSuperHirn parameters singleton class containing all static configuration variables
oCSuperHirnUtil
oCSVMDataData structure used in SVMWrapper
oCSvmTheoreticalSpectrumGenerator::SvmModelParameterSetSimple container storing the model parameters required for simulation
oCSvmTheoreticalSpectrumGeneratorSetLoads SvmTheoreticalSpectrumGenerator instances for different charges
oCSwathMapData structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2
oCSwathWindowLoaderClass to read a file describing the Swath Windows
oCSysInfoSome static functions to get system information
oCTargetedExperimentThis class stores an prediction of an SRM/MRM transition
oCTargetedExperiment
oCTextFileThis class provides some basic file handling methods for text files
oCFeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePatternHelper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked
oCTheoreticalSpectrumGenerationDialogTemplate
oCToolDescriptionInternalToolDescription Class
oCToolExternalDetails
oCToolHandler
oCTOPPASInputFileDialogTemplate
oCTOPPASInputFilesDialogTemplate
oCTOPPASIOMappingDialogTemplate
oCTOPPASOutputFilesDialogTemplate
oCTOPPASVertexNameDialogTemplate
oCTOPPBaseBase class for TOPP applications
oCTOPPASScene::TOPPProcessStores the information for a TOPP process
oCTOPPViewOpenDialogTemplate
oCTOPPViewPrefDialogTemplate
oCParam::ParamIterator::TraceInfoStruct that captures information on entered / left nodes for ParamIterator
oCIDDecoyProbability::Transformation_Struct to be used to store a transformation (used for fitting)
oCTransformationDescriptionGeneric description of a coordinate transformation
oCTransitionHelper
oCIsotopeWaveletTransform< PeakType >::TransSpectrumInternally (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
oCTransitionTSVReader::TSVTransitionInternal structure to represent a transition
oCTwoDOptimization::TwoDOptFunctor
oCunary_function
oCUniqueIdGeneratorA generator for unique ids
oCUniqueIdIndexer< RandomAccessContainer >A base class for random access containers for classes derived from UniqueIdInterface that adds functionality to convert a unique id into an index into the container
oCUniqueIdIndexer< ConsensusMap >
oCUniqueIdIndexer< FeatureMap >
oCUniqueIdInterfaceA base class defining a common interface for all classes having a unique id
oCCVTerm::Unit
oCSparseVector< Value >::ValueProxyClass ValueProxy allows the SparseVector to differentiate between writing and reading, so zeros can be ignored See "more effective c++" section 30
oCvector< T >STL class
oCVersionInfo::VersionDetails
oCVersionInfoVersion information class
oCTOPPASVertex::VertexRoundPackageInfo for one edge and round, to be passed to next node
oCWeightsRepresents a set of weights (double values and scaled with a certain precision their integer counterparts) with a quick access
oCWeightWrapperEncapsulated weight queries to simplify mono vs average weight computation
oCInclusionExclusionList::WindowDistance_Determine distance between two spectra
oCXMLFileBase class for loading/storing XML files that have a handler derived from XMLHandler
oCXTandemInfileNoteNote representation of bioml structure used by XTandem
oCbool
oCChromatogramPeakType
oCdouble
oCfloat
oCFloatDataArray
oCInt
oCIntegerDataArray
oCpair< std::string, long >
oCPeakT
oCsize_t
oCStringDataArray
oCUInt
\Cunsigned int

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:19:08 using doxygen 1.8.5