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OpenMS Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
AASequenceRepresentation of a peptide/protein sequence
AcquisitionInformation about one raw data spectrum that was combined with several other raw data spectra
AcquisitionInfoDescription of the combination of raw data to a single spectrum
AcquisitionInfoVisualizerClass that displays all meta information for AcquisitionInfo objects
AcquisitionVisualizerClass that displays all meta information for Acquisition objects
ANDIFileFile adapter for ANDI/MS files
ANDIHandlerRead-only File handler for ANDIFile (Version 1.0)
AreaIteratorForward iterator for an area of peaks in an experiment
AsymmetricStatisticsInternal class for asymmetric distributions
AveragePositionMaintain an average position by summing up positions with weights
AxisTickCalculatorCalculates ticks for a given value range
AxisWidgetWidget that represents an axis of a graph
BaseException base class
Base64Class to encode and decode Base64
BaseAlignmentBase alignment class
BaseMapMatcherThe base class of the map matching algorithm
BaseModelAbstract base class for all D-dimensional models
BasePairFinderThe base class of all element pair finding algorithms
BasePairwiseMapMatcherThe base class of all pairwise point matching algorithms
BaseSuperimposerThe base class of all superimposer algorithms
BaseVisualizerA base class for all visualizer classes
BasicStatisticsCalculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation
BernNormBernNorm scales the peaks by ranking them and then scaling them according to rank
BiGaussFitter1DBigaussian distribution fitter (1-dim.) approximated using linear interpolation
BiGaussModelBigaussian distribution approximated using linear interpolation
BigStringConcatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $)
BilinearInterpolationProvides access to bilinearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero
binary_function
BinnedRepBinned Representation of a PeakSpectrum (stick spectrum)
BinnedRepCompareFunctorBase class for compare functors of binned spectra which report the spectra similarity
BinnedRepMutualInformationMutual Information content which is calculated from binned stick spectra
BinnedRepSharedPeakCountCalculates the Shared Peak Count for two binned spectra
BinnedRepSpectrumContrastAngleCalculates the spectral contrast angle between two spectra in bin representation
BinnedRepSumAgreeingIntensitiesCalculates the sum of agreeing intensities for two spectra in binned representation
BufferOverflowBuffer overflow exception
CGAL::Cartesian
CGAL::Point_2
ColorSelectorA widget for selecting a color
ComplementFilterTotal intensity of peak pairs that could result from complementing fragments of charge state 1
ComplementMarkerComplementMarker marks peak pairs which could represent y - b ion pairs
ConsensusFeatureA 2-dimensional consensus feature
ConsensusIDCalculates a consensus ID from several ID runs
ConsensusMapA container for consensus elements
ConsensusPeakA 2-dimensional consensus peak
ConsensusXMLFileThis class provides Input functionality for ConsensusMaps and Output functionality for StarAlignments
ConsensusXMLHandlerXML Handler for a consensusXML
ContactPersonContact person information
ContactPersonVisualizerClass that displays all meta information for ContactPerson objects
ContinuousWaveletTransformThis class is the base class of the continuous wavelet transformation
ContinuousWaveletTransformNumIntegrationThis class computes the continuous wavelet transformation using a marr wavelet
ConversionErrorInvalid conversion exception
ConvexHull2DA 2-dimensional convex hull representation (conterclockwise)
DataFilterDialogDialog for creating and changing a DataFilter
DataFiltersDataFilter array providing some convenience functions
DataFilters::DataFilterRepresentation of a peak/feature filter combining FilterType, FilterOperation and a value
DataTableA class that provides some functions for displaying data
DataValueClass to hold a string or numeric value (UInt, Int, Real, DoubleReal)
DateDate Class
DateTimeDateTime Class
DBAdapterA class for accessing and storing data in a SQL database
DBConnectionA class for connecting to a SQL database
DBConnection::InvalidQueryException in case of an invalid Query
DBConnection::NotConnectedException in case of trying to execute a query without having established a database connection
DBoundingBoxA D-dimensional bounding box
DBSpectrumSelectorDialogDialog that allow selecting a spectrum from a DB
DefaultParamHandlerA base class for all classes handling default parameters
DelaunayPairFinderThis class implements an element pair finding algorithm
DelaunayPairFinder::GeometricTraits
DelaunayPairFinder::GeometricTraits::Construct_center_2
DelaunayPairFinder::Point
DigestionMeta information about digestion of a sample
DigestionVisualizerClass that displays all meta information of digestion objects
DIntervalBaseA base class for D-dimensional interval
DivisionByZeroDivision by zero error exception
DPeakA D-dimensional peak
DPeakArrayPeak container implemented as an array
DPeakConstReferenceArrayThis container holds pointer to the elements of another container
DPeakConstReferenceArray::DPeakConstReferenceArrayConstIteratorConstIterator for the DPeakConstReferenceArray
DPeakConstReferenceArray::DPeakConstReferenceArrayIteratorMutable iterator for the DPeakConstReferenceArray
DPositionRepresentation of a coordinate in D-dimensional space
DRangeA D-dimensional half-open interval
DRawDataPointD-dimensional raw data point
DRawDataPoint::IntensityLessCompare by getIntensity()
DRawDataPoint::NthPositionLessComparator for the i-th coordinate of the position
DRawDataPoint::PositionLessComparator for the position
DSpectrumRepresentation of a D-dimensional spectrum
DTA2DFileDTA2D File adapter
DTAFileFile adapter for DTA files
EdwardsLippertIteratorFinds all Peptide Candidates with given masses and given fasta file
EdwardsLippertIteratorTrypticEdwardsLippertIterator that only retrieves tryptic seqences
ElementRepresentation of an element
ElementDBStores elements
ElementNotFoundElement could not be found exception
ElementPairA pair of element in two different maps
EmgFitter1DExponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization
EmgFitter1D::DataHelper struct (contains the size of an area and a raw data container)
EmgModelExponentially modified gaussian distribution model for elution profiles
EmpiricalFormulaRepresentation of an empirical formula
EnhancedTabBarTab bar which is aware of double clicking and has a context menu to close it
EnzymaticDigestionClass for the enzymatic digestion of proteins
ExperimentalSettingsDescription of the experimental settings
ExperimentalSettingsVisualizerClass that displays all meta information for ExperimentalSettings objects
ExtendedIsotopeFitter1DExtended isotope distribution fitter (1-dim.) approximated using linear interpolation
ExtendedIsotopeModelExtended isotope distribution approximated using linear interpolation
ExternalAllocatorExternal allocator used in MSExperiment's std::vector to handle virtual memory, mapped to a swap file
ExternalAllocator::rebindRebind allocator to type U
ExternalAllocatorUniqueUnique settings for an ExternalAllocator
FactoryReturns FactoryProduct* based on the name of the desired concrete FactoryProduct
FactoryBaseBase class for Factory<T>
FactoryProductBase class for all classes T whose objects need to be constructed by Factory<T>
FASTAFileThis class serves for reading in FASTA files
FastaIteratorIterator over FASTA file
FastaIteratorInternIterator for a FASTA file
FeaFiModuleImplements a module of the FeatureFinder algorithm
FeatureA feature
Feature::OverallQualityLessCompare by getOverallQuality()
FeatureDechargerAn algorithm to decharge features (i.e. as found by FeatureFinder)
FeatureFinderThe main feature finder class
FeatureFinderAlgorithmAbstract base class for FeatureFinder algorithms
FeatureFinderAlgorithmPickedFeatureFinderAlgorithm for picked peaks
FeatureFinderAlgorithmPicked::IsotopePatternHelper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked
FeatureFinderAlgorithmPicked::MassTraceHelper struct for mass traces used in FeatureFinderAlgorithmPicked
FeatureFinderAlgorithmPicked::MassTracesHelper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked
FeatureFinderAlgorithmPicked::PeakInfoHelper structure that stores precalculated information for each peak used in FeatureFinderAlgorithmPicked
FeatureFinderAlgorithmPicked::SeedHelper structure for seeds used in FeatureFinderAlgorithmPicked
FeatureFinderAlgorithmPicked::TheoreticalIsotopePatternHelper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked
FeatureFinderAlgorithmSimpleFeatureFinderAlgorithm implementation using the Simple* modules
FeatureFinderAlgorithmSimplestFeatureFinderAlgorithm implementation using the Simple* modules
FeatureFinderDefsThe purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes
FeatureFinderDefs::NoSuccessorException that is thrown if a method a invalid IndexPair is given
FeatureFinderDefs::UnableToFitException used if a ModelFitter cannot fit a model i.e. data set with standard deviation of zero
FeatureMapA container for (composite) features
FeaturePairsHandlerXML Handler for a DFeaturePairVector
FeaturePairsXMLFileThis class provides Input/Output functionality for the class DFeaturePairVector
FeatureXMLFileThis class provides Input/Output functionality for feature maps
FeatureXMLHandlerXML Handler for a FeatureMap
FileBasic file handling operations
FileEmptyFile is empty
FileHandlerFacilitates file handling by file type recognition
FileNotFoundFile not found exception
FileNotReadableFile not readable exception
FilterFunctorA FilterFunctor extracts some spectrum characteristics for quality assessment
Fitter1DAbstract base class for all 1D-dimensional model fitter
FuzzyStringComparatorFuzzy comparison of strings, tolerates numeric differences
FuzzyStringComparator::AbortComparisonInternal exeption class
GaussFilterThis class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform raw data
GaussFitter1DGaussian distribution fitter (1-dim.) approximated using linear interpolation
GaussModelNormal distribution approximated using linear interpolation
GlobalExceptionHandlerOpenMS global exception handler
GoodDiffFilterGoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss
GradientRepresentation of a HPLC gradient
GradientVisualizerGradientVisualizer is a visualizer class for objects of type gradient
GridThis class represents a D-dimensional grid over a LC/MS map
GridCell2-dimensional grid cell over a map
GridFileProvides Input/Output functionality for instances of class DGrid
GridHandlerXML Handler for a vector of grid cells including their transformations
GroupA group of IndexTuple
HashFunctionGeneral Hash Function Template
HashMapGeneric Hash Map Class
HashMap::ConstIteratorHashMap const_iterator class
HashMap::IllegalKeyHashMap illegal key exception
HashMap::IteratorHashMap iterator class
HashMap::NodeHashMap node (internal use only)
HasScanModePredicate that determines if a spectrum has a certain scan mode
HierarchicalClusteringComplete or single linkage clustering based on DPosition<>
HistogramRepresentation of a histogram
HistogramDialogDialog that show a HistogramWidget
HistogramWidgetWidget which can visualize a histogram
HPLCRepresentation of a HPLC experiment
HPLCVisualizerClass that displays all meta information for HPLC objects
IDFeatureMapperAnnotates a FeatureMap instance with PeptideIdentification instances
IDFilterUsed to filter identifications by different criteria
IDSpectrumMapperAnnotate a MSExperiment instances with ProteinIdentification instances
IdXMLFileUsed to load and store IdXML files
IllegalArgumentSome Argument contains illegal values
IllegalPositionInvalid 3-dimensional position exception
IllegalSelfOperationIllegal self operation exception
IllegalTreeOperationIllegal tree operation exception
IncompatibleIteratorsIncompatible iterator exception
IndexOverflowInt overflow exception
IndexTupleThis class stores some needful information of an element
IndexTuple::IndexLessCompare by getOverallQuality()
IndexUnderflowInt underflow exception
INIFileEditorWindowShows the ParamEditor widget in a QMainWindow with a toolbar
InIntensityRangePredicate that determines if a peak lies inside/outside a specific intensity range
InMSLevelRangePredicate that determines if a spectrum lies inside/outside a specific MS level set
InMzRangePredicate that determines if a peak lies inside/outside a specific m/z range
InRTRangePredicate that determines if a spectrum lies inside/outside a specific retention time range
InspectInfileInspect input file adapter
InspectOutfileRepresentation of an Inspect outfile
InstrumentDescription of a MS instrument
InstrumentSettingsDescription of the settings a MS Instrument was run with
InstrumentSettingsVisualizerClass that displays all meta information for InstrumentSettings objects
InstrumentVisualizerClass that displays all meta information for HPLC objects
IntensityBalanceFilterIntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions
IntensityIteratorIntensity iterator for a FeatureFinderDefs::IndexSet
IntensityLessComparator that allows to compare the indices of two peaks by their intensity
InternalCalibrationA simple calibration method using linear interpolation of given reference masses
InterpolationModelAbstract class for 1D-models that are approximated using linear interpolation
InvalidIteratorInvalid iterator exception
InvalidParameterException indicating that an invalid parameter was handed over to an algorithm
InvalidRangeInvalid range exception
InvalidSizeInvalid UInt exception
InvalidValueInvalid value exception
IonDetectorDescription of a ion detector ( part of a MS Instrument )
IonDetectorVisualizerClass that displays all meta information for IonDetector objects
IonSourceDescription of a ion source ( Part of a MS Instrument )
IonSourceVisualizerClass that displays all meta information for IonSource objects
IsEmptySpectrumPredicate that determines if a spectrum is empty
IsotopeClusterStores information about an isotopic cluster (i.e. potential peptide charge variants)
IsotopeCluster::ChargedIndexSetIndex set with associated charge estimate
IsotopeDiffFilterIsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks
IsotopeDistributionIsotope distribution class
IsotopeFitter1DIsotope distribution fitter (1-dim.) approximated using linear interpolation
IsotopeMarkerIsotopeMarker marks peak pairs which could represent an ion and its isotope
IsotopeModelIsotope distribution approximated using linear interpolation
IsotopeWaveletImplements the isotope wavelet function
IsotopeWavelet::fi_Internal union for fast computation of the power function
IsotopeWaveletTransformA class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the IsotopeWaveletFF class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform
IsotopeWaveletTransform::BoxElement_Internally used data structure
iterator
LayerDataStruct that stores the data for one layer
LayerStatisticsDialogDialog showing statistics about the data of the current layer
LayerStatisticsDialog::MetaStatsValue_Struct representing the statistics about one meta information
LevMarqFitter1DAbstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization
LexicographicComparatorA 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
LibSVMEncoderServes for encoding sequences into feature vectors
LinearInterpolationProvides access to linearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero
LinearMappingThis class represents a linear coordinate transformation
LinearRegressionThis class offers functions to perform least-squares fits to a straight line model, $ Y(c,x) = c_0 + c_1 x $
LinearResamplerLinear Resampling of raw data
LmaGaussFitter1DGaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization
LmaGaussFitter1D::DataHelper struct (contains the size of an area and a raw data container)
LmaGaussModelNormal distribution model for elution profiles
LmaIsotopeFitter1DIsotope distribution fitter (1-dim.) approximated using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization
LmaIsotopeFitter1D::DataHelper struct (contains the size of an area, a raw data container, the relative abundance of i-th isotopic peak and the distance between consecutive isotopic peaks)
LmaIsotopeModelIsotope distribution approximated using linear interpolation
MapDewarperThis class applies a transformation as computed by class BaseMapMatcher to a set of features
MapMatcherRegressionMap matching using linear regression
MarkerMowerMarkerMower uses PeakMarker to find peaks, those that are not marked get removed
MascotInfileMascot input file adapter
MascotOutfileRepresentation of a Mascot output file
MascotXMLFileUsed to load MascotXML files
MascotXMLHandlerHandler that is used for parsing MascotXML data
MassAnalyzerDescripton of a mass analyzer ( Part of a MS Instrument )
MassAnalyzerVisualizerClass that displays all meta information for MassAnalyzer objects
MatrixA two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access
MaxLikeliFitter1DAbstract base class for all 1D-model fitters using maximum likelihood optimization
MemoryMapCross platform memory mapping
MetaInfoA Type-Name-Value tuple class
MetaInfoDescriptionDescription of the meta info added to each peak
MetaInfoDescriptionVisualizerClass that displays all meta information for MetaInfoDescription objects
MetaInfoInterfaceInterface for classes that can store arbitrary meta information (Type-Name-Value tupels)
MetaInfoRegistryRegistry which assigns unique integer indices to strings
MetaInfoVisualizerMetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member
MissingInformationNot all required information provided
ModelDescriptionStores the name and parameters of a model
ModelFitterTests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model
ModificationMeta information about chemical modification of a sample
ModificationVisualizerClass that displays all meta information of modification objects
ModifierRepImplements modification for suffix arrays
MorphFilterThis class is the baseclass of morphological filters
MSExperimentRepresentation of a mass spectrometry experiment
MSMetaDataExplorerA meta data visualization widget
MSSpectrumThe representation of a 1D spectrum
MSSpectrum::RTLessComparator for the retention time
MultiGradientA gradient of multiple colors and arbitrary distances between colors
MultiGradientSelectorA widget witch allows constructing gradients of multiple colors
MzDataExpSettHandlerXML handler for experimental settings of MzDataFile
MzDataFileFile adapter for MzData files
MzDataHandlerXML handler for MzDataFile
MzIteratorM/z iterator for a FeatureFinderDefs::IndexSet
MzXMLFileFile adapter for MzXML 2.1 files
MzXMLHandlerXML handlers for MzXMLFile
NeutralLossDiffFilterNeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained by a neutral loss
NeutralLossMarkerNeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water, ammonia)
NLargestNLargest removes all but the n largest peaks
NormalizerNormalizer normalizes the peak intensities
NotImplementedNot implemented exception
NullPointerNull pointer argument is invalid exception
OMSSAXMLFileUsed to load OMSSAXML files
OMSSAXMLHandlerHandler that is used for parsing OMSSAXML data
OpenDialogOpen spectrum dialog
OptimizePeakDeconvolutionThis class provides the deconvolution of peak regions using non-linear optimization
OptimizePickThis class provides the non-linear optimization of the peak paramters
OutOfGridOut of grid exception
OutOfMemoryOut of memory exception
OutOfRangeOut of range exception
pair
PairMatcherThe PairMatcher allows the matching of labeled features (features with a fixed distance)
PairMatcher::ComparatorCompare to pairs by comparing their qualities
ParamManagement and storage of parameters / INI files
Param::ParamEntryParameter entry used to store the actual information inside of a Param entry
Param::ParamIteratorForward const iterator for the Param class
Param::ParamIterator::TraceInfoStruct that captures information on entered / left nodes for ParamIterator
Param::ParamNodeNode inside a Param object which is used to build the internal tree
ParamEditorA GUI for editing or viewing a Param object
ParamEditorDelegateInternal delegate class for QTreeWidget
ParamTreeQTreeWidget that emits a signal whenever a new row is selected
ParamXMLHandlerXML Handler for Param files
ParentFilterParentfilter returns parent-ion charge and mass
ParentPeakMowerParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions
ParseErrorParse Error exception
Peak1DA 1-dimensional peak
Peak2DA 2-dimensional peak
PeakDensityFilterPeakDensityfilter calculates peak density
PeakFileOptionsOptions for loading files containing peak data
PeakIconClass for drawing icons with a QPainter
PeakMarkerPeakMarker marks peaks that seem to fulfill some criterion
PeakPickerThis class is the base class for every peak picker
PeakPickerCWTThis class implements a peak picking algorithm using wavelet techniques (as described by Lange et al. (2006) Proc. PSB-06)
PeakPickerCWT::PeakArea_Class for the internal peak representation
PeakShapeThis class is a internal representation (used by the PeakPickerCWT) of a peak shape
PeakShape::PositionLessComparator for the width
PeakShapeTypePeak shape type (asymmetric lorentzian or asymmetric hyperbolic secans squared)
PeakSpectrumCompareFunctorBase class for compare functors of spectra; compare functors returns a similiarity value of two spectra
PeakTypeEstimatorEstimates if the data of a spectrum is raw data or peak data
PenaltyFactorsClass for the penalty factors used during the optimization
PenaltyFactorsIntensityClass for the penalty factors used during the optimization
PepIteratorAbstract base class for different peptide iterators
PepNovoInfilePepNovo input file adapter
PepNovoOutfileRepresentation of a PepNovo output file
PeptideHitRepresentation of a peptide hit
PeptideHit::ScoreLessLesser predicate for scores of hits
PeptideHit::ScoreMoreGreater predicate for scores of hits
PeptideHitVisualizerClass that displays all meta information for PeptideHit objects
PeptideIdentificationRepresents the peptide hits for a spectrum
PeptideIdentificationVisualizerClass that displays all meta information for PeptideIdentification objects
PersistentObjectBase class for all persistent objects
PickedPeak1D1-dimensional picked peak
PickedPeak1D::WidthLessComparator for the width
PILISScoringThis class actually implements the E-value based scoring of PILIS
PointerComparatorWrapper 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
PoseClusteringAffineSuperimposerSuperimposer that uses a voting scheme to find a good affine transformation
PoseClusteringPairwiseMapMatcherThis class represents a point matching algorithm
PoseClusteringShiftSuperimposerSuperimposer that uses a voting scheme to find a good translation
PoseClusteringShiftSuperimposer::ShiftIntensity bounding box
PostconditionPostcondition failed exception
PreciseTimeTime class
PreconditionPrecondition failed exception
PrecursorPrecursor meta information
PrecursorPeakInternal class used to store some information about precursor ions
PrecursorVisualizerClass that displays all meta information for Precursor objects
PreprocessingFunctorBase class for Spectrum preprocessing classes
ProcessingMethodDescripton of the applied preprocessing steps
ProcessingMethodVisualizerClass that displays all meta information for ProcessingMethod objects
ProcessResourceOS based process restrictions
ProductModelClass for product models i.e. models with D independent dimensions
ProgressLoggerBase class for all classes that want to report their progess
ProteinHitRepresentation of a protein hit
ProteinHitVisualizerClass that displays all meta information for ProteinHit objects
ProteinIdentificationRepresentation of a peptide/protein ProteinIdentification
ProteinIdentification::SearchParametersSearch parameters of the DB search
ProteinIdentificationVisualizerClass that displays all meta information for ProteinIdentification objects
ProtonDistributionModelA proton distribution model to calculate the proton distribution over charged peptides
PTMXMLFileUsed to load and store PTMXML files
PTMXMLHandlerHandler that is used for parsing PTMXML data
QDate
QDateTime
QDialog
QGLWidget
QItemDelegate
QMainWindow
QTabBar
QTreeWidget
QWidget
RangeManagerHandles the managment of a position and intensity range
RawDataPoint1D1-dimensional raw data point
RawDataPoint1D::IntensityLessCompare by getIntensity()
RawDataPoint1D::PositionLessComparator for the position
RawDataPoint2D2-dimensional raw data point
RawDataPoint2D::IntensityLessCompare by getIntensity()
RawDataPoint2D::NthPositionLessComparator for the n-th coordinate of the position
RawDataPoint2D::PositionLessComparator for the position
RequiredParameterNotGivenA required parameter was not given
ResidueRepresentation of a residue
ResidueDBResidue data base which holds residues
ResidueModificationRepresentation of a modification
ReverseComparatorWrapper 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
ROCCurveROCCurves show the tradeoff in sensitivity and specitivity for binary classifiers using different cutoff values
ROCCurve::simsortdecPredicate for sort()
RtIteratorRetention time iterator for a FeatureFinderDefs::IndexSet
SampleMeta information about the sample
SampleTreatmentBase class for sample treatments (Digestion, Modification, Tagging, ...)
SampleVisualizerClass that displays all meta information of sample objects
SaveImageDialogDialog for saving an image
SavitzkyGolayFilterComputes the Savitzky-Golay filter coefficients using QR decomposition
ScalerScaler scales the peak by ranking the peaks and assigning intensity according to rank
SequestInfileSequest input file adapter
SequestOutfileRepresentation of a Sequest output file
SignalToNoiseEstimatorThis class represents the abstract base class of a signal to noise estimator
SignalToNoiseEstimator::GaussianEstimateProtected struct to store parameters my, sigma for a gaussian distribution
SignalToNoiseEstimatorMeanIterativeEstimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities
SignalToNoiseEstimatorMedianEstimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based)
SimpleExtenderImplements the extension phase of the FeatureFinder as described by Groepl et al. (2005)
SimpleExtender::IndexWithPriorityA helper structure to sort indizes by their priority
SimpleExtender::IndexWithPriority::PriorityLessCompares two indizes by priority
SimplePairFinderThis class implements a simple point pair finding algorithm
SimpleSeederSimple seeding class that uses the strongest peak as next seed
SingletonRegistryHolds pointers to unique instance of a singleton factory
SizeUnderflowUInt underflow exception
SmoothFilterBase class for all noise filter implementations
SoftwareDescription of the software used for processing
SoftwareVisualizerClass that displays all meta information for Software objects
SourceFileDescription of a file location, used to store the origin of (meta) data
SourceFileVisualizerClass that displays all meta information for SourceFile objects
SparseVectorBinned sparse vector implementation, which does not contain zero-elements
SparseVector::DoubleProxyClass DoubleProxy allows the SparseVector to differentiate between writing and reading, so zeros can be ignored
SparseVector::SparseVectorConstIteratorConst_iterator for SparseVector
SparseVector::SparseVectorIteratorIterator for SparseVector
Spectrum1DCanvasCanvas for visualization of one or several spectra
Spectrum1DGoToDialogSimple goto/set visible area dialog for exact placement of the viewing window
Spectrum1DPrefDialogPreferences dialog for Spectrum1DWidget
Spectrum1DWidgetWidget for visualization of several spectra
Spectrum2DCanvasCanvas for 2D-visualization of peak map and feature map data
Spectrum2DGoToDialogGoTo dialog used to zoom to a m/z and retention time range or to a feature
Spectrum2DPrefDialogPreferences dialog for Spectrum2DWidget
Spectrum2DWidgetWidget for 2D-visualization of peak map and feature map data
Spectrum3DCanvasCanvas for 3D-visualization of peak map data
Spectrum3DOpenGLCanvasOpenGL Canvas for 3D-visualization of map data
Spectrum3DPrefDialogPreferences dialog for Spectrum3DWidget
Spectrum3DWidgetWidget for 3D-visualization of map data
SpectrumAlignmentAligns the peaks of two spectra
SpectrumAlignmentScoreSimilarity score via spectra alignment
SpectrumCanvasBase class for visualization canvas classes
SpectrumCheapDPCorrSpectrumCheapDPCorr calculates an optimal alignment on stick spectra
SpectrumPrecursorComparatorSpectrumPrecursorComparator compares just the parent mass of two spectra
SpectrumSettingsRepresentation of 1D spectrum settings
SpectrumSettingsVisualizerClass that displays all meta information for SpectrumSettings objects
SpectrumWidgetBase class for spectrum widgets
SqrtMowerScales the intensity of peaks to the sqrt
StarAlignmentA star alignment class
StopWatchStopWatch Class
StringA more convenient string class
StringListString list
StringManagerHelper class for XML parsing that handles the memory management for conversions of Xerces strings
SuffixArrayAbstract class for suffix array
SuffixArrayPeptideFinderWrapper for easy use of sufArray
SuffixArraySeqanClass that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum
SuffixArrayTrypticCompressedClass that implements a suffix array for a String. It can be used to find peptide Candidates for a MS spectrum
SuffixArrayTrypticSeqanClass that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum
SVMWrapperServes as a wrapper for the libsvm
TaggingMeta information about tagging of a sample e.g. ICAT labeling
TaggingVisualizerClass that displays all meta information of tagging objects
TextFileThis class provides some basic file handling methods and facilitates reading, writing and handling text files
TheoreticalSpectrumGeneratorGenerates theoretical spectra with various options
ThresholdMowerThresholdMower removes all peaks below a Threshold
TICFilterTICFilter calculates TIC
TimeStampTime stamp class
TOFCalibrationThis class implements an external calibration for TOF data using external calibrant spectra
TOFCalibration::UnableToCalibrateInner Classes for Exception handling
ToolsDialogDialog for executing a TOPP Tool
TopHatFilterThis class represents a Top Hat baseline filter
TOPPBaseBase class for TOPP applications
TOPPBase::ParameterInformationStuct that captures all information of a parameter
TOPPViewBaseMain window of TOPPView tool
TOPPViewPrefDialogPreferences dialog for TOPPView
TrypticIteratorFinds all tryptic Peptides with every missed cleavage
TwoDOptimizationThis class provides the two-dimensional optimization of the picked peak parameters
TwoDOptimization::IndexLessComparator for the retention time
Ui::DataFilterDialogTemplate
Ui::LayerStatisticsDialogTemplate
Ui::OpenDialogTemplate
Ui::ParamEditorTemplate
Ui::Spectrum1DGoToDialogTemplate
Ui::Spectrum1DPrefDialogTemplate
Ui::Spectrum2DGoToDialogTemplate
Ui::Spectrum2DPrefDialogTemplate
Ui::Spectrum3DPrefDialogTemplate
Ui::TOPPViewPrefDialogTemplate
UnableToCreateFileUnable to create file exception
unary_function
UniqueIdGeneratorGenerator for unique IDs
UnregisteredParameterAn unregistered parameter was accessed
VersionInfoVersion information class
WindowMowerWindowMower augments the highest peaks in a sliding window
WrongParameterTypeA parameter was accessed with the wrong type
xercesc::DefaultHandler
xercesc::ErrorHandler
XMLFileBase class for loading/storing XML files that have a handler derived from XMLHandler
XMLHandlerBase class for XML handlers
XMLHandler::EndParsingSoftlyException that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file is needed)
XMLValidatorValidator for XML files
ZhangSimilarityScoreSimilarity score of Zhang

Generated Tue Apr 1 15:36:41 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1