In this namespace all the main OpenMS classes are located.
See Constants
See Exception
Classes | |
class | FeatureDecharger |
An algorithm to decharge features (i.e. as found by FeatureFinder). More... | |
class | ConsensusID |
Calculates a consensus ID from several ID runs. More... | |
class | IDFeatureMapper |
Annotates a FeatureMap instance with PeptideIdentification instances. More... | |
class | IDSpectrumMapper |
Annotate a MSExperiment instances with ProteinIdentification instances. More... | |
class | PILISScoring |
This class actually implements the E-value based scoring of PILIS. More... | |
class | ProtonDistributionModel |
A proton distribution model to calculate the proton distribution over charged peptides. More... | |
class | BaseAlignment |
Base alignment class. More... | |
class | BaseMapMatcher |
The base class of the map matching algorithm. More... | |
class | BasePairFinder |
The base class of all element pair finding algorithms. More... | |
class | BasePairwiseMapMatcher |
The base class of all pairwise point matching algorithms. More... | |
class | BaseSuperimposer |
The base class of all superimposer algorithms. More... | |
class | DelaunayPairFinder |
This class implements an element pair finding algorithm. More... | |
class | ElementPair |
A pair of element in two different maps. More... | |
class | Grid |
This class represents a D-dimensional grid over a LC/MS map. More... | |
class | GridCell |
2-dimensional grid cell over a map. More... | |
class | Group |
A group of IndexTuple. More... | |
class | IndexTuple |
This class stores some needful information of an element. More... | |
class | LinearMapping |
This class represents a linear coordinate transformation. More... | |
class | MapDewarper |
This class applies a transformation as computed by class BaseMapMatcher to a set of features. More... | |
class | MapMatcherRegression |
Map matching using linear regression. More... | |
class | PairMatcher |
The PairMatcher allows the matching of labeled features (features with a fixed distance). More... | |
class | PoseClusteringAffineSuperimposer |
Superimposer that uses a voting scheme to find a good affine transformation. More... | |
class | PoseClusteringPairwiseMapMatcher |
This class represents a point matching algorithm. More... | |
class | PoseClusteringShiftSuperimposer |
Superimposer that uses a voting scheme to find a good translation. More... | |
class | SimplePairFinder |
This class implements a simple point pair finding algorithm. More... | |
class | StarAlignment |
A star alignment class. More... | |
class | SVMWrapper |
Serves as a wrapper for the libsvm. More... | |
class | INIFileEditorWindow |
shows the ParamEditor widget in a QMainWindow with a toolbar More... | |
class | TOPPBase |
Base class for TOPP applications. More... | |
class | TOPPViewBase |
Main window of TOPPView tool. More... | |
class | AASequence |
Representation of a peptide/protein sequence. More... | |
class | EdwardsLippertIterator |
finds all Peptide Candidates with given masses and given fasta file More... | |
class | EdwardsLippertIteratorTryptic |
EdwardsLippertIterator that only retrieves tryptic seqences. More... | |
class | Element |
Representation of an element. More... | |
class | ElementDB |
Stores elements. More... | |
class | EmpiricalFormula |
Representation of an empirical formula. More... | |
class | EnzymaticDigestion |
Class for the enzymatic digestion of proteins. More... | |
class | IsotopeDistribution |
Isotope distribution class. More... | |
class | ModifierRep |
Implements modification for suffix arrays. More... | |
class | PepIterator |
Abstract base class for different peptide iterators. More... | |
class | Residue |
Representation of a residue. More... | |
class | ResidueDB |
residue data base which holds residues More... | |
class | ResidueModification |
Representation of a modification. More... | |
class | TheoreticalSpectrumGenerator |
Generates theoretical spectra with various options. More... | |
class | TrypticIterator |
finds all tryptic Peptides with every missed cleavage More... | |
class | BinnedRep |
Binned Representation of a PeakSpectrum (stick spectrum). More... | |
class | HierarchicalClustering |
Complete or single linkage clustering based on DPosition<>. More... | |
class | BinnedRepCompareFunctor |
Base class for compare functors of binned spectra which report the spectra similarity. More... | |
class | BinnedRepMutualInformation |
Mutual Information content which is calculated from binned stick spectra. More... | |
class | BinnedRepSharedPeakCount |
calculates the Shared Peak Count for two binned spectra More... | |
class | BinnedRepSpectrumContrastAngle |
calculates the spectral contrast angle between two spectra in bin representation More... | |
class | BinnedRepSumAgreeingIntensities |
calculates the sum of agreeing intensities for two spectra in binned representation More... | |
class | PeakSpectrumCompareFunctor |
Base class for compare functors of spectra; compare functors returns a similiarity value of two spectra. More... | |
class | SpectrumAlignment |
Aligns the peaks of two spectra. More... | |
class | SpectrumAlignmentScore |
Similarity score via spectra alignment. More... | |
class | SpectrumCheapDPCorr |
SpectrumCheapDPCorr calculates an optimal alignment on stick spectra. More... | |
class | SpectrumPrecursorComparator |
SpectrumPrecursorComparator compares just the parent mass of two spectra. More... | |
class | ZhangSimilarityScore |
Similarity score of Zhang. More... | |
class | Factory |
Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. More... | |
class | FactoryBase |
Base class for Factory<T>. More... | |
class | FactoryProduct |
Base class for all classes T whose objects need to be constructed by Factory<T>. More... | |
class | FuzzyStringComparator |
Fuzzy comparison of strings, tolerates numeric differences. More... | |
class | HashFunction |
General Hash Function Template. More... | |
class | ProgressLogger |
Base class for all classes that want to report their progess. More... | |
class | SingletonRegistry |
Holds pointers to unique instance of a singleton factory. More... | |
class | PreciseTime |
Time class. More... | |
class | TimeStamp |
Time stamp class. More... | |
class | VersionInfo |
Version information class. More... | |
class | BigString |
concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $) More... | |
class | ConvexHull2D |
A 2-dimensional convex hull representation (conterclockwise). More... | |
class | DataValue |
Class to hold a string or numeric value (UInt, Int, Real, DoubleReal). More... | |
class | Date |
Date Class. More... | |
class | DateTime |
DateTime Class. More... | |
class | DBoundingBox |
A D-dimensional bounding box. More... | |
class | DefaultParamHandler |
A base class for all classes handling default parameters. More... | |
class | DPosition |
Representation of a coordinate in D-dimensional space. More... | |
class | DRange |
A D-dimensional half-open interval. More... | |
class | HashMap |
Generic Hash Map Class. More... | |
struct | IsotopeCluster |
Stores information about an isotopic cluster (i.e. potential peptide charge variants). More... | |
class | Matrix |
A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access. More... | |
class | Param |
Management and storage of parameters / INI files. More... | |
class | SparseVector |
binned sparse vector implementation, which does not contain zero-elements More... | |
class | String |
A more convenient string class. More... | |
class | StringList |
String list. More... | |
class | SuffixArray |
abstract class for suffix array More... | |
class | SuffixArrayPeptideFinder |
wrapper for easy use of sufArray More... | |
class | SuffixArraySeqan |
Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum. More... | |
class | SuffixArrayTrypticCompressed |
Class that implements a suffix array for a String. It can be used to find peptide Candidates for a MS spectrum. More... | |
class | SuffixArrayTrypticSeqan |
Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum. More... | |
class | MorphFilter |
This class is the baseclass of morphological filters. More... | |
class | TopHatFilter |
This class represents a Top Hat baseline filter. More... | |
class | InternalCalibration |
A simple calibration method using linear interpolation of given reference masses. More... | |
class | TOFCalibration |
This class implements an external calibration for TOF data using external calibrant spectra. More... | |
class | DataFilters |
DataFilter array providing some convenience functions. More... | |
class | IDFilter |
used to filter identifications by different criteria More... | |
class | SignalToNoiseEstimator |
This class represents the abstract base class of a signal to noise estimator. More... | |
class | SignalToNoiseEstimatorMeanIterative |
Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities. More... | |
class | SignalToNoiseEstimatorMedian |
Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based). More... | |
class | GaussFilter |
This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform raw data. More... | |
class | SavitzkyGolayFilter |
Computes the Savitzky-Golay filter coefficients using QR decomposition. More... | |
class | SmoothFilter |
Base class for all noise filter implementations. More... | |
class | BernNorm |
BernNorm scales the peaks by ranking them and then scaling them according to rank. More... | |
class | ComplementFilter |
total intensity of peak pairs that could result from complementing fragments of charge state 1 More... | |
class | ComplementMarker |
ComplementMarker marks peak pairs which could represent y - b ion pairs. More... | |
class | FilterFunctor |
A FilterFunctor extracts some spectrum characteristics for quality assessment. More... | |
class | GoodDiffFilter |
GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid loss. More... | |
class | IntensityBalanceFilter |
IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions. More... | |
class | IsotopeDiffFilter |
IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks. More... | |
class | IsotopeMarker |
IsotopeMarker marks peak pairs which could represent an ion and its isotope. More... | |
class | LinearResampler |
Linear Resampling of raw data. More... | |
class | MarkerMower |
MarkerMower uses PeakMarker to find peaks, those that are not marked get removed. More... | |
class | NeutralLossDiffFilter |
NeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained by a neutral loss. More... | |
class | NeutralLossMarker |
NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water, ammonia). More... | |
class | NLargest |
NLargest removes all but the n largest peaks. More... | |
class | Normalizer |
Normalizer normalizes the peak intensities. More... | |
class | ParentFilter |
Parentfilter returns parent-ion charge and mass. More... | |
class | ParentPeakMower |
ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions. More... | |
class | PeakDensityFilter |
PeakDensityfilter calculates peak density. More... | |
class | PeakMarker |
PeakMarker marks peaks that seem to fulfill some criterion. More... | |
class | PreprocessingFunctor |
Base class for Spectrum preprocessing classes. More... | |
class | Scaler |
Scaler scales the peak by ranking the peaks and assigning intensity according to rank. More... | |
class | SqrtMower |
Scales the intensity of peaks to the sqrt. More... | |
class | ThresholdMower |
ThresholdMower removes all peaks below a Threshold. More... | |
class | TICFilter |
TICFilter calculates TIC. More... | |
class | WindowMower |
WindowMower augments the highest peaks in a sliding window. More... | |
class | ANDIFile |
File adapter for ANDI/MS files. More... | |
class | Base64 |
Class to encode and decode Base64. More... | |
class | ConsensusXMLFile |
This class provides Input functionality for ConsensusMaps and Output functionality for StarAlignments. More... | |
class | DBAdapter |
A class for accessing and storing data in a SQL database. More... | |
class | DBConnection |
A class for connecting to a SQL database. More... | |
class | DTA2DFile |
DTA2D File adapter. More... | |
class | DTAFile |
File adapter for DTA files. More... | |
class | FASTAFile |
This class serves for reading in FASTA files. More... | |
class | FastaIterator |
Iterator over FASTA file. More... | |
class | FastaIteratorIntern |
Iterator for a FASTA file. More... | |
class | FeaturePairsXMLFile |
This class provides Input/Output functionality for the class DFeaturePairVector. More... | |
class | FeatureXMLFile |
This class provides Input/Output functionality for feature maps. More... | |
class | FileHandler |
Facilitates file handling by file type recognition. More... | |
class | GridFile |
Provides Input/Output functionality for instances of class DGrid. More... | |
class | IdXMLFile |
Used to load and store IdXML files. More... | |
class | InspectInfile |
Inspect input file adapter. More... | |
class | InspectOutfile |
Representation of an Inspect outfile. More... | |
class | LibSVMEncoder |
Serves for encoding sequences into feature vectors. More... | |
class | MascotInfile |
Mascot input file adapter. More... | |
class | MascotOutfile |
Representation of a Mascot output file. More... | |
class | MascotXMLFile |
Used to load MascotXML files. More... | |
class | MzDataFile |
File adapter for MzData files. More... | |
class | MzXMLFile |
File adapter for MzXML 2.1 files. More... | |
class | OMSSAXMLFile |
Used to load OMSSAXML files. More... | |
class | PeakFileOptions |
Options for loading files containing peak data. More... | |
class | PeakTypeEstimator |
Estimates if the data of a spectrum is raw data or peak data. More... | |
class | PepNovoInfile |
PepNovo input file adapter. More... | |
class | PepNovoOutfile |
Representation of a PepNovo output file. More... | |
class | PersistentObject |
Base class for all persistent objects. More... | |
class | PTMXMLFile |
Used to load and store PTMXML files. More... | |
class | SequestInfile |
Sequest input file adapter. More... | |
class | SequestOutfile |
Representation of a Sequest output file. More... | |
class | TextFile |
This class provides some basic file handling methods and facilitates reading, writing and handling text files. More... | |
class | UniqueIdGenerator |
Generator for unique IDs. More... | |
class | XMLValidator |
Validator for XML files. More... | |
struct | 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. More... | |
struct | 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. More... | |
struct | 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. More... | |
class | ConsensusFeature |
A 2-dimensional consensus feature. More... | |
class | ConsensusMap |
A container for consensus elements. More... | |
class | ConsensusPeak |
A 2-dimensional consensus peak. More... | |
class | DPeak |
A D-dimensional peak. More... | |
class | DPeakArray |
Peak container implemented as an array. More... | |
class | DPeakConstReferenceArray |
This container holds pointer to the elements of another container. More... | |
class | DRawDataPoint |
D-dimensional raw data point. More... | |
class | DSpectrum |
Representation of a D-dimensional spectrum. More... | |
class | Feature |
A feature. More... | |
class | FeatureMap |
A container for (composite) features. More... | |
class | MSExperiment |
Representation of a mass spectrometry experiment. More... | |
class | MSSpectrum |
The representation of a 1D spectrum. More... | |
class | Peak1D |
A 1-dimensional peak. More... | |
class | Peak2D |
A 2-dimensional peak. More... | |
class | PickedPeak1D |
1-dimensional picked peak. More... | |
class | RangeManager |
Handles the managment of a position and intensity range. More... | |
class | InRTRange |
Predicate that determines if a spectrum lies inside/outside a specific retention time range. More... | |
class | InMSLevelRange |
Predicate that determines if a spectrum lies inside/outside a specific MS level set. More... | |
class | HasScanMode |
Predicate that determines if a spectrum has a certain scan mode. More... | |
class | IsEmptySpectrum |
Predicate that determines if a spectrum is empty. More... | |
class | InMzRange |
Predicate that determines if a peak lies inside/outside a specific m/z range. More... | |
class | InIntensityRange |
Predicate that determines if a peak lies inside/outside a specific intensity range. More... | |
class | RawDataPoint1D |
1-dimensional raw data point. More... | |
class | RawDataPoint2D |
2-dimensional raw data point. More... | |
class | Acquisition |
Information about one raw data spectrum that was combined with several other raw data spectra. More... | |
class | AcquisitionInfo |
Description of the combination of raw data to a single spectrum. More... | |
class | ContactPerson |
Contact person information. More... | |
class | Digestion |
Meta information about digestion of a sample. More... | |
class | ExperimentalSettings |
Description of the experimental settings. More... | |
class | Gradient |
Representation of a HPLC gradient. More... | |
class | HPLC |
Representation of a HPLC experiment. More... | |
class | Instrument |
Description of a MS instrument. More... | |
class | InstrumentSettings |
Description of the settings a MS Instrument was run with. More... | |
class | IonDetector |
Description of a ion detector ( part of a MS Instrument ). More... | |
class | IonSource |
Description of a ion source ( Part of a MS Instrument ). More... | |
class | MassAnalyzer |
Descripton of a mass analyzer ( Part of a MS Instrument ). More... | |
class | MetaInfo |
A Type-Name-Value tuple class. More... | |
class | MetaInfoDescription |
Description of the meta info added to each peak. More... | |
class | MetaInfoInterface |
Interface for classes that can store arbitrary meta information (Type-Name-Value tupels). More... | |
class | MetaInfoRegistry |
Registry which assigns unique integer indices to strings. More... | |
class | Modification |
Meta information about chemical modification of a sample. More... | |
class | PeptideHit |
Representation of a peptide hit. More... | |
class | PeptideIdentification |
Represents the peptide hits for a spectrum. More... | |
class | Precursor |
Precursor meta information. More... | |
class | ProcessingMethod |
Descripton of the applied preprocessing steps. More... | |
class | ProteinHit |
Representation of a protein hit. More... | |
class | ProteinIdentification |
Representation of a peptide/protein ProteinIdentification. More... | |
class | Sample |
Meta information about the sample. More... | |
class | SampleTreatment |
Base class for sample treatments (Digestion, Modification, Tagging, ...). More... | |
class | Software |
Description of the software used for processing. More... | |
class | SourceFile |
Description of a file location, used to store the origin of (meta) data. More... | |
class | SpectrumSettings |
Representation of 1D spectrum settings. More... | |
class | Tagging |
Meta information about tagging of a sample e.g. ICAT labeling. More... | |
class | ExternalAllocator |
External allocator used in MSExperiment's std::vector to handle virtual memory, mapped to a swap file. More... | |
class | ExternalAllocatorUnique |
Unique settings for an ExternalAllocator. More... | |
class | File |
Basic file handling operations. More... | |
class | MemoryMap |
Cross platform memory mapping. More... | |
class | ProcessResource |
OS based process restrictions. More... | |
class | StopWatch |
StopWatch Class. More... | |
class | BaseModel |
Abstract base class for all D-dimensional models. More... | |
class | BiGaussFitter1D |
Bigaussian distribution fitter (1-dim.) approximated using linear interpolation. More... | |
class | BiGaussModel |
Bigaussian distribution approximated using linear interpolation. More... | |
class | EmgFitter1D |
Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization. More... | |
class | EmgModel |
Exponentially modified gaussian distribution model for elution profiles. More... | |
class | ExtendedIsotopeFitter1D |
Extended isotope distribution fitter (1-dim.) approximated using linear interpolation. More... | |
class | ExtendedIsotopeModel |
Extended isotope distribution approximated using linear interpolation. More... | |
class | FeaFiModule |
Implements a module of the FeatureFinder algorithm. More... | |
class | FeatureFinder |
The main feature finder class. More... | |
class | FeatureFinderAlgorithm |
Abstract base class for FeatureFinder algorithms. More... | |
class | FeatureFinderAlgorithmPicked |
FeatureFinderAlgorithm for picked peaks. More... | |
class | FeatureFinderAlgorithmSimple |
FeatureFinderAlgorithm implementation using the Simple* modules. More... | |
class | FeatureFinderAlgorithmSimplest |
FeatureFinderAlgorithm implementation using the Simple* modules. More... | |
struct | FeatureFinderDefs |
The purpose of this struct is to provide definitions of classes and typedefs which are used throughout all FeatureFinder classes. More... | |
class | Fitter1D |
Abstract base class for all 1D-dimensional model fitter. More... | |
class | GaussFitter1D |
Gaussian distribution fitter (1-dim.) approximated using linear interpolation. More... | |
class | GaussModel |
Normal distribution approximated using linear interpolation. More... | |
class | InterpolationModel |
Abstract class for 1D-models that are approximated using linear interpolation. More... | |
class | IsotopeFitter1D |
Isotope distribution fitter (1-dim.) approximated using linear interpolation. More... | |
class | IsotopeModel |
Isotope distribution approximated using linear interpolation. More... | |
class | IsotopeWavelet |
Implements the isotope wavelet function. More... | |
class | IsotopeWaveletTransform |
A 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. More... | |
class | LevMarqFitter1D |
Abstract class for 1D-model fitter using Levenberg-Marquardt algorithm for parameter optimization. More... | |
class | LmaGaussFitter1D |
Gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization. More... | |
class | LmaGaussModel |
Normal distribution model for elution profiles. More... | |
class | LmaIsotopeFitter1D |
Isotope distribution fitter (1-dim.) approximated using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization. More... | |
class | LmaIsotopeModel |
Isotope distribution approximated using linear interpolation. More... | |
class | MaxLikeliFitter1D |
Abstract base class for all 1D-model fitters using maximum likelihood optimization. More... | |
class | ModelDescription |
Stores the name and parameters of a model. More... | |
class | ModelFitter |
Tests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model. More... | |
class | ProductModel |
Class for product models i.e. models with D independent dimensions. More... | |
class | SimpleExtender |
Implements the extension phase of the FeatureFinder as described by Groepl et al. (2005). More... | |
class | SimpleSeeder |
Simple seeding class that uses the strongest peak as next seed. More... | |
class | ContinuousWaveletTransform |
This class is the base class of the continuous wavelet transformation. More... | |
class | ContinuousWaveletTransformNumIntegration |
This class computes the continuous wavelet transformation using a marr wavelet. More... | |
class | OptimizePeakDeconvolution |
This class provides the deconvolution of peak regions using non-linear optimization. More... | |
class | OptimizePick |
This class provides the non-linear optimization of the peak paramters. More... | |
class | PeakPicker |
This class is the base class for every peak picker. More... | |
class | PeakPickerCWT |
This class implements a peak picking algorithm using wavelet techniques (as described by Lange et al. (2006) Proc. PSB-06). More... | |
class | PeakShape |
This class is a internal representation (used by the PeakPickerCWT) of a peak shape. More... | |
struct | PeakShapeType |
Peak shape type (asymmetric lorentzian or asymmetric hyperbolic secans squared). More... | |
class | TwoDOptimization |
This class provides the two-dimensional optimization of the picked peak parameters. More... | |
class | AxisTickCalculator |
Calculates ticks for a given value range. More... | |
class | AxisWidget |
Widget that represents an axis of a graph. More... | |
class | ColorSelector |
A widget for selecting a color. More... | |
class | DataTable |
A class that provides some functions for displaying data. More... | |
class | DataFilterDialog |
Dialog for creating and changing a DataFilter. More... | |
class | DBSpectrumSelectorDialog |
Dialog that allow selecting a spectrum from a DB. More... | |
class | HistogramDialog |
Dialog that show a HistogramWidget. More... | |
class | LayerStatisticsDialog |
Dialog showing statistics about the data of the current layer. More... | |
class | OpenDialog |
Open spectrum dialog. More... | |
class | SaveImageDialog |
Dialog for saving an image. More... | |
class | Spectrum1DGoToDialog |
simple goto/set visible area dialog for exact placement of the viewing window More... | |
class | Spectrum2DGoToDialog |
GoTo dialog used to zoom to a m/z and retention time range or to a feature. More... | |
class | ToolsDialog |
Dialog for executing a TOPP Tool. More... | |
class | EnhancedTabBar |
Tab bar which is aware of double clicking and has a context menu to close it. More... | |
class | HistogramWidget |
Widget which can visualize a histogram. More... | |
struct | LayerData |
Struct that stores the data for one layer. More... | |
class | MSMetaDataExplorer |
A meta data visualization widget. More... | |
class | MultiGradient |
A gradient of multiple colors and arbitrary distances between colors. More... | |
class | MultiGradientSelector |
A widget witch allows constructing gradients of multiple colors. More... | |
class | ParamEditor |
A GUI for editing or viewing a Param object. More... | |
class | PeakIcon |
Class for drawing icons with a QPainter. More... | |
class | Spectrum1DCanvas |
Canvas for visualization of one or several spectra. More... | |
class | Spectrum1DWidget |
Widget for visualization of several spectra. More... | |
class | Spectrum2DCanvas |
Canvas for 2D-visualization of peak map and feature map data. More... | |
class | Spectrum2DWidget |
Widget for 2D-visualization of peak map and feature map data. More... | |
class | Spectrum3DCanvas |
Canvas for 3D-visualization of peak map data. More... | |
class | Spectrum3DOpenGLCanvas |
OpenGL Canvas for 3D-visualization of map data. More... | |
class | Spectrum3DWidget |
Widget for 3D-visualization of map data. More... | |
class | SpectrumCanvas |
Base class for visualization canvas classes. More... | |
class | SpectrumWidget |
Base class for spectrum widgets. More... | |
class | AcquisitionInfoVisualizer |
Class that displays all meta information for AcquisitionInfo objects. More... | |
class | AcquisitionVisualizer |
Class that displays all meta information for Acquisition objects. More... | |
class | BaseVisualizer |
A base class for all visualizer classes. More... | |
class | ContactPersonVisualizer |
Class that displays all meta information for ContactPerson objects. More... | |
class | DigestionVisualizer |
Class that displays all meta information of digestion objects. More... | |
class | ExperimentalSettingsVisualizer |
Class that displays all meta information for ExperimentalSettings objects. More... | |
class | GradientVisualizer |
GradientVisualizer is a visualizer class for objects of type gradient. More... | |
class | HPLCVisualizer |
Class that displays all meta information for HPLC objects. More... | |
class | InstrumentSettingsVisualizer |
Class that displays all meta information for InstrumentSettings objects. More... | |
class | InstrumentVisualizer |
Class that displays all meta information for HPLC objects. More... | |
class | IonDetectorVisualizer |
Class that displays all meta information for IonDetector objects. More... | |
class | IonSourceVisualizer |
Class that displays all meta information for IonSource objects. More... | |
class | MassAnalyzerVisualizer |
Class that displays all meta information for MassAnalyzer objects. More... | |
class | MetaInfoDescriptionVisualizer |
Class that displays all meta information for MetaInfoDescription objects. More... | |
class | MetaInfoVisualizer |
MetaInfoVisualizer is a visualizer class for all classes that use one MetaInfo object as member. More... | |
class | ModificationVisualizer |
Class that displays all meta information of modification objects. More... | |
class | PeptideHitVisualizer |
Class that displays all meta information for PeptideHit objects. More... | |
class | PeptideIdentificationVisualizer |
Class that displays all meta information for PeptideIdentification objects. More... | |
class | PrecursorVisualizer |
Class that displays all meta information for Precursor objects. More... | |
class | ProcessingMethodVisualizer |
Class that displays all meta information for ProcessingMethod objects. More... | |
class | ProteinHitVisualizer |
Class that displays all meta information for ProteinHit objects. More... | |
class | ProteinIdentificationVisualizer |
Class that displays all meta information for ProteinIdentification objects. More... | |
class | SampleVisualizer |
Class that displays all meta information of sample objects. More... | |
class | SoftwareVisualizer |
Class that displays all meta information for Software objects. More... | |
class | SourceFileVisualizer |
Class that displays all meta information for SourceFile objects. More... | |
class | SpectrumSettingsVisualizer |
Class that displays all meta information for SpectrumSettings objects. More... | |
class | TaggingVisualizer |
Class that displays all meta information of tagging objects. More... | |
Namespaces | |
namespace | Constants |
Mathematical and physical constants namespace. | |
namespace | Exception |
Exception namespace. | |
namespace | Internal |
Namespace used to hide implementation details from users. | |
namespace | Math |
Math namespace. | |
namespace | OptimizationFunctions |
Namespace for all functions and classes needed for the gsl levenberg-marquard algorithm. | |
Typedefs | |
typedef double | intensity |
typedef OPENMS_INDEX_TYPE | Int |
Signed integer type. | |
typedef OPENMS_SIZE_TYPE | UInt |
Unsigned integer type. | |
typedef time_t | Time |
Time type. | |
typedef float | Real |
Real type. | |
typedef double | DoubleReal |
Double-precision real type. | |
typedef unsigned char | Byte |
Byte type. | |
typedef OPENMS_ULONG64_TYPE | PointerSizeUInt |
Pointer-sized unsigned int type. | |
typedef OPENMS_LONG64_TYPE | PointerSizeInt |
Pointer-sized signed int type. | |
typedef OPENMS_ULONG64_TYPE | UID |
A unique object ID. | |
typedef OPENMS_LONG64_TYPE | Offset64Int |
Offset type (64-bit). | |
typedef std::pair< unsigned int, unsigned int > | Idx |
typedef std::set< Idx > | IndexSet |
typedef MSSpectrum < RawDataPoint1D > | RawSpectrum |
Spectrum consisting of raw data points, with meta information. | |
typedef MSExperiment < RawDataPoint1D > | RawMap |
Two-dimensional map of raw data points, with meta information about experimental settings. | |
typedef MSSpectrum< Peak1D > | PeakSpectrum |
Spectrum consisting of peaks with meta information. | |
typedef MSExperiment< Peak1D > ::SpectrumType | PeakSpectrumE |
Spectrum consisting of peaks with meta information, which is contained in a PeakMap. | |
typedef MSExperiment< Peak1D > | PeakMap |
Two-dimensional map of peaks, with meta information about experimental settings. | |
Enumerations | |
enum | SVM_parameter_type { SVM_TYPE, KERNEL_TYPE, DEGREE, C, NU, P, GAMMA, PROBABILITY, SIGMA, BORDER_LENGTH } |
Parameters for the svm to be set from outside. More... | |
enum | SVM_kernel_type { OLIGO = 19, OLIGO_COMBINED } |
enum | ASCII { ASCII__BACKSPACE = '\b', ASCII__BELL = '\a', ASCII__CARRIAGE_RETURN = '\r', ASCII__HORIZONTAL_TAB = '\t', ASCII__NEWLINE = '\n', ASCII__RETURN = ASCII__NEWLINE, ASCII__SPACE = ' ', ASCII__TAB = ASCII__HORIZONTAL_TAB, ASCII__VERTICAL_TAB = '\v', ASCII__COLON = ':', ASCII__COMMA = ',', ASCII__EXCLAMATION_MARK = '!', ASCII__POINT = '.', ASCII__QUESTION_MARK = '?', ASCII__SEMICOLON = ';' } |
Functions | |
std::ostream & | operator<< (std::ostream &os, const Grid &grid) |
Print the content of Grid to a stream. | |
std::ostream & | operator<< (std::ostream &os, const GridCell &grid) |
Print the output to a stream. | |
template<typename ContainerT> | |
std::ostream & | operator<< (std::ostream &os, const Group< ContainerT > &cons) |
Print the contents to a stream. | |
template<typename ContainerT> | |
std::ostream & | operator<< (std::ostream &os, const IndexTuple< ContainerT > &cons) |
Print the contents to a stream. | |
std::ostream & | operator<< (std::ostream &os, const AASequence &peptide) |
std::istream & | operator>> (std::istream &os, const AASequence &peptide) |
std::ostream & | operator<< (std::ostream &, const Element &) |
std::ostream & | operator<< (std::ostream &, const EmpiricalFormula::EmpiricalFormula &) |
std::ostream & | operator<< (std::ostream &os, const Residue &residue) |
String | getResidueTypeName (Residue::ResidueType res_type) |
returns the ion name given as a residue type | |
std::ostream & | operator<< (std::ostream &os, const Exception::Base &e) |
std::ostream & | operator<< (std::ostream &os, const FactoryProduct &prod) |
Print the contents to a stream. | |
template<UInt D> | |
std::ostream & | operator<< (std::ostream &os, const DBoundingBox< D > &bounding_box) |
Print the contents to a stream. | |
template<UInt D> | |
DPosition< D > | operator * (DPosition< D > position, typename DPosition< D >::CoordinateType scalar) throw () |
Scalar multiplication (a bit inefficient). | |
template<UInt D> | |
DPosition< D > | operator * (typename DPosition< D >::CoordinateType scalar, DPosition< D > position) throw () |
Scalar multiplication (a bit inefficient). | |
template<UInt D> | |
std::ostream & | operator<< (std::ostream &os, const DPosition< D > &pos) |
Print the contents to a stream. | |
template<UInt D> | |
std::ostream & | operator<< (std::ostream &os, const DRange< D > &area) |
Print the contents to a stream. | |
template<typename Value> | |
std::ostream & | operator<< (std::ostream &os, const Matrix< Value > &matrix) |
Print the contents to a stream. | |
std::ostream & | operator<< (std::ostream &os, const Param ¶m) |
Output of Param to a stream. | |
template<class Cmp> | |
PointerComparator< Cmp > | pointerComparator (Cmp const &cmp) |
Make-function to create a PointerComparator from another comparator without the need to specify the template arguments. | |
template<class Cmp> | |
ReverseComparator< Cmp > | reverseComparator (Cmp const &cmp) |
Make-function to create a ReverseComparator from another comparator without the need to specify the template arguments. | |
template<typename Cmp1, typename Cmp2> | |
LexicographicComparator< Cmp1, Cmp2 > | lexicographicComparator (Cmp1 const &cmp1, Cmp2 const &cmp2) |
Make-function to create a LexicographicComparator from two other comparators without the need to specify the template arguments. | |
template<typename ContainerT> | |
std::ostream & | operator<< (std::ostream &os, const ConsensusFeature< ContainerT > &cons) |
Print the contents to a stream. | |
template<typename ConsensusElementT> | |
std::ostream & | operator<< (std::ostream &os, const ConsensusMap< ConsensusElementT > &cons_map) |
Print the contents of a ConsensusMap to a stream. | |
template<typename ContainerT> | |
std::ostream & | operator<< (std::ostream &os, const ConsensusPeak< ContainerT > &cons) |
Print the contents to a stream. | |
template<UInt D> | |
std::ostream & | operator<< (std::ostream &os, const DPeak< D > &peak) |
Print the contents to a stream. | |
template<typename PeakT, typename AllocT> | |
std::ostream & | operator<< (std::ostream &os, const DPeakArray< PeakT, AllocT > &array) |
Print the contents to a stream. | |
template<typename MapT> | |
std::ostream & | operator<< (std::ostream &os, const DPeakConstReferenceArray< MapT > &array) |
Print the contents to a stream. | |
template<UInt D> | |
std::ostream & | operator<< (std::ostream &os, const DRawDataPoint< D > &point) |
Print the contents to a stream. | |
template<typename Container> | |
std::ostream & | operator<< (std::ostream &os, const DSpectrum< Container > &rhs) |
Print the contents to a stream. | |
template<typename FeatureType> | |
std::ostream & | operator<< (std::ostream &os, const FeatureMap< FeatureType > &map) |
Print content of a feature map to a stream. | |
template<typename PeakT, typename AllocT> | |
std::ostream & | operator<< (std::ostream &os, const MSExperiment< PeakT, AllocT > &exp) |
Print the contents to a stream. | |
template<typename PeakT, typename AllocT> | |
std::ostream & | operator<< (std::ostream &os, const MSSpectrum< PeakT, AllocT > &spec) |
Print the contents to a stream. | |
std::ostream & | operator<< (std::ostream &os, const RawDataPoint1D &point) |
Print the contents to a stream. | |
std::ostream & | operator<< (std::ostream &os, const RawDataPoint2D &point) |
Print the contents to a stream. | |
std::ostream & | operator<< (std::ostream &os, const ExperimentalSettings &exp) |
Print the contents to a stream. | |
std::ostream & | operator<< (std::ostream &os, const SpectrumSettings &spec) |
Print the contents to a stream. | |
template<class T1, class T2> | |
bool | operator== (const ExternalAllocator< T1 > &, const ExternalAllocator< T2 > &) throw () |
return that all specializations of this allocator are NOT interchangeable | |
template<class T1, class T2> | |
bool | operator!= (const ExternalAllocator< T1 > &, const ExternalAllocator< T2 > &) throw () |
template<typename PeakType> | |
bool | comparator (const PeakType &a, const PeakType &b) |
std::ostream & | operator<< (std::ostream &os, const LayerData &rhs) |
Print the contents to a stream. | |
Specialized Hash Functions. | |
UInt | hashPointer (void *const ptr) throw () |
UInt | hashString (const char *str) throw () |
UInt | hashPJWString (const char *str) throw () |
UInt | hashElfString (const char *str) throw () |
template<typename T> | |
UInt | Hash (const T &key) throw () |
UInt | Hash (const String &s) throw () |
UInt | Hash (const std::string &s) throw () |
UInt | Hash (void *const &ptr) throw () |
UInt | getNextPrime (UInt l) throw () |
std::ostream & | operator<< (std::ostream &os, const PreciseTime &time) throw () |
std::ostream & | operator<< (std::ostream &os, const TimeStamp &stamp) throw () |
typedef std::pair<unsigned int,unsigned int> Idx |
typedef double intensity |
enum ASCII |
enum SVM_kernel_type |
enum SVM_parameter_type |
Parameters for the svm to be set from outside.
This type is used to specify the kind of parameter that is to be set or retrieved by the set/getParameter methods.
SVM_TYPE: the svm type cab be NU_SVR or EPSILON_SVR
KERNEL_TYPE: the kernel type
DEGREE: the degree for the polynomial- kernel
C: the C parameter of the svm NU: the nu parameter for nu-SVR P: the epsilon parameter for epsilon-SVR GAMMA: the gamma parameter of the POLY, RBF and SIGMOID kernel
bool OpenMS::comparator | ( | const PeakType & | a, | |
const PeakType & | b | |||
) | [inline] |
UInt OpenMS::getNextPrime | ( | UInt | l | ) | throw () |
Calculate the next prime number. This method returns the first prime number that is greater or equal to the number given as the argument. Only odd prime numbers are returned, the lowest number returned is 3.
String OpenMS::getResidueTypeName | ( | Residue::ResidueType | res_type | ) |
returns the ion name given as a residue type
UInt OpenMS::Hash | ( | void *const & | ptr | ) | throw () [inline] |
Pointer hash function. Use this function to hash pointers to objects.
UInt OpenMS::Hash | ( | const std::string & | s | ) | throw () [inline] |
string hash function. This method is optimized for the hashing of STL strings. In fact, it is only an inline wrapper aound hashString.
UInt OpenMS::Hash | ( | const String & | s | ) | throw () [inline] |
UInt OpenMS::Hash | ( | const T & | key | ) | throw () [inline] |
General default hash function. This method converts a given key to a UInt by calling (UInt)key
. If the key type T
is not convertible to UInt by default, a converter should be defined (operator UInt
).
key | the key to be hashed |
UInt OpenMS::hashElfString | ( | const char * | str | ) | throw () |
UInt OpenMS::hashPJWString | ( | const char * | str | ) | throw () |
UInt OpenMS::hashPointer | ( | void *const | ptr | ) | throw () |
UInt OpenMS::hashString | ( | const char * | str | ) | throw () |
LexicographicComparator< Cmp1, Cmp2 > lexicographicComparator | ( | Cmp1 const & | cmp1, | |
Cmp2 const & | cmp2 | |||
) | [inline] |
Make-function to create a LexicographicComparator from two other comparators without the need to specify the template arguments.
The usage is similar to pointerComparator() or reverseComparator(), which see.
DPosition<D> OpenMS::operator * | ( | typename DPosition< D >::CoordinateType | scalar, | |
DPosition< D > | position | |||
) | throw () [inline] |
Scalar multiplication (a bit inefficient).
DPosition<D> OpenMS::operator * | ( | DPosition< D > | position, | |
typename DPosition< D >::CoordinateType | scalar | |||
) | throw () [inline] |
Scalar multiplication (a bit inefficient).
bool OpenMS::operator!= | ( | const ExternalAllocator< T1 > & | , | |
const ExternalAllocator< T2 > & | ||||
) | throw () [inline] |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const LayerData & | rhs | |||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const SpectrumSettings & | spec | |||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const ExperimentalSettings & | exp | |||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const RawDataPoint2D & | point | |||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const RawDataPoint1D & | point | |||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const MSSpectrum< PeakT, AllocT > & | spec | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const MSExperiment< PeakT, AllocT > & | exp | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const FeatureMap< FeatureType > & | map | |||
) | [inline] |
Print content of a feature map to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const DSpectrum< Container > & | rhs | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const DRawDataPoint< D > & | point | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const DPeakConstReferenceArray< MapT > & | array | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const DPeakArray< PeakT, AllocT > & | array | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const DPeak< D > & | peak | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const ConsensusPeak< ContainerT > & | cons | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const ConsensusMap< ConsensusElementT > & | cons_map | |||
) | [inline] |
Print the contents of a ConsensusMap to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const ConsensusFeature< ContainerT > & | cons | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const Param & | param | |||
) |
Output of Param to a stream.
std::ostream & operator<< | ( | std::ostream & | os, | |
const Matrix< Value > & | matrix | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const DRange< D > & | area | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const DPosition< D > & | pos | |||
) | [inline] |
Print the contents to a stream.
std::ostream & operator<< | ( | std::ostream & | os, | |
const DBoundingBox< D > & | bounding_box | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const TimeStamp & | stamp | |||
) | throw () |
Print the contents of a TimeStamp object to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const PreciseTime & | time | |||
) | throw () |
Global stream operators for PreciseTime and TimeStamp Print the contents of a PreciseTime object to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const FactoryProduct & | prod | |||
) |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const Residue & | residue | |||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | , | |
const EmpiricalFormula::EmpiricalFormula & | ||||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | , | |
const Element & | ||||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const AASequence & | peptide | |||
) |
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const IndexTuple< ContainerT > & | cons | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const Group< ContainerT > & | cons | |||
) | [inline] |
Print the contents to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const GridCell & | grid | |||
) |
Print the output to a stream.
std::ostream& OpenMS::operator<< | ( | std::ostream & | os, | |
const Grid & | grid | |||
) |
Print the content of Grid to a stream.
bool OpenMS::operator== | ( | const ExternalAllocator< T1 > & | , | |
const ExternalAllocator< T2 > & | ||||
) | throw () [inline] |
return that all specializations of this allocator are NOT interchangeable
std::istream& OpenMS::operator>> | ( | std::istream & | os, | |
const AASequence & | peptide | |||
) |
PointerComparator< Cmp > pointerComparator | ( | Cmp const & | cmp | ) | [inline] |
Make-function to create a PointerComparator from another comparator without the need to specify the template arguments.
For example,
int i = 88, j = 99; if ( pointerComparator(std::less<int>())(&i,&j) ) { // yes, 88 < 99. }
ReverseComparator< Cmp > reverseComparator | ( | Cmp const & | cmp | ) | [inline] |
Make-function to create a ReverseComparator from another comparator without the need to specify the template arguments.
For example,
int i = 88, j = 99; if ( reverseComparator(std::less<int>())(j,i) ) { // yes, 99 > 88. }
Generated Tue Apr 1 15:36:41 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |