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OpenMS Namespace Reference


Detailed Description

Main OpenMS namespace.

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< IdxIndexSet
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< Peak1DPeakSpectrum
 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< Peak1DPeakMap
 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 &param)
 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 Documentation

typedef std::pair<unsigned int,unsigned int> Idx

typedef std::set<Idx> IndexSet

typedef double intensity


Enumeration Type Documentation

enum ASCII

Enumerator:
ASCII__BACKSPACE 
ASCII__BELL 
ASCII__CARRIAGE_RETURN 
ASCII__HORIZONTAL_TAB 
ASCII__NEWLINE 
ASCII__RETURN 
ASCII__SPACE 
ASCII__TAB 
ASCII__VERTICAL_TAB 
ASCII__COLON 
ASCII__COMMA 
ASCII__EXCLAMATION_MARK 
ASCII__POINT 
ASCII__QUESTION_MARK 
ASCII__SEMICOLON 

enum SVM_kernel_type

Enumerator:
OLIGO 
OLIGO_COMBINED 

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

Enumerator:
SVM_TYPE 
KERNEL_TYPE 
DEGREE 
C 
NU 
P 
GAMMA 
PROBABILITY 
SIGMA 
BORDER_LENGTH 


Function Documentation

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]

String hash function. This method is optimized for the hashing of OpenMS Strings. In fact, it is only an inline wrapper around hashString.

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).

Parameters:
key the key to be hashed
Returns:
UInt the hash index

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