OpenMS  2.6.0
File List
Here is a list of all files with brief descriptions:
 AAIndex.h
 AASequence.h
 AbsoluteQuantitation.h
 AbsoluteQuantitationMethod.h
 AbsoluteQuantitationMethodFile.h
 AbsoluteQuantitationStandards.h
 AbsoluteQuantitationStandardsFile.h
 AccurateMassSearch.cpp
 AccurateMassSearchEngine.h
 Acquisition.h
 AcquisitionInfo.h
 AcquisitionInfoVisualizer.h
 AcquisitionVisualizer.h
 AcqusHandler.h
 Adduct.h
 AhoCorasickAmbiguous.h
 Annotation1DCaret.h
 Annotation1DDistanceItem.h
 Annotation1DItem.h
 Annotation1DPeakItem.h
 Annotation1DTextItem.h
 Annotation1DVerticalLineItem.h
 Annotations1DContainer.h
 AppliedProcessingStep.h
 AreaIterator.h
 AScore.h
 AssayGeneratorMetabo.cpp
 AsymmetricStatistics.h
 AverageLinkage.h
 AveragePosition.h
 AxisPainter.h
 AxisTickCalculator.h
 AxisWidget.h
 BackgroundControl.h
 BackgroundIntensityBin.h
 Base64.h
 BaseFeature.h
 BaseGroupFinder.h
 BaseLabeler.h
 BaseLabeler_impl.h
 BaselineFilter.cpp
 BaseModel.h
 BaseModel_impl.h
 BaseSuperimposer.h
 BaseVisualizer.h
 BaseVisualizerGUI.h
 BasicProteinInferenceAlgorithm.h
 BasicStatistics.h
 BayesianProteinInferenceAlgorithm.h
 BernNorm.h
 BiGaussFitter1D.h
 BiGaussModel.h
 BilinearInterpolation.h
 BinaryTreeNode.h
 BinnedSharedPeakCount.h
 BinnedSpectralContrastAngle.h
 BinnedSpectrum.h
 BinnedSpectrumCompareFunctor.h
 BinnedSumAgreeingIntensities.h
 BSpline2d.h
 BuildInfo.h
 Bzip2Ifstream.h
 Bzip2InputStream.h
 CachedMzML.h
 CachedMzMLHandler.h
 CalibrationData.h
 CentroidData.h
 CentroidPeak.h
 Changelog.doxygen
 ChargePair.h
 ChromatogramExtractor.h
 ChromatogramExtractorAlgorithm.h
 ChromatogramPeak.h
 ChromatogramSettings.h
 ChromatogramTools.h
 ChromeleonFile.h
 ClassTest.h
 ClusterAnalyzer.h
 ClusteredMS2ConsensusSpectrum.h
 ClusterFunctor.h
 ClusterHierarchical.h
 ClusteringGrid.h
 ClusterMassTraces.cpp
 ClusterMassTracesByPrecursor.cpp
 CoarseIsotopePatternGenerator.h
 ColorSelector.h
 CometAdapter.cpp
 common-cmake-parameters.doxygen
 CommonDefs.h
 ComparatorUtils.h
 ComplementFilter.h
 ComplementMarker.h
 CompleteLinkage.h
 CompNovo.cpp
 CompNovoCID.cpp
 CompNovoIdentification.h
 CompNovoIdentificationBase.h
 CompNovoIdentificationCID.h
 CompNovoIonScoring.h
 CompNovoIonScoringBase.h
 CompNovoIonScoringCID.h
 Compomer.h
 CompressedInputSource.h
 ConfidenceScoring.h
 ConsensusFeature.h
 ConsensusID.cpp
 ConsensusIDAlgorithm.h
 ConsensusIDAlgorithmAverage.h
 ConsensusIDAlgorithmBest.h
 ConsensusIDAlgorithmIdentity.h
 ConsensusIDAlgorithmPEPIons.h
 ConsensusIDAlgorithmPEPMatrix.h
 ConsensusIDAlgorithmRanks.h
 ConsensusIDAlgorithmSimilarity.h
 ConsensusIDAlgorithmWorst.h
 ConsensusIsotopePattern.h
 ConsensusMap.h
 ConsensusMapMergerAlgorithm.h
 ConsensusMapNormalizer.cpp
 ConsensusMapNormalizerAlgorithmMedian.h
 ConsensusMapNormalizerAlgorithmQuantile.h
 ConsensusMapNormalizerAlgorithmThreshold.h
 ConsensusXMLFile.h
 ConsoleUtils.h
 Constants.h
 ConstRefVector.h
 ContactPerson.h
 ContactPersonVisualizer.h
 Contaminants.h
 ContinuousWaveletTransform.h
 ContinuousWaveletTransformNumIntegration.h
 ControlledVocabulary.h
 ConversionHelper.h
 ConvexHull2D.h
 CrossLinksDB.h
 CruxAdapter.cpp
 CsiFingerIdMzTabWriter.h
 CsvFile.h
 CubicSpline2d.h
 CVInspector.cpp
 CVMappingFile.h
 CVMappingRule.h
 CVMappings.h
 CVMappingTerm.h
 CVReference.h
 CVTerm.h
 CVTermList.h
 CVTermListInterface.h
 DataAccessHelper.h
 DataArrays.h
 DatabaseFilter.cpp
 DatabaseSuitability.cpp
 DataFilterDialog.h
 DataFilters.h
 DataFrameWriter.h
 DataProcessing.h
 DataProcessingSoftware.h
 DataProcessingStep.h
 DataProcessingVisualizer.h
 DataQuery.h
 DataSelectionTabs.h
 openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h
 openms/include/OpenMS/INTERFACES/DataStructures.h
 DataValue.h
 Date.h
 DateTime.h
 DBoundingBox.h
 DBSearchParam.h
 DBSuitability.h
 Decharger.cpp
 DecoyDatabase.cpp
 DecoyGenerator.h
 DefaultParamHandler.h
 openms/include/OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h
 superhirn/include/OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/Deisotoper.h
 DeMeanderize.cpp
 DeNovoAlgorithm.h
 DeNovoIdentification.h
 DeNovoIonScoring.h
 DeNovoPostScoring.h
 DetectabilitySimulation.h
 DIAHelper.h
 DIAPrescoring.h
 DIAScoring.h
 DIATreeTab.h
 Digestion.h
 DigestionEnzyme.h
 DigestionEnzymeDB.h
 DigestionEnzymeProtein.h
 DigestionEnzymeRNA.h
 DigestionVisualizer.h
 Digestor.cpp
 DigestorMotif.cpp
 DigestSimulation.h
 DIntervalBase.h
 DistanceMatrix.h
 DocumentIdentifier.h
 DocumentIdentifierVisualizer.h
 DocumentIDTagger.h
 DPeak.h
 DPosition.h
 DRange.h
 DTA2DFile.h
 DTAExtractor.cpp
 DTAFile.h
 EDTAFile.h
 EGHFitter1D.h
 EGHModel.h
 EGHTraceFitter.h
 EICExtractor.cpp
 Element.h
 ElementDB.h
 ElutionModelFitter.h
 ElutionPeakDetection.h
 EmgFitter1D.h
 EmgGradientDescent.h
 EmgModel.h
 EmgScoring.h
 EmpiricalFormula.h
 EnhancedTabBar.h
 EnhancedTabBarWidgetInterface.h
 EnhancedWorkspace.h
 EnumHelpers.h
 EnzymaticDigestion.h
 EnzymaticDigestionLogModel.h
 Epifany.cpp
 ERPairFinder.cpp
 EuclideanSimilarity.h
 Exception.h
 ExecutePipeline.cpp
 ExperimentalDesign.h
 ExperimentalDesignFile.h
 ExperimentalSettings.h
 ExperimentalSettingsVisualizer.h
 ExtendedIsotopeFitter1D.h
 ExtendedIsotopeModel.h
 ExternalCalibration.cpp
 ExternalCode.doxygen
 ExternalProcess.h
 ExternalProcessMBox.h
 Factory.h
 FactoryBase.h
 FalseDiscoveryRate.cpp
 FalseDiscoveryRate.h
 FAQ.doxygen
 FASTAContainer.h
 FASTAFile.h
 FastLowessSmoothing.h
 Feature.h
 FeatureDeconvolution.h
 FeatureDistance.h
 FeatureEditDialog.h
 FeatureFileOptions.h
 FeatureFinder.h
 FeatureFinderAlgorithm.h
 FeatureFinderAlgorithmIsotopeWavelet.h
 FeatureFinderAlgorithmMRM.h
 FeatureFinderAlgorithmPicked.h
 FeatureFinderAlgorithmPickedHelperStructs.h
 FeatureFinderAlgorithmSH.h
 FeatureFinderAlgorithmSHCtrl.h
 FeatureFinderCentroided.cpp
 FeatureFinderDefs.h
 FeatureFinderIdentification.cpp
 FeatureFinderIdentificationAlgorithm.h
 FeatureFinderIsotopeWavelet.cpp
 FeatureFinderMetabo.cpp
 FeatureFinderMetaboIdent.cpp
 FeatureFinderMRM.cpp
 FeatureFinderMultiplex.cpp
 FeatureFinderMultiplexAlgorithm.h
 FeatureFinderSuperHirn.cpp
 FeatureFindingMetabo.h
 FeatureGroupingAlgorithm.h
 FeatureGroupingAlgorithmKD.h
 FeatureGroupingAlgorithmLabeled.h
 FeatureGroupingAlgorithmQT.h
 FeatureGroupingAlgorithmUnlabeled.h
 FeatureHandle.h
 FeatureLCProfile.h
 FeatureLinkerBase.cpp
 FeatureLinkerLabeled.cpp
 FeatureLinkerUnlabeled.cpp
 FeatureLinkerUnlabeledKD.cpp
 FeatureLinkerUnlabeledQT.cpp
 FeatureMap.h
 FeatureMapping.h
 FeatureXMLFile.h
 FFEval.cpp
 FIAMSDataProcessor.h
 FIAMSScheduler.h
 FidHandler.h
 FidoAdapter.cpp
 File.h
 FileConverter.cpp
 FileFilter.cpp
 FileHandler.h
 FileInfo.cpp
 FileMerger.cpp
 FileTypes.h
 FileWatcher.h
 FilterFunctor.h
 FilterList.h
 FineIsotopePatternGenerator.h
 Fitter1D.h
 FlagSet.h
 FragmentMassError.h
 FTPeakDetectController.h
 FuzzyDiff.cpp
 FuzzyStringComparator.h
 FWHM.h
 GammaDistributionFitter.h
 GaussFilter.h
 GaussFilterAlgorithm.h
 GaussFitter.h
 GaussFitter1D.h
 GaussModel.h
 GaussTraceFitter.h
 GenericWrapper.cpp
 GlobalExceptionHandler.h
 GNPSExport.cpp
 GoodDiffFilter.h
 Gradient.h
 GradientVisualizer.h
 GridBasedCluster.h
 GridBasedClustering.h
 GridFeature.h
 GridSearch.h
 GUIHelpers.h
 GUIProgressLoggerImpl.h
 GumbelDistributionFitter.h
 GumbelMaxLikelihoodFitter.h
 GzipIfstream.h
 GzipInputStream.h
 HashGrid.h
 HDF5Connector.h
 Helpers.h
 HiddenMarkovModel.h
 HighResPrecursorMassCorrector.cpp
 Histogram.h
 HistogramDialog.h
 HistogramWidget.h
 HPLC.h
 HPLCVisualizer.h
 HyperScore.h
 IBSpectraFile.h
 ICPLLabeler.h
 IDBoostGraph.h
 IDConflictResolver.cpp
 IDConflictResolverAlgorithm.h
 IDDecoyProbability.cpp
 IDDecoyProbability.h
 Identification.h
 IdentificationData.h
 IdentificationDataConverter.h
 IdentificationHit.h
 IdentifiedCompound.h
 IdentifiedSequence.h
 IDExtractor.cpp
 IDFileConverter.cpp
 IDFilter.cpp
 IDFilter.h
 IDMapper.cpp
 IDMapper.h
 IDMassAccuracy.cpp
 IDMerger.cpp
 IDMergerAlgorithm.h
 IDPosteriorErrorProbability.cpp
 IDRipper.cpp
 IDRipper.h
 IDRTCalibration.cpp
 IDScoreGetterSetter.h
 IDScoreSwitcher.cpp
 IDScoreSwitcherAlgorithm.h
 IDSplitter.cpp
 IdXMLFile.h
 ILPDCWrapper.h
 ImageCreator.cpp
 IMSAlphabet.h
 IMSAlphabetParser.h
 IMSAlphabetTextParser.h
 IMSDataConsumer.h
 IMSElement.h
 IMSIsotopeDistribution.h
 IncludeExcludeTarget.h
 InclusionExclusionList.h
 InclusionExclusionListCreator.cpp
 IndexedMzMLDecoder.h
 IndexedMzMLFileLoader.h
 IndexedMzMLHandler.h
 INIFileEditor.cpp
 INIFileEditorWindow.cpp
 INIFileEditorWindow.h
 Init.h
 INIUpdater.cpp
 INIUpdater.h
 InputFile.h
 InputFileList.h
 InspectAdapter.cpp
 InspectInfile.h
 InspectOutfile.h
 install-linux-bin.doxygen
 install-linux.doxygen
 install-macs-bin.doxygen
 install-macs.doxygen
 install-win-bin.doxygen
 install-win.doxygen
 Instrument.h
 InstrumentSettings.h
 InstrumentSettingsVisualizer.h
 InstrumentVisualizer.h
 IntegerMassDecomposer.h
 IntensityBalanceFilter.h
 InternalCalibration.cpp
 InternalCalibration.h
 InterpolationModel.h
 IonDetector.h
 IonDetectorVisualizer.h
 IonizationSimulation.h
 IonMobilityScoring.h
 IonSource.h
 IonSourceVisualizer.h
 IsobaricAnalyzer.cpp
 IsobaricChannelExtractor.h
 IsobaricIsotopeCorrector.h
 IsobaricNormalizer.h
 IsobaricQuantifier.h
 IsobaricQuantifierStatistics.h
 IsobaricQuantitationMethod.h
 IsoSpecWrapper.h
 IsotopeCluster.h
 IsotopeDiffFilter.h
 IsotopeDistribution.h
 IsotopeDistributionCache.h
 IsotopeFitter1D.h
 IsotopeLabelingMDVs.h
 IsotopeMarker.h
 IsotopeModel.h
 IsotopePatternGenerator.h
 IsotopeWavelet.h
 IsotopeWaveletConstants.h
 IsotopeWaveletTransform.h
 IsotopicDist.h
 openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h
 openms/include/OpenMS/INTERFACES/ISpectrumAccess.h
 ITransition.h
 ItraqConstants.h
 ItraqEightPlexQuantitationMethod.h
 ItraqFourPlexQuantitationMethod.h
 ITRAQLabeler.h
 JavaInfo.h
 KDTree.h
 KDTreeFeatureMaps.h
 KDTreeFeatureNode.h
 KnownDevBugs.doxygen
 KroenikFile.h
 LabeledEval.cpp
 LabeledPairFinder.h
 LabelFreeLabeler.h
 LayerData.h
 LayerListView.h
 LayerStatisticsDialog.h
 LCElutionPeak.h
 LCMS.h
 LCMSCData.h
 LevMarqFitter1D.h
 LibSVMEncoder.h
 LinearInterpolation.h
 LinearRegression.h
 LinearRegressionWithoutIntercept.h
 LinearResampler.h
 LinearResamplerAlign.h
 ListEditor.h
 ListUtils.h
 ListUtilsIO.h
 LocalLinearMap.h
 LogConfigHandler.h
 LogStream.h
 LogWindow.h
 LowessSmoothing.h
 LPWrapper.h
 LuciphorAdapter.cpp
 openswathalgo/include/OpenMS/OPENSWATHALGO/Macros.h
 openms/include/OpenMS/CONCEPT/Macros.h
 MacrosTest.h
 Main.doxygen
 Map.h
 MapAlignerBase.h
 MapAlignerIdentification.cpp
 MapAlignerPoseClustering.cpp
 MapAlignerSpectrum.cpp
 MapAlignerTreeGuided.cpp
 MapAlignmentAlgorithmIdentification.h
 MapAlignmentAlgorithmKD.h
 MapAlignmentAlgorithmPoseClustering.h
 MapAlignmentAlgorithmSpectrumAlignment.h
 MapAlignmentAlgorithmTreeGuided.h
 MapAlignmentEvaluationAlgorithm.h
 MapAlignmentEvaluationAlgorithmPrecision.h
 MapAlignmentEvaluationAlgorithmRecall.h
 MapAlignmentTransformer.h
 MapNormalizer.cpp
 MapRTTransformer.cpp
 MapStatistics.cpp
 MapUtilities.h
 MaRaClusterAdapter.cpp
 MarkerMower.h
 MascotAdapter.cpp
 MascotAdapterOnline.cpp
 MascotGenericFile.h
 MascotInfile.h
 MascotRemoteQuery.h
 MascotXMLFile.h
 MascotXMLHandler.h
 MassAnalyzer.h
 MassAnalyzerVisualizer.h
 MassCalculator.cpp
 MassDecomposer.h
 MassDecomposition.h
 MassDecompositionAlgorithm.h
 MassExplainer.h
 MassTrace.h
 MasstraceCorrelator.h
 MassTraceDetection.h
 MassTraceExtractor.cpp
 MatchedIterator.h
 MathFunctions.h
 Matrix.h
 MatrixUtils.h
 MaxLikeliFitter1D.h
 MessagePasserFactory.h
 MetaboliteAdductDecharger.cpp
 MetaboliteFeatureDeconvolution.h
 MetaboliteSpectralMatcher.cpp
 MetaboliteSpectralMatching.h
 MetaboTargetedAssay.h
 MetaData.h
 MetaDataBrowser.h
 MetaInfo.h
 MetaInfoDescription.h
 MetaInfoDescriptionVisualizer.h
 MetaInfoInterface.h
 MetaInfoInterfaceUtils.h
 MetaInfoRegistry.h
 MetaInfoVisualizer.h
 MetaProSIP.cpp
 MissedCleavages.h
 MockObjects.h
 ModelDescription.h
 Modification.h
 ModificationDefinition.h
 ModificationDefinitionsSet.h
 ModificationsDB.h
 ModificationVisualizer.h
 ModifiedNASequenceGenerator.h
 ModifiedPeptideGenerator.h
 Modules.doxygen
 MoleculeParentMatch.h
 MoleculeQueryMatch.h
 MorpheusScore.h
 MorphologicalFilter.h
 MRMAssay.h
 MRMBatchFeatureSelector.h
 MRMDecoy.h
 MRMFeature.h
 MRMFeatureAccessOpenMS.h
 MRMFeatureFilter.h
 MRMFeatureFinderScoring.h
 MRMFeaturePicker.h
 MRMFeaturePickerFile.h
 MRMFeatureQC.h
 MRMFeatureQCFile.h
 MRMFeatureSelector.h
 MRMFragmentSelection.h
 MRMIonSeries.h
 MRMMapper.cpp
 MRMMapping.h
 MRMPairFinder.cpp
 MRMRTNormalizer.h
 MRMScoring.h
 MRMTransitionGroup.h
 MRMTransitionGroupPicker.cpp
 MRMTransitionGroupPicker.h
 MS1FeatureMerger.h
 MS2ConsensusSpectrum.h
 MS2Feature.h
 MS2File.h
 MS2Fragment.h
 Ms2IdentificationRate.h
 MS2Info.h
 Ms2SpectrumStats.h
 MSChromatogram.h
 MSDataAggregatingConsumer.h
 MSDataCachedConsumer.h
 MSDataChainingConsumer.h
 MSDataSqlConsumer.h
 MSDataStoringConsumer.h
 MSDataTransformingConsumer.h
 MSDataWritingConsumer.h
 MSExperiment.h
 MSFraggerAdapter.cpp
 MSGFPlusAdapter.cpp
 MsInspectFile.h
 MSNumpress.h
 MSNumpressCoder.h
 MSPeak.h
 MSPFile.h
 MSPGenericFile.h
 MSQuantifications.h
 MSSim.h
 MSSimulator.cpp
 MSSpectrum.h
 MSstatsConverter.cpp
 MSstatsFile.h
 MultiGradient.h
 MultiGradientSelector.h
 MultiplexClustering.h
 MultiplexDeltaMasses.h
 MultiplexDeltaMassesGenerator.h
 MultiplexFilteredMSExperiment.h
 MultiplexFilteredPeak.h
 MultiplexFiltering.h
 MultiplexFilteringCentroided.h
 MultiplexFilteringProfile.h
 MultiplexIsotopicPeakPattern.h
 MultiplexResolver.cpp
 MultiplexSatelliteCentroided.h
 MultiplexSatelliteProfile.h
 MyriMatchAdapter.cpp
 MzCalibration.h
 MzDataFile.h
 MzDataHandler.h
 MzDataValidator.h
 MzIdentMLDOMHandler.h
 MzIdentMLFile.h
 MzIdentMLHandler.h
 MzIdentMLValidator.h
 MzMLFile.h
 MzMLHandler.h
 MzMLHandlerHelper.h
 MzMLSpectrumDecoder.h
 MzMLSplitter.cpp
 MzMLSqliteHandler.h
 MzMLSqliteSwathHandler.h
 MzMLValidator.h
 MzQuantMLFile.h
 MzQuantMLHandler.h
 MzQuantMLValidator.h
 MzTab.h
 MzTabExporter.cpp
 MzTabFile.h
 MZTrafoModel.h
 MzXMLFile.h
 MzXMLHandler.h
 NASequence.h
 NetworkGetRequest.h
 NeutralLossDiffFilter.h
 NeutralLossMarker.h
 NLargest.h
 NNLS.h
 NoiseFilterGaussian.cpp
 NoiseFilterSGolay.cpp
 NonNegativeLeastSquaresSolver.h
 NoopMSDataConsumer.h
 Normalizer.h
 NovorAdapter.cpp
 NucleicAcidSearchEngine.cpp
 NucleicAcidSpectrumGenerator.h
 O18Labeler.h
 OfflinePrecursorIonSelection.h
 OMSSAAdapter.cpp
 OMSSACSVFile.h
 OMSSAXMLFile.h
 OnDiscMSExperiment.h
 OpenMS_Tutorial.doxygen
 OpenMS_Tutorial_html.doxygen
 OpenMSInfo.cpp
 OpenPepXL.cpp
 OpenPepXLAlgorithm.h
 OpenPepXLLF.cpp
 OpenPepXLLFAlgorithm.h
 OpenSwathAnalyzer.cpp
 OpenSwathAssayGenerator.cpp
 OpenSwathBase.h
 OpenSwathChromatogramExtractor.cpp
 OpenSwathConfidenceScoring.cpp
 OpenSwathDecoyGenerator.cpp
 OpenSwathDIAPreScoring.cpp
 OpenSwathFeatureXMLToTSV.cpp
 OpenSwathFileSplitter.cpp
 OpenSwathHelper.h
 OpenSwathMzMLFileCacher.cpp
 OpenSwathOSWWriter.h
 OpenSwathRewriteToFeatureXML.cpp
 OpenSwathRTNormalizer.cpp
 OpenSwathScores.h
 OpenSwathScoring.h
 OpenSwathTSVWriter.h
 OpenSwathWorkflow.cpp
 OpenSwathWorkflow.h
 OptimizePeakDeconvolution.h
 OptimizePick.h
 OPXLDataStructs.h
 OPXLHelper.h
 OPXLSpectrumProcessingAlgorithms.h
 OSWData.h
 OSWFile.h
 OutputDirectory.h
 Param.h
 ParamEditor.h
 ParameterInformation.h
 ParamXMLFile.h
 ParamXMLHandler.h
 ParentMolecule.h
 ParentMoleculeGroup.h
 ParentPeakMower.h
 Peak1D.h
 Peak2D.h
 PeakAlignment.h
 PeakFileOptions.h
 PeakIndex.h
 PeakIntegrator.h
 PeakIntensityPredictor.h
 PeakMarker.h
 PeakPickerCWT.h
 PeakPickerHiRes.cpp
 PeakPickerHiRes.h
 PeakPickerIterative.cpp
 PeakPickerIterative.h
 PeakPickerMaxima.h
 PeakPickerMRM.h
 PeakPickerSH.h
 PeakPickerWavelet.cpp
 PeakShape.h
 PeakSpectrumCompareFunctor.h
 PeakTypeEstimator.h
 PeakWidthEstimator.h
 PepNovoAdapter.cpp
 PepNovoInfile.h
 PepNovoOutfile.h
 PeptideAndProteinQuant.h
 PeptideEvidence.h
 PeptideHit.h
 PeptideHitVisualizer.h
 PeptideIdentification.h
 PeptideIdentificationVisualizer.h
 PeptideIndexer.cpp
 PeptideIndexing.h
 PeptideMass.h
 PeptideProteinResolution.h
 PepXMLFile.h
 PepXMLFileMascot.h
 PercolatorAdapter.cpp
 PercolatorFeatureSetHelper.h
 PercolatorOutfile.h
 PhosphoScoring.cpp
 Plot1DCanvas.h
 Plot1DGoToDialog.h
 Plot1DPrefDialog.h
 Plot1DWidget.h
 Plot2DCanvas.h
 Plot2DGoToDialog.h
 Plot2DPrefDialog.h
 Plot2DWidget.h
 Plot3DCanvas.h
 Plot3DOpenGLCanvas.h
 Plot3DPrefDialog.h
 Plot3DWidget.h
 PlotCanvas.h
 PlotWidget.h
 PoseClusteringAffineSuperimposer.h
 PoseClusteringShiftSuperimposer.h
 PosteriorErrorProbabilityModel.h
 PrecisionWrapper.h
 Precursor.h
 PrecursorCorrection.h
 PrecursorIonSelection.h
 PrecursorIonSelectionPreprocessing.h
 PrecursorIonSelector.cpp
 PrecursorMassCorrector.cpp
 PrecursorPurity.h
 PrecursorVisualizer.h
 ProcessData.h
 Product.h
 ProductModel.h
 ProductVisualizer.h
 ProgressLogger.h
 ProteaseDB.h
 ProteaseDigestion.h
 ProteinHit.h
 ProteinHitVisualizer.h
 ProteinIdentification.h
 ProteinIdentificationVisualizer.h
 ProteinInference.cpp
 ProteinInference.h
 ProteinQuantifier.cpp
 ProteinResolver.cpp
 ProteinResolver.h
 ProteomicsLFQ.cpp
 ProtonDistributionModel.h
 ProtXMLFile.h
 PScore.h
 PSLPFormulation.h
 PSMFeatureExtractor.cpp
 PSProteinInference.h
 PTModel.cpp
 PTMXMLFile.h
 PTMXMLHandler.h
 PTPredict.cpp
 PyOpenMS.doxygen
 PythonInfo.h
 PythonModuleRequirement.h
 PythonSelector.h
 QApplicationTOPP.cpp
 QApplicationTOPP.h
 QCBase.h
 QCCalculator.cpp
 QCEmbedder.cpp
 QCExporter.cpp
 QCExtractor.cpp
 QCImporter.cpp
 QCMerger.cpp
 QcMLFile.h
 QCShrinker.cpp
 QTCluster.h
 QTClusterFinder.h
 QuadraticRegression.h
 QualityControl.cpp
 QuantitativeExperimentalDesign.h
 QueryMatchGroup.h
 QuickStart.doxygen
 RAIICleanup.h
 RangeManager.h
 RangeUtils.h
 RANSAC.h
 RANSACModel.h
 RANSACModelLinear.h
 RANSACModelQuadratic.h
 RawData.h
 RawMSSignalSimulation.h
 RawTandemMSSignalSimulation.h
 ReactionMonitoringTransition.h
 RealMassDecomposer.h
 RecentFilesMenu.h
 RegressionUtils.h
 Resampler.cpp
 Residue.h
 ResidueDB.h
 ResidueModification.h
 Ribonucleotide.h
 RibonucleotideDB.h
 RichPeak2D.h
 RNADigestor.cpp
 RNAMassCalculator.cpp
 RNaseDB.h
 RNaseDigestion.h
 RNPxlFragmentAnnotationHelper.h
 RNPxlMarkerIonExtractor.h
 RNPxlModificationsGenerator.h
 RNPxlReport.h
 RNPxlSearch.cpp
 RNPxlXICFilter.cpp
 ROCCurve.h
 RTAlignment.h
 RTEvaluation.cpp
 RTModel.cpp
 RTPredict.cpp
 RTSimulation.h
 RWrapper.h
 Sample.h
 SampleTreatment.h
 SampleVisualizer.h
 SaveImageDialog.h
 SavitzkyGolayFilter.h
 Scaler.h
 ScanWindow.h
 ScanWindowVisualizer.h
 ScoredProcessingResult.h
 ScoreType.h
 Scoring.h
 SeedListGenerator.cpp
 SeedListGenerator.h
 SemanticValidator.cpp
 SemanticValidator.h
 SeqanIncludeWrapper.h
 SequenceCoverageCalculator.cpp
 SequestInfile.h
 SequestOutfile.h
 SHFeature.h
 SignalToNoiseEstimator.h
 SignalToNoiseEstimatorMeanIterative.h
 SignalToNoiseEstimatorMedian.h
 SignalToNoiseEstimatorMedianRapid.h
 SILACLabeler.h
 SimpleOpenMSSpectraAccessFactory.h
 SimplePairFinder.h
 SimpleSearchEngine.cpp
 SimpleSearchEngineAlgorithm.h
 SimpleSVM.h
 SimpleTSGXLMS.h
 SimTypes.h
 SingleLinkage.h
 SingletonRegistry.h
 SiriusAdapter.cpp
 SiriusAdapterAlgorithm.h
 SiriusFragmentAnnotation.h
 SiriusMSConverter.h
 SiriusMzTabWriter.h
 Software.h
 SoftwareVisualizer.h
 SONARScoring.h
 SourceFile.h
 SourceFileVisualizer.h
 SpecArrayFile.h
 SpecLibCreator.cpp
 SpecLibSearcher.cpp
 SpectraFilterBernNorm.cpp
 SpectraFilterMarkerMower.cpp
 SpectraFilterNLargest.cpp
 SpectraFilterNormalizer.cpp
 SpectraFilterParentPeakMower.cpp
 SpectraFilterScaler.cpp
 SpectraFilterSqrtMower.cpp
 SpectraFilterThresholdMower.cpp
 SpectraFilterWindowMower.cpp
 SpectraIDViewTab.h
 SpectraMerger.cpp
 SpectraMerger.h
 SpectraSTSearchAdapter.cpp
 SpectraSTSimilarityScore.h
 SpectraTreeTab.h
 SpectrumAccessOpenMS.h
 SpectrumAccessOpenMSCached.h
 SpectrumAccessOpenMSInMemory.h
 SpectrumAccessQuadMZTransforming.h
 SpectrumAccessSqMass.h
 SpectrumAccessTransforming.h
 SpectrumAddition.h
 SpectrumAlignment.h
 SpectrumAlignmentDialog.h
 SpectrumAlignmentScore.h
 SpectrumAnnotator.h
 SpectrumCheapDPCorr.h
 SpectrumHelper.h
 SpectrumHelpers.h
 SpectrumIdentification.h
 SpectrumLookup.h
 SpectrumMetaDataLookup.h
 SpectrumPrecursorComparator.h
 SpectrumSettings.h
 SpectrumSettingsVisualizer.h
 SplineBisection.h
 SplineInterpolatedPeaks.h
 SplinePackage.h
 SqliteConnector.h
 SqMassFile.h
 SqrtMower.h
 StablePairFinder.h
 StandardDeclarations.h
 StandardTypes.h
 StaticModification.cpp
 StatisticFunctions.h
 StatsHelpers.h
 SteinScottImproveScore.h
 StopWatch.h
 StreamHandler.h
 String.h
 StringListUtils.h
 StringUtils.h
 SuperHirnParameters.h
 SuperHirnUtil.h
 SvmTheoreticalSpectrumGenerator.h
 SvmTheoreticalSpectrumGeneratorSet.h
 SvmTheoreticalSpectrumGeneratorTrainer.cpp
 SvmTheoreticalSpectrumGeneratorTrainer.h
 SVMWrapper.h
 SVOutStream.h
 SwathFile.h
 SwathFileConsumer.h
 SwathLibraryStats.h
 SwathMap.h
 SwathMapMassCorrection.h
 SwathQC.h
 SwathTabWidget.h
 SwathWindowLoader.h
 SwathWizard.cpp
 SwathWizardBase.cpp
 SwathWizardBase.h
 SysInfo.h
 TableView.h
 Tagger.h
 Tagging.h
 TaggingVisualizer.h
 TargetedExperiment.h
 TargetedExperimentHelper.h
 TargetedFileConverter.cpp
 TargetedSpectraExtractor.h
 TextExporter.cpp
 TextFile.h
 TheoreticalSpectrumGenerationDialog.h
 TheoreticalSpectrumGenerator.h
 TheoreticalSpectrumGeneratorXLMS.h
 ThresholdMower.h
 TIC.h
 TICCalculator.cpp
 TICFilter.h
 TMTElevenPlexQuantitationMethod.h
 TMTSixPlexQuantitationMethod.h
 TMTSixteenPlexQuantitationMethod.h
 TMTTenPlexQuantitationMethod.h
 TOFCalibration.cpp
 TOFCalibration.h
 ToolDescription.h
 ToolDescriptionFile.h
 ToolDescriptionHandler.h
 ToolHandler.h
 ToolsDialog.h
 TOPP.doxygen
 TOPP_advanced.doxygen
 TOPP_concepts.doxygen
 TOPP_scripting.doxygen
 TOPP_Tutorial_html.doxygen
 TOPPAS.cpp
 TOPP_tutorial/TOPPAS.doxygen
 doxygen/public/TOPPAS.doxygen
 TOPPASBase.cpp
 TOPPASBase.h
 TOPPASEdge.h
 TOPPASInputFileDialog.h
 TOPPASInputFileListVertex.h
 TOPPASInputFilesDialog.h
 TOPPASIOMappingDialog.h
 TOPPASMergerVertex.h
 TOPPASOutputFileListVertex.h
 TOPPASOutputFilesDialog.h
 TOPPASResource.h
 TOPPASResources.h
 TOPPASScene.h
 TOPPASSplitterVertex.h
 TOPPASToolConfigDialog.h
 TOPPASToolVertex.h
 TOPPASTreeView.h
 TOPPASVertex.h
 TOPPASVertexNameDialog.h
 TOPPASWidget.h
 TOPPBase.h
 TOPPView.cpp
 TOPPView_calling_topp.doxygen
 TOPPView_interface.doxygen
 TOPPViewBase.cpp
 TOPPViewBase.h
 TOPPViewMenu.h
 TOPPViewOpenDialog.h
 TOPPViewPrefDialog.h
 TraceFitter.h
 TraMLFile.h
 TraMLHandler.h
 TraMLValidator.h
 TransformationDescription.h
 TransformationEvaluation.cpp
 TransformationModel.h
 TransformationModelBSpline.h
 TransformationModelInterpolated.h
 TransformationModelLinear.h
 TransformationModelLowess.h
 TransformationXMLFile.h
 TransitionExperiment.h
 TransitionHelper.h
 TransitionPQPFile.h
 Transitions.h
 TransitionTSVFile.h
 TreeView.h
 TriqlerConverter.cpp
 TriqlerFile.h
 TVControllerBase.h
 TVDIATreeTabController.h
 TVIdentificationViewController.h
 TVSpectraViewController.h
 TwoDOptimization.h
 TypeAsString.h
 Types.h
 UnimodXMLFile.h
 UnimodXMLHandler.h
 UniqueIdGenerator.h
 UniqueIdIndexer.h
 UniqueIdInterface.h
 UpdateCheck.h
 UTILS.doxygen
 VersionInfo.h
 Weights.h
 WeightWrapper.h
 WindowMower.h
 XFDR.cpp
 XFDRAlgorithm.h
 XMassFile.h
 XMLFile.h
 XMLHandler.h
 XMLValidator.cpp
 XMLValidator.h
 XQuestResultXMLFile.h
 XQuestResultXMLHandler.h
 XQuestScores.h
 XTandemAdapter.cpp
 XTandemInfile.h
 XTandemXMLFile.h
 ZhangSimilarityScore.h
 ZlibCompression.h