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
AdductInfo.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
AssayGeneratorMetaboSirius.cpp
AverageLinkage.h
AxisPainter.h
AxisTickCalculator.h
AxisWidget.h
Base64.h
BaseFeature.h
BaseGroupFinder.h
BaselineFilter.cpp
BaseModel.h
BaseModel_impl.h
BaseSuperimposer.h
BaseVisualizer.h
BaseVisualizerGUI.h
BasicProteinInferenceAlgorithm.h
BasicStatistics.h
BayesianProteinInferenceAlgorithm.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
Changelog.doxygen
ChargePair.h
ChromatogramExtractor.h
ChromatogramExtractorAlgorithm.h
ChromatogramPeak.h
ChromatogramSettings.h
ChromatogramTools.h
ChromeleonFile.h
ClassTest.h
ClusterAnalyzer.h
ClusterFunctor.h
ClusterHierarchical.h
ClusteringGrid.h
ClusterMassTraces.cpp
ClusterMassTracesByPrecursor.cpp
CoarseIsotopePatternGenerator.h
Colorizer.h
ColorSelector.h
CometAdapter.cpp
commit_messages.doxygen
common-cmake-parameters.doxygen
CommonDefs.h
CommonEnums.h
CompleteLinkage.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
ConsensusMap.h
ConsensusMapMergerAlgorithm.h
ConsensusMapNormalizer.cpp
ConsensusMapNormalizerAlgorithmMedian.h
ConsensusMapNormalizerAlgorithmQuantile.h
ConsensusMapNormalizerAlgorithmThreshold.h
ConsensusXMLFile.h
ConsensusXMLHandler.h
ConsoleUtils.h
Constants.h
ConstRefVector.h
ContactPerson.h
ContactPersonVisualizer.h
Contaminants.h
ControlledVocabulary.h
ConversionHelper.h
ConvexHull2D.h
CrossLinksDB.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
DataProcessingVisualizer.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
DeconvolvedSpectrum.h
DecoyDatabase.cpp
DecoyGenerator.h
DefaultParamHandler.h
Deisotoper.h
DeMeanderize.cpp
developer_coding_conventions.doxygen
developer_cpp_guide.doxygen
developer_faq.doxygen
developer_how_to_write_tests.doxygen
developer_tutorial.doxygen
DIAHelper.h
DIAPrescoring.h
DIAScoring.h
DIATreeTab.h
Digestion.h
DigestionEnzyme.h
DigestionEnzymeDB.h
DigestionEnzymeProtein.h
DigestionEnzymeRNA.h
DigestionVisualizer.h
Digestor.cpp
DigestorMotif.cpp
DimMapper.h
DIntervalBase.h
DistanceMatrix.h
DocumentIdentifier.h
DocumentIdentifierVisualizer.h
DPeak.h
DPosition.h
DRange.h
DTA2DFile.h
DTAExtractor.cpp
DTAFile.h
EDTAFile.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
Epifany.cpp
EuclideanSimilarity.h
Exception.h
ExecutePipeline.cpp
ExperimentalDesign.h
ExperimentalDesignFile.h
ExperimentalSettings.h
ExperimentalSettingsVisualizer.h
ExposedVector.h
ExtendedIsotopeFitter1D.h
ExtendedIsotopeModel.h
ExternalCalibration.cpp
ExternalCode.doxygen
ExternalProcess.h
ExternalProcessMBox.h
FAIMSHelper.h
FalseDiscoveryRate.cpp
FalseDiscoveryRate.h
FASTAContainer.h
FASTAFile.h
FastLowessSmoothing.h
Feature.h
FeatureDeconvolution.h
FeatureDistance.h
FeatureEditDialog.h
FeatureFileOptions.h
FeatureFinderAlgorithm.h
FeatureFinderAlgorithmMetaboIdent.h
FeatureFinderAlgorithmPicked.h
FeatureFinderAlgorithmPickedHelperStructs.h
FeatureFinderCentroided.cpp
FeatureFinderDefs.h
FeatureFinderIdentification.cpp
FeatureFinderIdentificationAlgorithm.h
FeatureFinderMetabo.cpp
FeatureFinderMetaboIdent.cpp
FeatureFinderMultiplex.cpp
FeatureFinderMultiplexAlgorithm.h
FeatureFindingMetabo.h
FeatureGroupingAlgorithm.h
FeatureGroupingAlgorithmKD.h
FeatureGroupingAlgorithmLabeled.h
FeatureGroupingAlgorithmQT.h
FeatureGroupingAlgorithmUnlabeled.h
FeatureHandle.h
FeatureLinkerBase.cpp
FeatureLinkerLabeled.cpp
FeatureLinkerUnlabeled.cpp
FeatureLinkerUnlabeledKD.cpp
FeatureLinkerUnlabeledQT.cpp
FeatureMap.h
FeatureMapping.h
FeatureOverlapFilter.h
FeatureSummary.h
FeatureXMLFile.h
FeatureXMLHandler.h
FIAMSDataProcessor.h
FIAMSScheduler.h
FidHandler.h
File.h
FileConverter.cpp
FileFilter.cpp
FileHandler.h
FileInfo.cpp
FileMerger.cpp
FileTypes.h
FileWatcher.h
FilterableList.h
FilterList.h
FineIsotopePatternGenerator.h
Fitter1D.h
FlagSet.h
FLASHDeconv.cpp
FLASHDeconvAlgorithm.h
FLASHDeconvFeatureFile.h
FLASHDeconvHelperStructs.h
FLASHDeconvSpectrumFile.h
FLASHDeconvTabWidget.h
FLASHDeconvWizard.cpp
FLASHDeconvWizardBase.cpp
FLASHDeconvWizardBase.h
FragmentMassError.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
GNPSMetaValueFile.h
GNPSMGFFile.h
GNPSQuantificationFile.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
HighResPrecursorMassCorrector.cpp
Histogram.h
HistogramDialog.h
HistogramWidget.h
HPLC.h
HPLCVisualizer.h
HyperScore.h
IBSpectraFile.h
IDBoostGraph.h
IDConflictResolver.cpp
IDConflictResolverAlgorithm.h
IDDecoyProbability.cpp
IDDecoyProbability.h
IdentificationData.h
IdentificationDataConverter.h
IdentificationSummary.h
IdentifiedCompound.h
IdentifiedMolecule.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
IMDataConverter.h
IMSAlphabet.h
IMSAlphabetParser.h
IMSAlphabetTextParser.h
IMSDataConsumer.h
IMSElement.h
IMSIsotopeDistribution.h
IMTypes.h
IncludeExcludeTarget.h
IndentedStream.h
IndexedMzMLDecoder.h
IndexedMzMLFileLoader.h
IndexedMzMLHandler.h
INIFileEditor.cpp
INIFileEditorWindow.cpp
INIFileEditorWindow.h
Init.h
INIUpdater.cpp
INIUpdater.h
include/OpenMS/METADATA/ID/InputFile.h
gui/include/OpenMS/VISUAL/InputFile.h
InputFileList.h
InspectInfile.h
InspectOutfile.h
install-linux.doxygen
install-macs.doxygen
install-win.doxygen
Instrument.h
InstrumentSettings.h
InstrumentSettingsVisualizer.h
InstrumentVisualizer.h
IntegerMassDecomposer.h
InternalCalibration.cpp
InternalCalibration.h
InterpolationModel.h
IonDetector.h
IonDetectorVisualizer.h
IonIdentityMolecularNetworking.h
IonMobilityBinning.cpp
IonMobilityScoring.h
IonSource.h
IonSourceVisualizer.h
IPeptideIds.h
IsobaricAnalyzer.cpp
IsobaricChannelExtractor.h
IsobaricIsotopeCorrector.h
IsobaricNormalizer.h
IsobaricQuantifier.h
IsobaricQuantifierStatistics.h
IsobaricQuantitationMethod.h
IsoSpecWrapper.h
IsotopeCluster.h
IsotopeDistribution.h
IsotopeFitter1D.h
IsotopeLabelingMDVs.h
IsotopeModel.h
IsotopePatternGenerator.h
openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h
openms/include/OpenMS/INTERFACES/ISpectrumAccess.h
ITransition.h
ItraqConstants.h
ItraqEightPlexQuantitationMethod.h
ItraqFourPlexQuantitationMethod.h
JavaInfo.h
JSONExporter.cpp
KDTree.h
KDTreeFeatureMaps.h
KDTreeFeatureNode.h
KroenikFile.h
LabeledPairFinder.h
LayerData1DBase.h
LayerData1DChrom.h
LayerData1DIonMobility.h
LayerData1DPeak.h
LayerDataBase.h
LayerDataChrom.h
LayerDataConsensus.h
LayerDataFeature.h
LayerDataIdent.h
LayerDataIonMobility.h
LayerDataPeak.h
LayerListView.h
LayerStatistics.h
LayerStatisticsDialog.h
LayerStoreData.h
LevMarqFitter1D.h
LinearInterpolation.h
LinearRegression.h
LinearRegressionWithoutIntercept.h
LinearResampler.h
LinearResamplerAlign.h
ListEditor.h
ListFilterDialog.h
ListUtils.h
ListUtilsIO.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
MapAlignerBase.h
MapAlignerIdentification.cpp
MapAlignerPoseClustering.cpp
MapAlignerTreeGuided.cpp
MapAlignmentAlgorithmIdentification.h
MapAlignmentAlgorithmKD.h
MapAlignmentAlgorithmPoseClustering.h
MapAlignmentAlgorithmTreeGuided.h
MapAlignmentEvaluationAlgorithm.h
MapAlignmentEvaluationAlgorithmPrecision.h
MapAlignmentEvaluationAlgorithmRecall.h
MapAlignmentTransformer.h
MapNormalizer.cpp
MapRTTransformer.cpp
MapStatistics.cpp
MapUtilities.h
MaRaClusterAdapter.cpp
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
MassFeatureTrace.h
MassTrace.h
MasstraceCorrelator.h
MassTraceDetection.h
MassTraceExtractor.cpp
MatchedIterator.h
MathFunctions.h
Matrix.h
MaxLikeliFitter1D.h
MessagePasserFactory.h
MetaboliteAdductDecharger.cpp
MetaboliteFeatureDeconvolution.h
MetaboliteSpectralMatcher.cpp
MetaboliteSpectralMatching.h
MetaboTargetedAssay.h
MetaboTargetedTargetDecoy.h
MetaData.h
MetaDataBrowser.h
MetaInfo.h
MetaInfoDescription.h
MetaInfoDescriptionVisualizer.h
MetaInfoInterface.h
MetaInfoInterfaceUtils.h
MetaInfoRegistry.h
MetaInfoVisualizer.h
MetaProSIP.cpp
MissedCleavages.h
MobilityPeak1D.h
MobilityPeak2D.h
Mobilogram.h
MockObjects.h
ModelDescription.h
Modification.h
ModificationDefinition.h
ModificationDefinitionsSet.h
ModificationsDB.h
ModificationVisualizer.h
ModifiedNASequenceGenerator.h
ModifiedPeptideGenerator.h
Modules.doxygen
MorpheusScore.h
MorphologicalFilter.h
MQEvidenceExporter.h
MQExporterHelper.h
MQMsmsExporter.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
MRMIonSeries.h
MRMMapper.cpp
MRMMapping.h
MRMPairFinder.cpp
MRMRTNormalizer.h
MRMScoring.h
MRMTransitionGroup.h
MRMTransitionGroupPicker.cpp
MRMTransitionGroupPicker.h
MS2File.h
Ms2IdentificationRate.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
MSPFile.h
MSPGenericFile.h
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
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
MzQCFile.h
MzTab.h
MzTabBase.h
MzTabExporter.cpp
MzTabFile.h
MzTabM.h
MzTabMFile.h
MZTrafoModel.h
MzXMLFile.h
MzXMLHandler.h
NASequence.h
NeedlemanWunsch.h
NeighborSeq.h
NetworkGetRequest.h
NLargest.h
NNLS.h
NoiseFilterGaussian.cpp
NoiseFilterSGolay.cpp
NonNegativeLeastSquaresSolver.h
NoopMSDataConsumer.h
Normalizer.h
NovorAdapter.cpp
NucleicAcidSearchEngine.cpp
NucleicAcidSpectrumGenerator.h
Observation.h
ObservationMatch.h
ObservationMatchGroup.h
OMSFile.h
OMSFileLoad.h
OMSFileStore.h
OMSSACSVFile.h
OMSSAXMLFile.h
OnDiscMSExperiment.h
OpenMSDatabasesInfo.cpp
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
OPXLDataStructs.h
OPXLHelper.h
OPXLSpectrumProcessingAlgorithms.h
OSWData.h
OSWFile.h
OutputDirectory.h
Painter1DBase.h
Painter2DBase.h
PainterBase.h
Param.h
ParamCTDFile.h
ParamCWLFile.h
ParamEditor.h
ParameterInformation.h
ParamJSONFile.h
ParamValue.h
ParamXMLFile.h
ParamXMLHandler.h
ParentGroup.h
ParentMatch.h
ParentSequence.h
Peak1D.h
Peak2D.h
PeakAlignment.h
PeakFileOptions.h
PeakGroup.h
PeakIndex.h
PeakIntegrator.h
PeakPickerChromatogram.h
PeakPickerHiRes.cpp
PeakPickerHiRes.h
PeakPickerIterative.cpp
PeakPickerIterative.h
PeakSpectrumCompareFunctor.h
PeakTypeEstimator.h
PeakWidthEstimator.h
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
PercolatorInfile.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
PrecursorPurity.h
PrecursorVisualizer.h
ProcessingSoftware.h
ProcessingStep.h
Product.h
ProductVisualizer.h
ProgressLogger.h
ProteaseDB.h
ProteaseDigestion.h
ProteinHit.h
ProteinHitVisualizer.h
ProteinIdentification.h
ProteinIdentificationVisualizer.h
ProteinInference.cpp
ProteinInference.h
ProteinQuantifier.cpp
ProteomicsLFQ.cpp
ProtXMLFile.h
PScore.h
PSMExplainedIonCurrent.h
PSMFeatureExtractor.cpp
PTMXMLFile.h
PTMXMLHandler.h
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
Qscore.h
QTCluster.h
QTClusterFinder.h
QuadraticRegression.h
QualityControl.cpp
Qvalue.h
RAIICleanup.h
RangeManager.h
RangeUtils.h
RankScaler.h
RANSAC.h
RANSACModel.h
RANSACModelLinear.h
RANSACModelQuadratic.h
ReactionMonitoringTransition.h
RealMassDecomposer.h
RecentFilesMenu.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
RNPxlXICFilter.cpp
ROCCurve.h
RTAlignment.h
RWrapper.h
SageAdapter.cpp
Sample.h
SampleTreatment.h
SampleVisualizer.h
SaveImageDialog.h
SavitzkyGolayFilter.h
ScanWindow.h
ScanWindowVisualizer.h
ScoredProcessingResult.h
ScoreType.h
Scoring.h
SearchEngineBase.h
SeedListGenerator.cpp
SeedListGenerator.h
SemanticValidator.cpp
SemanticValidator.h
SequenceCoverageCalculator.cpp
SequenceVisualizer.h
SequestInfile.h
SequestOutfile.h
SignalToNoiseEstimator.h
SignalToNoiseEstimatorMeanIterative.h
SignalToNoiseEstimatorMedian.h
SignalToNoiseEstimatorMedianRapid.h
SIMDe.h
SimpleOpenMSSpectraAccessFactory.h
SimpleSearchEngine.cpp
SimpleSearchEngineAlgorithm.h
SimpleSVM.h
SimpleTSGXLMS.h
SingleLinkage.h
SiriusExport.cpp
SiriusExportAlgorithm.h
SiriusFragmentAnnotation.h
SiriusMSConverter.h
Software.h
SoftwareVisualizer.h
SONARScoring.h
SourceFile.h
SourceFileVisualizer.h
SpecArrayFile.h
SpecLibCreator.cpp
SpecLibSearcher.cpp
SpectraFilterNLargest.cpp
SpectraFilterNormalizer.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
SpectrumCount.h
SpectrumHelper.h
SpectrumHelpers.h
SpectrumLookup.h
SpectrumMetaDataLookup.h
SpectrumPrecursorComparator.h
SpectrumSettings.h
SpectrumSettingsVisualizer.h
SplineBisection.h
SplineInterpolatedPeaks.h
SplinePackage.h
SqliteConnector.h
SqMassFile.h
SqrtScaler.h
StablePairFinder.h
StandardTypes.h
StaticModification.cpp
StatisticFunctions.h
StatsHelpers.h
SteinScottImproveScore.h
StopWatch.h
StreamHandler.h
String.h
StringConversions.h
StringListUtils.h
StringUtils.h
StringUtilsSimple.h
StringView.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
TMTEighteenPlexQuantitationMethod.h
TMTElevenPlexQuantitationMethod.h
TMTSixPlexQuantitationMethod.h
TMTSixteenPlexQuantitationMethod.h
TMTTenPlexQuantitationMethod.h
ToolDescription.h
ToolDescriptionFile.h
ToolDescriptionHandler.h
ToolHandler.h
ToolsDialog.h
TOPP.doxygen
TOPPAS.cpp
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
TOPPViewBase.cpp
TOPPViewBase.h
TOPPViewMenu.h
TOPPViewOpenDialog.h
TOPPViewPrefDialog.h
TraceFitter.h
TraMLFile.h
TraMLHandler.h
TraMLValidator.h
TransformationDescription.h
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
TVToolDiscovery.h
Types.h
UnimodXMLFile.h
UnimodXMLHandler.h
UniqueIdGenerator.h
UniqueIdIndexer.h
UniqueIdInterface.h
UpdateCheck.h
user_FAQ.doxygen
VersionInfo.h
Weights.h
WindowMower.h
WizardHelper.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