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Here is a list of all files with brief descriptions:
AAIndex.h
AASequence.h
AccurateMassSearch.C
AccurateMassSearchEngine.h
Acquisition.h
AcquisitionInfo.h
AcquisitionInfoVisualizer.h
AcquisitionVisualizer.h
AcqusHandler.h
AdditiveSeries.C
Adduct.h
Annotation1DDistanceItem.h
Annotation1DItem.h
Annotation1DPeakItem.h
Annotation1DTextItem.h
Annotations1DContainer.h
AreaIterator.h
AScore.h
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.C
BaseModel.h
BaseModel_impl.h
BaseSuperimposer.h
BaseVisualizer.h
BaseVisualizerGUI.h
BasicStatistics.h
BernNorm.h
BiGaussFitter1D.h
BiGaussModel.h
BigString.h
BilinearInterpolation.h
BinaryComposeFunctionAdapter.h
BinaryTreeNode.h
BinnedSharedPeakCount.h
BinnedSpectralContrastAngle.h
BinnedSpectrum.h
BinnedSpectrumCompareFunctor.h
BinnedSumAgreeingIntensities.h
Bzip2Ifstream.h
Bzip2InputStream.h
CachedmzML.h
CentroidData.h
CentroidPeak.h
Changelog.doxygen
ChargePair.h
ChromatogramExtractor.h
ChromatogramPeak.h
ChromatogramSettings.h
ChromatogramTools.h
ClassTest.h
ClusterAnalyzer.h
ClusteredMS2ConsensusSpectrum.h
ClusterFunctor.h
ClusterHierarchical.h
CodingConvention.doxygen
ColorSelector.h
ComparatorUtils.h
CompareFouriertransform.h
ComplementFilter.h
ComplementMarker.h
CompleteLinkage.h
CompNovo.C
CompNovoCID.C
CompNovoIdentification.h
CompNovoIdentificationBase.h
CompNovoIdentificationCID.h
CompNovoIonScoring.h
CompNovoIonScoringBase.h
CompNovoIonScoringCID.h
Compomer.h
CompressedInputSource.h
ConfidenceScoring.h
ConsensusFeature.h
ConsensusID.C
ConsensusID.h
ConsensusIsotopePattern.h
ConsensusMap.h
ConsensusMapNormalizer.C
ConsensusMapNormalizerAlgorithmMedian.h
ConsensusMapNormalizerAlgorithmQuantile.h
ConsensusMapNormalizerAlgorithmThreshold.h
ConsensusXMLFile.h
ConsoleUtils.h
Constants.h
ConstRefVector.h
ContactPerson.h
ContactPersonVisualizer.h
ContinuousWaveletTransform.h
ContinuousWaveletTransformNumIntegration.h
Contributing.doxygen
ControlledVocabulary.h
ConvertTraMLToTSV.C
ConvertTSVToTraML.C
ConvexHull2D.h
CPPGuide.doxygen
CsvFile.h
CVInspector.C
CVMappingFile.h
CVMappingRule.h
CVMappings.h
CVMappingTerm.h
CVReference.h
CVTerm.h
CVTermList.h
DataAccessHelper.h
DataFilterDialog.h
DataFilters.h
DataFrameWriter.h
DataProcessing.h
DataProcessingVisualizer.h
ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h
INTERFACES/DataStructures.h
DataValue.h
Date.h
DateTime.h
DBAdapter.h
DBConnection.h
DBExporter.C
DBImporter.C
DBOpenDialog.h
DBoundingBox.h
Decharger.C
DecoyDatabase.C
DefaultParamHandler.h
Deisotoper.h
DeMeanderize.C
DeNovoAlgorithm.h
DeNovoIdentification.h
DeNovoIonScoring.h
DeNovoPostScoring.h
DetectabilitySimulation.h
DIAHelper.h
DIAPrescoring.h
DIAScoring.h
Digestion.h
DigestionVisualizer.h
Digestor.C
DigestorMotif.C
DigestSimulation.h
DIntervalBase.h
DistanceMatrix.h
DocumentIdentifier.h
DocumentIdentifierVisualizer.h
DocumentIDTagger.h
DoubleList.h
DPeak.h
DPosition.h
DRange.h
DRichPeak.h
DTA2DFile.h
DTAExtractor.C
DTAFile.h
EDTAFile.h
EdwardsLippertIterator.h
EdwardsLippertIteratorTryptic.h
EGHFitter1D.h
EGHModel.h
EGHTraceFitter.h
EICExtractor.C
Element.h
ElementDB.h
ElutionPeakDetection.h
EmgFitter1D.h
EmgModel.h
EmgScoring.h
EmpiricalFormula.h
EnhancedTabBar.h
EnhancedTabBarWidgetInterface.h
EnhancedWorkspace.h
EnzymaticDigestion.h
ERPairFinder.C
EuclideanSimilarity.h
Exception.h
ExecutePipeline.C
ExperimentalSettings.h
ExperimentalSettingsVisualizer.h
ExtendedIsotopeFitter1D.h
ExtendedIsotopeModel.h
ExternalCode.doxygen
Factory.h
FactoryBase.h
FalseDiscoveryRate.C
FalseDiscoveryRate.h
public/FAQ.doxygen
internal/FAQ.doxygen
FASTAFile.h
FastaIterator.h
FastaIteratorIntern.h
FeaFiModule.h
Feature.h
FeatureDeconvolution.h
FeatureDistance.h
FeatureEditDialog.h
FeatureFileOptions.h
FeatureFinder.h
FeatureFinder_impl.h
FeatureFinderAlgorithm.h
FeatureFinderAlgorithm_impl.h
FeatureFinderAlgorithmIsotopeWavelet.h
FeatureFinderAlgorithmMRM.h
FeatureFinderAlgorithmPicked.h
FeatureFinderAlgorithmPickedHelperStructs.h
FeatureFinderAlgorithmSH.h
FeatureFinderAlgorithmSHCtrl.h
FeatureFinderAlgorithmSimple.h
FeatureFinderAlgorithmSimplest.h
FeatureFinderCentroided.C
FeatureFinderDefs.h
FeatureFinderIsotopeWavelet.C
FeatureFinderMetabo.C
FeatureFinderMRM.C
FeatureFinderRaw.C
FeatureFinderSuperHirn.C
FeatureFindingMetabo.h
FeatureGroupingAlgorithm.h
FeatureGroupingAlgorithmIdentification.h
FeatureGroupingAlgorithmLabeled.h
FeatureGroupingAlgorithmQT.h
FeatureGroupingAlgorithmUnlabeled.h
FeatureHandle.h
FeatureLCProfile.h
FeatureLinkerBase.C
FeatureLinkerLabeled.C
FeatureLinkerUnlabeled.C
FeatureLinkerUnlabeledQT.C
FeatureMap.h
FeatureXMLFile.h
FFEval.C
FidHandler.h
File.h
FileConverter.C
FileFilter.C
FileHandler.h
FileInfo.C
FileMerger.C
FileTypes.h
FileWatcher.h
FilterFunctor.h
Fitter1D.h
FTPeakDetectController.h
FuzzyDiff.C
FuzzyStringComparator.h
GammaDistributionFitter.h
GaussFilter.h
GaussFilterAlgorithm.h
GaussFitter.h
GaussFitter1D.h
GaussModel.h
GaussTraceFitter.h
GenericWrapper.C
GlobalExceptionHandler.h
GoodDiffFilter.h
Gradient.h
GradientVisualizer.h
GridFeature.h
GumbelDistributionFitter.h
GzipIfstream.h
GzipInputStream.h
HashGrid.h
HiddenMarkovModel.h
HierarchicalClustering.h
HighResPrecursorMassCorrector.C
Histogram.h
HistogramDialog.h
HistogramWidget.h
HPLC.h
HPLCVisualizer.h
ICPLLabeler.h
IDConflictResolver.C
IDDecoyProbability.C
IDDecoyProbability.h
Identification.h
IdentificationHit.h
IDEvaluationBase.C
IDEvaluationBase.h
IDEvaluator.C
IDEvaluatorGUI.C
IDExtractor.C
IDFileConverter.C
IDFilter.C
IDFilter.h
IDMapper.C
IDMapper.h
IDMassAccuracy.C
IDMerger.C
IDPosteriorErrorProbability.C
IDRipper.C
IDRipper.h
IDRTCalibration.C
IDSplitter.C
IdXMLFile.h
ILPDCWrapper.h
ImageCreator.C
IMSAlphabet.h
IMSAlphabetParser.h
IMSAlphabetTextParser.h
IMSElement.h
IMSIsotopeDistribution.h
IncludeExcludeTarget.h
InclusionExclusionList.h
InclusionExclusionListCreator.C
INIFileEditor.C
INIFileEditorWindow.C
INIFileEditorWindow.h
INIUpdater.C
INIUpdater.h
InspectAdapter.C
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.C
InternalCalibration.h
InterpolationModel.h
IntList.h
IonDetector.h
IonDetectorVisualizer.h
IonizationSimulation.h
IonSource.h
IonSourceVisualizer.h
IsobaricAnalyzer.C
IsobaricChannelExtractor.h
IsobaricIsotopeCorrector.h
IsobaricNormalizer.h
IsobaricQuantifier.h
IsobaricQuantifierStatistics.h
IsobaricQuantitationMethod.h
IsotopeCluster.h
IsotopeDiffFilter.h
IsotopeDistribution.h
IsotopeDistributionCache.h
IsotopeFitter1D.h
IsotopeMarker.h
IsotopeModel.h
IsotopeWavelet.h
IsotopeWaveletConstants.h
IsotopeWaveletCudaKernel.h
IsotopeWaveletParallelFor.h
IsotopeWaveletTransform.h
IsotopicDist.h
ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h
INTERFACES/ISpectrumAccess.h
ITransition.h
ITRAQAnalyzer.C
ItraqChannelExtractor.h
ItraqConstants.h
ItraqEightPlexQuantitationMethod.h
ItraqFourPlexQuantitationMethod.h
ITRAQLabeler.h
ItraqQuantifier.h
KnownDevBugs.doxygen
KroenikFile.h
LabeledEval.C
LabeledPairFinder.h
LabelFreeLabeler.h
LayerData.h
LayerStatisticsDialog.h
LCElutionPeak.h
LCMS.h
LCMSCData.h
LevMarqFitter1D.h
LibSVMEncoder.h
LinearInterpolation.h
LinearRegression.h
LinearResampler.h
LinearResamplerAlign.h
ListEditor.h
LmaGaussFitter1D.h
LmaGaussModel.h
LmaIsotopeFitter1D.h
LmaIsotopeModel.h
LocalLinearMap.h
LogConfigHandler.h
LogStream.h
LowessSmoothing.h
LPWrapper.h
Macros.h
Main.doxygen
Map.h
MapAlignerBase.h
MapAlignerIdentification.C
MapAlignerPoseClustering.C
MapAlignerSpectrum.C
MapAlignmentAlgorithm.h
MapAlignmentAlgorithmIdentification.h
MapAlignmentAlgorithmPoseClustering.h
MapAlignmentAlgorithmSpectrumAlignment.h
MapAlignmentEvaluation.C
MapAlignmentEvaluationAlgorithm.h
MapAlignmentEvaluationAlgorithmPrecision.h
MapAlignmentEvaluationAlgorithmRecall.h
MapAlignmentTransformer.h
MapNormalizer.C
MapRTTransformer.C
MapStatistics.C
MarkerMower.h
MascotAdapter.C
MascotAdapterOnline.C
MascotGenericFile.h
MascotInfile.h
MascotRemoteQuery.h
MascotXMLFile.h
MascotXMLHandler.h
MassAnalyzer.h
MassAnalyzerVisualizer.h
MassCalculator.C
MassDecomposer.h
MassDecomposition.h
MassDecompositionAlgorithm.h
MassExplainer.h
MassTrace.h
MassTraceDetection.h
MassTraceExtractor.C
MathFunctions.h
Matrix.h
MaxLikeliFitter1D.h
MetaDataBrowser.h
MetaInfo.h
MetaInfoDescription.h
MetaInfoDescriptionVisualizer.h
MetaInfoInterface.h
MetaInfoRegistry.h
MetaInfoVisualizer.h
MockObjects.h
ModelDescription.h
ModelFitter.h
Modification.h
ModificationDefinition.h
ModificationDefinitionsSet.h
ModificationsDB.h
ModificationVisualizer.h
ModifierRep.h
Modules.doxygen
MorphologicalFilter.h
MRMDecoy.h
MRMFeature.h
MRMFeatureAccessOpenMS.h
MRMFeatureFinderScoring.h
MRMFragmentSelection.h
MRMMapper.C
MRMPairFinder.C
MRMRTNormalizer.h
MRMScoring.h
MRMTransitionGroup.h
MRMTransitionGroupPicker.h
MS1FeatureMerger.h
MS2ConsensusSpectrum.h
MS2Feature.h
MS2File.h
MS2Fragment.h
MS2Info.h
MSChromatogram.h
MSExperiment.h
MsInspectFile.h
MSPeak.h
MSPFile.h
MSQuantifications.h
MSSim.h
MSSimulator.C
MSSpectrum.h
MultiGradient.h
MultiGradientSelector.h
MyriMatchAdapter.C
MzDataFile.h
MzDataHandler.h
MzDataValidator.h
MzIdentMLFile.h
MzIdentMLHandler.h
MzIdentMLValidator.h
MzMLFile.h
MzMLHandler.h
MzMLValidator.h
MzQuantMLFile.h
MzQuantMLHandler.h
MzQuantMLValidator.h
MzTab.h
MzTabExporter.C
MzTabFile.h
MzXMLFile.h
MzXMLHandler.h
NeutralLossDiffFilter.h
NeutralLossMarker.h
NLargest.h
NNLS.h
NoiseFilterGaussian.C
NoiseFilterSGolay.C
NonNegativeLeastSquaresSolver.h
Normalizer.h
O18Labeler.h
OfflinePrecursorIonSelection.h
OMSSAAdapter.C
OMSSACSVFile.h
OMSSAXMLFile.h
OpenMS_Tutorial.doxygen
OpenMS_Tutorial_html.doxygen
OpenMSInfo.C
OpenSwathAnalyzer.C
OpenSwathChromatogramExtractor.C
OpenSwathConfidenceScoring.C
OpenSwathDecoyGenerator.C
OpenSwathDIAPreScoring.C
OpenSwathFeatureXMLToTSV.C
OpenSwathHelper.h
OpenSwathMzMLFileCacher.C
OpenSwathRewriteToFeatureXML.C
OpenSwathRTNormalizer.C
OptimizePeakDeconvolution.h
OptimizePick.h
Param.h
ParamEditor.h
ParameterInformation.h
ParamXMLFile.h
ParamXMLHandler.h
ParentPeakMower.h
Peak1D.h
Peak2D.h
PeakAlignment.h
PeakFileOptions.h
PeakIndex.h
PeakIntensityPredictor.h
PeakMarker.h
PeakPickerCWT.h
PeakPickerHiRes.C
PeakPickerHiRes.h
PeakPickerSH.h
PeakPickerWavelet.C
PeakShape.h
PeakSpectrumCompareFunctor.h
PeakTypeEstimator.h
PeakWidthEstimator.h
PepIterator.h
PepNovoAdapter.C
PepNovoInfile.h
PepNovoOutfile.h
PeptideAndProteinQuant.h
PeptideEvidence.h
PeptideHit.h
PeptideHitVisualizer.h
PeptideIdentification.h
PeptideIdentificationVisualizer.h
PeptideIndexer.C
PepXMLFile.h
PepXMLFileMascot.h
PersistentObject.h
PhosphoScoring.C
PILISCrossValidation.h
PILISIdentification.C
PILISIdentification.h
PILISModel.h
PILISModelCV.C
PILISModelGenerator.h
PILISModelTrainer.C
PILISNeutralLossModel.h
PILISScoring.h
PILISSpectraGenerator.C
PoseClusteringAffineSuperimposer.h
PoseClusteringShiftSuperimposer.h
PosteriorErrorProbabilityModel.h
Precursor.h
PrecursorIonSelection.h
PrecursorIonSelectionPreprocessing.h
PrecursorIonSelector.C
PrecursorMassCorrector.C
PrecursorVisualizer.h
ProcessData.h
Product.h
ProductModel.h
ProductVisualizer.h
ProgressLogger.h
ProteinHit.h
ProteinHitVisualizer.h
ProteinIdentification.h
ProteinIdentificationVisualizer.h
ProteinInference.C
ProteinInference.h
ProteinQuantifier.C
ProteinResolver.C
ProteinResolver.h
ProtonDistributionModel.h
ProtXMLFile.h
PSLPFormulation.h
PSProteinInference.h
PTModel.C
PTMXMLFile.h
PTMXMLHandler.h
PTPredict.C
PyOpenMS.doxygen
QApplicationTOPP.C
QApplicationTOPP.h
QCCalculator.C
QCEmbedder.C
QCExporter.C
QCExtractor.C
QCImporter.C
QCMerger.C
QcMLFile.h
QCShrinker.C
QTCluster.h
QTClusterFinder.h
QuantitativeExperimentalDesign.h
QuickStart.doxygen
RangeManager.h
RangeUtils.h
RawData.h
RawMSSignalSimulation.h
RawTandemMSSignalSimulation.h
ReactionMonitoringTransition.h
RealMassDecomposer.h
Resampler.C
Residue.h
ResidueDB.h
ResidueModification.h
RichPeak1D.h
RichPeak2D.h
RNPxl.C
RNPxlXICFilter.C
ROCCurve.h
RTEvaluation.C
RTModel.C
RTPredict.C
RTSimulation.h
Sample.h
SampleTreatment.h
SampleVisualizer.h
SaveImageDialog.h
SavitzkyGolayFilter.h
Scaler.h
ScanWindow.h
ScanWindowVisualizer.h
Scoring.h
SeedListGenerator.C
SeedListGenerator.h
SemanticValidator.C
SemanticValidator.h
SeqanIncludeWrapper.h
SequenceCoverageCalculator.C
SequestAdapter.C
SequestInfile.h
SequestOutfile.h
SHFeature.h
SignalToNoiseEstimator.h
SignalToNoiseEstimatorMeanIterative.h
SignalToNoiseEstimatorMedian.h
SILACAnalyzer.C
SILACAnalyzer.h
SILACClustering.h
SILACFilter.h
SILACFiltering.h
SILACLabeler.h
SILACPattern.h
SILACPoint.h
SimpleExtender.h
SimpleOpenMSSpectraAccessFactory.h
SimplePairFinder.h
SimpleSeeder.h
SimTypes.h
SingleLinkage.h
SingletonRegistry.h
Software.h
SoftwareVisualizer.h
SourceFile.h
SourceFileVisualizer.h
SparseVector.h
SpecArrayFile.h
SpecLibCreator.C
SpecLibSearcher.C
SpectraFilterBernNorm.C
SpectraFilterMarkerMower.C
SpectraFilterNLargest.C
SpectraFilterNormalizer.C
SpectraFilterParentPeakMower.C
SpectraFilterScaler.C
SpectraFilterSqrtMower.C
SpectraFilterThresholdMower.C
SpectraFilterWindowMower.C
SpectraIdentificationViewWidget.h
SpectraMerger.C
SpectraMerger.h
SpectraSTSimilarityScore.h
SpectraViewWidget.h
Spectrum1DCanvas.h
Spectrum1DGoToDialog.h
Spectrum1DPrefDialog.h
Spectrum1DWidget.h
Spectrum2DCanvas.h
Spectrum2DGoToDialog.h
Spectrum2DPrefDialog.h
Spectrum2DWidget.h
Spectrum3DCanvas.h
Spectrum3DOpenGLCanvas.h
Spectrum3DPrefDialog.h
Spectrum3DWidget.h
SpectrumAccessOpenMS.h
SpectrumAccessOpenMSCached.h
SpectrumAddition.h
SpectrumAlignment.h
SpectrumAlignmentDialog.h
SpectrumAlignmentScore.h
SpectrumCanvas.h
SpectrumCheapDPCorr.h
SpectrumHelpers.h
SpectrumIdentification.h
SpectrumPrecursorComparator.h
SpectrumSettings.h
SpectrumSettingsVisualizer.h
SpectrumWidget.h
SqrtMower.h
StablePairFinder.h
StandardTypes.h
StatisticFunctions.h
StatsHelpers.h
SteinScottImproveScore.h
StopWatch.h
StreamHandler.h
String.h
StringList.h
SuffixArray.h
SuffixArrayPeptideFinder.h
SuffixArraySeqan.h
SuffixArrayTrypticCompressed.h
SuffixArrayTrypticSeqan.h
SuperHirnParameters.h
SuperHirnUtil.h
SvmTheoreticalSpectrumGenerator.h
SvmTheoreticalSpectrumGeneratorSet.h
SvmTheoreticalSpectrumGeneratorTrainer.C
SvmTheoreticalSpectrumGeneratorTrainer.h
SVMWrapper.h
SVOutStream.h
Tagging.h
TaggingVisualizer.h
TargetedExperiment.h
TargetedExperimentHelper.h
TextExporter.C
TextFile.h
TheoreticalSpectrumGenerationDialog.h
TheoreticalSpectrumGenerator.h
ThresholdMower.h
TICFilter.h
TMTAnalyzer.C
TMTSixPlexQuantitationMethod.h
TOFCalibration.C
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.C
TOPP_tutorial/TOPPAS.doxygen
doxygen/public/TOPPAS.doxygen
TOPPASBase.C
TOPPASBase.h
TOPPASEdge.h
TOPPASInputFileDialog.h
TOPPASInputFileListVertex.h
TOPPASInputFilesDialog.h
TOPPASIOMappingDialog.h
TOPPASLogWindow.h
TOPPASMergerVertex.h
TOPPASOutputFileListVertex.h
TOPPASOutputFilesDialog.h
TOPPASResource.h
TOPPASResources.h
TOPPASScene.h
TOPPASTabBar.h
TOPPASToolConfigDialog.h
TOPPASToolVertex.h
TOPPASTreeView.h
TOPPASVertex.h
TOPPASVertexNameDialog.h
TOPPASWidget.h
TOPPBase.h
TOPPView.C
TOPPView_calling_topp.doxygen
TOPPView_interface.doxygen
TOPPViewBase.C
TOPPViewBase.h
TOPPViewBehaviorInterface.h
TOPPViewIdentificationViewBehavior.h
TOPPViewOpenDialog.h
TOPPViewPrefDialog.h
TOPPViewSpectraViewBehavior.h
TraceFitter.h
TraMLFile.h
TraMLHandler.h
TraMLValidator.h
TransformationDescription.h
TransformationEvaluation.C
TransformationModel.h
TransformationXMLFile.h
TransitionExperiment.h
TransitionHelper.h
Transitions.h
TransitionTSVReader.h
TrypticIterator.h
TwoDOptimization.h
Types.h
UnaryComposeFunctionAdapter.h
UnimodXMLFile.h
UnimodXMLHandler.h
UniqueIdGenerator.h
UniqueIdIndexer.h
UniqueIdInterface.h
UTILS.doxygen
VersionInfo.h
Weights.h
WeightWrapper.h
WindowMower.h
XMassFile.h
XMLFile.h
XMLHandler.h
XMLValidator.C
XMLValidator.h
XTandemAdapter.C
XTandemInfile.h
XTandemInfileXMLHandler.h
XTandemXMLFile.h
ZhangSimilarityScore.h
OpenMS / TOPP release 1.11.1
Documentation generated on Thu Nov 14 2013 11:20:59 using doxygen 1.8.5