All Classes

AccurateMassAdjuster Aligner Aligner.FeaturePairSelector Aligner.HybridFeaturePairSelector Aligner.MassFeaturePairSelector Aligner.MassOrMzFeaturePairSelector Aligner.MzFeaturePairSelector Aligner.PeptideFeaturePairSelector AmtDatabase AmtDatabaseBuilder AmtDatabaseCreatorCommandLineModule AmtDatabaseDiagnosticCommandLineModule AmtDatabaseManager AmtDatabaseManagerCommandLineModule AmtDatabaseMatcher AmtDatabaseMatcherCommandLineModule AmtExtraInfoDef AmtFeatureSetMatcher AmtFeatureSetMatcher.FeatureMatchingResult AmtFeatureSetMatcherFactory AMTFileRestrictor AmtPeptideEntry AmtPeptideEntry.AmtPeptideModificationStateEntry AmtPeptideEntry.AmtPeptideObservation AmtRunEntry AmtTsvReader AmtTsvReader.AmtTsvRow AmtUtilities AmtXmlReader AmtXmlWriter AnalyzeICAT AnalyzeICAT.IsotopicLabel Application ArgumentDefinitionFactory ArgumentValidationException AwtPropertyBag BackgroundRemover BaseAmtFeatureSetMatcherImpl BaseArgumentDefinitionImpl BaseCommandLineModuleImpl BaseCommandLineTest BaseFeatureStrategy BaseFeatureStrategy.StatusListener BaseFeatureStrategyModular BaseImagePanelLayer BasePeakCombiner BaseViewerTest BooleanArgumentDefinition BrowserController BucketedPeptideArray CalibrateFeatureMassesCLM CalibrateMzxmlMassesCLM ChartDialog Clusterer2D Clusterer2D.Clusterable Clusterer2D.ClusterDimensionSplitCalculator Clusterer2D.DefaultClusterDimensionSplitCalculator Clusterer2D.TreeEntry ClusteringFeatureSetMatcher CommandFileRunner CommandFileRunner.CommandFileRunnerAction CommandLineArgumentDefinition CommandLineModule CommandLineModuleDiscoverer CommandLineModuleExecutionException ConvertFeatureFileCommandLineModule ConvertHelper ConvertHelper.ChargeWrapper ConvertHelper.DateFriendlyStringConverter ConvertHelper.LenientDateConverter ConvertHelper.LenientTimestampConverter ConvertHelper.MyBooleanConverter ConvertHelper.PercentWrapper CoverageCalculatorAction CPASBrowser CPASBrowser.BrowseCPASAction CPASBrowser.CPASConnectionDialog CPASBrowser.CPASConnectionInformation CPASBrowser.CPASFileChooser CPASClientCommandLineModule CPASTreeBuilder CPASTreeBuilder.UserObjectWrapper DecimalArgumentDefinition DecimalListArgumentDefinition DeconvoluteCommandLineModule Deconvoluter DefaultFeatureScorer DefaultPeakCombiner DeltaMassArgumentDefinition DeltaMassArgumentDefinition.DeltaMassWithType DetectAdductsCLM DirectoryToReadArgumentDefinition DumpWindow2D DumpWindow2DCommandLineModule EnumeratedValuesArgumentDefinition ExtractEdgeFeatures ExtractFeatureRangesAction ExtractFeatureRangesAction.ExtractFeatureRangesDialog ExtractFeatureRangesAction.FeatureScanner ExtractMaxima2D ExtractRunsFromPepXmlCommandLineModule FastaFileArgumentDefinition Feature Feature.IntensityDescComparator Feature.MassAscComparator Feature.MzAscComparator Feature.MzDistAscComparator Feature.MzScanAscComparator Feature.PeaksKLComparatorDesc Feature.ScanAscComparator FeatureAsMap FeatureClusterer FeatureClusterer.FeatureClusterable FeatureClusterer.FeatureMassHydroClusterable FeatureClusterer.FeatureMassScanClusterable FeatureClusterer.FeatureMassTimeClusterable FeatureClusterer.FeatureMzHydroClusterable FeatureClusterer.FeatureMzScanClusterable FeatureClusterer.FeatureMzTimeClusterable FeatureExtractor FeatureExtractor.StatusListener FeatureExtraInformationDef FeatureFileArgumentDefinition FeatureFinder FeatureFindingBroker FeatureGrouper FeaturePepXmlWriter FeatureScorer FeatureSelectionFrame FeatureSelectionFrame.FeatureSelectionDialog FeatureSelectionFrame.FeatureSelectionDialog.BrowseEditor FeatureSelectionFrame.FeatureSelectionDialog.ColorEditor FeatureSelectionFrame.FeatureSelectionDialog.ColorRenderer FeatureSelectionFrame.FeatureSelectionDialog.FeatureFrame FeatureSelectionFrame.FeatureSelectionDialog.NumberRenderer FeatureSelectionFrame.FeatureSelectionDialog.Optimizer FeatureSelectionParamsCommandLineModule FeatureSet FeatureSet.FeatureSelector FeatureSetMatcherCommandLineModule FeatureStrategy FeatureStrategyCentroided FeatureStrategyCombined FeatureStrategyGrossFeatures FeatureStrategyPeakClusters FeatureStrategyPeakClustersOld FeatureStrategyPeaks FeatureStrategyPeaks2 FeatureStrategySpectrumFit FeatureStrategyUsingWindow FeatureStrategyUsingWindow2D FeatureStrategyWavelet FeatureStrategyWavelet2D FeatureStrategyWavelet2D.SmoothWavelet FeatureStrategyWindow FeatureTableModel FileToReadArgumentDefinition FileToWriteArgumentDefinition FilterFeaturesCommandLineModule FilterFeaturesTest FindPeptidesCommandLineModule FindPeptidesTest Haar HeatMapFrame HeatMapPanel HtmlGenerator HydrophobicityAlgorithmAnalyzerCLM HydrophobicityNormalizer IcatCommandLineModule ImagePanel ImagePanelLayer IntegerArgumentDefinition IntensityPlot IntensityPlot.ColorMap IntensityPlot.CyanMap IntensityPlot.FireMap IntensityPlot.GrayMap IntensityPlot.InvFireMap IntensityPlot.RainbowMap IsotopicLabelExtraInfoDef ListenerHelper Localizer Localizer.FontActionListener Localizer.LanguageActionListener MassAccuracyCommandLineModule MassCalibrationUtilities ModificationListArgumentDefinition MS2Correct MS2ExtraInfoDef MS2ExtraInfoDef.PeptideProphetAscComparator MS2ExtraInfoDef.PeptideProphetDescComparator MSDetailPanel MSDetailPanel.DetailDialog MSDetailPanel.Show3DAction MSDetailPanel.ShowDialogAction MSImageComponent MSImageComponent.SaveImageAction MSRun MSRunInfoAction MzXmlWriter Normalizer OpenFastaDialog OpenFastaDialog.OpenFastaAction OpenFileAction PanelWithBarChart PanelWithBoxAndWhiskerChart PanelWithChart PanelWithHistogram PanelWithLineChart PanelWithRPerspectivePlot PanelWithScatterPlot PanelWithVenn PeakCombiner PeakExtractor PeptideArrayAnalyzer PeptideArrayAnalyzerCommandLineModule PeptideArrayCommandLineModule PeptideArrayTest PeptideCompareCommandLineModule PeptideMatcher PepXmlChannelSplitter PlotMassCalibrationCLM PopulateMS2TimesCLM PropertiesPane ProteinDisplay ProteinMatcher ProteinMatcherFrame ProteinMatcherFrame.ProteinMatcherAction ProteinRollupCommandLineModule Q3 QuantCommandLineModule RInterface RunCommandFileCommandLineModule SaveImageCommandLineModule SaveMzxmlWindowCommandLineModule SavePartialMzxmlDialog SavePartialMzxmlDialog.SavePartialMzxmlAction ScatterPlotDialog ScrollableImage SelectedForCIDFinder SelectedForCIDFinder.ResultsDialog SelectedForCIDFinder.SelectedForCIDFinderAction SharedProperties Smooth2D SmootherCreator SpecifyModuleArgumentsFrame SpecifyModuleArgumentsFrame.ChooseCommandDialog SpecifyModuleArgumentsFrame.RunCommandAction Spectrum Spectrum.CentroidedPeak Spectrum.FeatureBase Spectrum.Peak SpectrumChartFactory SpectrumComponent SpectrumComponent.SpinnerRunModel SpectrumDataSet SpectrumResampler SpectrumXYSeries SRMCommandLineModule SRMCommandLineModule.SRMTransition SRMCommandLineModule.SRMTransition.MeanMzAscComparator SRMCommandLineModule.SRMTransition.PrecursorMzComparator StringArgumentDefinition Surface SurfaceFrame TableSorter TempFileManager TestRunner TestUtilities TimeExtraInfoDef WaveletPeakExtractor Window2DFeatureSetMatcher WorkbenchFileChooser WorkbenchFrame WorkbenchFrame.HelpAction WorkbenchFrame.SupportAction WorkbenchFrame.UrlAction