Hierarchy For All Packages

Package Hierarchies:

org.fhcrc.cpl.toolbox, org.fhcrc.cpl.toolbox.commandline, org.fhcrc.cpl.toolbox.commandline.arguments, org.fhcrc.cpl.toolbox.datastructure, org.fhcrc.cpl.toolbox.filehandler, org.fhcrc.cpl.toolbox.gui, org.fhcrc.cpl.toolbox.gui.chart, org.fhcrc.cpl.toolbox.gui.widget, org.fhcrc.cpl.toolbox.normalize, org.fhcrc.cpl.toolbox.proteomics, org.fhcrc.cpl.toolbox.proteomics.commandline.arguments, org.fhcrc.cpl.toolbox.proteomics.feature, org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo, org.fhcrc.cpl.toolbox.proteomics.feature.filehandler, org.fhcrc.cpl.toolbox.proteomics.feature.matching, org.fhcrc.cpl.toolbox.proteomics.filehandler, org.fhcrc.cpl.toolbox.proteomics.gui, org.fhcrc.cpl.toolbox.statistics, org.fhcrc.cpl.toolbox.test, org.fhcrc.cpl.toolbox.test.commandline, org.fhcrc.cpl.viewer, org.fhcrc.cpl.viewer.align, org.fhcrc.cpl.viewer.align.commandline, org.fhcrc.cpl.viewer.amt, org.fhcrc.cpl.viewer.amt.commandline, org.fhcrc.cpl.viewer.commandline, org.fhcrc.cpl.viewer.commandline.modules, org.fhcrc.cpl.viewer.database, org.fhcrc.cpl.viewer.database.dbclasses, org.fhcrc.cpl.viewer.database.loader, org.fhcrc.cpl.viewer.feature, org.fhcrc.cpl.viewer.feature.extraction, org.fhcrc.cpl.viewer.feature.extraction.strategy, org.fhcrc.cpl.viewer.gui, org.fhcrc.cpl.viewer.gui.util, org.fhcrc.cpl.viewer.mrm, org.fhcrc.cpl.viewer.mrm.commandline, org.fhcrc.cpl.viewer.mrm.utilities, org.fhcrc.cpl.viewer.ms2, org.fhcrc.cpl.viewer.ms2.commandline, org.fhcrc.cpl.viewer.ms2.gui, org.fhcrc.cpl.viewer.qa, org.fhcrc.cpl.viewer.qa.commandline, org.fhcrc.cpl.viewer.quant, org.fhcrc.cpl.viewer.quant.commandline, org.fhcrc.cpl.viewer.quant.gui, org.fhcrc.cpl.viewer.test, org.fhcrc.cpl.viewer.test.commandline, org.fhcrc.cpl.viewer.util

Class Hierarchy

• java.lang.Object
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • org.fhcrc.cpl.viewer.gui.ChooseCommandDialog.RunCommandAction
    • org.fhcrc.cpl.viewer.CommandFileRunner.CommandFileRunnerAction
    • org.fhcrc.cpl.viewer.gui.CoverageCalculatorAction (implements java.beans.PropertyChangeListener)
    • org.fhcrc.cpl.viewer.gui.ExtractFeatureRangesAction (implements java.beans.PropertyChangeListener)
    • org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame (implements java.beans.PropertyChangeListener)
    • org.fhcrc.cpl.viewer.gui.MSDetailPanel.Show3DAction
    • org.fhcrc.cpl.viewer.gui.MSDetailPanel.ShowDialogAction
    • org.fhcrc.cpl.viewer.gui.MSImageComponent.SaveImageAction
    • org.fhcrc.cpl.viewer.gui.MSRunInfoAction
    • org.fhcrc.cpl.viewer.gui.OpenFastaDialog.OpenFastaAction
    • org.fhcrc.cpl.viewer.gui.OpenFileAction
    • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.FindProteinsMatchedInMS2Action
    • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.LoadMS2RegressionAction
    • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.LoadOffsetFeatureSetAction
    • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.MatchProteinsFromFastaAction
    • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.ProteinMatcherAction
    • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.SaveFastaAction
    • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.SetParametersAction
    • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.ShowPredictedHydroTimePlotAction
    • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.WritePepXmlMs2RegressionAction
    • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.CreateChartsAction
    • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.ExitAction
    • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.FilterPepXMLAction
    • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.HelpAction
    • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.OpenFileAction
    • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.ProteinSummaryAction
    • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.SaveAction
    • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.SummaryChartsAction
    • org.fhcrc.cpl.viewer.gui.SavePartialMzxmlDialog.SavePartialMzxmlAction
    • org.fhcrc.cpl.viewer.gui.SelectedForCIDFinder.SelectedForCIDFinderAction (implements java.beans.PropertyChangeListener)
    • org.fhcrc.cpl.viewer.gui.WorkbenchFrame.AutoZoomAction
    • org.fhcrc.cpl.viewer.gui.WorkbenchFrame.ExitAction
    • org.fhcrc.cpl.viewer.gui.WorkbenchFrame.HeatMapAction (implements java.beans.PropertyChangeListener)
    • org.fhcrc.cpl.viewer.gui.WorkbenchFrame.LockYAxisAction
    • org.fhcrc.cpl.viewer.gui.WorkbenchFrame.QurateAction
    • org.fhcrc.cpl.viewer.gui.WorkbenchFrame.UrlAction
      • org.fhcrc.cpl.viewer.gui.WorkbenchFrame.HelpAction
      • org.fhcrc.cpl.viewer.gui.WorkbenchFrame.SupportAction
  • javax.swing.AbstractCellEditor (implements javax.swing.CellEditor, java.io.Serializable)
    • javax.swing.DefaultCellEditor (implements javax.swing.table.TableCellEditor, javax.swing.tree.TreeCellEditor)
      • org.fhcrc.cpl.viewer.mrm.utilities.NumberTableCellEditor
    • org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame.FeatureSelectionDialog.BrowseEditor (implements java.awt.event.ActionListener, javax.swing.table.TableCellEditor)
    • org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame.FeatureSelectionDialog.ColorEditor (implements java.awt.event.ActionListener, javax.swing.table.TableCellEditor)
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • org.fhcrc.cpl.toolbox.proteomics.MS2ModificationList
  • org.fhcrc.cpl.toolbox.AbstractConvertHelper
    • org.fhcrc.cpl.viewer.util.ConvertHelper
  • org.fhcrc.cpl.toolbox.AbstractConvertHelper.NullSafeConverter (implements org.apache.commons.beanutils.Converter)
  • org.jfree.data.general.AbstractDataset (implements java.lang.Cloneable, org.jfree.data.general.Dataset, java.io.ObjectInputValidation, java.io.Serializable)
    • org.jfree.data.general.AbstractSeriesDataset (implements java.io.Serializable, org.jfree.data.general.SeriesChangeListener, org.jfree.data.general.SeriesDataset)
      • org.jfree.data.xy.AbstractXYDataset (implements org.jfree.data.xy.XYDataset)
        • org.jfree.data.xy.AbstractIntervalXYDataset (implements org.jfree.data.xy.IntervalXYDataset)
          • org.fhcrc.cpl.viewer.gui.SpectrumDataSet
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • org.fhcrc.cpl.toolbox.datastructure.BoundMap (implements java.io.Serializable)
  • javax.swing.AbstractSpinnerModel (implements javax.swing.SpinnerModel)
    • javax.swing.SpinnerNumberModel (implements java.io.Serializable)
      • org.fhcrc.cpl.viewer.gui.SpectrumComponent.SpinnerRunModel
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • javax.swing.table.DefaultTableModel (implements java.io.Serializable)
      • org.fhcrc.cpl.viewer.gui.SelectedForCIDFinder.ResultsDialog.ResultsDialogTableModel
    • org.fhcrc.cpl.viewer.gui.FeatureTableModel
    • org.fhcrc.cpl.viewer.mrm.utilities.PeaksTableModel
  • org.fhcrc.cpl.viewer.feature.extraction.AccurateMassAdjuster
  • org.fhcrc.cpl.viewer.amt.AcrylamideHydrophobicityAdjuster
  • org.fhcrc.cpl.viewer.align.Aligner
    • org.fhcrc.cpl.viewer.align.QuantileRegressionAligner
    • org.fhcrc.cpl.viewer.align.SplineAligner
  • org.fhcrc.cpl.viewer.align.Aligner.HybridFeaturePairSelector (implements org.fhcrc.cpl.viewer.align.Aligner.FeaturePairSelector)
  • org.fhcrc.cpl.viewer.align.Aligner.MassOrMzFeaturePairSelector (implements org.fhcrc.cpl.viewer.align.Aligner.FeaturePairSelector)
    • org.fhcrc.cpl.viewer.align.Aligner.MassFeaturePairSelector (implements org.fhcrc.cpl.viewer.align.Aligner.FeaturePairSelector)
    • org.fhcrc.cpl.viewer.align.Aligner.MzFeaturePairSelector (implements org.fhcrc.cpl.viewer.align.Aligner.FeaturePairSelector)
  • org.fhcrc.cpl.viewer.align.Aligner.PeptideFeaturePairSelector (implements org.fhcrc.cpl.viewer.align.Aligner.FeaturePairSelector)
  • org.fhcrc.cpl.viewer.amt.AmtDatabase (implements java.lang.Cloneable)
  • org.fhcrc.cpl.viewer.amt.AmtDatabaseBuilder
  • org.fhcrc.cpl.viewer.amt.AmtDatabaseFeatureSetGenerator
  • org.fhcrc.cpl.viewer.amt.AmtDatabaseManager
  • org.fhcrc.cpl.viewer.amt.AmtDatabaseMatcher
  • org.fhcrc.cpl.viewer.amt.AmtDatabaseMatcher.PeptideProphetComparatorDesc (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.amt.AmtFeatureSetMatcherFactory
  • org.fhcrc.cpl.viewer.amt.AMTFileRestrictor
  • org.fhcrc.cpl.viewer.amt.AmtLabeledQuant
  • org.fhcrc.cpl.viewer.amt.AmtMatchedProtein
  • org.fhcrc.cpl.viewer.amt.AmtMatchedProtein.AmtMatchedPeptide
  • org.fhcrc.cpl.viewer.amt.AmtMatchProbabilityAssigner
  • org.fhcrc.cpl.viewer.amt.AmtPeptideEntry
  • org.fhcrc.cpl.viewer.amt.AmtPeptideEntry.AmtPeptideModificationStateEntry
  • org.fhcrc.cpl.viewer.amt.AmtPeptideEntry.AmtPeptideObservation
  • org.fhcrc.cpl.viewer.amt.AmtRunEntry
  • org.fhcrc.cpl.viewer.amt.AmtTsvReader
  • org.fhcrc.cpl.viewer.amt.AmtTsvReader.AmtTsvRow
  • org.fhcrc.cpl.viewer.amt.AmtUtilities
  • org.fhcrc.cpl.viewer.amt.AmtXmlReader
  • org.fhcrc.cpl.viewer.amt.AmtXmlWriter
  • org.fhcrc.cpl.toolbox.proteomics.feature.AnalyzeICAT
  • org.fhcrc.cpl.toolbox.proteomics.feature.AnalyzeICAT.IsotopicLabel
  • org.fhcrc.cpl.viewer.Application (implements org.fhcrc.cpl.toolbox.ApplicationContext.ApplicationContextProvider)
  • org.fhcrc.cpl.toolbox.ApplicationContext
  • org.fhcrc.cpl.toolbox.ApplicationContext.DefaultApplicationContext (implements org.fhcrc.cpl.toolbox.ApplicationContext.ApplicationContextProvider)
  • junit.framework.Assert
    • junit.framework.TestCase (implements junit.framework.Test)
      • org.fhcrc.cpl.toolbox.test.BaseCommandTest
        • org.fhcrc.cpl.toolbox.test.commandline.BaseCommandLineTest
          • org.fhcrc.cpl.viewer.test.commandline.FilterFeaturesTest (implements junit.framework.Test)
          • org.fhcrc.cpl.viewer.test.commandline.FindPeptidesTest (implements junit.framework.Test)
          • org.fhcrc.cpl.viewer.test.commandline.PeptideArrayTest (implements junit.framework.Test)
      • org.fhcrc.cpl.toolbox.filehandler.TabLoader.TabLoaderTestCase
  • org.jfree.chart.axis.Axis (implements java.lang.Cloneable, java.io.Serializable)
    • org.jfree.chart.axis.ValueAxis (implements java.lang.Cloneable, org.jfree.util.PublicCloneable, java.io.Serializable)
      • org.jfree.chart.axis.NumberAxis (implements java.lang.Cloneable, java.io.Serializable)
        • org.fhcrc.cpl.viewer.mrm.utilities.CenterZoomNumberAxis
  • org.fhcrc.cpl.viewer.feature.extraction.BackgroundRemover
  • org.fhcrc.cpl.toolbox.commandline.arguments.BaseArgumentDefinitionImpl (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.commandline.arguments.BooleanArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.commandline.arguments.DecimalArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.commandline.arguments.DecimalListArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.commandline.arguments.DeltaMassArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.commandline.arguments.EnumeratedValuesArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.commandline.arguments.FileArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
      • org.fhcrc.cpl.toolbox.commandline.arguments.DirectoryToReadArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
      • org.fhcrc.cpl.toolbox.commandline.arguments.DirectoryToWriteArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
      • org.fhcrc.cpl.toolbox.commandline.arguments.FileToReadArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
        • org.fhcrc.cpl.toolbox.proteomics.commandline.arguments.FastaFileArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
        • org.fhcrc.cpl.toolbox.proteomics.commandline.arguments.FeatureFileArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
      • org.fhcrc.cpl.toolbox.commandline.arguments.FileToWriteArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.commandline.arguments.FileToReadListArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.commandline.arguments.IntegerArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.proteomics.commandline.arguments.ModificationListArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.commandline.arguments.StringArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
    • org.fhcrc.cpl.toolbox.commandline.arguments.StringListArgumentDefinition (implements org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition)
  • org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
    • org.fhcrc.cpl.viewer.commandline.modules.BaseViewerCommandLineModuleImpl
      • org.fhcrc.cpl.viewer.align.commandline.AlignCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.amt.commandline.AmtDatabaseDiagnosticCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.amt.commandline.AmtDatabaseFeatureSetCreatorCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.amt.commandline.AmtDatabaseManagerCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.amt.commandline.AmtDatabaseMatcherCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.amt.commandline.AmtLabeledQuantCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.CalculateFDRCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.CalibrateFeatureMassesCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.CalibrateMzxmlMassesCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.amt.commandline.CombineAmtMs2FilesCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.CombinePepXmlFilesCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.CompareFastasCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.ConsensusFeatureFileCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.ConvertFeatureFileCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.CorrectPrecursorMzCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.CreateIndexCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.DeconvoluteCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
        • org.fhcrc.cpl.viewer.quant.commandline.QuantCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
          • org.fhcrc.cpl.viewer.quant.commandline.IcatCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.DetectAdductsCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.DumpWindow2DCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.FeatureSelectionParamsCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
        • org.fhcrc.cpl.viewer.amt.commandline.AmtDatabaseCreatorCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
        • org.fhcrc.cpl.viewer.ms2.commandline.ExtractRunsFromPepXmlCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
        • org.fhcrc.cpl.viewer.commandline.modules.FilterFeaturesCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
        • org.fhcrc.cpl.viewer.align.commandline.PeptideArrayCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.FeatureSetMatcherCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.FilterPeptideRegexpCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.FilterPepXmlCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.FilterReverseDBHitsCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.FindIndistinguishableProteinsCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.FindPeptidesCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.FindSearchScoreCutoffForFARCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.quant.commandline.FlagQuantEventsCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.FlipPepXMLRatiosCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.GuessProteinsFromFastaCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.HydrophobicityAlgorithmAnalyzerCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.MassAccuracyCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.mrm.commandline.MRMCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.MS2ScanViewerCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.align.commandline.PeptideArrayAnalyzerCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.PeptideCompareCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.PeptidePeakModellerCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.quant.commandline.PeptideQuantVisualizationCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.quant.commandline.PeptideRatioVariationCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.PickTargetedMS2CandidatesCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.PlotDeltaMassesCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.PlotFeatureAttributesCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.PlotMassCalibrationCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.PlotMs1Ms2ScanCountsCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.PopulateMS2TimesCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.PostProcessPepXMLCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.ProteinFractionsSpreadsheetCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.quant.commandline.ProteinQuantChartsCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.amt.commandline.ProteinRollupCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.ProtXmlCompareCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.quant.commandline.Q3CommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.qa.commandline.QAExperimentCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.qa.commandline.QAProtXMLCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.ReverseFastaCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.quant.commandline.ReviewQuantitationCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.RunCommandFileCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.SaveImageCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.SaveMzxmlWindowCommandLineModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.SpectralCountCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.SpreadsheetMergeCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.ms2.commandline.SummarizeProtXmlCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.UserManualCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
      • org.fhcrc.cpl.viewer.commandline.modules.ViewSpectrumChartCLM (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
    • org.fhcrc.cpl.toolbox.commandline.DemoCommandModule (implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule)
  • org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.BaseFeatureSetFileHandler
    • org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.APMLFeatureFileHandler (implements org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.FeatureSetFileHandler)
    • org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.HardklorFeatureFileHandler (implements org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.FeatureSetFileHandler)
    • org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.NativeTSVFeatureFileHandler (implements org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.FeatureSetFileHandler)
    • org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.PepXMLFeatureFileHandler (implements org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.FeatureSetFileHandler)
  • org.fhcrc.cpl.toolbox.proteomics.feature.matching.BaseFeatureSetMatcherImpl (implements org.fhcrc.cpl.toolbox.proteomics.feature.matching.FeatureSetMatcher)
    • org.fhcrc.cpl.toolbox.proteomics.feature.matching.ClusteringFeatureSetMatcher (implements org.fhcrc.cpl.toolbox.proteomics.feature.matching.FeatureSetMatcher)
    • org.fhcrc.cpl.toolbox.proteomics.feature.matching.RecursiveFeatureSetMatcher (implements org.fhcrc.cpl.toolbox.proteomics.feature.matching.FeatureSetMatcher)
  • org.fhcrc.cpl.toolbox.proteomics.feature.matching.BaseFeatureSetMatcherImpl.FeatureElutionClosenessToBaseFeatureComparatorDesc (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.feature.extraction.strategy.BaseFeatureStrategy (implements org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategy)
    • org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategyWindow
      • org.fhcrc.cpl.viewer.feature.extraction.strategy.BaseFeatureStrategyModular
        • org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategyPeakClusters
          • org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategyPeakClustersNegCharge
        • org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategySmallMolecule
  • org.fhcrc.cpl.toolbox.gui.BaseImagePanelLayer (implements org.fhcrc.cpl.toolbox.gui.ImagePanelLayer)
    • org.fhcrc.cpl.viewer.gui.MSImageComponent.MSImagePanel.FeatureSetImagePanelLayer
    • org.fhcrc.cpl.viewer.gui.MSImageComponent.MSImagePanel.TopPanelLayer
  • org.fhcrc.cpl.viewer.feature.extraction.BasePeakCombiner (implements org.fhcrc.cpl.viewer.feature.extraction.PeakCombiner)
    • org.fhcrc.cpl.viewer.feature.extraction.DefaultPeakCombiner
    • org.fhcrc.cpl.viewer.feature.extraction.SmallMoleculePeakCombiner
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.BasePepXmlWriter
    • org.fhcrc.cpl.toolbox.proteomics.feature.FeaturePepXmlWriter
  • org.fhcrc.cpl.toolbox.statistics.BasicStatistics
  • org.fhcrc.cpl.viewer.database.dbclasses.BioSequenceDBC
  • org.fhcrc.cpl.toolbox.datastructure.BoundMap.TestBean
  • org.fhcrc.cpl.toolbox.BrowserController
  • org.fhcrc.cpl.viewer.align.BucketedPeptideArray (implements java.lang.Runnable)
  • org.fhcrc.cpl.viewer.ms2.commandline.CalculateFDRCLM.SearchScoreComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.gui.chart.ChartDialog.ResizeListener (implements java.awt.event.ComponentListener)
  • org.fhcrc.cpl.viewer.gui.ChooseCommandDialog.RunCommandAction.ChooseModuleListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.gui.ChooseCommandDialog.RunCommandAction.ExecuteModuleListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.toolbox.commandline.CLMUserManualGenerator
    • org.fhcrc.cpl.viewer.ViewerUserManualGenerator
  • org.fhcrc.cpl.toolbox.proteomics.Clusterer2D
    • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureClusterer
  • org.fhcrc.cpl.toolbox.proteomics.Clusterer2D.BucketSummary
  • org.fhcrc.cpl.toolbox.proteomics.Clusterer2D.ClusterDimensionSplitCalculator
    • org.fhcrc.cpl.toolbox.proteomics.Clusterer2D.DefaultClusterDimensionSplitCalculator
  • org.fhcrc.cpl.toolbox.proteomics.Clusterer2D.TreeEntry (implements java.lang.Comparable<T>)
  • org.fhcrc.cpl.viewer.CommandFileRunner
  • org.fhcrc.cpl.toolbox.commandline.CommandLineModuleDiscoverer
    • org.fhcrc.cpl.viewer.commandline.ViewerCommandLineModuleDiscoverer
  • org.fhcrc.cpl.toolbox.commandline.CommandLineModuleUtilities
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.AbstractButton (implements java.awt.ItemSelectable, javax.swing.SwingConstants)
          • javax.swing.JToggleButton (implements javax.accessibility.Accessible)
            • javax.swing.JCheckBox (implements javax.accessibility.Accessible)
              • org.fhcrc.cpl.viewer.mrm.utilities.MRMBooleanRenderer (implements javax.swing.table.TableCellRenderer, javax.swing.plaf.UIResource)
        • javax.swing.JFileChooser (implements javax.accessibility.Accessible)
          • org.fhcrc.cpl.viewer.gui.WorkbenchFileChooser
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • javax.swing.table.DefaultTableCellRenderer (implements java.io.Serializable, javax.swing.table.TableCellRenderer)
            • org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame.FeatureSelectionDialog.NumberRenderer
            • org.fhcrc.cpl.viewer.mrm.utilities.MRMNumberTableRenderer
            • org.fhcrc.cpl.viewer.quant.gui.QuantEventsSummaryTable.CurationStatusRenderer
            • org.fhcrc.cpl.viewer.quant.gui.QuantEventsSummaryTable.FlagQuantStatusRenderer
          • org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame.FeatureSelectionDialog.ColorRenderer (implements javax.swing.table.TableCellRenderer)
          • org.fhcrc.cpl.viewer.mrm.utilities.MRMDaughterTableRenderer (implements javax.swing.table.TableCellRenderer)
          • org.fhcrc.cpl.viewer.gui.MRMDialog.MRMTransitionTableRenderer (implements javax.swing.table.TableCellRenderer)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • org.fhcrc.cpl.viewer.gui.HeatMapPanel (implements java.awt.event.ComponentListener, java.beans.PropertyChangeListener)
          • org.fhcrc.cpl.toolbox.gui.HtmlGenerator
          • org.fhcrc.cpl.toolbox.gui.ImagePanel
          • org.fhcrc.cpl.viewer.gui.MRMDialog.coloredMRMListRenderer (implements javax.swing.ListCellRenderer)
          • org.fhcrc.cpl.viewer.ms2.gui.MS2ScanViewer
          • org.fhcrc.cpl.viewer.ms2.gui.MS2ScanViewer.MultiMS2ScanViewer
          • org.fhcrc.cpl.toolbox.gui.chart.MultiChartDisplayPanel
            • org.fhcrc.cpl.toolbox.gui.chart.DropdownMultiChartDisplayPanel
            • org.fhcrc.cpl.toolbox.gui.chart.TabbedMultiChartDisplayPanel
          • org.fhcrc.cpl.toolbox.gui.chart.PanelWithChart
            • org.fhcrc.cpl.toolbox.gui.chart.PanelWithBarChart
              • org.fhcrc.cpl.viewer.quant.gui.PanelWithProteinRatiosChart
            • org.fhcrc.cpl.toolbox.gui.chart.PanelWithBlindImageChart
              • org.fhcrc.cpl.toolbox.gui.chart.PanelWithRPairsPlot
              • org.fhcrc.cpl.toolbox.gui.chart.PanelWithRPerspectivePlot
            • org.fhcrc.cpl.toolbox.gui.chart.PanelWithBoxAndWhiskerChart
            • org.fhcrc.cpl.toolbox.gui.chart.PanelWithHeatMap
              • org.fhcrc.cpl.viewer.gui.util.PanelWithFractionatedExpHeatMap
              • org.fhcrc.cpl.viewer.quant.gui.PanelWithSpectrumChart
            • org.fhcrc.cpl.toolbox.gui.chart.PanelWithHistogram
            • org.fhcrc.cpl.toolbox.gui.chart.PanelWithLineChart
              • org.fhcrc.cpl.toolbox.gui.chart.PanelWithPeakChart
            • org.fhcrc.cpl.toolbox.gui.chart.PanelWithPieChart
            • org.fhcrc.cpl.toolbox.gui.chart.PanelWithScatterPlot
          • org.fhcrc.cpl.viewer.quant.gui.PanelWithLogRatioHistAndFields
          • org.fhcrc.cpl.toolbox.gui.chart.PanelWithVenn
          • org.fhcrc.cpl.viewer.gui.SurfaceFrame
        • javax.swing.JPopupMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
          • org.fhcrc.cpl.viewer.gui.MSImageComponent.RightMousePopupMenu
          • org.fhcrc.cpl.viewer.gui.PropertiesPane.RightMousePopupMenu
          • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.ProteinTablePopupMenu
        • javax.swing.JScrollPane (implements javax.accessibility.Accessible, javax.swing.ScrollPaneConstants)
          • org.fhcrc.cpl.toolbox.gui.HtmlViewerPanel
        • javax.swing.JTable (implements javax.accessibility.Accessible, javax.swing.event.CellEditorListener, javax.swing.event.ListSelectionListener, javax.swing.event.RowSorterListener, javax.swing.Scrollable, javax.swing.event.TableColumnModelListener, javax.swing.event.TableModelListener)
          • org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame.FeatureSelectionDialog.FeatureFrame.FeatureTable
          • org.fhcrc.cpl.viewer.quant.gui.ProteinSummarySelectorFrame.ProteinSummaryTable
          • org.fhcrc.cpl.viewer.quant.QuantEvent.QuantEventPropertiesTable
          • org.fhcrc.cpl.viewer.quant.gui.QuantEventsSummaryTable
        • org.fhcrc.cpl.toolbox.gui.ScrollableImage (implements java.awt.event.MouseMotionListener, javax.swing.Scrollable)
          • org.fhcrc.cpl.viewer.gui.MSDetailPanel
          • org.fhcrc.cpl.viewer.gui.MSImageComponent.MSImagePanel
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.fhcrc.cpl.toolbox.gui.chart.ChartDialog
              • org.fhcrc.cpl.toolbox.gui.chart.ScatterPlotDialog
            • org.fhcrc.cpl.viewer.gui.ChooseCommandDialog
            • org.fhcrc.cpl.viewer.gui.ExtractFeatureRangesAction.ExtractFeatureRangesDialog
            • org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame.FeatureSelectionDialog
            • org.fhcrc.cpl.toolbox.gui.InteractiveModuleFrame
              • org.fhcrc.cpl.viewer.gui.ViewerInteractiveModuleFrame
            • org.fhcrc.cpl.viewer.gui.MSDetailPanel.DetailDialog
            • org.fhcrc.cpl.viewer.gui.OpenFastaDialog (implements java.beans.PropertyChangeListener)
            • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame
            • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.ParametersDialog
            • org.fhcrc.cpl.viewer.quant.gui.ProteinQuantSummaryFrame
            • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer
            • org.fhcrc.cpl.viewer.gui.SavePartialMzxmlDialog
            • org.fhcrc.cpl.viewer.gui.SelectedForCIDFinder.ResultsDialog
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame.FeatureSelectionDialog.FeatureFrame
            • org.fhcrc.cpl.viewer.gui.HeatMapFrame
            • org.fhcrc.cpl.viewer.gui.MRMDialog (implements java.io.Serializable)
            • org.fhcrc.cpl.viewer.quant.gui.ProteinSummarySelectorFrame
            • org.fhcrc.cpl.toolbox.gui.widget.SplashFrame
            • org.fhcrc.cpl.viewer.gui.WorkbenchFrame (implements java.beans.PropertyChangeListener)
  • org.fhcrc.cpl.viewer.util.ConvertHelper.ChargeWrapper (implements org.apache.commons.beanutils.Converter)
  • org.fhcrc.cpl.viewer.util.ConvertHelper.DateFriendlyStringConverter (implements org.apache.commons.beanutils.Converter)
  • org.fhcrc.cpl.viewer.util.ConvertHelper.LenientDateConverter (implements org.apache.commons.beanutils.Converter)
  • org.fhcrc.cpl.viewer.util.ConvertHelper.LenientTimestampConverter (implements org.apache.commons.beanutils.Converter)
  • org.fhcrc.cpl.viewer.util.ConvertHelper.MyBooleanConverter (implements org.apache.commons.beanutils.Converter)
  • org.fhcrc.cpl.viewer.util.ConvertHelper.PercentWrapper (implements org.apache.commons.beanutils.Converter)
  • org.fhcrc.cpl.toolbox.CPUTimer
  • org.fhcrc.cpl.toolbox.gui.chart.CrosshairChangeListener (implements org.jfree.chart.event.ChartProgressListener)
  • org.fhcrc.cpl.toolbox.proteomics.feature.Deconvoluter (implements java.lang.Cloneable)
  • org.fhcrc.cpl.viewer.feature.extraction.DefaultFeatureScorer (implements org.fhcrc.cpl.viewer.feature.extraction.FeatureScorer)
  • javax.swing.DefaultListSelectionModel (implements java.lang.Cloneable, javax.swing.ListSelectionModel, java.io.Serializable)
    • org.fhcrc.cpl.viewer.gui.MRMDialog.peaksTableSelectionModel
  • org.fhcrc.cpl.toolbox.commandline.arguments.DeltaMassArgumentDefinition.DeltaMassWithType
  • org.fhcrc.cpl.toolbox.datastructure.DoubleArray
  • org.fhcrc.cpl.toolbox.gui.chart.DropdownMultiChartDisplayPanel.ComboListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.toolbox.gui.chart.DropdownMultiChartDisplayPanel.SlideshowManager (implements java.lang.Runnable)
  • org.fhcrc.cpl.viewer.DumpWindow2D
  • org.fhcrc.cpl.viewer.mrm.ElutionCurve
  • org.fhcrc.cpl.viewer.mrm.ElutionCurveStrategy
    • org.fhcrc.cpl.viewer.mrm.BasicElutionCurveStrategy
    • org.fhcrc.cpl.viewer.mrm.BasicLowIntensityElutionCurveStrategy
    • org.fhcrc.cpl.viewer.mrm.NoiseSubtractionElutionCurveStrategy
    • org.fhcrc.cpl.viewer.mrm.ThermoElutionCurveStrategy
  • org.fhcrc.cpl.viewer.util.ElutionDataPoint
  • org.fhcrc.cpl.viewer.database.dbclasses.ExperimentRunDBC
  • org.fhcrc.cpl.viewer.feature.ExtractEdgeFeatures
  • org.fhcrc.cpl.viewer.gui.ExtractFeatureRangesAction.FeatureScanner (implements java.lang.Runnable)
  • org.fhcrc.cpl.viewer.feature.ExtractMaxima2D
  • org.fhcrc.cpl.viewer.database.loader.FastaDBLoader
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.FastaLoader
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.FastaLoader.ProteinIterator (implements java.util.Iterator<E>)
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.FastaValidator
  • org.fhcrc.cpl.toolbox.proteomics.feature.Feature.IntensityDescComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.feature.Feature.MassAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.feature.Feature.MzAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.feature.Feature.MzDistAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.feature.Feature.MzScanAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.feature.Feature.PeaksKLComparatorDesc (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.feature.Feature.ScanAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.feature.Feature.ScanChargeMzAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureClusterer.FeatureClusterable (implements org.fhcrc.cpl.toolbox.proteomics.Clusterer2D.Clusterable)
    • org.fhcrc.cpl.viewer.amt.AmtUtilities.FeatureMassHydroClusterable
    • org.fhcrc.cpl.viewer.amt.AmtUtilities.FeatureMzHydroClusterable
    • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureClusterer.FeatureMassScanClusterable
    • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureClusterer.FeatureMassTimeClusterable
    • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureClusterer.FeatureMzScanClusterable
    • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureClusterer.FeatureMzTimeClusterable
  • org.fhcrc.cpl.viewer.feature.FeatureExtractor
    • org.fhcrc.cpl.viewer.feature.FeatureStrategySpectrumFit
    • org.fhcrc.cpl.viewer.feature.FeatureStrategyUsingWindow
      • org.fhcrc.cpl.viewer.feature.FeatureStrategyCentroided
      • org.fhcrc.cpl.viewer.feature.FeatureStrategyCombined
      • org.fhcrc.cpl.viewer.feature.FeatureStrategyGrossFeatures
      • org.fhcrc.cpl.viewer.feature.FeatureStrategyPeakClustersOld
        • org.fhcrc.cpl.viewer.feature.FeatureStrategyPeaks2
      • org.fhcrc.cpl.viewer.feature.FeatureStrategyPeaks
      • org.fhcrc.cpl.viewer.feature.FeatureStrategyUsingWindow2D
        • org.fhcrc.cpl.viewer.feature.FeatureStrategyWavelet2D
      • org.fhcrc.cpl.viewer.feature.FeatureStrategyWavelet
  • org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.FeatureExtraInformationDef
    • org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.AmtExtraInfoDef
    • org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.IsotopicLabelExtraInfoDef
    • org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.MS2ExtraInfoDef
    • org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.TimeExtraInfoDef
  • org.fhcrc.cpl.viewer.feature.extraction.FeatureFinder
  • org.fhcrc.cpl.viewer.feature.extraction.FeatureFindingBroker
  • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureGrouper
  • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureMassCalibrationUtilities
  • org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame.FeatureSelectionDialog.Optimizer (implements java.lang.Runnable)
  • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureSet (implements java.lang.Cloneable)
  • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureSet.FeatureSelector (implements java.lang.Cloneable)
  • org.fhcrc.cpl.toolbox.proteomics.feature.matching.FeatureSetMatcher.FeatureMatchingResult
  • org.fhcrc.cpl.toolbox.commandline.arguments.FileArgumentDefinition.GUIFileChooserButtonListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.ms2.commandline.FindSearchScoreCutoffForFARCLM.PeptideProphetComparatorDesc (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.ms2.commandline.FindSearchScoreCutoffForFARCLM.SearchScoreComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.datastructure.FloatArray
  • org.fhcrc.cpl.toolbox.datastructure.FloatRange (implements java.io.Serializable)
  • org.fhcrc.cpl.viewer.ms2.Fractionation2DUtilities
  • org.fhcrc.cpl.viewer.ms2.Fractionation2DUtilities.FractionatedAMTDatabaseStructure
  • org.fhcrc.cpl.viewer.ms2.Fractionation2DUtilities.FractionatedExperimentStructure
  • org.fhcrc.cpl.viewer.database.dbclasses.GeneDBC
  • org.fhcrc.cpl.viewer.ms2.GeneMappingUtilities
  • org.fhcrc.cpl.viewer.ms2.GeneMappingUtilities.InfoForGene
  • org.fhcrc.cpl.viewer.util.Haar
  • org.fhcrc.cpl.viewer.database.HibernateManager
  • org.fhcrc.cpl.toolbox.gui.HtmlViewerPanel.MyHyperLinkListener (implements javax.swing.event.HyperlinkListener)
  • org.fhcrc.cpl.toolbox.proteomics.Hydrophobicity3
  • org.fhcrc.cpl.viewer.amt.HydrophobicityNormalizer
  • org.fhcrc.cpl.toolbox.proteomics.IdPattern
  • org.fhcrc.cpl.toolbox.datastructure.IntegerArray
  • org.fhcrc.cpl.toolbox.proteomics.gui.IntensityPlot (implements java.io.Serializable)
  • org.fhcrc.cpl.toolbox.proteomics.gui.IntensityPlot.ColorMap
    • org.fhcrc.cpl.toolbox.proteomics.gui.IntensityPlot.CyanMap
    • org.fhcrc.cpl.toolbox.proteomics.gui.IntensityPlot.FancyMap
    • org.fhcrc.cpl.toolbox.proteomics.gui.IntensityPlot.FireMap
    • org.fhcrc.cpl.toolbox.proteomics.gui.IntensityPlot.GrayMap
    • org.fhcrc.cpl.toolbox.proteomics.gui.IntensityPlot.InvFireMap
    • org.fhcrc.cpl.toolbox.proteomics.gui.IntensityPlot.RainbowMap
  • org.fhcrc.cpl.toolbox.gui.InteractiveModuleFrame.ArgHelpListener (implements java.awt.event.MouseListener)
  • org.fhcrc.cpl.toolbox.gui.InteractiveModuleFrame.ArgRequiredListener (implements java.awt.event.MouseListener)
  • org.fhcrc.cpl.toolbox.gui.ListenerHelper
  • org.fhcrc.cpl.viewer.Localizer
  • org.fhcrc.cpl.viewer.Localizer.FontActionListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.Localizer.LanguageActionListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.quant.gui.LogRatioHistMouseListener.SelectedRegionOverlay (implements org.jfree.chart.panel.Overlay)
  • org.fhcrc.cpl.toolbox.proteomics.MassCalibrationUtilities
  • org.fhcrc.cpl.toolbox.proteomics.MassUtilities
  • org.fhcrc.cpl.toolbox.statistics.MatrixUtil
  • org.fhcrc.cpl.toolbox.proteomics.ModifiedAminoAcid
  • java.awt.event.MouseAdapter (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.MouseWheelListener)
    • org.fhcrc.cpl.toolbox.gui.chart.ChartMouseAndMotionListener
      • org.fhcrc.cpl.viewer.quant.gui.LogRatioHistMouseListener
    • org.fhcrc.cpl.toolbox.gui.chart.PanelWithBlindImageChart.PopupListener
  • org.fhcrc.cpl.viewer.mrm.MRMDaughter (implements org.fhcrc.cpl.viewer.mrm.PlotDataSupplier)
  • org.fhcrc.cpl.viewer.mrm.MRMDaughter.MeanMzAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.mrm.MRMDaughter.PrecursorMzComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.gui.MRMDialog.daughterRangeAxisChangeListener (implements org.jfree.chart.event.AxisChangeListener)
  • org.fhcrc.cpl.viewer.gui.MRMDialog.defaultGraphZone (implements org.fhcrc.cpl.viewer.mrm.utilities.graphZone)
  • org.fhcrc.cpl.viewer.gui.MRMDialog.domainAxisZoomCoordinator (implements org.jfree.chart.event.AxisChangeListener)
  • org.fhcrc.cpl.viewer.gui.MRMDialog.originalReParser (implements org.fhcrc.cpl.viewer.gui.MRMDialog.mzXML2TransitionArray)
  • org.fhcrc.cpl.viewer.gui.MRMDialog.peaksTableListener (implements javax.swing.event.TableModelListener)
  • org.fhcrc.cpl.viewer.gui.MRMDialog.PeaksTableListSelectionListener (implements javax.swing.event.ListSelectionListener)
  • org.fhcrc.cpl.viewer.gui.MRMDialog.thermoReParser (implements org.fhcrc.cpl.viewer.gui.MRMDialog.mzXML2TransitionArray)
  • org.fhcrc.cpl.viewer.gui.MRMDialog.transitionListSelectionListener (implements javax.swing.event.ListSelectionListener)
  • org.fhcrc.cpl.viewer.gui.MRMDialog.zoomedGraphZone (implements org.fhcrc.cpl.viewer.mrm.utilities.graphZone)
  • org.fhcrc.cpl.viewer.gui.MRMDialog.zoomToCurveGraphZone (implements org.fhcrc.cpl.viewer.mrm.utilities.graphZone)
  • org.fhcrc.cpl.viewer.mrm.utilities.MRMerMouseListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • org.fhcrc.cpl.viewer.mrm.MRMTransition (implements org.fhcrc.cpl.viewer.mrm.PlotDataSupplier)
  • org.fhcrc.cpl.viewer.mrm.MRMTransition.PrecursorMzComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.MS2Correct
  • org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.MS2ExtraInfoDef.PeptideProphetAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.MS2ExtraInfoDef.PeptideProphetDescComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.MS2Loader
    • org.fhcrc.cpl.toolbox.proteomics.filehandler.PepXmlLoader
  • org.fhcrc.cpl.toolbox.proteomics.MS2Modification
  • org.fhcrc.cpl.viewer.ms2.commandline.MS2ScanViewerCLM.MS2ScanChangedListener (implements javax.swing.event.ChangeListener)
  • org.fhcrc.cpl.viewer.gui.MSImageComponent
  • org.fhcrc.cpl.viewer.gui.MSImageComponent.ColorActionListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.gui.MSImageComponent.LayerAdjustmentListener (implements java.awt.event.AdjustmentListener)
  • org.fhcrc.cpl.viewer.gui.MSImageComponent.RightPopupListener (implements javax.swing.event.PopupMenuListener)
  • org.fhcrc.cpl.toolbox.proteomics.MSRun (implements java.io.Serializable)
  • org.fhcrc.cpl.toolbox.proteomics.MSRun.MSScan (implements org.fhcrc.cpl.toolbox.proteomics.Scan, java.io.Serializable)
  • org.fhcrc.cpl.toolbox.gui.chart.MultiChartDisplayPanel.ResizeListener (implements java.awt.event.ComponentListener)
  • org.fhcrc.cpl.toolbox.gui.chart.MultiChartDisplayPanel.TabFocusListener (implements javax.swing.event.ChangeListener)
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.MzXmlWriter
  • org.fhcrc.cpl.toolbox.normalize.Normalizer
  • org.fhcrc.cpl.viewer.gui.OpenFastaDialog.PepDisplay
  • org.fhcrc.cpl.viewer.gui.OpenFastaDialog.PeptideTableSelectionListener (implements javax.swing.event.ListSelectionListener)
  • org.fhcrc.cpl.toolbox.datastructure.Pair<Type1,Type2> (implements java.util.Map.Entry<K,V>, java.io.Serializable)
  • org.fhcrc.cpl.toolbox.gui.chart.PanelWithBlindImageChart.ResizeListener (implements java.awt.event.ComponentListener)
  • org.fhcrc.cpl.toolbox.gui.chart.PanelWithLineChart.NullLabelGenerator (implements org.jfree.chart.labels.XYItemLabelGenerator)
  • org.fhcrc.cpl.viewer.quant.gui.PanelWithLogRatioHistAndFields.LogRatioHistogramListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.toolbox.gui.chart.PanelWithRPerspectivePlot.LineVariables
  • org.fhcrc.cpl.viewer.quant.PeakOverlapCorrection
  • org.fhcrc.cpl.toolbox.proteomics.Peptide
  • org.fhcrc.cpl.viewer.align.PeptideArrayAnalyzer
  • org.fhcrc.cpl.viewer.database.dbclasses.PeptideDBC
  • org.fhcrc.cpl.toolbox.proteomics.PeptideGenerator (implements java.lang.Runnable)
  • org.fhcrc.cpl.toolbox.proteomics.PeptideGenerator.CommandLinePeptideListener (implements org.fhcrc.cpl.toolbox.proteomics.PeptideGenerator.PeptideListener)
  • org.fhcrc.cpl.viewer.database.dbclasses.PeptideHitDBC
  • org.fhcrc.cpl.viewer.amt.PeptideMatcher
  • org.fhcrc.cpl.toolbox.proteomics.PeptideUtilities
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.PepXmlAnalysisResultHandler
    • org.fhcrc.cpl.toolbox.proteomics.filehandler.PeptideProphetHandler
    • org.fhcrc.cpl.toolbox.proteomics.filehandler.Q3Handler
    • org.fhcrc.cpl.toolbox.proteomics.filehandler.XPressHandler
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.PepXmlAnalysisResultHandler.PepXmlAnalysisResult
    • org.fhcrc.cpl.toolbox.proteomics.filehandler.PeptideProphetHandler.PeptideProphetResult
    • org.fhcrc.cpl.toolbox.proteomics.filehandler.RelativeQuantAnalysisResult
      • org.fhcrc.cpl.toolbox.proteomics.filehandler.Q3Handler.Q3Result
      • org.fhcrc.cpl.toolbox.proteomics.filehandler.XPressHandler.XPressResult
  • org.fhcrc.cpl.viewer.util.PepXmlChannelSplitter
  • org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.PepXMLFeatureFileHandler.PepXMLFeatureSetIterator (implements java.util.Iterator<E>)
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.PepXmlLoader.FractionIterator (implements java.util.Iterator<E>)
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.PepXmlLoader.PeptideIterator (implements java.util.Iterator<E>)
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.PepXmlLoader.PepXmlFraction
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.PepXmlLoader.PepXmlPeptide
  • org.fhcrc.cpl.viewer.ms2.commandline.PickTargetedMS2CandidatesCLM.PeptideCountsComparatorDesc (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.gui.PropertiesPane
  • org.fhcrc.cpl.toolbox.PropertyBag
    • org.fhcrc.cpl.toolbox.gui.AwtPropertyBag
  • org.fhcrc.cpl.toolbox.proteomics.Protein
  • org.fhcrc.cpl.toolbox.proteomics.Protein.Alias
  • org.fhcrc.cpl.toolbox.proteomics.Protein.HeaderComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.Protein.LookupComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.Protein.SequenceComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.database.dbclasses.ProteinDBC
  • org.fhcrc.cpl.viewer.amt.ProteinDisplay
  • org.fhcrc.cpl.viewer.database.loader.ProteinGeneMapDBLoader
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.ProteinGroup
  • org.fhcrc.cpl.viewer.database.dbclasses.ProteinGroupDBC
  • org.fhcrc.cpl.viewer.database.dbclasses.ProteinHitDBC
  • org.fhcrc.cpl.viewer.amt.ProteinMatcher
  • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.ProteinMS1MatchesComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame.ProteinMS1PercentCoverageComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.quant.gui.ProteinQuantSummaryFrame.ChartBuilderWorker.ProgressBarUpdater (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.quant.gui.ProteinQuantSummaryFrame.EventsTableListSelectionHandler (implements javax.swing.event.ListSelectionListener)
  • org.fhcrc.cpl.viewer.quant.gui.ProteinQuantSummaryFrame.LogRatioHistogramListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.quant.gui.ProteinQuantSummaryFrame.ProteinTableListSelectionHandler (implements javax.swing.event.ListSelectionListener)
  • org.fhcrc.cpl.viewer.quant.gui.ProteinQuantSummaryFrame.ProteinTableLogRatioHistogramListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.database.dbclasses.ProteinSearchDBC
  • org.fhcrc.cpl.viewer.quant.gui.ProteinSummarySelectorFrame.LogRatioHistogramListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.quant.gui.ProteinSummarySelectorFrame.ProteinRatioAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.ProteinUtilities
  • org.fhcrc.cpl.toolbox.proteomics.ProteomicsRegressionUtilities
  • org.fhcrc.cpl.viewer.ms2.commandline.ProtXmlCompareCLM.ProteinInfo
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.ProtXmlReader
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.ProtXmlReader.Peptide
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.ProtXmlReader.Protein (implements java.lang.Cloneable)
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.ProtXmlReader.ProteinGroupIterator (implements java.util.Iterator<E>)
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.ProtXmlReader.QuantitationRatio
  • org.fhcrc.cpl.viewer.quant.Q3
  • org.fhcrc.cpl.viewer.quant.Q3.IsotopicLabel
  • org.fhcrc.cpl.viewer.qa.QAUtilities
  • org.fhcrc.cpl.viewer.quant.QuantEvent
  • org.fhcrc.cpl.viewer.quant.QuantEvent.PeptideSequenceAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.quant.QuantEvent.PeptideSequenceAscFractionAscChargeModificationsAscRatioAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.quant.QuantEvent.ProteinPeptideFractionChargeModificationsRatioAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.quant.QuantEvent.RatioAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.quant.QuantEvent.ScanAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.quant.QuantEventAssessor
  • org.fhcrc.cpl.viewer.quant.QuantEventAssessor.QuantEventAssessment
  • org.fhcrc.cpl.viewer.quant.QuantEventAssessor.QuantPeakSetSummary
  • org.fhcrc.cpl.viewer.quant.gui.QuantEventsSummaryTable.JSliderRenderer (implements javax.swing.table.TableCellRenderer)
  • org.fhcrc.cpl.viewer.quant.gui.QuantEventsSummaryTable.QuantEventChangeListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.EventSummaryTableListSelectionHandler (implements javax.swing.event.ListSelectionListener)
  • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.LeftPanelResizeListener (implements java.awt.event.ComponentListener)
  • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.ProteinSelectedActionListener (implements java.awt.event.ActionListener)
  • org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer.RightPanelResizeListener (implements java.awt.event.ComponentListener)
  • org.fhcrc.cpl.toolbox.proteomics.QuantitationUtilities
  • org.fhcrc.cpl.viewer.quant.gui.QuantitationVisualizer
  • org.fhcrc.cpl.viewer.quant.gui.QuantitationVisualizer.ModResidueMassAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.statistics.RegressionUtilities
  • org.fhcrc.cpl.toolbox.statistics.RegressionUtilities.AnovaResult
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.RelativeQuantAnalysisSummary
    • org.fhcrc.cpl.toolbox.proteomics.filehandler.Q3AnalysisSummary
    • org.fhcrc.cpl.toolbox.proteomics.filehandler.XPressAnalysisSummary
  • org.fhcrc.cpl.toolbox.statistics.RInterface
  • org.fhcrc.cpl.toolbox.Rounder
  • javax.swing.RowFilter<M,I>
    • org.fhcrc.cpl.viewer.quant.gui.ProteinSummarySelectorFrame.ProteinSummaryTable.RatioRowFilter
    • org.fhcrc.cpl.viewer.quant.gui.QuantEventsSummaryTable.RatioRowFilter
  • org.fhcrc.cpl.viewer.gui.SelectedForCIDFinder
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.SensitivitySummary
    • org.fhcrc.cpl.toolbox.proteomics.filehandler.PeptideProphetSummary
  • org.fhcrc.cpl.toolbox.proteomics.filehandler.SensitivitySummary.ProbabilityInfo (implements java.lang.Comparable<T>)
  • org.jfree.data.general.Series (implements java.lang.Cloneable, java.io.Serializable)
    • org.jfree.data.xy.XYSeries (implements java.lang.Cloneable, java.io.Serializable)
      • org.fhcrc.cpl.viewer.gui.SpectrumXYSeries
  • org.fhcrc.cpl.toolbox.filehandler.SimpleXMLEventRewriter
  • org.fhcrc.cpl.toolbox.filehandler.SimpleXMLEventRewriter.SimpleEndElement (implements org.fhcrc.cpl.toolbox.filehandler.SimpleXMLEventRewriter.SimpleElement)
  • org.fhcrc.cpl.toolbox.filehandler.SimpleXMLEventRewriter.SimpleSpaceElement (implements org.fhcrc.cpl.toolbox.filehandler.SimpleXMLEventRewriter.SimpleElement)
  • org.fhcrc.cpl.toolbox.filehandler.SimpleXMLEventRewriter.SimpleStartElement (implements org.fhcrc.cpl.toolbox.filehandler.SimpleXMLEventRewriter.SimpleElement)
  • org.fhcrc.cpl.viewer.feature.Smooth2D
    • org.fhcrc.cpl.viewer.feature.FeatureStrategyWavelet2D.SmoothWavelet
  • org.fhcrc.cpl.viewer.feature.extraction.SmootherCreator
  • org.fhcrc.cpl.toolbox.datastructure.SpatialQuadrantTreeNode.DataPointXComparatorAsc (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.datastructure.SpatialQuadrantTreeNode.DataPointYComparatorAsc (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.datastructure.SpatialQuadrantTreeNode.DistanceToInterestingPointComparatorAsc (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.toolbox.proteomics.feature.Spectrum
  • org.fhcrc.cpl.toolbox.proteomics.feature.Spectrum.Peak
    • org.fhcrc.cpl.toolbox.proteomics.feature.Feature (implements java.lang.Cloneable)
      • org.fhcrc.cpl.toolbox.proteomics.feature.FeatureAsMap (implements java.util.Map<K,V>)
        • org.fhcrc.cpl.viewer.align.PeptideArrayAnalyzer.FeatureAsMapWithIdAndFile
    • org.fhcrc.cpl.toolbox.proteomics.feature.Spectrum.CentroidedPeak
  • org.fhcrc.cpl.viewer.gui.SpectrumChartFactory
  • org.fhcrc.cpl.viewer.gui.SpectrumChartFactory.NullLabelGenerator (implements org.jfree.chart.labels.XYItemLabelGenerator)
  • org.fhcrc.cpl.viewer.gui.SpectrumComponent
  • org.fhcrc.cpl.viewer.feature.extraction.SpectrumResampler
  • org.fhcrc.cpl.toolbox.filehandler.Stax2DomBuilder
  • org.fhcrc.cpl.viewer.gui.Surface
  • org.fhcrc.cpl.toolbox.gui.SwingUtils<T,V>
  • javax.swing.SwingWorker<T,V> (implements java.util.concurrent.RunnableFuture<V>)
    • org.fhcrc.cpl.toolbox.gui.widget.SwingWorkerWithProgressBarDialog<T,V>
      • org.fhcrc.cpl.viewer.quant.gui.ProteinQuantSummaryFrame.ChartBuilderWorker
  • org.fhcrc.cpl.toolbox.filehandler.TabLoader
  • org.fhcrc.cpl.toolbox.filehandler.TabLoader._RowMap (implements java.util.Map<K,V>)
  • org.fhcrc.cpl.toolbox.filehandler.TabLoader.ColumnDescriptor
  • org.fhcrc.cpl.toolbox.filehandler.TabLoader.TabLoaderIterator (implements java.util.Iterator<E>)
  • org.fhcrc.cpl.toolbox.filehandler.TabWriter
  • org.fhcrc.cpl.toolbox.filehandler.TempFileManager
  • junit.framework.TestSuite (implements junit.framework.Test)
    • org.fhcrc.cpl.viewer.test.TestRunner
  • org.fhcrc.cpl.toolbox.test.TestUtilities
  • org.fhcrc.cpl.toolbox.TextProvider
  • java.lang.Thread (implements java.lang.Runnable)
    • org.fhcrc.cpl.toolbox.statistics.RInterface.RErrorReaderThread
    • org.fhcrc.cpl.toolbox.statistics.RInterface.RReaderThread
    • org.fhcrc.cpl.toolbox.statistics.RInterface.RWriterThread
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.fhcrc.cpl.toolbox.commandline.arguments.ArgumentValidationException
      • org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException
  • org.fhcrc.cpl.viewer.mrm.TransitionDefinition
  • org.fhcrc.cpl.viewer.mrm.TransitionDefinition.TransitionDefinitionPeptideMZAscComparator (implements java.util.Comparator<T>)
  • org.fhcrc.cpl.viewer.mrm.TransitionDefinitionHeader
  • org.fhcrc.cpl.viewer.mrm.TransitionDefinitionHeader.AQUApair
  • org.fhcrc.cpl.viewer.mrm.TransitionDefinitionParser
    • org.fhcrc.cpl.viewer.mrm.TSVTransitionDefinitionParser
  • org.fhcrc.cpl.toolbox.datastructure.Tree<T>
    • org.fhcrc.cpl.toolbox.datastructure.InOrderBinaryTree<T>
  • org.fhcrc.cpl.toolbox.datastructure.Tree2D
  • org.fhcrc.cpl.toolbox.datastructure.TreeNode<T>
    • org.fhcrc.cpl.toolbox.datastructure.BinaryTreeNode<T>
    • org.fhcrc.cpl.toolbox.datastructure.ParentAwareTreeNode<T>
      • org.fhcrc.cpl.toolbox.datastructure.SpatialQuadrantTreeNode<T>
  • org.fhcrc.cpl.viewer.mrm.Utils
  • org.fhcrc.cpl.viewer.commandline.ViewerCommandModuleUtilities
  • org.fhcrc.cpl.viewer.feature.extraction.WaveletPeakExtractor (implements org.fhcrc.cpl.viewer.feature.extraction.PeakExtractor)
  • org.fhcrc.cpl.toolbox.proteomics.feature.matching.Window2DFeatureSetMatcher
  • org.fhcrc.cpl.toolbox.filehandler.XMLStreamReaderWrapper (implements javax.xml.stream.XMLStreamReader)
    • org.fhcrc.cpl.toolbox.filehandler.SimpleXMLStreamReader

Interface Hierarchy

• org.fhcrc.cpl.viewer.align.Aligner.FeaturePairSelector
• org.fhcrc.cpl.toolbox.ApplicationContext.ApplicationContextProvider
• org.fhcrc.cpl.viewer.feature.extraction.strategy.BaseFeatureStrategy.StatusListener
• org.fhcrc.cpl.toolbox.proteomics.Clusterer2D.Clusterable
• org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition
• org.fhcrc.cpl.toolbox.commandline.CommandLineModule
• org.fhcrc.cpl.viewer.feature.FeatureExtractor.StatusListener
• org.fhcrc.cpl.viewer.feature.extraction.FeatureScorer
• org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.FeatureSetFileHandler
• org.fhcrc.cpl.toolbox.proteomics.feature.matching.FeatureSetMatcher
• org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategy
• org.fhcrc.cpl.viewer.mrm.utilities.graphZone
• org.fhcrc.cpl.toolbox.gui.ImagePanelLayer
• org.fhcrc.cpl.viewer.gui.MRMDialog.mzXML2TransitionArray
• org.fhcrc.cpl.viewer.feature.extraction.PeakCombiner
• org.fhcrc.cpl.viewer.feature.extraction.PeakExtractor
• org.fhcrc.cpl.toolbox.proteomics.PeptideGenerator.PeptideListener
• org.fhcrc.cpl.viewer.mrm.PlotDataSupplier
• org.fhcrc.cpl.toolbox.proteomics.Scan
• org.fhcrc.cpl.viewer.util.SharedProperties
• org.fhcrc.cpl.toolbox.filehandler.SimpleXMLEventRewriter.SimpleElement
• org.fhcrc.cpl.toolbox.datastructure.XYDataPoint

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.fhcrc.cpl.viewer.gui.MRMDialog.peaksData
    • org.fhcrc.cpl.viewer.util.ElutionDataPoint.timeUnits
    • org.fhcrc.cpl.viewer.util.ElutionDataPoint.intensityUnits