Hierarchy For All Packages

Package Hierarchies:

• eu.isas.peptideshaker,
• eu.isas.peptideshaker.cmd,
• eu.isas.peptideshaker.export,
• eu.isas.peptideshaker.export.sections,
• eu.isas.peptideshaker.fileimport,
• eu.isas.peptideshaker.followup,
• eu.isas.peptideshaker.gui,
• eu.isas.peptideshaker.gui.export,
• eu.isas.peptideshaker.gui.filtering,
• eu.isas.peptideshaker.gui.parameters,
• eu.isas.peptideshaker.gui.pride,
• eu.isas.peptideshaker.gui.protein_inference,
• eu.isas.peptideshaker.gui.protein_sequence,
• eu.isas.peptideshaker.gui.start,
• eu.isas.peptideshaker.gui.tablemodels,
• eu.isas.peptideshaker.gui.tabpanels,
• eu.isas.peptideshaker.parameters,
• eu.isas.peptideshaker.preferences,
• eu.isas.peptideshaker.processing,
• eu.isas.peptideshaker.protein_inference,
• eu.isas.peptideshaker.ptm,
• eu.isas.peptideshaker.recalibration,
• eu.isas.peptideshaker.scoring,
• eu.isas.peptideshaker.scoring.maps,
• eu.isas.peptideshaker.scoring.maps.specific,
• eu.isas.peptideshaker.scoring.psm_scoring,
• eu.isas.peptideshaker.scoring.targetdecoy,
• eu.isas.peptideshaker.stirred,
• eu.isas.peptideshaker.stirred.modules,
• eu.isas.peptideshaker.utils,
• eu.isas.peptideshaker.validation

Class Hierarchy

• java.lang.Object
  • com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli (implements java.util.concurrent.Callable<V>)
    • eu.isas.peptideshaker.cmd.IdentificationParametersCLI
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • javax.swing.table.DefaultTableModel (implements java.io.Serializable)
      • eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel
      • eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel
      • eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel
      • com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
        • eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel
        • eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
        • eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
  • eu.isas.peptideshaker.scoring.psm_scoring.BestMatchSelection
  • eu.isas.peptideshaker.cmd.CLIExportMethods
  • com.compomics.software.CompomicsWrapper
    • eu.isas.peptideshaker.PeptideShakerWrapper
  • 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.JPanel (implements javax.accessibility.Accessible)
          • eu.isas.peptideshaker.gui.tabpanels.AnnotationPanel
          • eu.isas.peptideshaker.gui.tabpanels.GOEAPanel
          • eu.isas.peptideshaker.gui.ImageIconPanel
          • eu.isas.peptideshaker.gui.JumpToPanel
          • eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel
          • eu.isas.peptideshaker.gui.tabpanels.OverviewPanel (implements eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanelParent)
          • eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel (implements eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanelParent)
          • eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphPanel
          • eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel
          • eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel.JmolPanel
          • eu.isas.peptideshaker.gui.tabpanels.QCPanel
          • eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel
          • eu.isas.peptideshaker.gui.tabpanels.ValidationPanel
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • eu.isas.peptideshaker.gui.pride.DatabaseHelpDialog
            • eu.isas.peptideshaker.gui.parameters.DisplayPreferencesDialog
            • eu.isas.peptideshaker.gui.export.FeaturesExportDialog
            • eu.isas.peptideshaker.gui.filtering.FiltersDialog
            • eu.isas.peptideshaker.gui.export.FollowUpExportDialog
            • eu.isas.peptideshaker.gui.FractionDetailsDialog
            • eu.isas.peptideshaker.gui.start.GettingStartedDialog
            • eu.isas.peptideshaker.gui.IdToSpectrumFileMappingDialog
            • eu.isas.peptideshaker.gui.export.InclusionListExportDialog
            • eu.isas.peptideshaker.gui.MatchValidationDialog
            • eu.isas.peptideshaker.gui.export.MethodsSectionDialog
            • eu.isas.peptideshaker.gui.ModificationDialog
            • eu.isas.peptideshaker.gui.ModificationSiteInferenceDialog
            • eu.isas.peptideshaker.gui.export.MzIdentMLExportDialog
            • eu.isas.peptideshaker.gui.NewDialog
            • eu.isas.peptideshaker.gui.pride.PrideDataTypeSelectionDialog
            • eu.isas.peptideshaker.gui.pride.PrideFreeTextSearchDialog
            • eu.isas.peptideshaker.gui.pride.PridePrivateDataDialog
            • eu.isas.peptideshaker.gui.pride.PrideReshakeSetupDialog
            • eu.isas.peptideshaker.gui.pride.PrideSearchParametersDialog
            • eu.isas.peptideshaker.gui.parameters.ProjectDetailsDialog
            • eu.isas.peptideshaker.gui.parameters.ProjectParametersDialog
            • eu.isas.peptideshaker.gui.pride.ProjectsFilterDialog
            • eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceDialog
            • eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphLegendDialog
            • eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphSelectionDialog
            • eu.isas.peptideshaker.gui.protein_inference.ProteinInferencePeptideLevelDialog
            • eu.isas.peptideshaker.gui.export.PtmSelectionDialog
            • eu.isas.peptideshaker.gui.SaveDialog
            • eu.isas.peptideshaker.gui.parameters.SpectrumColorsDialog
            • eu.isas.peptideshaker.gui.parameters.SpectrumCountingSettingsDialog
            • eu.isas.peptideshaker.gui.WelcomeDialog
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • eu.isas.peptideshaker.gui.PeptideShakerGUI (implements java.awt.datatransfer.ClipboardOwner, com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent, com.compomics.util.gui.error_handlers.notification.NotificationDialogParent)
            • eu.isas.peptideshaker.gui.pride.PrideReshakeGUI
  • eu.isas.peptideshaker.followup.DeepLcExport
  • eu.isas.peptideshaker.utils.DeepLcUtils
  • eu.isas.peptideshaker.utils.DisplayFeaturesGenerator
  • com.compomics.util.experiment.personalization.ExperimentObject (implements java.io.Serializable)
    • eu.isas.peptideshaker.preferences.DisplayParameters
    • com.compomics.util.io.json.JsonMarshaller
      • eu.isas.peptideshaker.utils.ExportFactoryMarshaller
    • eu.isas.peptideshaker.ptm.ModificationLocalizationScorer
    • eu.isas.peptideshaker.parameters.PeptideShakerParameters (implements com.compomics.util.experiment.personalization.UrParameter)
    • eu.isas.peptideshaker.preferences.ProjectDetails
    • eu.isas.peptideshaker.scoring.PSMaps (implements com.compomics.util.experiment.personalization.UrParameter)
    • eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap (implements java.io.Serializable)
      • eu.isas.peptideshaker.scoring.maps.specific.ModificationSpecificMap
      • eu.isas.peptideshaker.scoring.maps.specific.SimpleSpecificMap
    • eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap
    • eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults (implements java.io.Serializable)
  • eu.isas.peptideshaker.followup.FastaExport
  • eu.isas.peptideshaker.fileimport.FileImporter
  • eu.isas.peptideshaker.cmd.FollowUpCLIInputBean
  • eu.isas.peptideshaker.gui.tabpanels.GOEAPanel.QuickGoTerm
  • eu.isas.peptideshaker.gui.tabpanels.GOEAPanel.QuickGoTerm.DummyResults
  • eu.isas.peptideshaker.protein_inference.GroupSimplification
  • eu.isas.peptideshaker.stirred.modules.IdImporter
  • eu.isas.peptideshaker.followup.InclusionListExport
  • eu.isas.peptideshaker.scoring.maps.InputMap (implements java.io.Serializable)
  • eu.isas.peptideshaker.validation.MatchesValidator
  • eu.isas.peptideshaker.followup.Ms2PipExport
  • eu.isas.peptideshaker.utils.Ms2PipUtils
  • eu.isas.peptideshaker.cmd.MzidCLIInputBean
  • eu.isas.peptideshaker.export.MzIdentMLExport
  • eu.isas.peptideshaker.cmd.PathSettingsCLI
  • eu.isas.peptideshaker.cmd.PathSettingsCLIInputBean
  • eu.isas.peptideshaker.protein_inference.PeptideChecker
  • eu.isas.peptideshaker.PeptideShaker
  • eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean
  • eu.isas.peptideshaker.cmd.PeptideShakerIdentificationParametersCLIParams
  • eu.isas.peptideshaker.export.PeptideShakerMethods
  • eu.isas.peptideshaker.preferences.PeptideShakerPathParameters
  • eu.isas.peptideshaker.PeptideShakerZipFileChecker
  • eu.isas.peptideshaker.followup.PepXmlExport
  • eu.isas.peptideshaker.followup.PercolatorExport
  • eu.isas.peptideshaker.utils.PercolatorUtils
  • eu.isas.peptideshaker.followup.ProgenesisExport
  • eu.isas.peptideshaker.export.ProjectExport
  • eu.isas.peptideshaker.utils.Properties
  • eu.isas.peptideshaker.gui.protein_sequence.ProteinAnnotations (implements org.jfree.chart.labels.CategoryToolTipGenerator)
  • eu.isas.peptideshaker.protein_inference.ProteinInference
  • eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphPanel.ProteinInferenceVertexRenderer (implements edu.uci.ics.jung.visualization.renderers.Renderer.Vertex<V,E>)
  • eu.isas.peptideshaker.processing.ProteinProcessor
  • eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel
  • eu.isas.peptideshaker.followup.ProteoformExport
  • eu.isas.peptideshaker.export.sections.PsAnnotationSection
  • eu.isas.peptideshaker.export.PsdbExporter
  • eu.isas.peptideshaker.export.PSExportFactory (implements com.compomics.util.io.export.ExportFactory)
  • eu.isas.peptideshaker.export.PsExportStyle (implements com.compomics.util.io.export.WorkbookStyle)
  • eu.isas.peptideshaker.export.sections.PsFragmentSection
  • eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection
  • eu.isas.peptideshaker.export.sections.PsInputFilterSection
  • eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable (implements java.lang.Runnable)
  • eu.isas.peptideshaker.fileimport.PsmImporter
  • eu.isas.peptideshaker.fileimport.PsmImportRunnable (implements java.lang.Runnable)
  • eu.isas.peptideshaker.processing.PsmProcessor
  • eu.isas.peptideshaker.processing.PsmProcessorRunnable (implements java.lang.Runnable)
  • eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer
  • eu.isas.peptideshaker.export.sections.PsPeptideSection
  • eu.isas.peptideshaker.export.sections.PsProjectSection
  • eu.isas.peptideshaker.export.sections.PsProteinSection
  • eu.isas.peptideshaker.export.sections.PsPsmSection
  • eu.isas.peptideshaker.export.sections.PsPtmScoringSection
  • eu.isas.peptideshaker.export.sections.PsSearchParametersSection
  • eu.isas.peptideshaker.export.sections.PsSpectrumCountingSection
  • eu.isas.peptideshaker.export.sections.PsValidationSection
  • eu.isas.peptideshaker.utils.PsZipUtils
  • eu.isas.peptideshaker.followup.RecalibrationExporter
  • eu.isas.peptideshaker.cmd.ReportCLIInputBean
  • eu.isas.peptideshaker.gui.protein_sequence.ResidueAnnotation
  • eu.isas.peptideshaker.recalibration.RunMzDeviation
  • eu.isas.peptideshaker.followup.SpectrumExporter
  • eu.isas.peptideshaker.recalibration.SpectrumRecalibrator
  • eu.isas.peptideshaker.utils.StarHider
  • eu.isas.peptideshaker.stirred.Stirred
  • eu.isas.peptideshaker.cmd.StirredCLI
  • eu.isas.peptideshaker.cmd.StirredOptionsBean
  • eu.isas.peptideshaker.stirred.modules.StirRunnable (implements java.lang.Runnable)
  • eu.isas.peptideshaker.protein_inference.TagMapper
  • eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint (implements java.io.Serializable)
  • eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries
  • eu.isas.peptideshaker.scoring.psm_scoring.TieBreaker
  • eu.isas.peptideshaker.utils.Tips
  • eu.isas.peptideshaker.export.UnipeptExport
  • eu.isas.peptideshaker.preferences.UserParameters (implements java.io.Serializable)
  • eu.isas.peptideshaker.preferences.UserPreferencesParent
    • eu.isas.peptideshaker.utils.PsdbParent (implements java.lang.AutoCloseable)
      • eu.isas.peptideshaker.cmd.FollowUpCLI
      • eu.isas.peptideshaker.cmd.MzidCLI
      • eu.isas.peptideshaker.cmd.PeptideShakerCLI (implements java.util.concurrent.Callable<V>)
      • eu.isas.peptideshaker.cmd.ReportCLI

Interface Hierarchy

• eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanelParent

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • eu.isas.peptideshaker.cmd.StirredOptions
    • eu.isas.peptideshaker.cmd.ReportCLIParams
    • eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
    • eu.isas.peptideshaker.cmd.PathSettingsCLIParams
    • eu.isas.peptideshaker.cmd.MzidCLIParams
    • eu.isas.peptideshaker.cmd.FollowUpCLIParams
    • eu.isas.peptideshaker.followup.SpectrumExporter.ExportType
    • eu.isas.peptideshaker.followup.ProgenesisExport.ExportType
    • eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat
    • eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType
    • eu.isas.peptideshaker.followup.FastaExport.ExportType
    • eu.isas.peptideshaker.gui.MatchValidationDialog.MatchType
    • eu.isas.peptideshaker.gui.JumpToPanel.JumpType
    • eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey (implements com.compomics.software.settings.PathKey)
    • eu.isas.peptideshaker.protein_inference.ProteinInference.GroupSimplificationOption