Hierarchy For All Packages

Package Hierarchies:

• ubic.erminej,
• ubic.erminej.analysis,
• ubic.erminej.data,
• ubic.erminej.gui,
• ubic.erminej.gui.analysis,
• ubic.erminej.gui.file,
• ubic.erminej.gui.geneset,
• ubic.erminej.gui.geneset.details,
• ubic.erminej.gui.geneset.edit,
• ubic.erminej.gui.geneset.table,
• ubic.erminej.gui.geneset.tree,
• ubic.erminej.gui.table,
• ubic.erminej.gui.util

Class Hierarchy

• java.lang.Object
  • ubic.erminej.analysis.AbstractLongTask
    • ubic.erminej.analysis.AbstractGeneSetPvalGenerator
      • ubic.erminej.analysis.CorrelationPvalGenerator
      • ubic.erminej.analysis.GeneSetResamplingPvalGenerator
        • ubic.erminej.analysis.ExperimentScoreQuickPvalGenerator
      • ubic.erminej.analysis.OraPvalGenerator
      • ubic.erminej.analysis.RocPvalGenerator
    • ubic.erminej.analysis.AbstractResamplingGeneSetScore (implements ubic.erminej.analysis.NullDistributionGenerator)
      • ubic.erminej.analysis.GeneSetResamplingBackgroundDistributionGenerator
      • ubic.erminej.analysis.ResamplingCorrelationGeneSetScore
    • ubic.erminej.analysis.MultipleTestCorrector
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel
    • ubic.erminej.gui.geneset.table.GeneSetTableModel
    • ubic.erminej.gui.geneset.ProbeTableModel
    • ubic.erminej.gui.geneset.SimpleGeneSetListTableModel
  • ubic.erminej.data.AnnotationFileFetcher
  • ubic.erminej.classScoreCMD
  • ubic.erminej.ClassScoreSimple
  • ubic.erminej.gui.util.Colors
  • 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.JFileChooser (implements javax.accessibility.Accessible)
          • ubic.erminej.gui.geneset.details.DetailsOutputDataFileChooser
          • ubic.erminej.gui.geneset.details.DetailsOutputImageFileChooser
          • ubic.erminej.gui.geneset.details.JGeneScoreFileChooser
          • ubic.erminej.gui.geneset.details.JRawFileChooser
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • ubic.erminej.gui.table.JBarGraphCellRenderer (implements javax.swing.table.TableCellRenderer)
          • ubic.erminej.gui.util.JLinkLabel (implements java.lang.Comparable<T>)
          • ubic.erminej.gui.table.JMatrixCellRenderer (implements javax.swing.table.TableCellRenderer)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • ubic.erminej.gui.StartupPanel
          • ubic.erminej.gui.util.WizardStep
            • ubic.erminej.gui.analysis.AnalysisWizardStep1
            • ubic.erminej.gui.analysis.AnalysisWizardStep2 (implements java.awt.event.KeyListener)
            • ubic.erminej.gui.analysis.AnalysisWizardStep3
            • ubic.erminej.gui.analysis.AnalysisWizardStep4
            • ubic.erminej.gui.analysis.AnalysisWizardStep5
            • ubic.erminej.gui.geneset.edit.GeneSetWizardStep1
            • ubic.erminej.gui.geneset.edit.GeneSetWizardStep1A
            • ubic.erminej.gui.geneset.edit.GeneSetWizardStep2
            • ubic.erminej.gui.geneset.edit.GeneSetWizardStep3
        • javax.swing.JPopupMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
          • ubic.erminej.gui.geneset.GeneSetPanelPopupMenu
        • javax.swing.JScrollPane (implements javax.accessibility.Accessible, javax.swing.ScrollPaneConstants)
          • ubic.erminej.gui.geneset.GeneSetPanel
            • ubic.erminej.gui.geneset.table.GeneSetTablePanel
            • ubic.erminej.gui.geneset.tree.GeneSetTreePanel
        • javax.swing.table.JTableHeader (implements javax.accessibility.Accessible, javax.swing.event.TableColumnModelListener)
          • ubic.erminej.gui.table.JVerticalHeaderRenderer (implements javax.swing.table.TableCellRenderer)
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • ubic.erminej.gui.AboutBox
            • ubic.erminej.gui.file.AnnotationListFrame
            • ubic.erminej.gui.AppDialog
              • ubic.erminej.gui.file.DataDirectoryDialog
            • ubic.erminej.gui.geneset.details.GeneUrlDialog
            • ubic.erminej.gui.SaveAnalysisDialog
            • ubic.erminej.gui.util.ScrollingTextAreaDialog
            • ubic.erminej.gui.util.Wizard
              • ubic.erminej.gui.analysis.AnalysisWizard
              • ubic.erminej.gui.geneset.edit.GeneSetWizard
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • ubic.erminej.gui.geneset.details.GeneSetDetailsFrame
            • ubic.erminej.gui.geneset.details.GeneSetRankingContextWindow
            • ubic.erminej.gui.JHistViewer
            • ubic.erminej.gui.MainFrame
            • ubic.erminej.gui.analysis.MultiFuncDiagWindow
  • ubic.erminej.data.DataIOUtils
  • javax.swing.tree.DefaultMutableTreeNode (implements java.lang.Cloneable, javax.swing.tree.MutableTreeNode, java.io.Serializable)
    • ubic.erminej.gui.geneset.tree.GeneSetTreeNode
  • javax.swing.tree.DefaultTreeModel (implements java.io.Serializable, javax.swing.tree.TreeModel)
    • ubic.erminej.gui.geneset.tree.FilteredGeneSetTreeModel
  • ubic.erminej.ErmineJGui
  • javax.swing.filechooser.FileFilter
    • ubic.erminej.gui.file.DataFileFilter
    • ubic.erminej.gui.file.ImageFileFilter
    • ubic.erminej.gui.file.XMLFileFilter
  • ubic.erminej.data.Gene (implements java.lang.Comparable<T>)
  • ubic.erminej.data.GeneAnnotationParser
  • ubic.erminej.data.GeneAnnotations
  • ubic.erminej.data.GeneScores
  • ubic.erminej.data.GeneSet
  • ubic.erminej.data.GeneSetDetails
  • ubic.erminej.data.GeneSetDetailsImageWriter
  • ubic.erminej.data.GeneSetMapTools
  • ubic.erminej.analysis.GeneSetPvalRun
  • ubic.erminej.data.GeneSetResult (implements java.lang.Comparable<T>)
    • ubic.erminej.data.EmptyGeneSetResult
  • ubic.erminej.data.GeneSetTerm (implements java.lang.Comparable<T>)
  • ubic.erminej.data.GeneSetTerms
  • ubic.erminej.data.GOParser
  • ubic.erminej.gui.util.GuiUtil
  • ubic.erminej.gui.HelpHelper
  • ubic.erminej.data.Histogram
  • ubic.erminej.gui.util.MatrixPreviewer
  • ubic.erminej.data.Multifunctionality
  • ubic.erminej.gui.analysis.Plotting
  • java.awt.geom.Point2D (implements java.lang.Cloneable)
    • java.awt.Point (implements java.io.Serializable)
      • ubic.erminej.gui.table.MatrixPoint (implements java.lang.Comparable<T>)
  • ubic.erminej.data.Probe
  • ubic.erminej.ResultsFileReader
  • ubic.erminej.ResultsPrinter
  • ubic.erminej.analysis.ScoreQuantiles
  • ubic.erminej.SettingsHolder
    • ubic.erminej.Settings
  • ubic.basecode.util.StatusDebugLogger (implements ubic.basecode.util.StatusViewer)
    • ubic.erminej.gui.util.StatusJlabel
  • java.lang.Thread (implements java.lang.Runnable)
    • ubic.erminej.Analyzer
  • ubic.erminej.data.UserDefinedGeneSetManager

Interface Hierarchy

• ubic.erminej.analysis.NullDistributionGenerator

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.erminej.SettingsHolder.GeneScoreMethod
    • ubic.erminej.SettingsHolder.Method
    • ubic.erminej.SettingsHolder.MultiProbeHandling
    • ubic.erminej.SettingsHolder.MultiTestCorrMethod
    • ubic.erminej.data.UserDefinedGeneSetManager.GeneSetFileFormat
    • ubic.erminej.data.GeneAnnotationParser.Format