Hierarchy For All Packages

Package Hierarchies:

• be.svlandeg.diffany.console,
• be.svlandeg.diffany.core.algorithms,
• be.svlandeg.diffany.core.io,
• be.svlandeg.diffany.core.networks,
• be.svlandeg.diffany.core.progress,
• be.svlandeg.diffany.core.project,
• be.svlandeg.diffany.core.semantics,
• be.svlandeg.diffany.core.visualstyle,
• be.svlandeg.diffany.cytoscape,
• be.svlandeg.diffany.cytoscape.actions,
• be.svlandeg.diffany.cytoscape.gui,
• be.svlandeg.diffany.cytoscape.internal,
• be.svlandeg.diffany.cytoscape.tasks,
• be.svlandeg.diffany.cytoscape.vizmapper,
• be.svlandeg.diffany.examples,
• be.svlandeg.diffany.study.osmotic,
• be.svlandeg.diffany.study.osmotic.arabidopsis

Class Hierarchy

• java.lang.Object
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • org.cytoscape.application.swing.AbstractCyAction (implements org.cytoscape.application.swing.CyAction)
      • be.svlandeg.diffany.cytoscape.actions.LoadExampleAction
      • be.svlandeg.diffany.cytoscape.actions.RunProjectAction
      • be.svlandeg.diffany.cytoscape.actions.UpdateVisualStyleAction
  • org.cytoscape.service.util.AbstractCyActivator (implements org.osgi.framework.BundleActivator)
    • be.svlandeg.diffany.cytoscape.internal.CyActivator
  • javax.swing.AbstractListModel<E> (implements javax.swing.ListModel<E>, java.io.Serializable)
    • be.svlandeg.diffany.cytoscape.gui.ModeDropDownModel (implements javax.swing.ComboBoxModel<E>)
    • be.svlandeg.diffany.cytoscape.gui.ProjectDropDownModel (implements javax.swing.ComboBoxModel<E>)
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • be.svlandeg.diffany.cytoscape.gui.EdgeFilterTableModel
    • be.svlandeg.diffany.cytoscape.gui.SelectionTableModel
  • be.svlandeg.diffany.cytoscape.vizmapper.AbstractVisualDiffanyStyle
    • be.svlandeg.diffany.cytoscape.vizmapper.VisualDiffStyle
    • be.svlandeg.diffany.cytoscape.vizmapper.VisualSourceStyle
  • be.svlandeg.diffany.core.networks.Attribute
  • be.svlandeg.diffany.core.algorithms.CalculateDiff
  • 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.JMenuItem (implements javax.accessibility.Accessible, javax.swing.MenuElement)
            • javax.swing.JMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
              • be.svlandeg.diffany.cytoscape.gui.ExtraOptionsMenu (implements java.awt.event.ActionListener, java.util.Observer)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • be.svlandeg.diffany.cytoscape.gui.TabPane (implements java.awt.event.ActionListener, javax.swing.event.ChangeListener, org.cytoscape.application.swing.CytoPanelComponent, javax.swing.event.ListSelectionListener, java.util.Observer, javax.swing.event.TableModelListener)
  • be.svlandeg.diffany.core.networks.Condition
  • be.svlandeg.diffany.cytoscape.CyNetworkBridge
  • be.svlandeg.diffany.cytoscape.CyProject
  • be.svlandeg.diffany.cytoscape.CyProject.CyNetworkPair
  • be.svlandeg.diffany.console.DiffanyOptions
  • be.svlandeg.diffany.core.networks.Edge
  • be.svlandeg.diffany.core.algorithms.EdgeByEdge
  • be.svlandeg.diffany.core.algorithms.EdgeComparison
  • be.svlandeg.diffany.core.algorithms.EdgeComparison.IntermediateComparison
  • be.svlandeg.diffany.core.networks.EdgeDefinition
  • be.svlandeg.diffany.core.visualstyle.EdgeDrawing
    • be.svlandeg.diffany.core.visualstyle.TreeEdgeDrawing
      • be.svlandeg.diffany.core.visualstyle.DefaultDiffEdgeDrawing
      • be.svlandeg.diffany.core.visualstyle.DefaultSourceEdgeDrawing
  • be.svlandeg.diffany.core.networks.EdgeGenerator
  • be.svlandeg.diffany.core.io.EdgeIO
  • be.svlandeg.diffany.core.semantics.EdgeOntology
    • be.svlandeg.diffany.core.semantics.TreeEdgeOntology
      • be.svlandeg.diffany.core.semantics.DefaultEdgeOntology
  • be.svlandeg.diffany.core.visualstyle.EdgeStyle
  • be.svlandeg.diffany.examples.ExampleCode
  • be.svlandeg.diffany.cytoscape.vizmapper.ExtraDiffanyVisMappings (implements be.svlandeg.diffany.cytoscape.vizmapper.ExtraVisMappings)
  • be.svlandeg.diffany.study.osmotic.arabidopsis.GenePrinter
  • be.svlandeg.diffany.examples.GenericExample
    • be.svlandeg.diffany.examples.ActivityFlowTest
    • be.svlandeg.diffany.examples.Bandyopadhyay2010
    • be.svlandeg.diffany.examples.ConflictingEdgesTest
    • be.svlandeg.diffany.examples.FuzzyNetworks
    • be.svlandeg.diffany.examples.FuzzyNetworks2
    • be.svlandeg.diffany.examples.Ideker2011
    • be.svlandeg.diffany.examples.MultipleConditionTest
    • be.svlandeg.diffany.examples.OsmoticSampleTest
    • be.svlandeg.diffany.examples.OsmoticUseCase
    • be.svlandeg.diffany.examples.ProcessTest
  • be.svlandeg.diffany.study.osmotic.arabidopsis.KinaseData
  • be.svlandeg.diffany.cytoscape.tasks.LoadExampleTask (implements org.cytoscape.work.Task)
  • be.svlandeg.diffany.cytoscape.tasks.LoadExampleTaskFactory (implements org.cytoscape.work.TaskFactory)
  • be.svlandeg.diffany.core.project.LogEntry
  • be.svlandeg.diffany.core.project.Logger
  • be.svlandeg.diffany.study.osmotic.arabidopsis.MapID
  • be.svlandeg.diffany.console.MetaOptions
  • be.svlandeg.diffany.core.networks.Network
    • be.svlandeg.diffany.core.networks.ConsensusNetwork
    • be.svlandeg.diffany.core.networks.DifferentialNetwork
    • be.svlandeg.diffany.core.networks.InputNetwork
      • be.svlandeg.diffany.core.networks.ConditionNetwork
      • be.svlandeg.diffany.core.networks.ReferenceNetwork
  • be.svlandeg.diffany.study.osmotic.NetworkAnalysis
  • be.svlandeg.diffany.core.algorithms.NetworkCleaning
  • be.svlandeg.diffany.study.osmotic.NetworkConstruction
  • be.svlandeg.diffany.cytoscape.gui.NetworkEntry
  • be.svlandeg.diffany.core.io.NetworkIO
  • be.svlandeg.diffany.core.networks.Node
  • be.svlandeg.diffany.core.algorithms.NodeComparison
  • be.svlandeg.diffany.core.io.NodeIO
  • be.svlandeg.diffany.core.semantics.NodeMapper
  • java.util.Observable
    • be.svlandeg.diffany.cytoscape.Model (implements org.cytoscape.model.events.NetworkAddedListener, org.cytoscape.model.events.NetworkDestroyedListener, org.cytoscape.model.events.RowsSetListener, org.cytoscape.application.events.SetCurrentNetworkViewListener)
  • be.svlandeg.diffany.core.networks.OutputNetworkPair
  • be.svlandeg.diffany.study.osmotic.OverexpressionData
  • be.svlandeg.diffany.study.osmotic.OverexpressionIO
  • be.svlandeg.diffany.study.osmotic.arabidopsis.PPIdata
  • be.svlandeg.diffany.core.progress.ProgressListener
    • be.svlandeg.diffany.cytoscape.tasks.RunProjectTask (implements org.cytoscape.work.Task)
    • be.svlandeg.diffany.core.progress.StandardProgressListener
  • be.svlandeg.diffany.core.project.Project
  • be.svlandeg.diffany.study.osmotic.arabidopsis.RegData
  • be.svlandeg.diffany.core.project.Run
  • be.svlandeg.diffany.study.osmotic.RunAnalysis
  • be.svlandeg.diffany.core.project.RunConfiguration
    • be.svlandeg.diffany.core.project.RunDiffConfiguration
  • be.svlandeg.diffany.console.RunConsole
  • be.svlandeg.diffany.core.project.RunOutput
  • be.svlandeg.diffany.console.RunProject
  • be.svlandeg.diffany.cytoscape.tasks.RunProjectTaskFactory (implements org.cytoscape.work.TaskFactory)
  • be.svlandeg.diffany.core.progress.ScheduledTask
  • be.svlandeg.diffany.cytoscape.internal.Services
  • be.svlandeg.diffany.cytoscape.SessionListener (implements org.cytoscape.session.events.SessionAboutToBeSavedListener, org.cytoscape.session.events.SessionLoadedListener)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • be.svlandeg.diffany.cytoscape.InvalidRunConfigurationException
  • be.svlandeg.diffany.core.algorithms.Unification
  • be.svlandeg.diffany.cytoscape.tasks.UpdateVisualStyleTask (implements org.cytoscape.work.Task)
  • be.svlandeg.diffany.cytoscape.tasks.UpdateVisualStyleTaskFactory (implements org.cytoscape.work.TaskFactory)

Interface Hierarchy

• be.svlandeg.diffany.cytoscape.vizmapper.ExtraVisMappings

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • be.svlandeg.diffany.core.algorithms.CalculateDiff.RunMode
    • be.svlandeg.diffany.core.visualstyle.EdgeStyle.ArrowHead
    • be.svlandeg.diffany.cytoscape.Model.OverlapOperator
    • be.svlandeg.diffany.cytoscape.Model.ComparisonMode
    • be.svlandeg.diffany.cytoscape.CyNetworkBridge.NetworkType