Package org.cytoscape.application

Interface CyApplicationManager

public interface CyApplicationManager
Basic access to current and/or currently selected networks, views and rendering engines in an instance of Cytoscape.

Module: application-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>application-api</artifactId>
</dependency>

Cytoscape Backwards Compatibility (API Interface): We expect that this interface will be used but not implemented by developers using this interface. As such, we reserve the right to add methods to the interface as part of minor version upgrades. We will not remove methods for any changes other than major version upgrades.

  • Method Details

    • getCurrentNetwork

      CyNetwork getCurrentNetwork()
      Provides access to the current network.
      Returns:
      the current network or null if there is no current network

    • setCurrentNetwork

      void setCurrentNetwork​(CyNetwork net)
      Sets the current network to the specified network. If the passed network is different from the current one, a SetCurrentNetworkEvent is fired. If the passed network is not yet selected, any selected networks are unselected before the passed one is selected. That means that the SetSelectedNetworksEvent can also be fired.
      Parameters:
      net - The network that will become the current network (it can be null).

    • getCurrentNetworkView

      CyNetworkView getCurrentNetworkView()
      Returns the current network view.
      Returns:
      the current network view or null if no network is currently being visualized

    • setCurrentNetworkView

      void setCurrentNetworkView​(CyNetworkView netView)
      Sets the current network view to the specified network view.
      Parameters:
      netView - The network view to become the current network view (it can be null).

    • getSelectedNetworks

      List<CyNetwork> getSelectedNetworks()
      Returns the list of selected networks.
      Returns:
      The list of selected networks.

    • getSelectedNetworkViews

      List<CyNetworkView> getSelectedNetworkViews()
      Returns the list of selected network views.
      Returns:
      The list of selected network views.

    • setSelectedNetworkViews

      void setSelectedNetworkViews​(List<CyNetworkView> views)
      Sets the specified network views as selected.
      Parameters:
      views - The list of network views to be selected.

    • setSelectedNetworks

      void setSelectedNetworks​(List<CyNetwork> nets)
      Sets the networks specified as selected.
      Parameters:
      nets - The networks to be selected.

    • getCurrentRenderingEngine

      RenderingEngine<CyNetwork> getCurrentRenderingEngine()
      Returns the rendering engine associated with the current network view.
      Returns:
      The rendering engine associated with the current network view.

    • setCurrentRenderingEngine

      void setCurrentRenderingEngine​(RenderingEngine<CyNetwork> engine)
      Sets the current rendering engine.
      Parameters:
      engine - The rendering engine that should be made current.

    • getCurrentTable

      CyTable getCurrentTable()
      Returns the currently active table.
      Returns:
      the currently active CyTable or null if no table is currently being visualized

    • setCurrentTable

      void setCurrentTable​(CyTable table)
      Sets the currently active table.
      Parameters:
      table - The table that should be made current (it can be null).

    • reset

      void reset()
      Releases all currently held references and resources.

      Cytoscape Backwards Compatibility (DO NOT USE): This method may change or be removed in future minor version upgrades of Cytoscape. It is not safe for Apps to call or override this method.

    • getCurrentNetworkViewRenderer

      NetworkViewRenderer getCurrentNetworkViewRenderer()
      Returns the NetworkViewRenderer associated with the current RenderingEngine.
      Returns:
      the NetworkViewRenderer associated with the current RenderingEngine

    • getDefaultNetworkViewRenderer

      NetworkViewRenderer getDefaultNetworkViewRenderer()
      Returns the NetworkViewRenderer that should be used to create CyNetworkViews.
      Returns:
      the NetworkViewRenderer that should be used to create CyNetworkViews.

    • setDefaultNetworkViewRenderer

      void setDefaultNetworkViewRenderer​(NetworkViewRenderer renderer)
      Sets the NetworkViewRenderer that should be used to create CyNetworkViews.
      Parameters:
      renderer - the NetworkViewRenderer that should be used by default.

    • getNetworkViewRenderer

      NetworkViewRenderer getNetworkViewRenderer​(String rendererId)
      Returns the NetworkViewRenderer that has the passed id or null if it doesn't exist.
      Parameters:
      rendererId -
      Returns:
      the NetworkViewRenderer that should be used to create CyNetworkViews

    • getNetworkViewRendererSet

      Set<NetworkViewRenderer> getNetworkViewRendererSet()
      Returns a set with all the NetworkViewRenderer objects that have been registered.
      Returns:
      the complete set of all the currently known renderers

    • getDefaultTableViewRenderer

      TableViewRenderer getDefaultTableViewRenderer()
      Returns the TableViewRenderer that should be used to create CyTableViews.
      Returns:
      the TableViewRenderer that should be used to create CyTableViews.

    • setDefaultTableViewRenderer

      void setDefaultTableViewRenderer​(TableViewRenderer renderer)
      Sets the TableViewRenderer that should be used to create CyTableViews.
      Parameters:
      renderer - the TableViewRenderer that should be used by default.

    • getTableViewRenderer

      TableViewRenderer getTableViewRenderer​(String rendererId)
      Returns the TableViewRenderer that has the passed id or null if it doesn't exist.
      Parameters:
      rendererId -
      Returns:
      the TableViewRenderer that should be used to create CyTableViews

    • getTableViewRendererSet

      Set<TableViewRenderer> getTableViewRendererSet()
      Returns a set with all the TableViewRenderer objects that have been registered.
      Returns:
      the complete set of all the currently known renderers

    • getCurrentDirectory

      File getCurrentDirectory()
      Get the current working directory.
      Returns:
      a File pointing to the current working directory as set in Properties, or user.dir if a value is not set (or if the set value is not a valid directory)

    • setCurrentDirectory

      boolean setCurrentDirectory​(File dir)
      Set the current working directory.
      Parameters:
      dir - a File object pointing to an existing directory
      Returns:
      true if successful, false if the specified File is not a directory or does not exist