Refactored_Menu

Refactored Menu

The following is a tentative plan for the new menu bar.

File

[http://chianti.ucsd.edu/kono/images/newMenu.png]

Since the basic file format for 2.3 and later is Session (.cys), we the save and load functions are now called import/export.

• New

  • Network

    • Empty Network - Cytoscape Editor will be called from here.

      • COMMENT from AllanK: Kei, what if somebody wants to edit an existing network? That wouldn't be possible under this scheme.

    • From selected nodes, all edges (Ctrl-N)
    • From Selected nodes, selected edges (Shift+Ctrl-N)
    • Clone current network - Copy current network and create a new one.
  • Session - Clean current workspace (networks and attributes) and start a new session.

• Open - Open the session file. Current session will be lost (dialog box will appear).

• Save - Save current session into a CYS file. Overwrite existing session file.

• Save As... - Save the session with new name. File chooser will pop-up.

• (Separator)

• Import

  • Network (Ctrl-L) - Load network files: SIF, GML, or XGMML.
  • Node Attributes
  • Edge Attributes
  • Expression Matrix File (Ctrl-E)
  • Gene Ontology

• Export

  • Network and Attributes as XGMML
  • Network as GML
• (Separator)

• Print (Ctrl-P) -- Print out current network as a graphic.

• Quit (Ctrl-Q) -- Quit from Cytoscape. Confirmation dialog will appear.

Edit

Data

CytoPanels menu item is implemented as a submenu of this.

• Network Panel - This is on Cytopanel 1.
• Attribute Browser (F5)
• Advanced Panel - This is on Cytopanel 3. Default is off.
• (Separator)

• CytoPanels

  • Cytopanel 1 (Ctrl-1)
  • Cytopanel 2 (Ctrl-2)
  • Cytopanel 3 (Ctrl-3)

Select

View

Formerly called Layout and Visualization.

Plugins

List of loaded plugins will be displayed here. Same as 2.2.

Help

Basically, this is same as 2.2.

• Contents (F1)
• Context Sensitive (Shift+F1)
• (Separator)
• About