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.

      • COMMENT from Kei: Editor will be called from New AND Edit Menu. I think this is more intuitive UI.

    • 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.

      • COMMENT from AllanK: Would these come up with the editor enabled or disabled? If disabled, then do we need an item on the File menu for enabling editing?

  • 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 (SBML & KEGG importer may be added).

  • Node Attributes
  • Edge Attributes
  • Expression Matrix File (Ctrl-E)
  • Gene Ontology

• Export

  • Network and Attributes as XGMML
  • Network as GML
  • Network as SIF
  • Node Attributes
  • Edge Attributes
  • Network as graphics... - PDF,GIF, etc.
  • Use user XST... - export network using user XSL template.
• (Separator)

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

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

Edit

• Undo

• Redo

• (Separator)

• Edit current network

  • Cytoscape Editor menu items will be inserted here (Is this possible, Allan?)

    • COMMENT from AllanK: I think this should work. The reason that I originally had the SetEditor command on the File menu was that, in the current Cytoscape, the Edit menu commands were all disabled if there was no network loaded, so no way to set up an editor if there was not a network already loaded.

• Delete Selected Nodes/Edges

• Create View

• Destroy View

• Destroy Network

• Squiggle

  • Enable/Disable (F12)
  • Clear
• (Separator)

• Prederence

Data

CytoPanels menu item is implemented as a submenu of this. Maybe renamed something like Desktop, since menu items under this section manage layout/states of the panels on the Cytoscape desktop.

• Network Panel - This is on Cytopanel 1.

• Attribute Browser (F5)

• Advanced Panel - This is on Cytopanel 3. Default is off.

• Show/Hide Overview - ON/OFF the overview window on Cytopanel 1

• (Separator)

• CytoPanels

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

Select

Basically filter is doing selection. So it should be under this menu item.

• Mouse Drag Selects

• Nodes

  • (Submenu items are same as 2.2)

• Edges

  • (Submenu itess are same as 2.2)

• Select all nodes and edges

• Deselect all nodes and edges

• (Separator)

• Use Filters (F7) - Filter plugin will be called from here.

View

Formerly called Layout and Visualization.

• Rotate/Scale Network

• Align/Distribute Nodes

• (Separator)

• yFiles Layouts

  • (Submenu items are same as 2.2)

• jgraph Layouts

  • (Submenu items TBD)

• native Layouts

  • (Submenu will include our hierarchical and spring embedded layouts and possibly others)
• (Separator)

• Set Vizmapper

• Lock/Unlock Viz Mapper

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