Diff for "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.
  • 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

• Undo

• Redo

• (Separator)

• Edit current network - calls Cytoscape Editor (Is this possible, Allan?)

• 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 renames something like "Desktop" since menu items under this section manages layout/states of the panels.

• 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

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

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