Differences between revisions 9 and 13 (spanning 4 versions)
Revision 9 as of 2006-02-23 01:05:30
Size: 2007
Editor: cosiapat1
Comment:
Revision 13 as of 2006-02-23 02:15:14
Size: 3155
Editor: KeiichiroOno
Comment:
Deletions are marked like this. Additions are marked like this.
Line 6: Line 6:

[http://chianti.ucsd.edu/kono/images/newMenu.png]
Line 8: Line 11:
 * New  * '''''New'''''
Line 12: Line 15:
           * '''COMMENT''' ''from Kei: Editor will be called from New AND Edit Menu. I think this is more intuitive UI.''
Line 14: Line 18:
      * Clone current network - Copy current network and create a new one.
Line 15: Line 20:
 * 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.
 * Open - Open the session file. Current session will be lost (dialog box will appear).
 * '''''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.
Line 19: Line 24:
 * Import  * '''''Import'''''
Line 25: Line 30:
 * Export  * '''''Export'''''
Line 29: Line 34:
 * Print (Ctrl-P) -- Print out current network as a graphic.
 * Quit (Ctrl-Q) -- Quit from Cytoscape. Confirmation dialog will appear.
 * '''''Print''''' (Ctrl-P) -- Print out current network as a graphic.
 * '''''Quit''''' (Ctrl-Q) -- Quit from Cytoscape. Confirmation dialog will appear.
Line 32: Line 37:
 * '''''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'''''
Line 34: Line 52:
''CytoPanels'' menu item is implemented as a submenu of this. ''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.
Line 45: Line 64:
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.

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

Refactored_Menu (last edited 2009-02-12 01:03:41 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

MoinMoin Appliance - Powered by TurnKey Linux