Diff for "Refactored_Menu"

Differences between revisions 1 and 12 (spanning 11 versions)

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)
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.

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

-  ← Revision 1 as of 2006-02-21 21:37:03 →
  Size: 84
  Editor: KeiichiroOno
  Comment:
+  ← Revision 12 as of 2006-02-23 02:01:24 →
  Size: 2626
  Editor: KeiichiroOno
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-=== Refactored Menu Items ===
+=== Refactored Menu ===
 Line 3:
-(under construction)
+The following is a tentative plan for the new menu bar.

----

==== File ====
-Line 5:
+Line 7:
- * File

 * Data

 * View
+[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)

 * '''''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.

 * 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