Diff for "Refactored_Menu"

Differences between revisions 14 and 15

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 (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.
(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?)
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 manage 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.
How/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.

Apply Spring Embedded Layout
(Layout algorithms provided as plugins are inserted here.)
(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

-  ← Revision 14 as of 2006-02-23 02:25:57 →
  Size: 3598
  Editor: KeiichiroOno
  Comment:
+  ← Revision 15 as of 2006-02-23 02:33:27 →
  Size: 3755
  Editor: KeiichiroOno
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 25:
-    * Network (Ctrl-L) - Load network files: SIF, GML, or XGMML.
+    * Network (Ctrl-L) - Load network files: SIF, GML, or XGMML (SBML & KEGG importer may be added).
 Line 33:
+    * Network as SIF

    * Node Attributes

    * Edge Attributes

    * Network as graphics... - PDF,GIF, etc.
-Line 53:
+Line 57:
-''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.
+''CytoPanels'' menu item is implemented as a submenu of this.  Maybe renames something like '''''Desktop''''' since menu items under this section manage layout/states of the panels.