Size: 424
Comment:
|
Size: 3598
Comment:
|
Deletions are marked like this. | Additions are marked like this. |
Line 7: | Line 7: |
[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. |
|
Line 8: | Line 37: |
* '''''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''''' |
|
Line 9: | Line 53: |
''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. * '''''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) |
|
Line 10: | Line 66: |
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. |
|
Line 12: | Line 79: |
* '''''Apply Spring Embedded Layout''''' * (Layout algorithms provided as plugins are inserted here.) * (Separator) * '''''Set Vizmapper''''' * '''''Lock/Unlock Viz Mapper''''' |
|
Line 18: | Line 91: |
* Contents (F1) * Context Sensitive (Shift+F1) * About |
* '''''Contents''''' (F1) * '''''Context Sensitive''''' (Shift+F1) * (Separator) * '''''About''''' |
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.
- Network
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
- 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 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.
How/Hide Overview - ON/OFF the overview window on Cytopanel 1
- (Separator)
- 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