Differences between revisions 10 and 15 (spanning 5 versions)
← Revision 10 as of 2006-02-23 01:35:44 →
Size: 2062
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.
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 * New  * '''''New'''''
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           * '''COMMENT''' ''from Kei: Editor will be called from New AND Edit Menu. I think this is more intuitive UI.''
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      * Clone current network - Copy current network and create a new one.
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 * 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 22: Line 24:
 * Import
    * Network (Ctrl-L) - Load network files: SIF, GML, or XGMML. 		 * '''''Import'''''
    * Network (Ctrl-L) - Load network files: SIF, GML, or XGMML (SBML & KEGG importer may be added).
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 * Export  * '''''Export'''''
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    * Network as SIF
    * Node Attributes
    * Edge Attributes
    * Network as graphics... - PDF,GIF, etc.
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 * 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.
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 * '''''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'''''
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''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. 		''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
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 * CytoPanels  * '''''CytoPanels'''''
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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 50: Line 83:

 * '''''Apply Spring Embedded Layout'''''
 * (Layout algorithms provided as plugins are inserted here.)
 * (Separator)
 * '''''Set Vizmapper'''''
 * '''''Lock/Unlock Viz Mapper'''''
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 * Contents (F1)
 * Context Sensitive (Shift+F1) 		 * '''''Contents''''' (F1)
 * '''''Context Sensitive''''' (Shift+F1)
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 * About  * '''''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.

  • 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

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.

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