ProMoT Visual Editor

Setup A: Start ProMoT server and GUI -> load the logical library Promot/trunk/promot/kb/SignalTransd/structure/struct-ana-library.mdl​ -> load the logical toymodel from tutorial Promot/trunk/promot/kb/SignalTransd/structure/toymodel_tutorial/LOAD_toymodel.mdl​ -> Open the Visual Editor for the browser tree node "cell" by double click.

Setup B: Start ProMoT server and GUI -> load Promot/trunk/promot/kb/practical-bio/LOAD.mdl​ which includes the library (reduced-library) for dynamic modeling -> Open the browser tree for "dynamic-model", for "mapk_modules" and double click to "raf-ras_modu" to open the Visual Editor for this class

The Functionality needed for the setups should be tested in browser tests, see: testplan)
Setup A is applied to tests 1., 2., 3., 4., 5., 7., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18.
Setup B is applied to tests 11., 12.,

1. Open the menu "Model" -> "Save as", type in the dialog "cell2" and click to the button "OK". A new class appears in the browser tree with name "cell2" with the same mdl-code like cell. !!! Save changes has to be tested. !!!
2. Click to "X" in the upper right corner or choose the menu action "Model" -> "Close" and the editor disappears.
3. Open the browser tree for "struct-library" and "compound"
   • Drag from the ProMoTTreeNode "drug" to the Modules-palette and release. The class is now available in the Palette.
   • Drag from the ProMoTTreeNode "nucleus" to the ConstructionArea and release. A new Slot with name "nucleus0" is created at the coordinates where released.
4. Drag from the class "source" in the Modules-palette to the ConstructionArea, a new instance is created with name "source0" at the coordinates where released.
5. Setup A and test 3 -> then click with right mouse button to the class "drug" in the Modules-palette and choose delete. The class disappears.
6. Disposing a slot in the ConstructionArea of the PaletteWindow is tested in the junit test Promot/trunk/promot/src/gui/org/mpg/dcts/promot/vizedit/cmds/CmdDisposeTest.java​
7. Double click to the class nucleus and a new visual editor with the corresponding class opens.
8. Rename connected and unconnected slots is tested in junit test Promot/trunk/promot/src/gui/org/mpg/dcts/promot/test/CmdRenameTest.java​, tests are still enhanceable.
9. Insert a "kinase" and an "and-2" slot by drag and drop from the Modules-palette, then drag an edge from the port of "kinase" to the "input1" port of "and-2". A new link with a linknode placed at the "kinase" port will be created.
10. Press the mouse over the slot named "nucleus" and move the mouse around, mouse release will place the "nucleus" slot at another place. Now press the cursor-key and the selected slot will also move.
11. Propagate a terminal from a slots port
    • logical gate terminal & logical compound terminal:
      Use Setup A, insert a new slot "and-2" by Drag and Drop from the modules palette, right click on the new node and choose 'Connect Terminals' -> 'Propagate input 1' from the context menu, a new 'term-struct-input' named 'input1' is created and connected to the input1-terminal of the 'and_2';
      Now insert a new slot "kinase" by Drag and Drop from the modules palette, right click on the new node and choose 'Connect Terminals' -> 'Propagate input' from the context menu, a 'struct-adapter-compound' is inserted and its input-terminal is propagated. There is also a LinkNode created for the link between the compound and the adapter and placed on the compound terminal.
    • dynamic terminals:
      Use Setup B, insert a new slot "storage-intra" by Drag and Drop from the modules palette, right click on the new node and choose 'Connect Terminals' -> 'Propagate cf' from the context menu, an 'adapter-flux' is inserted and its term-reaction-flux is propagated to the modules border. There is also a LinkNode created for the link between the storage and the adapter and placed on the storage terminal.
12. Copy&Paste a selection of slots (inside one/ between two editors)
13. EditDetailsDialog (see detailed tests)
14. Elevate a modules content to the current level (de-modularization)
15. Create a new class from a selection (modularization)
16. Choose from the menu 'Model'->'Export Graphics'->'Save Graphics to EPS', choose a target directory for the export, type a name and click to 'Save'. Repeat for the formats gif and gif-icon. Check the created files.
17. Drag a rectangle around the nodes "r1_a1", "r1", "r2", "not_lr" "not_r1_r2_a2" to select them, then choose 'Edit'->'Set Map Number' from the menu. Type '2' in the dialog and click to OK. Check the mdl code in the browser, if parameters are written for the slots.
18. Set parameter to selection
19. Setting the model size is tested in Promot/trunk/promot/src/gui/org/mpg/dcts/promot/vizedit/cmds/CmdSetModelSizeTest.java​
20. Fitting the model size to module content is also tested in Promot/trunk/promot/src/gui/org/mpg/dcts/promot/vizedit/cmds/CmdSetModelSizeTest.java​