| 46 | | 7. Import/export layout [[BR]] Save layout (Model --> Export --> Export Layout) in a file (e.g. layout.graphml) in your home directory, change editing mode to 'Editing', move the compounds 'lig1' and 'ph2' slightly, move the edge handle of inhibition edge '!r1-->not_r1_r2_a2' slightly, import layout (Model --> Import --> Import Layout) from a file (e.g. layout.graphml). The positions of the compounds 'lig1' and 'ph2' and edge handle of inhibition edge '!r1-->not_r1_r2_a2' should be the same as before. [[BR]] --> TODO: use JUnit test. |
| 47 | | |
| 48 | | 8. Import/export attributes [[BR]] Save node attribute 'Map Number' (Model --> Export --> Export Attributes) in a file (e.g. node_attrs.txt) in your home directory, edit file node_attrs.txt by changing in the first line 'Map Number' to 'Test' and in the second line '1' to '5', import attribute file (Model --> Import --> Import Attributes). Copy the 'Logical Network Scenario' and for 'Node Fill Color' set the map attribute to 'Test'. Two row should appear showing the values '1' and '5'. Now set for value '1' a blue color, for value '5' a red color. The node 'k1' in the module 'cell' should be colored red, all other nodes should colored blue [[BR]] --> TODO: use JUnit test. |
| 49 | | |
| 50 | | 9. Export graphics [[BR]] Open export dialog (Model --> Export --> Export Graphics), a dialog should appear with six options for formats (eps, ps, svg, emf, png, gif), export the view with each of the formats using default options. The results should look like the view in the Visual Explorer but without any layers (status, overview, grid) |
| 51 | | 10. Export logical model [[BR]] Output logical model with default options, click button 'Generate Model', export should perform without errors, check resulting files, click button 'Close' should exit the dialog. [[BR]] --> TODO: use JUnit test. [[BR]] |
| 52 | | 11. Edit scenarios, new/copy/rename/remove/mappings [[BR]] |
| 53 | | |
| 54 | | 8. Load user-defined (local) scenarios [[BR]] Load user-defined scenarios from USER_HOME. Check console output. Two cases: |
| 55 | | 1. No file '.!PromotVizScenarios' in USER_HOME. When open the Visual Explorer a default scenario 'Default (Editable)' is created. Check 'Edit Scenarios'-dialog (Edit --> Edit Scenario...). |
| 56 | | 2. File '.!PromotVizScenarios' in USER_HOME exists. Check 'Edit Scenarios'-dialog (Edit --> Edit Scenario...). In the dialog local scenarios (indicated in the name by a prefixed [L]) have to be present. |
| 57 | | |
| 58 | | 9. Save user-defined (local) scenarios (to USER_HOME) [[BR]] Save user-defined scenarios to USER_HOME. Check console output. Check file '.!PromotVizScenarios' in the USER_HOME of existence and correct time stamp. |
| 59 | | |
| 60 | | 10. Exit with/without dialog [[BR]] Closing the visual explorer requires to check the local scenarios. If the initial local scenarios are equal to the current local scenarios (no changes) the Visual Explorer exit promptly. If the initial local scenarios are not equal to the current local scenarios (changes are made during exploration) a dialog is opened in order to make sure the user really wants to save the local scenarios (options: Save, Discard, Close). Button 'Save' saves the scenarios as described in (9), button 'Discard' just close the dialog, button 'Close' exits the Visual Explorer with no saving. |
| | 44 | 7. Import/export layout [[BR]] Save layout (Model --> Export --> Export Layout) in a file (e.g. layout.graphml) in your home directory, change editing mode to 'Editing', move the compounds 'lig1' and 'ph2' slightly, move the edge handle of inhibition edge '!r1-->not_r1_r2_a2' slightly, import layout (Model --> Import --> Import Layout) from a file (e.g. layout.graphml). The positions of the compounds 'lig1' and 'ph2' and edge handle of inhibition edge '!r1-->not_r1_r2_a2' should be the same as before. [[BR]] --> TODO: use JUnit test. [[BR]][[BR]] |
| | 45 | 8. Import/export attributes [[BR]] Save node attribute 'Map Number' (Model --> Export --> Export Attributes) in a file (e.g. node_attrs.txt) in your home directory, edit file node_attrs.txt by changing in the first line 'Map Number' to 'Test' and in the second line '1' to '5', import attribute file (Model --> Import --> Import Attributes). Copy the 'Logical Network Scenario' and for 'Node Fill Color' set the map attribute to 'Test'. Two row should appear showing the values '1' and '5'. Now set for value '1' a blue color, for value '5' a red color. The node 'k1' in the module 'cell' should be colored red, all other nodes should colored blue [[BR]] --> TODO: use JUnit test.[[BR]][[BR]] |
| | 46 | 9. Export graphics [[BR]] Open export dialog (Model --> Export --> Export Graphics), a dialog should appear with six options for formats (eps, ps, svg, emf, png, gif), export the view with each of the formats using default options. The results should look like the view in the Visual Explorer but without any layers (status, overview, grid). [[BR]][[BR]] |
| | 47 | 10. Export logical model [[BR]] Output logical model with default options, click button 'Generate Model', export should perform without errors, check resulting files, click button 'Close' should exit the dialog. [[BR]] --> TODO: use JUnit test. [[BR]][[BR]] |
| | 48 | 11. Edit scenarios, new/copy/rename/remove mappings. [[BR]][[BR]] |
| | 49 | 12. Load user-defined (local) scenarios [[BR]] Load user-defined scenarios from USER_HOME. Check console output. Two cases: |
| | 50 | a. No file '.!PromotVizScenarios' in USER_HOME. When open the Visual Explorer a default scenario 'Default (Editable)' is created. Check 'Edit Scenarios'-dialog (Edit --> Edit Scenario...). |
| | 51 | b. File '.!PromotVizScenarios' in USER_HOME exists. Check 'Edit Scenarios'-dialog (Edit --> Edit Scenario...). In the dialog local scenarios (indicated in the name by a prefixed [L]) have to be present. [[BR]][[BR]] |
| | 52 | 13. Save user-defined (local) scenarios (to USER_HOME) [[BR]] Save user-defined scenarios to USER_HOME. Check console output. Check file '.!PromotVizScenarios' in the USER_HOME of existence and correct time stamp.[[BR]][[BR]] |
| | 53 | 14. Exit with/without dialog [[BR]] Closing the visual explorer requires to check the local scenarios. If the initial local scenarios are equal to the current local scenarios (no changes) the Visual Explorer exit promptly. If the initial local scenarios are not equal to the current local scenarios (changes are made during exploration) a dialog is opened in order to make sure the user really wants to save the local scenarios (options: Save, Discard, Close). Button 'Save' saves the scenarios as described in (13), button 'Discard' just close the dialog, button 'Close' exits the Visual Explorer with no saving. [[BR]][[BR]] |
| 64 | | 11. Orthogonal layout [[BR]] Apply an orthogonal layout to the network, all edges represented by polylines (not straight lines) must be drawn in an orthogonal style. |
| 65 | | |
| 66 | | 12. Flat layout [[BR]] Apply a flat layout to the network, all basic compounds are scaled to the same size (compare compounds in different modules, e.g. 'k1' in cell and 'tf1' in nucleus) |
| 67 | | |
| 68 | | 13. Adjust node size [[BR]] Extend node width to label length, ... |
| 69 | | |
| 70 | | 12. Grid layer on/off [[BR]] A grid overlaying the entire canvas should appear/disappear by switching option on/off. |
| 71 | | |
| 72 | | 13. Squiggle layer on/off [[BR]] With option on and pressed left mouse button, a line is drawn, release mouse button should stop drawing, drawings can be switched on/off. |
| 73 | | |
| 74 | | 14. Status layer on/off [[BR]] With option on, a text box appears in the right lower corner showing the name of the current scenario (default: Logical Scenario) and the current navigation mode (default: Hierarchy Zoom), display can be switched on/off. |
| 75 | | |
| 76 | | 15. Overview layer on/off [[BR]] With option on, a overview window of the entire canvas appears in the right lower corner, can be switched on/off. |
| 77 | | |
| 78 | | 16. Legend layer for Visual Scenarios on/off/correct mappings [[BR]] A window should appear showing the mappings used in the current visual scenario. Press the button 'Close' to exit the dialog, can be switched on/off. |
| 79 | | |
| 80 | | 17. Navigation mode: Interactive Zoom [[BR]] Select navigation mode 'Interactive Zoom', in the status layer the current mode should be entitled 'Interactive Zoom': |
| | 57 | 15. Orthogonal layout [[BR]] Apply an orthogonal layout to the network (Edit --> Layout --> Orthogonal Layout), all edges represented by polylines (not straight lines) must be drawn in an orthogonal style. [[BR]][[BR]] |
| | 58 | 16. Flat layout [[BR]] Apply a flat layout to the network (Edit --> Layout --> Flat Layout), all basic compounds are scaled to the same size (compare compounds in different modules, e.g. 'k1' in cell and 'tf1' in nucleus). [[BR]][[BR]] |
| | 59 | 17. Adjust node width [[BR]] Call action (Edit --> Layout --> Extend Node Width To Label), all nodes with really long labels should adjust their width to the label length. [[BR]][[BR]] |
| | 60 | 18. Grid layer on/off [[BR]] A grid overlaying the entire canvas should appear/disappear by switching option on/off. [[BR]][[BR]] |
| | 61 | 19. Squiggle layer on/off [[BR]] With option on and pressed left mouse button, a line is drawn, release mouse button should stop drawing, drawings can be switched on/off. [[BR]][[BR]] |
| | 62 | 20. Status layer on/off [[BR]] With option on, a text box appears in the right lower corner showing the name of the current scenario (default: Logical Scenario) and the current navigation mode (default: Hierarchy Zoom), display can be switched on/off. [[BR]][[BR]] |
| | 63 | 21. Overview layer on/off [[BR]] With option on, a overview window of the entire canvas appears in the right lower corner, can be switched on/off. [[BR]][[BR]] |
| | 64 | 22. Legend layer for Visual Scenarios on/off/correct mappings [[BR]] A window should appear showing the mappings used in the current visual scenario. Press the button 'Close' to exit the dialog, can be switched on/off. [[BR]][[BR]] |
| | 65 | 23. Navigation mode: Interactive Zoom [[BR]] Select navigation mode 'Interactive Zoom', in the status layer the current mode should be entitled 'Interactive Zoom': |
| 108 | | * hold down left button + ctrl + drag should move (pan) the entire network. |
| 109 | | |
| 110 | | 22. Show (all) icons on/off [[BR]] With option on, all icons are shown also for complex modules, can be toggled on/off. |
| 111 | | |
| 112 | | 23. Show (all) details on/off [[BR]] With option off, the content (nodes, edges, icons, labels) disappears, can be toggled on/off. |
| 113 | | |
| 114 | | 24. Show (all) labels on/off [[BR]] With option off, labels of all nodes (also in hierarchy) disappear, can be toggled on/off. |
| 115 | | |
| 116 | | 25. Show (all) label boxes on/off [[BR]] With option on, all label boxes of nodes (also in hierarchy) are drawn, option is disabled if (24) is off, can be toggled on/off. |
| 117 | | |
| 118 | | 26. Edge: Zoom to Source [[BR]] Choose navigation mode 'Hierarchy Zoom', click on compound 'cell' (automatic zoom to compound 'cell'), right click on reaction edge between compound 'k3p1' and compound 'ph1', choose 'Zoom To Source' from context menu (automatic zoom to compound 'k3p1'), compound 'k3p1' should be enlarged. |
| 119 | | |
| 120 | | 27. Edge: Zoom to Target [[BR]] Choose navigation mode 'Hierarchy Zoom', click on compound 'cell' (automatic zoom to compound 'cell'), right click on reaction edge between compound 'k3p1' and compound 'ph1', choose 'Zoom To Target' from context menu (automatic zoom to compound 'ph1'), compound 'ph1' should be enlarged. |
| 121 | | |
| 122 | | 28. Edge: Zoom along Edge [[BR]] Choose navigation mode 'Hierarchy Zoom', click on compound 'cell' (automatic zoom to compound 'cell'), right click on reaction edge between compound 'a1' and compound 'ph2', choose 'Zoom along Edge' from context menu (automatic zoom to compound 'a1' followed by moving the view along the path in the edge direction until compound 'ph2' is reached), compound 'ph2' should be enlarged. |
| 123 | | |
| 124 | | 29. Search for node/edge in network [[BR]] Search for the compound '!r2' (attribute == !PromotName, Case sensitive == on, Display options == Highlight, Navigation Options == Hierarchy Zoom), click button 'Search', compound '!r2' is emphasized by 'Global Highlight Node Color' (default red color) applied on the node border, display should zoom to compound '!r2', click button 'Clear' should remove the string input in the dialog and the highlight border color. [[BR]][[BR]] |
| 125 | | Search for the edges with interaction type 'inhibition' (attribute == !InteractionType, Case sensitive == off, Display options == Highlight, Navigation Options == None), click button 'Search', edges 'ph1-->a1_not_ph1_k1' and '!r1-->not_r1_r2_a2' are emphasized by 'Global Highlight Edge Color' (default red color) applied on the edge color, no zoom should be applied, click button 'Clear' should remove the string input in the dialog and the highlight border color. |
| 126 | | |
| 127 | | 30. Check model type [[BR]] Check the correct interpretation of the loaded model. Four cases:[[BR]] |
| 128 | | 1. Using Setup A, a logical model should be loaded, in the 'Statistics' dialog the model type should be 'Logical Model', default scenario should be 'Logical Network'. |
| 129 | | 2. Using Setup B, a dynamical model should be loaded, in the 'Statistics' dialog the model type should be 'Dynamical Model', default scenario should be 'Visual Editor'. |
| 130 | | 3. Using Setup C, a SBML model should be loaded, in the 'Statistics' dialog the model type should be 'SBML Model', default scenario should be 'SBML Model'. |
| 131 | | 4. Using Setup D, a unknown model type should be loaded, in the 'Statistics' dialog the model type should be 'Unknown Model', default scenario should be 'Visual Editor'. |
| | 89 | * hold down left button + ctrl + drag should move (pan) the entire network. [[BR]][[BR]] |
| | 90 | 28. Show (all) icons on/off [[BR]] With option on, all icons are shown also for complex modules, can be toggled on/off. [[BR]][[BR]] |
| | 91 | 29. Show (all) details on/off [[BR]] With option off, the content (nodes, edges, icons, labels) disappears, can be toggled on/off. [[BR]][[BR]] |
| | 92 | 30. Show (all) labels on/off [[BR]] With option off, labels of all nodes (also in hierarchy) disappear, can be toggled on/off. [[BR]][[BR]] |
| | 93 | 31. Show (all) label boxes on/off [[BR]] With option on, all label boxes of nodes (also in hierarchy) are drawn, option is disabled if (24) is off, can be toggled on/off. [[BR]][[BR]] |
| | 94 | 32. Edge: Zoom to Source [[BR]] Choose navigation mode 'Hierarchy Zoom', click on compound 'cell' (automatic zoom to compound 'cell'), right click on reaction edge between compound 'k3p1' and compound 'ph1', choose 'Zoom To Source' from context menu (automatic zoom to compound 'k3p1'), compound 'k3p1' should be enlarged. [[BR]][[BR]] |
| | 95 | 33. Edge: Zoom to Target [[BR]] Choose navigation mode 'Hierarchy Zoom', click on compound 'cell' (automatic zoom to compound 'cell'), right click on reaction edge between compound 'k3p1' and compound 'ph1', choose 'Zoom To Target' from context menu (automatic zoom to compound 'ph1'), compound 'ph1' should be enlarged. [[BR]][[BR]] |
| | 96 | 34. Edge: Zoom along Edge [[BR]] Choose navigation mode 'Hierarchy Zoom', click on compound 'cell' (automatic zoom to compound 'cell'), right click on reaction edge between compound 'a1' and compound 'ph2', choose 'Zoom along Edge' from context menu (automatic zoom to compound 'a1' followed by moving the view along the path in the edge direction until compound 'ph2' is reached), compound 'ph2' should be enlarged. [[BR]][[BR]] |
| | 97 | 35. Search for node/edge in network [[BR]] Search for the compound '!r2' (attribute == !PromotName, Case sensitive == on, Display options == Highlight, Navigation Options == Hierarchy Zoom), click button 'Search', compound '!r2' is emphasized by 'Global Highlight Node Color' (default red color) applied on the node border, display should zoom to compound '!r2', click button 'Clear' should remove the string input in the dialog and the highlight border color. [[BR]] |
| | 98 | Search for the edges with interaction type 'inhibition' (attribute == !InteractionType, Case sensitive == off, Display options == Highlight, Navigation Options == None), click button 'Search', edges 'ph1-->a1_not_ph1_k1' and '!r1-->not_r1_r2_a2' are emphasized by 'Global Highlight Edge Color' (default red color) applied on the edge color, no zoom should be applied, click button 'Clear' should remove the string input in the dialog and the highlight border color. [[BR]][[BR]] |
| | 99 | 36. Check model type [[BR]] Check the correct interpretation of the loaded model. Four cases:[[BR]] |
| | 100 | a. Using Setup A, a logical model should be loaded, in the 'Statistics' dialog the model type should be 'Logical Model', default scenario should be 'Logical Network'. |
| | 101 | b. Using Setup B, a dynamical model should be loaded, in the 'Statistics' dialog the model type should be 'Dynamical Model', default scenario should be 'Visual Editor'. |
| | 102 | c. Using Setup C, a SBML model should be loaded, in the 'Statistics' dialog the model type should be 'SBML Model', default scenario should be 'SBML Model'. |
| | 103 | d. Using Setup D, a unknown model type should be loaded, in the 'Statistics' dialog the model type should be 'Unknown Model', default scenario should be 'Visual Editor'. |
