| b1ab172 | Daniel Packer | 16 July 2012, 17:13:01 UTC | branch for my work this week of july 16 | 16 July 2012, 17:13:01 UTC |
| ad7e0ca | Daniel Packer | 16 July 2012, 16:22:34 UTC | moved macosx specific launch options to the macosx platform tab. | 16 July 2012, 16:22:34 UTC |
| f5dfff9 | Adam | 08 July 2012, 22:24:55 UTC | - put regex in place for matching simulation errors. - Extract line from sim errors, - some formatting changes. | 08 July 2012, 22:24:55 UTC |
| e5135dc | Adam | 08 July 2012, 22:06:14 UTC | Formatting changes. | 08 July 2012, 22:06:14 UTC |
| 6b23f6d | Adam | 08 July 2012, 21:43:35 UTC | - New BNGParser version - Added new 'Custom' perspective with all views closable and available. - Added menu for adding views to perspectives - Disable limits that keep editors in certain views. - Console interaction with Parameter Scan now uses relative paths. TODO - use a real regex in console errors. | 08 July 2012, 21:43:35 UTC |
| bb3ecbf | Adam | 27 June 2012, 23:34:04 UTC | Made progress towards links to simulation errors from the console. Also it looks like a lot of old bng files did not make it into the last commit. | 27 June 2012, 23:34:04 UTC |
| cfbb033 | Adam | 14 June 2012, 21:25:01 UTC | | 14 June 2012, 21:25:01 UTC |
| dd6787b | Adam | 14 June 2012, 21:20:09 UTC | for pattern matching. | 14 June 2012, 21:20:09 UTC |
| b67ca08 | Adam | 14 June 2012, 21:03:37 UTC | Beginning of Console Hyperlink stuff. | 14 June 2012, 21:03:37 UTC |
| 0c74578 | Adam | 04 May 2012, 18:06:45 UTC | | 04 May 2012, 18:06:45 UTC |
| 301ea87 | Adam | 26 April 2012, 22:39:24 UTC | Update BNGParser. | 26 April 2012, 22:39:24 UTC |
| b2f17a5 | Adam | 26 April 2012, 22:24:43 UTC | removed the old parser lib | 26 April 2012, 22:24:43 UTC |
| c1612f8 | Adam | 26 April 2012, 22:23:15 UTC | Added the new BNGParser. Updated the simulator so that it manually cancels windows run_network and NFSim executables based on the PID printed in the BNG2.pl log. | 26 April 2012, 22:23:15 UTC |
| b1a170e | Adam | 26 April 2012, 15:39:06 UTC | | 26 April 2012, 15:39:06 UTC |
| a46131a | Adam | 26 April 2012, 13:45:40 UTC | Reorganizing and deleting results chart model files. | 26 April 2012, 13:45:40 UTC |
| dc42a68 | Adam | 26 April 2012, 03:41:28 UTC | Removed a lot of the old Navigator code. There are still some data types to remove after some dependency analysis. | 26 April 2012, 03:41:28 UTC |
| 5d3cf95 | Adam | 26 April 2012, 03:34:16 UTC | Results are now shown in a multipage editor. | 26 April 2012, 03:34:16 UTC |
| 165ecad | Adam | 25 April 2012, 22:10:25 UTC | Added some example classes for wiki tutorials. Added a few icons. | 25 April 2012, 22:10:25 UTC |
| 2fe929a | Adam | 24 April 2012, 18:40:40 UTC | scaled architecture overview image | 24 April 2012, 18:40:40 UTC |
| a48c9ab | Adam | 24 April 2012, 18:28:41 UTC | Added architecture overview image. Some small random changes. Mostly cleanup. | 24 April 2012, 18:28:41 UTC |
| a3c39b5 | Adam | 17 April 2012, 01:41:05 UTC | Start of massive documentation and cleaning effort. | 17 April 2012, 01:41:05 UTC |
| c974d4d | Adam | 03 April 2012, 14:11:41 UTC | Included the new scan_var.pl script in the distributionresources copy of BNG. Support the new scan_var.pl: removed my -bngPath argument and use BNGPATH environment variable in the ProcessBuilder. Started organizing files for bnga editor. Removed some old directories. | 03 April 2012, 14:11:41 UTC |
| 1685162 | Adam | 30 March 2012, 20:42:04 UTC | Removed old errorview files. Update the simulation so that it uses ProcessBuilder, and fixed some platform specific issues. Started the separation of models and actions. | 30 March 2012, 20:42:04 UTC |
| ed08b09 | Adam | 14 March 2012, 16:36:13 UTC | distribution resources and test files. | 14 March 2012, 16:36:13 UTC |
| 7a5c220 | Adam | 13 March 2012, 16:43:31 UTC | Simulation and Parameter Scans are now able to be cancelled. | 13 March 2012, 16:43:31 UTC |
| d93da6e | Adam | 29 February 2012, 21:59:21 UTC | Changed the way that the results directory was set for simulations and parameter scans. Other minor bug fixes. | 29 February 2012, 21:59:21 UTC |
| 8609225 | Adam | 25 February 2012, 01:23:36 UTC | The file browser is updated when there are changes from the simulator. Just sent the test release. | 25 February 2012, 01:23:36 UTC |
| 73898b6 | Adam | 23 February 2012, 23:52:10 UTC | Added IMarkers and IAnnotations for errors. Next is to add them for search/link occurance. | 23 February 2012, 23:52:10 UTC |
| 4b5fdf9 | Adam | 21 February 2012, 16:09:46 UTC | Added the CNF. Working on hiding editors from perspectives. | 21 February 2012, 16:09:46 UTC |
| 84350ef | Adam | 16 February 2012, 21:38:46 UTC | Just before 2.0a | 16 February 2012, 21:38:46 UTC |
| 6200c2a | Adam | 14 February 2012, 21:53:07 UTC | Fixed bug that gave all Bond ids the same value, which only allowed a single rule per edge. Fixed a bug that added both forward and reverse versions of a bidirectional rule to a an edge. Added the edge properties. Added the component properties. Added the molecule properties. Refactored for more clearly labled attributes in rules. | 14 February 2012, 21:53:07 UTC |
| 0f13e5d | Adam | 07 February 2012, 01:01:26 UTC | The Properties view is set up using IPropertySource objects, but I may change the way it is done so that references to the original objects are in the contact map and then implement iadaptable... we'll see. | 07 February 2012, 01:01:26 UTC |
| f6eb9b6 | Adam | 03 February 2012, 20:30:02 UTC | Moved all of the file opening functionality from the model navigator to a static utility class. Finished the error reporting capabilities. The table viewer shows errors from the open files, and clicking on the rows of the table will select the text that has the error. | 03 February 2012, 20:30:02 UTC |
| 1f93a7e | Adam | 31 January 2012, 22:10:58 UTC | Overhauled the contact map selection and part listening class. Editors opening and closing are handled in much smoother way. All of the known bugs in the contact map except for the tooltips issues have been fixed (update issues, redraw issues, issues with closing the last cmap, memory leaks, etc). Also added new problem view feature. Instead of using a console for the modeling phase, the user now has a table that shows all of the errors that are in currently open files. The file labels are still too long, but I will fix that later. Also completed the functionality for creating new projects and updated the images for the file explorer context menu. Cleaned some old files that were no longer used. Updated errout filters for ANTLR so that the errors are parsed and converted to BNGLModel structures that are open for the whole workspace to use through property change listeners. Updated the way that the abstract syntax tree is updated so that less code is used and it's more efficient. Removed old debugging statements. | 31 January 2012, 22:10:58 UTC |
| 150c8b0 | Adam | 06 January 2012, 03:41:35 UTC | | 06 January 2012, 03:41:35 UTC |
| c580daa | Adam | 06 January 2012, 02:54:05 UTC | AFter removing 1.5 support | 06 January 2012, 02:54:05 UTC |
| 80760fa | Adam | 04 January 2012, 21:45:21 UTC | Final commit before switching to Java 1.6 | 04 January 2012, 21:45:21 UTC |
| 100f109 | Adam | 04 January 2012, 19:15:45 UTC | There should not be any platform dependent libraries left, so I moved them all to the 'lib' folder. Eclipse should handle all of the cross-platform details. | 04 January 2012, 19:15:45 UTC |
| 09192a9 | Adam | 04 January 2012, 19:15:31 UTC | There should not be any platform dependent libraries left, so I moved them all to the 'lib' folder. Eclipse should handle all of the cross-platform details. | 04 January 2012, 19:15:31 UTC |
| 46392ff | Adam | 04 January 2012, 19:15:18 UTC | There should not be any platform dependent libraries left, so I moved them all to the 'lib' folder. Eclipse should handle all of the cross-platform details. | 04 January 2012, 19:15:18 UTC |
| 3303398 | Adam | 22 December 2011, 23:46:13 UTC | | 22 December 2011, 23:46:13 UTC |
| 0592b9d | Adam | 22 December 2011, 15:54:20 UTC | The context menu in the results browser now allows for comparisons of files. | 22 December 2011, 15:54:20 UTC |
| d2ba0f1 | Adam | 22 December 2011, 14:42:06 UTC | The Net and BNGL files are now able to be displayed in the results viewer. | 22 December 2011, 14:42:06 UTC |
| 83f09bf | Adam | 21 December 2011, 21:57:13 UTC | Added icons for the views and perspectives. | 21 December 2011, 21:57:13 UTC |
| 7288a0c | Adam | 21 December 2011, 20:24:35 UTC | - The contact map is now aligned in the border properly and in a way that is consistent with the overview. - The contact map now updates correctly on an editor switch. - All of the perspectives now share the same navigator. I was able to remove some packages because of this. - The double click listener for the navigator now uses delegation to call a specific double click listener depending on the shown perspective. - The perspective buttons are now all shown by default. - The simulation view has been given a new layout and is a little bit cleaner. It does not scroll, but I don't think that is an urgent issue. | 21 December 2011, 20:24:35 UTC |
| a479b8b | Adam | 19 December 2011, 04:01:54 UTC | Species Graph works in the results pane. | 19 December 2011, 04:01:54 UTC |
| 50f3dee | Adam | 17 December 2011, 01:31:43 UTC | | 17 December 2011, 01:31:43 UTC |
| c4354ef | Adam | 16 December 2011, 15:31:09 UTC | Changed the name of the InfluenceGraph stuff to be the full name and not IGraph. This commit is the semi-final rough draft version before results analysis features are added. | 16 December 2011, 15:31:09 UTC |
| bc3cb43 | Adam | 16 December 2011, 15:29:38 UTC | Removed these tests because they are out of date. The complete implementation of the BioNetGenUtility is not very testable. | 16 December 2011, 15:29:38 UTC |
| 4fa8fe3 | Adam | 16 December 2011, 04:52:59 UTC | | 16 December 2011, 04:52:59 UTC |
| aa76f44 | Adam | 14 December 2011, 15:35:08 UTC | Simulation and parameter scanning both work at a basic level with the interface. TODO: - Figure out a new way to report the script output to the console. - Figure out how to have a separate console output stream for each running job (like eclipse) - Figure out how to cancel a job (either at the user’s request or after some kind of error); - Error Reporting. | 14 December 2011, 15:35:08 UTC |
| 2e926b8 | Adam | 09 December 2011, 21:48:22 UTC | Made some progress on parameter scan. Still need to hook up the gui and run tests. | 09 December 2011, 21:48:22 UTC |
| 322d666 | Adam | 02 December 2011, 21:44:35 UTC | Many changes. There are compile errors still, but I had to save this code. - started simulation stuff. - organized layouts according to meeting with bio team. - added placeholder packages for all visual aspects. - added icons. - started working with results views. | 02 December 2011, 21:44:35 UTC |
| ae9352b | Adam | 14 November 2011, 21:18:22 UTC | Moved data structures for the bng ast reader to the appropriate package. | 14 November 2011, 21:18:22 UTC |
| ad984fb | Adam | 14 November 2011, 21:13:12 UTC | Moved the java 1.5 support files to the core. | 14 November 2011, 21:13:12 UTC |
| 133fd82 | Adam | 14 November 2011, 20:45:36 UTC | Moved all of the prefuse stuff to the core package. This may not be where it should stay, but I'm trying to really partition all of the code into segments that could be separated by different plug-ins. | 14 November 2011, 20:45:36 UTC |
| b7ab94d | Adam | 14 November 2011, 20:42:17 UTC | Moved the LayeredPane into the prefuse package. | 14 November 2011, 20:42:17 UTC |
| ed008b4 | Adam | 14 November 2011, 20:39:28 UTC | Moved the navigator models into the appropriate package. | 14 November 2011, 20:39:28 UTC |
| 0fe6683 | Adam | 14 November 2011, 20:08:44 UTC | Moved model building objects into appropriate packages. Also making progress with error reporting. | 14 November 2011, 20:08:44 UTC |
| 5454f83 | Adam | 11 November 2011, 23:12:11 UTC | Core functionality almost done. Models are produced upon saves and property change listeners can be registered to receive updates. Next is to get the errors from the ast and display them. | 11 November 2011, 23:12:11 UTC |
| 473a667 | Adam | 09 November 2011, 21:41:37 UTC | | 09 November 2011, 21:41:37 UTC |
| 06fb7cd | Adam | 09 November 2011, 21:19:59 UTC | Reorganizing most of the packages. I would really like to write new functionality as separate plug-ins, however, my time is short and we need stuff to work. | 09 November 2011, 21:19:59 UTC |
| 4318b34 | Adam | 03 November 2011, 19:11:18 UTC | Making progress on syntax highlighting. | 03 November 2011, 19:11:18 UTC |
| ba9763c | Adam | 27 October 2011, 18:06:39 UTC | Small changes and set images for file system interaction. | 27 October 2011, 18:06:39 UTC |
| 6cd0457 | Adam | 23 October 2011, 20:01:10 UTC | Added interactive functionality to file browser (new directory, delete, refresh) | 23 October 2011, 20:01:10 UTC |
| 7adbef5 | Adam | 17 October 2011, 19:19:50 UTC | Contact map basically done. Work started on igraph. Work started on navigator context menu and filesystem integration. | 17 October 2011, 19:19:50 UTC |
| 9852fad | Adam | 04 October 2011, 16:09:14 UTC | | 04 October 2011, 16:09:14 UTC |
| 7f3218c | Adam | 04 October 2011, 16:06:25 UTC | | 04 October 2011, 16:06:25 UTC |
| f7091e9 | Adam | 30 September 2011, 19:33:21 UTC | Starting IGraph | 30 September 2011, 19:33:21 UTC |
| 1187b40 | Adam | 22 September 2011, 19:24:44 UTC | Committing everything before I start changing the contact map overview. | 22 September 2011, 19:24:44 UTC |
| f25419e | Adam | 16 September 2011, 19:32:10 UTC | | 16 September 2011, 19:32:10 UTC |
| 1ddcf36 | Adam | 16 September 2011, 19:27:02 UTC | Random and many changes for today. | 16 September 2011, 19:27:02 UTC |
| 5f1d8af | Adam | 15 September 2011, 06:29:25 UTC | Added new code for ContactMap production | 15 September 2011, 06:29:25 UTC |
| 8c36e58 | Adam | 31 August 2011, 18:31:43 UTC | First commit of the RCP tool. RuleBender is not finished yet. | 31 August 2011, 18:31:43 UTC |
