| 70a0f1a | lonelyjoeparker | 16 October 2017, 19:52:42 UTC | ResultsPrinterSimple runnable .jar file. Includes -h help option. | 16 October 2017, 19:52:42 UTC |
| d71ec08 | lonelyjoeparker | 16 October 2017, 19:50:03 UTC | more docs | 16 October 2017, 19:50:03 UTC |
| 442bc38 | lonelyjoeparker | 16 October 2017, 19:41:14 UTC | updated javadoc (nb encoding ISO-8859-1) | 16 October 2017, 19:41:14 UTC |
| 3eb2f85 | lonelyjoeparker | 16 October 2017, 18:40:40 UTC | Proper documentation for output statistics. Closes #61. | 16 October 2017, 18:40:40 UTC |
| 97d2763 | lonelyjoeparker | 16 October 2017, 13:15:00 UTC | .gitignore additions (benchmarking, launch script etc) | 16 October 2017, 13:15:00 UTC |
| bc2dc5a | lonelyjoeparker | 24 July 2017, 10:58:16 UTC | basic example files | 24 July 2017, 10:58:16 UTC |
| cbbcfca | lonelyjoeparker | 24 July 2017, 10:57:38 UTC | basic example files | 24 July 2017, 10:57:38 UTC |
| 2155636 | Joe Parker | 19 July 2017, 14:41:39 UTC | Create ConvergenceInputs.md | 19 July 2017, 14:41:39 UTC |
| 717c68a | Joe Parker | 19 July 2017, 09:26:39 UTC | More detailed version info | 19 July 2017, 09:26:39 UTC |
| e920e02 | Joe Parker | 13 July 2017, 22:29:21 UTC | Add screenshots and benchmarking statement. | 13 July 2017, 22:29:21 UTC |
| 79b8cc8 | lonelyjoeparker | 13 July 2017, 22:28:19 UTC | png of figure for benchmarks | 13 July 2017, 22:28:19 UTC |
| df55b63 | lonelyjoeparker | 13 July 2017, 22:03:41 UTC | benchmarking data, scripts and plots; GUI screengrabs | 13 July 2017, 22:03:41 UTC |
| a92ee5b | lonelyjoeparker | 12 July 2017, 11:00:33 UTC | Benchmarking: try/catch the preload so an iteration will exit(1) if hung. | 12 July 2017, 11:00:33 UTC |
| 6fdf9bd | lonelyjoeparker | 11 July 2017, 22:15:51 UTC | results for benchmarking on linux box | 11 July 2017, 22:15:51 UTC |
| cf024f9 | lonelyjoeparker | 11 July 2017, 22:09:09 UTC | scripts to benchmark CONTEXT | 11 July 2017, 22:09:09 UTC |
| f110344 | lonelyjoeparker | 11 July 2017, 18:23:45 UTC | add benchmarking option (pass arg at command line to load/process/close dir) | 11 July 2017, 18:23:45 UTC |
| 4aac6b3 | lonelyjoeparker | 11 July 2017, 18:18:10 UTC | Merge branch 'master' of https://github.com/lonelyjoeparker/qmul-genome-convergence-pipeline | 11 July 2017, 18:18:10 UTC |
| eaff20e | lonelyjoeparker | 11 July 2017, 18:16:43 UTC | For benchmarking: pass a file (directory) on the command line as arg to trigger preload / process / shutdown cycle. | 11 July 2017, 18:16:43 UTC |
| 594227e | lonelyjoeparker | 11 July 2017, 15:58:37 UTC | doc updates, all fine... | 11 July 2017, 15:58:37 UTC |
| 64e0e7d | lonelyjoeparker | 11 July 2017, 15:57:56 UTC | Colless and root height and number of tips below all now implemented/checked. Closing #57. | 11 July 2017, 15:57:56 UTC |
| 1c16d64 | Joe Parker | 11 July 2017, 10:18:59 UTC | Update CONTEXT_versions.md | 11 July 2017, 10:18:59 UTC |
| 8e311bb | Joe Parker | 10 July 2017, 20:23:48 UTC | Update CONTEXT_versions.md | 10 July 2017, 20:23:48 UTC |
| d296daa | Joe Parker | 10 July 2017, 20:18:39 UTC | Update CONTEXT.md | 10 July 2017, 20:18:39 UTC |
| df06ac4 | Joe Parker | 10 July 2017, 20:16:13 UTC | Update CONTEXT.md | 10 July 2017, 20:16:13 UTC |
| 2da2b2b | lonelyjoeparker | 10 July 2017, 19:45:38 UTC | release version v0.8.4 prerelease | 10 July 2017, 19:45:38 UTC |
| 7966948 | lonelyjoeparker | 10 July 2017, 19:34:03 UTC | Upversion to 0.8.4 - Phylogeny import NEXUS trees #59: Closing w/limited support (not BEAST or MrBayes rate/branch annotations or TRANSLATE block, most other) - Phylogeny stats scrollpane/jtable UI, export phylogeny stats #58: closing. - Test data etc should be in the right places. - Version string -> 0.8.4 prerelease - UI (menu+hotkey) improvements to support the above. | 10 July 2017, 19:34:03 UTC |
| 1a3f5c3 | lonelyjoeparker | 10 July 2017, 12:39:17 UTC | Added a .ser file from the older tests. Most of the older TreeNode tests now passing. Still need to look at the Colless imbalance (#57) | 10 July 2017, 12:39:17 UTC |
| 3060daa | lonelyjoeparker | 10 July 2017, 12:21:11 UTC | Refactored input data structure and dependent binary locations for junit testing. _Most_ of the data and binaries for ASR and phylogeny classes' tests should now be within the project working directory (e.g. ./junit, ./junit-test-inputs, and ./bin-dependencies). Most of the PAML/codeml and raxML wrappers have not been retested or are failing though - need to raise a new issue. | 10 July 2017, 12:21:11 UTC |
| de21b71 | lonelyjoeparker | 08 July 2017, 21:15:28 UTC | t's all good, merge weekly work Merge branch 'master' of https://github.com/lonelyjoeparker/qmul-genome-convergence-pipeline | 08 July 2017, 21:15:28 UTC |
| 924b07e | lonelyjoeparker | 08 July 2017, 21:05:52 UTC | First attempt at #46, tested against TreeStat v1.7.4. Passing: Tree Length Cherry Count Internal Length External Length External : Internal Treeness Seem correct in test trees but TreeStat gives odd implementations: Tree Height To do: Tree Imbalance (Colless) | 08 July 2017, 21:05:52 UTC |
| 91ab34e | lonelyjoeparker | 07 July 2017, 19:09:26 UTC | wireframe for tree stats (#46) | 07 July 2017, 19:09:26 UTC |
| 0499c4f | Joe Parker | 06 July 2017, 00:44:45 UTC | Update CONTEXT.md | 06 July 2017, 00:44:45 UTC |
| 280cb3d | Joe Parker | 06 July 2017, 00:36:40 UTC | Update CONTEXT_versions.md | 06 July 2017, 00:36:40 UTC |
| ef392a8 | Joe Parker | 06 July 2017, 00:19:25 UTC | Update README.md | 06 July 2017, 00:19:25 UTC |
| c118721 | Joe Parker | 06 July 2017, 00:15:45 UTC | Update README.md | 06 July 2017, 00:15:45 UTC |
| 172cb71 | lonelyjoeparker | 06 July 2017, 00:09:48 UTC | update bin snapshots | 06 July 2017, 00:09:48 UTC |
| 5d1d89c | lonelyjoeparker | 05 July 2017, 23:59:34 UTC | Alignment file imports tightened up considerably, so moving to 0.8.3. | 05 July 2017, 23:59:34 UTC |
| c9f4860 | lonelyjoeparker | 05 July 2017, 23:00:11 UTC | Closes #42. Sequence translation now done via static access to EnnumeratedTranslator* classes' translate() method. EnnumeratedTranslatorOrthodoxCodons.translate() will get most of the most common, but EnnumeratedTranslatorFullCodons.translate() will usually be needed. | 05 July 2017, 23:00:11 UTC |
| 7acc381 | lonelyjoeparker | 05 July 2017, 15:37:38 UTC | Various UI improvements to plotting frame including summary statistics calculation for alignments. | 05 July 2017, 15:37:38 UTC |
| 3e8f4e1 | lonelyjoeparker | 04 July 2017, 21:27:01 UTC | Horizontal scrolling for AA and NT alignment panes linked (jerkily...) Closes #54 | 04 July 2017, 21:27:01 UTC |
| 211d87b | lonelyjoeparker | 04 July 2017, 20:03:08 UTC | snapshot v0.8.2 | 04 July 2017, 20:03:08 UTC |
| f614078 | lonelyjoeparker | 04 July 2017, 14:33:32 UTC | Rename AlignmentsTableModel -> AlignmentsModel (for consistency) | 04 July 2017, 14:33:32 UTC |
| cd94a95 | lonelyjoeparker | 04 July 2017, 13:16:10 UTC | AlignmentsModel updated to correctly parse table data to Double[] for plotting. Addresses #52 | 04 July 2017, 13:16:10 UTC |
| 2c2a824 | lonelyjoeparker | 04 July 2017, 09:53:43 UTC | eclipse .launch files | 04 July 2017, 09:53:43 UTC |
| 55744df | lonelyjoeparker | 04 July 2017, 09:44:18 UTC | adding .classpath to .gitignore | 04 July 2017, 09:44:18 UTC |
| 34d2443 | lonelyjoeparker | 04 July 2017, 00:02:30 UTC | Changes up to 0.8.2: - add text dump of alignment statistics - first implementation of statistics plotting via XChart New dependencies: - XChart 3.3.1 | 04 July 2017, 00:02:30 UTC |
| 73a41c8 | lonelyjoeparker | 20 April 2017, 11:50:56 UTC | Add eclipse IDE .launch config file and github issue template. | 20 April 2017, 11:50:56 UTC |
| fc9d48a | lonelyjoeparker | 12 July 2016, 20:29:45 UTC | added ISSUE_TEMPLATE | 12 July 2016, 20:29:45 UTC |
| 37e064a | lonelyjoeparker | 01 November 2015, 11:11:23 UTC | Added public method to force the data model's last row to update the seleciton in the view JTable | 01 November 2015, 11:11:23 UTC |
| 7393712 | lonelyjoeparker | 31 October 2015, 18:50:15 UTC | (very) Partially addresses issue #50 (duplicate taxon names not importing correctly leading to incorrect taxon counts in phylip exports): the number of taxon counts in export step now taken directly from taxaListArray.length() not numberOfTaxa. However this is only a partial fix - doesn't even slightly address the causal issue (duplicate taxon names behaviour not well defined in imports) at all. | 31 October 2015, 18:50:15 UTC |
| 07411ef | lonelyjoeparker | 30 October 2015, 15:40:23 UTC | Added option to set minimum line length in chars (currently defaults to >1, in the case of fastq files this is no good as need to grep out '+' lines..) | 30 October 2015, 15:40:23 UTC |
| b7527b2 | lonelyjoeparker | 30 October 2015, 14:21:04 UTC | .DS_Store added to .gitignore | 30 October 2015, 14:21:04 UTC |
| 77ae2ff | lonelyjoeparker | 28 August 2015, 18:19:55 UTC | Test specifications for translation mode switching (orthodox, unorthodox and 2 debug modes) | 28 August 2015, 18:19:55 UTC |
| 5742f56 | lonelyjoeparker | 26 August 2015, 15:51:12 UTC | Implemented first test (true positive) of orthodox translate on orthodox input (true/true=pass) | 26 August 2015, 15:51:12 UTC |
| ef0dc8f | lonelyjoeparker | 26 August 2015, 15:50:32 UTC | Made all input sequences same length so no padding should occur in ASR import (no gaps expected on translation) | 26 August 2015, 15:50:32 UTC |
| 9baaae3 | lonelyjoeparker | 26 August 2015, 15:39:12 UTC | Added example fasta files that should pass/fail under various conditions (contain gaps, ambiguity characters, invalid characters etc) | 26 August 2015, 15:39:12 UTC |
| 6e53007 | lonelyjoeparker | 25 August 2015, 18:30:25 UTC | Setting up test harness framework including input files for AlignedSequenceRepresentation.translate() using AlignmentTranslationTable enum to specify translation hash options behaviour at runtime. (towards issue #42) | 25 August 2015, 18:30:25 UTC |
| ac84a34 | lonelyjoeparker | 25 August 2015, 17:56:55 UTC | Merge branch 'master' of https://github.com/lonelyjoeparker/qmul-genome-convergence-pipeline | 25 August 2015, 17:56:55 UTC |
| f53856a | lonelyjoeparker | 25 August 2015, 17:56:24 UTC | Changed to use example input file from trunk/examples | 25 August 2015, 17:56:24 UTC |
| 7fe9c3c | Joe Parker | 25 August 2015, 17:49:20 UTC | Formatted a bit better | 25 August 2015, 17:49:20 UTC |
| 97cfe76 | Joe Parker | 25 August 2015, 15:29:05 UTC | Update README.md | 25 August 2015, 15:29:05 UTC |
| 6dcc4cd | Joe Parker | 25 August 2015, 15:28:12 UTC | Added right-click hint | 25 August 2015, 15:28:12 UTC |
| 5fa3d1c | Joe Parker | 25 August 2015, 15:27:03 UTC | Create readme and right-click hint | 25 August 2015, 15:27:03 UTC |
| 7ee1a86 | Joe Parker | 25 August 2015, 15:22:00 UTC | Added right-click hint | 25 August 2015, 15:22:00 UTC |
| c2d9da9 | Joe Parker | 25 August 2015, 15:20:53 UTC | Update CONTEXT.md | 25 August 2015, 15:20:53 UTC |
| 0f9cfbb | Joe Parker | 25 August 2015, 15:16:33 UTC | Create README.md | 25 August 2015, 15:16:33 UTC |
| e81fb20 | lonelyjoeparker | 25 August 2015, 15:13:36 UTC | Added compressed example directory | 25 August 2015, 15:13:36 UTC |
| a3ae55b | lonelyjoeparker | 25 August 2015, 15:05:09 UTC | Merge branch 'master' of https://github.com/lonelyjoeparker/qmul-genome-convergence-pipeline | 25 August 2015, 15:05:09 UTC |
| d60663b | lonelyjoeparker | 25 August 2015, 15:04:25 UTC | Adding example files and directory structure for v0.8.1 CONTEXT | 25 August 2015, 15:04:25 UTC |
| 0e179c4 | Joe Parker | 25 August 2015, 14:49:33 UTC | Added information for 0.8.1 version | 25 August 2015, 14:49:33 UTC |
| 48baba6 | Joe Parker | 25 August 2015, 14:44:19 UTC | Updated reference to v0.8.1 | 25 August 2015, 14:44:19 UTC |
| ae0f2d2 | Joe Parker | 25 August 2015, 14:42:41 UTC | Updated reference to v0.8.1 | 25 August 2015, 14:42:41 UTC |
| 469b6ff | lonelyjoeparker | 25 August 2015, 14:39:24 UTC | Version updated to v0.8.1 incorporating fixes to issues #45 #44 #39. | 25 August 2015, 14:39:24 UTC |
| 190ab1c | lonelyjoeparker | 25 August 2015, 14:36:23 UTC | v0.8.1 executable binary Adds fixes to issues #45 #44 #39. | 25 August 2015, 14:36:23 UTC |
| 86db9d8 | lonelyjoeparker | 25 August 2015, 14:34:18 UTC | Fixes issue #45 (slowness rendering - added repaint() to scrollbar listener) | 25 August 2015, 14:34:18 UTC |
| 58c758d | lonelyjoeparker | 25 August 2015, 11:27:16 UTC | Resolves issue #44 (polytomies not rendered correctly) | 25 August 2015, 11:27:16 UTC |
| 36cc770 | lonelyjoeparker | 24 August 2015, 19:01:13 UTC | Updated comments to TreeNode to highlight issue #44 for work | 24 August 2015, 19:01:13 UTC |
| 3d8deb7 | lonelyjoeparker | 24 August 2015, 18:53:01 UTC | Tree phylogeny display obtains max Xpos from branches and use that (+10 px) to position tips. Resolves X-pos issue for tip labels. | 24 August 2015, 18:53:01 UTC |
| fb74d32 | lonelyjoeparker | 24 August 2015, 18:33:48 UTC | updated addBatch listener to show last-added phylogeny in display panel. | 24 August 2015, 18:33:48 UTC |
| 2b72a87 | lonelyjoeparker | 24 August 2015, 18:07:53 UTC | Renaming PhylogenyDisplayPanel -> DisplayPhylogenyPanel for consistency. Mounting phylogeny display in a scroll pane and other UI tweaks including swapping phylogenies | 24 August 2015, 18:07:53 UTC |
| 570b467 | lonelyjoeparker | 24 August 2015, 15:53:44 UTC | Rename for consistency with DisplayAlignment / DisplayAlignmentPanel | 24 August 2015, 15:53:44 UTC |
| bb807a9 | lonelyjoeparker | 24 August 2015, 14:40:44 UTC | debug only, print selected row info | 24 August 2015, 14:40:44 UTC |
| e795c13 | lonelyjoeparker | 24 August 2015, 14:20:57 UTC | more refactoring - deleted redundant (and duplicate) dir | 24 August 2015, 14:20:57 UTC |
| 7224c97 | lonelyjoeparker | 24 August 2015, 14:18:30 UTC | trunk/src moved to src | 24 August 2015, 14:18:30 UTC |
| fd5d48a | lonelyjoeparker | 24 August 2015, 14:14:36 UTC | Updated javadoc (autogenerated/eclipse) | 24 August 2015, 14:14:36 UTC |
| 8573431 | lonelyjoeparker | 24 August 2015, 14:12:24 UTC | Updated javadoc (autogenerated/eclipse) | 24 August 2015, 14:12:24 UTC |
| 0b69705 | lonelyjoeparker | 24 August 2015, 14:09:45 UTC | Remove empty dir src | 24 August 2015, 14:09:45 UTC |
| 52fc304 | Joe Parker | 21 August 2015, 13:09:57 UTC | Added project email, roadmap *Email joe+CONTEXT@kitson-consulting.co.uk *No roadmap defined yet, but listed for completeness. | 21 August 2015, 13:09:57 UTC |
| 6317cff | Joe Parker | 20 August 2015, 18:12:23 UTC | Update README_SimpleMRCASubstitutionDetector.md | 20 August 2015, 18:12:23 UTC |
| ee497fd | Joe Parker | 20 August 2015, 18:10:31 UTC | Update README.md | 20 August 2015, 18:10:31 UTC |
| ab766d1 | Joe Parker | 20 August 2015, 17:47:54 UTC | Update README_SimpleMRCASubstitutionDetector.md | 20 August 2015, 17:47:54 UTC |
| 2601597 | Joe Parker | 20 August 2015, 17:46:01 UTC | Update README.md | 20 August 2015, 17:46:01 UTC |
| 46691de | Joe Parker | 20 August 2015, 17:44:59 UTC | Update README.md | 20 August 2015, 17:44:59 UTC |
| 8bd1f5e | Joe Parker | 20 August 2015, 17:44:20 UTC | Depdendencies and packaged libraries (build path) information | 20 August 2015, 17:44:20 UTC |
| d16f2d0 | Joe Parker | 20 August 2015, 17:33:35 UTC | Create README_CONTEXT-PhylogenomicDatasetBrowser.md | 20 August 2015, 17:33:35 UTC |
| 92cc205 | Joe Parker | 20 August 2015, 17:32:15 UTC | Update CONTEXT.md | 20 August 2015, 17:32:15 UTC |
| 5d9d1b5 | lonelyjoeparker | 20 August 2015, 17:28:34 UTC | Executable jarfile build of 0.8 prerelease version | 20 August 2015, 17:28:34 UTC |
| c5d8f34 | lonelyjoeparker | 20 August 2015, 17:18:55 UTC | Tidying up deletions; renamed PDB to CONTEXTPDB | 20 August 2015, 17:18:55 UTC |
| 05f2de9 | lonelyjoeparker | 20 August 2015, 17:16:11 UTC | Merge branch 'master' of https://github.com/lonelyjoeparker/qmul-genome-convergence-pipeline | 20 August 2015, 17:16:11 UTC |
| db8d328 | lonelyjoeparker | 20 August 2015, 17:14:52 UTC | Various updates related to tidying up GUI for 0.8 prerelease: * Renamed to CONTEXT * About JFrame showing credits * Implemented all versioning info via CONTEXTVersion class * Implemented user-selected destination for alignment stats textfile to dump in .tdf format to * Implemented JFrame to display statistics' definitions * Updated project URLs on github | 20 August 2015, 17:14:52 UTC |
