Ben Soares [Tue, 4 Apr 2023 15:27:48 +0000 (16:27 +0100)]
JAL-629 More consistent printing of --arguments. Example nf-core argfile
Ben Soares [Tue, 4 Apr 2023 10:37:45 +0000 (11:37 +0100)]
JAL-629 Remove debugging comment
Ben Soares [Tue, 4 Apr 2023 10:36:50 +0000 (11:36 +0100)]
JAL-629 --initsubstitutions as a bootstrap arg, new tests
Ben Soares [Mon, 3 Apr 2023 22:31:28 +0000 (23:31 +0100)]
JAL-629 sort files from java glob for predictability. reduce maxdepth of walkfiletree
Ben Soares [Mon, 3 Apr 2023 18:22:06 +0000 (19:22 +0100)]
JAL-629 Removed --headless to fix CommandsTest
Ben Soares [Mon, 3 Apr 2023 17:04:37 +0000 (18:04 +0100)]
JAL-629 added setprop. More filename based substitutions enabled. Test for these.
Ben Soares [Thu, 30 Mar 2023 15:25:58 +0000 (16:25 +0100)]
JAL-629 More extensive tests with real files being opened
Ben Soares [Thu, 30 Mar 2023 15:25:34 +0000 (16:25 +0100)]
JAL-629 fix bug for opening single named file with no args
Ben Soares [Thu, 30 Mar 2023 13:10:57 +0000 (14:10 +0100)]
JAL-629 Don't use new ArgParser if there are no --args and some -args
Ben Soares [Thu, 30 Mar 2023 08:34:55 +0000 (09:34 +0100)]
JAL-629 fix SubVals npe
Ben Soares [Wed, 29 Mar 2023 23:01:12 +0000 (00:01 +0100)]
JAL-629 extensive tests for ArgParser features
Ben Soares [Wed, 29 Mar 2023 22:31:46 +0000 (23:31 +0100)]
JAL-629 Added --opennew --nonews --nosplash. Added java globbing for = e.g. --open=**/*.fa. General debugging of argparser features for tests
Ben Soares [Tue, 28 Mar 2023 10:17:23 +0000 (11:17 +0100)]
JAL-629 Opening files in new windows. not working yet
Ben Soares [Sat, 25 Mar 2023 21:32:08 +0000 (21:32 +0000)]
JAL-629 open initial non-Arg arguments as files in separate alignment frames
Ben Soares [Sat, 25 Mar 2023 01:05:19 +0000 (01:05 +0000)]
JAL-629 improvements to argparser toString. Improvements to cli paeFile structure selection. Allow label subval for paefile
Ben Soares [Fri, 24 Mar 2023 00:20:30 +0000 (00:20 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Fri, 24 Mar 2023 00:19:42 +0000 (00:19 +0000)]
JAL-629 Test tidyup
James Procter [Thu, 23 Mar 2023 11:52:19 +0000 (11:52 +0000)]
Merge branch 'patch/JAL-4153_flakyJvCacheableInputBoxTest' into develop
Ben Soares [Thu, 23 Mar 2023 01:50:13 +0000 (01:50 +0000)]
JAL-629 don't clear appProps in tests
Ben Soares [Thu, 23 Mar 2023 01:11:40 +0000 (01:11 +0000)]
JAL-629 refactor ArgParser and helper classes all to jalview.bin.argparser to remove static classes. Clear properties after tests.
Ben Soares [Tue, 21 Mar 2023 19:54:47 +0000 (19:54 +0000)]
JAL-629 null checks for Desktop.instance.closeAll(). Props re-loaded after CommandsTest.
James Procter [Mon, 20 Mar 2023 17:00:10 +0000 (17:00 +0000)]
JAL-4153 longer Thread.sleep() calls in the hope that the test might pass on Bamboo
James Procter [Mon, 20 Mar 2023 16:26:18 +0000 (16:26 +0000)]
JAL-4150 test and quick patch copying code from AlignFrame.paste() to Desktop.paste() so internal paste works from popup menu
Ben Soares [Sat, 18 Mar 2023 22:37:10 +0000 (22:37 +0000)]
JAL-629 restore original tests memory settings
Ben Soares [Sat, 18 Mar 2023 22:36:00 +0000 (22:36 +0000)]
JAL-629 restore original tests memory settings
Ben Soares [Sat, 18 Mar 2023 22:12:31 +0000 (22:12 +0000)]
JAL-629 Check for new commandsSuccess before quit
Ben Soares [Sat, 18 Mar 2023 21:59:10 +0000 (21:59 +0000)]
JAL-629 move getdown update to earlier stage
Ben Soares [Sat, 18 Mar 2023 20:48:50 +0000 (20:48 +0000)]
JAL-629 Back to forking tests
Ben Soares [Fri, 17 Mar 2023 21:15:30 +0000 (21:15 +0000)]
JAL-629 All applications System.exits going through Jalview.exit
Ben Soares [Fri, 17 Mar 2023 18:16:12 +0000 (18:16 +0000)]
JAL-629 whittling down options for successful tests
Ben Soares [Fri, 17 Mar 2023 18:09:46 +0000 (18:09 +0000)]
JAL-629 whittling down options for successful tests
Ben Soares [Fri, 17 Mar 2023 12:50:21 +0000 (12:50 +0000)]
JAL-629 whittling down options for successful tests
Ben Soares [Fri, 17 Mar 2023 12:40:12 +0000 (12:40 +0000)]
JAL-629 whittling down options for successful tests
Ben Soares [Fri, 17 Mar 2023 11:33:55 +0000 (11:33 +0000)]
JAL-629 more memory to tests task
Ben Soares [Fri, 17 Mar 2023 10:40:03 +0000 (10:40 +0000)]
JAL-629 add in jvmArgs for memory for tests and keep increased clover memory
Ben Soares [Fri, 17 Mar 2023 10:32:29 +0000 (10:32 +0000)]
JAL-629 remove jvmArgs for memory for tests. Increase clover memory
Ben Soares [Fri, 17 Mar 2023 10:25:53 +0000 (10:25 +0000)]
JAL-629 Add in jvmArgs for memory for tests
Ben Soares [Thu, 16 Mar 2023 21:31:12 +0000 (21:31 +0000)]
JAL-629 closer to normal gradle settings with just increased test memory
Ben Soares [Thu, 16 Mar 2023 18:51:13 +0000 (18:51 +0000)]
JAL-629 increase test JVM size
Ben Soares [Thu, 16 Mar 2023 18:36:54 +0000 (18:36 +0000)]
JAL-629 failFast and new threads for each test
Ben Soares [Thu, 16 Mar 2023 16:46:49 +0000 (16:46 +0000)]
JAL-629 increased memory for clover
Ben Soares [Thu, 16 Mar 2023 16:41:00 +0000 (16:41 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/r2_11_2_alphafold/JAL-629-new_temp_test_branch
Ben Soares [Thu, 16 Mar 2023 16:40:50 +0000 (16:40 +0000)]
JAL-629 revert metal laf
Ben Soares [Thu, 16 Mar 2023 14:22:51 +0000 (14:22 +0000)]
JAL-629 Set Metal as default LAF for build server tests
Ben Soares [Thu, 16 Mar 2023 10:41:20 +0000 (10:41 +0000)]
JAL-629 fixed a test failing when run without a Jalview.main() having been started in another task
Ben Soares [Wed, 15 Mar 2023 01:00:21 +0000 (01:00 +0000)]
JAL-3833 fixed HiDPI test for macOS
Ben Soares [Wed, 15 Mar 2023 00:48:45 +0000 (00:48 +0000)]
JAL-629 Commands more objecty, less classy. FileLoader with sync option (or rather default async flag). Tests adjusted.
Ben Soares [Mon, 13 Mar 2023 19:52:26 +0000 (19:52 +0000)]
JAL-629 teardown in CommandsTest
Ben Soares [Sun, 12 Mar 2023 01:13:59 +0000 (01:13 +0000)]
JAL-629 Allow substitutions of {} = defaultCounter, {n} = autoCounter, {++n} = incremented autoCounter on args involving an output filename.
Ben Soares [Sat, 11 Mar 2023 12:45:18 +0000 (12:45 +0000)]
JAL-629 --substitutions --nosubstitutions flags, --nil[{++n}] just in case needed
Ben Soares [Sat, 11 Mar 2023 00:43:01 +0000 (00:43 +0000)]
JAL-629 Auto and Default count incrementer args. Flags for output filename replacements.
Ben Soares [Sat, 11 Mar 2023 00:12:45 +0000 (00:12 +0000)]
JAL-629 start of CommandsTest. More ArgParserTests.
Ben Soares [Fri, 10 Mar 2023 14:53:23 +0000 (14:53 +0000)]
JAL-629 start of tests and more examples
Ben Soares [Thu, 9 Mar 2023 23:56:15 +0000 (23:56 +0000)]
JAL-629 start of tests
Ben Soares [Thu, 9 Mar 2023 16:29:19 +0000 (16:29 +0000)]
JAL-629 --argfile=glob implemented. Remove reference seq from pAE Matrix annotation label
Ben Soares [Wed, 8 Mar 2023 15:56:02 +0000 (15:56 +0000)]
JAL-629 --close individually for each AlignFrame opened now allows batch processing of jobs in one jalview instance
Ben Soares [Wed, 8 Mar 2023 15:12:50 +0000 (15:12 +0000)]
JAL-629 improved comment and return speed of StringUtils.replaceLast()
Ben Soares [Wed, 8 Mar 2023 15:06:39 +0000 (15:06 +0000)]
JAL-629 --quiet [no stdout], --quiet --quiet [no stderr]. Tidied up BootstrapArgs. Multiple --argfile=... can be used.
Ben Soares [Wed, 8 Mar 2023 13:32:44 +0000 (13:32 +0000)]
JAL-629 Fix --headless for new args. Fix progressbar for non-headless commands. Add an --argfile=... feature
Ben Soares [Wed, 8 Mar 2023 13:31:23 +0000 (13:31 +0000)]
JAL-629 stash some TFType and PAEFile info into a PDBEntry
Ben Soares [Mon, 6 Mar 2023 20:43:45 +0000 (20:43 +0000)]
JAL-629 Fix null AlignPanel. More descriptive label of pAE Matrix allows 'Add reference annotation' to be enabled for subsequent PDB+PAE files.
Ben Soares [Fri, 3 Mar 2023 22:59:11 +0000 (22:59 +0000)]
JAL-629 Improved consistency of ArgParser classes (use of ArgValuesMap). Added setting, checking and fetching ID value for ArgValues to allow easier linking of arguments. Added argIndex for boolean Args. Made noDuplicates (no duplicate values) an Arg Option.
Ben Soares [Thu, 2 Mar 2023 23:02:27 +0000 (23:02 +0000)]
JAL-629 slight tidy up
Ben Soares [Thu, 2 Mar 2023 22:22:09 +0000 (22:22 +0000)]
JAL-629 Removal of unnecessary methods. Set pLTTD tempfac for EBIAlfafold. Simplify adding cmannot.
Ben Soares [Thu, 2 Mar 2023 13:31:03 +0000 (13:31 +0000)]
JAL-629 Some refactoring to allow more flexible use of PAE files. Not working as desired yet
Ben Soares [Tue, 28 Feb 2023 18:29:20 +0000 (18:29 +0000)]
JAL-629 Firm up bootstrapArgs. Correct '-colour' in test. Separate --headless and -headless for now to avoid premature exit for -headless (fixes tests).
Ben Soares [Mon, 27 Feb 2023 23:54:45 +0000 (23:54 +0000)]
JAL-629 add AF examples for FER1_SPIOL. Link and display PAE matrix annotation
Ben Soares [Mon, 27 Feb 2023 15:05:09 +0000 (15:05 +0000)]
JAL-629 Fix Exceptions when running with CLI not headless
Ben Soares [Mon, 27 Feb 2023 14:16:00 +0000 (14:16 +0000)]
JAL-629 Guesstimate whether to set pLDDT with PDB file
Ben Soares [Mon, 27 Feb 2023 10:04:43 +0000 (10:04 +0000)]
JAL-629 JAL-4124 JAL-3855 remove deleted debugging test file from tests
Ben Soares [Mon, 27 Feb 2023 09:52:13 +0000 (09:52 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Mon, 27 Feb 2023 09:47:23 +0000 (09:47 +0000)]
JAL-629 removed debug prints. added .cif. added some comments/code-markers
Ben Soares [Sun, 26 Feb 2023 19:43:10 +0000 (19:43 +0000)]
JAL-629 PAE matrix file guesstimate from filename
Ben Soares [Fri, 24 Feb 2023 17:23:52 +0000 (17:23 +0000)]
JAL-629 Position GUI widgets for PDF file options. Remove icon from StructureChooser frame.
James Procter [Fri, 24 Feb 2023 17:10:02 +0000 (17:10 +0000)]
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - additional test case
James Procter [Fri, 24 Feb 2023 16:44:48 +0000 (16:44 +0000)]
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)
Ben Soares [Fri, 24 Feb 2023 16:23:09 +0000 (16:23 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Fri, 24 Feb 2023 15:54:38 +0000 (15:54 +0000)]
JAL-629 add widgets to StructureChooser for tempfac choice and pae matrix file
James Procter [Fri, 24 Feb 2023 15:26:30 +0000 (15:26 +0000)]
Merge branch 'features/JAL-3858_PAEsInProjects' into develop
James Procter [Fri, 24 Feb 2023 15:13:37 +0000 (15:13 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts:
src/jalview/bin/Jalview.java
Ben Soares [Fri, 24 Feb 2023 14:43:38 +0000 (14:43 +0000)]
JAL-629 helper function for getting sensible structure (or other arg value)
Ben Soares [Fri, 24 Feb 2023 12:54:35 +0000 (12:54 +0000)]
JAL-629 better test fixes. --props=... instead of --debug
Ben Soares [Fri, 24 Feb 2023 11:52:19 +0000 (11:52 +0000)]
JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups
Ben Soares [Thu, 23 Feb 2023 19:21:24 +0000 (19:21 +0000)]
JAL-629 test fixing
Ben Soares [Thu, 23 Feb 2023 17:01:05 +0000 (17:01 +0000)]
JAL-629 Add debug messages for more failing tests
Ben Soares [Thu, 23 Feb 2023 16:21:49 +0000 (16:21 +0000)]
JAL-629 fixed a Log4j test by adding --debug arg
Ben Soares [Thu, 23 Feb 2023 16:21:19 +0000 (16:21 +0000)]
JAL-629 bootstrap args and properties. Remember index of args for 'previous structure' defaulting of other args
Ben Soares [Thu, 23 Feb 2023 16:19:25 +0000 (16:19 +0000)]
JAL-629 nf-core sample alignment files and a2m versions
Ben Soares [Thu, 23 Feb 2023 16:18:40 +0000 (16:18 +0000)]
JAL-629 fix a PAEMatrix casting error
James Procter [Thu, 23 Feb 2023 12:08:00 +0000 (12:08 +0000)]
JAL-3858 new MatrixType JAX-RI POJO
James Procter [Thu, 23 Feb 2023 11:58:09 +0000 (11:58 +0000)]
JAL-4133 update validChar width when font is changed so characters are suppressed for small widths
James Procter [Wed, 22 Feb 2023 22:14:15 +0000 (22:14 +0000)]
JAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project
James Procter [Wed, 22 Feb 2023 22:02:20 +0000 (22:02 +0000)]
JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests.
James Procter [Wed, 22 Feb 2023 14:24:04 +0000 (14:24 +0000)]
JAL-1551 source formatting
James Procter [Wed, 22 Feb 2023 14:23:56 +0000 (14:23 +0000)]
JAL-3858 simple test for PAE matrix recovery
James Procter [Wed, 22 Feb 2023 14:23:15 +0000 (14:23 +0000)]
JAL-3858 construct a PAE direct from float array
Ben Soares [Wed, 22 Feb 2023 14:04:25 +0000 (14:04 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Wed, 22 Feb 2023 14:04:03 +0000 (14:04 +0000)]
JAL-4064 JAL-4054 Corrected the tgz top-level dir from './Contents' to 'Contents' for mac JRE bundles for install4j (not strictly used, but might be in the future).
James Procter [Wed, 22 Feb 2023 13:34:54 +0000 (13:34 +0000)]
JAL-629 make sure we show GUI when not driven programmatically
James Procter [Wed, 22 Feb 2023 12:43:25 +0000 (12:43 +0000)]
JAL-4095 slightly better threshold setting and todos for improvement