Ben Soares [Thu, 31 Aug 2023 21:11:18 +0000 (22:11 +0100)]
JAL-3830 Remove dock icon for -h too
Ben Soares [Thu, 17 Aug 2023 11:47:57 +0000 (12:47 +0100)]
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into improvement/JAL-3830_remove_dock_icon_in_headless_mode
Ben Soares [Thu, 17 Aug 2023 11:43:26 +0000 (12:43 +0100)]
JAL-3830 JAL-4160 Remove --noheadless as --gui does this. Simplifies wrapper scripts
Ben Soares [Wed, 16 Aug 2023 23:02:26 +0000 (00:02 +0100)]
JAL-3830 JAL-3421 Conda launch script for 2.11.3 and new CLI with OS compatibility from installer launch script
Ben Soares [Wed, 16 Aug 2023 16:48:07 +0000 (17:48 +0100)]
Merge branch 'develop' into improvement/JAL-3830_remove_dock_icon_in_headless_mode
Ben Soares [Wed, 16 Aug 2023 16:48:00 +0000 (17:48 +0100)]
JAL-4160 JAL-3830 Improvements to the jalview.sh bash script especially when not in .app bundle on mac.
Ben Soares [Wed, 16 Aug 2023 16:46:51 +0000 (17:46 +0100)]
JAL-3820 JAL-4189 Use the same LaunchUtils methods to check java executable symlinks in getdown.
Ben Soares [Wed, 16 Aug 2023 16:45:56 +0000 (17:45 +0100)]
JAL-3820 JAL-4189 Move checks for java executable symlinks to LaunchUtils ready for use in getdown
Ben Soares [Fri, 11 Aug 2023 13:44:07 +0000 (14:44 +0100)]
JAL-629 Much better way of dealing with list of filenames/URLs without an --open argument. Added tests for these and fixed multiple STDOUT files.
Ben Soares [Thu, 10 Aug 2023 20:41:45 +0000 (21:41 +0100)]
JAL-629 more tests for stdout
Ben Soares [Thu, 10 Aug 2023 16:29:17 +0000 (17:29 +0100)]
JAL-629 STDOUT documentation. Opt.STDOUT narrower option. Fix for subvals and STDOUT detection.
Ben Soares [Thu, 10 Aug 2023 15:31:15 +0000 (16:31 +0100)]
JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console.errPrintln. Fix command line tests. Add test for STDOUT output file.
Ben Soares [Thu, 10 Aug 2023 09:50:14 +0000 (10:50 +0100)]
JAL-629 Method to use for printStackTrace
Ben Soares [Wed, 9 Aug 2023 23:23:50 +0000 (00:23 +0100)]
JAL-629 Move more stdout messages to stderr when outputting file to stdout
Ben Soares [Wed, 9 Aug 2023 16:21:34 +0000 (17:21 +0100)]
JAL-629 Default to FASTA if no format given for output to STDOUT
Ben Soares [Wed, 9 Aug 2023 16:16:18 +0000 (17:16 +0100)]
JAL-629 Enable output to STDOUT when specifying output filename as '-'. Must check other output is suppressed.
Ben Soares [Fri, 28 Jul 2023 11:38:51 +0000 (12:38 +0100)]
JAL-4064 Added more recognisable display names to macOS DMG architectures
James Procter [Sat, 22 Jul 2023 09:54:57 +0000 (11:54 +0200)]
JAL-4243 Jalview 2.11.2.7’s biotool record as JSON complete with update instructions as a README
James Procter [Thu, 20 Jul 2023 07:33:17 +0000 (08:33 +0100)]
JAL-3855 tree title for PAE matrix tree is PAE Matrix (method) for (structure) (sequence)
James Procter [Thu, 20 Jul 2023 07:21:11 +0000 (08:21 +0100)]
JAL-3855 auto select clusters and fix up colouring/propagation on calculation & tree display
James Procter [Wed, 19 Jul 2023 06:50:25 +0000 (07:50 +0100)]
Merge branch 'patch/JAL-3855_fixup_pae' into develop
James Procter [Tue, 18 Jul 2023 19:57:44 +0000 (20:57 +0100)]
Merge branch 'develop' into patch/JAL-3855_fixup_pae
James Procter [Tue, 18 Jul 2023 19:51:21 +0000 (20:51 +0100)]
JAL-4153 comments re patch incorrectly committed under JAL-4513
Ben Soares [Tue, 18 Jul 2023 17:00:42 +0000 (18:00 +0100)]
JAL-4513 move comments
Ben Soares [Tue, 18 Jul 2023 15:58:01 +0000 (16:58 +0100)]
JAL-4513 now re-add the SwingUtilities.invokeAndWait() with minimal sleep
James Procter [Tue, 18 Jul 2023 15:17:12 +0000 (16:17 +0100)]
JAL-3855 PAE matrices are transposed on import from JSON so returned contact vectors correspond to errors predicted when superposing at a given column position
James Procter [Tue, 18 Jul 2023 15:05:44 +0000 (16:05 +0100)]
JAL-3855 JAL-4124 test checks asymmetric matrices are stored and restored correctly
James Procter [Tue, 18 Jul 2023 14:45:27 +0000 (15:45 +0100)]
JAL-3858 fix off-by-one in matrix visualisation and interactive tooltip
James Procter [Tue, 18 Jul 2023 14:44:07 +0000 (15:44 +0100)]
JAL-3858 flip diagonal so matrix visualisation is top left to bottom right
James Procter [Tue, 18 Jul 2023 14:40:31 +0000 (15:40 +0100)]
JAL-3858 annotation .height is bigger than graphHeight so adjacent PAE matrices are clearly separated
Ben Soares [Tue, 18 Jul 2023 13:38:34 +0000 (14:38 +0100)]
JAL-4513 reduce wait to invoke fail
Ben Soares [Tue, 18 Jul 2023 13:19:15 +0000 (14:19 +0100)]
JAL-4513 add a SwingUtilities.invokeAndWait() to see what happens
Ben Soares [Mon, 17 Jul 2023 16:38:31 +0000 (17:38 +0100)]
JAL-3599 Updated default eclipse to 'latest' and made jalviewjsLaunchTest timeouts a bit more flexible
James Procter [Mon, 17 Jul 2023 10:15:07 +0000 (11:15 +0100)]
JAL-4119 TRACE level console message reporting download URL for sifts. Also more informative message when ‘Sifts Mapping Failed’ is reported as an exception - since this message can be reported when some chains in the PDB file do not match sequences being associated (but others do!!).
James Procter [Mon, 17 Jul 2023 09:41:43 +0000 (10:41 +0100)]
JAL-4090 JAL-4165 known issue
James Procter [Mon, 17 Jul 2023 09:40:04 +0000 (10:40 +0100)]
JAL-4090 JAL-4165 known issue
James Procter [Mon, 17 Jul 2023 09:27:23 +0000 (10:27 +0100)]
JAL-4223 add testdata for test
James Procter [Mon, 17 Jul 2023 09:25:45 +0000 (10:25 +0100)]
JAL-4090 mark JAL-4178 and JAL-4142 as known issues
James Procter [Mon, 17 Jul 2023 06:31:00 +0000 (07:31 +0100)]
JAL-4217 move Commands.structureImageTest to testTask1
James Procter [Wed, 12 Jul 2023 07:33:54 +0000 (08:33 +0100)]
JAL-4223 - test and patch to ensure numbering matches sequence data from RNAML file
James Procter [Mon, 10 Jul 2023 09:12:48 +0000 (10:12 +0100)]
Merge branch 'improvement/JAL-3830_remove_dock_icon_in_headless_mode' into develop
James Procter [Fri, 7 Jul 2023 16:54:19 +0000 (17:54 +0100)]
Merge branch 'patch/JAL-4195_cli_eps_export_npe' into develop
James Procter [Fri, 7 Jul 2023 16:53:28 +0000 (17:53 +0100)]
JAL-4217 JAL-629 built in 25s time out waiting for structure viewer to load data before attempting to grab an image.
James Procter [Fri, 7 Jul 2023 16:02:00 +0000 (17:02 +0100)]
JAL-4090 update 2.11.3.0 release notes (with in-progress bits too) and what's new
James Procter [Fri, 7 Jul 2023 14:18:08 +0000 (15:18 +0100)]
Merge branch 'patch/JAL-4119_sifts_ftp_split' into develop
James Procter [Fri, 7 Jul 2023 14:03:09 +0000 (15:03 +0100)]
Merge branch 'develop' into patch/JAL-4195_cli_eps_export_npe
James Procter [Fri, 7 Jul 2023 13:58:52 +0000 (14:58 +0100)]
JAL-4195 add exception handling for all other CommandsTest tests and remove errant class-level @Test tag
James Procter [Fri, 7 Jul 2023 13:42:20 +0000 (14:42 +0100)]
JAL-4221 update description when transferring annotation and no description already set
James Procter [Fri, 7 Jul 2023 13:18:44 +0000 (14:18 +0100)]
JAL-629 even more console debug for --structureviewer opening arguments
James Procter [Thu, 6 Jul 2023 17:17:14 +0000 (18:17 +0100)]
JAL-629 liberal defensive coding, comments about refactoring and DEBUG output for --structureimage
James Procter [Thu, 6 Jul 2023 17:16:24 +0000 (18:16 +0100)]
JAL-629 make —structure image work again after threading it off
James Procter [Thu, 6 Jul 2023 16:35:17 +0000 (17:35 +0100)]
JAL-4217 catch case when the structure viewer doesn't get added to the desktop window (possible knock on for flatlaf JAL-3416)
James Procter [Thu, 6 Jul 2023 15:52:29 +0000 (16:52 +0100)]
JAL-4217 interruptedExceptions should also break any wait loops
James Procter [Thu, 6 Jul 2023 15:49:23 +0000 (16:49 +0100)]
JAL-2292 verify mixed case alignment actually aligns
James Procter [Thu, 6 Jul 2023 15:00:03 +0000 (16:00 +0100)]
JAL-4217 wrap imageExport CLI method's call to imageExport in a separate thread and hang around until it completes…
James Procter [Thu, 6 Jul 2023 14:23:29 +0000 (15:23 +0100)]
JAL-4217 wrap imageExport CLI method's call to imageExport in an invokeAndWait
James Procter [Wed, 5 Jul 2023 12:42:57 +0000 (13:42 +0100)]
Merge branch 'patch/JAL-2292_caseSensitivePAE' into develop
James Procter [Wed, 5 Jul 2023 12:41:14 +0000 (13:41 +0100)]
Merge branch 'patch/JAL-4213_addref_with_selection' into develop
James Procter [Tue, 4 Jul 2023 11:54:58 +0000 (12:54 +0100)]
Merge branch 'merge/from_2_11_2_7_to_2_11_3_0' into develop
James Procter [Fri, 30 Jun 2023 16:25:46 +0000 (17:25 +0100)]
JAL-4117 JAL-1551 source licensing
James Procter [Fri, 30 Jun 2023 15:02:43 +0000 (16:02 +0100)]
JAL-4117 Fri June 30th release of 2.11.2.7 with Jalview Plausible analytics
James Procter [Fri, 30 Jun 2023 11:58:55 +0000 (12:58 +0100)]
JAL-4217 try really hard to shut down and dispose of Desktop resources and any lurking threads
James Procter [Thu, 29 Jun 2023 16:31:00 +0000 (17:31 +0100)]
JAL-4216 release notes
James Procter [Thu, 29 Jun 2023 14:38:22 +0000 (15:38 +0100)]
JAL-4216 compute size of annotation using start/end of sequence and given length. This might not work...
James Procter [Fri, 30 Jun 2023 10:23:52 +0000 (11:23 +0100)]
Merge branch 'task/JAL-4001_Plausible_API' into develop
Ben Soares [Fri, 30 Jun 2023 01:37:20 +0000 (02:37 +0100)]
JAL-4001 Added a random id to User-Agent to ensure separate visits recorded in Plausible. Changed default URL to self-hosted site
James Procter [Thu, 29 Jun 2023 08:55:51 +0000 (09:55 +0100)]
Merge branch 'task/JAL-4001_Plausible_API' into develop
James Procter [Wed, 28 Jun 2023 14:29:43 +0000 (15:29 +0100)]
JAL-4117 JAL-4001 plausible analytics release notes and privacy docs
James Procter [Wed, 25 Jan 2023 15:33:22 +0000 (15:33 +0000)]
JAL-4090 update from 2.11.2.7 JAL-4117 - version bump and release notes for JAL-4116
James Procter [Thu, 29 Jun 2023 07:13:44 +0000 (08:13 +0100)]
JAL-4001 analytics url provided by https://jalview.org/services/config/analytics/url
Ben Soares [Wed, 28 Jun 2023 14:46:20 +0000 (15:46 +0100)]
JAL-4001 change Plausible discovery URL
Ben Soares [Wed, 28 Jun 2023 14:01:21 +0000 (15:01 +0100)]
JAL-4001 remove stray --headless mode analytic
Ben Soares [Wed, 28 Jun 2023 13:57:56 +0000 (14:57 +0100)]
Merge branch 'task/JAL-4001_Plausible_API' into improvement/JAL-3830_remove_dock_icon_in_headless_mode
Ben Soares [Wed, 28 Jun 2023 13:55:48 +0000 (14:55 +0100)]
JAL-3820 add java and java.exe from JAVAHOME to list of likely JVMs
Ben Soares [Wed, 28 Jun 2023 13:28:33 +0000 (14:28 +0100)]
JAL-4001 remove headless code from analytics
Ben Soares [Wed, 28 Jun 2023 13:26:11 +0000 (14:26 +0100)]
JAL-4001 Remove analytics for --headless mode
Ben Soares [Tue, 27 Jun 2023 12:35:30 +0000 (13:35 +0100)]
JAL-4001 Added useful props information
Ben Soares [Mon, 26 Jun 2023 12:34:26 +0000 (13:34 +0100)]
Merge branch 'develop' into improvement/JAL-3830_remove_dock_icon_in_headless_mode
Ben Soares [Thu, 22 Jun 2023 20:53:32 +0000 (21:53 +0100)]
Merge branch 'develop' into task/JAL-4001_Plausible_API
Ben Soares [Thu, 22 Jun 2023 16:09:26 +0000 (17:09 +0100)]
JAL-4001 Fix default API url
James Procter [Thu, 22 Jun 2023 15:39:34 +0000 (17:39 +0200)]
JAL-4213 don’t pass active selection when actioning the addReferenceAnnotation
James Procter [Thu, 22 Jun 2023 15:38:07 +0000 (17:38 +0200)]
JAL-4213 - document the addReferenceAnnotations method’s behaviour when given a selection
Ben Soares [Thu, 22 Jun 2023 15:06:40 +0000 (16:06 +0100)]
JAL-4001 Added 'installation' property.
James Procter [Thu, 22 Jun 2023 15:00:31 +0000 (17:00 +0200)]
JAL-2292 - ensure mapping is built for equal symbols with mismatched case
Ben Soares [Thu, 22 Jun 2023 14:52:52 +0000 (15:52 +0100)]
JAL-4001 Added lookup to https://jalview.org/config/analytics/url to check API base url. Changed terminology to match Plausible API
Ben Soares [Thu, 22 Jun 2023 13:35:12 +0000 (14:35 +0100)]
JAL-4019 corrected to '>' to '>=' for percentage comparisons
James Procter [Wed, 21 Jun 2023 11:24:27 +0000 (13:24 +0200)]
Merge branch 'patch/JAL-4196_structure_viewer_synchronising' into develop
Ben Soares [Wed, 21 Jun 2023 11:01:34 +0000 (12:01 +0100)]
JAL-4001 Rationalise user-agent string into HttpUtils
Ben Soares [Wed, 21 Jun 2023 07:42:33 +0000 (08:42 +0100)]
JAL-4001 Change wording from google to plausible or generic analytics
Ben Soares [Tue, 20 Jun 2023 22:10:36 +0000 (23:10 +0100)]
JAL-4001 rename the init method
Ben Soares [Tue, 20 Jun 2023 17:53:21 +0000 (18:53 +0100)]
JAL-4001 Working Plausible analytics
Ben Soares [Tue, 20 Jun 2023 15:33:20 +0000 (16:33 +0100)]
JAL-4001 Plausible class
Ben Soares [Tue, 20 Jun 2023 09:17:33 +0000 (10:17 +0100)]
JAL-4001 Added a genuine client_id (from gtag). Added /debug/mp/collect with response content
Ben Soares [Sat, 17 Jun 2023 21:19:20 +0000 (22:19 +0100)]
JAL-4001 Check --nousagestats before doing analytics in headless mode
Ben Soares [Fri, 16 Jun 2023 19:40:03 +0000 (20:40 +0100)]
JAL-3830 Take account of --gui taking precedence over --headless
Ben Soares [Fri, 16 Jun 2023 15:09:45 +0000 (16:09 +0100)]
JAL-3830 Look for --headless mode and add -Djava.awt.headless=true to java invocation to remove icon from dock in macos
Ben Soares [Fri, 16 Jun 2023 14:22:52 +0000 (15:22 +0100)]
JAL-4001 Add a _geo=1 to query string and JSON. Add a headless flag to path and JSON, and send analytics in headless mode if USAGESTATS=true.
Ben Soares [Fri, 16 Jun 2023 14:21:06 +0000 (15:21 +0100)]
JAL-4001 Remove jgoogleanalytics code and jar
Ben Soares [Fri, 16 Jun 2023 09:09:12 +0000 (10:09 +0100)]
JAL-4001 make page_location the same encoding as the old jgoogleanalytics
Ben Soares [Thu, 15 Jun 2023 19:20:15 +0000 (20:20 +0100)]
JAL-4001 Changed for Java 8 compatibility