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 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
Ben Soares [Wed, 14 Jun 2023 22:21:02 +0000 (23:21 +0100)]
JAL-4001 Trying to see extra information in GA dashboard
Ben Soares [Wed, 14 Jun 2023 12:41:36 +0000 (13:41 +0100)]
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
Ben Soares [Tue, 13 Jun 2023 11:16:10 +0000 (12:16 +0100)]
JAL-3599 Tidyup for all OS to use ScheduledExecutor
Ben Soares [Mon, 12 Jun 2023 08:14:10 +0000 (09:14 +0100)]
JAL-3599 replaced a build dependency for jalviewjsLaunchTest
Ben Soares [Sun, 11 Jun 2023 18:11:35 +0000 (19:11 +0100)]
JAL-3599 Cater for macOS. ScheduledExecutor timeout implemented
Ben Soares [Sun, 11 Jun 2023 14:38:17 +0000 (15:38 +0100)]
JAL-3599 Cater for macOS. --timeout not working yet
Ben Soares [Fri, 9 Jun 2023 16:32:34 +0000 (17:32 +0100)]
JAL-3599 Make jalviewjs dependOn jalviewjsLaunchTest. Change jalviewjsLaunchTest to only stop the task (not trigger a failure) if chrome not found. Remove deliberate NPE.
Ben Soares [Fri, 9 Jun 2023 15:48:32 +0000 (16:48 +0100)]
JAL-3599 Deliberate NPE to see if build plan fails
Ben Soares [Fri, 9 Jun 2023 14:12:51 +0000 (15:12 +0100)]
JAL-3599 fixed placement of 'First Run' file for chromium profile
Ben Soares [Fri, 9 Jun 2023 11:21:46 +0000 (12:21 +0100)]
JAL-3599 --no-sandbox --disable-gpu and Thorium flatpak on build server
Ben Soares [Fri, 9 Jun 2023 10:15:17 +0000 (11:15 +0100)]
JAL-3599 STDOUT and STDERR saved and sent to System.out/err
Ben Soares [Fri, 9 Jun 2023 10:02:34 +0000 (11:02 +0100)]
JAL-3599 Not redirecting STDOUT or STDERR just for build server debuggin
Ben Soares [Fri, 9 Jun 2023 09:48:43 +0000 (10:48 +0100)]
JAL-3599 More stderr/stdout output to logs when anything
Ben Soares [Fri, 9 Jun 2023 09:38:54 +0000 (10:38 +0100)]
JAL-3599 More stderr/stdout output to logs when failed
Ben Soares [Fri, 9 Jun 2023 08:14:02 +0000 (09:14 +0100)]
JAL-3599 increase real and virtual time chrome runs for to 60s (in real-time this is still about 3s)
Ben Soares [Thu, 8 Jun 2023 19:58:49 +0000 (20:58 +0100)]
JAL-3599 gradle tasks to test JalviewJS launches in a chrome or chromium browser
Ben Soares [Thu, 8 Jun 2023 16:37:13 +0000 (17:37 +0100)]
JAL-4001 Only send defaultParams for application_launch event
Ben Soares [Thu, 8 Jun 2023 16:21:28 +0000 (17:21 +0100)]
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
Ben Soares [Thu, 8 Jun 2023 10:12:17 +0000 (11:12 +0100)]
JAL-3416 FlatLaf SystemInfo failing in JalviewJS. Look and Feel not relevant to JalviewJS so setLookAndFeel commented out for j2s with @j2sIgnore
Ben Soares [Thu, 8 Jun 2023 07:16:06 +0000 (08:16 +0100)]
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
James Procter [Thu, 8 Jun 2023 07:09:46 +0000 (08:09 +0100)]
Merge branch 'patch/JAL-4195_cli_eps_export_npe' into develop
Ben Soares [Wed, 7 Jun 2023 21:30:30 +0000 (22:30 +0100)]
JAL-4001 Javadoc for the method to use
James Procter [Wed, 7 Jun 2023 19:59:59 +0000 (20:59 +0100)]
JAL-4195 add exception handling for all image output ops - still need to refactor messaging to the UI
James Procter [Wed, 7 Jun 2023 16:16:01 +0000 (17:16 +0100)]
Merge branch 'patch/JAL-4195_cli_eps_export_npe' into develop
James Procter [Wed, 7 Jun 2023 16:13:55 +0000 (17:13 +0100)]
JAL-4195 catch thrown exceptions (if any) during image export and report as an error.
Ben Soares [Wed, 7 Jun 2023 15:52:00 +0000 (16:52 +0100)]
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
Ben Soares [Wed, 7 Jun 2023 15:41:37 +0000 (16:41 +0100)]
Merge branch 'develop' into improvement/JAL-4193_cl_arg_prevent_startup_file
Ben Soares [Wed, 7 Jun 2023 14:37:22 +0000 (15:37 +0100)]
JAL-4001 Added more params for application_launch
Ben Soares [Wed, 7 Jun 2023 13:41:16 +0000 (14:41 +0100)]
JAL-4001 removed a test param
Ben Soares [Wed, 7 Jun 2023 13:40:14 +0000 (14:40 +0100)]
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
Ben Soares [Wed, 7 Jun 2023 13:39:56 +0000 (14:39 +0100)]
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
Ben Soares [Wed, 7 Jun 2023 13:39:49 +0000 (14:39 +0100)]
JAL-4001 GA4 tracking is now ENABLED. Currently logging a page_view like the website with a schemeless, domainless path the same as the UA tracking, as well as a custom application_launch event with the path_location, separate app_name and version parameters
James Procter [Wed, 7 Jun 2023 13:02:11 +0000 (14:02 +0100)]
JAL-4195 tidy up desktop instances after creating them
James Procter [Tue, 6 Jun 2023 17:42:42 +0000 (18:42 +0100)]
JAL-4195 report full stack trace for exceptions raised when exporting an image
James Procter [Tue, 6 Jun 2023 17:38:02 +0000 (18:38 +0100)]
JAL-4160 --colour can now take user defined scheme names and colour scheme-spec definition lines as its value
James Procter [Tue, 6 Jun 2023 16:59:35 +0000 (17:59 +0100)]
JAL-4160 JAL-4195 wait around until alignFrame calculators are finished before trying to output an image
James Procter [Tue, 6 Jun 2023 16:58:18 +0000 (17:58 +0100)]
JAL-1551 formatting and javadoc for ArgParser rather than // comments
James Procter [Tue, 6 Jun 2023 16:49:18 +0000 (17:49 +0100)]
JAL-629 - remove TODO from jalview.bin.Jalview since it is now done via jalview.bin.Commands
James Procter [Tue, 6 Jun 2023 15:31:03 +0000 (16:31 +0100)]
JAL-4195 Debug message indicating creation of an image file should come before we make the call to create the file !
James Procter [Tue, 6 Jun 2023 15:30:04 +0000 (16:30 +0100)]
JAL-1551 a bit of javadoc for Jalview.testoutput methods
Ben Soares [Mon, 5 Jun 2023 19:26:42 +0000 (20:26 +0100)]
JAL-4001 debugging statements
Ben Soares [Mon, 5 Jun 2023 17:34:58 +0000 (18:34 +0100)]
JAL-4001 untested GA4 client code
Ben Soares [Mon, 5 Jun 2023 14:17:45 +0000 (15:17 +0100)]
JAL-4001 most of google analytics client
Ben Soares [Mon, 5 Jun 2023 10:30:39 +0000 (11:30 +0100)]
JAL-4001 start of GA4 client class
James Procter [Fri, 2 Jun 2023 11:13:36 +0000 (12:13 +0100)]
JAL-4090 update 2.11.3.0 release notes for recent merges
Ben Soares [Fri, 2 Jun 2023 10:10:03 +0000 (11:10 +0100)]
JAL-3521 Updated debian build.gradle in utils/debian/debian_build.gradle and patch file
Ben Soares [Fri, 2 Jun 2023 08:57:01 +0000 (09:57 +0100)]
JAL-4001 Spanish translation
Ben Soares [Fri, 2 Jun 2023 08:05:38 +0000 (09:05 +0100)]
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
Ben Soares [Thu, 1 Jun 2023 17:16:56 +0000 (18:16 +0100)]
Merge branch 'develop' into improvement/JAL-4193_cl_arg_prevent_startup_file
Ben Soares [Thu, 1 Jun 2023 16:10:08 +0000 (17:10 +0100)]
JAL-629 changes merged in from develop fixed it. Deleted duplicate example PAE file.
Ben Soares [Thu, 1 Jun 2023 16:01:58 +0000 (17:01 +0100)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Thu, 1 Jun 2023 16:01:36 +0000 (17:01 +0100)]
JAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToStructure(). not fixed yet
Ben Soares [Thu, 1 Jun 2023 14:50:09 +0000 (15:50 +0100)]
JAL-4001 Changed title+message to MessageManager
Ben Soares [Thu, 1 Jun 2023 14:49:33 +0000 (15:49 +0100)]
JAL-629 added data for test
Ben Soares [Thu, 1 Jun 2023 14:07:18 +0000 (15:07 +0100)]
JAL-4193 JAL-4194 sessionProperties layer in Cache, CLI arg Opts to deal with -Pkey=val and set sessionProperties. Documentation for it.
James Procter [Thu, 1 Jun 2023 13:58:17 +0000 (14:58 +0100)]
Merge branch 'features/JAL-4134_use_annotation_row_for_colours_and_groups' into develop
major improvements: JAL-4134 column tree is only computed when requested. group colours on PAE matrix row can be hidden.
JAL-1556 new popup menu options to select/colour by annotation row.
JAL-4089 selected columns used to (re)compute superposition
JAL-4190 escape in tree panel clears active selection
JAL-4182 patch fixes copy of annotation for sub-sequence
JAL-4177 patch fixes add view/new view not being disabled when loading structures from local file via structure chooser
JAL-4123 outstanding work to make 'default' do the right thing when a model is imported manually and a PAE is also provided.
James Procter [Thu, 1 Jun 2023 13:19:25 +0000 (14:19 +0100)]
Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups
James Procter [Thu, 1 Jun 2023 12:56:53 +0000 (13:56 +0100)]
JAL-4134 properly resolve positions in associated aligned sequence for matrix group column-wise selection actions in tree and annotation panel
Ben Soares [Thu, 1 Jun 2023 08:46:48 +0000 (09:46 +0100)]
JAL-629 better reference text for --nousagestats
James Procter [Tue, 30 May 2023 16:13:01 +0000 (17:13 +0100)]
JAL-4134 repaint the tree or alignment view(s) when column selections change
James Procter [Tue, 30 May 2023 16:12:19 +0000 (17:12 +0100)]
JAL-4134 highlight selected column nodes on the linked alignment view using getMappedPositionsFor
Ben Soares [Tue, 30 May 2023 10:36:12 +0000 (11:36 +0100)]
JAL-629 JAL-4121 Added documentation to Help docs and Usage statement
Ben Soares [Tue, 30 May 2023 09:59:05 +0000 (10:59 +0100)]
JAL-4121 adjust test name
Ben Soares [Tue, 30 May 2023 09:53:40 +0000 (10:53 +0100)]
JAL-629 Better formatting of Arg.Opt options in usage statement
Ben Soares [Tue, 30 May 2023 07:54:57 +0000 (08:54 +0100)]
JAL-4121 slight refactoring of method name and added tests for headless assumptions/settings
James Procter [Mon, 29 May 2023 17:05:51 +0000 (18:05 +0100)]
JAL-4190 - escape clears selected nodes
James Procter [Mon, 29 May 2023 17:03:08 +0000 (18:03 +0100)]
JAL-4134 JAL-2349 test & fixed implementation(ish) for getMappedPositionsFor(seq,from,to)
James Procter [Mon, 29 May 2023 13:56:22 +0000 (14:56 +0100)]
Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups
Ben Soares [Sat, 27 May 2023 21:47:45 +0000 (22:47 +0100)]
JAL-4121 Added a NPE check caught in tests. Added --gui to relevant tests.
Ben Soares [Sat, 27 May 2023 18:46:33 +0000 (19:46 +0100)]
JAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt.OUTPUT to Opt.OUTPUTFILE for clarity. isHeadless() method sets policy for headless mode including assumption of headless if there's an Opt.OUTPUTFILE Arg.
Ben Soares [Fri, 26 May 2023 15:45:37 +0000 (16:45 +0100)]
JAL-4125 Fixed non-closing external viewers, also added options for default behaviour for both normal quit and forced quit
James Procter [Fri, 26 May 2023 14:11:28 +0000 (15:11 +0100)]
JAL-4134 internationalise popup menu entries and show a ‘tree calculation in progress’ progress bar in align panel.
James Procter [Fri, 26 May 2023 12:20:16 +0000 (13:20 +0100)]
JAL-1556 fix bad import
James Procter [Fri, 26 May 2023 11:57:41 +0000 (12:57 +0100)]
Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups
Conflicts:
src/jalview/gui/AnnotationLabels.java
James Procter [Fri, 26 May 2023 11:52:58 +0000 (12:52 +0100)]
JAL-1556 initial implementation - no tests as yet but ‘works’
Ben Soares [Fri, 26 May 2023 11:07:26 +0000 (12:07 +0100)]
JAL-629 dispose of non-displaying StructureChooser, removes zombie entry in Window menu
Ben Soares [Fri, 26 May 2023 09:11:57 +0000 (10:11 +0100)]
Merge branch 'develop' into feature/JAL-3416_update_to_flatlaf_3.1.1_with_unpacked_native_libraries
Ben Soares [Thu, 25 May 2023 23:45:53 +0000 (00:45 +0100)]
JAL-3416 JAL-3820 FlatLaf default for everyone, including Windows. Add jalview_local.bat and .ps1 on Windows installation.
Ben Soares [Thu, 25 May 2023 19:19:53 +0000 (20:19 +0100)]
JAL-3416 better path name
James Procter [Thu, 25 May 2023 16:37:52 +0000 (17:37 +0100)]
JAL-4134 popup menu and annotation row property to control display of display of column group colouring on matrix
Ben Soares [Thu, 25 May 2023 16:34:49 +0000 (17:34 +0100)]
JAL-3820 JAL-3830 improvements to script launching. Icon on macOS. Fixed CLASSPATH.
James Procter [Thu, 25 May 2023 15:29:31 +0000 (16:29 +0100)]
JAL-2381 don’t need to set description, dbrefs etc for subsequence returned by getSubSequence(started)
James Procter [Thu, 25 May 2023 15:28:36 +0000 (16:28 +0100)]
JAL-2381 copy and paste sequence also copies contact matrix annotation
James Procter [Thu, 25 May 2023 14:05:40 +0000 (15:05 +0100)]
Merge branch 'bug/JAL-4186_space_in_sequence_name_causes_empty_modal' into develop
Ben Soares [Thu, 25 May 2023 12:55:37 +0000 (13:55 +0100)]
JAL-3820 Create and use 'Jalview app' symblinks to java executable. Fixes grouped naming in linux taskbar, possibly macOS dock, still to check.
Ben Soares [Thu, 25 May 2023 09:44:40 +0000 (10:44 +0100)]
JAL-3416 remove old flatlaf jars from j8lib
Ben Soares [Thu, 25 May 2023 07:35:09 +0000 (08:35 +0100)]
JAL-4186 fixed a test
Ben Soares [Thu, 25 May 2023 00:39:36 +0000 (01:39 +0100)]
JAL-4186 Turn JvOptionPane Callable<Void> handlers back into Runnable for jalviewjs (now working)
Ben Soares [Wed, 24 May 2023 23:41:50 +0000 (00:41 +0100)]
JAL-4186 attempts to work in jalviewjs, still not working
Ben Soares [Wed, 24 May 2023 16:28:25 +0000 (17:28 +0100)]
JAL-4186 fix dialog. broken in JalviewJS
Ben Soares [Wed, 24 May 2023 11:50:08 +0000 (12:50 +0100)]
JAL-3416 slightly improved colours for tabber pane tabs
Ben Soares [Wed, 24 May 2023 08:49:24 +0000 (09:49 +0100)]
JAL-3416 Updated flatlaf libraries. Native libraries are extracted automatically by flatlaf apparently.
Ben Soares [Tue, 23 May 2023 22:24:30 +0000 (23:24 +0100)]
JAL-629 Updated help docs and fixed structure image subvalues
Ben Soares [Tue, 23 May 2023 13:33:38 +0000 (14:33 +0100)]
JAL-629 Added --structureimage code and formatting args/subvals. Added tests for structure image. Added docs for structure image.
Ben Soares [Mon, 22 May 2023 19:42:02 +0000 (20:42 +0100)]
JAL-629 --structureimage with formatting args.