Jim Procter [Thu, 22 Jul 2021 19:36:13 +0000 (20:36 +0100)]
JAL-3853 patch sequence annotation report code and tweak the test. When merging from 2.11.2 develop there will be conflicts that need merging re HTMLXML tags
Jim Procter [Thu, 22 Jul 2021 17:04:01 +0000 (18:04 +0100)]
JAL-3848 ensure annotation from a service gets a calcId so it can be updated and tracked across multiple views - nb - service.getId() probably isn’t the right value to use for this!
Jim Procter [Thu, 22 Jul 2021 17:02:19 +0000 (18:02 +0100)]
JAL-3848 don’t include sequence limits in sequence id as it confuses slivka-0.8’s jalview-feature-file creation script
Jim Procter [Thu, 22 Jul 2021 17:00:55 +0000 (18:00 +0100)]
JAL-3848 - actually test the Slivka and JABAWS disorder services - nb still need asserts to verify the disorder annotation from Slivka looks like Jabaws
Mateusz Warowny [Wed, 21 Jul 2021 16:08:38 +0000 (18:08 +0200)]
JAL-3848 print exception for failed align jobs
Mateusz Warowny [Wed, 21 Jul 2021 16:06:57 +0000 (18:06 +0200)]
JAL-3848 add latest slivka-client fixes.
Mateusz Warowny [Fri, 9 Jul 2021 11:09:43 +0000 (13:09 +0200)]
Merge branch 'bug/JAL-3849_aacon-parameters' into improvement/JAL-3848_slivka_0.8
Mateusz Warowny [Fri, 9 Jul 2021 10:38:17 +0000 (12:38 +0200)]
JAL-3690 Remove references to old AlignCalcManager.
Mateusz Warowny [Thu, 8 Jul 2021 13:39:16 +0000 (15:39 +0200)]
JAL-3848 SlivkaParamSet: reformat code and add service description.
Mateusz Warowny [Tue, 6 Jul 2021 13:42:38 +0000 (15:42 +0200)]
JAL-3848 Update slivka client library.
Mateusz Warowny [Thu, 8 Jul 2021 13:43:22 +0000 (15:43 +0200)]
JAL-3849 Remove join() which blocked the ui.
Mateusz Warowny [Mon, 22 Feb 2021 12:20:38 +0000 (13:20 +0100)]
Merge branch 'bug/JAL-3809_ws_params_dialog_fix' into alpha/JAL-3066_Jalview_212_slivka-integration
Mateusz Warowny [Mon, 22 Feb 2021 12:05:40 +0000 (13:05 +0100)]
Merge branch 'bug/JAL-3810_annotation_ws_stopping_abruptly' into bug/JAL-3809_ws_params_dialog_fix
Mateusz Warowny [Wed, 3 Feb 2021 18:48:32 +0000 (19:48 +0100)]
JAL-3809 - Fixed param edit dialog for jalviewjs.
Edit settings dialog now works asynchronously.
Annotation services still do not add annotations to the sequences.
Mateusz Warowny [Mon, 22 Feb 2021 11:48:21 +0000 (12:48 +0100)]
Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration
Mateusz [Thu, 21 Jan 2021 15:44:25 +0000 (16:44 +0100)]
Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration
Mateusz Warowny [Fri, 5 Feb 2021 14:49:34 +0000 (15:49 +0100)]
JAL-3810 - Add trace method to javascript implementation of Logger
Mateusz Warowny [Fri, 5 Feb 2021 14:48:58 +0000 (15:48 +0100)]
JAL-3810 - Replace log.trace() calls with log.debug()
Mateusz [Wed, 27 Jan 2021 14:36:07 +0000 (15:36 +0100)]
JAL-3690 Introduce AlignCalcManager2 tests.
Mateusz [Fri, 22 Jan 2021 14:20:31 +0000 (15:20 +0100)]
Merge branch 'Jalview-JS/develop' into feature/JAL-3690_callback-based-web-services
Mateusz [Tue, 19 Jan 2021 17:29:42 +0000 (18:29 +0100)]
JAL-3690 AlignCalcManager - add full support for oneshot workers
Mateusz [Tue, 19 Jan 2021 16:10:27 +0000 (17:10 +0100)]
JAL-3690 AACon ws menu entry fix.
Mateusz [Mon, 18 Jan 2021 16:50:46 +0000 (17:50 +0100)]
JAL-3690 Allow unregistered workers to be run with CalcManager.
Mateusz [Mon, 18 Jan 2021 16:50:17 +0000 (17:50 +0100)]
JAL-3690 Fix typo in enum name in slivka client.
Mateusz [Fri, 15 Jan 2021 18:21:47 +0000 (19:21 +0100)]
JAL-3690 Fixed slivka wsmenu categories.
Mateusz [Mon, 18 Jan 2021 12:51:00 +0000 (13:51 +0100)]
Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services' into feature/JAL-3690_callback-based-web-services
Ben Soares [Mon, 11 Jan 2021 21:30:56 +0000 (21:30 +0000)]
JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle
Ben Soares [Mon, 11 Jan 2021 21:28:56 +0000 (21:28 +0000)]
JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty
Jim Procter [Fri, 18 Dec 2020 11:37:02 +0000 (11:37 +0000)]
JAL-3690 recoded AWSThread to use javax.swing.Timer (see https://github.com/BobHanson/java2script/issues/195#issuecomment-
747695834 )- web service submission works, but doesn’t seem to be happening as a background task.
Jim Procter [Thu, 17 Dec 2020 16:31:10 +0000 (16:31 +0000)]
JAL-3690 patch out use of java.streams/spliterator not supported in java2script (yet)
Jim Procter [Tue, 15 Dec 2020 19:04:36 +0000 (19:04 +0000)]
JAL-3690 tweak J2S direct DB access registration for jalview, compbio and other sites
Jim Procter [Tue, 15 Dec 2020 18:46:26 +0000 (18:46 +0000)]
JAL-3690 direct access to slivka, compbio, jalview.org and localhost/loopback.
Jim Procter [Tue, 15 Dec 2020 18:45:32 +0000 (18:45 +0000)]
JAL-3690 patch out need for java.time in j2s (see https://github.com/BobHanson/java2script/issues/194 )
Jim Procter [Tue, 15 Dec 2020 18:42:37 +0000 (18:42 +0000)]
JAL-3690 patch out spinning animation for web service jobs
Jim Procter [Tue, 15 Dec 2020 11:53:50 +0000 (11:53 +0000)]
JAL-3690 disable proxy server for JalviewJS
Jim Procter [Mon, 14 Dec 2020 19:58:34 +0000 (19:58 +0000)]
Merge branch 'Jalview-JS/develop' into merge_js_develop
also patched new code from JAL-3690 refactorings
Jim Procter [Mon, 14 Dec 2020 16:27:15 +0000 (16:27 +0000)]
Merge branch 'Jalview-JS/develop_j2s_v3_2_9_j11' into Jalview-JS/develop
Mateusz [Fri, 11 Dec 2020 14:33:14 +0000 (15:33 +0100)]
JAL-3690 Let's enable web services (seriously this time)
Jim Procter [Thu, 10 Dec 2020 17:50:05 +0000 (17:50 +0000)]
JAL-3223 - update swingjs to 3.2.9-j11
Mateusz Waronwy [Fri, 27 Nov 2020 16:01:14 +0000 (17:01 +0100)]
JAL-3690 List.copyOf() workaround
Mateusz Waronwy [Fri, 13 Nov 2020 15:51:38 +0000 (16:51 +0100)]
JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker
Mateusz Waronwy [Thu, 12 Nov 2020 15:13:36 +0000 (16:13 +0100)]
JAL-3690 - fixed state inconsistency when restarting the calcworker
Mateusz Waronwy [Wed, 11 Nov 2020 18:42:48 +0000 (19:42 +0100)]
JAL-3690 partially reworked AlignCalcManager
todo:
- modify SeqAnnotationServiceCalcWorker to implement PollableAlignCalcWorkerI
- fix race condition where worker state gets overriden by the old job (QUEUED to IDLE)
Mateusz Waronwy [Mon, 26 Oct 2020 12:20:00 +0000 (13:20 +0100)]
JAL-3690 - introduce shutdown method that cleans up manager's resources.
Mateusz Waronwy [Wed, 21 Oct 2020 14:18:05 +0000 (16:18 +0200)]
JAL-3690 Documentation for AlignCalcListener
Mateusz Waronwy [Wed, 21 Oct 2020 13:54:13 +0000 (15:54 +0200)]
JAL-3690 Catch and notify about worker cancellation separately.
Mateusz Waronwy [Wed, 21 Oct 2020 13:51:06 +0000 (15:51 +0200)]
JAL-3690 Fix concurrent modification exception when workers are cancelled
Mateusz Waronwy [Wed, 21 Oct 2020 13:45:42 +0000 (15:45 +0200)]
JAL-3690 Documentation for AlignCalcManagerI2
Mateusz Warowny [Sun, 2 Aug 2020 17:12:26 +0000 (18:12 +0100)]
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager
Ben Soares [Fri, 25 Sep 2020 08:39:02 +0000 (09:39 +0100)]
JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle
Ben Soares [Thu, 24 Sep 2020 17:16:17 +0000 (18:16 +0100)]
JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...
Ben Soares [Fri, 4 Sep 2020 17:29:41 +0000 (18:29 +0100)]
JAL-3679 Added externally specified plugins dir to J2sPlugin check
Mateusz Warowny [Wed, 22 Jul 2020 13:13:00 +0000 (14:13 +0100)]
JAL-3690 changed AWSThread to use Timer instead
Mateusz Warowny [Fri, 17 Jul 2020 12:43:39 +0000 (13:43 +0100)]
JAL-3690 alternative servers menu fix
Mateusz Warowny [Fri, 17 Jul 2020 10:59:21 +0000 (11:59 +0100)]
JAL-3690 restore jws1 JPred
Mateusz Warowny [Thu, 16 Jul 2020 12:37:22 +0000 (13:37 +0100)]
JAL-3690 switching to CompletableFuture to allow chaining
Mateusz Warowny [Wed, 15 Jul 2020 16:39:59 +0000 (17:39 +0100)]
JAL-3690 mark JalviewChangeSupport as deprecated
Mateusz Warowny [Wed, 15 Jul 2020 16:39:21 +0000 (17:39 +0100)]
JAL-3690 refactoring web-services discovery
Mateusz Warowny [Thu, 9 Jul 2020 14:43:01 +0000 (15:43 +0100)]
Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/merge_212_JalviewJS_2112
Conflicts:
src/jalview/gui/Desktop.java
src/jalview/gui/Preferences.java
src/jalview/jbgui/GPreferences.java
Mateusz Warowny [Thu, 9 Jul 2020 13:23:51 +0000 (14:23 +0100)]
Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/JAL-3066_Jalview_212_slivka-integration
Mateusz Warowny [Wed, 8 Jul 2020 14:27:01 +0000 (15:27 +0100)]
JAL-3683 retrieve job status to output stream
Mateusz Warowny [Wed, 8 Jul 2020 11:59:38 +0000 (12:59 +0100)]
JAL-6386 update slivka client for j2s compatibility
Mateusz Warowny [Wed, 8 Jul 2020 12:44:08 +0000 (13:44 +0100)]
Merge branch 'feature/JAL-3515-slivka-preferences' into alpha/JAL-3066_Jalview_212_slivka-integration
gmungoc [Tue, 30 Jun 2020 11:12:09 +0000 (12:12 +0100)]
JAL-3446 unused imports removed
gmungoc [Thu, 18 Jun 2020 14:43:51 +0000 (15:43 +0100)]
JAL-3648 resize annotation panel after dragging to resize graph height
Jim Procter [Mon, 29 Jun 2020 17:39:41 +0000 (18:39 +0100)]
JAL-3493 fix patch for 2.11.1_js (nb - these changes should not be merged to 2.11.2!)
Jim Procter [Mon, 29 Jun 2020 16:46:57 +0000 (17:46 +0100)]
JAL-3675 2.11.1.1 release notes
Jim Procter [Mon, 29 Jun 2020 16:24:29 +0000 (17:24 +0100)]
JAL-3493 clear search highlights when escape/deselect all
Conflicts:
src/jalview/gui/AlignFrame.java
patch migrated to src/jalview/gui/AligmentPanel.java
Jim Procter [Mon, 29 Jun 2020 16:19:19 +0000 (17:19 +0100)]
JAL-3493 failing test - creates a highlight and column selection and then called the deselect all alignfjame action and checks if highlight and selection are still present.
Conflicts:
test/jalview/gui/SeqCanvasTest.java
BobHanson [Thu, 18 Jun 2020 16:00:32 +0000 (11:00 -0500)]
JAL-3659 unnecessary duplication -- test is made in previous block
BobHanson [Thu, 18 Jun 2020 15:57:28 +0000 (10:57 -0500)]
JAL-3446 unintentially left training message in code.
Jim Procter [Wed, 17 Jun 2020 12:49:24 +0000 (13:49 +0100)]
JAL-3662 JAL-3660 JAL-3561 source formatting
Jim Procter [Wed, 17 Jun 2020 12:24:09 +0000 (13:24 +0100)]
Merge branch 'cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat' into Jalview-JS/develop
Jim Procter [Tue, 16 Jun 2020 16:12:54 +0000 (17:12 +0100)]
JAL-3660 JAL-3561 output alignment as requested file format as validated by FileFormats - report if format cannot be resolved or FileFormatI does not support export.
Merged jbp patch for 2.11.1.0 to rhanson's Jalview-JS/develop reworking of args parsing
Jim Procter [Tue, 16 Jun 2020 16:11:32 +0000 (17:11 +0100)]
JAL-3561 JAL-3660 check resolved FileFormatI instances are equivalent to verify format is as expected in test
Jim Procter [Fri, 20 Mar 2020 13:12:39 +0000 (13:12 +0000)]
JAL-3561 failing test verifying expected fileformat produced during commandlineoperation tests
BobHanson [Tue, 16 Jun 2020 23:09:57 +0000 (18:09 -0500)]
JAL-3659 proper headless check; skips setProperty for JS
BobHanson [Tue, 16 Jun 2020 23:00:51 +0000 (18:00 -0500)]
JAL-3662 simple fix for CLI not using right format for output of
alignment.
BobHanson [Tue, 16 Jun 2020 12:51:05 +0000 (07:51 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
BobHanson [Tue, 16 Jun 2020 12:44:20 +0000 (07:44 -0500)]
JAL-3446 -- YEIKS! two checkURLLinks calls!
gmungoc [Tue, 16 Jun 2020 12:00:49 +0000 (13:00 +0100)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
gmungoc [Tue, 16 Jun 2020 12:00:29 +0000 (13:00 +0100)]
JAL-3583 better handling of null or empty tooltip on annotation
gmungoc [Tue, 16 Jun 2020 11:47:12 +0000 (12:47 +0100)]
JAL-3446 defer size calculations until panel added to window
BobHanson [Tue, 16 Jun 2020 11:23:01 +0000 (06:23 -0500)]
JAL-3446 proper call for headless state
BobHanson [Tue, 16 Jun 2020 04:23:26 +0000 (23:23 -0500)]
JAL-3446 CommandLineOperation test
- cleaner headless check when adding JInternalFrame to Desktop
instance.
BobHanson [Tue, 16 Jun 2020 03:07:02 +0000 (22:07 -0500)]
JAL-3446 CommandLineOperation test
- headless check must be before Desktop.getInstance(), as you can't
make an instance of JFrame() when headless.
BobHanson [Tue, 16 Jun 2020 03:05:44 +0000 (22:05 -0500)]
JAL-3446 CTRL-DOWN check for headless operation
BobHanson [Mon, 15 Jun 2020 17:55:05 +0000 (12:55 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
BobHanson [Mon, 15 Jun 2020 17:54:52 +0000 (12:54 -0500)]
JAL-3657 SwingJS HashMap.putEntries() coding mistake.
soares [Mon, 15 Jun 2020 14:21:01 +0000 (15:21 +0100)]
JAL-3658 Now only making cores from utils/jalviewjs/classlists/*.txt
gmungoc [Mon, 15 Jun 2020 09:20:15 +0000 (10:20 +0100)]
JAL-3446 breaking change redacted
gmungoc [Mon, 15 Jun 2020 07:24:41 +0000 (08:24 +0100)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
BobHanson [Sun, 14 Jun 2020 03:10:54 +0000 (22:10 -0500)]
JAL-3445 BSML BBB file format.
- merge of BSML test branch.
- includes BSMLFileTest
- preliminary; does not read complement
- See Jalview-JS/develop/temp/bbb.dtd.pdf
BobHanson [Sun, 14 Jun 2020 02:42:30 +0000 (21:42 -0500)]
JAL-3653 SwingJS support for indeterminate JProgressBar
BobHanson [Sat, 13 Jun 2020 21:37:52 +0000 (16:37 -0500)]
JAL-3487 Splash screen
- cleaner code, more comments
- adds SwingJS support for 1-ms image finalization
(using JSToolkit.dispatch instead of invokeLater
BobHanson [Sat, 13 Jun 2020 17:30:28 +0000 (12:30 -0500)]
JAL-3487 Splash screen
- JS now uses StateMachine
- simple example of how StateMachine works.
BobHanson [Sat, 13 Jun 2020 14:41:14 +0000 (09:41 -0500)]
Merge branch 'Jalview-JS/develop.JAL-3445-BSML-reader' into Jalview-JS/develop
BobHanson [Fri, 12 Jun 2020 14:02:20 +0000 (09:02 -0500)]
JAL-3446 SwingJS update
-fixes desktop frame not taking focus when clicked, so not processing
menu shortcuts
BobHanson [Fri, 12 Jun 2020 13:32:44 +0000 (08:32 -0500)]
JAL-3664 shortcuts in Desktop not working from AlignFrame
- missing test for JInternalFrame in JComponent.processKeyBindings
soares [Fri, 12 Jun 2020 11:24:55 +0000 (12:24 +0100)]
JAL-3446 fixing a bad merge, sorry
git://source.jalview.org / jalview.git / log