Jim Procter [Tue, 29 Nov 2022 17:05:07 +0000 (17:05 +0000)]
JAL-3066 remove git conflict file
Jim Procter [Tue, 29 Nov 2022 17:03:19 +0000 (17:03 +0000)]
JAL-3362 JAL-3066 patch out not-yet supported thenCompare in slivka ws menu builder
Jim Procter [Tue, 29 Nov 2022 15:38:59 +0000 (15:38 +0000)]
JAL-3066 catch exceptions and report slivka server discovery status on Console
Jim Procter [Tue, 29 Nov 2022 15:34:41 +0000 (15:34 +0000)]
Merge branch 'JAL-3878_web_services_overhaul' into try-to-update-slivka-jar
JAL-3066 JAL-3362 Update 2.12 alpha with latest slivka-client.jar
Conflicts:
src/jalview/bin/Cache.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/Desktop.java
src/jalview/workers/AlignCalcManager.java
src/jalview/ws/jws2/JPredThread.java
src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
src/jalview/ws/slivkaws/SlivkaWSInstance.java
swingjs/ver/3.3.1/SwingJS-site.zip
swingjs/ver/3.3.1/timestamp
Jim Procter [Mon, 28 Nov 2022 20:58:26 +0000 (20:58 +0000)]
version 2.12 in RELEASE file for JAL-3362 2.12 alpha
Jim Procter [Mon, 28 Nov 2022 20:47:07 +0000 (20:47 +0000)]
Merge branch 'develop' into merged_2_11_2_0_to_2_12
updates JAL-3362 2.12 alpha with 2.11.2.5 release changes. Still has failing tests.
Conflicts:
THIRDPARTYLIBS
build.gradle
gradle.properties
help/help/html/features/preferences.html
help/help/html/releases.html
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/datamodel/SequenceI.java
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureEditor.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OptsAndParamsPage.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/SplashScreen.java
src/jalview/gui/SplitFrame.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/UserQuestionnaireCheck.java
src/jalview/gui/VamsasApplication.java
src/jalview/gui/WsJobParameters.java
src/jalview/gui/WsParamSetManager.java
src/jalview/io/BackupFiles.java
src/jalview/io/ModellerDescription.java
src/jalview/io/NewickFile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/javascript/log4j/Logger.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
src/jalview/jbgui/GCutAndPasteTransfer.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GPreferences.java
src/jalview/project/Jalview2XML.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/urls/IdentifiersUrlProvider.java
src/jalview/util/HttpUtils.java
src/jalview/util/MappingUtils.java
src/jalview/util/MessageManager.java
src/jalview/util/Platform.java
src/jalview/util/StringUtils.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/ws/AWSThread.java
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/gui/MsaWSThread.java
src/jalview/ws/jws1/Discoverer.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
src/jalview/ws/jws2/Jws2Client.java
src/jalview/ws/jws2/Jws2Discoverer.java
src/jalview/ws/jws2/MsaWSClient.java
src/jalview/ws/rest/HttpResultSet.java
src/jalview/ws/rest/RestClient.java
src/jalview/ws/rest/RestJobThread.java
src/jalview/ws/utils/UrlDownloadClient.java
src/jalview/xml/binding/jalview/DoubleVector.java
src/jalview/xml/binding/jalview/JalviewModel.java
test/jalview/bin/CommandLineOperations.java
test/jalview/ext/jmol/JmolCommandsTest.java
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/gui/AlignmentPanelTest.java
test/jalview/gui/AnnotationChooserTest.java
test/jalview/gui/AnnotationRowFilterTest.java
test/jalview/gui/JvSwingUtilsTest.java
test/jalview/gui/SeqCanvasTest.java
test/jalview/gui/SequenceRendererTest.java
test/jalview/gui/StructureChooserTest.java
test/jalview/io/SequenceAnnotationReportTest.java
test/jalview/project/Jalview2xmlTests.java
test/jalview/renderer/OverviewResColourFinderTest.java
test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
test/jalview/schemes/ClustalxColourSchemeTest.java
test/jalview/structure/StructureSelectionManagerTest.java
test/jalview/util/ColorUtilsTest.java
test/jalview/workers/AlignCalcManagerTest.java
test/jalview/ws/gui/Jws2ParamView.java
test/jalview/ws/sifts/SiftsClientTest.java
Jim Procter [Mon, 21 Nov 2022 17:02:08 +0000 (17:02 +0000)]
Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD
Ben Soares [Wed, 26 Oct 2022 08:13:24 +0000 (09:13 +0100)]
JAL-3416 (and others) increasing number of STDERR lines used for jalview.bin.CommandLineOperations tests for increased robustness
Ben Soares [Tue, 25 Oct 2022 12:07:19 +0000 (13:07 +0100)]
JAL-3416 Making FlatLaF default for macs due to a problem with VAqua not starting on macs
Jim Procter [Tue, 11 Oct 2022 15:53:25 +0000 (16:53 +0100)]
JAL-4065 final fix for 2.11.2.5 - 5pm BST release
Jim Procter [Tue, 11 Oct 2022 15:16:01 +0000 (16:16 +0100)]
JAL-4065 revised to avoid a visit from the apostrophe police
Jim Procter [Tue, 11 Oct 2022 14:43:36 +0000 (15:43 +0100)]
JAL-4073 update tests
Jim Procter [Tue, 11 Oct 2022 14:26:59 +0000 (15:26 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Jim Procter [Tue, 11 Oct 2022 14:24:32 +0000 (15:24 +0100)]
JAL-4073 fix PEBCAK failure
Ben Soares [Tue, 11 Oct 2022 13:43:10 +0000 (14:43 +0100)]
JAL-4014 Changed gecos display names to match labels in help
Jim Procter [Tue, 11 Oct 2022 12:10:29 +0000 (13:10 +0100)]
JAL-4065 revised whatsNew to make sense !
Jim Procter [Tue, 11 Oct 2022 10:32:05 +0000 (11:32 +0100)]
JAL-4065 release 2.11.2.5 date is 11th Oct
Jim Procter [Fri, 7 Oct 2022 14:53:01 +0000 (15:53 +0100)]
JAL-4065 update citations for Pfam and Rfam and added the Interpro citation
Jim Procter [Fri, 7 Oct 2022 14:19:21 +0000 (15:19 +0100)]
JAL-4065 2.11.2.5 release version bump
Jim Procter [Fri, 7 Oct 2022 14:14:08 +0000 (15:14 +0100)]
JAL-4065 release notes and updated release date for 2.11.2.5
Jim Procter [Thu, 6 Oct 2022 17:13:09 +0000 (18:13 +0100)]
stable url for PFAM retrieval via interpro api :) JAL-4073
Jim Procter [Thu, 6 Oct 2022 11:31:14 +0000 (12:31 +0100)]
JAL-1551 formatting
Jim Procter [Thu, 6 Oct 2022 11:22:09 +0000 (12:22 +0100)]
JAL-4065 release notes for JAL-4073 JAL-4074
Jim Procter [Thu, 6 Oct 2022 11:21:28 +0000 (12:21 +0100)]
JAL-4073 Pfam retrieval now works via a template including $PFAMID$ and $ALTYPE$ (full, seed, etc). Also changed name of PFAM_BASEURL_KEY to PFAM_INTERPRO_URL_TEMPLATE to avoid misconfiguration
Jim Procter [Thu, 6 Oct 2022 11:19:13 +0000 (12:19 +0100)]
Patch for JAL-4074 - any content ending in ‘gzip’ recognised as a gzipped stream to decompress
Jim Procter [Thu, 15 Sep 2022 11:21:03 +0000 (12:21 +0100)]
JAL-4065 release notes for JAL-4014 and JAL-4063 in 2.11.2.5
Jim Procter [Thu, 15 Sep 2022 11:17:10 +0000 (12:17 +0100)]
JAL-4065 - new release notes featuring JAL-3612 fix
Jim Procter [Wed, 14 Sep 2022 11:19:13 +0000 (12:19 +0100)]
Merge branch 'bug/JAL-3612_overviewFeatureOrdering' into develop
Ben Soares [Tue, 23 Aug 2022 10:29:18 +0000 (11:29 +0100)]
JAL-4014 JAL-4063 Added gecos colourScheme names (INFO message) and fixed Clustal colourScheme name
Jim Procter [Mon, 8 Aug 2022 17:48:01 +0000 (18:48 +0100)]
JAL-4046 release on 9th August 2022
Jim Procter [Mon, 8 Aug 2022 17:28:15 +0000 (18:28 +0100)]
JAL-4046 JAL-3993 imports reformatting
Jim Procter [Mon, 8 Aug 2022 17:27:29 +0000 (18:27 +0100)]
JAL-4046 JAL-3993 patch for 2.11.2.4 release
Jim Procter [Mon, 8 Aug 2022 17:09:54 +0000 (18:09 +0100)]
JAL-4046 release notes for JAL-3991
Jim Procter [Mon, 8 Aug 2022 17:01:19 +0000 (18:01 +0100)]
Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup' into develop
Jim Procter [Mon, 8 Aug 2022 16:50:39 +0000 (17:50 +0100)]
JAL-4046 release notes for JAL-4014 - gecos colourschemes
Jim Procter [Mon, 8 Aug 2022 16:16:14 +0000 (17:16 +0100)]
Merge branch 'improvement/JAL-4014_gecos_colour_schemes' into develop
Jim Procter [Mon, 8 Aug 2022 16:06:24 +0000 (17:06 +0100)]
JAL-4056 documented in release notes for JAL-4043
Jim Procter [Mon, 8 Aug 2022 15:46:04 +0000 (16:46 +0100)]
Merge branch 'patch/JAL-4036_uniprot_fts_legacy_endpoint' into develop
Jim Procter [Mon, 8 Aug 2022 15:42:21 +0000 (16:42 +0100)]
JAL-4043 what’s new, updated help images and release notes for JAL-4034 (3d beacons button)
Jim Procter [Mon, 8 Aug 2022 15:17:49 +0000 (16:17 +0100)]
JAL-4034 show the loading spinner when switching between tabs
Jim Procter [Mon, 8 Aug 2022 13:47:31 +0000 (14:47 +0100)]
Merge branch 'features/JAL-4034_improve_3dbeacons_button_and_ux' into develop
Ben Soares [Mon, 1 Aug 2022 10:32:43 +0000 (11:32 +0100)]
JAL-4056 fixed tl;dr section of doc/building.md
Ben Soares [Tue, 26 Jul 2022 17:01:48 +0000 (18:01 +0100)]
JAL-4036 Fixed the virus_host_id query field
Ben Soares [Tue, 26 Jul 2022 17:01:27 +0000 (18:01 +0100)]
JAL-4036 Added text to help about different number and date range acceptable formats
Ben Soares [Mon, 25 Jul 2022 16:09:43 +0000 (17:09 +0100)]
JAL-4036 updated help about new UniProt API
Ben Soares [Mon, 25 Jul 2022 10:00:52 +0000 (11:00 +0100)]
JAL-4036 moved a comment block
Ben Soares [Mon, 25 Jul 2022 09:57:51 +0000 (10:57 +0100)]
JAL-4034 button looks better also on other OSes with the 0 vertical insets
Ben Soares [Sun, 24 Jul 2022 16:37:59 +0000 (17:37 +0100)]
JAL-4034 add round corners to 3DB confirmation button with icon on a mac
Ben Soares [Fri, 22 Jul 2022 17:17:34 +0000 (18:17 +0100)]
JAL-4036 Changes made from code review CR-JAL-265
Ben Soares [Fri, 22 Jul 2022 10:55:16 +0000 (11:55 +0100)]
JAL-4036 Add getDbName to the GFTSPanelI and add an index code message to the index dropdown tooltip as appropriate
Ben Soares [Fri, 22 Jul 2022 10:06:24 +0000 (11:06 +0100)]
JAL-4036 removing the query field code from the dropdown indexes
Ben Soares [Thu, 21 Jul 2022 20:00:49 +0000 (21:00 +0100)]
JAL-4036 Don't autosearch changing index when autosearch is de-selected
Ben Soares [Thu, 21 Jul 2022 20:00:15 +0000 (21:00 +0100)]
JAL-4036 add search fieldname to dropdown list
Ben Soares [Thu, 21 Jul 2022 19:59:22 +0000 (20:59 +0100)]
JAL-4036 removed often duplicated pluralisation in message
Ben Soares [Thu, 21 Jul 2022 19:58:06 +0000 (20:58 +0100)]
JAL-4036 New configuration, target and pagination process for 2022-07 new Uniprot API
Jim Procter [Wed, 20 Jul 2022 14:51:16 +0000 (15:51 +0100)]
JAL-4046 started release notes for 2.11.2.4 patch release
Jim Procter [Wed, 20 Jul 2022 14:44:03 +0000 (15:44 +0100)]
JAL-4045 - don't apply distribution dependent scale factor to the axis lines!
Ben Soares [Fri, 15 Jul 2022 17:38:33 +0000 (18:38 +0100)]
JAL-4034 Use the new non-modal JDialog for 3DBeacons uniprot lookup confirmation. Link dialog to GStructureChooser's frame so it can moveToFront. Minor improvement to Search 3DB button appearance
Ben Soares [Fri, 15 Jul 2022 17:37:04 +0000 (18:37 +0100)]
JAL-4034 Allow request for non-modal JDialog, which puts the Runnable action into the button click listener (similar to JalviewJS)
Ben Soares [Tue, 12 Jul 2022 11:13:28 +0000 (12:13 +0100)]
JAL-4034 change to jalview property name
Ben Soares [Tue, 12 Jul 2022 10:58:35 +0000 (11:58 +0100)]
JAL-4034 showConfirmDialog works for both desktop and jalviewjs
Ben Soares [Mon, 11 Jul 2022 16:14:56 +0000 (17:14 +0100)]
JAL-4034 Non-blocking 3D Beacons query after warning dialog
Ben Soares [Mon, 11 Jul 2022 15:25:17 +0000 (16:25 +0100)]
JAL-4034 allow a jalview_property to set the threshold level
Jim Procter [Tue, 5 Jul 2022 21:52:27 +0000 (22:52 +0100)]
JAL-4012 release date bump and JAL-4004 tweak to include current version in generated whatsNew.html
Jim Procter [Mon, 4 Jul 2022 17:04:13 +0000 (18:04 +0100)]
JAL-4034 fix #3 change uniprot ref fetch dialog to a ‘warning’ shown when many ids have to be retrieved
Jim Procter [Mon, 4 Jul 2022 16:59:14 +0000 (17:59 +0100)]
JAL-4034 Fix #2 show an icon and a button to press to initiate search
Jim Procter [Mon, 4 Jul 2022 16:58:01 +0000 (17:58 +0100)]
JAL-4034 fix 1 - reword button
Jim Procter [Mon, 4 Jul 2022 14:58:04 +0000 (15:58 +0100)]
JAL-4012 updated release date and whats new for 2.11.2.3
Jim Procter [Fri, 1 Jul 2022 13:08:52 +0000 (14:08 +0100)]
JAL-4012 tweak release notes wording for legacy.uniprot
Jim Procter [Fri, 1 Jul 2022 12:55:20 +0000 (13:55 +0100)]
Merge branch 'patch/JAL-4036_uniprot_fts_legacy_endpoint' into develop
Jim Procter [Fri, 1 Jul 2022 12:44:40 +0000 (13:44 +0100)]
JAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and update to release notes and what’s new
Jim Procter [Thu, 30 Jun 2022 16:37:02 +0000 (17:37 +0100)]
JAL-4036 use the legacy endpoint (and report the FTS query when debug/trace enabled)
Ben Soares [Tue, 28 Jun 2022 12:32:51 +0000 (13:32 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop
Ben Soares [Tue, 28 Jun 2022 12:31:55 +0000 (13:31 +0100)]
JAL-1988 Don't put Quit in the File menu if there's a handler for it
Ben Soares [Thu, 23 Jun 2022 15:02:46 +0000 (16:02 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop
Ben Soares [Thu, 23 Jun 2022 14:28:46 +0000 (15:28 +0100)]
JAL-1988 Check for setHandler capability to avoid About and Preferences menu options disappearing into a void
Ben Soares [Fri, 17 Jun 2022 16:10:52 +0000 (17:10 +0100)]
JAL-3027 Avoid FlatLAF Desktop class is JalviewJS
Jim Procter [Wed, 15 Jun 2022 15:17:59 +0000 (16:17 +0100)]
JAL-4012 release notes for JAL-1988,JAL-3416
Jim Procter [Wed, 15 Jun 2022 14:54:56 +0000 (15:54 +0100)]
JAL-1988 JAL-3416 avoid unnecessary static flag
Jim Procter [Wed, 15 Jun 2022 14:54:19 +0000 (15:54 +0100)]
JAL-3418 JAL-1988 don’t need java version check anymore
Jim Procter [Wed, 15 Jun 2022 14:41:53 +0000 (15:41 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop
Ben Soares [Mon, 13 Jun 2022 17:32:22 +0000 (18:32 +0100)]
JAL-1988 Hack to ensure Quit dialog box is moved to front
Ben Soares [Mon, 13 Jun 2022 17:14:11 +0000 (18:14 +0100)]
JAL-1988 Moved APQHandlers to jalview.jbgui and called from jalview.jbgui.GDesktop. Use result to not add About and Preferences to normal menus.
Ben Soares [Mon, 13 Jun 2022 16:22:52 +0000 (17:22 +0100)]
Merge branch 'develop' into improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option
Ben Soares [Mon, 13 Jun 2022 15:20:12 +0000 (16:20 +0100)]
JAL-4004 Fix missing whatsNew.html when not building with RELEASE channel set
Jim Procter [Mon, 13 Jun 2022 11:24:07 +0000 (12:24 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_flatlaf_osx_apqhandler' into improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option
Jim Procter [Mon, 13 Jun 2022 11:22:31 +0000 (12:22 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into improvement/JAL-1988+JAL-3416_flatlaf_osx_apqhandler
Ben Soares [Mon, 13 Jun 2022 10:43:35 +0000 (11:43 +0100)]
JAL-3416 remove flat as default for linux
Ben Soares [Mon, 13 Jun 2022 10:20:50 +0000 (11:20 +0100)]
JAL-1988 JAL-3416 Using the flatlaf-extras About, Preferences and Quit handler system to set APQhandler for both J9+ and now Java 8
Ben Soares [Mon, 13 Jun 2022 10:18:31 +0000 (11:18 +0100)]
JAL-3416 Added some mac specific FlatLAF settings. Note this is not the default macOS LaF, this is only when -Dlaf=flat is set on a mac when running Jalview
Ben Soares [Mon, 13 Jun 2022 10:17:04 +0000 (11:17 +0100)]
JAL-3416 updated FlatLAF libraries to 2.3. Added the flatlaf-extras library
Jim Procter [Thu, 9 Jun 2022 13:25:39 +0000 (14:25 +0100)]
JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation
Jim Procter [Thu, 9 Jun 2022 13:07:04 +0000 (14:07 +0100)]
Merge branch 'bug/JAL-4020_add_pymolwin_paths' into develop
Jim Procter [Thu, 9 Jun 2022 13:03:55 +0000 (14:03 +0100)]
JAL-4004 add the autogenerated whatsNew.html and releases.html to .gitignore
Jim Procter [Thu, 9 Jun 2022 11:35:26 +0000 (12:35 +0100)]
JAL-4014 release notes for JAL-4026 patches
Jim Procter [Thu, 9 Jun 2022 11:16:08 +0000 (12:16 +0100)]
JAL-4026 increase timeouts for command line ops
Jim Procter [Thu, 9 Jun 2022 10:20:22 +0000 (11:20 +0100)]
JAL-4026 ignore StructureSelectionManager events if no viewer is available to act on them
Jim Procter [Thu, 9 Jun 2022 09:38:44 +0000 (10:38 +0100)]
JAL-4026 always wait 50ms before checking if the calculation worker is still running so it has time to start.
Jim Procter [Thu, 9 Jun 2022 07:18:31 +0000 (08:18 +0100)]
JAL-4026 update the viewport’s wrapped width after calculating it
Jim Procter [Wed, 8 Jun 2022 14:17:16 +0000 (15:17 +0100)]
JAL-4014 release notes for JAL-4023 and JAL-4024
git://source.jalview.org / jalview.git / log