Mateusz Warowny [Fri, 28 Jul 2023 10:59:16 +0000 (12:59 +0200)]
JAL-4241 Create sequence mapping before adjusting annotations
Mateusz Warowny [Fri, 28 Jul 2023 10:37:32 +0000 (12:37 +0200)]
--- Adding issue comments
James Procter [Tue, 4 Jul 2023 14:16:44 +0000 (15:16 +0100)]
Merge branch 'mmw/Release_2_12_ws_merge' into development/Release_2_12_Branch
Mateusz Warowny [Mon, 27 Mar 2023 15:34:06 +0000 (17:34 +0200)]
JAL-4155 Replace unsafe casting to AlignmentPanel with generics
James Procter [Thu, 23 Mar 2023 14:51:32 +0000 (14:51 +0000)]
JAL-4155 Viewport holds a reference to its AlignmentViewPanel - getter on gui.AlignViewport casts interface to gui.AlignmentPanel
Mateusz Warowny [Fri, 24 Mar 2023 15:34:00 +0000 (16:34 +0100)]
JAL-4154 Remove not-bamboo flag from testGetVisibleWidth
Mateusz Warowny [Fri, 24 Mar 2023 15:18:55 +0000 (16:18 +0100)]
JAL-4154 Update AlignmentPanelTest to use new forArch method
Mateusz Warowny [Fri, 24 Mar 2023 15:16:15 +0000 (16:16 +0100)]
JAL-4154 Add Platform.forArch method.
Platform.forArch allows to specify constants that depend on
architecture.
Mateusz Warowny [Tue, 28 Mar 2023 12:57:43 +0000 (14:57 +0200)]
Merge branch 'JAL-4152-typed-singleton-provider' into mmw/Release_2_12_ws_merge
Mateusz Warowny [Tue, 28 Mar 2023 11:54:56 +0000 (13:54 +0200)]
Merge branch 'development/Release_2_12_Branch' into mmw/Release_2_12_ws_merge
Mateusz Warowny [Fri, 24 Mar 2023 15:44:38 +0000 (16:44 +0100)]
JAL-4152 Remove redundant casts from getInstance usages.
Mateusz Warowny [Wed, 22 Mar 2023 11:50:47 +0000 (12:50 +0100)]
JAL-4152 Make return type of getInstance a generic type
Mateusz Warowny [Fri, 17 Mar 2023 13:49:19 +0000 (14:49 +0100)]
JAL-4146 Fix SeqCanvasTest setup
Mateusz Warowny [Wed, 15 Mar 2023 11:47:51 +0000 (12:47 +0100)]
JAL-4146 Change occurrences of <br/> to <br>
Mateusz Warowny [Tue, 14 Mar 2023 14:03:39 +0000 (15:03 +0100)]
JAL-4146 Patch parseColourString test to expect null for "-1"
Mateusz Warowny [Wed, 1 Mar 2023 15:22:31 +0000 (16:22 +0100)]
JAL-4136 Replace uses of isBlank with isEmpty
Mateusz Warowny [Fri, 24 Feb 2023 15:02:31 +0000 (16:02 +0100)]
JAL-4135 replace stream.toString(Charset) calls with stream.toString(String)
The former variant was introduced in java 10 and is not implemented in java2script.
Mateusz Warowny [Wed, 22 Feb 2023 13:28:59 +0000 (14:28 +0100)]
JAL-4130 Replace Collection#forEach call with for loop
Mateusz Warowny [Wed, 22 Feb 2023 13:27:43 +0000 (14:27 +0100)]
JAL-4130 Avoid using thenComparing of the Comparator interface
Mateusz Warowny [Fri, 17 Feb 2023 12:28:26 +0000 (13:28 +0100)]
JAL-4131 Replace usages of requireNonNullElse
Mateusz Warowny [Wed, 15 Feb 2023 14:11:28 +0000 (15:11 +0100)]
JAL-4130 Workaround the j2s issue with final variables inside lambdas
Mateusz Warowny [Mon, 6 Feb 2023 14:29:48 +0000 (15:29 +0100)]
JAL-3878 Change Cache.log calls to Console
Mateusz Warowny [Mon, 6 Feb 2023 13:04:59 +0000 (14:04 +0100)]
Merge branch 'JAL-3878_ws-overhaul-3' into mmw/Release_2_12_ws_merge
Jim Procter [Fri, 20 Jan 2023 23:41:35 +0000 (23:41 +0000)]
Merge branch 'develop' into development/Release_2_12_Branch_JAL-4102_21126_merge
Jim Procter [Fri, 20 Jan 2023 23:40:08 +0000 (23:40 +0000)]
Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
Jim Procter [Fri, 20 Jan 2023 23:39:28 +0000 (23:39 +0000)]
JAL-4114 model_page_url not required in v2.0 response
Jim Procter [Fri, 20 Jan 2023 23:15:09 +0000 (23:15 +0000)]
JAL-4102 update 2.12 from 2.11.2.6 patch release - JAL-3416 JAL-2353 JAL-4104 JAL-4114
Jim Procter [Fri, 20 Jan 2023 23:03:12 +0000 (23:03 +0000)]
JAL-4102 update date and release notes for 2.11.2.6
Jim Procter [Fri, 20 Jan 2023 22:53:26 +0000 (22:53 +0000)]
Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
Jim Procter [Fri, 20 Jan 2023 22:52:55 +0000 (22:52 +0000)]
Merge branch 'patch/Release_2_11_2_6_Branch' into develop
Jim Procter [Fri, 20 Jan 2023 20:48:43 +0000 (20:48 +0000)]
JAL-2353 primary ref candidates that should be promoted should preserve original version string
Jim Procter [Fri, 20 Jan 2023 20:44:47 +0000 (20:44 +0000)]
JAL-4114 missing mock server response
Jim Procter [Fri, 20 Jan 2023 17:53:48 +0000 (17:53 +0000)]
JAL-4114 only rank model qualities that are computed with the same method, and uprank models with pLDDT over other types of models in the same model type category
Jim Procter [Fri, 20 Jan 2023 17:52:52 +0000 (17:52 +0000)]
JAL-4114 alphafold now marked as AB-INITIO so adjust ranking in categories
Jim Procter [Fri, 20 Jan 2023 17:50:53 +0000 (17:50 +0000)]
JAL-4114 additional warnings when PDBe doesn’t return as many responses as queries made to it when adding in additional metadata
Jim Procter [Fri, 20 Jan 2023 17:49:38 +0000 (17:49 +0000)]
JAL-4114 patch REST client for changed JSON schema in 3D beacons v2 API
Jim Procter [Fri, 20 Jan 2023 17:49:16 +0000 (17:49 +0000)]
JAL-4114 formatting
Jim Procter [Fri, 20 Jan 2023 17:48:04 +0000 (17:48 +0000)]
JAL-4114 updated mock tests and responses for v2.0 api
Jim Procter [Fri, 6 Jan 2023 16:52:30 +0000 (16:52 +0000)]
Merge branch 'improvement/JAL-4111_suffixed_DEVELOP_channels' into development/Release_2_12_Branch
Ben Soares [Fri, 6 Jan 2023 13:53:44 +0000 (13:53 +0000)]
JAL-4111 Added commit and date text to splashscreens of all channels
Ben Soares [Thu, 5 Jan 2023 20:18:57 +0000 (20:18 +0000)]
JAL-4111 improvement to convert -draw argument
Ben Soares [Thu, 5 Jan 2023 20:07:00 +0000 (20:07 +0000)]
JAL-4111 Use ImageMagick to add commit and build time text to DMG and getdown splash images
Ben Soares [Thu, 5 Jan 2023 13:38:00 +0000 (13:38 +0000)]
JAL-4111 Fixed channel.props to allow replacement of __SUFFIX__. Generic background images with 'branch version' for getdown and DMG
Benedict Soares (Staff) [Thu, 5 Jan 2023 00:19:00 +0000 (00:19 +0000)]
JAL-4111 fixed DMG background image for generic Develop-X.XX app name, and new DS_Store
Ben Soares [Thu, 22 Dec 2022 00:51:44 +0000 (00:51 +0000)]
JAL-4111 Allow -PCHANNEL=DEVELOP-version for new appbase. Add a utils/channel/develop-2.12 dir with new getdown images.
Jim Procter [Wed, 21 Dec 2022 15:37:58 +0000 (15:37 +0000)]
JAL-3362 update release to 2.12
Jim Procter [Fri, 16 Dec 2022 16:46:14 +0000 (16:46 +0000)]
JAL-4110 added line to build.gradle that allows stdout and stderr from tests to be viewed when run via gradle. Currently commented out.
Jim Procter [Fri, 16 Dec 2022 16:45:18 +0000 (16:45 +0000)]
JAL-4109 examine -Djalview.loglevel on startup to decide what the default log level should be
Jim Procter [Fri, 16 Dec 2022 16:33:28 +0000 (16:33 +0000)]
JAL-4107 JAL-4108 updated testNG and other test dependencies
Jim Procter [Fri, 16 Dec 2022 13:22:39 +0000 (13:22 +0000)]
JAL-4107 patching tests after merge
Jim Procter [Fri, 16 Dec 2022 13:21:17 +0000 (13:21 +0000)]
JAL-4107 fix merge and avoid NPE
Jim Procter [Fri, 16 Dec 2022 13:18:27 +0000 (13:18 +0000)]
JAL-4107 remove old jMol jar
Jim Procter [Wed, 14 Dec 2022 17:09:09 +0000 (17:09 +0000)]
JAL-4107 fix test compilation issues
Jim Procter [Wed, 14 Dec 2022 16:01:09 +0000 (16:01 +0000)]
Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
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/jws1/JPredClient.java
src/jalview/ws/jws1/JPredThread.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 [Tue, 13 Dec 2022 17:29:01 +0000 (17:29 +0000)]
Merge branch 'alpha/origin_2022_JAL-3066_Jalview_212_slivka-integration' into spike/jims/dec_2022_2112_to_212_JAL-3066_slikva_integration
Conflicts:
src/jalview/bin/Cache.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
Mateusz Warowny [Mon, 12 Dec 2022 15:24:47 +0000 (16:24 +0100)]
WIP
Jim Procter [Wed, 30 Nov 2022 11:51:02 +0000 (11:51 +0000)]
JAL-4102 bump version number
Jim Procter [Wed, 30 Nov 2022 11:34:45 +0000 (11:34 +0000)]
JAL-4102 2.11.2.6 hotfix release notes - JAL-4101 JAL-2353
Ben Soares [Tue, 29 Nov 2022 13:20:54 +0000 (13:20 +0000)]
JAL-4101 Updated Rfam* tests
Ben Soares [Tue, 29 Nov 2022 13:15:32 +0000 (13:15 +0000)]
JAL-4101 Updated DEFAULT_RFAM_BASEURL
Jim Procter [Sun, 30 Oct 2022 23:19:57 +0000 (23:19 +0000)]
JAL-2353 patch for Ensembl refs from uniprot - needs test and checking !
Ben Soares [Tue, 29 Nov 2022 13:20:54 +0000 (13:20 +0000)]
JAL-4101 Updated Rfam* tests
Ben Soares [Tue, 29 Nov 2022 13:15:32 +0000 (13:15 +0000)]
JAL-4101 Updated DEFAULT_RFAM_BASEURL
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 15:54:16 +0000 (16:54 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 15:16:37 +0000 (16:16 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 14:44:01 +0000 (15:44 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 14:43:36 +0000 (15:43 +0100)]
JAL-4073 update tests
Jim Procter [Tue, 11 Oct 2022 14:28:03 +0000 (15:28 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 12:10:56 +0000 (13:10 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 10:32:29 +0000 (11:32 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 14:19:54 +0000 (15:19 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 14:14:42 +0000 (15:14 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 17:14:19 +0000 (18:14 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 11:36:33 +0000 (12:36 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 11:21:51 +0000 (12:21 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 11:17:59 +0000 (12:17 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
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 17:49:08 +0000 (18:49 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 8 Aug 2022 17:48:01 +0000 (18:48 +0100)]
JAL-4046 release on 9th August 2022
git://source.jalview.org / jalview.git / log