Jim Procter [Fri, 3 Jun 2022 13:13:41 +0000 (14:13 +0100)]
JAL-4021 todo & fix FileFormat tests
Jim Procter [Fri, 3 Jun 2022 10:37:14 +0000 (11:37 +0100)]
JAL-1953 2.11.2 with Archeopteryx!
Minimal patches and Merge branch 'kjvdh/features/PhylogenyViewer' into merge/2_11_2/PhylogenyViewer
also restored last kjvdh build of forester to j8 and j11lib directories
Conflicts:
.classpath
j8lib/forester.jar
resources/lang/Messages.properties
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/fts/core/GFTSPanel.java
src/jalview/fts/service/pdb/PDBFTSPanel.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SplashScreen.java
src/jalview/gui/StructureViewerBase.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/FileLoader.java
src/jalview/io/HtmlSvgOutput.java
src/jalview/project/Jalview2XML.java
src/jalview/schemabinding/version2/JalviewModelSequence.java
src/jalview/util/DBRefUtils.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/DasSequenceFeatureFetcher.java
src/jalview/ws/jws2/Jws2Discoverer.java
utils/jalviewjs/buildxml/build.xml
Jim Procter [Thu, 2 Jun 2022 16:31:52 +0000 (17:31 +0100)]
Revert "JAL-2799 all tabs now get mouse listeners and Jalview switches tree view"
This reverts commit
62f2ed464010270830afcfe954647a51dfb5114b.
Jim Procter [Thu, 2 Jun 2022 16:23:47 +0000 (17:23 +0100)]
minimal fixes - probably not valid since forester jar out of sync
Jim Procter [Thu, 2 Jun 2022 15:05:51 +0000 (16:05 +0100)]
Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh/features/PhylogenyViewer_tabbedsupport
Update from Release 2.11.2 develop branch JAL-1953
Conflicts:
.classpath
.project
resources/lang/Messages.properties
src/jalview/bin/Jalview.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/fts/core/GFTSPanel.java
src/jalview/fts/service/pdb/PDBFTSPanel.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/CalculationChooser.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/Desktop.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SplashScreen.java
src/jalview/gui/StructureViewerBase.java
src/jalview/gui/TreePanel.java
src/jalview/gui/WebserviceInfo.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/FileLoader.java
src/jalview/io/HtmlSvgOutput.java
src/jalview/io/NewickFile.java
src/jalview/math/Matrix.java
src/jalview/math/MatrixI.java
src/jalview/util/MappingUtils.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/DasSequenceFeatureFetcher.java
src/jalview/ws/jws2/Jws2Discoverer.java
utils/eclipse/org.eclipse.jdt.core.jalview.prefs
utils/eclipse/org.eclipse.jdt.ui.prefs
Jim Procter [Wed, 11 May 2022 14:50:10 +0000 (15:50 +0100)]
Merge branch 'patch/JAL-4008_jabaws_2_2_1_patch' into doc/release_2_11_2_3
Jim Procter [Wed, 11 May 2022 12:44:36 +0000 (13:44 +0100)]
JAL-4012 JAL-4008 release notes for Jalview 2.11.2.3
Jim Procter [Tue, 10 May 2022 16:56:51 +0000 (17:56 +0100)]
JAL-4008 update jabaws client to 2.2.1 - definitely no log4j references !
Jim Procter [Tue, 19 Apr 2022 14:04:00 +0000 (15:04 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 19 Apr 2022 14:03:23 +0000 (15:03 +0100)]
JAL-3992 bump version and report updates in 2.11.2.2 release notes
Jim Procter [Tue, 19 Apr 2022 14:02:17 +0000 (15:02 +0100)]
Merge branch 'bug/JAL-3997_NPE_in_wrapped_mode' into develop
Jim Procter [Tue, 19 Apr 2022 13:57:56 +0000 (14:57 +0100)]
Merge branch 'bug/JAL-3365_extendedDSSP_via_stockholm' into develop
Jim Procter [Mon, 18 Apr 2022 13:49:47 +0000 (14:49 +0100)]
JAL-3997 check for tooltip being null before checking equivalence to last tooltip string
Jim Procter [Mon, 18 Apr 2022 12:27:14 +0000 (13:27 +0100)]
Merge branch 'task/JAL-3992_update_docs' into bug/JAL-3365_extendedDSSP_via_stockholm
Jim Procter [Mon, 18 Apr 2022 11:51:59 +0000 (12:51 +0100)]
JAL-3992 fix path
Jim Procter [Sat, 16 Apr 2022 12:36:06 +0000 (13:36 +0100)]
JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files
Jim Procter [Wed, 13 Apr 2022 15:13:40 +0000 (16:13 +0100)]
JAL-3992 shift+arrow to jump to next gap/residue in cursor/keyboard editing mode
Jim Procter [Tue, 5 Apr 2022 19:48:38 +0000 (20:48 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 5 Apr 2022 19:44:48 +0000 (20:44 +0100)]
JAL-3990 release notes and what’s new
Jim Procter [Tue, 5 Apr 2022 17:50:33 +0000 (18:50 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 5 Apr 2022 17:37:11 +0000 (18:37 +0100)]
JAL-3981 patch tests and remove errant imports
Jim Procter [Tue, 5 Apr 2022 17:15:28 +0000 (18:15 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 5 Apr 2022 17:14:52 +0000 (18:14 +0100)]
JAL-3990 gradle spotlessApply
Jim Procter [Tue, 5 Apr 2022 17:12:13 +0000 (18:12 +0100)]
JAL-3990 release notes for 2.11.2.1 patch release
Jim Procter [Tue, 5 Apr 2022 16:57:40 +0000 (17:57 +0100)]
Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop
Jim Procter [Thu, 31 Mar 2022 22:11:44 +0000 (23:11 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 31 Mar 2022 19:44:49 +0000 (20:44 +0100)]
JAL-3983 release note for JAL-3985
Jim Procter [Thu, 31 Mar 2022 19:42:53 +0000 (20:42 +0100)]
Merge branch 'bug/JAL-3085_avoid_414_error_for_PDBFTS' into develop
Jim Procter [Thu, 31 Mar 2022 14:17:46 +0000 (15:17 +0100)]
JAL-3085 update tests and mock responses, new P0dtd1 testcase
Jim Procter [Thu, 31 Mar 2022 13:06:28 +0000 (14:06 +0100)]
JAL-3985 formatting
Jim Procter [Thu, 31 Mar 2022 13:06:04 +0000 (14:06 +0100)]
JAL-3985 split PDB id queries into multiple queries so server doesn’t 414
Jim Procter [Wed, 30 Mar 2022 17:35:07 +0000 (18:35 +0100)]
Merge branch 'patch/JAL-3976_3dbeaconsnull' into develop
Jim Procter [Wed, 30 Mar 2022 16:32:19 +0000 (17:32 +0100)]
JAL-3976 fix mock PDBFTS query & responses
Jim Procter [Wed, 30 Mar 2022 15:56:41 +0000 (16:56 +0100)]
JAL-3983 known issue note for JAL-3984
Jim Procter [Wed, 30 Mar 2022 15:54:33 +0000 (16:54 +0100)]
JAL-3983 release notes for JAL-3975 and known issue note for JAL-3984
Jim Procter [Wed, 30 Mar 2022 15:52:27 +0000 (16:52 +0100)]
Merge branch 'bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog' into develop
Jim Procter [Wed, 30 Mar 2022 15:51:44 +0000 (16:51 +0100)]
JAL-360 JAL-3975 update parent for text colour dialog - doesn't seem to help but we live in hope..
Ben Soares [Tue, 15 Mar 2022 17:13:01 +0000 (17:13 +0000)]
JAL-360 JAL-3975 make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after JvOptionPane action.
Jim Procter [Wed, 30 Mar 2022 15:15:43 +0000 (16:15 +0100)]
JAL-3983 update release notes for JAL-3973
Jim Procter [Wed, 30 Mar 2022 15:12:51 +0000 (16:12 +0100)]
JAL-3973 exclude the original RELEASE file so gradle doesn't complain of duplicate entries in the tarball
Jim Procter [Wed, 30 Mar 2022 14:49:09 +0000 (15:49 +0100)]
Merge branch 'bug/JAL-3973_source_tarball_not_building' into develop
Jim Procter [Wed, 30 Mar 2022 14:45:01 +0000 (15:45 +0100)]
JAL-3983 release 2.11.2.1 date and release notes
Jim Procter [Fri, 25 Mar 2022 14:31:18 +0000 (14:31 +0000)]
JAL-3980 JAL-3979 TODOs
Jim Procter [Fri, 25 Mar 2022 14:30:17 +0000 (14:30 +0000)]
JAL-3980 defensive copy - inefficient but fixes bug
Jim Procter [Fri, 25 Mar 2022 14:16:21 +0000 (14:16 +0000)]
JAL-3981 Additional line breaks - sort of helps
Jim Procter [Thu, 24 Mar 2022 17:02:10 +0000 (17:02 +0000)]
JAL-3981 strategic newlines to help speed up Java's html parser
Jim Procter [Wed, 23 Mar 2022 12:22:41 +0000 (12:22 +0000)]
JAL-3976 skip entries with null values when analyzing
Jim Procter [Wed, 23 Mar 2022 12:22:15 +0000 (12:22 +0000)]
JAL-3976 update tests
Ben Soares [Sun, 13 Mar 2022 21:00:24 +0000 (21:00 +0000)]
Append git.hash and git.branch to RELEASE file stored in tarball. When compiling, if not in git repo use git.branch and git.hash from RELEASE file.
Ben Soares [Fri, 11 Mar 2022 09:31:57 +0000 (09:31 +0000)]
JAL-3973 This fixes the gradle build when not in a git repo. (Part 1 of the issue)
Jalview Development Admin [Thu, 10 Mar 2022 17:40:40 +0000 (17:40 +0000)]
Merge branch 'master' into releases/Release_2_11_2_Branch
Jalview Development Admin [Thu, 10 Mar 2022 01:34:08 +0000 (01:34 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jalview Development Admin [Thu, 10 Mar 2022 01:29:53 +0000 (01:29 +0000)]
JAL-3746 bump release date to 10th March - after UoD network maintenance
Jalview Development Admin [Thu, 10 Mar 2022 01:28:58 +0000 (01:28 +0000)]
JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(
Jim Procter [Wed, 9 Mar 2022 17:31:53 +0000 (17:31 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jalview Development Admin [Wed, 9 Mar 2022 16:51:38 +0000 (16:51 +0000)]
JAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert
Jim Procter [Wed, 9 Mar 2022 10:12:18 +0000 (10:12 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 9 Mar 2022 10:11:56 +0000 (10:11 +0000)]
JAL-3746 JAL-3841 fix README typo
Jim Procter [Wed, 9 Mar 2022 08:14:14 +0000 (08:14 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 9 Mar 2022 08:09:45 +0000 (08:09 +0000)]
JAL-3746 more docs tweaking and release notes
Jim Procter [Wed, 9 Mar 2022 07:59:03 +0000 (07:59 +0000)]
Merge branch 'spike/try_spotless_JAL-3438' into develop
Jim Procter [Tue, 8 Mar 2022 21:58:37 +0000 (21:58 +0000)]
JAL-3746 apply copyright to tests
Jim Procter [Tue, 8 Mar 2022 21:56:25 +0000 (21:56 +0000)]
JAL-3746 apply copyright to source
Jim Procter [Tue, 8 Mar 2022 21:30:05 +0000 (21:30 +0000)]
JAL-3438 spotless for 2.11.2.0
Jim Procter [Tue, 8 Mar 2022 20:40:15 +0000 (20:40 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 8 Mar 2022 20:39:47 +0000 (20:39 +0000)]
JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes
Jim Procter [Tue, 8 Mar 2022 18:53:09 +0000 (18:53 +0000)]
JAL-3108 updated Ensembl client and model species names
Jim Procter [Tue, 8 Mar 2022 18:18:56 +0000 (18:18 +0000)]
JAL-3746 new release date for 2.11.2
Jim Procter [Tue, 8 Mar 2022 18:13:27 +0000 (18:13 +0000)]
JAL-3746 JAL-3103 java.awt.Desktop.showURL method mechanism release notes
Jim Procter [Tue, 8 Mar 2022 17:41:04 +0000 (17:41 +0000)]
Merge branch 'bug/JAL-3103_browser_launcher_problems_macos_and_linux' into develop
Ben Soares [Tue, 8 Mar 2022 12:26:28 +0000 (12:26 +0000)]
JAL-3103 updated help doc to remove default browser choice
Ben Soares [Tue, 8 Mar 2022 12:14:45 +0000 (12:14 +0000)]
JAL-3103 Removed code and unused widgets for defaultBrowser
Ben Soares [Tue, 8 Mar 2022 12:03:11 +0000 (12:03 +0000)]
JAL-3103 Remove BrowserLauncher2 and use Desktop.browse(url) with wrapper methods
Ben Soares [Tue, 8 Mar 2022 00:39:04 +0000 (00:39 +0000)]
JAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS
Ben Soares [Tue, 8 Mar 2022 00:34:55 +0000 (00:34 +0000)]
JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-needed exception handling from jalview code for openURL. Change Default browser input to JComboBox populated by BrowserLauncher2
Jim Procter [Mon, 7 Mar 2022 20:12:04 +0000 (20:12 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 7 Mar 2022 20:07:36 +0000 (20:07 +0000)]
JAL-3647 release notes for JAL-1842 JAL-3509 JAL-3881, JAL-3884 JAL-3632 JAL-3633 and report JAL-3764 as a known issue
Jim Procter [Mon, 7 Mar 2022 17:52:44 +0000 (17:52 +0000)]
JAL-3685 - two single quotes when replacements are present in i18n message
Ben Soares [Mon, 7 Mar 2022 17:51:47 +0000 (17:51 +0000)]
JAL-3103 Switched to (a wrapper around) BrowserLauncher2
Jim Procter [Fri, 4 Mar 2022 17:19:40 +0000 (17:19 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 4 Mar 2022 17:19:17 +0000 (17:19 +0000)]
JAL-3647 release notes for hdpi/laf scaling JAL-3608 JAL-3609 JAL-3552
Jim Procter [Fri, 4 Mar 2022 16:38:01 +0000 (16:38 +0000)]
JAL-3746 structure mapping preference docs for JAL-3817
Jim Procter [Fri, 5 Feb 2021 17:03:12 +0000 (17:03 +0000)]
JAL-3746 JAL-3811 document SHOW_JWS2_SERVICES user preference and provide new menu option for ‘one off’ JABAWS discovery if preference is disabled.
Jim Procter [Fri, 5 Feb 2021 17:05:03 +0000 (17:05 +0000)]
JAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and user preference ‘NOHTMLTEMPLATES’ to disable download of templates from GitHub repository
Jim Procter [Fri, 5 Feb 2021 17:07:18 +0000 (17:07 +0000)]
JAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disables jalview pinging jalview.org/services/identifiers to get a list of URL link templates for viewing database crossreferences
Jim Procter [Fri, 5 Feb 2021 17:07:54 +0000 (17:07 +0000)]
JAL-3746 JAL-3814 don’t automatically launch the news browser when the desktop is first opened
Jim Procter [Fri, 5 Feb 2021 17:01:09 +0000 (17:01 +0000)]
JAL-3746 JAL-3814 NONEWS property
Jim Procter [Fri, 4 Mar 2022 15:57:52 +0000 (15:57 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 4 Mar 2022 15:41:06 +0000 (15:41 +0000)]
JAL-3608 JAL-3830 tweaked the what’s new text and updated helpTOC
Jim Procter [Fri, 4 Mar 2022 15:26:25 +0000 (15:26 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 4 Mar 2022 15:26:03 +0000 (15:26 +0000)]
JAL-3608 JAL-3830 simplified command line docs a bit
Jim Procter [Fri, 4 Mar 2022 14:36:11 +0000 (14:36 +0000)]
Merge branch 'doc/JAL-3608+JAL-3830_added_to_help_docs' into develop
Ben Soares [Fri, 4 Mar 2022 13:48:54 +0000 (13:48 +0000)]
JAL-3830 added command line to whatsnew and releases
Ben Soares [Fri, 4 Mar 2022 13:38:29 +0000 (13:38 +0000)]
JAL-3830 Added new command line usage to docs
Ben Soares [Fri, 4 Mar 2022 12:19:35 +0000 (12:19 +0000)]
JAL-3608 added to LaF documentation
Ben Soares [Thu, 3 Mar 2022 15:38:47 +0000 (15:38 +0000)]
JAL-3830 fix broken/buggy install4j9 setting of executeSetupApp=false still running setupApp
Jim Procter [Wed, 2 Mar 2022 20:51:16 +0000 (20:51 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 2 Mar 2022 20:50:54 +0000 (20:50 +0000)]
Merge branch 'bug/JAL-3962_awt_dll_problem' into develop
Jim Procter [Wed, 2 Mar 2022 20:50:02 +0000 (20:50 +0000)]
JAL-3746 release notes for JAL-3867
Jim Procter [Wed, 2 Mar 2022 18:12:13 +0000 (18:12 +0000)]
JAL-3746 release note for JAL-3907 building Jalview with j17
git://source.jalview.org / jalview.git / log