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.
James Procter [Thu, 23 Mar 2023 11:52:19 +0000 (11:52 +0000)]
Merge branch 'patch/JAL-4153_flakyJvCacheableInputBoxTest' into develop
James Procter [Mon, 20 Mar 2023 17:00:10 +0000 (17:00 +0000)]
JAL-4153 longer Thread.sleep() calls in the hope that the test might pass on Bamboo
James Procter [Mon, 20 Mar 2023 16:26:18 +0000 (16:26 +0000)]
JAL-4150 test and quick patch copying code from AlignFrame.paste() to Desktop.paste() so internal paste works from popup menu
James Procter [Fri, 24 Feb 2023 17:10:02 +0000 (17:10 +0000)]
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - additional test case
James Procter [Fri, 24 Feb 2023 16:44:48 +0000 (16:44 +0000)]
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)
James Procter [Fri, 24 Feb 2023 15:26:30 +0000 (15:26 +0000)]
Merge branch 'features/JAL-3858_PAEsInProjects' into develop
James Procter [Fri, 24 Feb 2023 15:13:37 +0000 (15:13 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts:
src/jalview/bin/Jalview.java
Ben Soares [Fri, 24 Feb 2023 12:54:35 +0000 (12:54 +0000)]
JAL-629 better test fixes. --props=... instead of --debug
Ben Soares [Fri, 24 Feb 2023 11:52:19 +0000 (11:52 +0000)]
JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups
Ben Soares [Thu, 23 Feb 2023 19:21:24 +0000 (19:21 +0000)]
JAL-629 test fixing
Ben Soares [Thu, 23 Feb 2023 17:01:05 +0000 (17:01 +0000)]
JAL-629 Add debug messages for more failing tests
Ben Soares [Thu, 23 Feb 2023 16:21:49 +0000 (16:21 +0000)]
JAL-629 fixed a Log4j test by adding --debug arg
Ben Soares [Thu, 23 Feb 2023 16:21:19 +0000 (16:21 +0000)]
JAL-629 bootstrap args and properties. Remember index of args for 'previous structure' defaulting of other args
Ben Soares [Thu, 23 Feb 2023 16:19:25 +0000 (16:19 +0000)]
JAL-629 nf-core sample alignment files and a2m versions
Ben Soares [Thu, 23 Feb 2023 16:18:40 +0000 (16:18 +0000)]
JAL-629 fix a PAEMatrix casting error
James Procter [Thu, 23 Feb 2023 12:08:00 +0000 (12:08 +0000)]
JAL-3858 new MatrixType JAX-RI POJO
James Procter [Thu, 23 Feb 2023 11:58:09 +0000 (11:58 +0000)]
JAL-4133 update validChar width when font is changed so characters are suppressed for small widths
James Procter [Wed, 22 Feb 2023 22:14:15 +0000 (22:14 +0000)]
JAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project
James Procter [Wed, 22 Feb 2023 22:02:20 +0000 (22:02 +0000)]
JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests.
James Procter [Wed, 22 Feb 2023 14:24:04 +0000 (14:24 +0000)]
JAL-1551 source formatting
James Procter [Wed, 22 Feb 2023 14:23:56 +0000 (14:23 +0000)]
JAL-3858 simple test for PAE matrix recovery
James Procter [Wed, 22 Feb 2023 14:23:15 +0000 (14:23 +0000)]
JAL-3858 construct a PAE direct from float array
Ben Soares [Wed, 22 Feb 2023 14:04:25 +0000 (14:04 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Wed, 22 Feb 2023 14:04:03 +0000 (14:04 +0000)]
JAL-4064 JAL-4054 Corrected the tgz top-level dir from './Contents' to 'Contents' for mac JRE bundles for install4j (not strictly used, but might be in the future).
James Procter [Wed, 22 Feb 2023 13:34:54 +0000 (13:34 +0000)]
JAL-629 make sure we show GUI when not driven programmatically
James Procter [Wed, 22 Feb 2023 12:43:25 +0000 (12:43 +0000)]
JAL-4095 slightly better threshold setting and todos for improvement
James Procter [Wed, 22 Feb 2023 12:42:58 +0000 (12:42 +0000)]
JAL-4095 magic fill behaviour is PAE specific
Ben Soares [Wed, 22 Feb 2023 12:40:43 +0000 (12:40 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
James Procter [Wed, 22 Feb 2023 12:38:00 +0000 (12:38 +0000)]
JAL-3858 JAL-2381 allow different linear shading schemes for selected/non-selected regions of contact matrix heat map
James Procter [Wed, 22 Feb 2023 12:05:22 +0000 (12:05 +0000)]
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type, with actual matrix type stored in calcId
Ben Soares [Tue, 21 Feb 2023 13:41:37 +0000 (13:41 +0000)]
JAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS
Ben Soares [Mon, 20 Feb 2023 23:04:09 +0000 (23:04 +0000)]
JAL-3416 Turn off (partial) flatlaf scaling for HiDPI in Linux and Java 8 - Some GUI parts unusable
Ben Soares [Mon, 20 Feb 2023 17:48:16 +0000 (17:48 +0000)]
JAL-4064 JAL-4054 Correct names of mac arch installer DMG files
Ben Soares [Mon, 20 Feb 2023 15:42:14 +0000 (15:42 +0000)]
Merge branch 'develop' into improvement/JAL-4111_suffixed_DEVELOP_channels
Ben Soares [Mon, 20 Feb 2023 10:46:11 +0000 (10:46 +0000)]
JAL-4128 Catch RasterFormatException caused whilst resizing Overview window, recalculate OverviewDimensions od instead. Prevent negative OverviewDimensions being set to avoid problem with vertically fully shrunk overview window 'losing' the alignement canvas.
Ben Soares [Mon, 20 Feb 2023 10:09:46 +0000 (10:09 +0000)]
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
James Procter [Thu, 16 Feb 2023 13:14:11 +0000 (13:14 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts:
src/jalview/bin/Jalview.java
James Procter [Thu, 16 Feb 2023 12:25:41 +0000 (12:25 +0000)]
JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
James Procter [Wed, 15 Feb 2023 15:25:53 +0000 (15:25 +0000)]
Merge branch 'develop' into feature/JAL-1713_overviewInProject
James Procter [Wed, 15 Feb 2023 14:43:32 +0000 (14:43 +0000)]
Passing test for JAL-4127 failing on the JAL-1713 branch
James Procter [Wed, 15 Feb 2023 13:59:29 +0000 (13:59 +0000)]
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
Ben Soares [Mon, 13 Feb 2023 22:42:58 +0000 (22:42 +0000)]
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
Ben Soares [Mon, 13 Feb 2023 22:41:51 +0000 (22:41 +0000)]
JAL-4125 Spanish translations
Ben Soares [Mon, 13 Feb 2023 20:18:00 +0000 (20:18 +0000)]
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
Ben Soares [Mon, 13 Feb 2023 19:16:08 +0000 (19:16 +0000)]
JAL-4125 Move confirmation of closing external viewer windows into the quit handler, and allow all to close or not in closeViewer whilst quitting.
James Procter [Mon, 13 Feb 2023 17:28:45 +0000 (17:28 +0000)]
Merge branch 'develop' into feature/JAL-1713_overviewInProject
James Procter [Fri, 10 Feb 2023 17:05:30 +0000 (17:05 +0000)]
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
James Procter [Fri, 10 Feb 2023 16:26:37 +0000 (16:26 +0000)]
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
James Procter [Fri, 10 Feb 2023 16:23:53 +0000 (16:23 +0000)]
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
James Procter [Fri, 10 Feb 2023 16:03:32 +0000 (16:03 +0000)]
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
Ben Soares [Thu, 9 Feb 2023 01:38:20 +0000 (01:38 +0000)]
JAL-4125 Additions to JvOptionPane and QuitHandler with StructureViewerBase handling closed frame during quit differently. Still not working as dialog content does not appear until after quithandling thread has finished (it's blocking EDT). Need to break the doDesktopQuit Callable up into sections, that add another bit to the end when necessary.
Ben Soares [Fri, 3 Feb 2023 21:10:51 +0000 (21:10 +0000)]
JAL-629 Fasta sequence id reading whitespace fix. Flexioble pae json keys and structure. Headless fixes. Logging fixes (MessageManager -- test broken). ArgParser and Console helper methods. Commands added e.g. --colour=gecos:flower.
Ben Soares [Fri, 3 Feb 2023 20:57:43 +0000 (20:57 +0000)]
JAL-629 "updated" json-simple
James Procter [Fri, 3 Feb 2023 14:18:44 +0000 (14:18 +0000)]
JAL-1551 remove temp file in src
James Procter [Fri, 3 Feb 2023 14:14:49 +0000 (14:14 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
James Procter [Tue, 31 Jan 2023 16:17:49 +0000 (16:17 +0000)]
JAL-1713 update from Jalview 2.11.3 develop
Merge branch 'develop' into feature/JAL-1713_overviewInProject
regenerated jaxb classes to resolve conflicts
Ben Soares [Mon, 30 Jan 2023 12:17:27 +0000 (12:17 +0000)]
JAL-1988 Make sensible choices if only the opening file has been opened, and alter the message if an alignment has been fetched but not changed
Ben Soares [Thu, 26 Jan 2023 17:06:40 +0000 (17:06 +0000)]
JAL-4118 remove unnecessary sleep from QuitHandlerTest
Ben Soares [Thu, 26 Jan 2023 16:44:51 +0000 (16:44 +0000)]
JAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possible problem with filename with dirs in passed to BackupFiles.
Ben Soares [Thu, 26 Jan 2023 11:49:36 +0000 (11:49 +0000)]
JAL-1988 Add a sleep to file save test to give time for file to save
Ben Soares [Thu, 26 Jan 2023 11:10:37 +0000 (11:10 +0000)]
JAL-629 example files from nf-core
Ben Soares [Thu, 26 Jan 2023 11:10:04 +0000 (11:10 +0000)]
JAL-629 helper eclipse CLI run
Ben Soares [Thu, 26 Jan 2023 11:09:47 +0000 (11:09 +0000)]
JAL-629 adjust arg type for tempfac-shading -- was grabbing next argument
James Procter [Wed, 25 Jan 2023 15:28:48 +0000 (15:28 +0000)]
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
James Procter [Wed, 25 Jan 2023 13:05:54 +0000 (13:05 +0000)]
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
James Procter [Tue, 24 Jan 2023 18:20:55 +0000 (18:20 +0000)]
JAL-4090 Release 2.11.3.0 release notes and version bump
James Procter [Tue, 24 Jan 2023 17:41:02 +0000 (17:41 +0000)]
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into develop
James Procter [Tue, 24 Jan 2023 08:18:39 +0000 (08:18 +0000)]
JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation
James Procter [Tue, 24 Jan 2023 07:51:00 +0000 (07:51 +0000)]
JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..
James Procter [Tue, 24 Jan 2023 07:49:39 +0000 (07:49 +0000)]
JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time
James Procter [Tue, 24 Jan 2023 07:48:54 +0000 (07:48 +0000)]
JAL-629 don’t carry on Jalview.main if we’ve already processed command line args another way
James Procter [Tue, 24 Jan 2023 07:48:07 +0000 (07:48 +0000)]
JAL-629 don’t trash user’s system property file when adjusting settings to process CL args
James Procter [Tue, 24 Jan 2023 07:46:53 +0000 (07:46 +0000)]
JAL-629 don’t complain for Unary args
James Procter [Tue, 24 Jan 2023 07:46:34 +0000 (07:46 +0000)]
JAL-629 labelled breaks are frowned upon by everyone
James Procter [Tue, 24 Jan 2023 06:27:46 +0000 (06:27 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into features/r2_11_2_alphafold/JAL-629
James Procter [Tue, 24 Jan 2023 06:26:15 +0000 (06:26 +0000)]
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
Ben Soares [Mon, 23 Jan 2023 23:57:06 +0000 (23:57 +0000)]
JAL-629 Attempts to add PAE to structure. --headless working. Make HTML output single threaded in headless mode. Delete an editor temp file.
James Procter [Mon, 23 Jan 2023 20:17:42 +0000 (20:17 +0000)]
JAL-4104 JAL-4102 update help docs with script to add jalview command line tool to osx path
Jim Procter [Mon, 23 Jan 2023 09:32:43 +0000 (09:32 +0000)]
JAL-4102 whatsNew for 2.11.2.6
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 23:03:12 +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
Ben Soares [Wed, 18 Jan 2023 15:52:10 +0000 (15:52 +0000)]
JAL-629 make sequence id key 'seqid'
Ben Soares [Tue, 17 Jan 2023 17:01:45 +0000 (17:01 +0000)]
JAL-3416 No longer needed
Ben Soares [Tue, 17 Jan 2023 10:44:50 +0000 (10:44 +0000)]
Merge branch 'develop' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Mon, 16 Jan 2023 23:21:25 +0000 (23:21 +0000)]
JAL-3416 More tweaking of FlatLaf. Problem with macOS themed FlatLaf solved with new DesktopManager
Ben Soares [Wed, 11 Jan 2023 13:04:47 +0000 (13:04 +0000)]
JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as 'all saved' after initial opening
Ben Soares [Wed, 11 Jan 2023 11:55:53 +0000 (11:55 +0000)]
JAL-629 added Alphafold cif, pdb and PAE json files to examples/AlphaFold