jalview.git
19 months agoJAL-4154 Update AlignmentPanelTest to use new forArch method
Mateusz Warowny [Fri, 24 Mar 2023 15:18:55 +0000 (16:18 +0100)]
JAL-4154 Update AlignmentPanelTest to use new forArch method

19 months agoJAL-4154 Add Platform.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.

19 months agoMerge branch 'patch/JAL-4153_flakyJvCacheableInputBoxTest' into develop
James Procter [Thu, 23 Mar 2023 11:52:19 +0000 (11:52 +0000)]
Merge branch 'patch/JAL-4153_flakyJvCacheableInputBoxTest' into develop

19 months agoJAL-4153 longer Thread.sleep() calls in the hope that the test might pass on Bamboo
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

19 months agoJAL-4150 test and quick patch copying code from AlignFrame.paste() to Desktop.paste...
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

20 months agoJAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of...
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

20 months agoJAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of...
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?)

20 months agoMerge branch 'features/JAL-3858_PAEsInProjects' into develop
James Procter [Fri, 24 Feb 2023 15:26:30 +0000 (15:26 +0000)]
Merge branch 'features/JAL-3858_PAEsInProjects' into develop

20 months agoMerge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects features/JAL-3858_PAEsInProjects
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

20 months agoJAL-629 better test fixes. --props=... instead of --debug
Ben Soares [Fri, 24 Feb 2023 12:54:35 +0000 (12:54 +0000)]
JAL-629 better test fixes. --props=... instead of --debug

20 months agoJAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code...
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

20 months agoJAL-629 test fixing
Ben Soares [Thu, 23 Feb 2023 19:21:24 +0000 (19:21 +0000)]
JAL-629 test fixing

20 months agoJAL-629 Add debug messages for more failing tests
Ben Soares [Thu, 23 Feb 2023 17:01:05 +0000 (17:01 +0000)]
JAL-629 Add debug messages for more failing tests

20 months agoJAL-629 fixed a Log4j test by adding --debug arg
Ben Soares [Thu, 23 Feb 2023 16:21:49 +0000 (16:21 +0000)]
JAL-629 fixed a Log4j test by adding --debug arg

20 months agoJAL-629 bootstrap args and properties. Remember index of args for 'previous structure...
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

20 months agoJAL-629 nf-core sample alignment files and a2m versions
Ben Soares [Thu, 23 Feb 2023 16:19:25 +0000 (16:19 +0000)]
JAL-629 nf-core sample alignment files and a2m versions

20 months agoJAL-629 fix a PAEMatrix casting error
Ben Soares [Thu, 23 Feb 2023 16:18:40 +0000 (16:18 +0000)]
JAL-629 fix a PAEMatrix casting error

20 months agoJAL-3858 new MatrixType JAX-RI POJO
James Procter [Thu, 23 Feb 2023 12:08:00 +0000 (12:08 +0000)]
JAL-3858 new MatrixType JAX-RI POJO

20 months agoJAL-4133 update validChar width when font is changed so characters are suppressed...
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

20 months agoJAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project
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

20 months agoJAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset...
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.

20 months agoJAL-1551 source formatting
James Procter [Wed, 22 Feb 2023 14:24:04 +0000 (14:24 +0000)]
JAL-1551 source formatting

20 months agoJAL-3858 simple test for PAE matrix recovery
James Procter [Wed, 22 Feb 2023 14:23:56 +0000 (14:23 +0000)]
JAL-3858 simple test for PAE matrix recovery

20 months agoJAL-3858 construct a PAE direct from float array
James Procter [Wed, 22 Feb 2023 14:23:15 +0000 (14:23 +0000)]
JAL-3858 construct a PAE direct from float array

20 months agoMerge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Wed, 22 Feb 2023 14:04:25 +0000 (14:04 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629

20 months agoJAL-4064 JAL-4054 Corrected the tgz top-level dir from './Contents' to 'Contents...
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).

20 months agoJAL-629 make sure we show GUI when not driven programmatically
James Procter [Wed, 22 Feb 2023 13:34:54 +0000 (13:34 +0000)]
JAL-629 make sure we show GUI when not driven programmatically

20 months agoJAL-4095 slightly better threshold setting and todos for improvement
James Procter [Wed, 22 Feb 2023 12:43:25 +0000 (12:43 +0000)]
JAL-4095 slightly better threshold setting and todos for improvement

20 months agoJAL-4095 magic fill behaviour is PAE specific
James Procter [Wed, 22 Feb 2023 12:42:58 +0000 (12:42 +0000)]
JAL-4095 magic fill behaviour is PAE specific

20 months agoMerge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Wed, 22 Feb 2023 12:40:43 +0000 (12:40 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629

20 months agoJAL-3858 JAL-2381 allow different linear shading schemes for selected/non-selected...
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

20 months agoJAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type...
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

20 months agoJAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS
Ben Soares [Tue, 21 Feb 2023 13:41:37 +0000 (13:41 +0000)]
JAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS

20 months agoJAL-3416 Turn off (partial) flatlaf scaling for HiDPI in Linux and Java 8 - Some...
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

20 months agoJAL-4064 JAL-4054 Correct names of mac arch installer DMG files
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

20 months agoMerge branch 'develop' into improvement/JAL-4111_suffixed_DEVELOP_channels improvement/JAL-4111_suffixed_DEVELOP_channels
Ben Soares [Mon, 20 Feb 2023 15:42:14 +0000 (15:42 +0000)]
Merge branch 'develop' into improvement/JAL-4111_suffixed_DEVELOP_channels

20 months agoJAL-4128 Catch RasterFormatException caused whilst resizing Overview window, recalcul... bug/JAL-4128_resizing_overview_with_solid_drags_causes_exception
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.

20 months agoMerge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_p... bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
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

20 months agoMerge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
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

20 months agoJAL-1713 don’t close an automatically created overview window for projects from Jalvi...
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

20 months agoMerge branch 'develop' into feature/JAL-1713_overviewInProject
James Procter [Wed, 15 Feb 2023 15:25:53 +0000 (15:25 +0000)]
Merge branch 'develop' into feature/JAL-1713_overviewInProject

20 months agoPassing test for JAL-4127 failing on the JAL-1713 branch
James Procter [Wed, 15 Feb 2023 14:43:32 +0000 (14:43 +0000)]
Passing test for JAL-4127 failing on the JAL-1713 branch

20 months agoJAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list...
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

20 months agoMerge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_p...
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

20 months agoJAL-4125 Spanish translations
Ben Soares [Mon, 13 Feb 2023 22:41:51 +0000 (22:41 +0000)]
JAL-4125 Spanish translations

20 months agoMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into bug/JAL-4125_f...
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

20 months agoJAL-4125 Move confirmation of closing external viewer windows into the quit handler...
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.

20 months agoMerge branch 'develop' into feature/JAL-1713_overviewInProject
James Procter [Mon, 13 Feb 2023 17:28:45 +0000 (17:28 +0000)]
Merge branch 'develop' into feature/JAL-1713_overviewInProject

20 months agoJAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved...
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!)

20 months agoFix for JAL-4126 - don’t automatically create a threshold line when no threshold...
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

20 months agoJAL-4126 comment out closeAll - so we can visually check the alignment frame as it...
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

20 months agoJAL-4126 failing test - colour scheme appears to be being created and configured...
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.

20 months agoJAL-4125 Additions to JvOptionPane and QuitHandler with StructureViewerBase handling...
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.

20 months agoJAL-629 Fasta sequence id reading whitespace fix. Flexioble pae json keys and structu...
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.

20 months agoJAL-629 "updated" json-simple
Ben Soares [Fri, 3 Feb 2023 20:57:43 +0000 (20:57 +0000)]
JAL-629 "updated" json-simple

20 months agoJAL-1551 remove temp file in src
James Procter [Fri, 3 Feb 2023 14:18:44 +0000 (14:18 +0000)]
JAL-1551 remove temp file in src

20 months agoMerge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
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

21 months agoJAL-1713 update from Jalview 2.11.3 develop
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

21 months agoJAL-1988 Make sensible choices if only the opening file has been opened, and alter... merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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

21 months agoJAL-4118 remove unnecessary sleep from QuitHandlerTest
Ben Soares [Thu, 26 Jan 2023 17:06:40 +0000 (17:06 +0000)]
JAL-4118 remove unnecessary sleep from QuitHandlerTest

21 months agoJAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possib...
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.

21 months agoJAL-1988 Add a sleep to file save test to give time for file to save
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

21 months agoJAL-629 example files from nf-core
Ben Soares [Thu, 26 Jan 2023 11:10:37 +0000 (11:10 +0000)]
JAL-629 example files from nf-core

21 months agoJAL-629 helper eclipse CLI run
Ben Soares [Thu, 26 Jan 2023 11:10:04 +0000 (11:10 +0000)]
JAL-629 helper eclipse CLI run

21 months agoJAL-629 adjust arg type for tempfac-shading -- was grabbing next argument
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

21 months agoJAL-4116 relegate the failed to promote warning to Console.debug so most users won...
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).

21 months agoMerge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
James Procter [Wed, 25 Jan 2023 13:05:54 +0000 (13:05 +0000)]
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop

21 months agoJAL-4090 Release 2.11.3.0 release notes and version bump
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

21 months agoMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into develop
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

21 months agoJAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequen...
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

21 months agoJAL-629 suggest not breaking out of the structure processing loop if just one structu...
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..

21 months agoJAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure...
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

21 months agoJAL-629 don’t carry on Jalview.main if we’ve already processed command line args...
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

21 months agoJAL-629 don’t trash user’s system property file when adjusting settings to process...
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

21 months agoJAL-629 don’t complain for Unary args
James Procter [Tue, 24 Jan 2023 07:46:53 +0000 (07:46 +0000)]
JAL-629 don’t complain for Unary args

21 months agoJAL-629 labelled breaks are frowned upon by everyone
James Procter [Tue, 24 Jan 2023 07:46:34 +0000 (07:46 +0000)]
JAL-629 labelled breaks are frowned upon by everyone

21 months agoMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into features/r2_11_2_alp...
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

21 months agoMerge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphaf... features/r2_11_2_alphafold/JAL-2349_JAL-3855
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

21 months agoJAL-629 Attempts to add PAE to structure. --headless working. Make HTML output single...
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.

21 months agoJAL-4104 JAL-4102 update help docs with script to add jalview command line tool to... Release_2_11_2_6
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

21 months agoJAL-4102 whatsNew for 2.11.2.6
Jim Procter [Mon, 23 Jan 2023 09:32:43 +0000 (09:32 +0000)]
JAL-4102 whatsNew for 2.11.2.6

21 months agoMerge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
Jim Procter [Fri, 20 Jan 2023 23:40:08 +0000 (23:40 +0000)]
Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop

21 months agoJAL-4114 model_page_url not required in v2.0 response patch/JAL-4114_updated_3dbeacons_api
Jim Procter [Fri, 20 Jan 2023 23:39:28 +0000 (23:39 +0000)]
JAL-4114 model_page_url not required in v2.0 response

21 months agoJAL-4102 update date and release notes for 2.11.2.6
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

21 months agoMerge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
Jim Procter [Fri, 20 Jan 2023 22:53:26 +0000 (22:53 +0000)]
Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop

21 months agoMerge branch 'patch/Release_2_11_2_6_Branch' 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

21 months agoJAL-2353 primary ref candidates that should be promoted should preserve original... patch/Release_2_11_2_6_Branch
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

21 months agoJAL-4114 missing mock server response
Jim Procter [Fri, 20 Jan 2023 20:44:47 +0000 (20:44 +0000)]
JAL-4114 missing mock server response

21 months agoJAL-4114 only rank model qualities that are computed with the same method, and uprank...
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

21 months agoJAL-4114 alphafold now marked as AB-INITIO so adjust ranking in categories
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

21 months agoJAL-4114 additional warnings when PDBe doesn’t return as many responses as queries...
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

21 months agoJAL-4114 patch REST client for changed JSON schema in 3D beacons v2 API
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

21 months agoJAL-4114 formatting
Jim Procter [Fri, 20 Jan 2023 17:49:16 +0000 (17:49 +0000)]
JAL-4114 formatting

21 months agoJAL-4114 updated mock tests and responses for v2.0 api
Jim Procter [Fri, 20 Jan 2023 17:48:04 +0000 (17:48 +0000)]
JAL-4114 updated mock tests and responses for v2.0 api

21 months agoJAL-629 make sequence id key 'seqid'
Ben Soares [Wed, 18 Jan 2023 15:52:10 +0000 (15:52 +0000)]
JAL-629 make sequence id key 'seqid'

21 months agoJAL-3416 No longer needed
Ben Soares [Tue, 17 Jan 2023 17:01:45 +0000 (17:01 +0000)]
JAL-3416 No longer needed

21 months agoMerge branch 'develop' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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

21 months agoJAL-3416 More tweaking of FlatLaf. Problem with macOS themed FlatLaf solved with...
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

21 months agoJAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as 'all saved' after initial opening
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

21 months agoJAL-629 added Alphafold cif, pdb and PAE json files to examples/AlphaFold
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