jalview.git
3 months agoMerge branch 'develop' into features/JAL-34_comparing_msas features/JAL-34_comparing_msas features/JAL-4366_foldseek_3di_viewing
James Procter [Tue, 23 Jan 2024 15:14:07 +0000 (15:14 +0000)]
Merge branch 'develop' into features/JAL-34_comparing_msas

3 months agoJAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is...
James Procter [Wed, 10 Jan 2024 15:51:52 +0000 (15:51 +0000)]
JAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is in progress

3 months agoMerge branch 'features/JAL-4366_foldseek_3di_viewing' into features/JAL-34_comparing_msas
James Procter [Tue, 23 Jan 2024 14:42:58 +0000 (14:42 +0000)]
Merge branch 'features/JAL-4366_foldseek_3di_viewing' into features/JAL-34_comparing_msas

3 months agoJAL-4371 minimal test and move PDBEntryUtils to correct package
James Procter [Tue, 23 Jan 2024 14:41:59 +0000 (14:41 +0000)]
JAL-4371 minimal test and move PDBEntryUtils to correct package

3 months agoJAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is...
James Procter [Wed, 10 Jan 2024 15:51:52 +0000 (15:51 +0000)]
JAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is in progress

3 months agoJAL-4369 uniprotkb - try to avoid another redirect response
James Procter [Wed, 10 Jan 2024 10:26:26 +0000 (10:26 +0000)]
JAL-4369 uniprotkb - try to avoid another redirect response

3 months agoJAL-4369 use rest.uniprot.org as fetch domain
James Procter [Tue, 9 Jan 2024 18:36:12 +0000 (18:36 +0000)]
JAL-4369 use rest.uniprot.org as fetch domain
t pu# Please enter the commit message for your changes. Lines starting

3 months agoMerge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executa...
James Procter [Tue, 23 Jan 2024 13:39:04 +0000 (13:39 +0000)]
Merge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch' into develop

3 months agoMerge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' into...
James Procter [Tue, 23 Jan 2024 13:34:35 +0000 (13:34 +0000)]
Merge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' into develop

3 months agoJAL-4373 Setting the jvmmempc and jvmmemmax strings from the Arg.getName() for consis... bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch
Ben Soares [Fri, 19 Jan 2024 17:00:46 +0000 (17:00 +0000)]
JAL-4373 Setting the jvmmempc and jvmmemmax strings from the Arg.getName() for consistency. Updated some comments.

3 months agoJAL-4373 Fix Main-Class and other attribute settings in the shadowJar manifest. It...
Ben Soares [Fri, 19 Jan 2024 16:11:14 +0000 (16:11 +0000)]
JAL-4373 Fix Main-Class and other attribute settings in the shadowJar manifest. It requires a 'dummy' Jar task with the correct settings.

3 months agoJAL-34 fix up comparison annotation so it gets shown and scaled properly
James Procter [Thu, 18 Jan 2024 17:34:24 +0000 (17:34 +0000)]
JAL-34 fix up comparison annotation so it gets shown and scaled properly

3 months agoJAL-34 mouse over ruler in one alignment highlights location of aligned positions...
James Procter [Thu, 18 Jan 2024 10:08:17 +0000 (10:08 +0000)]
JAL-34 mouse over ruler in one alignment highlights location of aligned positions in the other alignment. Really notice a need to allow those positions to be persisted without ultraprecise mouse control

3 months agoJAL-34 - quick hack to see how we can do alignment comparison for splitframes linking...
James Procter [Wed, 17 Jan 2024 18:14:37 +0000 (18:14 +0000)]
JAL-34 - quick hack to see how we can do alignment comparison for splitframes linking 1:1 mapped alignments

3 months agoJAL-4366 JAL-728 show 3di-Mat based quality in the overview when gecos-3di is enabled
James Procter [Tue, 16 Jan 2024 17:28:40 +0000 (17:28 +0000)]
JAL-4366 JAL-728 show 3di-Mat based quality in the overview when gecos-3di is enabled

3 months agoJAL-4366 JAL-728 simple hack to use 3di matrix when gecos-3di is enabled
James Procter [Tue, 16 Jan 2024 17:28:04 +0000 (17:28 +0000)]
JAL-4366 JAL-728 simple hack to use 3di matrix when gecos-3di is enabled

3 months agoJAL-4366 JAL-4371 allow cruft after inferred pdb ids, ex 1xyz_A.pdb yields 1xyzA
James Procter [Mon, 15 Jan 2024 17:16:03 +0000 (17:16 +0000)]
JAL-4366 JAL-4371 allow cruft after inferred pdb ids, ex 1xyz_A.pdb yields 1xyzA

3 months agoJAL-4366 JAL-3947 avoid ambiguity for multi character chain codes in mapping test
James Procter [Sun, 14 Jan 2024 15:05:43 +0000 (15:05 +0000)]
JAL-4366 JAL-3947 avoid ambiguity for multi character chain codes in mapping test

3 months agoJAL-4366 JAL-4371 tighten up detection of chain code and allow two-character codes...
James Procter [Sun, 14 Jan 2024 15:05:10 +0000 (15:05 +0000)]
JAL-4366 JAL-4371 tighten up detection of chain code and allow two-character codes JAL-3947

3 months agoJAL-4366 revive broken alignDNAasDNA test
James Procter [Sun, 14 Jan 2024 15:03:13 +0000 (15:03 +0000)]
JAL-4366 revive broken alignDNAasDNA test

3 months agoJAL-4366 JAL-4371 fix imports
James Procter [Sun, 14 Jan 2024 13:43:16 +0000 (13:43 +0000)]
JAL-4366 JAL-4371 fix imports

3 months agoJAL-4366 avoid corrupting map when no complete mapping available for chain to sequence
James Procter [Sun, 14 Jan 2024 13:35:29 +0000 (13:35 +0000)]
JAL-4366 avoid corrupting map when no complete mapping available for chain to sequence

3 months agoJAL-4366 JAL-4371 refactor and fix up code inferring potential PDB IDs & Chaincode...
James Procter [Sun, 14 Jan 2024 13:33:57 +0000 (13:33 +0000)]
JAL-4366 JAL-4371  refactor and fix up code inferring potential PDB IDs & Chaincode from ID strings to PDBEntryUtils

3 months agoJAL-4366 provide options for updating (or not) the linked alignment or existing align...
James Procter [Fri, 12 Jan 2024 14:04:12 +0000 (14:04 +0000)]
JAL-4366 provide options for updating (or not) the linked alignment or existing alignment when opening a split frame

3 months agoJAL-4366 fixed wrinkles in reconstructing peptide alignment using 3di alignment.... spikes/JAL-4366_3di_msa_forfoldseeks
James Procter [Fri, 12 Jan 2024 11:50:57 +0000 (11:50 +0000)]
JAL-4366 fixed wrinkles in reconstructing peptide alignment using 3di alignment. Need to work though UX paths to ensure all different combinations work

3 months agoJAL-4366 fix reconstruction of peptide alignment...
James Procter [Thu, 11 Jan 2024 17:17:15 +0000 (17:17 +0000)]
JAL-4366 fix reconstruction of peptide alignment...

3 months agoJAL-4366 test reconstruction of peptide alignment given 3di alignment and peptide...
James Procter [Thu, 11 Jan 2024 17:16:57 +0000 (17:16 +0000)]
JAL-4366 test reconstruction of peptide alignment given 3di alignment and peptide seqs

3 months agoJAL-4366 use dataset sequences for building the mapping
James Procter [Thu, 11 Jan 2024 17:16:28 +0000 (17:16 +0000)]
JAL-4366 use dataset sequences for building the mapping

3 months agoJAL-4371 make the PDB fetcher use simple naming 1xyzA when retrieving 1xyz:A from...
James Procter [Thu, 11 Jan 2024 17:15:20 +0000 (17:15 +0000)]
JAL-4371 make the PDB fetcher use simple naming 1xyzA when retrieving 1xyz:A from PDBe - configure via PDB_CHAIN_NAME = (SIMPLE|LEGACY)

3 months agoJAL-3466 higher ‘crummy alignment’ threshold when deciding to create an identity...
James Procter [Thu, 11 Jan 2024 15:30:35 +0000 (15:30 +0000)]
JAL-3466 higher ‘crummy alignment’ threshold when deciding to create an identity mapping for PDB with exact length match to a sequence in the alignment

3 months agoJAL-4366 remove some tortuous repetition in computeMapping, so SIFTs failures result...
James Procter [Thu, 11 Jan 2024 15:15:28 +0000 (15:15 +0000)]
JAL-4366 remove some tortuous repetition in computeMapping, so SIFTs failures result in NW mappings being created in the same way as if sifts mappings was disabled in preferences.

3 months agoJAL-4366 incomplete test verifying a 3di alignment can be reconstructed for a peptide...
James Procter [Thu, 11 Jan 2024 14:45:33 +0000 (14:45 +0000)]
JAL-4366 incomplete test verifying a 3di alignment can be reconstructed for a peptide msa and 3di sequences

3 months agoJAL-4366 new mapping type for 3di/protein sequence relationships
James Procter [Thu, 11 Jan 2024 14:45:01 +0000 (14:45 +0000)]
JAL-4366 new mapping type for 3di/protein sequence relationships

3 months agoJAL-4366 allow a 3di alignment to be loaded and shown as a split frame with existing...
James Procter [Thu, 11 Jan 2024 14:44:32 +0000 (14:44 +0000)]
JAL-4366 allow a 3di alignment to be loaded and shown as a split frame with existing AA alignment

3 months agoJAL-4368 Only set a colour scheme if --colour is given or it's not a JVP file bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately
Ben Soares [Fri, 5 Jan 2024 17:28:36 +0000 (17:28 +0000)]
JAL-4368 Only set a colour scheme if --colour is given or it's not a JVP file

4 months agoJAL-4366 account for 3dmat matrix in tests
James Procter [Sun, 17 Dec 2023 20:25:04 +0000 (20:25 +0000)]
JAL-4366 account for 3dmat matrix in tests

4 months agoJAL-4366 1:1 mapping requires exact sequence length match - still not sufficient...
James Procter [Sat, 16 Dec 2023 08:43:55 +0000 (08:43 +0000)]
JAL-4366 1:1 mapping requires exact sequence length match - still not sufficient for 3di case - will need a molecule type

4 months agoJAL-789 pairwise alignment via calculations dialog, allowing score model to be changed
James Procter [Sat, 16 Dec 2023 08:43:06 +0000 (08:43 +0000)]
JAL-789 pairwise alignment via calculations dialog, allowing score model to be changed

4 months agoJAL-4366 mat3di score model
James Procter [Sat, 16 Dec 2023 08:41:16 +0000 (08:41 +0000)]
JAL-4366 mat3di score model

4 months agoJAL-4366 hacked in a 1:1 mapping
James Procter [Fri, 15 Dec 2023 14:17:24 +0000 (14:17 +0000)]
JAL-4366 hacked in a 1:1 mapping

4 months agoJAL-1551 formatting
James Procter [Fri, 15 Dec 2023 13:57:50 +0000 (13:57 +0000)]
JAL-1551 formatting

4 months agoJAL-4366 build a mapping to a PDBChain with an arbitrary SequenceMapping
James Procter [Fri, 15 Dec 2023 13:56:57 +0000 (13:56 +0000)]
JAL-4366 build a mapping to a PDBChain with an arbitrary SequenceMapping

4 months agoJAL-4366 compute coverage on each side of the pairwise alignment
James Procter [Fri, 15 Dec 2023 13:56:07 +0000 (13:56 +0000)]
JAL-4366 compute coverage on each side of the pairwise alignment

4 months agoJAL-4356 update release notes
James Procter [Thu, 14 Dec 2023 15:39:20 +0000 (15:39 +0000)]
JAL-4356 update release notes

4 months agoMerge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...
James Procter [Thu, 14 Dec 2023 15:28:08 +0000 (15:28 +0000)]
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into develop

4 months agoMerge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...
James Procter [Tue, 12 Dec 2023 20:55:49 +0000 (20:55 +0000)]
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment

4 months agoJAL-4353 wait for files to be written fully before comparing size with older file
James Procter [Tue, 12 Dec 2023 17:20:04 +0000 (17:20 +0000)]
JAL-4353 wait for files to be written fully before comparing size with older file

4 months agoJAL-4217 singleThread all tests
James Procter [Tue, 12 Dec 2023 17:18:48 +0000 (17:18 +0000)]
JAL-4217 singleThread all tests

4 months agoMerge branch 'bug/JAL-2934proportionalScrolling' into develop
James Procter [Thu, 14 Dec 2023 14:16:38 +0000 (14:16 +0000)]
Merge branch 'bug/JAL-2934proportionalScrolling' into develop

4 months agoMerge branch 'develop' into bug/JAL-2934proportionalScrolling bug/JAL-2934proportionalScrolling
James Procter [Thu, 14 Dec 2023 14:14:15 +0000 (14:14 +0000)]
Merge branch 'develop' into bug/JAL-2934proportionalScrolling

4 months agoJAL-4353 bigger tighter test
Ben Soares [Tue, 12 Dec 2023 17:49:35 +0000 (17:49 +0000)]
JAL-4353 bigger tighter test

4 months agoJAL-4217 don’t try and export an image when Jmol is also trying to repaint
James Procter [Tue, 12 Dec 2023 17:17:17 +0000 (17:17 +0000)]
JAL-4217 don’t try and export an image when Jmol is also trying to repaint

4 months agoMerge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...
Ben Soares [Tue, 12 Dec 2023 17:13:45 +0000 (17:13 +0000)]
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' of https://source.jalview.org/git/jalview into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment

4 months agoMerge branch 'develop' into bug/JAL-4353_cannot_output_multiple_different_structure_i...
James Procter [Tue, 12 Dec 2023 16:02:14 +0000 (16:02 +0000)]
Merge branch 'develop' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment

4 months agoJAL-4217 close internal frame on the swing thread to avoid deadlock
James Procter [Tue, 12 Dec 2023 15:48:32 +0000 (15:48 +0000)]
JAL-4217 close internal frame on the swing thread to avoid deadlock

4 months agoJAL-4353 helper method and test for primary/secondary and auxiliary arguments with...
Ben Soares [Tue, 12 Dec 2023 15:47:26 +0000 (15:47 +0000)]
JAL-4353 helper method and test for primary/secondary and auxiliary arguments with --structure pdb0 --structureimage png0a --bgcolour col0a --structureimagepng0b --bgcolour col0b --structure pdb1 --...

4 months agoMerge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...
James Procter [Tue, 12 Dec 2023 12:37:04 +0000 (12:37 +0000)]
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into develop

4 months agoJAL-4353 failing test
James Procter [Tue, 12 Dec 2023 12:36:51 +0000 (12:36 +0000)]
JAL-4353 failing test

4 months agoJAL-4353 fix assert that successive test output files get bigger in structureImageOut...
James Procter [Tue, 12 Dec 2023 12:36:36 +0000 (12:36 +0000)]
JAL-4353 fix assert that successive test output files get bigger in structureImageOutputTest and argFilesGlobAndSubstitutionsTest

4 months agoJAL-4192 more specific info about versions needed
James Procter [Mon, 11 Dec 2023 17:31:38 +0000 (17:31 +0000)]
JAL-4192 more specific info about versions needed

4 months agoJAL-4353 re-used random color code
Ben Soares [Wed, 6 Dec 2023 22:00:06 +0000 (22:00 +0000)]
JAL-4353 re-used random color code

4 months agoJAL-4353 Preserve the user given 'linkedId' with ArgValue, to help with deciding...
Ben Soares [Wed, 6 Dec 2023 17:41:35 +0000 (17:41 +0000)]
JAL-4353 Preserve the user given 'linkedId' with ArgValue, to help with deciding if user deliberately set a wildcard linkedId (or --all), to inform value of sub-args.

4 months agoJAL-4356 bump RELEASE
James Procter [Wed, 6 Dec 2023 14:37:04 +0000 (14:37 +0000)]
JAL-4356 bump RELEASE

4 months agoJAL-4356 new release notes and whats new for 2.11.3.3 and JAL-840 release notes
James Procter [Wed, 6 Dec 2023 14:21:11 +0000 (14:21 +0000)]
JAL-4356 new release notes and whats new for 2.11.3.3 and JAL-840 release notes

4 months agoMerge branch 'patch/JAL-840_clustalx_docs_fix' into develop
James Procter [Wed, 6 Dec 2023 14:14:12 +0000 (14:14 +0000)]
Merge branch 'patch/JAL-840_clustalx_docs_fix' into develop

4 months agoMerge branch 'bug/JAL-2934proportionalScrolling' into develop
James Procter [Wed, 6 Dec 2023 13:48:54 +0000 (13:48 +0000)]
Merge branch 'bug/JAL-2934proportionalScrolling' into develop

4 months agoJAL-4353 Add a 'random' colour to produce a random colour.
Ben Soares [Wed, 6 Dec 2023 11:02:32 +0000 (11:02 +0000)]
JAL-4353 Add a 'random' colour to produce a random colour.

4 months agoJAL-4353 Add secondary Types for Args, for STRUCTUREIMAGE Type and restrict structure...
Ben Soares [Tue, 5 Dec 2023 14:15:53 +0000 (14:15 +0000)]
JAL-4353 Add secondary Types for Args, for STRUCTUREIMAGE Type and restrict structureimages between structures on the same open alignment

5 months agoJAL-4243 Updated bio.tools record and JSON (version number)
Ben Soares [Fri, 1 Dec 2023 12:05:27 +0000 (12:05 +0000)]
JAL-4243 Updated bio.tools record and JSON (version number)

5 months agoJAL-4351 update release notes for JAL-4342
James Procter [Thu, 30 Nov 2023 16:55:24 +0000 (16:55 +0000)]
JAL-4351 update release notes for JAL-4342

5 months agoMerge branch 'patch/JAL-4342_emptyannotationsexport' into develop
James Procter [Thu, 30 Nov 2023 16:51:09 +0000 (16:51 +0000)]
Merge branch 'patch/JAL-4342_emptyannotationsexport' into develop

5 months agoJAL-4342 test and patch checking annotation csv export contains the annotations on... patch/JAL-4342_emptyannotationsexport
James Procter [Thu, 30 Nov 2023 15:39:14 +0000 (15:39 +0000)]
JAL-4342 test and patch checking annotation csv export contains the annotations on the alignment or a specific exported annotation

5 months agoPatch fixes JAL-4165 - added to release notes JAL-4351
James Procter [Thu, 30 Nov 2023 15:17:41 +0000 (15:17 +0000)]
Patch fixes JAL-4165 - added to release notes JAL-4351

5 months agoJAL-4351 2.11.3.2 scheduled for 1st December release
James Procter [Thu, 30 Nov 2023 15:06:04 +0000 (15:06 +0000)]
JAL-4351 2.11.3.2 scheduled for 1st December release

5 months agoMerge branch 'bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_squa...
James Procter [Thu, 30 Nov 2023 14:32:45 +0000 (14:32 +0000)]
Merge branch 'bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square-FIXED_from_develop' into develop

5 months agoJAL-4344 careful application of -Djava.awt.headless=true to avoid Jmol problem. Using...
Ben Soares [Thu, 30 Nov 2023 12:51:54 +0000 (12:51 +0000)]
JAL-4344 careful application of -Djava.awt.headless=true to avoid Jmol problem. Using -Dapple.awt.headless=true instead for macOS. Fixed in install and conda shell scripts and also in jalview.bin.Launcher.

5 months agoJAL-4343 fix insufficient-caffeine error - add whats new for 2.11.3.1
James Procter [Wed, 22 Nov 2023 10:43:58 +0000 (10:43 +0000)]
JAL-4343 fix insufficient-caffeine error - add whats new for 2.11.3.1

5 months agoJAL-4343 release today, update notes for JAL-4348 and what’s new for release
James Procter [Wed, 22 Nov 2023 10:38:41 +0000 (10:38 +0000)]
JAL-4343 release today, update notes for JAL-4348 and what’s new for release

5 months agoMerge branch 'patch/JAL-4345_pae_epas1_doubleclick' into develop
James Procter [Wed, 22 Nov 2023 10:28:18 +0000 (10:28 +0000)]
Merge branch 'patch/JAL-4345_pae_epas1_doubleclick' into develop

5 months agoJAL-4345 patch and release notes patch/JAL-4345_pae_epas1_doubleclick
James Procter [Tue, 21 Nov 2023 18:02:57 +0000 (18:02 +0000)]
JAL-4345 patch and release notes

5 months agoJAL-4348 Add newer versions of Chimera and ChimeraX to the version whitelist
Ben Soares [Mon, 20 Nov 2023 13:40:53 +0000 (13:40 +0000)]
JAL-4348 Add newer versions of Chimera and ChimeraX to the version whitelist

5 months agoJAL-4343 patch for JAL-4347 uniprot non-pos feature parsing
James Procter [Mon, 20 Nov 2023 11:34:03 +0000 (11:34 +0000)]
JAL-4343 patch for JAL-4347 uniprot non-pos feature parsing

5 months agoJAL-4343 release notes for JAL-4340 and JAL-4243
James Procter [Fri, 17 Nov 2023 16:05:27 +0000 (16:05 +0000)]
JAL-4343 release notes for JAL-4340 and JAL-4243

5 months agoJAL-4343 bump version
James Procter [Fri, 17 Nov 2023 16:01:01 +0000 (16:01 +0000)]
JAL-4343 bump version

5 months agoJAL-4243 Updated bio.tools record for 2.11.3.0
Ben Soares [Thu, 16 Nov 2023 20:03:30 +0000 (20:03 +0000)]
JAL-4243 Updated bio.tools record for 2.11.3.0

5 months agoJAL-4340 Change launch scripts to be xresources to set executable permission bit...
Ben Soares [Thu, 16 Nov 2023 11:34:50 +0000 (11:34 +0000)]
JAL-4340 Change launch scripts to be xresources to set executable permission bit where needed

5 months agoJAL-4090 JAL-4334 patch in release notes
James Procter [Wed, 15 Nov 2023 16:16:27 +0000 (16:16 +0000)]
JAL-4090 JAL-4334 patch in release notes

5 months agoMerge branch 'bug/JAL-4334_unknownstartenduniprotfeatures' into develop
James Procter [Wed, 15 Nov 2023 16:10:02 +0000 (16:10 +0000)]
Merge branch 'bug/JAL-4334_unknownstartenduniprotfeatures' into develop

5 months agoMerge branch 'patch/JAL-4222_100s_timeout_on_imagexport' into develop
James Procter [Wed, 15 Nov 2023 16:09:35 +0000 (16:09 +0000)]
Merge branch 'patch/JAL-4222_100s_timeout_on_imagexport' into develop

5 months agoJAL-4273 actually pass startSeq etc on to rendering code when rendering for image...
James Procter [Wed, 15 Nov 2023 15:33:06 +0000 (15:33 +0000)]
JAL-4273 actually pass startSeq etc on to rendering code when rendering for image export

5 months agoJAL-4090 fix up release notes new known issues
James Procter [Wed, 15 Nov 2023 15:24:40 +0000 (15:24 +0000)]
JAL-4090 fix up release notes new known issues

5 months agoJAL-4222 bail if we wait too long for Jmol to save an image patch/JAL-4222_100s_timeout_on_imagexport
James Procter [Wed, 15 Nov 2023 15:02:43 +0000 (15:02 +0000)]
JAL-4222 bail if we wait too long for Jmol to save an image

5 months agoJAL-4090 blocker patch JAL-3772 tidy up groovy console when closed rather than callin...
James Procter [Wed, 15 Nov 2023 14:54:31 +0000 (14:54 +0000)]
JAL-4090 blocker patch JAL-3772 tidy up groovy console when closed rather than calling its exit and hanging

5 months agoJAL-4090 JAL-4334 position status when start, end or pos is unknown is stored in... bug/JAL-4334_unknownstartenduniprotfeatures
James Procter [Wed, 15 Nov 2023 14:31:08 +0000 (14:31 +0000)]
JAL-4090 JAL-4334 position status when start, end or pos is unknown is stored in start_status,end_status,pos_status properties

5 months agoJAL-4090 JAL-4338 known defect
James Procter [Wed, 15 Nov 2023 11:54:33 +0000 (11:54 +0000)]
JAL-4090 JAL-4338 known defect

5 months agoJAL-4090 release 15th November 2023
James Procter [Wed, 15 Nov 2023 11:48:43 +0000 (11:48 +0000)]
JAL-4090 release 15th November 2023

5 months agoJAL-4090 JAL-3858 fix up PAE docs - drop the EBI image example
James Procter [Wed, 15 Nov 2023 11:48:30 +0000 (11:48 +0000)]
JAL-4090 JAL-3858 fix up PAE docs - drop the EBI image example

5 months agoJAL-4090 JAL-1551 source license
James Procter [Mon, 13 Nov 2023 18:36:35 +0000 (18:36 +0000)]
JAL-4090 JAL-1551 source license

5 months agoJAL-4090 relese date 14th Nov 2023
James Procter [Mon, 13 Nov 2023 18:16:46 +0000 (18:16 +0000)]
JAL-4090 relese date 14th Nov 2023

5 months agoJAL-4236 don’t look for headers in JalviewJS
James Procter [Mon, 13 Nov 2023 17:19:11 +0000 (17:19 +0000)]
JAL-4236 don’t look for headers in JalviewJS