Jim Procter [Fri, 15 Nov 2024 17:08:29 +0000 (17:08 +0000)]
Merge branch 'spikes/JAL-4366_3di_msa_forfoldseeks' into spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure
Conflicts:
resources/lang/Messages.properties
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
src/jalview/api/AlignViewportI.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/gui/CalculationChooser.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/workers/SecondaryStructureConsensusThread.java
Jim Procter [Fri, 15 Nov 2024 13:55:47 +0000 (13:55 +0000)]
Merge branch 'develop' into features/JAL-4366_foldseek_3di_viewing
Jim Procter [Wed, 13 Nov 2024 18:19:44 +0000 (18:19 +0000)]
JAL-2275 JAL-3921 JAL-4077 release notes JAL-4090
Jim Procter [Wed, 13 Nov 2024 18:16:58 +0000 (18:16 +0000)]
Merge branch 'patch/JAL-4077_jmolsaveloadwindows' into develop
Jim Procter [Wed, 13 Nov 2024 16:00:35 +0000 (16:00 +0000)]
JAL-4077 JAL-1551 formatting
Jim Procter [Wed, 13 Nov 2024 16:00:22 +0000 (16:00 +0000)]
JAL-4077 JAL-3921 TRACE level reporting of Jmol modelfilenames
Jim Procter [Wed, 13 Nov 2024 15:59:36 +0000 (15:59 +0000)]
JAL-3921 escape and transform file paths for Jmol scripting environment
Jim Procter [Wed, 13 Nov 2024 15:58:51 +0000 (15:58 +0000)]
JAL-4077 JAL-3921 match up transformed windows filepaths in Jmol's datamodel to original path in Jalview so associations work
Jim Procter [Wed, 13 Nov 2024 15:54:59 +0000 (15:54 +0000)]
JAL-4077 translate between Java/windows and Jmol 14.31.53 script/internal model representation of local and network file paths
Jim Procter [Tue, 12 Nov 2024 15:37:59 +0000 (15:37 +0000)]
JAL-4077 additional trace output to help track down temporary files saved/loaded for sesions
Jim Procter [Tue, 12 Nov 2024 15:36:44 +0000 (15:36 +0000)]
JAL-4077 JAL-3921 even more generous incremental backoff and warnings to log and GUI if the saved structure session file was zero length
Jim Procter [Tue, 12 Nov 2024 12:51:14 +0000 (12:51 +0000)]
JAL-4077 patched sessionSave(File ) command and test for Jmol so it actually escapes backslashes
Jim Procter [Mon, 11 Nov 2024 17:41:44 +0000 (17:41 +0000)]
JAL-4482 JAL-4490 release notes
Jim Procter [Mon, 11 Nov 2024 17:37:28 +0000 (17:37 +0000)]
Merge branch 'bug/JAL-4482_gradle_task_linkCheck_fails' into develop
Jim Procter [Mon, 11 Nov 2024 16:34:19 +0000 (16:34 +0000)]
JAL-4490 JAL-4474 release notes (preemptive but hopeful that it works!)
Jim Procter [Mon, 11 Nov 2024 16:32:19 +0000 (16:32 +0000)]
Merge branch 'JAL-4474_jalview.ps1_not_working' into develop
Jim Procter [Mon, 11 Nov 2024 16:05:09 +0000 (16:05 +0000)]
JAL-4490 release notes for JAL-4485 et al.
Jim Procter [Mon, 11 Nov 2024 16:03:53 +0000 (16:03 +0000)]
Merge branch 'improvement/JAL-4485_not_finding_chimerax_on_managed_desktop' into develop
Jim Procter [Mon, 11 Nov 2024 16:02:03 +0000 (16:02 +0000)]
JAL-4490 bump version and release notes
Ben Soares [Mon, 11 Nov 2024 15:55:57 +0000 (15:55 +0000)]
JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor
Renia Correya [Thu, 7 Nov 2024 10:09:50 +0000 (10:09 +0000)]
JAL-4435 Menu option and colouring for sec struct providers
Added menu option in tree panel for the users to choose between coloured
lines or labels or none for secondary structure providers in tree panel.
Code changes for using jcolorbrewer colouring palette
Ben Soares [Wed, 6 Nov 2024 14:44:57 +0000 (14:44 +0000)]
JAL-4485 Tests for FileUtils.getMatchingVersionedFilesTest()
Ben Soares [Wed, 6 Nov 2024 12:33:08 +0000 (12:33 +0000)]
JAL-4485 Not using whitelist, just file glob and blacklist
Ben Soares [Wed, 6 Nov 2024 12:32:15 +0000 (12:32 +0000)]
JAL-4485 Better var name and using FileUtils method in StructureManager
Ben Soares [Wed, 6 Nov 2024 12:13:53 +0000 (12:13 +0000)]
JAL-4485 Extracted the whitelist/blacklist fileglob finding code into FileUtils for more generic use
Ben Soares [Wed, 6 Nov 2024 00:52:50 +0000 (00:52 +0000)]
JAL-4485 Fix the template path for Windows Chimera/X executable. Added more debugging for path finding.
Ben Soares [Wed, 6 Nov 2024 00:51:45 +0000 (00:51 +0000)]
JAL-4487 Escape backslash file separators when looking for file globs. Fixed a CLI and a debugging NPE.
Ben Soares [Tue, 5 Nov 2024 17:30:21 +0000 (17:30 +0000)]
JAL-4485 Path fix for macOS Application*s*
Ben Soares [Tue, 5 Nov 2024 16:35:42 +0000 (16:35 +0000)]
JAL-4485 Initially look for all installations of Chimera/X and add to the pathlist if version is not in the blacklist
Ben Soares [Fri, 1 Nov 2024 17:37:54 +0000 (17:37 +0000)]
JAL-4485 Extra debugging for Chimera/X and PyMol launches
Ben Soares [Fri, 1 Nov 2024 11:41:56 +0000 (11:41 +0000)]
JAL-4474 Added -Force option to all Get-Item calls in Readlink-f function in jalview.ps1
James Procter [Tue, 29 Oct 2024 21:32:30 +0000 (21:32 +0000)]
JAL-4473 JAL-4467 release notes
James Procter [Tue, 29 Oct 2024 21:29:09 +0000 (21:29 +0000)]
Merge branch 'bug/JAL-4467_getdownArchive_task_fails' into develop
James Procter [Mon, 28 Oct 2024 16:57:12 +0000 (16:57 +0000)]
JAL-4473 release date 29th Oct 2024
James Procter [Mon, 28 Oct 2024 16:34:18 +0000 (16:34 +0000)]
JAL-4473 release notes for JAL-4380
Ben Soares [Tue, 2 Apr 2024 19:27:50 +0000 (20:27 +0100)]
JAL-4380 Improved annotation tooltips especially secondary structure tooltips
Ben Soares [Tue, 20 Feb 2024 15:35:22 +0000 (15:35 +0000)]
JAL-4380 Added information to annotation tooltips when description is not present
James Procter [Fri, 25 Oct 2024 14:41:49 +0000 (15:41 +0100)]
Merge branch 'patch/fix_JAL-4470_JAL-4471_for_2_11_4_1' into develop
Renia Correya [Fri, 18 Oct 2024 12:06:20 +0000 (13:06 +0100)]
Merge branch 'feature/JAL-4476_reformat_ss_consensus_annotation_labels' into feature/JAL-4386_JAL-4435_reformat_node_labels
Renia Correya [Fri, 18 Oct 2024 11:58:14 +0000 (12:58 +0100)]
Merge branch 'feature/JAL-4386_JAL-4435_coloured_lines_for_providers' into feature/JAL-4386_JAL-4435_reformat_node_labels
Renia Correya [Wed, 16 Oct 2024 13:29:33 +0000 (14:29 +0100)]
JAL-4435 Append numbers to group names if there is a naming conflict
Renia Correya [Wed, 16 Oct 2024 12:59:40 +0000 (13:59 +0100)]
JAL-4435 Added Show Secondary Structure Providers menu in tree panel
THis change is for secondary structure similarity tree panel. Secondary structure providers will be displayed as internal node labels if this menu option is selected. The labels will be displayed only if the node count is greater than 3.
Renia Correya [Fri, 11 Oct 2024 14:56:22 +0000 (15:56 +0100)]
JAL-4435 Added coloured dashed lines for secondary structure providers.
Renia Correya [Tue, 8 Oct 2024 11:45:54 +0000 (12:45 +0100)]
JAL-4476 Reformat secondary structure consensus annotation labels
Renia Correya [Tue, 8 Oct 2024 11:22:06 +0000 (12:22 +0100)]
JAL-4435 Reformatting tree node labels and tree sub group names
Jim Procter [Fri, 4 Oct 2024 16:06:44 +0000 (17:06 +0100)]
JAL-4473 whatsNew 2.11.4.1
Jim Procter [Fri, 4 Oct 2024 15:08:23 +0000 (16:08 +0100)]
JAL-4473 new jalview patch release
Jim Procter [Fri, 4 Oct 2024 15:06:49 +0000 (16:06 +0100)]
fix for JAL-4471 - secondary structure similarity tree can only be computed for sequence-associated annotation(s)
Jim Procter [Fri, 4 Oct 2024 15:03:38 +0000 (16:03 +0100)]
JAL-4470 fix: check for workers!=null before checking its empty...
Ben Soares [Fri, 20 Sep 2024 15:42:53 +0000 (16:42 +0100)]
JAL-4467 Take account of presource and xresource in the getdownArchiveBuild task
Jim Procter [Wed, 18 Sep 2024 01:52:21 +0000 (02:52 +0100)]
JAL-4418 release notes typos
Jim Procter [Wed, 18 Sep 2024 00:27:36 +0000 (01:27 +0100)]
JAL-4418 bump release date to 18th September 2024
Jim Procter [Wed, 18 Sep 2024 00:26:47 +0000 (01:26 +0100)]
JAL-4418 fix up help TOC copypaste error
Jim Procter [Tue, 17 Sep 2024 22:53:40 +0000 (23:53 +0100)]
JAL-4418 more documentation tweaks - getting Jen Fleming's name correct
Jim Procter [Tue, 17 Sep 2024 22:23:57 +0000 (23:23 +0100)]
JAL-4418 JAL-4428 CHANNEL=RELEASE has a different path for the jni jars
Jim Procter [Tue, 17 Sep 2024 20:39:49 +0000 (21:39 +0100)]
JAL-4418 fix link case for linkcheck and window menu documentation update
Jim Procter [Tue, 17 Sep 2024 20:21:28 +0000 (21:21 +0100)]
JAL-4159 pasimap viewer image for docs
Jim Procter [Tue, 17 Sep 2024 20:17:57 +0000 (21:17 +0100)]
JAL-4418 JAL-4090 known defect report for JAL-4349
Jim Procter [Tue, 17 Sep 2024 19:34:33 +0000 (20:34 +0100)]
JAL-4414 JAL-1054 fix irrelevant failing network test for JAL-4418 2.11.4.0 release
Jim Procter [Tue, 17 Sep 2024 16:57:42 +0000 (17:57 +0100)]
Merge branch 'bug/JAL-1054_broken_test' into develop
Jim Procter [Tue, 17 Sep 2024 16:05:09 +0000 (17:05 +0100)]
JAL-4418 documentation for 4461
Jim Procter [Tue, 17 Sep 2024 15:56:03 +0000 (16:56 +0100)]
JAL-4418 documentation for ss annotation row preference and auto show (JAL-4425 JAL-4392)
Jim Procter [Tue, 17 Sep 2024 15:35:20 +0000 (16:35 +0100)]
JAL-4418 JAL-4442 quit racecondition patch
Jim Procter [Tue, 17 Sep 2024 15:32:55 +0000 (16:32 +0100)]
Merge branch 'JAL-4442_cant_quit_jalview_on_windows_11' into develop
Jim Procter [Tue, 17 Sep 2024 15:26:45 +0000 (16:26 +0100)]
JAL-4418 release 2.11.4.0 today!
Jim Procter [Tue, 17 Sep 2024 15:24:53 +0000 (16:24 +0100)]
JAL-4418 JAL-4392 show/hide group associated secondary structure consensus and document autohide of secondary structure consensus
JAL-4464 also knowndefect for not storing/restoring group associated secondary structure consensus
Jim Procter [Tue, 17 Sep 2024 11:09:00 +0000 (12:09 +0100)]
Merge branch 'improvement/JAL-4461_select_format_from_extension' into develop
Jim Procter [Mon, 16 Sep 2024 16:28:09 +0000 (17:28 +0100)]
JAL-4392 JAL-4425 commented out code to allow consensus to be hidden automatically when just one sequence is shown
Jim Procter [Mon, 16 Sep 2024 16:20:46 +0000 (17:20 +0100)]
Merge branch 'patch/JAL-4392_hide_ssconsensus_if_no_data' into develop
Jim Procter [Mon, 16 Sep 2024 15:57:33 +0000 (16:57 +0100)]
Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
Jim Procter [Mon, 16 Sep 2024 15:50:49 +0000 (16:50 +0100)]
JAL-4392 autohide the secondary structure consensus annotation by setting AlignmentAnnotation.hasData to false so it is not displayed in view
Renia Correya [Mon, 16 Sep 2024 14:59:55 +0000 (20:29 +0530)]
JAL-4427 Added test cases and a minor correction
Jim Procter [Mon, 16 Sep 2024 14:39:34 +0000 (15:39 +0100)]
JAL-4392 don't show SS consensus for DNA alignments
Ben Soares [Mon, 16 Sep 2024 08:18:44 +0000 (09:18 +0100)]
JAL-4461 Move SwingUtils to darrylbu.util.SwingUtils, more appropriate
Jim Procter [Fri, 13 Sep 2024 17:09:29 +0000 (18:09 +0100)]
JAL-4418 release notes for JAL-4461 - nb need to document the new option in the built in help
Jim Procter [Fri, 13 Sep 2024 17:06:36 +0000 (18:06 +0100)]
Merge branch 'improvement/JAL-4461_select_format_from_extension' into develop
Ben Soares [Fri, 13 Sep 2024 16:05:24 +0000 (17:05 +0100)]
JAL-4461 Tests for JalviewFileChooser.defaultSaveFileFormat() and a slight fix to the code
Jim Procter [Fri, 13 Sep 2024 15:21:10 +0000 (16:21 +0100)]
Merge branch 'feature/JAL-4386_JAL-4435_trees_from_annotations_on_alignment_2114_update' into trial_merge_JAL-4386
# Conflicts:
# src/jalview/analysis/AAFrequency.java
# src/jalview/analysis/AlignmentUtils.java
# src/jalview/analysis/PaSiMap.java
# src/jalview/analysis/ccAnalysis.java
# src/jalview/analysis/scoremodels/ScoreModels.java
# src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
# src/jalview/api/AlignViewportI.java
# src/jalview/datamodel/SequenceGroup.java
# src/jalview/gui/PaSiMapPanel.java
# src/jalview/gui/PairwiseAlignPanel.java
# src/jalview/gui/PopupMenu.java
# src/jalview/gui/SliderPanel.java
# src/jalview/jbgui/GAlignFrame.java
# src/jalview/jbgui/GPaSiMapPanel.java
# src/jalview/project/Jalview2XML.java
# src/jalview/renderer/AnnotationRenderer.java
# src/jalview/renderer/ResidueShader.java
# src/jalview/util/Constants.java
# src/jalview/viewmodel/AlignmentViewport.java
# test/jalview/analysis/AlignmentUtilsTests.java
Ben Soares [Fri, 13 Sep 2024 14:26:23 +0000 (15:26 +0100)]
JAL-4461 Adding in a number of properties that control the default save_as format. See issue for details.
Jim Procter [Fri, 13 Sep 2024 13:53:03 +0000 (14:53 +0100)]
Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
Jim Procter [Fri, 13 Sep 2024 13:38:50 +0000 (14:38 +0100)]
JAL-4418 sign off JAL-4454 and convert markdown header to html for whatsNew 'experimental'
Ben Soares [Fri, 13 Sep 2024 10:20:54 +0000 (11:20 +0100)]
JAL-4461 Change JalviewFileFilter to use LinkedHashSet for extensions. Add list of extensions to 'By extensions' tooltip.
Jim Procter [Thu, 12 Sep 2024 16:17:22 +0000 (17:17 +0100)]
Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
Jim Procter [Thu, 12 Sep 2024 16:16:43 +0000 (17:16 +0100)]
JAL-4418 sign off JAL-4427 JAL-4451 fix
Jim Procter [Thu, 12 Sep 2024 15:57:41 +0000 (16:57 +0100)]
Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
Ben Soares [Thu, 12 Sep 2024 15:52:01 +0000 (16:52 +0100)]
JAL-4461 Added a dynamic tooltip to give more information when 'By extension' is the selected File Type. Utilising MIT licensed SwingUtils.getDescendantsByClass() to delve into the JFileChooser.
Jim Procter [Thu, 12 Sep 2024 13:57:29 +0000 (14:57 +0100)]
JAL-4461 fix up formatting and remove old comment
Jim Procter [Thu, 12 Sep 2024 13:56:31 +0000 (14:56 +0100)]
JAL-4461 after autodetection, update the filechooser dialog and let the user hit OK again to confirm the autodetected format
Ben Soares [Thu, 12 Sep 2024 13:12:59 +0000 (14:12 +0100)]
JAL-4461 Change labelling of All-known-alignment-files to Select-format-from-extension for Save-as file chooser
Ben Soares [Thu, 12 Sep 2024 12:29:49 +0000 (13:29 +0100)]
JAL-4460 Don't display the All-known-alignment-files format when a JalviewFileChooser is made with acceptAny set to false (usually a Save-as dialog)
Jim Procter [Thu, 12 Sep 2024 10:04:37 +0000 (11:04 +0100)]
JAL-4454 make sure 2.11.4.0-test is stripped - *for reals*
Jim Procter [Wed, 11 Sep 2024 17:01:24 +0000 (18:01 +0100)]
JAL-4418 release notes for JAL-4460
Jim Procter [Wed, 11 Sep 2024 16:59:04 +0000 (17:59 +0100)]
Merge branch 'bug/JAL-4460_alignment_save_as_format_not_registering' into develop
Jim Procter [Wed, 11 Sep 2024 16:43:22 +0000 (17:43 +0100)]
JAL-4454 make sure 2.11.4.0-test is stripped
Ben Soares [Wed, 11 Sep 2024 16:24:33 +0000 (17:24 +0100)]
JAL-4460 In save as, set format from file extension if a multi-format file filter is selected
Ben Soares [Wed, 11 Sep 2024 15:51:49 +0000 (16:51 +0100)]
JAL-4460 Don't add .aln for an 'All known formats...' filename
Ben Soares [Wed, 11 Sep 2024 15:23:43 +0000 (16:23 +0100)]
JAL-4460 Update currentFileFormat /after/ new format selection
Jim Procter [Wed, 11 Sep 2024 14:34:09 +0000 (15:34 +0100)]
JAL-4418 JAL-4428,JAL-4421,JAL-3393 release notes
Jim Procter [Wed, 11 Sep 2024 14:29:08 +0000 (15:29 +0100)]
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
Jim Procter [Wed, 11 Sep 2024 14:25:52 +0000 (15:25 +0100)]
JAL-4428 codesign jnilibs
git://source.jalview.org / jalview.git / log