Ben Soares [Sat, 2 Sep 2023 14:15:00 +0000 (15:15 +0100)]
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Sat, 2 Sep 2023 14:14:51 +0000 (15:14 +0100)]
JAL-629 Add accessors for argParser and bootstrapArgs
Ben Soares [Fri, 1 Sep 2023 23:03:39 +0000 (00:03 +0100)]
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Fri, 1 Sep 2023 23:03:21 +0000 (00:03 +0100)]
JAL-629 Save structure frames in project files when opened and saved in headless mode
Ben Soares [Fri, 1 Sep 2023 22:27:53 +0000 (23:27 +0100)]
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Fri, 1 Sep 2023 22:27:38 +0000 (23:27 +0100)]
JAL-629 Fix --structureimage and options
Ben Soares [Thu, 31 Aug 2023 21:11:40 +0000 (22:11 +0100)]
Merge branch 'improvement/JAL-3830_remove_dock_icon_in_headless_mode' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Thu, 31 Aug 2023 21:11:18 +0000 (22:11 +0100)]
JAL-3830 Remove dock icon for -h too
Ben Soares [Thu, 31 Aug 2023 15:49:25 +0000 (16:49 +0100)]
Merge branch 'features/r2_11_2_alphafold/JAL-629' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Thu, 31 Aug 2023 15:49:10 +0000 (16:49 +0100)]
JAL-629 Small buglet with getting --seqid
Ben Soares [Thu, 31 Aug 2023 15:10:57 +0000 (16:10 +0100)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Tue, 29 Aug 2023 14:15:16 +0000 (15:15 +0100)]
Merge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBinder_error_message' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Tue, 29 Aug 2023 14:14:50 +0000 (15:14 +0100)]
JAL-4255 better grammar
Ben Soares [Tue, 29 Aug 2023 13:17:36 +0000 (14:17 +0100)]
JAL-4255 Updated THIRDPARTYLIBS
Ben Soares [Tue, 29 Aug 2023 12:58:25 +0000 (13:58 +0100)]
Merge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBinder_error_message' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Tue, 29 Aug 2023 12:58:14 +0000 (13:58 +0100)]
JAL-4255 Added slf4j-nop jar and upgraded to last 1.x release
Ben Soares [Mon, 28 Aug 2023 19:17:32 +0000 (20:17 +0100)]
Merge branch 'develop' into merge/big_merge_of_bens_stuff_before_2_11_3_0
James Procter [Mon, 28 Aug 2023 11:26:28 +0000 (12:26 +0100)]
JAL-4090 JAL-4250 JAL-4253 JAL-325 release notes and THIRDPARTYLIB
James Procter [Mon, 28 Aug 2023 11:18:09 +0000 (12:18 +0100)]
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into develop
James Procter [Mon, 28 Aug 2023 11:10:37 +0000 (12:10 +0100)]
JAL-4253 drop the bottom line so it lines up with the vertical of group border.
Ben Soares [Thu, 24 Aug 2023 18:54:43 +0000 (19:54 +0100)]
Merge branch 'develop' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Thu, 24 Aug 2023 18:53:56 +0000 (19:53 +0100)]
Merge branch 'features/r2_11_2_alphafold/JAL-629' into develop
Ben Soares [Thu, 24 Aug 2023 18:53:36 +0000 (19:53 +0100)]
JAL-629 Avoid hidden options dialog when saving in headless mode
Ben Soares [Thu, 24 Aug 2023 17:43:19 +0000 (18:43 +0100)]
Merge branch 'bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Thu, 24 Aug 2023 16:54:47 +0000 (17:54 +0100)]
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Thu, 24 Aug 2023 16:54:37 +0000 (17:54 +0100)]
JAL-4250 Fix bug in vector rendition where more than one secondary structure loses the glyphline.
Ben Soares [Thu, 24 Aug 2023 12:18:02 +0000 (13:18 +0100)]
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Thu, 24 Aug 2023 12:17:42 +0000 (13:17 +0100)]
JAL-4250 Much simplified glyph creation removing most need for differences between vector/bitmap generation. Careful testing done to ensure no gaps in vector or high or low res bitmap.
Ben Soares [Wed, 23 Aug 2023 15:06:08 +0000 (16:06 +0100)]
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Wed, 23 Aug 2023 15:05:03 +0000 (16:05 +0100)]
JAL-4250 Fix one word bug for 'af.createEPS(file, renderer)' (was af.createEPS(file, name)'. Everything else is formatting changes.
Ben Soares [Wed, 23 Aug 2023 09:21:07 +0000 (10:21 +0100)]
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Wed, 23 Aug 2023 09:20:46 +0000 (10:20 +0100)]
JAL-4250 Updated jfreesvg to fix round stroke in linegraph.
Ben Soares [Wed, 23 Aug 2023 07:58:11 +0000 (08:58 +0100)]
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Wed, 23 Aug 2023 00:07:29 +0000 (01:07 +0100)]
JAL-4250 Simplification of polygons and adjustments to calculations in secondary structure for vector rendition. Corrected rounding error for line graph with round stroke to give joined up appearance in vector rendition.
Ben Soares [Mon, 21 Aug 2023 13:09:03 +0000 (14:09 +0100)]
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Mon, 21 Aug 2023 13:08:36 +0000 (14:08 +0100)]
JAL-4250 revert green to bright green
Ben Soares [Mon, 21 Aug 2023 11:16:07 +0000 (12:16 +0100)]
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Mon, 21 Aug 2023 10:55:42 +0000 (11:55 +0100)]
JAL-4250 Conservative setting of ANTIALIAS and readjustment of glyphs to avoid scrolling artifacts by pixel-out positioned glyphs
Ben Soares [Fri, 18 Aug 2023 16:16:55 +0000 (17:16 +0100)]
JAL-4250 Make secondary structure annotation shapes antialiased and outlined in the same colour for better shape definition.
Ben Soares [Fri, 18 Aug 2023 14:36:13 +0000 (15:36 +0100)]
Merge branch 'improvement/JAL-4206_improve_JalviewFileChooser_for_flatlaf' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Fri, 18 Aug 2023 14:33:53 +0000 (15:33 +0100)]
Merge branch 'bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Fri, 18 Aug 2023 13:35:41 +0000 (14:35 +0100)]
Merge branch 'improvement/JAL-4212_remove_macos_test_java_icons' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Fri, 18 Aug 2023 13:34:52 +0000 (14:34 +0100)]
Merge branch 'feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Fri, 18 Aug 2023 13:34:14 +0000 (14:34 +0100)]
Merge branch 'improvement/JAL-3830_remove_dock_icon_in_headless_mode' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Fri, 18 Aug 2023 13:34:00 +0000 (14:34 +0100)]
Merge branch 'bug/JAL-4242_exception_when_pressing_escape_in_fetch_from_URL_dialog' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares [Fri, 18 Aug 2023 13:33:40 +0000 (14:33 +0100)]
JAL-3416 Remove full height separators between new curved tabs
Ben Soares [Fri, 18 Aug 2023 11:26:45 +0000 (12:26 +0100)]
JAL-3416 flatlaf and flatlaf-extras 3.2 jars
Ben Soares [Fri, 18 Aug 2023 09:03:13 +0000 (10:03 +0100)]
JAL-4242 null check on getValue() return
Ben Soares [Thu, 17 Aug 2023 11:47:57 +0000 (12:47 +0100)]
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into improvement/JAL-3830_remove_dock_icon_in_headless_mode
Ben Soares [Thu, 17 Aug 2023 11:43:26 +0000 (12:43 +0100)]
JAL-3830 JAL-4160 Remove --noheadless as --gui does this. Simplifies wrapper scripts
James Procter [Sun, 23 Jul 2023 07:27:47 +0000 (09:27 +0200)]
JAL-4090 JAL-4243 bio.tools json file release notes
Ben Soares [Wed, 16 Aug 2023 23:02:26 +0000 (00:02 +0100)]
JAL-3830 JAL-3421 Conda launch script for 2.11.3 and new CLI with OS compatibility from installer launch script
Ben Soares [Wed, 16 Aug 2023 16:48:07 +0000 (17:48 +0100)]
Merge branch 'develop' into improvement/JAL-3830_remove_dock_icon_in_headless_mode
Ben Soares [Wed, 16 Aug 2023 16:48:00 +0000 (17:48 +0100)]
JAL-4160 JAL-3830 Improvements to the jalview.sh bash script especially when not in .app bundle on mac.
Ben Soares [Wed, 16 Aug 2023 16:46:51 +0000 (17:46 +0100)]
JAL-3820 JAL-4189 Use the same LaunchUtils methods to check java executable symlinks in getdown.
Ben Soares [Wed, 16 Aug 2023 16:45:56 +0000 (17:45 +0100)]
JAL-3820 JAL-4189 Move checks for java executable symlinks to LaunchUtils ready for use in getdown
Ben Soares [Fri, 11 Aug 2023 13:44:07 +0000 (14:44 +0100)]
JAL-629 Much better way of dealing with list of filenames/URLs without an --open argument. Added tests for these and fixed multiple STDOUT files.
Ben Soares [Thu, 10 Aug 2023 20:41:45 +0000 (21:41 +0100)]
JAL-629 more tests for stdout
Ben Soares [Thu, 10 Aug 2023 16:29:17 +0000 (17:29 +0100)]
JAL-629 STDOUT documentation. Opt.STDOUT narrower option. Fix for subvals and STDOUT detection.
Ben Soares [Thu, 10 Aug 2023 15:31:15 +0000 (16:31 +0100)]
JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console.errPrintln. Fix command line tests. Add test for STDOUT output file.
Ben Soares [Thu, 10 Aug 2023 09:50:14 +0000 (10:50 +0100)]
JAL-629 Method to use for printStackTrace
Ben Soares [Wed, 9 Aug 2023 23:23:50 +0000 (00:23 +0100)]
JAL-629 Move more stdout messages to stderr when outputting file to stdout
Ben Soares [Wed, 9 Aug 2023 16:21:34 +0000 (17:21 +0100)]
JAL-629 Default to FASTA if no format given for output to STDOUT
Ben Soares [Wed, 9 Aug 2023 16:16:18 +0000 (17:16 +0100)]
JAL-629 Enable output to STDOUT when specifying output filename as '-'. Must check other output is suppressed.
Ben Soares [Wed, 9 Aug 2023 12:07:43 +0000 (13:07 +0100)]
JAL-244 Fix window size narrow adjustment not becoming a manual adjustment clash
Ben Soares [Tue, 8 Aug 2023 11:37:54 +0000 (12:37 +0100)]
JAL-244 Added light grey marks to indicate regions to resize the margins
Ben Soares [Tue, 8 Aug 2023 00:28:54 +0000 (01:28 +0100)]
JAL-244 Fix mismatched vertical positioning of sequences and their labels in wrap mode with margin adjustment enabled
Ben Soares [Mon, 7 Aug 2023 11:28:53 +0000 (12:28 +0100)]
JAL-244 Avoid working on the Ids Graphics object when we don't mean to
Ben Soares [Fri, 4 Aug 2023 15:28:09 +0000 (16:28 +0100)]
JAL-244 Adjust wrapped alignment widths to always maintain a visible wrapped sequence width (and also avoid zero divisions)
Ben Soares [Wed, 2 Aug 2023 15:16:01 +0000 (16:16 +0100)]
JAL-244 Fix buglet with automatic change in id column width not being recorded. More tests includeing wrapped format.
Ben Soares [Tue, 1 Aug 2023 19:22:14 +0000 (20:22 +0100)]
JAL-244 More control of automatic idWidth adjustments. Added tests.
Ben Soares [Tue, 1 Aug 2023 08:39:25 +0000 (09:39 +0100)]
Merge branch 'develop' into feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels
Ben Soares [Fri, 28 Jul 2023 11:38:51 +0000 (12:38 +0100)]
JAL-4064 Added more recognisable display names to macOS DMG architectures
Ben Soares [Thu, 27 Jul 2023 19:18:50 +0000 (20:18 +0100)]
Merge branch 'develop' into feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels
Ben Soares [Thu, 27 Jul 2023 19:14:25 +0000 (20:14 +0100)]
JAL-244 Allow wrap manual adjustments to be smaller than the actual id widths.
Ben Soares [Thu, 27 Jul 2023 16:28:48 +0000 (17:28 +0100)]
JAL-244 Allow adjusting Id column width in wrap mode. Set Id column width in gui and image output with --wrap mode.
Ben Soares [Tue, 25 Jul 2023 08:18:47 +0000 (09:18 +0100)]
JAL-244 testing without AlignFrame for --wrap
James Procter [Sat, 22 Jul 2023 09:54:57 +0000 (11:54 +0200)]
JAL-4243 Jalview 2.11.2.7’s biotool record as JSON complete with update instructions as a README
Ben Soares [Fri, 21 Jul 2023 16:23:24 +0000 (17:23 +0100)]
JAL-244 Fixed idWidth labels in headless mode for non-wrap alignments
Ben Soares [Thu, 20 Jul 2023 11:32:43 +0000 (12:32 +0100)]
JAL-244 More accurate width calculation, allow increased id width adjustment after manual adjustment
Ben Soares [Thu, 20 Jul 2023 09:36:50 +0000 (10:36 +0100)]
JAL-244 test files
James Procter [Thu, 20 Jul 2023 07:33:17 +0000 (08:33 +0100)]
JAL-3855 tree title for PAE matrix tree is PAE Matrix (method) for (structure) (sequence)
James Procter [Thu, 20 Jul 2023 07:21:11 +0000 (08:21 +0100)]
JAL-3855 auto select clusters and fix up colouring/propagation on calculation & tree display
Ben Soares [Wed, 19 Jul 2023 23:34:55 +0000 (00:34 +0100)]
JAL-244 Changes to Annotation labels width now adjusts the overall idWidth if larger than the alignment idWidth. Will not shrink the width if a manual adjustment has been made. Can be overridden by preference. Also fixed buglet of scroll bar not adjusting with manual changes to idWidth.
James Procter [Wed, 19 Jul 2023 06:50:25 +0000 (07:50 +0100)]
Merge branch 'patch/JAL-3855_fixup_pae' into develop
James Procter [Tue, 18 Jul 2023 19:57:44 +0000 (20:57 +0100)]
Merge branch 'develop' into patch/JAL-3855_fixup_pae
James Procter [Tue, 18 Jul 2023 19:51:21 +0000 (20:51 +0100)]
JAL-4153 comments re patch incorrectly committed under JAL-4513
Ben Soares [Tue, 18 Jul 2023 17:00:42 +0000 (18:00 +0100)]
JAL-4513 move comments
Ben Soares [Tue, 18 Jul 2023 15:58:01 +0000 (16:58 +0100)]
JAL-4513 now re-add the SwingUtilities.invokeAndWait() with minimal sleep
James Procter [Tue, 18 Jul 2023 15:17:12 +0000 (16:17 +0100)]
JAL-3855 PAE matrices are transposed on import from JSON so returned contact vectors correspond to errors predicted when superposing at a given column position
James Procter [Tue, 18 Jul 2023 15:05:44 +0000 (16:05 +0100)]
JAL-3855 JAL-4124 test checks asymmetric matrices are stored and restored correctly
James Procter [Tue, 18 Jul 2023 14:45:27 +0000 (15:45 +0100)]
JAL-3858 fix off-by-one in matrix visualisation and interactive tooltip
James Procter [Tue, 18 Jul 2023 14:44:07 +0000 (15:44 +0100)]
JAL-3858 flip diagonal so matrix visualisation is top left to bottom right
James Procter [Tue, 18 Jul 2023 14:40:31 +0000 (15:40 +0100)]
JAL-3858 annotation .height is bigger than graphHeight so adjacent PAE matrices are clearly separated
Ben Soares [Tue, 18 Jul 2023 13:38:34 +0000 (14:38 +0100)]
JAL-4513 reduce wait to invoke fail
Ben Soares [Tue, 18 Jul 2023 13:19:15 +0000 (14:19 +0100)]
JAL-4513 add a SwingUtilities.invokeAndWait() to see what happens
Ben Soares [Mon, 17 Jul 2023 16:38:31 +0000 (17:38 +0100)]
JAL-3599 Updated default eclipse to 'latest' and made jalviewjsLaunchTest timeouts a bit more flexible
James Procter [Mon, 17 Jul 2023 10:15:07 +0000 (11:15 +0100)]
JAL-4119 TRACE level console message reporting download URL for sifts. Also more informative message when ‘Sifts Mapping Failed’ is reported as an exception - since this message can be reported when some chains in the PDB file do not match sequences being associated (but others do!!).
James Procter [Mon, 17 Jul 2023 09:41:43 +0000 (10:41 +0100)]
JAL-4090 JAL-4165 known issue
James Procter [Mon, 17 Jul 2023 09:40:04 +0000 (10:40 +0100)]
JAL-4090 JAL-4165 known issue
git://source.jalview.org / jalview.git / log