Ben Soares [Mon, 11 Sep 2023 23:21:10 +0000 (00:21 +0100)]
Merge branch 'improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed' into bug/JAL-4277_dirname_substitution_always_absolute
Ben Soares [Mon, 11 Sep 2023 23:19:12 +0000 (00:19 +0100)]
JAL-4277 --mkdirs with cautious refusal for paths with ..
Ben Soares [Mon, 11 Sep 2023 23:16:44 +0000 (00:16 +0100)]
JAL-4284 JAL-4285 Deal with output files/images consistently with --overwrite check. Gather batch process errors together to output at the end of processing.
Ben Soares [Fri, 8 Sep 2023 14:37:23 +0000 (15:37 +0100)]
JAL-4262 Make an excepetion for STDOUT filename in old style arguments detection
Ben Soares [Fri, 8 Sep 2023 13:43:26 +0000 (14:43 +0100)]
Merge branch 'bug/JAL-4277_dirname_substitution_always_absolute' into improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed
Ben Soares [Fri, 8 Sep 2023 13:43:09 +0000 (14:43 +0100)]
JAL-4262 Dialog for GUI and WARN for CLI of old style arguments, or mixed arguments \(with exit\). Changed Jalview.exit to use an enum for exit code to avoid collisions.
Ben Soares [Thu, 7 Sep 2023 22:43:42 +0000 (23:43 +0100)]
Merge branch 'develop' into bug/JAL-4277_dirname_substitution_always_absolute
Ben Soares [Thu, 7 Sep 2023 22:28:24 +0000 (23:28 +0100)]
JAL-4277 fixed and improved tests
James Procter [Thu, 7 Sep 2023 17:00:54 +0000 (18:00 +0100)]
JAL-4090 release notes for JAL-244 JAL-901 JAL-4260 JAL-4189 JAL-2910
Ben Soares [Thu, 7 Sep 2023 16:05:07 +0000 (17:05 +0100)]
JAL-4277 Corrected choice of all or last opened linkedIds. Better wildcard syntactic sugar for output files. Fixed all tests for new defaults.
James Procter [Thu, 7 Sep 2023 16:00:19 +0000 (17:00 +0100)]
JAL-4279 suppress error dialogs raised by file loader when working in batch mode
James Procter [Thu, 7 Sep 2023 15:28:46 +0000 (16:28 +0100)]
JAL-4279 move on if the file doesn't exist, or Identify fails for the file.
James Procter [Thu, 7 Sep 2023 15:26:40 +0000 (16:26 +0100)]
JAL-4279 catch exceptions with fileLoader and report when we don’t get an alignment frame after trying to import a given file before moving on.
James Procter [Thu, 7 Sep 2023 10:21:23 +0000 (11:21 +0100)]
JAL-4090 JAL-4160 JAL-4274 image export dimensions and scale factor configurable via .jalview_properties as well as command line
Ben Soares [Thu, 7 Sep 2023 11:01:10 +0000 (12:01 +0100)]
JAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTIID and Opt.MULTI to Opt.MULTIVALUE. Remove filename value open* as trigger for applying an output file to all globbed files opened in the last --open, and make it the default option for globbed files opened. Adjust 2 test data for removed 'open*'.
James Procter [Thu, 7 Sep 2023 09:45:43 +0000 (10:45 +0100)]
JAL-4273 release notes for visible adjuster marks, and patch so they are not rendered during figure export
James Procter [Thu, 7 Sep 2023 09:08:26 +0000 (10:08 +0100)]
JAL-4090 report JAL-4261 known issue
James Procter [Wed, 6 Sep 2023 14:28:14 +0000 (15:28 +0100)]
JAL-4260 attempt to rejig paging when id width is adjusted whilst in wrapped mode.
James Procter [Wed, 6 Sep 2023 13:45:13 +0000 (14:45 +0100)]
JAL-4258 remove unnecessary ‘this’
James Procter [Wed, 6 Sep 2023 13:44:33 +0000 (14:44 +0100)]
JAL-4259 construct a new SequenceRenderer when rendering an MSA to an exporter
James Procter [Wed, 6 Sep 2023 11:39:44 +0000 (12:39 +0100)]
JAL-629 javadoc on new setMapping variant for structureselectionmanager
James Procter [Wed, 6 Sep 2023 11:28:10 +0000 (12:28 +0100)]
JAL-629 reinstate INFO level stack trace from StructureChooser service exceptions and suppress external service queries when viewing structures via Command-line import
James Procter [Wed, 6 Sep 2023 10:48:11 +0000 (11:48 +0100)]
JAL-629 javadoc
James Procter [Tue, 5 Sep 2023 16:03:42 +0000 (17:03 +0100)]
JAL-629 remove structure viewer from the list of structure viewer base instances when its closeViewer method is called
James Procter [Tue, 5 Sep 2023 16:03:02 +0000 (17:03 +0100)]
JAL-629 use JalviewStructureDisplayI in place of StructureViewerBase
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.
git://source.jalview.org / jalview.git / log