James Procter [Thu, 28 Sep 2023 16:39:51 +0000 (17:39 +0100)]
JAL-3858 improved contactInterval computation and added detailed test coverage for ContactGeometry
- contactInterval.cStart/cEnd and pStart/pEnd are now base-0 inclusive ranges, always less than contactHeight and graphHeight
- change in mapFor behaviour so cStart/cEnd and pStart/pEnd are always just one mapped range, not as many as requested to cover mapFor(pFrom,pTo)
James Procter [Tue, 26 Sep 2023 10:59:56 +0000 (11:59 +0100)]
JAL-3858 JAL-4090 pae matrix docs. WIP
James Procter [Tue, 26 Sep 2023 10:59:08 +0000 (11:59 +0100)]
JAL-3858 JAL-4090 avoid NPE when given out of bound column ranges when requesting ContactList
James Procter [Mon, 25 Sep 2023 16:55:38 +0000 (17:55 +0100)]
JAL-3858 JAL-4090 PAE documentation..
James Procter [Mon, 25 Sep 2023 16:55:15 +0000 (17:55 +0100)]
JAL-3858 minimum value for a range is used to shade ranges in PAE map
James Procter [Mon, 25 Sep 2023 16:54:44 +0000 (17:54 +0100)]
JAL-3858 javadoc and slightly revised green linear shading - still not a perfect match to EBI AlphaFold
James Procter [Mon, 25 Sep 2023 16:40:54 +0000 (17:40 +0100)]
JAL-3858 report PAE range with sensible precision
James Procter [Fri, 22 Sep 2023 15:56:42 +0000 (16:56 +0100)]
JAL-4090 fix link...
James Procter [Fri, 22 Sep 2023 11:05:07 +0000 (12:05 +0100)]
JAL-4090 smaller associate PDB file panel image in docs
James Procter [Thu, 21 Sep 2023 16:27:46 +0000 (17:27 +0100)]
JAL-4090 what’s new and additional help docs for JAL-3858 JAL-3855
James Procter [Thu, 21 Sep 2023 16:26:48 +0000 (17:26 +0100)]
JAL-4090 JAL-4262 JAL-4265 release notes
James Procter [Thu, 21 Sep 2023 16:25:48 +0000 (17:25 +0100)]
JAL-1551 javadoc for mapUtils
James Procter [Thu, 21 Sep 2023 16:20:27 +0000 (17:20 +0100)]
JAL-3855 disable the AlphaFold DB entry in Sequence Fetcher - see JAL-4287 for an alternative (and perhaps preferred way) of fetching proteins with alphafold structures.
James Procter [Thu, 21 Sep 2023 16:17:01 +0000 (17:17 +0100)]
JAL-3858 JAL-3855 documentation for import and display PAE from alphafold and JSON format flat files for Import 3D structure from file
James Procter [Thu, 21 Sep 2023 11:44:19 +0000 (12:44 +0100)]
Merge branch 'merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285' into develop
Ben Soares [Thu, 21 Sep 2023 08:57:22 +0000 (09:57 +0100)]
JAL-4265 Use ColourUtils.parseColourString() for consistency with the rest of Jalview (and it's better). Change documentation to match new hexstring format
Ben Soares [Thu, 21 Sep 2023 08:29:39 +0000 (09:29 +0100)]
Merge branch 'develop' into merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285
Ben Soares [Wed, 20 Sep 2023 17:09:45 +0000 (18:09 +0100)]
JAL-4265 Use ColorUtils.parseColourString() and adjust documentation to use un-hashed hex-string for consistency with other Jalview uses of parseColourString(). When adding 2 structures and 2 structureimages I am now getting a NPE for String[] files = getStructureFiles(); in AAStructureBindingModel, and when using bgcolour for the first structureimage, losing the residues in the second structure image. Will need to investigate when I'm back
James Procter [Wed, 20 Sep 2023 17:03:37 +0000 (18:03 +0100)]
JAL-4285 don’t say you are reporting warnings/errors when there are none..
James Procter [Wed, 20 Sep 2023 17:02:41 +0000 (18:02 +0100)]
JAL-4265 JAL-4286 reinstated explicit restoreSession method because Jmol’s LOAD files command does not behave the same way as restore STATE. Also added defensive check for unexpected exceptions if the state restore trashes the Jmol/Jalview binding
James Procter [Wed, 20 Sep 2023 16:59:26 +0000 (17:59 +0100)]
JAL-4265 JAL-4267 added a ‘restoreSession’ StructureViewer.getBinding() method that allows a snapshot to be explicitly reloaded in place.
James Procter [Wed, 20 Sep 2023 15:42:28 +0000 (16:42 +0100)]
JAL-4195 JAL-1069 JAL-4160 errors in Cache should go to Console.stderr
James Procter [Wed, 20 Sep 2023 15:36:48 +0000 (16:36 +0100)]
Merge branch 'reviews/merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285' into develop
James Procter [Wed, 20 Sep 2023 14:14:05 +0000 (15:14 +0100)]
JAL-4217 - try to invokeAndWait on Desktop.closeAll() to avoid Jmol redraw blocking close
James Procter [Wed, 20 Sep 2023 13:23:09 +0000 (14:23 +0100)]
JAL-4274 fix test failure message typo
James Procter [Wed, 20 Sep 2023 13:22:11 +0000 (14:22 +0100)]
JAL-4265 bail early when attempting to export a view from other viewers than Jmol, and use viewType independent methods as much as possible.
James Procter [Wed, 20 Sep 2023 13:13:57 +0000 (14:13 +0100)]
JAL-4265 JAL-4267 allow injection of custom commands outside of Viewer binding model
James Procter [Wed, 20 Sep 2023 13:13:07 +0000 (14:13 +0100)]
JAL-4265 back out redundant ‘saveState’ and ‘restoreState’ StructureCommandsI methods.
Ben Soares [Wed, 20 Sep 2023 11:17:17 +0000 (12:17 +0100)]
JAL-4265 Added saveState and restoreState to interface with no-op methods in abstract class
Ben Soares [Wed, 20 Sep 2023 10:41:27 +0000 (11:41 +0100)]
JAL-629 Explanation of \{m\} in case anyone actually wants it
Ben Soares [Wed, 20 Sep 2023 10:23:05 +0000 (11:23 +0100)]
JAL-629 Add link and example for BioJS image output
Ben Soares [Wed, 20 Sep 2023 10:19:59 +0000 (11:19 +0100)]
JAL-629 Make arguments appear correctly using all non-breaking hyphens
Ben Soares [Wed, 20 Sep 2023 10:15:57 +0000 (11:15 +0100)]
JAL-629 Added/corrected/tidied documentation
Ben Soares [Tue, 19 Sep 2023 23:42:34 +0000 (00:42 +0100)]
JAL-629 JAL-4265 JAL-4269 Updated help Documentation
Ben Soares [Tue, 19 Sep 2023 23:32:46 +0000 (00:32 +0100)]
JAL-629 JAL-4265 JAL-4269 Updated help Documentation
Ben Soares [Tue, 19 Sep 2023 21:36:19 +0000 (22:36 +0100)]
JAL-4265 Change to use JmolCommands
Ben Soares [Tue, 19 Sep 2023 09:48:29 +0000 (10:48 +0100)]
JAL-629 Allow multiple structure images for multiple structure files for the one alignment. Add a {structurebasename} etc and {m} substitution which must be handled differently (on the fly) to other substitutions.
Ben Soares [Sat, 16 Sep 2023 20:14:42 +0000 (21:14 +0100)]
JAL-4250 Fixed blue arrows in drawStemAnnot()
Ben Soares [Sat, 16 Sep 2023 15:56:54 +0000 (16:56 +0100)]
JAL-629 Fix a test and omit an incorrect error message for structureviewer=none
Ben Soares [Sat, 16 Sep 2023 12:28:53 +0000 (13:28 +0100)]
JAL-4265 Added --bgcolour for --structureimage output. Saves and restores Jmol state before and after colour changes and export. Added 'set antialiasdisplay on' by default for all Jmol viewers.
Ben Soares [Sat, 16 Sep 2023 11:24:31 +0000 (12:24 +0100)]
JAL-4269 Now using --width, --height, --scale for both --image and --structureimage. Multiple --image and --structureimage can be specified with --imagecolour allowing changes of colour. --width etc only apply to that particular image.
Ben Soares [Thu, 14 Sep 2023 13:16:17 +0000 (14:16 +0100)]
Merge branch 'develop' into feature/JAL-4274_configurable_bitmap_export_preferences
Ben Soares [Wed, 13 Sep 2023 19:33:20 +0000 (20:33 +0100)]
JAL-4274 comments to help follow the tests
Ben Soares [Wed, 13 Sep 2023 19:26:38 +0000 (20:26 +0100)]
JAL-4274 Tests for BIS defaults and overrides
Ben Soares [Wed, 13 Sep 2023 16:28:11 +0000 (17:28 +0100)]
JAL-4274 Use Cache BITMAP_* if no other image restrictions given
Ben Soares [Wed, 13 Sep 2023 12:32:33 +0000 (13:32 +0100)]
JAL-4262 Made deprecation warning properly modal
Ben Soares [Tue, 12 Sep 2023 11:32:00 +0000 (12:32 +0100)]
JAL-4262 Allow HTML in the dialog box for link to CLI documentation
Ben Soares [Tue, 12 Sep 2023 10:17:16 +0000 (11:17 +0100)]
JAL-4277 No longer using getCanonicalPath() for parent dir -- fix test
Ben Soares [Tue, 12 Sep 2023 09:43:20 +0000 (10:43 +0100)]
JAL-4285 Better checkFiles processing. Better dialog.
Ben Soares [Tue, 12 Sep 2023 01:23:45 +0000 (02:23 +0100)]
JAL-629 updated tests
Ben Soares [Tue, 12 Sep 2023 01:05:07 +0000 (02:05 +0100)]
JAL-4285 JAL-4262 Added a scrollable dialog to display errors. Moved old-style CLI warning so it appears above Jalview desktop.
Ben Soares [Mon, 11 Sep 2023 23:33:15 +0000 (00:33 +0100)]
JAL-4001 corrected analytics message labels
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