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2023-09-20	Ben Soares	JAL-629 Add link and example for BioJS image output	commit \| commitdiff \| tree
2023-09-20	Ben Soares	JAL-629 Make arguments appear correctly using all non...	commit \| commitdiff \| tree
2023-09-20	Ben Soares	JAL-629 Added/corrected/tidied documentation	commit \| commitdiff \| tree
2023-09-19	Ben Soares	JAL-629 JAL-4265 JAL-4269 Updated help Documentation	commit \| commitdiff \| tree
2023-09-19	Ben Soares	JAL-629 JAL-4265 JAL-4269 Updated help Documentation	commit \| commitdiff \| tree
2023-09-19	Ben Soares	JAL-4265 Change to use JmolCommands	commit \| commitdiff \| tree
2023-09-19	Ben Soares	JAL-629 Allow multiple structure images for multiple...	commit \| commitdiff \| tree
2023-09-16	Ben Soares	JAL-4250 Fixed blue arrows in drawStemAnnot()	commit \| commitdiff \| tree
2023-09-16	Ben Soares	JAL-629 Fix a test and omit an incorrect error message...	commit \| commitdiff \| tree
2023-09-16	Ben Soares	JAL-4265 Added --bgcolour for --structureimage output...	commit \| commitdiff \| tree
2023-09-16	Ben Soares	JAL-4269 Now using --width, --height, --scale for both...	commit \| commitdiff \| tree
2023-09-14	Ben Soares	Merge branch 'develop' into feature/JAL-4274_configurable_bi...	commit \| commitdiff \| tree
2023-09-13	Ben Soares	JAL-4274 comments to help follow the tests	commit \| commitdiff \| tree
2023-09-13	Ben Soares	JAL-4274 Tests for BIS defaults and overrides	commit \| commitdiff \| tree
2023-09-13	Ben Soares	JAL-4274 Use Cache BITMAP_* if no other image restrictions...	commit \| commitdiff \| tree
2023-09-13	Ben Soares	JAL-4262 Made deprecation warning properly modal	commit \| commitdiff \| tree
2023-09-12	Ben Soares	JAL-4262 Allow HTML in the dialog box for link to CLI...	commit \| commitdiff \| tree
2023-09-12	Ben Soares	JAL-4277 No longer using getCanonicalPath() for parent...	commit \| commitdiff \| tree
2023-09-12	Ben Soares	JAL-4285 Better checkFiles processing. Better dialog.	commit \| commitdiff \| tree
2023-09-12	Ben Soares	JAL-629 updated tests	commit \| commitdiff \| tree
2023-09-12	Ben Soares	JAL-4285 JAL-4262 Added a scrollable dialog to display...	commit \| commitdiff \| tree
2023-09-11	Ben Soares	JAL-4001 corrected analytics message labels	commit \| commitdiff \| tree
2023-09-11	Ben Soares	Merge branch 'improvement/JAL-4262_deprecation_warning_when_...	commit \| commitdiff \| tree
2023-09-11	Ben Soares	JAL-4277 --mkdirs with cautious refusal for paths with ..	commit \| commitdiff \| tree
2023-09-11	Ben Soares	JAL-4284 JAL-4285 Deal with output files/images consistently...	commit \| commitdiff \| tree
2023-09-08	Ben Soares	JAL-4262 Make an excepetion for STDOUT filename in...	commit \| commitdiff \| tree
2023-09-08	Ben Soares	Merge branch 'bug/JAL-4277_dirname_substitution_always_absol...	commit \| commitdiff \| tree
2023-09-08	Ben Soares	JAL-4262 Dialog for GUI and WARN for CLI of old style...	commit \| commitdiff \| tree
2023-09-07	Ben Soares	Merge branch 'develop' into bug/JAL-4277_dirname_substitutio...	commit \| commitdiff \| tree
2023-09-07	Ben Soares	JAL-4277 fixed and improved tests	commit \| commitdiff \| tree
2023-09-07	Ben Soares	JAL-4277 Corrected choice of all or last opened linkedIds...	commit \| commitdiff \| tree
2023-09-07	Ben Soares	JAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTIID...	commit \| commitdiff \| tree
2023-09-02	Ben Soares	Merge branch 'feature/JAL-629_--output_-_means_output_to_STD...	commit \| commitdiff \| tree
2023-09-02	Ben Soares	JAL-629 Add accessors for argParser and bootstrapArgs	commit \| commitdiff \| tree
2023-09-01	Ben Soares	Merge branch 'feature/JAL-629_--output_-_means_output_to_STD...	commit \| commitdiff \| tree
2023-09-01	Ben Soares	JAL-629 Save structure frames in project files when...	commit \| commitdiff \| tree
2023-09-01	Ben Soares	Merge branch 'feature/JAL-629_--output_-_means_output_to_STD...	commit \| commitdiff \| tree
2023-09-01	Ben Soares	JAL-629 Fix --structureimage and options	commit \| commitdiff \| tree
2023-08-31	Ben Soares	Merge branch 'improvement/JAL-3830_remove_dock_icon_in_headl...	commit \| commitdiff \| tree
2023-08-31	Ben Soares	JAL-3830 Remove dock icon for -h too	commit \| commitdiff \| tree
2023-08-31	Ben Soares	Merge branch 'features/r2_11_2_alphafold/JAL-629' into...	commit \| commitdiff \| tree
2023-08-31	Ben Soares	JAL-629 Small buglet with getting --seqid	commit \| commitdiff \| tree
2023-08-31	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-08-29	Ben Soares	Merge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBinder_...	commit \| commitdiff \| tree
2023-08-29	Ben Soares	JAL-4255 better grammar	commit \| commitdiff \| tree
2023-08-29	Ben Soares	JAL-4255 Updated THIRDPARTYLIBS	commit \| commitdiff \| tree
2023-08-29	Ben Soares	Merge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBinder_...	commit \| commitdiff \| tree
2023-08-29	Ben Soares	JAL-4255 Added slf4j-nop jar and upgraded to last 1...	commit \| commitdiff \| tree
2023-08-28	Ben Soares	Merge branch 'develop' into merge/big_merge_of_bens_stuff_be...	commit \| commitdiff \| tree
2023-08-24	Ben Soares	Merge branch 'develop' into merge/big_merge_of_bens_stuff_be...	commit \| commitdiff \| tree
2023-08-24	Ben Soares	Merge branch 'features/r2_11_2_alphafold/JAL-629' into...	commit \| commitdiff \| tree
2023-08-24	Ben Soares	JAL-629 Avoid hidden options dialog when saving in...	commit \| commitdiff \| tree
2023-08-24	Ben Soares	Merge branch 'bug/JAL-4214_system_freeze_when_opening_file_u...	commit \| commitdiff \| tree
2023-08-24	Ben Soares	Merge branch 'improvement/JAL-4250_secondary_structure_annot...	commit \| commitdiff \| tree
2023-08-24	Ben Soares	JAL-4250 Fix bug in vector rendition where more than...	commit \| commitdiff \| tree
2023-08-24	Ben Soares	Merge branch 'improvement/JAL-4250_secondary_structure_annot...	commit \| commitdiff \| tree
2023-08-24	Ben Soares	JAL-4250 Much simplified glyph creation removing most...	commit \| commitdiff \| tree
2023-08-23	Ben Soares	Merge branch 'improvement/JAL-4250_secondary_structure_annot...	commit \| commitdiff \| tree
2023-08-23	Ben Soares	JAL-4250 Fix one word bug for 'af.createEPS(file, renderer...	commit \| commitdiff \| tree
2023-08-23	Ben Soares	Merge branch 'improvement/JAL-4250_secondary_structure_annot...	commit \| commitdiff \| tree
2023-08-23	Ben Soares	JAL-4250 Updated jfreesvg to fix round stroke in linegraph.	commit \| commitdiff \| tree
2023-08-23	Ben Soares	Merge branch 'improvement/JAL-4250_secondary_structure_annot...	commit \| commitdiff \| tree
2023-08-23	Ben Soares	JAL-4250 Simplification of polygons and adjustments...	commit \| commitdiff \| tree
2023-08-21	Ben Soares	Merge branch 'improvement/JAL-4250_secondary_structure_annot...	commit \| commitdiff \| tree
2023-08-21	Ben Soares	JAL-4250 revert green to bright green	commit \| commitdiff \| tree
2023-08-21	Ben Soares	Merge branch 'improvement/JAL-4250_secondary_structure_annot...	commit \| commitdiff \| tree
2023-08-21	Ben Soares	JAL-4250 Conservative setting of ANTIALIAS and readjustment...	commit \| commitdiff \| tree
2023-08-18	Ben Soares	JAL-4250 Make secondary structure annotation shapes...	commit \| commitdiff \| tree
2023-08-18	Ben Soares	Merge branch 'improvement/JAL-4206_improve_JalviewFileChoose...	commit \| commitdiff \| tree
2023-08-18	Ben Soares	Merge branch 'bug/JAL-4214_system_freeze_when_opening_file_u...	commit \| commitdiff \| tree
2023-08-18	Ben Soares	Merge branch 'improvement/JAL-4212_remove_macos_test_java_ic...	commit \| commitdiff \| tree
2023-08-18	Ben Soares	Merge branch 'feature/JAL-244_Automatically_adjust_left_marg...	commit \| commitdiff \| tree
2023-08-18	Ben Soares	Merge branch 'improvement/JAL-3830_remove_dock_icon_in_headl...	commit \| commitdiff \| tree
2023-08-18	Ben Soares	Merge branch 'bug/JAL-4242_exception_when_pressing_escape_in...	commit \| commitdiff \| tree
2023-08-18	Ben Soares	JAL-3416 Remove full height separators between new...	commit \| commitdiff \| tree
2023-08-18	Ben Soares	JAL-3416 flatlaf and flatlaf-extras 3.2 jars	commit \| commitdiff \| tree
2023-08-18	Ben Soares	JAL-4242 null check on getValue() return	commit \| commitdiff \| tree
2023-08-17	Ben Soares	Merge branch 'feature/JAL-629_--output_-_means_output_to_STD...	commit \| commitdiff \| tree
2023-08-17	Ben Soares	JAL-3830 JAL-4160 Remove --noheadless as --gui does...	commit \| commitdiff \| tree
2023-08-16	Ben Soares	JAL-3830 JAL-3421 Conda launch script for 2.11.3 and...	commit \| commitdiff \| tree
2023-08-16	Ben Soares	Merge branch 'develop' into improvement/JAL-3830_remove_dock...	commit \| commitdiff \| tree
2023-08-16	Ben Soares	JAL-4160 JAL-3830 Improvements to the jalview.sh bash...	commit \| commitdiff \| tree
2023-08-16	Ben Soares	JAL-3820 JAL-4189 Use the same LaunchUtils methods...	commit \| commitdiff \| tree
2023-08-16	Ben Soares	JAL-3820 JAL-4189 Move checks for java executable symlinks...	commit \| commitdiff \| tree
2023-08-11	Ben Soares	JAL-629 Much better way of dealing with list of filenames...	commit \| commitdiff \| tree
2023-08-10	Ben Soares	JAL-629 more tests for stdout	commit \| commitdiff \| tree
2023-08-10	Ben Soares	JAL-629 STDOUT documentation. Opt.STDOUT narrower...	commit \| commitdiff \| tree
2023-08-10	Ben Soares	JAL-629 Change all stdout and stderr output to use...	commit \| commitdiff \| tree
2023-08-10	Ben Soares	JAL-629 Method to use for printStackTrace	commit \| commitdiff \| tree
2023-08-09	Ben Soares	JAL-629 Move more stdout messages to stderr when outputting...	commit \| commitdiff \| tree
2023-08-09	Ben Soares	JAL-629 Default to FASTA if no format given for output...	commit \| commitdiff \| tree
2023-08-09	Ben Soares	JAL-629 Enable output to STDOUT when specifying output...	commit \| commitdiff \| tree
2023-08-09	Ben Soares	JAL-244 Fix window size narrow adjustment not becoming...	commit \| commitdiff \| tree
2023-08-08	Ben Soares	JAL-244 Added light grey marks to indicate regions...	commit \| commitdiff \| tree
2023-08-08	Ben Soares	JAL-244 Fix mismatched vertical positioning of sequences...	commit \| commitdiff \| tree
2023-08-07	Ben Soares	JAL-244 Avoid working on the Ids Graphics object when...	commit \| commitdiff \| tree
2023-08-04	Ben Soares	JAL-244 Adjust wrapped alignment widths to always maintain...	commit \| commitdiff \| tree
2023-08-02	Ben Soares	JAL-244 Fix buglet with automatic change in id column...	commit \| commitdiff \| tree
2023-08-01	Ben Soares	JAL-244 More control of automatic idWidth adjustments...	commit \| commitdiff \| tree
2023-08-01	Ben Soares	Merge branch 'develop' into feature/JAL-244_Automatically_ad...	commit \| commitdiff \| tree
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