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JAL-629 Fix --nodebug turning off debug mode from properties
2023-10-19 Ben SoaresJAL-629 Fix --nodebug turning off debug mode from properties
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2023-10-19 Ben SoaresJAL-4298 comment markers
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2023-10-19 Ben SoaresMerge branch 'improvement/JAL-3783_upgrade_to_groovy...
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2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from...
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2023-10-19 Ben SoaresMerge branch 'improvement/JAL-3783_upgrade_to_groovy...
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2023-10-18 Ben SoaresJAL-629 Run non-alignframe linked groovy scripts. ...
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2023-10-18 Ben SoaresJAL-4262 Fix the nonblockingdialog so that Jalview...
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2023-10-13 Ben SoaresJAL-3783 Updated groovy jars. Requires javaparser...
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2023-10-13 Ben SoaresJAL-3783 Updated build process to allow multiple groovy...
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2023-10-12 Ben SoaresJAL-3772 Fix the logic of prompt to save URL loaded...
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2023-10-12 Ben SoaresJAL-629 null check and neatening code
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2023-10-11 Ben SoaresJAL-629 correct a timeout. Correct passing html flag.
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2023-10-11 Ben SoaresJAL-629 Add a timeout to modal dialogs for command...
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2023-10-11 Ben SoaresJAL-629 Change getdown not to add -open argument
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2023-10-11 Ben SoaresJAL-629 Remove argfiles from the hashset of used argfiles...
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2023-10-11 Ben SoaresJAL-3772 Preference to NOT prompt to save remotely...
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2023-10-11 Ben SoaresJAL-4298 Added diagnostics and minor dimension changes...
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2023-10-05 Ben SoaresJAL-4298 Fixed initial log level to see .jalview_properties...
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2023-10-03 Ben SoaresJAL-4001 Only use acquireDialogQueue and releaseDialogQueue...
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2023-09-21 Ben SoaresJAL-4265 Use ColourUtils.parseColourString() for consistency...
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2023-09-21 Ben SoaresMerge branch 'develop' into merge/JAL-4262+JAL-4265...
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2023-09-20 Ben SoaresJAL-4265 Use ColorUtils.parseColourString() and adjust...
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2023-09-20 Ben SoaresJAL-4265 Added saveState and restoreState to interface...
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2023-09-20 Ben SoaresJAL-629 Explanation of \{m\} in case anyone actually...
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2023-09-20 Ben SoaresJAL-629 Add link and example for BioJS image output
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2023-09-20 Ben SoaresJAL-629 Make arguments appear correctly using all non...
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2023-09-20 Ben SoaresJAL-629 Added/corrected/tidied documentation
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2023-09-19 Ben SoaresJAL-629 JAL-4265 JAL-4269 Updated help Documentation
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2023-09-19 Ben SoaresJAL-629 JAL-4265 JAL-4269 Updated help Documentation
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2023-09-19 Ben SoaresJAL-4265 Change to use JmolCommands
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2023-09-19 Ben SoaresJAL-629 Allow multiple structure images for multiple...
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2023-09-16 Ben SoaresJAL-4250 Fixed blue arrows in drawStemAnnot()
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2023-09-16 Ben SoaresJAL-629 Fix a test and omit an incorrect error message...
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2023-09-16 Ben SoaresJAL-4265 Added --bgcolour for --structureimage output...
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2023-09-16 Ben SoaresJAL-4269 Now using --width, --height, --scale for both...
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2023-09-14 Ben SoaresMerge branch 'develop' into feature/JAL-4274_configurable_bi...
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2023-09-13 Ben SoaresJAL-4274 comments to help follow the tests
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2023-09-13 Ben SoaresJAL-4274 Tests for BIS defaults and overrides
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2023-09-13 Ben SoaresJAL-4274 Use Cache BITMAP_* if no other image restrictions...
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2023-09-13 Ben SoaresJAL-4262 Made deprecation warning properly modal
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2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI...
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2023-09-12 Ben SoaresJAL-4277 No longer using getCanonicalPath() for parent...
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2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog.
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2023-09-12 Ben SoaresJAL-629 updated tests
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2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display...
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2023-09-11 Ben SoaresJAL-4001 corrected analytics message labels
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2023-09-11 Ben SoaresMerge branch 'improvement/JAL-4262_deprecation_warning_when_...
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2023-09-11 Ben SoaresJAL-4277 --mkdirs with cautious refusal for paths with ..
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2023-09-11 Ben SoaresJAL-4284 JAL-4285 Deal with output files/images consistently...
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2023-09-08 Ben SoaresJAL-4262 Make an excepetion for STDOUT filename in...
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2023-09-08 Ben SoaresMerge branch 'bug/JAL-4277_dirname_substitution_always_absol...
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2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style...
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2023-09-07 Ben SoaresMerge branch 'develop' into bug/JAL-4277_dirname_substitutio...
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2023-09-07 Ben SoaresJAL-4277 fixed and improved tests
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2023-09-07 Ben SoaresJAL-4277 Corrected choice of all or last opened linkedIds...
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2023-09-07 Ben SoaresJAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTIID...
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2023-09-02 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_to_STD...
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2023-09-02 Ben SoaresJAL-629 Add accessors for argParser and bootstrapArgs
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2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_to_STD...
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2023-09-01 Ben SoaresJAL-629 Save structure frames in project files when...
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2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_to_STD...
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2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options
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2023-08-31 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_headl...
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2023-08-31 Ben SoaresJAL-3830 Remove dock icon for -h too
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2023-08-31 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
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2023-08-31 Ben SoaresJAL-629 Small buglet with getting --seqid
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2023-08-31 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
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2023-08-29 Ben SoaresMerge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBinder_...
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2023-08-29 Ben SoaresJAL-4255 better grammar
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2023-08-29 Ben SoaresJAL-4255 Updated THIRDPARTYLIBS
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2023-08-29 Ben SoaresMerge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBinder_...
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2023-08-29 Ben SoaresJAL-4255 Added slf4j-nop jar and upgraded to last 1...
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2023-08-28 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stuff_be...
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2023-08-24 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stuff_be...
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2023-08-24 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
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2023-08-24 Ben SoaresJAL-629 Avoid hidden options dialog when saving in...
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2023-08-24 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_file_u...
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2023-08-24 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_annot...
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2023-08-24 Ben SoaresJAL-4250 Fix bug in vector rendition where more than...
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2023-08-24 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_annot...
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2023-08-24 Ben SoaresJAL-4250 Much simplified glyph creation removing most...
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2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_annot...
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2023-08-23 Ben SoaresJAL-4250 Fix one word bug for 'af.createEPS(file, renderer...
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2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_annot...
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2023-08-23 Ben SoaresJAL-4250 Updated jfreesvg to fix round stroke in linegraph.
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2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_annot...
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2023-08-23 Ben SoaresJAL-4250 Simplification of polygons and adjustments...
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2023-08-21 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_annot...
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2023-08-21 Ben SoaresJAL-4250 revert green to bright green
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2023-08-21 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_annot...
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2023-08-21 Ben SoaresJAL-4250 Conservative setting of ANTIALIAS and readjustment...
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2023-08-18 Ben SoaresJAL-4250 Make secondary structure annotation shapes...
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2023-08-18 Ben SoaresMerge branch 'improvement/JAL-4206_improve_JalviewFileChoose...
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2023-08-18 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_file_u...
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2023-08-18 Ben SoaresMerge branch 'improvement/JAL-4212_remove_macos_test_java_ic...
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2023-08-18 Ben SoaresMerge branch 'feature/JAL-244_Automatically_adjust_left_marg...
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2023-08-18 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_headl...
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2023-08-18 Ben SoaresMerge branch 'bug/JAL-4242_exception_when_pressing_escape_in...
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2023-08-18 Ben SoaresJAL-3416 Remove full height separators between new...
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2023-08-18 Ben SoaresJAL-3416 flatlaf and flatlaf-extras 3.2 jars
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