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2023-12-15	Ben Soares	JAL-4290 Move some annotation visibility settings to...	commit \| commitdiff \| tree
2023-12-12	Ben Soares	JAL-4353 bigger tighter test	commit \| commitdiff \| tree
2023-12-12	Ben Soares	Merge branch 'bug/JAL-4353_cannot_output_multiple_different_...	commit \| commitdiff \| tree
2023-12-12	Ben Soares	JAL-4353 helper method and test for primary/secondary...	commit \| commitdiff \| tree
2023-12-06	Ben Soares	JAL-4353 re-used random color code	commit \| commitdiff \| tree
2023-12-06	Ben Soares	JAL-4353 Preserve the user given 'linkedId' with ArgValue...	commit \| commitdiff \| tree
2023-12-06	Ben Soares	JAL-4353 Add a 'random' colour to produce a random...	commit \| commitdiff \| tree
2023-12-05	Ben Soares	JAL-4353 Add secondary Types for Args, for STRUCTUREIMAGE...	commit \| commitdiff \| tree
2023-12-01	Ben Soares	JAL-4243 Updated bio.tools record and JSON (version...	commit \| commitdiff \| tree
2023-11-30	Ben Soares	JAL-4344 careful application of -Djava.awt.headless...	commit \| commitdiff \| tree
2023-11-20	Ben Soares	JAL-4348 Add newer versions of Chimera and ChimeraX...	commit \| commitdiff \| tree
2023-11-16	Ben Soares	JAL-4243 Updated bio.tools record for 2.11.3.0	commit \| commitdiff \| tree
2023-11-16	Ben Soares	JAL-4340 Change launch scripts to be xresources to...	commit \| commitdiff \| tree
2023-11-09	Ben Soares	JAL-4090 minor missing word correction to whatsnew	commit \| commitdiff \| tree
2023-10-31	Ben Soares	JAL-4319 Downgrade shadow(Jar) module to stop triggering...	commit \| commitdiff \| tree
2023-10-25	Ben Soares	Merge branch 'develop' into bug/JAL-4289_group_boundary_not_...	commit \| commitdiff \| tree
2023-10-20	Ben Soares	JAL-4298 Update help docs to reflect Groovy changes	commit \| commitdiff \| tree
2023-10-20	Ben Soares	JAL-4298 Remove a stray return in the processGroovyScript...	commit \| commitdiff \| tree
2023-10-20	Ben Soares	JAL-4298 another implicated line	commit \| commitdiff \| tree
2023-10-19	Ben Soares	Merge branch 'patch/JAL-4298_synchronize_consoledoc...	commit \| commitdiff \| tree
2023-10-19	Ben Soares	JAL-629 Fix --nodebug turning off debug mode from properties	commit \| commitdiff \| tree
2023-10-19	Ben Soares	JAL-4298 comment markers	commit \| commitdiff \| tree
2023-10-19	Ben Soares	Merge branch 'improvement/JAL-3783_upgrade_to_groovy...	commit \| commitdiff \| tree
2023-10-19	Ben Soares	JAL-4305 Isolate and unify the Jalview object from...	commit \| commitdiff \| tree
2023-10-19	Ben Soares	Merge branch 'improvement/JAL-3783_upgrade_to_groovy...	commit \| commitdiff \| tree
2023-10-18	Ben Soares	JAL-629 Run non-alignframe linked groovy scripts. ...	commit \| commitdiff \| tree
2023-10-18	Ben Soares	JAL-4262 Fix the nonblockingdialog so that Jalview...	commit \| commitdiff \| tree
2023-10-13	Ben Soares	JAL-3783 Updated groovy jars. Requires javaparser...	commit \| commitdiff \| tree
2023-10-13	Ben Soares	JAL-3783 Updated build process to allow multiple groovy...	commit \| commitdiff \| tree
2023-10-12	Ben Soares	JAL-3772 Fix the logic of prompt to save URL loaded...	commit \| commitdiff \| tree
2023-10-12	Ben Soares	JAL-629 null check and neatening code	commit \| commitdiff \| tree
2023-10-11	Ben Soares	JAL-629 correct a timeout. Correct passing html flag.	commit \| commitdiff \| tree
2023-10-11	Ben Soares	JAL-629 Add a timeout to modal dialogs for command...	commit \| commitdiff \| tree
2023-10-11	Ben Soares	JAL-629 Change getdown not to add -open argument	commit \| commitdiff \| tree
2023-10-11	Ben Soares	JAL-629 Remove argfiles from the hashset of used argfiles...	commit \| commitdiff \| tree
2023-10-11	Ben Soares	JAL-3772 Preference to NOT prompt to save remotely...	commit \| commitdiff \| tree
2023-10-11	Ben Soares	JAL-4298 Added diagnostics and minor dimension changes...	commit \| commitdiff \| tree
2023-10-05	Ben Soares	JAL-4298 Fixed initial log level to see .jalview_properties...	commit \| commitdiff \| tree
2023-10-03	Ben Soares	JAL-4001 Only use acquireDialogQueue and releaseDialogQueue...	commit \| commitdiff \| tree
2023-10-03	Ben Soares	Merge branch 'develop' into bug/JAL-4289_group_boundary_not_...	commit \| commitdiff \| tree
2023-10-02	Ben Soares	JAL-4289 In fastPaint(), don't render one more than...	commit \| commitdiff \| tree
2023-09-21	Ben Soares	JAL-4265 Use ColourUtils.parseColourString() for consistency...	commit \| commitdiff \| tree
2023-09-21	Ben Soares	Merge branch 'develop' into merge/JAL-4262+JAL-4265...	commit \| commitdiff \| tree
2023-09-20	Ben Soares	JAL-4265 Use ColorUtils.parseColourString() and adjust...	commit \| commitdiff \| tree
2023-09-20	Ben Soares	JAL-4265 Added saveState and restoreState to interface...	commit \| commitdiff \| tree
2023-09-20	Ben Soares	JAL-629 Explanation of \{m\} in case anyone actually...	commit \| commitdiff \| tree
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
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