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2023-06-09	Ben Soares	JAL-3599 STDOUT and STDERR saved and sent to System...	commit \| commitdiff \| tree
2023-06-09	Ben Soares	JAL-3599 Not redirecting STDOUT or STDERR just for...	commit \| commitdiff \| tree
2023-06-09	Ben Soares	JAL-3599 More stderr/stdout output to logs when anything	commit \| commitdiff \| tree
2023-06-09	Ben Soares	JAL-3599 More stderr/stdout output to logs when failed	commit \| commitdiff \| tree
2023-06-09	Ben Soares	JAL-3599 increase real and virtual time chrome runs...	commit \| commitdiff \| tree
2023-06-08	Ben Soares	JAL-3599 gradle tasks to test JalviewJS launches in...	commit \| commitdiff \| tree
2023-06-08	Ben Soares	JAL-3416 FlatLaf SystemInfo failing in JalviewJS. ...	commit \| commitdiff \| tree
2023-06-07	Ben Soares	Merge branch 'develop' into improvement/JAL-4193_cl_arg_prev...	commit \| commitdiff \| tree
2023-06-02	Ben Soares	JAL-3521 Updated debian build.gradle in utils/debian...	commit \| commitdiff \| tree
2023-06-01	Ben Soares	Merge branch 'develop' into improvement/JAL-4193_cl_arg_prev...	commit \| commitdiff \| tree
2023-06-01	Ben Soares	JAL-629 changes merged in from develop fixed it. Deleted...	commit \| commitdiff \| tree
2023-06-01	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-06-01	Ben Soares	JAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToStructu...	commit \| commitdiff \| tree
2023-06-01	Ben Soares	JAL-629 added data for test	commit \| commitdiff \| tree
2023-06-01	Ben Soares	JAL-4193 JAL-4194 sessionProperties layer in Cache...	commit \| commitdiff \| tree
2023-06-01	Ben Soares	JAL-629 better reference text for --nousagestats	commit \| commitdiff \| tree
2023-05-30	Ben Soares	JAL-629 JAL-4121 Added documentation to Help docs and...	commit \| commitdiff \| tree
2023-05-30	Ben Soares	JAL-4121 adjust test name	commit \| commitdiff \| tree
2023-05-30	Ben Soares	JAL-629 Better formatting of Arg.Opt options in usage...	commit \| commitdiff \| tree
2023-05-30	Ben Soares	JAL-4121 slight refactoring of method name and added...	commit \| commitdiff \| tree
2023-05-27	Ben Soares	JAL-4121 Added a NPE check caught in tests. Added ...	commit \| commitdiff \| tree
2023-05-27	Ben Soares	JAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt...	commit \| commitdiff \| tree
2023-05-26	Ben Soares	JAL-4125 Fixed non-closing external viewers, also added...	commit \| commitdiff \| tree
2023-05-26	Ben Soares	JAL-629 dispose of non-displaying StructureChooser...	commit \| commitdiff \| tree
2023-05-26	Ben Soares	Merge branch 'develop' into feature/JAL-3416_update_to_flatl...	commit \| commitdiff \| tree
2023-05-25	Ben Soares	JAL-3416 JAL-3820 FlatLaf default for everyone, including...	commit \| commitdiff \| tree
2023-05-25	Ben Soares	JAL-3416 better path name	commit \| commitdiff \| tree
2023-05-25	Ben Soares	JAL-3820 JAL-3830 improvements to script launching...	commit \| commitdiff \| tree
2023-05-25	Ben Soares	JAL-3820 Create and use 'Jalview app' symblinks to...	commit \| commitdiff \| tree
2023-05-25	Ben Soares	JAL-3416 remove old flatlaf jars from j8lib	commit \| commitdiff \| tree
2023-05-25	Ben Soares	JAL-4186 fixed a test	commit \| commitdiff \| tree
2023-05-25	Ben Soares	JAL-4186 Turn JvOptionPane Callable<Void> handlers...	commit \| commitdiff \| tree
2023-05-24	Ben Soares	JAL-4186 attempts to work in jalviewjs, still not working	commit \| commitdiff \| tree
2023-05-24	Ben Soares	JAL-4186 fix dialog. broken in JalviewJS	commit \| commitdiff \| tree
2023-05-24	Ben Soares	JAL-3416 slightly improved colours for tabber pane...	commit \| commitdiff \| tree
2023-05-24	Ben Soares	JAL-3416 Updated flatlaf libraries. Native libraries...	commit \| commitdiff \| tree
2023-05-23	Ben Soares	JAL-629 Updated help docs and fixed structure image...	commit \| commitdiff \| tree
2023-05-23	Ben Soares	JAL-629 Added --structureimage code and formatting...	commit \| commitdiff \| tree
2023-05-22	Ben Soares	JAL-629 --structureimage with formatting args.	commit \| commitdiff \| tree
2023-05-21	Ben Soares	JAL-629 Clarify sections of arguments with --help-all...	commit \| commitdiff \| tree
2023-05-20	Ben Soares	JAL-4187 JAL-629 JAL-3830 small adjustments after further...	commit \| commitdiff \| tree
2023-05-20	Ben Soares	JAL-3416 Ensure setFrameIcon(null) is set for remaining...	commit \| commitdiff \| tree
2023-05-20	Ben Soares	JAL-3416 Removed another internal Frame icon from title bar	commit \| commitdiff \| tree
2023-05-20	Ben Soares	JAL-4187 JAL-629 JAL-3830 adjustments to Cygwin and...	commit \| commitdiff \| tree
2023-05-20	Ben Soares	JAL-4160 JAL-3830 Improve jalview.bin.Launcher for...	commit \| commitdiff \| tree
2023-05-20	Ben Soares	JAL-4160 JAL-3830 Improve jalview.bin.Launcher for...	commit \| commitdiff \| tree
2023-05-19	Ben Soares	JAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for...	commit \| commitdiff \| tree
2023-05-19	Ben Soares	JAL-629 Fix missing icon for command line launch	commit \| commitdiff \| tree
2023-05-19	Ben Soares	JAL-629 Updated debian helpers for new command line	commit \| commitdiff \| tree
2023-05-19	Ben Soares	JAL-629 Updated launching scripts to 1) not insert...	commit \| commitdiff \| tree
2023-05-19	Ben Soares	JAL-629 Added Arg.Types and additional --help-type...	commit \| commitdiff \| tree
2023-05-18	Ben Soares	JAL-629 fixes to typed args	commit \| commitdiff \| tree
2023-05-18	Ben Soares	JAL-629 Added 'Type' to args and argvalues	commit \| commitdiff \| tree
2023-05-18	Ben Soares	JAL-629 fixes to help docs	commit \| commitdiff \| tree
2023-05-17	Ben Soares	JAL-629 Tidy up tests and replaced methods before merge...	commit \| commitdiff \| tree
2023-05-17	Ben Soares	JAL-629 Changed some old -arg to --arg in help docs...	commit \| commitdiff \| tree
2023-05-17	Ben Soares	JAL-629 tidying the help docs	commit \| commitdiff \| tree
2023-05-17	Ben Soares	JAL-629 delete stray files	commit \| commitdiff \| tree
2023-05-17	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-05-16	Ben Soares	JAL-629 Finished documentation for new command lines.	commit \| commitdiff \| tree
2023-05-16	Ben Soares	JAL-629 Ensure precedence of named linked ID values...	commit \| commitdiff \| tree
2023-05-15	Ben Soares	JAL-629 More help text	commit \| commitdiff \| tree
2023-05-15	Ben Soares	Revert "JAL-629 Add a --threads argument to allow a...	commit \| commitdiff \| tree
2023-05-15	Ben Soares	JAL-629 Add a --threads argument to allow a limited...	commit \| commitdiff \| tree
2023-05-14	Ben Soares	JAL-629 add an {extension} substitution	commit \| commitdiff \| tree
2023-05-13	Ben Soares	JAL-629 launcher shell script uses jalview.bin.Launcher...	commit \| commitdiff \| tree
2023-05-12	Ben Soares	JAL-629 More docs	commit \| commitdiff \| tree
2023-05-12	Ben Soares	JAL-629 extra test for --output open*.ext when used...	commit \| commitdiff \| tree
2023-05-12	Ben Soares	JAL-629 Added --opened arg which is like limiting ...	commit \| commitdiff \| tree
2023-05-11	Ben Soares	JAL-629 Add some shortnames to args. Add Opt.OUTPUT...	commit \| commitdiff \| tree
2023-05-11	Ben Soares	JAL-629 Move clarguments documentation to default....	commit \| commitdiff \| tree
2023-05-11	Ben Soares	JAL-629 Fix --tempfac. Hide non-working --notempfac...	commit \| commitdiff \| tree
2023-05-11	Ben Soares	JAL-629 Added linkedId to ArgValuesMap for reference...	commit \| commitdiff \| tree
2023-05-10	Ben Soares	JAL-629 Check Arg options for obtaining boolean or...	commit \| commitdiff \| tree
2023-05-10	Ben Soares	JAL-629 Catch a NPE, fix a test	commit \| commitdiff \| tree
2023-05-10	Ben Soares	JAL-629 More docs. Usage statement. Adjust some logging...	commit \| commitdiff \| tree
2023-05-09	Ben Soares	JAL-629 Add --seqid for non-subval use, make arg value...	commit \| commitdiff \| tree
2023-05-09	Ben Soares	JAL-629 update a subval for structureviewer in the...	commit \| commitdiff \| tree
2023-05-09	Ben Soares	JAL-629 more docs	commit \| commitdiff \| tree
2023-05-09	Ben Soares	JAL-629 change --renderer to --textrenderer to be more...	commit \| commitdiff \| tree
2023-05-05	Ben Soares	JAL-629 test fixes	commit \| commitdiff \| tree
2023-05-04	Ben Soares	JAL-629 Moved additional CommandLineOperationsNG tests...	commit \| commitdiff \| tree
2023-05-04	Ben Soares	JAL-629 More NG arguments: --features, --annotations...	commit \| commitdiff \| tree
2023-05-03	Ben Soares	JAL-629 a bit more documentation	commit \| commitdiff \| tree
2023-05-03	Ben Soares	JAL-629 added eps and imagemap. Added --output and...	commit \| commitdiff \| tree
2023-05-02	Ben Soares	JAL-629 Changed --newframe and --allframes to --new...	commit \| commitdiff \| tree
2023-05-02	Ben Soares	JAL-629 Add --renderer arg/subval for vector output...	commit \| commitdiff \| tree
2023-05-01	Ben Soares	JAL-629 fix lang label names after adjusting colour...	commit \| commitdiff \| tree
2023-05-01	Ben Soares	JAL-629 real life test for --allframes	commit \| commitdiff \| tree
2023-04-30	Ben Soares	JAL-629 Change behaviour of --open GLOB to increment...	commit \| commitdiff \| tree
2023-04-29	Ben Soares	JAL-629 Only log to console FAILED tests	commit \| commitdiff \| tree
2023-04-29	Ben Soares	JAL-629 Added --all arg, [*] linkedId and functionality...	commit \| commitdiff \| tree
2023-04-28	Ben Soares	JAL-629 Fixed the argfile1 after subval separator change	commit \| commitdiff \| tree
2023-04-28	Ben Soares	JAL-629 Fixed the argfiletests after subval separator...	commit \| commitdiff \| tree
2023-04-28	Ben Soares	JAL-629 Fixed the argfile after subval separator change	commit \| commitdiff \| tree
2023-04-28	Ben Soares	JAL-629 Change colour scheme shortnames to something...	commit \| commitdiff \| tree
2023-04-28	Ben Soares	JAL-4167 Now we don't fail testTasks on No Matching...	commit \| commitdiff \| tree
2023-04-27	Ben Soares	JAL-629 Part-way to honouring --tests argument	commit \| commitdiff \| tree
2023-04-27	Ben Soares	JAL-629 start of help text	commit \| commitdiff \| tree
2023-04-27	Ben Soares	JAL-629 changed args in tests	commit \| commitdiff \| tree
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