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[jalview.git] / src / jalview / bin / Jalview.java

2023-09-14	Ben Soares	Merge branch 'develop' into feature/JAL-4274_configurab...	blob \| commitdiff
2023-09-13	Ben Soares	JAL-4262 Made deprecation warning properly modal bug/JAL-4277_dirname_substitution_always_absolute	blob \| commitdiff \| diff to current
2023-09-12	Ben Soares	JAL-4262 Allow HTML in the dialog box for link to CLI...	blob \| commitdiff \| diff to current
2023-09-12	Ben Soares	JAL-4285 Better checkFiles processing. Better dialog.	blob \| commitdiff \| diff to current
2023-09-12	Ben Soares	JAL-4285 JAL-4262 Added a scrollable dialog to display...	blob \| commitdiff \| diff to current
2023-09-11	Ben Soares	JAL-4001 corrected analytics message labels	blob \| commitdiff \| diff to current
2023-09-08	Ben Soares	JAL-4262 Dialog for GUI and WARN for CLI of old style...	blob \| commitdiff \| diff to current
2023-09-07	James Procter	JAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI	blob \| commitdiff \| diff to current
2023-09-06	James Procter	JAL-629 javadoc	blob \| commitdiff \| diff to current
2023-09-02	Ben Soares	Merge branch 'feature/JAL-629_--output_-_means_output_t...	blob \| commitdiff \| diff to current
2023-09-02	Ben Soares	JAL-629 Add accessors for argParser and bootstrapArgs feature/JAL-629_--output_-_means_output_to_STDOUT	blob \| commitdiff \| diff to current
2023-09-01	Ben Soares	Merge branch 'feature/JAL-629_--output_-_means_output_t...	blob \| commitdiff \| diff to current
2023-09-01	Ben Soares	JAL-629 Fix --structureimage and options	blob \| commitdiff \| diff to current
2023-08-18	Ben Soares	Merge branch 'improvement/JAL-3830_remove_dock_icon_in_...	blob \| commitdiff \| diff to current
2023-08-18	Ben Soares	JAL-3416 Remove full height separators between new... improvement/JAL-3416_FlatLaf_3.2	blob \| commitdiff \| diff to current
2023-08-10	Ben Soares	JAL-629 Change all stdout and stderr output to use...	blob \| commitdiff \| diff to current
2023-08-09	Ben Soares	JAL-629 Move more stdout messages to stderr when output...	blob \| commitdiff \| diff to current
2023-06-28	Ben Soares	JAL-4001 remove stray --headless mode analytic	blob \| commitdiff \| diff to current
2023-06-28	Ben Soares	Merge branch 'task/JAL-4001_Plausible_API' into improve...	blob \| commitdiff \| diff to current
2023-06-28	Ben Soares	JAL-4001 Remove analytics for --headless mode	blob \| commitdiff \| diff to current
2023-06-21	Ben Soares	JAL-4001 Rationalise user-agent string into HttpUtils	blob \| commitdiff \| diff to current
2023-06-21	Ben Soares	JAL-4001 Change wording from google to plausible or...	blob \| commitdiff \| diff to current
2023-06-20	Ben Soares	JAL-4001 rename the init method	blob \| commitdiff \| diff to current
2023-06-17	Ben Soares	JAL-4001 Check --nousagestats before doing analytics...	blob \| commitdiff \| diff to current
2023-06-16	Ben Soares	JAL-3830 Look for --headless mode and add -Djava.awt...	blob \| commitdiff \| diff to current
2023-06-16	Ben Soares	JAL-4001 Add a _geo=1 to query string and JSON. Add...	blob \| commitdiff \| diff to current
2023-06-08	Ben Soares	Merge branch 'develop' into task/JAL-4001_migrate_googl...	blob \| commitdiff \| diff to current
2023-06-08	Ben Soares	JAL-3416 FlatLaf SystemInfo failing in JalviewJS. ...	blob \| commitdiff \| diff to current
2023-06-08	Ben Soares	Merge branch 'develop' into task/JAL-4001_migrate_googl...	blob \| commitdiff \| diff to current
2023-06-07	James Procter	JAL-4195 add exception handling for all image output...	blob \| commitdiff \| diff to current
2023-06-07	James Procter	Merge branch 'patch/JAL-4195_cli_eps_export_npe' into...	blob \| commitdiff \| diff to current
2023-06-07	Ben Soares	Merge branch 'develop' into task/JAL-4001_migrate_googl...	blob \| commitdiff \| diff to current
2023-06-06	James Procter	JAL-629 - remove TODO from jalview.bin.Jalview since...	blob \| commitdiff \| diff to current
2023-06-06	James Procter	JAL-1551 a bit of javadoc for Jalview.testoutput methods	blob \| commitdiff \| diff to current
2023-06-01	Ben Soares	JAL-4001 Changed title+message to MessageManager	blob \| commitdiff \| diff to current
2023-06-01	Ben Soares	JAL-4193 JAL-4194 sessionProperties layer in Cache...	blob \| commitdiff \| diff to current
2023-05-30	Ben Soares	JAL-4121 slight refactoring of method name and added...	blob \| commitdiff \| diff to current
2023-05-27	Ben Soares	JAL-4121 Added a NPE check caught in tests. Added ...	blob \| commitdiff \| diff to current
2023-05-27	Ben Soares	JAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt...	blob \| commitdiff \| diff to current
2023-05-26	Ben Soares	JAL-4125 Fixed non-closing external viewers, also added...	blob \| commitdiff \| diff to current
2023-05-25	Ben Soares	JAL-3416 JAL-3820 FlatLaf default for everyone, includi...	blob \| commitdiff \| diff to current
2023-05-24	Ben Soares	JAL-3416 slightly improved colours for tabber pane...	blob \| commitdiff \| diff to current
2023-05-23	Ben Soares	JAL-629 Added --structureimage code and formatting...	blob \| commitdiff \| diff to current
2023-05-22	Ben Soares	JAL-629 --structureimage with formatting args.	blob \| commitdiff \| diff to current
2023-05-19	Ben Soares	JAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for...	blob \| commitdiff \| diff to current
2023-05-19	Ben Soares	JAL-629 Added Arg.Types and additional --help-type...	blob \| commitdiff \| diff to current
2023-05-18	Ben Soares	JAL-629 fixes to typed args	blob \| commitdiff \| diff to current
2023-05-18	Ben Soares	JAL-629 Added 'Type' to args and argvalues	blob \| commitdiff \| diff to current
2023-05-11	Ben Soares	JAL-629 Fix --tempfac. Hide non-working --notempfac...	blob \| commitdiff \| diff to current
2023-05-11	Ben Soares	JAL-629 Added linkedId to ArgValuesMap for reference...	blob \| commitdiff \| diff to current
2023-05-10	Ben Soares	JAL-629 More docs. Usage statement. Adjust some logging...	blob \| commitdiff \| diff to current
2023-05-04	Ben Soares	JAL-629 More NG arguments: --features, --annotations...	blob \| commitdiff \| diff to current
2023-05-03	Ben Soares	JAL-629 added eps and imagemap. Added --output and...	blob \| commitdiff \| diff to current
2023-04-26	Ben Soares	JAL-629 JAL-4167 Added args to tests. Fixed potential...	blob \| commitdiff \| diff to current
2023-04-24	Ben Soares	JAL-629 Add --nowebdiscovery. Distinguish arg=="open...	blob \| commitdiff \| diff to current
2023-04-22	Ben Soares	JAL-629 Test and fix --annotation --ssannotation args...	blob \| commitdiff \| diff to current
2023-04-19	Ben Soares	JAL-629 Now showing temp fac and secondary structure...	blob \| commitdiff \| diff to current
2023-04-12	Ben Soares	JAL-629 parse SubVals once with ArgValue. Ensure SubVal...	blob \| commitdiff \| diff to current
2023-04-04	Ben Soares	JAL-629 Start of Usage statement	blob \| commitdiff \| diff to current
2023-04-04	Ben Soares	JAL-629 --initsubstitutions as a bootstrap arg, new...	blob \| commitdiff \| diff to current
2023-04-03	Ben Soares	JAL-629 added setprop. More filename based substitution...	blob \| commitdiff \| diff to current
2023-03-29	Ben Soares	JAL-629 Added --opennew --nonews --nosplash. Added...	blob \| commitdiff \| diff to current
2023-03-28	Ben Soares	JAL-629 Opening files in new windows. not working yet	blob \| commitdiff \| diff to current
2023-03-23	Ben Soares	JAL-629 refactor ArgParser and helper classes all to...	blob \| commitdiff \| diff to current
2023-03-18	Ben Soares	JAL-629 Check for new commandsSuccess before quit	blob \| commitdiff \| diff to current
2023-03-18	Ben Soares	JAL-629 move getdown update to earlier stage	blob \| commitdiff \| diff to current
2023-03-17	Ben Soares	JAL-629 All applications System.exits going through...	blob \| commitdiff \| diff to current
2023-03-16	Ben Soares	JAL-629 revert metal laf	blob \| commitdiff \| diff to current
2023-03-16	Ben Soares	JAL-629 Set Metal as default LAF for build server tests	blob \| commitdiff \| diff to current
2023-03-15	Ben Soares	JAL-629 Commands more objecty, less classy. FileLoader...	blob \| commitdiff \| diff to current
2023-03-09	Ben Soares	JAL-629 --argfile=glob implemented. Remove reference...	blob \| commitdiff \| diff to current
2023-03-08	Ben Soares	JAL-629 --quiet [no stdout], --quiet --quiet [no stderr...	blob \| commitdiff \| diff to current
2023-03-08	Ben Soares	JAL-629 Fix --headless for new args. Fix progressbar...	blob \| commitdiff \| diff to current
2023-02-28	Ben Soares	JAL-629 Firm up bootstrapArgs. Correct '-colour' in...	blob \| commitdiff \| diff to current
2023-02-27	Ben Soares	JAL-629 Fix Exceptions when running with CLI not headless	blob \| commitdiff \| diff to current
2023-02-24	James Procter	Merge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects	blob \| commitdiff \| diff to current
2023-02-23	Ben Soares	JAL-629 bootstrap args and properties. Remember index...	blob \| commitdiff \| diff to current
2023-02-22	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	blob \| commitdiff \| diff to current
2023-02-20	Ben Soares	JAL-3416 Turn off (partial) flatlaf scaling for HiDPI...	blob \| commitdiff \| diff to current
2023-02-16	James Procter	Merge branch 'features/r2_11_2_alphafold/JAL-629' into...	blob \| commitdiff \| diff to current
2023-02-03	Ben Soares	JAL-629 Fasta sequence id reading whitespace fix. Flexi...	blob \| commitdiff \| diff to current
2023-01-30	Ben Soares	JAL-1988 Make sensible choices if only the opening... merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064	blob \| commitdiff \| diff to current
2023-01-24	James Procter	JAL-629 don’t carry on Jalview.main if we’ve already...	blob \| commitdiff \| diff to current
2023-01-23	Ben Soares	JAL-629 Attempts to add PAE to structure. --headless...	blob \| commitdiff \| diff to current
2023-01-16	Ben Soares	JAL-3416 More tweaking of FlatLaf. Problem with macOS...	blob \| commitdiff \| diff to current
2023-01-11	Ben Soares	JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as...	blob \| commitdiff \| diff to current
2023-01-06	Ben Soares	JAL-3416 More explicit setting of FlatLaf macOS theme	blob \| commitdiff \| diff to current
2023-01-06	Ben Soares	JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme...	blob \| commitdiff \| diff to current
2022-11-23	Ben Soares	JAL-629 Doing things with the command line arguments	blob \| commitdiff \| diff to current
2022-11-16	Ben Soares	Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG...	blob \| commitdiff \| diff to current
2022-11-16	Ben Soares	JAL-3416 make flatlaf default for linux improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf	blob \| commitdiff \| diff to current
2022-11-04	Ben Soares	JAL-1998 JAL-3772 JAL-3416 Merge conflict resolution...	blob \| commitdiff \| diff to current
2022-11-02	Ben Soares	JAL-1988 JAL-3772 Moving packages to somewhere more...	blob \| commitdiff \| diff to current
2022-11-01	Ben Soares	JAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE	blob \| commitdiff \| diff to current
2022-10-27	Ben Soares	Merge branch 'develop' into bug/JAL-1988_JAL-3772_impro...	blob \| commitdiff \| diff to current
2022-10-25	Ben Soares	JAL-3416 Making FlatLaF default for macs due to a probl...	blob \| commitdiff \| diff to current
2022-10-24	Ben Soares	JAL-1988 JAL-3772 Non-blocking modal dialogs for unsave...	blob \| commitdiff \| diff to current
2022-09-23	Ben Soares	JAL-1988 JAL-3772 Quit confirmation dialog boxes with...	blob \| commitdiff \| diff to current
2022-08-08	Jim Procter	Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a...	blob \| commitdiff \| diff to current
2022-06-13	Jim Procter	Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS...	blob \| commitdiff \| diff to current
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