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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / bin / Jalview.java
2023-10-20 James ProcterMerge branch 'improvement/JAL-3783_upgrade_to_groovy... commit | commitdiff
2023-10-20 Ben SoaresJAL-4298 Remove a stray return in the processGroovyScri... commit | commitdiff
2023-10-19 Ben SoaresJAL-629 Fix --nodebug turning off debug mode from prope... commit | commitdiff
2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from... commit | commitdiff
2023-10-11 Ben SoaresJAL-629 correct a timeout. Correct passing html flag. commit | commitdiff
2023-10-11 Ben SoaresJAL-629 Add a timeout to modal dialogs for command... commit | commitdiff
2023-10-05 Ben SoaresJAL-4298 Fixed initial log level to see .jalview_proper... commit | commitdiff
2023-09-14 Ben SoaresMerge branch 'develop' into feature/JAL-4274_configurab... commit | commitdiff
2023-09-13 Ben SoaresJAL-4262 Made deprecation warning properly modal bug/JAL-4277_dirname_substitution_always_absolute commit | commitdiff
2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI... commit | commitdiff
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog. commit | commitdiff
2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display... commit | commitdiff
2023-09-11 Ben SoaresJAL-4001 corrected analytics message labels commit | commitdiff
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style... commit | commitdiff
2023-09-07 James ProcterJAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI commit | commitdiff
2023-09-06 James ProcterJAL-629 javadoc commit | commitdiff
2023-09-02 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... commit | commitdiff
2023-09-02 Ben SoaresJAL-629 Add accessors for argParser and bootstrapArgs feature/JAL-629_--output_-_means_output_to_STDOUT commit | commitdiff
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... commit | commitdiff
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options commit | commitdiff
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_... commit | commitdiff
2023-08-18 Ben SoaresJAL-3416 Remove full height separators between new... improvement/JAL-3416_FlatLaf_3.2 commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2023-08-09 Ben SoaresJAL-629 Move more stdout messages to stderr when output... commit | commitdiff
2023-06-28 Ben SoaresJAL-4001 remove stray --headless mode analytic commit | commitdiff
2023-06-28 Ben SoaresMerge branch 'task/JAL-4001_Plausible_API' into improve... commit | commitdiff
2023-06-28 Ben SoaresJAL-4001 Remove analytics for --headless mode commit | commitdiff
2023-06-22 Ben SoaresJAL-4001 Release_2_11_2 branch with Plausible analytics commit | commitdiff
2023-06-21 Ben SoaresJAL-4001 Rationalise user-agent string into HttpUtils commit | commitdiff
2023-06-21 Ben SoaresJAL-4001 Change wording from google to plausible or... commit | commitdiff
2023-06-20 Ben SoaresJAL-4001 rename the init method commit | commitdiff
2023-06-17 Ben SoaresJAL-4001 Check --nousagestats before doing analytics... commit | commitdiff
2023-06-16 Ben SoaresJAL-3830 Look for --headless mode and add -Djava.awt... commit | commitdiff
2023-06-16 Ben SoaresJAL-4001 Add a _geo=1 to query string and JSON. Add... commit | commitdiff
2023-06-08 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl... commit | commitdiff
2023-06-08 Ben SoaresJAL-3416 FlatLaf SystemInfo failing in JalviewJS. ... commit | commitdiff
2023-06-08 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl... commit | commitdiff
2023-06-07 James ProcterJAL-4195 add exception handling for all image output... commit | commitdiff
2023-06-07 James ProcterMerge branch 'patch/JAL-4195_cli_eps_export_npe' into... commit | commitdiff
2023-06-07 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl... commit | commitdiff
2023-06-06 James ProcterJAL-629 - remove TODO from jalview.bin.Jalview since... commit | commitdiff
2023-06-06 James ProcterJAL-1551 a bit of javadoc for Jalview.testoutput methods commit | commitdiff
2023-06-01 Ben SoaresJAL-4001 Changed title+message to MessageManager commit | commitdiff
2023-06-01 Ben SoaresJAL-4193 JAL-4194 sessionProperties layer in Cache... commit | commitdiff
2023-05-30 Ben SoaresJAL-4121 slight refactoring of method name and added... commit | commitdiff
2023-05-27 Ben SoaresJAL-4121 Added a NPE check caught in tests. Added ... commit | commitdiff
2023-05-27 Ben SoaresJAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt... commit | commitdiff
2023-05-26 Ben SoaresJAL-4125 Fixed non-closing external viewers, also added... commit | commitdiff
2023-05-25 Ben SoaresJAL-3416 JAL-3820 FlatLaf default for everyone, includi... commit | commitdiff
2023-05-24 Ben SoaresJAL-3416 slightly improved colours for tabber pane... commit | commitdiff
2023-05-23 Ben SoaresJAL-629 Added --structureimage code and formatting... commit | commitdiff
2023-05-22 Ben SoaresJAL-629 --structureimage with formatting args. commit | commitdiff
2023-05-19 Ben SoaresJAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for... commit | commitdiff
2023-05-19 Ben SoaresJAL-629 Added Arg.Types and additional --help-type... commit | commitdiff
2023-05-18 Ben SoaresJAL-629 fixes to typed args commit | commitdiff
2023-05-18 Ben SoaresJAL-629 Added 'Type' to args and argvalues commit | commitdiff
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac... commit | commitdiff
2023-05-11 Ben SoaresJAL-629 Added linkedId to ArgValuesMap for reference... commit | commitdiff
2023-05-10 Ben SoaresJAL-629 More docs. Usage statement. Adjust some logging... commit | commitdiff
2023-05-04 Ben SoaresJAL-629 More NG arguments: --features, --annotations... commit | commitdiff
2023-05-03 Ben SoaresJAL-629 added eps and imagemap. Added --output and... commit | commitdiff
2023-04-26 Ben SoaresJAL-629 JAL-4167 Added args to tests. Fixed potential... commit | commitdiff
2023-04-24 Ben SoaresJAL-629 Add --nowebdiscovery. Distinguish arg=="open... commit | commitdiff
2023-04-22 Ben SoaresJAL-629 Test and fix --annotation --ssannotation args... commit | commitdiff
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... commit | commitdiff
2023-04-12 Ben SoaresJAL-629 parse SubVals once with ArgValue. Ensure SubVal... commit | commitdiff
2023-04-04 Ben SoaresJAL-629 Start of Usage statement commit | commitdiff
2023-04-04 Ben SoaresJAL-629 --initsubstitutions as a bootstrap arg, new... commit | commitdiff
2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitution... commit | commitdiff
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added... commit | commitdiff
2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet commit | commitdiff
2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to... commit | commitdiff
2023-03-18 Ben SoaresJAL-629 Check for new commandsSuccess before quit commit | commitdiff
2023-03-18 Ben SoaresJAL-629 move getdown update to earlier stage commit | commitdiff
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... commit | commitdiff
2023-03-16 Ben SoaresJAL-629 revert metal laf commit | commitdiff
2023-03-16 Ben SoaresJAL-629 Set Metal as default LAF for build server tests commit | commitdiff
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader... commit | commitdiff
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference... commit | commitdiff
2023-03-08 Ben SoaresJAL-629 --quiet [no stdout], --quiet --quiet [no stderr... commit | commitdiff
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar... commit | commitdiff
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in... commit | commitdiff
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless commit | commitdiff
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects commit | commitdiff
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index... commit | commitdiff
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff
2023-02-20 Ben SoaresJAL-3416 Turn off (partial) flatlaf scaling for HiDPI... commit | commitdiff
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... commit | commitdiff
2023-01-30 Ben SoaresJAL-1988 Make sensible choices if only the opening... merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064 commit | commitdiff
2023-01-24 James ProcterJAL-629 don’t carry on Jalview.main if we’ve already... commit | commitdiff
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... commit | commitdiff
2023-01-16 Ben SoaresJAL-3416 More tweaking of FlatLaf. Problem with macOS... commit | commitdiff
2023-01-11 Ben SoaresJAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as... commit | commitdiff
2023-01-06 Ben SoaresJAL-3416 More explicit setting of FlatLaf macOS theme commit | commitdiff
2023-01-06 Ben SoaresJAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme... commit | commitdiff
2022-11-23 Ben SoaresJAL-629 Doing things with the command line arguments commit | commitdiff
2022-11-16 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG... commit | commitdiff
2022-11-16 Ben SoaresJAL-3416 make flatlaf default for linux improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf commit | commitdiff
2022-11-04 Ben SoaresJAL-1998 JAL-3772 JAL-3416 Merge conflict resolution... commit | commitdiff
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