Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview / bin / Jalview.java
2024-07-31 Ben SoaresJAL-3631 Changes to Getdown to call getdown-launcher...
2024-06-27 Ben SoaresJAL-3631 Add property to let log4j know we're not runni...
2024-06-27 Ben SoaresJAL-3631 Log4j logging to .jalview.log file when reques...
2024-06-25 Ben SoaresJAL-3631 JAL-3384 Install4j launch now redirects STDOUT...
2024-06-19 Ben SoaresJAL-3631 Rename/rationalise informational system proper...
2024-06-14 Ben SoaresJAL-3631 JAL-4104 More consistent system property names...
2024-06-13 Ben SoaresJAL-3845 Add a popup error message, with instructions...
2024-06-12 Ben SoaresJAL-3631 Name changes to system properties and a fallba...
2024-05-15 Ben SoaresJAL-4409 Refactoring to allow easier reuse of classes...
2024-05-14 Ben SoaresJAL-4414 Add a FileNotFoundException when identifying...
2023-10-20 James ProcterMerge branch 'improvement/JAL-3783_upgrade_to_groovy...
2023-10-20 Ben SoaresJAL-4298 Remove a stray return in the processGroovyScri...
2023-10-19 Ben SoaresJAL-629 Fix --nodebug turning off debug mode from prope...
2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from...
2023-10-11 Ben SoaresJAL-629 correct a timeout. Correct passing html flag.
2023-10-11 Ben SoaresJAL-629 Add a timeout to modal dialogs for command...
2023-10-05 Ben SoaresJAL-4298 Fixed initial log level to see .jalview_proper...
2023-09-14 Ben SoaresMerge branch 'develop' into feature/JAL-4274_configurab...
2023-09-13 Ben SoaresJAL-4262 Made deprecation warning properly modal bug/JAL-4277_dirname_substitution_always_absolute
2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI...
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog.
2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display...
2023-09-11 Ben SoaresJAL-4001 corrected analytics message labels
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style...
2023-09-07 James ProcterJAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI
2023-09-06 James ProcterJAL-629 javadoc
2023-09-02 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t...
2023-09-02 Ben SoaresJAL-629 Add accessors for argParser and bootstrapArgs feature/JAL-629_--output_-_means_output_to_STDOUT
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t...
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_...
2023-08-18 Ben SoaresJAL-3416 Remove full height separators between new... improvement/JAL-3416_FlatLaf_3.2
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use...
2023-08-09 Ben SoaresJAL-629 Move more stdout messages to stderr when output...
2023-06-28 Ben SoaresJAL-4001 remove stray --headless mode analytic
2023-06-28 Ben SoaresMerge branch 'task/JAL-4001_Plausible_API' into improve...
2023-06-28 Ben SoaresJAL-4001 Remove analytics for --headless mode
2023-06-22 Ben SoaresJAL-4001 Release_2_11_2 branch with Plausible analytics
2023-06-21 Ben SoaresJAL-4001 Rationalise user-agent string into HttpUtils
2023-06-21 Ben SoaresJAL-4001 Change wording from google to plausible or...
2023-06-20 Ben SoaresJAL-4001 rename the init method
2023-06-17 Ben SoaresJAL-4001 Check --nousagestats before doing analytics...
2023-06-16 Ben SoaresJAL-3830 Look for --headless mode and add -Djava.awt...
2023-06-16 Ben SoaresJAL-4001 Add a _geo=1 to query string and JSON. Add...
2023-06-08 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl...
2023-06-08 Ben SoaresJAL-3416 FlatLaf SystemInfo failing in JalviewJS. ...
2023-06-08 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl...
2023-06-07 James ProcterJAL-4195 add exception handling for all image output...
2023-06-07 James ProcterMerge branch 'patch/JAL-4195_cli_eps_export_npe' into...
2023-06-07 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl...
2023-06-06 James ProcterJAL-629 - remove TODO from jalview.bin.Jalview since...
2023-06-06 James ProcterJAL-1551 a bit of javadoc for Jalview.testoutput methods
2023-06-01 Ben SoaresJAL-4001 Changed title+message to MessageManager
2023-06-01 Ben SoaresJAL-4193 JAL-4194 sessionProperties layer in Cache...
2023-05-30 Ben SoaresJAL-4121 slight refactoring of method name and added...
2023-05-27 Ben SoaresJAL-4121 Added a NPE check caught in tests. Added ...
2023-05-27 Ben SoaresJAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt...
2023-05-26 Ben SoaresJAL-4125 Fixed non-closing external viewers, also added...
2023-05-25 Ben SoaresJAL-3416 JAL-3820 FlatLaf default for everyone, includi...
2023-05-24 Ben SoaresJAL-3416 slightly improved colours for tabber pane...
2023-05-23 Ben SoaresJAL-629 Added --structureimage code and formatting...
2023-05-22 Ben SoaresJAL-629 --structureimage with formatting args.
2023-05-19 Ben SoaresJAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for...
2023-05-19 Ben SoaresJAL-629 Added Arg.Types and additional --help-type...
2023-05-18 Ben SoaresJAL-629 fixes to typed args
2023-05-18 Ben SoaresJAL-629 Added 'Type' to args and argvalues
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac...
2023-05-11 Ben SoaresJAL-629 Added linkedId to ArgValuesMap for reference...
2023-05-10 Ben SoaresJAL-629 More docs. Usage statement. Adjust some logging...
2023-05-04 Ben SoaresJAL-629 More NG arguments: --features, --annotations...
2023-05-03 Ben SoaresJAL-629 added eps and imagemap. Added --output and...
2023-04-26 Ben SoaresJAL-629 JAL-4167 Added args to tests. Fixed potential...
2023-04-24 Ben SoaresJAL-629 Add --nowebdiscovery. Distinguish arg=="open...
2023-04-22 Ben SoaresJAL-629 Test and fix --annotation --ssannotation args...
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure...
2023-04-12 Ben SoaresJAL-629 parse SubVals once with ArgValue. Ensure SubVal...
2023-04-04 Ben SoaresJAL-629 Start of Usage statement
2023-04-04 Ben SoaresJAL-629 --initsubstitutions as a bootstrap arg, new...
2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitution...
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added...
2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet
2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to...
2023-03-18 Ben SoaresJAL-629 Check for new commandsSuccess before quit
2023-03-18 Ben SoaresJAL-629 move getdown update to earlier stage
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through...
2023-03-16 Ben SoaresJAL-629 revert metal laf
2023-03-16 Ben SoaresJAL-629 Set Metal as default LAF for build server tests
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader...
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference...
2023-03-08 Ben SoaresJAL-629 --quiet [no stdout], --quiet --quiet [no stderr...
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar...
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in...
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index...
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-02-20 Ben SoaresJAL-3416 Turn off (partial) flatlaf scaling for HiDPI...
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi...
2023-01-30 Ben SoaresJAL-1988 Make sensible choices if only the opening... merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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