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JAL-3820 JAL-4189 Move checks for java executable symlinks to LaunchUtils ready for...
[jalview.git] / src / jalview / bin /
2023-04-27 Ben SoaresJAL-629 allow opening URL as only argument(s) tree | commitdiff
2023-04-26 Ben SoaresJAL-629 JAL-4167 Added args to tests. Fixed potential... tree | commitdiff
2023-04-24 Ben SoaresJAL-629 Add --nowebdiscovery. Distinguish arg=="open... tree | commitdiff
2023-04-23 Ben SoaresJAL-629 Change --open to --append and --opennew to... tree | commitdiff
2023-04-22 Ben SoaresJAL-629 Test and fix --annotation --ssannotation args... tree | commitdiff
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... tree | commitdiff
2023-04-14 Ben SoaresJAL-629 Adding PAE and TFType at structure loading... tree | commitdiff
2023-04-12 Ben SoaresJAL-629 Fix non-multi string bootstrap arg bug. tree | commitdiff
2023-04-12 Ben SoaresJAL-629 parse SubVals once with ArgValue. Ensure SubVal... tree | commitdiff
2023-04-12 Ben SoaresJAL-629 allow argfiles in argfiles, but avoid looping... tree | commitdiff
2023-04-12 Ben SoaresJAL-629 allow comments in argfiles '#' tree | commitdiff
2023-04-05 Ben SoaresJAL-629 Tests for FileUtils. Tidying counter substituti... tree | commitdiff
2023-04-04 Ben SoaresJAL-629 more info in usage statement tree | commitdiff
2023-04-04 Ben SoaresJAL-629 Start of Usage statement tree | commitdiff
2023-04-04 Ben SoaresJAL-629 More consistent printing of --arguments. Exampl... tree | commitdiff
2023-04-04 Ben SoaresJAL-629 Remove debugging comment tree | commitdiff
2023-04-04 Ben SoaresJAL-629 --initsubstitutions as a bootstrap arg, new... tree | commitdiff
2023-04-03 Ben SoaresJAL-629 sort files from java glob for predictability... tree | commitdiff
2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitution... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 fix bug for opening single named file with... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 Don't use new ArgParser if there are no --args... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 fix SubVals npe tree | commitdiff
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added... tree | commitdiff
2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet tree | commitdiff
2023-03-25 Ben SoaresJAL-629 open initial non-Arg arguments as files in... tree | commitdiff
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement... tree | commitdiff
2023-03-24 Ben SoaresJAL-629 Test tidyup tree | commitdiff
2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to... tree | commitdiff
2023-03-18 Ben SoaresJAL-629 Check for new commandsSuccess before quit tree | commitdiff
2023-03-18 Ben SoaresJAL-629 move getdown update to earlier stage tree | commitdiff
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... tree | commitdiff
2023-03-16 Ben SoaresJAL-629 revert metal laf tree | commitdiff
2023-03-16 Ben SoaresJAL-629 Set Metal as default LAF for build server tests tree | commitdiff
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader... tree | commitdiff
2023-03-12 Ben SoaresJAL-629 Allow substitutions of {} = defaultCounter... tree | commitdiff
2023-03-11 Ben SoaresJAL-629 --substitutions --nosubstitutions flags, -... tree | commitdiff
2023-03-11 Ben SoaresJAL-629 Auto and Default count incrementer args. Flags... tree | commitdiff
2023-03-10 Ben SoaresJAL-629 start of tests and more examples tree | commitdiff
2023-03-09 Ben SoaresJAL-629 start of tests tree | commitdiff
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 --close individually for each AlignFrame opened... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 --quiet [no stdout], --quiet --quiet [no stderr... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar... tree | commitdiff
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ... tree | commitdiff
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... tree | commitdiff
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in... tree | commitdiff
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless tree | commitdiff
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some... tree | commitdiff
2023-02-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects tree | commitdiff
2023-02-24 Ben SoaresJAL-629 helper function for getting sensible structure... tree | commitdiff
2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies... tree | commitdiff
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index... tree | commitdiff
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-20 Ben SoaresJAL-3416 Turn off (partial) flatlaf scaling for HiDPI... tree | commitdiff
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... tree | 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 tree | commitdiff
2023-01-26 Ben SoaresJAL-629 adjust arg type for tempfac-shading -- was... tree | commitdiff
2023-01-24 James ProcterJAL-629 hacked in --tempfac-shading - hardcoded to... tree | commitdiff
2023-01-24 James ProcterJAL-629 suggest not breaking out of the structure proce... tree | commitdiff
2023-01-24 James ProcterJAL-629 don’t carry on Jalview.main if we’ve already... tree | commitdiff
2023-01-24 James ProcterJAL-629 don’t trash user’s system property file when... tree | commitdiff
2023-01-24 James ProcterJAL-629 don’t complain for Unary args tree | commitdiff
2023-01-24 James ProcterJAL-629 labelled breaks are frowned upon by everyone tree | commitdiff
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... tree | commitdiff
2023-01-18 Ben SoaresJAL-629 make sequence id key 'seqid' tree | commitdiff
2023-01-16 Ben SoaresJAL-3416 More tweaking of FlatLaf. Problem with macOS... tree | commitdiff
2023-01-11 Ben SoaresJAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as... tree | commitdiff
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... tree | commitdiff
2023-01-06 Ben SoaresJAL-3416 More explicit setting of FlatLaf macOS theme tree | commitdiff
2023-01-06 Ben SoaresJAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme... tree | commitdiff
2022-12-19 Ben SoaresJAL-629 Add image output and quit tree | commitdiff
2022-12-15 Ben SoaresJAL-629 move SubId to more logical place. Attempt remov... tree | commitdiff
2022-12-14 Ben SoaresJAL-629 Open Structure Viewer from cmdline tree | commitdiff
2022-12-09 Ben SoaresJAL-629 null check, fixed tests! tree | commitdiff
2022-12-08 Ben SoaresJAL-629 stray code deleted tree | commitdiff
2022-12-08 Ben SoaresJAL-629 Allow attachment of pAE file to a particular... tree | commitdiff
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options tree | commitdiff
2022-11-23 Ben SoaresJAL-629 Doing things with the command line arguments tree | commitdiff
2022-11-16 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG... tree | commitdiff
2022-11-16 Ben SoaresJAL-3416 make flatlaf default for linux improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf tree | commitdiff
2022-11-04 Ben SoaresJAL-1998 JAL-3772 JAL-3416 Merge conflict resolution... tree | commitdiff
2022-11-02 Ben SoaresJAL-1988 JAL-3772 Moving packages to somewhere more... tree | commitdiff
2022-11-01 Ben SoaresJAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE tree | commitdiff
2022-10-27 Ben SoaresMerge branch 'develop' into bug/JAL-1988_JAL-3772_impro... tree | commitdiff
2022-10-25 Ben SoaresJAL-3416 Making FlatLaF default for macs due to a probl... tree | commitdiff
2022-10-24 Ben SoaresJAL-1988 JAL-3772 Non-blocking modal dialogs for unsave... tree | commitdiff
2022-09-23 Ben SoaresJAL-1988 JAL-3772 Quit confirmation dialog boxes with... tree | commitdiff
2022-09-23 Ben SoaresJAL-3676 extra information about jalview_properties... tree | commitdiff
2022-08-08 Jim ProcterMerge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a... tree | commitdiff
2022-06-13 Jim ProcterMerge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS... tree | commitdiff
2022-06-13 Ben SoaresJAL-3416 remove flat as default for linux tree | commitdiff
2022-06-13 Ben SoaresJAL-3416 Added some mac specific FlatLAF settings.... tree | commitdiff
2022-04-06 Ben SoaresJAL-3991 JAVA_COMPILE_VERSION put into build_properties... tree | commitdiff
2022-03-18 Ben SoaresJAL-3978 Using getdowninstanceappdir and getdowninstanc... tree | commitdiff
2022-03-18 Ben SoaresJAL-3978 New tasks to build archive 'old' dir with... tree | commitdiff
2022-03-08 Jim ProcterJAL-3746 apply copyright to source tree | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 tree | commitdiff
2022-03-08 Ben SoaresJAL-3103 Removed code and unused widgets for defaultBrowser tree | commitdiff
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