JAL-629 Change behaviour of --open GLOB to increment defaultLinkedId to allow --allfr...
[jalview.git] / src / jalview / bin /
2023-04-30 Ben SoaresJAL-629 Change behaviour of --open GLOB to increment...
2023-04-29 Ben SoaresJAL-629 Added --all arg, [*] linkedId and functionality...
2023-04-28 Ben SoaresJAL-629 Change colour scheme shortnames to something...
2023-04-27 Ben SoaresJAL-629 Fixed appending URLs
2023-04-27 Ben SoaresJAL-629 Changed --increment to --newframe to make sense...
2023-04-27 Ben SoaresJAL-629 allow opening URL as only argument(s)
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...
2023-04-23 Ben SoaresJAL-629 Change --open to --append and --opennew to...
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...
2023-04-14 Ben SoaresJAL-629 Adding PAE and TFType at structure loading...
2023-04-12 Ben SoaresJAL-629 Fix non-multi string bootstrap arg bug.
2023-04-12 Ben SoaresJAL-629 parse SubVals once with ArgValue. Ensure SubVal...
2023-04-12 Ben SoaresJAL-629 allow argfiles in argfiles, but avoid looping...
2023-04-12 Ben SoaresJAL-629 allow comments in argfiles '#'
2023-04-05 Ben SoaresJAL-629 Tests for FileUtils. Tidying counter substituti...
2023-04-04 Ben SoaresJAL-629 more info in usage statement
2023-04-04 Ben SoaresJAL-629 Start of Usage statement
2023-04-04 Ben SoaresJAL-629 More consistent printing of --arguments. Exampl...
2023-04-04 Ben SoaresJAL-629 Remove debugging comment
2023-04-04 Ben SoaresJAL-629 --initsubstitutions as a bootstrap arg, new...
2023-04-03 Ben SoaresJAL-629 sort files from java glob for predictability...
2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitution...
2023-03-30 Ben SoaresJAL-629 fix bug for opening single named file with...
2023-03-30 Ben SoaresJAL-629 Don't use new ArgParser if there are no --args...
2023-03-30 Ben SoaresJAL-629 fix SubVals npe
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
2023-03-25 Ben SoaresJAL-629 open initial non-Arg arguments as files in...
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement...
2023-03-24 Ben SoaresJAL-629 Test tidyup
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...
2023-03-12 Ben SoaresJAL-629 Allow substitutions of {} = defaultCounter...
2023-03-11 Ben SoaresJAL-629 --substitutions --nosubstitutions flags, -...
2023-03-11 Ben SoaresJAL-629 Auto and Default count incrementer args. Flags...
2023-03-10 Ben SoaresJAL-629 start of tests and more examples
2023-03-09 Ben SoaresJAL-629 start of tests
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference...
2023-03-08 Ben SoaresJAL-629 --close individually for each AlignFrame opened...
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...
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ...
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use...
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
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some...
2023-02-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects
2023-02-24 Ben SoaresJAL-629 helper function for getting sensible structure...
2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies...
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
2023-01-26 Ben SoaresJAL-629 adjust arg type for tempfac-shading -- was...
2023-01-24 James ProcterJAL-629 hacked in --tempfac-shading - hardcoded to...
2023-01-24 James ProcterJAL-629 suggest not breaking out of the structure proce...
2023-01-24 James ProcterJAL-629 don’t carry on Jalview.main if we’ve already...
2023-01-24 James ProcterJAL-629 don’t trash user’s system property file when...
2023-01-24 James ProcterJAL-629 don’t complain for Unary args
2023-01-24 James ProcterJAL-629 labelled breaks are frowned upon by everyone
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless...
2023-01-18 Ben SoaresJAL-629 make sequence id key 'seqid'
2023-01-16 Ben SoaresJAL-3416 More tweaking of FlatLaf. Problem with macOS...
2023-01-11 Ben SoaresJAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as...
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification...
2023-01-06 Ben SoaresJAL-3416 More explicit setting of FlatLaf macOS theme
2023-01-06 Ben SoaresJAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme...
2022-12-19 Ben SoaresJAL-629 Add image output and quit
2022-12-15 Ben SoaresJAL-629 move SubId to more logical place. Attempt remov...
2022-12-14 Ben SoaresJAL-629 Open Structure Viewer from cmdline
2022-12-09 Ben SoaresJAL-629 null check, fixed tests!
2022-12-08 Ben SoaresJAL-629 stray code deleted
2022-12-08 Ben SoaresJAL-629 Allow attachment of pAE file to a particular...
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options
2022-11-23 Ben SoaresJAL-629 Doing things with the command line arguments
2022-11-16 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG...
2022-11-16 Ben SoaresJAL-3416 make flatlaf default for linux improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf
2022-11-04 Ben SoaresJAL-1998 JAL-3772 JAL-3416 Merge conflict resolution...
2022-11-02 Ben SoaresJAL-1988 JAL-3772 Moving packages to somewhere more...
2022-11-01 Ben SoaresJAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE
2022-10-27 Ben SoaresMerge branch 'develop' into bug/JAL-1988_JAL-3772_impro...
2022-10-25 Ben SoaresJAL-3416 Making FlatLaF default for macs due to a probl...
2022-10-24 Ben SoaresJAL-1988 JAL-3772 Non-blocking modal dialogs for unsave...
2022-09-23 Ben SoaresJAL-1988 JAL-3772 Quit confirmation dialog boxes with...
2022-09-23 Ben SoaresJAL-3676 extra information about jalview_properties...
2022-08-08 Jim ProcterMerge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a...
2022-06-13 Jim ProcterMerge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS...
2022-06-13 Ben SoaresJAL-3416 remove flat as default for linux
2022-06-13 Ben SoaresJAL-3416 Added some mac specific FlatLAF settings....
2022-04-06 Ben SoaresJAL-3991 JAVA_COMPILE_VERSION put into build_properties...
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