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JAL-629 Added --structureimage code and formatting args/subvals. Added tests for...
[jalview.git] / src / jalview / bin /
2023-05-23 Ben SoaresJAL-629 Added --structureimage code and formatting... tree | commitdiff
2023-05-22 Ben SoaresJAL-629 --structureimage with formatting args. tree | commitdiff
2023-05-21 Ben SoaresJAL-629 Clarify sections of arguments with --help-all... tree | commitdiff
2023-05-20 Ben SoaresJAL-4187 JAL-629 JAL-3830 small adjustments after furth... tree | commitdiff
2023-05-20 Ben SoaresJAL-4187 JAL-629 JAL-3830 adjustments to Cygwin and... tree | commitdiff
2023-05-20 Ben SoaresJAL-4160 JAL-3830 Improve jalview.bin.Launcher for... tree | commitdiff
2023-05-20 Ben SoaresJAL-4160 JAL-3830 Improve jalview.bin.Launcher for... tree | commitdiff
2023-05-19 Ben SoaresJAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for... tree | commitdiff
2023-05-19 Ben SoaresJAL-629 Added Arg.Types and additional --help-type... tree | commitdiff
2023-05-18 Ben SoaresJAL-629 fixes to typed args tree | commitdiff
2023-05-18 Ben SoaresJAL-629 Added 'Type' to args and argvalues tree | commitdiff
2023-05-16 Ben SoaresJAL-629 Ensure precedence of named linked ID values... tree | commitdiff
2023-05-15 Ben SoaresRevert "JAL-629 Add a --threads argument to allow a... tree | commitdiff
2023-05-15 Ben SoaresJAL-629 Add a --threads argument to allow a limited... tree | commitdiff
2023-05-14 Ben SoaresJAL-629 add an {extension} substitution tree | commitdiff
2023-05-13 Ben SoaresJAL-629 launcher shell script uses jalview.bin.Launcher... tree | commitdiff
2023-05-12 Ben SoaresJAL-629 Added --opened arg which is like limiting ... tree | commitdiff
2023-05-11 Ben SoaresJAL-629 Add some shortnames to args. Add Opt.OUTPUT... tree | commitdiff
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac... tree | commitdiff
2023-05-11 Ben SoaresJAL-629 Added linkedId to ArgValuesMap for reference... tree | commitdiff
2023-05-10 Ben SoaresJAL-629 Check Arg options for obtaining boolean or... tree | commitdiff
2023-05-10 Ben SoaresJAL-629 Catch a NPE, fix a test tree | commitdiff
2023-05-10 Ben SoaresJAL-629 More docs. Usage statement. Adjust some logging... tree | commitdiff
2023-05-09 Ben SoaresJAL-629 Add --seqid for non-subval use, make arg value... tree | commitdiff
2023-05-09 Ben SoaresJAL-629 change --renderer to --textrenderer to be more... tree | commitdiff
2023-05-04 Ben SoaresJAL-629 More NG arguments: --features, --annotations... tree | commitdiff
2023-05-03 Ben SoaresJAL-629 added eps and imagemap. Added --output and... tree | commitdiff
2023-05-02 Ben SoaresJAL-629 Changed --newframe and --allframes to --new... tree | commitdiff
2023-05-02 Ben SoaresJAL-629 Add --renderer arg/subval for vector output... tree | commitdiff
2023-04-30 Ben SoaresJAL-629 Change behaviour of --open GLOB to increment... tree | commitdiff
2023-04-29 Ben SoaresJAL-629 Added --all arg, [*] linkedId and functionality... tree | commitdiff
2023-04-28 Ben SoaresJAL-629 Change colour scheme shortnames to something... tree | commitdiff
2023-04-27 Ben SoaresJAL-629 Fixed appending URLs tree | commitdiff
2023-04-27 Ben SoaresJAL-629 Changed --increment to --newframe to make sense... tree | commitdiff
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
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