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2023-05-16	Ben Soares	JAL-629 Finished documentation for new command lines.	commit \| commitdiff \| tree
2023-05-16	Ben Soares	JAL-629 Ensure precedence of named linked ID values...	commit \| commitdiff \| tree
2023-05-15	Ben Soares	JAL-629 More help text	commit \| commitdiff \| tree
2023-05-15	Ben Soares	Revert "JAL-629 Add a --threads argument to allow a...	commit \| commitdiff \| tree
2023-05-15	Ben Soares	JAL-629 Add a --threads argument to allow a limited...	commit \| commitdiff \| tree
2023-05-14	Ben Soares	JAL-629 add an {extension} substitution	commit \| commitdiff \| tree
2023-05-13	Ben Soares	JAL-629 launcher shell script uses jalview.bin.Launcher...	commit \| commitdiff \| tree
2023-05-12	Ben Soares	JAL-629 More docs	commit \| commitdiff \| tree
2023-05-12	Ben Soares	JAL-629 extra test for --output open*.ext when used...	commit \| commitdiff \| tree
2023-05-12	Ben Soares	JAL-629 Added --opened arg which is like limiting ...	commit \| commitdiff \| tree
2023-05-11	Ben Soares	JAL-629 Add some shortnames to args. Add Opt.OUTPUT...	commit \| commitdiff \| tree
2023-05-11	Ben Soares	JAL-629 Move clarguments documentation to default....	commit \| commitdiff \| tree
2023-05-11	Ben Soares	JAL-629 Fix --tempfac. Hide non-working --notempfac...	commit \| commitdiff \| tree
2023-05-11	Ben Soares	JAL-629 Added linkedId to ArgValuesMap for reference...	commit \| commitdiff \| tree
2023-05-10	Ben Soares	JAL-629 Check Arg options for obtaining boolean or...	commit \| commitdiff \| tree
2023-05-10	Ben Soares	JAL-629 Catch a NPE, fix a test	commit \| commitdiff \| tree
2023-05-10	Ben Soares	JAL-629 More docs. Usage statement. Adjust some logging...	commit \| commitdiff \| tree
2023-05-09	Ben Soares	JAL-629 Add --seqid for non-subval use, make arg value...	commit \| commitdiff \| tree
2023-05-09	Ben Soares	JAL-629 update a subval for structureviewer in the...	commit \| commitdiff \| tree
2023-05-09	Ben Soares	JAL-629 more docs	commit \| commitdiff \| tree
2023-05-09	Ben Soares	JAL-629 change --renderer to --textrenderer to be more...	commit \| commitdiff \| tree
2023-05-05	Ben Soares	JAL-629 test fixes	commit \| commitdiff \| tree
2023-05-04	Ben Soares	JAL-629 Moved additional CommandLineOperationsNG tests...	commit \| commitdiff \| tree
2023-05-04	Ben Soares	JAL-629 More NG arguments: --features, --annotations...	commit \| commitdiff \| tree
2023-05-03	Ben Soares	JAL-629 a bit more documentation	commit \| commitdiff \| tree
2023-05-03	Ben Soares	JAL-629 added eps and imagemap. Added --output and...	commit \| commitdiff \| tree
2023-05-02	Ben Soares	JAL-629 Changed --newframe and --allframes to --new...	commit \| commitdiff \| tree
2023-05-02	Ben Soares	JAL-629 Add --renderer arg/subval for vector output...	commit \| commitdiff \| tree
2023-05-01	Ben Soares	JAL-629 fix lang label names after adjusting colour...	commit \| commitdiff \| tree
2023-05-01	Ben Soares	JAL-629 real life test for --allframes	commit \| commitdiff \| tree
2023-04-30	Ben Soares	JAL-629 Change behaviour of --open GLOB to increment...	commit \| commitdiff \| tree
2023-04-29	Ben Soares	JAL-629 Only log to console FAILED tests	commit \| commitdiff \| tree
2023-04-29	Ben Soares	JAL-629 Added --all arg, [*] linkedId and functionality...	commit \| commitdiff \| tree
2023-04-28	Ben Soares	JAL-629 Fixed the argfile1 after subval separator change	commit \| commitdiff \| tree
2023-04-28	Ben Soares	JAL-629 Fixed the argfiletests after subval separator...	commit \| commitdiff \| tree
2023-04-28	Ben Soares	JAL-629 Fixed the argfile after subval separator change	commit \| commitdiff \| tree
2023-04-28	Ben Soares	JAL-629 Change colour scheme shortnames to something...	commit \| commitdiff \| tree
2023-04-28	Ben Soares	JAL-4167 Now we don't fail testTasks on No Matching...	commit \| commitdiff \| tree
2023-04-27	Ben Soares	JAL-629 Part-way to honouring --tests argument	commit \| commitdiff \| tree
2023-04-27	Ben Soares	JAL-629 start of help text	commit \| commitdiff \| tree
2023-04-27	Ben Soares	JAL-629 changed args in tests	commit \| commitdiff \| tree
2023-04-27	Ben Soares	JAL-629 Fixed appending URLs	commit \| commitdiff \| tree
2023-04-27	Ben Soares	JAL-629 Changed --increment to --newframe to make sense...	commit \| commitdiff \| tree
2023-04-27	Ben Soares	JAL-629 allow opening URL as only argument(s)	commit \| commitdiff \| tree
2023-04-27	Ben Soares	JAL-4167 Added OVERALL summary to bash output	commit \| commitdiff \| tree
2023-04-26	Ben Soares	JAL-4167 Added colours to bash output	commit \| commitdiff \| tree
2023-04-26	Ben Soares	JAL-4167 Allow a test to run in multiple testTasks	commit \| commitdiff \| tree
2023-04-26	Ben Soares	JAL-629 shorter wait times for this test	commit \| commitdiff \| tree
2023-04-26	Ben Soares	JAL-4167 Adjustments to get clover to work with normal...	commit \| commitdiff \| tree
2023-04-26	Ben Soares	JAL-4167 Adjustments to get clover to work with normal...	commit \| commitdiff \| tree
2023-04-26	Ben Soares	JAL-4167 Adjustments to get clover to work	commit \| commitdiff \| tree
2023-04-26	Ben Soares	JAL-629 JAL-4167 Added args to tests. Fixed potential...	commit \| commitdiff \| tree
2023-04-24	Ben Soares	JAL-629 Add --nowebdiscovery. Distinguish arg=="open...	commit \| commitdiff \| tree
2023-04-24	Ben Soares	JAL-629 Put commandsTest.jvprops in the right place	commit \| commitdiff \| tree
2023-04-24	Ben Soares	JAL-629 loaded props from arg in failing build server...	commit \| commitdiff \| tree
2023-04-24	Ben Soares	JAL-629 Dynamic sleep in test, more diagnostics	commit \| commitdiff \| tree
2023-04-24	Ben Soares	JAL-629 Dynamic sleep in test	commit \| commitdiff \| tree
2023-04-24	Ben Soares	JAL-629 Move diagnostics to the right place	commit \| commitdiff \| tree
2023-04-24	Ben Soares	JAL-629 Diagnosis output for failing test	commit \| commitdiff \| tree
2023-04-24	Ben Soares	JAL-629 Count VISIBLE annotations for tests	commit \| commitdiff \| tree
2023-04-24	Ben Soares	JAL-629 attempt to fix tests on build server (more...	commit \| commitdiff \| tree
2023-04-23	Ben Soares	JAL-629 single threaded test for viewer window for...	commit \| commitdiff \| tree
2023-04-23	Ben Soares	JAL-629 even longer wait for viewer window for build...	commit \| commitdiff \| tree
2023-04-23	Ben Soares	JAL-629 longer wait for viewer window for build server	commit \| commitdiff \| tree
2023-04-23	Ben Soares	JAL-629 Change --open to --append and --opennew to...	commit \| commitdiff \| tree
2023-04-22	Ben Soares	JAL-629 Test and fix --annotation --ssannotation args...	commit \| commitdiff \| tree
2023-04-19	Ben Soares	JAL-629 Now showing temp fac and secondary structure...	commit \| commitdiff \| tree
2023-04-14	Ben Soares	JAL-629 Adding PAE and TFType at structure loading...	commit \| commitdiff \| tree
2023-04-12	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 deleted test output file from repo	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 mild improvement to test	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 Fixed ~ based test for build server	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 Add substituteHomeDir to getDirname(). Tighten...	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 Put old -props back as will now use old parser	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 Fix non-multi string bootstrap arg bug.	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 setprop test disabled as feature is disabled	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 parse SubVals once with ArgValue. Ensure SubVals...	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 allow argfiles in argfiles, but avoid looping...	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 allow comments in argfiles '#'	commit \| commitdiff \| tree
2023-04-12	Ben Soares	JAL-629 DON'T use quotation marks in argfiles as they...	commit \| commitdiff \| tree
2023-04-05	Ben Soares	JAL-629 Tests for FileUtils. Tidying counter substitutions...	commit \| commitdiff \| tree
2023-04-04	Ben Soares	JAL-629 more info in usage statement	commit \| commitdiff \| tree
2023-04-04	Ben Soares	JAL-629 Start of Usage statement	commit \| commitdiff \| tree
2023-04-04	Ben Soares	JAL-629 More consistent printing of --arguments. Example...	commit \| commitdiff \| tree
2023-04-04	Ben Soares	JAL-629 Remove debugging comment	commit \| commitdiff \| tree
2023-04-04	Ben Soares	JAL-629 --initsubstitutions as a bootstrap arg, new...	commit \| commitdiff \| tree
2023-04-03	Ben Soares	JAL-629 sort files from java glob for predictability...	commit \| commitdiff \| tree
2023-04-03	Ben Soares	JAL-629 Removed --headless to fix CommandsTest	commit \| commitdiff \| tree
2023-04-03	Ben Soares	JAL-629 added setprop. More filename based substitutions...	commit \| commitdiff \| tree
2023-03-30	Ben Soares	JAL-629 More extensive tests with real files being...	commit \| commitdiff \| tree
2023-03-30	Ben Soares	JAL-629 fix bug for opening single named file with...	commit \| commitdiff \| tree
2023-03-30	Ben Soares	JAL-629 Don't use new ArgParser if there are no --args...	commit \| commitdiff \| tree
2023-03-30	Ben Soares	JAL-629 fix SubVals npe	commit \| commitdiff \| tree
2023-03-29	Ben Soares	JAL-629 extensive tests for ArgParser features	commit \| commitdiff \| tree
2023-03-29	Ben Soares	JAL-629 Added --opennew --nonews --nosplash. Added...	commit \| commitdiff \| tree
2023-03-28	Ben Soares	JAL-629 Opening files in new windows. not working yet	commit \| commitdiff \| tree
2023-03-25	Ben Soares	JAL-629 open initial non-Arg arguments as files in...	commit \| commitdiff \| tree
2023-03-25	Ben Soares	JAL-629 improvements to argparser toString. Improvements...	commit \| commitdiff \| tree
2023-03-24	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-03-24	Ben Soares	JAL-629 Test tidyup	commit \| commitdiff \| tree
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