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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
2023-03-23	Ben Soares	JAL-629 don't clear appProps in tests	commit \| commitdiff \| tree
2023-03-23	Ben Soares	JAL-629 refactor ArgParser and helper classes all to...	commit \| commitdiff \| tree
2023-03-21	Ben Soares	JAL-629 null checks for Desktop.instance.closeAll(...	commit \| commitdiff \| tree
2023-03-18	Ben Soares	JAL-629 restore original tests memory settings	commit \| commitdiff \| tree
2023-03-18	Ben Soares	JAL-629 restore original tests memory settings	commit \| commitdiff \| tree
2023-03-18	Ben Soares	JAL-629 Check for new commandsSuccess before quit	commit \| commitdiff \| tree
2023-03-18	Ben Soares	JAL-629 move getdown update to earlier stage	commit \| commitdiff \| tree
2023-03-18	Ben Soares	JAL-629 Back to forking tests	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 All applications System.exits going through...	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 whittling down options for successful tests	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 whittling down options for successful tests	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 whittling down options for successful tests	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 whittling down options for successful tests	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 more memory to tests task	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 add in jvmArgs for memory for tests and keep...	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 remove jvmArgs for memory for tests. Increase...	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 Add in jvmArgs for memory for tests	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 closer to normal gradle settings with just...	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 increase test JVM size	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 failFast and new threads for each test	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 increased memory for clover	commit \| commitdiff \| tree
2023-03-16	Ben Soares	Merge branch 'features/r2_11_2_alphafold/JAL-629' into...	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 revert metal laf	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 Set Metal as default LAF for build server tests	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 fixed a test failing when run without a Jalview...	commit \| commitdiff \| tree
2023-03-15	Ben Soares	JAL-3833 fixed HiDPI test for macOS	commit \| commitdiff \| tree
2023-03-15	Ben Soares	JAL-629 Commands more objecty, less classy. FileLoader...	commit \| commitdiff \| tree
2023-03-13	Ben Soares	JAL-629 teardown in CommandsTest	commit \| commitdiff \| tree
2023-03-12	Ben Soares	JAL-629 Allow substitutions of {} = defaultCounter...	commit \| commitdiff \| tree
2023-03-11	Ben Soares	JAL-629 --substitutions --nosubstitutions flags, -...	commit \| commitdiff \| tree
2023-03-11	Ben Soares	JAL-629 Auto and Default count incrementer args. Flags...	commit \| commitdiff \| tree
2023-03-11	Ben Soares	JAL-629 start of CommandsTest. More ArgParserTests.	commit \| commitdiff \| tree
2023-03-10	Ben Soares	JAL-629 start of tests and more examples	commit \| commitdiff \| tree
2023-03-09	Ben Soares	JAL-629 start of tests	commit \| commitdiff \| tree
2023-03-09	Ben Soares	JAL-629 --argfile=glob implemented. Remove reference...	commit \| commitdiff \| tree
2023-03-08	Ben Soares	JAL-629 --close individually for each AlignFrame opened...	commit \| commitdiff \| tree
2023-03-08	Ben Soares	JAL-629 improved comment and return speed of StringUtils...	commit \| commitdiff \| tree
2023-03-08	Ben Soares	JAL-629 --quiet [no stdout], --quiet --quiet [no stderr...	commit \| commitdiff \| tree
2023-03-08	Ben Soares	JAL-629 Fix --headless for new args. Fix progressbar...	commit \| commitdiff \| tree
2023-03-08	Ben Soares	JAL-629 stash some TFType and PAEFile info into a PDBEntry	commit \| commitdiff \| tree
2023-03-06	Ben Soares	JAL-629 Fix null AlignPanel. More descriptive label...	commit \| commitdiff \| tree
2023-03-03	Ben Soares	JAL-629 Improved consistency of ArgParser classes ...	commit \| commitdiff \| tree
2023-03-02	Ben Soares	JAL-629 slight tidy up	commit \| commitdiff \| tree
2023-03-02	Ben Soares	JAL-629 Removal of unnecessary methods. Set pLTTD tempfac...	commit \| commitdiff \| tree
2023-03-02	Ben Soares	JAL-629 Some refactoring to allow more flexible use...	commit \| commitdiff \| tree
2023-02-28	Ben Soares	JAL-629 Firm up bootstrapArgs. Correct '-colour' in...	commit \| commitdiff \| tree
2023-02-27	Ben Soares	JAL-629 add AF examples for FER1_SPIOL. Link and display...	commit \| commitdiff \| tree
2023-02-27	Ben Soares	JAL-629 Fix Exceptions when running with CLI not headless	commit \| commitdiff \| tree
2023-02-27	Ben Soares	JAL-629 Guesstimate whether to set pLDDT with PDB file	commit \| commitdiff \| tree
2023-02-27	Ben Soares	JAL-629 JAL-4124 JAL-3855 remove deleted debugging...	commit \| commitdiff \| tree
2023-02-27	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-02-27	Ben Soares	JAL-629 removed debug prints. added .cif. added some...	commit \| commitdiff \| tree
2023-02-26	Ben Soares	JAL-629 PAE matrix file guesstimate from filename	commit \| commitdiff \| tree
2023-02-24	Ben Soares	JAL-629 Position GUI widgets for PDF file options....	commit \| commitdiff \| tree
2023-02-24	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-02-24	Ben Soares	JAL-629 add widgets to StructureChooser for tempfac...	commit \| commitdiff \| tree
2023-02-24	Ben Soares	JAL-629 helper function for getting sensible structure...	commit \| commitdiff \| tree
2023-02-24	Ben Soares	JAL-629 better test fixes. --props=... instead of ...	commit \| commitdiff \| tree
2023-02-24	Ben Soares	JAL-629 Made ArgValuesMap helper class, simplifies...	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 test fixing	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 Add debug messages for more failing tests	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 fixed a Log4j test by adding --debug arg	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 bootstrap args and properties. Remember index...	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 nf-core sample alignment files and a2m versions	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 fix a PAEMatrix casting error	commit \| commitdiff \| tree
2023-02-22	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
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