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JAL-629 Change --open to --append and --opennew to --open. Make --open(new) part...
2023-04-23 Ben SoaresJAL-629 Change --open to --append and --opennew to...
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2023-04-22 Ben SoaresJAL-629 Test and fix --annotation --ssannotation args...
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2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure...
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2023-04-14 Ben SoaresJAL-629 Adding PAE and TFType at structure loading...
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2023-04-12 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
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2023-04-12 Ben SoaresJAL-629 deleted test output file from repo
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2023-04-12 Ben SoaresJAL-629 mild improvement to test
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2023-04-12 Ben SoaresJAL-629 Fixed ~ based test for build server
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2023-04-12 Ben SoaresJAL-629 Add substituteHomeDir to getDirname(). Tighten...
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2023-04-12 Ben SoaresJAL-629 Put old -props back as will now use old parser
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2023-04-12 Ben SoaresJAL-629 Fix non-multi string bootstrap arg bug.
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2023-04-12 Ben SoaresJAL-629 setprop test disabled as feature is disabled
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2023-04-12 Ben SoaresJAL-629 parse SubVals once with ArgValue. Ensure SubVals...
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2023-04-12 Ben SoaresJAL-629 allow argfiles in argfiles, but avoid looping...
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2023-04-12 Ben SoaresJAL-629 allow comments in argfiles '#'
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2023-04-12 Ben SoaresJAL-629 DON'T use quotation marks in argfiles as they...
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2023-04-05 Ben SoaresJAL-629 Tests for FileUtils. Tidying counter substitutions...
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2023-04-04 Ben SoaresJAL-629 more info in usage statement
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2023-04-04 Ben SoaresJAL-629 Start of Usage statement
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2023-04-04 Ben SoaresJAL-629 More consistent printing of --arguments. Example...
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2023-04-04 Ben SoaresJAL-629 Remove debugging comment
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2023-04-04 Ben SoaresJAL-629 --initsubstitutions as a bootstrap arg, new...
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2023-04-03 Ben SoaresJAL-629 sort files from java glob for predictability...
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2023-04-03 Ben SoaresJAL-629 Removed --headless to fix CommandsTest
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2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitutions...
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2023-03-30 Ben SoaresJAL-629 More extensive tests with real files being...
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2023-03-30 Ben SoaresJAL-629 fix bug for opening single named file with...
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2023-03-30 Ben SoaresJAL-629 Don't use new ArgParser if there are no --args...
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2023-03-30 Ben SoaresJAL-629 fix SubVals npe
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2023-03-29 Ben SoaresJAL-629 extensive tests for ArgParser features
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2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added...
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2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet
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2023-03-25 Ben SoaresJAL-629 open initial non-Arg arguments as files in...
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2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvements...
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2023-03-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
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2023-03-24 Ben SoaresJAL-629 Test tidyup
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2023-03-23 Ben SoaresJAL-629 don't clear appProps in tests
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2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to...
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2023-03-21 Ben SoaresJAL-629 null checks for Desktop.instance.closeAll(...
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2023-03-18 Ben SoaresJAL-629 restore original tests memory settings
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2023-03-18 Ben SoaresJAL-629 restore original tests memory settings
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2023-03-18 Ben SoaresJAL-629 Check for new commandsSuccess before quit
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2023-03-18 Ben SoaresJAL-629 move getdown update to earlier stage
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2023-03-18 Ben SoaresJAL-629 Back to forking tests
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2023-03-17 Ben SoaresJAL-629 All applications System.exits going through...
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2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests
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2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests
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2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests
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2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests
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2023-03-17 Ben SoaresJAL-629 more memory to tests task
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2023-03-17 Ben SoaresJAL-629 add in jvmArgs for memory for tests and keep...
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2023-03-17 Ben SoaresJAL-629 remove jvmArgs for memory for tests. Increase...
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2023-03-17 Ben SoaresJAL-629 Add in jvmArgs for memory for tests
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2023-03-16 Ben SoaresJAL-629 closer to normal gradle settings with just...
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2023-03-16 Ben SoaresJAL-629 increase test JVM size
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2023-03-16 Ben SoaresJAL-629 failFast and new threads for each test
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2023-03-16 Ben SoaresJAL-629 increased memory for clover
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2023-03-16 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
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2023-03-16 Ben SoaresJAL-629 revert metal laf
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2023-03-16 Ben SoaresJAL-629 Set Metal as default LAF for build server tests
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2023-03-16 Ben SoaresJAL-629 fixed a test failing when run without a Jalview...
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2023-03-15 Ben SoaresJAL-3833 fixed HiDPI test for macOS
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2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader...
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2023-03-13 Ben SoaresJAL-629 teardown in CommandsTest
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2023-03-12 Ben SoaresJAL-629 Allow substitutions of {} = defaultCounter...
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2023-03-11 Ben SoaresJAL-629 --substitutions --nosubstitutions flags, -...
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2023-03-11 Ben SoaresJAL-629 Auto and Default count incrementer args. Flags...
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2023-03-11 Ben SoaresJAL-629 start of CommandsTest. More ArgParserTests.
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2023-03-10 Ben SoaresJAL-629 start of tests and more examples
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2023-03-09 Ben SoaresJAL-629 start of tests
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2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference...
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2023-03-08 Ben SoaresJAL-629 --close individually for each AlignFrame opened...
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2023-03-08 Ben SoaresJAL-629 improved comment and return speed of StringUtils...
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2023-03-08 Ben SoaresJAL-629 --quiet [no stdout], --quiet --quiet [no stderr...
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2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar...
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2023-03-08 Ben SoaresJAL-629 stash some TFType and PAEFile info into a PDBEntry
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2023-03-06 Ben SoaresJAL-629 Fix null AlignPanel. More descriptive label...
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2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ...
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2023-03-02 Ben SoaresJAL-629 slight tidy up
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2023-03-02 Ben SoaresJAL-629 Removal of unnecessary methods. Set pLTTD tempfac...
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2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use...
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2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in...
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2023-02-27 Ben SoaresJAL-629 add AF examples for FER1_SPIOL. Link and display...
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2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless
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2023-02-27 Ben SoaresJAL-629 Guesstimate whether to set pLDDT with PDB file
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2023-02-27 Ben SoaresJAL-629 JAL-4124 JAL-3855 remove deleted debugging...
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2023-02-27 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
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2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some...
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2023-02-26 Ben SoaresJAL-629 PAE matrix file guesstimate from filename
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2023-02-24 Ben SoaresJAL-629 Position GUI widgets for PDF file options....
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2023-02-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
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2023-02-24 Ben SoaresJAL-629 add widgets to StructureChooser for tempfac...
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2023-02-24 Ben SoaresJAL-629 helper function for getting sensible structure...
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2023-02-24 Ben SoaresJAL-629 better test fixes. --props=... instead of ...
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2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies...
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2023-02-23 Ben SoaresJAL-629 test fixing
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2023-02-23 Ben SoaresJAL-629 Add debug messages for more failing tests
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2023-02-23 Ben SoaresJAL-629 fixed a Log4j test by adding --debug arg
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2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index...
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2023-02-23 Ben SoaresJAL-629 nf-core sample alignment files and a2m versions
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