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jalview.git
2023-04-14 Ben SoaresJAL-629 Adding PAE and TFType at structure loading... commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 deleted test output file from repo commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 mild improvement to test commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 Fixed ~ based test for build server commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 Add substituteHomeDir to getDirname(). Tighten... commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 Put old -props back as will now use old parser commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 Fix non-multi string bootstrap arg bug. commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 setprop test disabled as feature is disabled commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 parse SubVals once with ArgValue. Ensure SubVal... commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 allow argfiles in argfiles, but avoid looping... commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 allow comments in argfiles '#' commit | commitdiff | tree | snapshot
2023-04-12 Ben SoaresJAL-629 DON'T use quotation marks in argfiles as they... commit | commitdiff | tree | snapshot
2023-04-05 Ben SoaresJAL-629 Tests for FileUtils. Tidying counter substituti... commit | commitdiff | tree | snapshot
2023-04-04 Ben SoaresJAL-629 more info in usage statement commit | commitdiff | tree | snapshot
2023-04-04 Ben SoaresJAL-629 Start of Usage statement commit | commitdiff | tree | snapshot
2023-04-04 Ben SoaresJAL-629 More consistent printing of --arguments. Exampl... commit | commitdiff | tree | snapshot
2023-04-04 Ben SoaresJAL-629 Remove debugging comment commit | commitdiff | tree | snapshot
2023-04-04 Ben SoaresJAL-629 --initsubstitutions as a bootstrap arg, new... commit | commitdiff | tree | snapshot
2023-04-03 Ben SoaresJAL-629 sort files from java glob for predictability... commit | commitdiff | tree | snapshot
2023-04-03 Ben SoaresJAL-629 Removed --headless to fix CommandsTest commit | commitdiff | tree | snapshot
2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitution... commit | commitdiff | tree | snapshot
2023-03-31 James ProcterMerge branch 'features/JAL-4134_treeviewerforcolumns... feature/JAL-4162_Read_and_write_Relaxed_PHYLIP_format new_feature/JAL-4019_ambiguous_base_colourscheme commit | commitdiff | tree | snapshot
2023-03-30 Ben SoaresJAL-629 More extensive tests with real files being... commit | commitdiff | tree | snapshot
2023-03-30 Ben SoaresJAL-629 fix bug for opening single named file with... commit | commitdiff | tree | snapshot
2023-03-30 Ben SoaresJAL-629 Don't use new ArgParser if there are no --args... commit | commitdiff | tree | snapshot
2023-03-30 Ben SoaresJAL-629 fix SubVals npe commit | commitdiff | tree | snapshot
2023-03-29 Ben SoaresJAL-629 extensive tests for ArgParser features commit | commitdiff | tree | snapshot
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added... commit | commitdiff | tree | snapshot
2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet commit | commitdiff | tree | snapshot
2023-03-25 Ben SoaresJAL-629 open initial non-Arg arguments as files in... commit | commitdiff | tree | snapshot
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement... commit | commitdiff | tree | snapshot
2023-03-24 James ProcterMerge branch 'develop' into features/JAL-4134_treeviewe... commit | commitdiff | tree | snapshot
2023-03-24 James ProcterJAL-4158 first attempt at stashing colours for contact... commit | commitdiff | tree | snapshot
2023-03-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-03-24 Ben SoaresJAL-629 Test tidyup commit | commitdiff | tree | snapshot
2023-03-23 James ProcterMerge branch 'patch/JAL-4153_flakyJvCacheableInputBoxTe... commit | commitdiff | tree | snapshot
2023-03-23 Ben SoaresJAL-629 don't clear appProps in tests commit | commitdiff | tree | snapshot
2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to... commit | commitdiff | tree | snapshot
2023-03-21 Ben SoaresJAL-629 null checks for Desktop.instance.closeAll(... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 override default hasTree so PAE tree is saved! commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4153 longer Thread.sleep() calls in the hope that... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 - missing Jalview project JAXB class - st... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterMerge branch 'develop' into features/JAL-4134_treeviewe... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4150 test and quick patch copying code from AlignFr... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-2349 JAL-4134 Console log messages for contact... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 propagate column selection changes in tree... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 fix off-by-one in selection commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 fix NPEs when matrix not resolved or alignment... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 better popup menu name ‘Tree for Contact Matrix’ commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-2349 test TODOs commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-2349 fix off by one when resolving columns for... commit | commitdiff | tree | snapshot
2023-03-18 Ben SoaresJAL-629 restore original tests memory settings commit | commitdiff | tree | snapshot
2023-03-18 Ben SoaresJAL-629 restore original tests memory settings commit | commitdiff | tree | snapshot
2023-03-18 Ben SoaresJAL-629 Check for new commandsSuccess before quit commit | commitdiff | tree | snapshot
2023-03-18 Ben SoaresJAL-629 move getdown update to earlier stage commit | commitdiff | tree | snapshot
2023-03-18 Ben SoaresJAL-629 Back to forking tests commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests commit | commitdiff | tree | snapshot
2023-03-17 James ProcterJAL-4134 fix up column selection when hidden regions... commit | commitdiff | tree | snapshot
2023-03-17 James ProcterJAL-4134 store/restore Newick tree for PAE annotation row commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 whittling down options for successful tests commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 more memory to tests task commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 add in jvmArgs for memory for tests and keep... commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 remove jvmArgs for memory for tests. Increase... commit | commitdiff | tree | snapshot
2023-03-17 Ben SoaresJAL-629 Add in jvmArgs for memory for tests commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 closer to normal gradle settings with just... commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 increase test JVM size commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 failFast and new threads for each test commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 increased memory for clover commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 revert metal laf commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 Set Metal as default LAF for build server tests commit | commitdiff | tree | snapshot
2023-03-16 Ben SoaresJAL-629 fixed a test failing when run without a Jalview... commit | commitdiff | tree | snapshot
2023-03-15 James ProcterJAL-4091 JAL-4147 - revised annotation label display... commit | commitdiff | tree | snapshot
2023-03-15 James ProcterJAL-4091 JAL-629 ‘Add Reference Annotations’ takes... commit | commitdiff | tree | snapshot
2023-03-15 James ProcterJAL-2349 don’t clobber existing label/description... commit | commitdiff | tree | snapshot
2023-03-15 James ProcterJAL-4134 JAL-3855 store/restore groups, tree and thresh... commit | commitdiff | tree | snapshot
2023-03-15 Ben SoaresJAL-3833 fixed HiDPI test for macOS commit | commitdiff | tree | snapshot
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader... commit | commitdiff | tree | snapshot
2023-03-13 Ben SoaresJAL-629 teardown in CommandsTest commit | commitdiff | tree | snapshot
2023-03-12 Ben SoaresJAL-629 Allow substitutions of {} = defaultCounter... commit | commitdiff | tree | snapshot
2023-03-11 Ben SoaresJAL-629 --substitutions --nosubstitutions flags, -... commit | commitdiff | tree | snapshot
2023-03-11 Ben SoaresJAL-629 Auto and Default count incrementer args. Flags... commit | commitdiff | tree | snapshot
2023-03-11 Ben SoaresJAL-629 start of CommandsTest. More ArgParserTests. commit | commitdiff | tree | snapshot
2023-03-10 Ben SoaresJAL-629 start of tests and more examples commit | commitdiff | tree | snapshot
2023-03-09 Ben SoaresJAL-629 start of tests commit | commitdiff | tree | snapshot
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 --close individually for each AlignFrame opened... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 improved comment and return speed of StringUtil... commit | commitdiff | tree | snapshot
2023-03-08 James ProcterJAL-2349 handle matrix_clicked on mouse_release rather... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 --quiet [no stdout], --quiet --quiet [no stderr... commit | commitdiff | tree | snapshot
2023-03-08 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 stash some TFType and PAEFile info into a PDBEntry commit | commitdiff | tree | snapshot
2023-03-06 Ben SoaresJAL-629 Fix null AlignPanel. More descriptive label... commit | commitdiff | tree | snapshot
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ... commit | commitdiff | tree | snapshot
2023-03-02 Ben SoaresJAL-629 slight tidy up commit | commitdiff | tree | snapshot
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