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JAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToStructure(). not fixed yet
[jalview.git] / src /
2023-06-01 Ben SoaresJAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt... tree | commitdiff
2023-05-30 Ben SoaresJAL-629 JAL-4121 Added documentation to Help docs and... tree | commitdiff
2023-05-30 Ben SoaresJAL-629 Better formatting of Arg.Opt options in usage... tree | commitdiff
2023-05-30 Ben SoaresJAL-4121 slight refactoring of method name and added... tree | commitdiff
2023-05-27 Ben SoaresJAL-4121 Added a NPE check caught in tests. Added ... tree | commitdiff
2023-05-27 Ben SoaresJAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt... tree | commitdiff
2023-05-26 Ben SoaresJAL-4125 Fixed non-closing external viewers, also added... tree | commitdiff
2023-05-26 Ben SoaresJAL-629 dispose of non-displaying StructureChooser... tree | commitdiff
2023-05-26 Ben SoaresMerge branch 'develop' into feature/JAL-3416_update_to_... feature/JAL-3416_update_to_flatlaf_3.1.1_with_unpacked_native_libraries tree | commitdiff
2023-05-25 Ben SoaresJAL-3416 JAL-3820 FlatLaf default for everyone, includi... tree | commitdiff
2023-05-25 Ben SoaresJAL-3820 JAL-3830 improvements to script launching... tree | commitdiff
2023-05-25 Ben SoaresJAL-3820 Create and use 'Jalview app' symblinks to... tree | commitdiff
2023-05-25 Ben SoaresJAL-4186 Turn JvOptionPane Callable<Void> handlers... tree | commitdiff
2023-05-24 Ben SoaresJAL-4186 attempts to work in jalviewjs, still not working tree | commitdiff
2023-05-24 Ben SoaresJAL-4186 fix dialog. broken in JalviewJS tree | commitdiff
2023-05-24 Ben SoaresJAL-3416 slightly improved colours for tabber pane... tree | commitdiff
2023-05-23 Ben SoaresJAL-629 Updated help docs and fixed structure image... tree | commitdiff
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-3416 Ensure setFrameIcon(null) is set for remaining... tree | commitdiff
2023-05-20 Ben SoaresJAL-3416 Removed another internal Frame icon from title bar 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
2023-05-17 Ben SoaresJAL-629 Tidy up tests and replaced methods before merge... tree | commitdiff
2023-05-17 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-05-17 James ProcterJAL-4184 export description line in stockholm patch/JAL-4184_description_stockholm 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
2023-05-05 Ben SoaresJAL-629 test fixes 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 SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-04-12 Ben SoaresJAL-629 Add substituteHomeDir to getDirname(). Tighten... 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 More extensive tests with real files being... 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 James ProcterJAL-4158 first attempt at stashing colours for contact... tree | commitdiff
2023-03-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... 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
2023-03-20 James ProcterJAL-4134 override default hasTree so PAE tree is saved! tree | commitdiff
2023-03-20 James ProcterJAL-4134 - missing Jalview project JAXB class - st... tree | commitdiff
2023-03-20 James ProcterMerge branch 'develop' into features/JAL-4134_treeviewe... tree | commitdiff
2023-03-20 James ProcterJAL-4150 test and quick patch copying code from AlignFr... tree | commitdiff
2023-03-20 James ProcterJAL-2349 JAL-4134 Console log messages for contact... tree | commitdiff
2023-03-20 James ProcterJAL-4134 propagate column selection changes in tree... tree | commitdiff
2023-03-20 James ProcterJAL-4134 fix off-by-one in selection tree | commitdiff
2023-03-20 James ProcterJAL-4134 fix NPEs when matrix not resolved or alignment... tree | commitdiff
2023-03-20 James ProcterJAL-4134 better popup menu name ‘Tree for Contact Matrix’ tree | commitdiff
2023-03-20 James ProcterJAL-2349 fix off by one when resolving columns for... tree | commitdiff
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