2023-05-18 |
James Procter | JAL-4134 column grouping model and methods moved to... |
tree | commitdiff |
2023-05-18 |
Ben Soares | JAL-629 Added 'Type' to args and argvalues |
tree | commitdiff |
2023-05-18 |
James Procter | JAL-4134 formatting |
tree | commitdiff |
2023-05-18 |
James Procter | JAL-4134 properly specify BinaryNode as a typed generic... |
tree | commitdiff |
2023-05-17 |
Ben Soares | JAL-629 Tidy up tests and replaced methods before merge... |
tree | commitdiff |
2023-05-17 |
Ben Soares | Merge branch 'develop' into features/r2_11_2_alphafold... |
tree | commitdiff |
2023-05-17 |
James Procter | JAL-4184 export description line in stockholm patch/JAL-4184_description_stockholm |
tree | commitdiff |
2023-05-16 |
Ben Soares | JAL-629 Ensure precedence of named linked ID values... |
tree | commitdiff |
2023-05-16 |
James Procter | JAL-4089 - if no centerViewOn commands are given, don... |
tree | commitdiff |
2023-05-15 |
James Procter | JAL-4182 patch - map selection group onto sequence... |
tree | commitdiff |
2023-05-15 |
Ben Soares | Revert "JAL-629 Add a --threads argument to allow a... |
tree | commitdiff |
2023-05-15 |
Ben Soares | JAL-629 Add a --threads argument to allow a limited... |
tree | commitdiff |
2023-05-14 |
James Procter | JAL-2349 fix up tests for Java 11 compatibility and... |
tree | commitdiff |
2023-05-14 |
James Procter | JAL-2349 store/restore mappable contact matrix in proje... |
tree | commitdiff |
2023-05-14 |
Ben Soares | JAL-629 add an {extension} substitution |
tree | commitdiff |
2023-05-13 |
James Procter | JAL-2349 JAL-3855 PAE tests covers ContactListI.getMapp... |
tree | commitdiff |
2023-05-13 |
James Procter | JAL-2349 JAL-3855 helper method to make it easy to... |
tree | commitdiff |
2023-05-13 |
Ben Soares | JAL-629 launcher shell script uses jalview.bin.Launcher... |
tree | commitdiff |
2023-05-12 |
James Procter | JAL-2349 allow PAE or other contact matrices to hold... |
tree | commitdiff |
2023-05-12 |
Ben Soares | JAL-629 Added --opened arg which is like limiting ... |
tree | commitdiff |
2023-05-11 |
Ben Soares | JAL-629 Add some shortnames to args. Add Opt.OUTPUT... |
tree | commitdiff |
2023-05-11 |
Ben Soares | JAL-629 Fix --tempfac. Hide non-working --notempfac... |
tree | commitdiff |
2023-05-11 |
Ben Soares | JAL-629 Added linkedId to ArgValuesMap for reference... |
tree | commitdiff |
2023-05-10 |
Ben Soares | JAL-629 Check Arg options for obtaining boolean or... |
tree | commitdiff |
2023-05-10 |
Ben Soares | JAL-629 Catch a NPE, fix a test |
tree | commitdiff |
2023-05-10 |
Ben Soares | JAL-629 More docs. Usage statement. Adjust some logging... |
tree | commitdiff |
2023-05-09 |
Ben Soares | JAL-629 Add --seqid for non-subval use, make arg value... |
tree | commitdiff |
2023-05-09 |
Ben Soares | JAL-629 change --renderer to --textrenderer to be more... |
tree | commitdiff |
2023-05-05 |
Ben Soares | JAL-629 test fixes |
tree | commitdiff |
2023-05-04 |
Ben Soares | JAL-629 More NG arguments: --features, --annotations... |
tree | commitdiff |
2023-05-03 |
Ben Soares | JAL-629 added eps and imagemap. Added --output and... |
tree | commitdiff |
2023-05-02 |
Ben Soares | JAL-629 Changed --newframe and --allframes to --new... |
tree | commitdiff |
2023-05-02 |
Ben Soares | JAL-629 Add --renderer arg/subval for vector output... |
tree | commitdiff |
2023-05-01 |
James Procter | Merge branch 'features/JAL-4134_treeviewerforcolumns... |
tree | commitdiff |
2023-05-01 |
James Procter | JAL-4177 disable ‘Cancel’ as well - since we as yet... features/JAL-4134_treeviewerforcolumns |
tree | commitdiff |
2023-05-01 |
James Procter | JAL-4177 disable add/new view when an import is started. |
tree | commitdiff |
2023-05-01 |
James Procter | JAL-4123 JAL-3914 JAL-3858 tweak wording and layout... |
tree | commitdiff |
2023-05-01 |
James Procter | JAL-4134 double click to select column groups |
tree | commitdiff |
2023-05-01 |
James Procter | JAL-3858 report errors when trying to parse JSON to... |
tree | commitdiff |
2023-04-30 |
Ben Soares | JAL-629 Change behaviour of --open GLOB to increment... |
tree | commitdiff |
2023-04-29 |
Ben Soares | JAL-629 Added --all arg, [*] linkedId and functionality... |
tree | commitdiff |
2023-04-28 |
Ben Soares | JAL-629 Change colour scheme shortnames to something... |
tree | commitdiff |
2023-04-27 |
Ben Soares | JAL-629 Fixed appending URLs |
tree | commitdiff |
2023-04-27 |
Ben Soares | JAL-629 Changed --increment to --newframe to make sense... |
tree | commitdiff |
2023-04-27 |
Ben Soares | JAL-629 allow opening URL as only argument(s) |
tree | commitdiff |
2023-04-26 |
Ben Soares | JAL-629 JAL-4167 Added args to tests. Fixed potential... |
tree | commitdiff |
2023-04-24 |
Ben Soares | JAL-629 Add --nowebdiscovery. Distinguish arg=="open... |
tree | commitdiff |
2023-04-23 |
Ben Soares | JAL-629 Change --open to --append and --opennew to... |
tree | commitdiff |
2023-04-22 |
Ben Soares | JAL-629 Test and fix --annotation --ssannotation args... |
tree | commitdiff |
2023-04-19 |
Ben Soares | JAL-629 Now showing temp fac and secondary structure... |
tree | commitdiff |
2023-04-14 |
Ben Soares | JAL-629 Adding PAE and TFType at structure loading... |
tree | commitdiff |
2023-04-12 |
Ben Soares | Merge branch 'develop' into features/r2_11_2_alphafold... |
tree | commitdiff |
2023-04-12 |
Ben Soares | JAL-629 Add substituteHomeDir to getDirname(). Tighten... |
tree | commitdiff |
2023-04-12 |
Ben Soares | JAL-629 Fix non-multi string bootstrap arg bug. |
tree | commitdiff |
2023-04-12 |
Ben Soares | JAL-629 parse SubVals once with ArgValue. Ensure SubVal... |
tree | commitdiff |
2023-04-12 |
Ben Soares | JAL-629 allow argfiles in argfiles, but avoid looping... |
tree | commitdiff |
2023-04-12 |
Ben Soares | JAL-629 allow comments in argfiles '#' |
tree | commitdiff |
2023-04-05 |
Ben Soares | JAL-629 Tests for FileUtils. Tidying counter substituti... |
tree | commitdiff |
2023-04-04 |
Ben Soares | JAL-629 more info in usage statement |
tree | commitdiff |
2023-04-04 |
Ben Soares | JAL-629 Start of Usage statement |
tree | commitdiff |
2023-04-04 |
Ben Soares | JAL-629 More consistent printing of --arguments. Exampl... |
tree | commitdiff |
2023-04-04 |
Ben Soares | JAL-629 Remove debugging comment |
tree | commitdiff |
2023-04-04 |
Ben Soares | JAL-629 --initsubstitutions as a bootstrap arg, new... |
tree | commitdiff |
2023-04-03 |
Ben Soares | JAL-629 sort files from java glob for predictability... |
tree | commitdiff |
2023-04-03 |
Ben Soares | JAL-629 added setprop. More filename based substitution... |
tree | commitdiff |
2023-03-30 |
Ben Soares | JAL-629 More extensive tests with real files being... |
tree | commitdiff |
2023-03-30 |
Ben Soares | JAL-629 fix bug for opening single named file with... |
tree | commitdiff |
2023-03-30 |
Ben Soares | JAL-629 Don't use new ArgParser if there are no --args... |
tree | commitdiff |
2023-03-30 |
Ben Soares | JAL-629 fix SubVals npe |
tree | commitdiff |
2023-03-29 |
Ben Soares | JAL-629 Added --opennew --nonews --nosplash. Added... |
tree | commitdiff |
2023-03-28 |
Ben Soares | JAL-629 Opening files in new windows. not working yet |
tree | commitdiff |
2023-03-25 |
Ben Soares | JAL-629 open initial non-Arg arguments as files in... |
tree | commitdiff |
2023-03-25 |
Ben Soares | JAL-629 improvements to argparser toString. Improvement... |
tree | commitdiff |
2023-03-24 |
James Procter | JAL-4134 - store colours in annotation row, so colour... |
tree | commitdiff |
2023-03-24 |
James Procter | JAL-4158 first attempt at stashing colours for contact... |
tree | commitdiff |
2023-03-24 |
Ben Soares | Merge branch 'develop' into features/r2_11_2_alphafold... |
tree | commitdiff |
2023-03-24 |
Ben Soares | JAL-629 Test tidyup |
tree | commitdiff |
2023-03-23 |
Ben Soares | JAL-629 refactor ArgParser and helper classes all to... |
tree | commitdiff |
2023-03-20 |
James Procter | JAL-4134 override default hasTree so PAE tree is saved! |
tree | commitdiff |
2023-03-20 |
James Procter | JAL-4134 - missing Jalview project JAXB class - st... |
tree | commitdiff |
2023-03-20 |
James Procter | Merge branch 'develop' into features/JAL-4134_treeviewe... |
tree | commitdiff |
2023-03-20 |
James Procter | JAL-4150 test and quick patch copying code from AlignFr... |
tree | commitdiff |
2023-03-20 |
James Procter | JAL-2349 JAL-4134 Console log messages for contact... |
tree | commitdiff |
2023-03-20 |
James Procter | JAL-4134 propagate column selection changes in tree... |
tree | commitdiff |
2023-03-20 |
James Procter | JAL-4134 fix off-by-one in selection |
tree | commitdiff |
2023-03-20 |
James Procter | JAL-4134 fix NPEs when matrix not resolved or alignment... |
tree | commitdiff |
2023-03-20 |
James Procter | JAL-4134 better popup menu name ‘Tree for Contact Matrix’ |
tree | commitdiff |
2023-03-20 |
James Procter | JAL-2349 fix off by one when resolving columns for... |
tree | commitdiff |
2023-03-18 |
Ben Soares | JAL-629 Check for new commandsSuccess before quit |
tree | commitdiff |
2023-03-18 |
Ben Soares | JAL-629 move getdown update to earlier stage |
tree | commitdiff |
2023-03-17 |
Ben Soares | JAL-629 All applications System.exits going through... |
tree | commitdiff |
2023-03-17 |
James Procter | JAL-4134 fix up column selection when hidden regions... |
tree | commitdiff |
2023-03-17 |
James Procter | JAL-4134 store/restore Newick tree for PAE annotation row |
tree | commitdiff |
2023-03-16 |
Ben Soares | JAL-629 revert metal laf |
tree | commitdiff |
2023-03-16 |
Ben Soares | JAL-629 Set Metal as default LAF for build server tests |
tree | commitdiff |
2023-03-15 |
James Procter | JAL-4091 JAL-4147 - revised annotation label display... |
tree | commitdiff |
2023-03-15 |
James Procter | JAL-4091 JAL-629 ‘Add Reference Annotations’ takes... |
tree | commitdiff |
2023-03-15 |
James Procter | JAL-2349 don’t clobber existing label/description... |
tree | commitdiff |
2023-03-15 |
James Procter | JAL-4134 JAL-3855 store/restore groups, tree and thresh... |
tree | commitdiff |
2023-03-15 |
Ben Soares | JAL-629 Commands more objecty, less classy. FileLoader... |
tree | commitdiff |
next |