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Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups
[jalview.git] / src /
2023-05-19 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... tree | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply tree | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply tree | commitdiff
2023-05-18 James ProcterJAL-4134 support recovery of mapped positions for raw... tree | commitdiff
2023-05-18 James ProcterJAL-4134 colour by annotation needs distinct annotation... tree | commitdiff
2023-05-18 James ProcterJAL-4134 column grouping model and methods moved to... tree | commitdiff
2023-05-18 James ProcterJAL-4134 formatting tree | commitdiff
2023-05-18 James ProcterJAL-4134 properly specify BinaryNode as a typed generic... 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
2023-05-16 James ProcterJAL-4089 - if no centerViewOn commands are given, don... tree | commitdiff
2023-05-15 James ProcterJAL-4182 patch - map selection group onto sequence... 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 James ProcterJAL-2349 fix up tests for Java 11 compatibility and... tree | commitdiff
2023-05-14 James ProcterJAL-2349 store/restore mappable contact matrix in proje... tree | commitdiff
2023-05-14 Ben SoaresJAL-629 add an {extension} substitution tree | commitdiff
2023-05-13 James ProcterJAL-2349 JAL-3855 PAE tests covers ContactListI.getMapp... tree | commitdiff
2023-05-13 James ProcterJAL-2349 JAL-3855 helper method to make it easy to... tree | commitdiff
2023-05-13 Ben SoaresJAL-629 launcher shell script uses jalview.bin.Launcher... tree | commitdiff
2023-05-12 James ProcterJAL-2349 allow PAE or other contact matrices to hold... 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
2023-05-01 James ProcterMerge branch 'features/JAL-4134_treeviewerforcolumns... tree | commitdiff
2023-05-01 James ProcterJAL-4177 disable ‘Cancel’ as well - since we as yet... features/JAL-4134_treeviewerforcolumns tree | commitdiff
2023-05-01 James ProcterJAL-4177 disable add/new view when an import is started. tree | commitdiff
2023-05-01 James ProcterJAL-4123 JAL-3914 JAL-3858 tweak wording and layout... tree | commitdiff
2023-05-01 James ProcterJAL-4134 double click to select column groups tree | commitdiff
2023-05-01 James ProcterJAL-3858 report errors when trying to parse JSON to... 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-4134 - store colours in annotation row, so colour... 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
2023-03-18 Ben SoaresJAL-629 Check for new commandsSuccess before quit tree | commitdiff
2023-03-18 Ben SoaresJAL-629 move getdown update to earlier stage tree | commitdiff
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... tree | commitdiff
2023-03-17 James ProcterJAL-4134 fix up column selection when hidden regions... tree | commitdiff
2023-03-17 James ProcterJAL-4134 store/restore Newick tree for PAE annotation row tree | commitdiff
2023-03-16 Ben SoaresJAL-629 revert metal laf tree | commitdiff
2023-03-16 Ben SoaresJAL-629 Set Metal as default LAF for build server tests tree | commitdiff
2023-03-15 James ProcterJAL-4091 JAL-4147 - revised annotation label display... tree | commitdiff
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