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JAL-3855 auto select clusters and fix up colouring/propagation on calculation & tree...
[jalview.git] / src / jalview /
2023-05-26 James ProcterJAL-4134 internationalise popup menu entries and show... tree | commitdiff
2023-05-26 James ProcterJAL-1556 fix bad import tree | commitdiff
2023-05-26 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... tree | commitdiff
2023-05-26 James ProcterJAL-1556 initial implementation - no tests as yet but... 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 James ProcterJAL-4134 popup menu and annotation row property to... tree | commitdiff
2023-05-25 Ben SoaresJAL-3820 JAL-3830 improvements to script launching... tree | commitdiff
2023-05-25 James ProcterJAL-2381 don’t need to set description, dbrefs etc... tree | commitdiff
2023-05-25 James ProcterJAL-2381 copy and paste sequence also copies contact... 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
2023-05-22 James ProcterJAL-4134 map between column and node selections better... tree | commitdiff
2023-05-22 James ProcterJAL-4134 efficiency improvement tree | commitdiff
2023-05-22 James ProcterJAL-629 javadoc on StructureSelectionManager.computeMapping tree | commitdiff
2023-05-22 James ProcterJAL-4134 only build tree when showing it in the tree... tree | commitdiff
2023-05-22 James ProcterJAL-4134 catch NPE - though in principle this should... tree | commitdiff
2023-05-22 James ProcterMerge branch 'JAL-1551_2_11_3_spotlett' into features... tree | commitdiff
2023-05-22 James ProcterJAL-1551 spotless 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 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... tree | commitdiff
2023-05-19 Ben SoaresJAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for... tree | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply tree | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply tree | commitdiff
2023-05-19 Ben SoaresJAL-629 Added Arg.Types and additional --help-type... 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 Ben SoaresJAL-629 fixes to typed args tree | commitdiff
2023-05-18 James ProcterJAL-4134 column grouping model and methods moved to... tree | commitdiff
2023-05-18 Ben SoaresJAL-629 Added 'Type' to args and argvalues 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
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