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jalview.git
2023-06-09 James ProcterJAL-4041 failing tests to verify we can resolve mixture... bug/JAL-4041_no_3dbeacons_when_no_uniprotseq commit | commitdiff | tree | snapshot
2023-06-08 Ben SoaresJAL-3416 FlatLaf SystemInfo failing in JalviewJS. ... commit | commitdiff | tree | snapshot
2023-06-08 James ProcterMerge branch 'patch/JAL-4195_cli_eps_export_npe' into... commit | commitdiff | tree | snapshot
2023-06-07 James ProcterJAL-4195 add exception handling for all image output... commit | commitdiff | tree | snapshot
2023-06-07 James ProcterMerge branch 'patch/JAL-4195_cli_eps_export_npe' into... commit | commitdiff | tree | snapshot
2023-06-07 James ProcterJAL-4195 catch thrown exceptions (if any) during image... commit | commitdiff | tree | snapshot
2023-06-07 Ben SoaresMerge branch 'develop' into improvement/JAL-4193_cl_arg... improvement/JAL-4193_cl_arg_prevent_startup_file commit | commitdiff | tree | snapshot
2023-06-07 James ProcterJAL-4195 tidy up desktop instances after creating them commit | commitdiff | tree | snapshot
2023-06-06 James ProcterJAL-4195 report full stack trace for exceptions raised... commit | commitdiff | tree | snapshot
2023-06-06 James ProcterJAL-4160 --colour can now take user defined scheme... commit | commitdiff | tree | snapshot
2023-06-06 James ProcterJAL-4160 JAL-4195 wait around until alignFrame calculat... commit | commitdiff | tree | snapshot
2023-06-06 James ProcterJAL-1551 formatting and javadoc for ArgParser rather... commit | commitdiff | tree | snapshot
2023-06-06 James ProcterJAL-629 - remove TODO from jalview.bin.Jalview since... commit | commitdiff | tree | snapshot
2023-06-06 James ProcterJAL-4195 Debug message indicating creation of an image... commit | commitdiff | tree | snapshot
2023-06-06 James ProcterJAL-1551 a bit of javadoc for Jalview.testoutput methods commit | commitdiff | tree | snapshot
2023-06-02 James ProcterJAL-4090 update 2.11.3.0 release notes for recent merges commit | commitdiff | tree | snapshot
2023-06-02 Ben SoaresJAL-3521 Updated debian build.gradle in utils/debian... commit | commitdiff | tree | snapshot
2023-06-01 Ben SoaresMerge branch 'develop' into improvement/JAL-4193_cl_arg... commit | commitdiff | tree | snapshot
2023-06-01 Ben SoaresJAL-629 changes merged in from develop fixed it. Delet... commit | commitdiff | tree | snapshot
2023-06-01 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-06-01 Ben SoaresJAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt... commit | commitdiff | tree | snapshot
2023-06-01 Ben SoaresJAL-629 added data for test commit | commitdiff | tree | snapshot
2023-06-01 Ben SoaresJAL-4193 JAL-4194 sessionProperties layer in Cache... commit | commitdiff | tree | snapshot
2023-06-01 James ProcterMerge branch 'features/JAL-4134_use_annotation_row_for_... commit | commitdiff | tree | snapshot
2023-06-01 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... commit | commitdiff | tree | snapshot
2023-06-01 James ProcterJAL-4134 properly resolve positions in associated align... features/JAL-4134_use_annotation_row_for_colours_and_groups commit | commitdiff | tree | snapshot
2023-06-01 Ben SoaresJAL-629 better reference text for --nousagestats commit | commitdiff | tree | snapshot
2023-05-30 James ProcterJAL-4134 repaint the tree or alignment view(s) when... commit | commitdiff | tree | snapshot
2023-05-30 James ProcterJAL-4134 highlight selected column nodes on the linked... commit | commitdiff | tree | snapshot
2023-05-30 Ben SoaresJAL-629 JAL-4121 Added documentation to Help docs and... commit | commitdiff | tree | snapshot
2023-05-30 Ben SoaresJAL-4121 adjust test name commit | commitdiff | tree | snapshot
2023-05-30 Ben SoaresJAL-629 Better formatting of Arg.Opt options in usage... commit | commitdiff | tree | snapshot
2023-05-30 Ben SoaresJAL-4121 slight refactoring of method name and added... commit | commitdiff | tree | snapshot
2023-05-29 James ProcterJAL-4190 - escape clears selected nodes commit | commitdiff | tree | snapshot
2023-05-29 James ProcterJAL-4134 JAL-2349 test & fixed implementation(ish)... commit | commitdiff | tree | snapshot
2023-05-29 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... commit | commitdiff | tree | snapshot
2023-05-27 Ben SoaresJAL-4121 Added a NPE check caught in tests. Added ... commit | commitdiff | tree | snapshot
2023-05-27 Ben SoaresJAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt... commit | commitdiff | tree | snapshot
2023-05-26 Ben SoaresJAL-4125 Fixed non-closing external viewers, also added... commit | commitdiff | tree | snapshot
2023-05-26 James ProcterJAL-4134 internationalise popup menu entries and show... commit | commitdiff | tree | snapshot
2023-05-26 James ProcterJAL-1556 fix bad import commit | commitdiff | tree | snapshot
2023-05-26 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... commit | commitdiff | tree | snapshot
2023-05-26 James ProcterJAL-1556 initial implementation - no tests as yet but... commit | commitdiff | tree | snapshot
2023-05-26 Ben SoaresJAL-629 dispose of non-displaying StructureChooser... commit | commitdiff | tree | snapshot
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 commit | commitdiff | tree | snapshot
2023-05-25 Ben SoaresJAL-3416 JAL-3820 FlatLaf default for everyone, includi... commit | commitdiff | tree | snapshot
2023-05-25 Ben SoaresJAL-3416 better path name commit | commitdiff | tree | snapshot
2023-05-25 James ProcterJAL-4134 popup menu and annotation row property to... commit | commitdiff | tree | snapshot
2023-05-25 Ben SoaresJAL-3820 JAL-3830 improvements to script launching... commit | commitdiff | tree | snapshot
2023-05-25 James ProcterJAL-2381 don’t need to set description, dbrefs etc... commit | commitdiff | tree | snapshot
2023-05-25 James ProcterJAL-2381 copy and paste sequence also copies contact... commit | commitdiff | tree | snapshot
2023-05-25 James ProcterMerge branch 'bug/JAL-4186_space_in_sequence_name_cause... commit | commitdiff | tree | snapshot
2023-05-25 Ben SoaresJAL-3820 Create and use 'Jalview app' symblinks to... commit | commitdiff | tree | snapshot
2023-05-25 Ben SoaresJAL-3416 remove old flatlaf jars from j8lib commit | commitdiff | tree | snapshot
2023-05-25 Ben SoaresJAL-4186 fixed a test commit | commitdiff | tree | snapshot
2023-05-25 Ben SoaresJAL-4186 Turn JvOptionPane Callable<Void> handlers... commit | commitdiff | tree | snapshot
2023-05-24 Ben SoaresJAL-4186 attempts to work in jalviewjs, still not working commit | commitdiff | tree | snapshot
2023-05-24 Ben SoaresJAL-4186 fix dialog. broken in JalviewJS commit | commitdiff | tree | snapshot
2023-05-24 Ben SoaresJAL-3416 slightly improved colours for tabber pane... commit | commitdiff | tree | snapshot
2023-05-24 Ben SoaresJAL-3416 Updated flatlaf libraries. Native libraries... commit | commitdiff | tree | snapshot
2023-05-23 Ben SoaresJAL-629 Updated help docs and fixed structure image... commit | commitdiff | tree | snapshot
2023-05-23 Ben SoaresJAL-629 Added --structureimage code and formatting... commit | commitdiff | tree | snapshot
2023-05-22 Ben SoaresJAL-629 --structureimage with formatting args. commit | commitdiff | tree | snapshot
2023-05-22 James ProcterJAL-4134 map between column and node selections better... commit | commitdiff | tree | snapshot
2023-05-22 James ProcterJAL-4134 efficiency improvement commit | commitdiff | tree | snapshot
2023-05-22 James ProcterJAL-629 javadoc on StructureSelectionManager.computeMapping commit | commitdiff | tree | snapshot
2023-05-22 James ProcterJAL-4134 only build tree when showing it in the tree... commit | commitdiff | tree | snapshot
2023-05-22 James ProcterJAL-4134 catch NPE - though in principle this should... commit | commitdiff | tree | snapshot
2023-05-22 James ProcterMerge branch 'JAL-1551_2_11_3_spotlett' into features... commit | commitdiff | tree | snapshot
2023-05-22 James ProcterMerge branch 'spotless_2' into JAL-1551_2_11_3_spotlett commit | commitdiff | tree | snapshot
2023-05-22 James ProcterJAL-1551 spotless commit | commitdiff | tree | snapshot
2023-05-21 Ben SoaresJAL-629 Clarify sections of arguments with --help-all... commit | commitdiff | tree | snapshot
2023-05-20 Ben SoaresJAL-4187 JAL-629 JAL-3830 small adjustments after furth... commit | commitdiff | tree | snapshot
2023-05-20 Ben SoaresJAL-3416 Ensure setFrameIcon(null) is set for remaining... commit | commitdiff | tree | snapshot
2023-05-20 Ben SoaresJAL-3416 Removed another internal Frame icon from title bar commit | commitdiff | tree | snapshot
2023-05-20 Ben SoaresJAL-4187 JAL-629 JAL-3830 adjustments to Cygwin and... commit | commitdiff | tree | snapshot
2023-05-20 Ben SoaresJAL-4160 JAL-3830 Improve jalview.bin.Launcher for... commit | commitdiff | tree | snapshot
2023-05-20 Ben SoaresJAL-4160 JAL-3830 Improve jalview.bin.Launcher for... commit | commitdiff | tree | snapshot
2023-05-19 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... commit | commitdiff | tree | snapshot
2023-05-19 Ben SoaresJAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for... commit | commitdiff | tree | snapshot
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff | tree | snapshot
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff | tree | snapshot
2023-05-19 Ben SoaresJAL-629 Fix missing icon for command line launch commit | commitdiff | tree | snapshot
2023-05-19 Ben SoaresJAL-629 Updated debian helpers for new command line commit | commitdiff | tree | snapshot
2023-05-19 Ben SoaresJAL-629 Updated launching scripts to 1) not insert... commit | commitdiff | tree | snapshot
2023-05-19 Ben SoaresJAL-629 Added Arg.Types and additional --help-type... commit | commitdiff | tree | snapshot
2023-05-18 James ProcterJAL-4134 support recovery of mapped positions for raw... commit | commitdiff | tree | snapshot
2023-05-18 James ProcterJAL-4134 colour by annotation needs distinct annotation... commit | commitdiff | tree | snapshot
2023-05-18 Ben SoaresJAL-629 fixes to typed args commit | commitdiff | tree | snapshot
2023-05-18 James ProcterJAL-4134 column grouping model and methods moved to... commit | commitdiff | tree | snapshot
2023-05-18 Ben SoaresJAL-629 Added 'Type' to args and argvalues commit | commitdiff | tree | snapshot
2023-05-18 Ben SoaresJAL-629 fixes to help docs commit | commitdiff | tree | snapshot
2023-05-18 James ProcterJAL-4134 formatting commit | commitdiff | tree | snapshot
2023-05-18 James ProcterJAL-4134 properly specify BinaryNode as a typed generic... commit | commitdiff | tree | snapshot
2023-05-17 Ben SoaresJAL-629 Tidy up tests and replaced methods before merge... commit | commitdiff | tree | snapshot
2023-05-17 Ben SoaresJAL-629 Changed some old -arg to --arg in help docs... commit | commitdiff | tree | snapshot
2023-05-17 Ben SoaresJAL-629 tidying the help docs commit | commitdiff | tree | snapshot
2023-05-17 Ben SoaresJAL-629 delete stray files commit | commitdiff | tree | snapshot
2023-05-17 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-05-17 James ProcterJAL-4184 release notes commit | commitdiff | tree | snapshot
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