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JAL-4206 Added recentlyOpenedCellRenderer to better display the Recently Opened JList...
[jalview.git] / src /
2023-06-14 Ben SoaresJAL-4206 Added recentlyOpenedCellRenderer to better... tree | commitdiff
2023-06-13 Ben SoaresJAL-3416 Removed a few more JInternalFrame icons with... tree | commitdiff
2023-06-09 Ben SoaresJAL-3599 Make jalviewjs dependOn jalviewjsLaunchTest... tree | commitdiff
2023-06-09 Ben SoaresJAL-3599 Deliberate NPE to see if build plan fails tree | commitdiff
2023-06-08 Ben SoaresJAL-3599 gradle tasks to test JalviewJS launches in... tree | commitdiff
2023-06-08 Ben SoaresJAL-3416 FlatLaf SystemInfo failing in JalviewJS. ... tree | commitdiff
2023-06-07 James ProcterJAL-4195 add exception handling for all image output... tree | commitdiff
2023-06-07 James ProcterMerge branch 'patch/JAL-4195_cli_eps_export_npe' into... tree | commitdiff
2023-06-07 James ProcterJAL-4195 catch thrown exceptions (if any) during image... tree | commitdiff
2023-06-07 James ProcterJAL-4195 tidy up desktop instances after creating them tree | commitdiff
2023-06-06 James ProcterJAL-4195 report full stack trace for exceptions raised... tree | commitdiff
2023-06-06 James ProcterJAL-4160 --colour can now take user defined scheme... tree | commitdiff
2023-06-06 James ProcterJAL-4160 JAL-4195 wait around until alignFrame calculat... tree | commitdiff
2023-06-06 James ProcterJAL-1551 formatting and javadoc for ArgParser rather... tree | commitdiff
2023-06-06 James ProcterJAL-629 - remove TODO from jalview.bin.Jalview since... tree | commitdiff
2023-06-06 James ProcterJAL-4195 Debug message indicating creation of an image... tree | commitdiff
2023-06-06 James ProcterJAL-1551 a bit of javadoc for Jalview.testoutput methods tree | commitdiff
2023-06-01 Ben SoaresMerge branch 'develop' into improvement/JAL-4193_cl_arg... tree | commitdiff
2023-06-01 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-06-01 Ben SoaresJAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt... tree | commitdiff
2023-06-01 Ben SoaresJAL-4193 JAL-4194 sessionProperties layer in Cache... tree | commitdiff
2023-06-01 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... tree | commitdiff
2023-06-01 James ProcterJAL-4134 properly resolve positions in associated align... features/JAL-4134_use_annotation_row_for_colours_and_groups tree | commitdiff
2023-05-30 James ProcterJAL-4134 repaint the tree or alignment view(s) when... tree | commitdiff
2023-05-30 James ProcterJAL-4134 highlight selected column nodes on the linked... 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
2023-05-29 James ProcterJAL-4190 - escape clears selected nodes tree | commitdiff
2023-05-29 James ProcterJAL-4134 JAL-2349 test & fixed implementation(ish)... tree | commitdiff
2023-05-29 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... 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 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
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