jalview.git
2023-05-30 James ProcterJAL-4134 repaint the tree or alignment view(s) when...
2023-05-30 James ProcterJAL-4134 highlight selected column nodes on the linked...
2023-05-29 James ProcterJAL-4190 - escape clears selected nodes
2023-05-29 James ProcterJAL-4134 JAL-2349 test & fixed implementation(ish)...
2023-05-29 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot...
2023-05-27 Ben SoaresJAL-4121 Added a NPE check caught in tests. Added ...
2023-05-27 Ben SoaresJAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt...
2023-05-26 Ben SoaresJAL-4125 Fixed non-closing external viewers, also added...
2023-05-26 James ProcterJAL-4134 internationalise popup menu entries and show...
2023-05-26 James ProcterJAL-1556 fix bad import
2023-05-26 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot...
2023-05-26 James ProcterJAL-1556 initial implementation - no tests as yet but...
2023-05-26 Ben SoaresJAL-629 dispose of non-displaying StructureChooser...
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
2023-05-25 Ben SoaresJAL-3416 JAL-3820 FlatLaf default for everyone, includi...
2023-05-25 Ben SoaresJAL-3416 better path name
2023-05-25 James ProcterJAL-4134 popup menu and annotation row property to...
2023-05-25 Ben SoaresJAL-3820 JAL-3830 improvements to script launching...
2023-05-25 James ProcterJAL-2381 don’t need to set description, dbrefs etc...
2023-05-25 James ProcterJAL-2381 copy and paste sequence also copies contact...
2023-05-25 James ProcterMerge branch 'bug/JAL-4186_space_in_sequence_name_cause...
2023-05-25 Ben SoaresJAL-3820 Create and use 'Jalview app' symblinks to...
2023-05-25 Ben SoaresJAL-3416 remove old flatlaf jars from j8lib
2023-05-25 Ben SoaresJAL-4186 fixed a test
2023-05-25 Ben SoaresJAL-4186 Turn JvOptionPane Callable<Void> handlers...
2023-05-24 Ben SoaresJAL-4186 attempts to work in jalviewjs, still not working
2023-05-24 Ben SoaresJAL-4186 fix dialog. broken in JalviewJS
2023-05-24 Ben SoaresJAL-3416 slightly improved colours for tabber pane...
2023-05-24 Ben SoaresJAL-3416 Updated flatlaf libraries. Native libraries...
2023-05-23 Ben SoaresJAL-629 Updated help docs and fixed structure image...
2023-05-23 Ben SoaresJAL-629 Added --structureimage code and formatting...
2023-05-22 Ben SoaresJAL-629 --structureimage with formatting args.
2023-05-22 James ProcterJAL-4134 map between column and node selections better...
2023-05-22 James ProcterJAL-4134 efficiency improvement
2023-05-22 James ProcterJAL-629 javadoc on StructureSelectionManager.computeMapping
2023-05-22 James ProcterJAL-4134 only build tree when showing it in the tree...
2023-05-22 James ProcterJAL-4134 catch NPE - though in principle this should...
2023-05-22 James ProcterMerge branch 'JAL-1551_2_11_3_spotlett' into features...
2023-05-22 James ProcterMerge branch 'spotless_2' into JAL-1551_2_11_3_spotlett
2023-05-22 James ProcterJAL-1551 spotless
2023-05-21 Ben SoaresJAL-629 Clarify sections of arguments with --help-all...
2023-05-20 Ben SoaresJAL-4187 JAL-629 JAL-3830 small adjustments after furth...
2023-05-20 Ben SoaresJAL-3416 Ensure setFrameIcon(null) is set for remaining...
2023-05-20 Ben SoaresJAL-3416 Removed another internal Frame icon from title bar
2023-05-20 Ben SoaresJAL-4187 JAL-629 JAL-3830 adjustments to Cygwin and...
2023-05-20 Ben SoaresJAL-4160 JAL-3830 Improve jalview.bin.Launcher for...
2023-05-20 Ben SoaresJAL-4160 JAL-3830 Improve jalview.bin.Launcher for...
2023-05-19 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot...
2023-05-19 Ben SoaresJAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for...
2023-05-19 James ProcterJAL-1551 spotlessApply
2023-05-19 James ProcterJAL-1551 spotlessApply
2023-05-19 Ben SoaresJAL-629 Fix missing icon for command line launch
2023-05-19 Ben SoaresJAL-629 Updated debian helpers for new command line
2023-05-19 Ben SoaresJAL-629 Updated launching scripts to 1) not insert...
2023-05-19 Ben SoaresJAL-629 Added Arg.Types and additional --help-type...
2023-05-18 James ProcterJAL-4134 support recovery of mapped positions for raw...
2023-05-18 James ProcterJAL-4134 colour by annotation needs distinct annotation...
2023-05-18 Ben SoaresJAL-629 fixes to typed args
2023-05-18 James ProcterJAL-4134 column grouping model and methods moved to...
2023-05-18 Ben SoaresJAL-629 Added 'Type' to args and argvalues
2023-05-18 Ben SoaresJAL-629 fixes to help docs
2023-05-18 James ProcterJAL-4134 formatting
2023-05-18 James ProcterJAL-4134 properly specify BinaryNode as a typed generic...
2023-05-17 Ben SoaresJAL-629 Tidy up tests and replaced methods before merge...
2023-05-17 Ben SoaresJAL-629 Changed some old -arg to --arg in help docs...
2023-05-17 Ben SoaresJAL-629 tidying the help docs
2023-05-17 Ben SoaresJAL-629 delete stray files
2023-05-17 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-05-17 James ProcterJAL-4184 release notes
2023-05-17 James ProcterMerge branch 'patch/JAL-4184_description_stockholm...
2023-05-17 James ProcterJAL-4184 export description line in stockholm patch/JAL-4184_description_stockholm
2023-05-17 James ProcterJAL-4184 failing test for description export and re...
2023-05-16 Ben SoaresJAL-629 Finished documentation for new command lines.
2023-05-16 Ben SoaresJAL-629 Ensure precedence of named linked ID values...
2023-05-16 James ProcterJAL-4089 - if no centerViewOn commands are given, don...
2023-05-15 Ben SoaresJAL-629 More help text
2023-05-15 James ProcterJAL-4182 patch - map selection group onto sequence...
2023-05-15 Ben SoaresRevert "JAL-629 Add a --threads argument to allow a...
2023-05-15 James ProcterJAL-4182 failing test
2023-05-15 Ben SoaresJAL-629 Add a --threads argument to allow a limited...
2023-05-14 James ProcterJAL-2349 fix up tests for Java 11 compatibility and...
2023-05-14 James ProcterJAL-4134 add tree distance engine test to functional
2023-05-14 James ProcterJAL-2349 store/restore mappable contact matrix in proje...
2023-05-14 Ben SoaresJAL-629 add an {extension} substitution
2023-05-13 James ProcterJAL-2349 JAL-3855 PAE tests covers ContactListI.getMapp...
2023-05-13 James ProcterJAL-2349 JAL-3855 helper method to make it easy to...
2023-05-13 Ben SoaresJAL-629 launcher shell script uses jalview.bin.Launcher...
2023-05-12 Ben SoaresJAL-629 More docs
2023-05-12 James ProcterJAL-2349 allow PAE or other contact matrices to hold...
2023-05-12 Ben SoaresJAL-629 extra test for --output open*.ext when used...
2023-05-12 Ben SoaresJAL-629 Added --opened arg which is like limiting ...
2023-05-11 Ben SoaresJAL-629 Add some shortnames to args. Add Opt.OUTPUT...
2023-05-11 Ben SoaresJAL-629 Move clarguments documentation to default....
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac...
2023-05-11 Ben SoaresJAL-629 Added linkedId to ArgValuesMap for reference...
2023-05-10 Ben SoaresJAL-629 Check Arg options for obtaining boolean or...
2023-05-10 Ben SoaresJAL-629 Catch a NPE, fix a test
2023-05-10 Ben SoaresJAL-629 More docs. Usage statement. Adjust some logging...
2023-05-09 Ben SoaresJAL-629 Add --seqid for non-subval use, make arg value...
2023-05-09 Ben SoaresJAL-629 update a subval for structureviewer in the...
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