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jalview.git
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
2023-05-30 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
2023-05-29 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
2023-05-17 James ProcterMerge branch 'patch/JAL-4184_description_stockholm... commit | commitdiff | tree | snapshot
2023-05-17 James ProcterJAL-4184 export description line in stockholm patch/JAL-4184_description_stockholm commit | commitdiff | tree | snapshot
2023-05-17 James ProcterJAL-4184 failing test for description export and re... commit | commitdiff | tree | snapshot
2023-05-16 Ben SoaresJAL-629 Finished documentation for new command lines. commit | commitdiff | tree | snapshot
2023-05-16 Ben SoaresJAL-629 Ensure precedence of named linked ID values... commit | commitdiff | tree | snapshot
2023-05-16 James ProcterJAL-4089 - if no centerViewOn commands are given, don... commit | commitdiff | tree | snapshot
2023-05-15 Ben SoaresJAL-629 More help text commit | commitdiff | tree | snapshot
2023-05-15 James ProcterJAL-4182 patch - map selection group onto sequence... commit | commitdiff | tree | snapshot
2023-05-15 Ben SoaresRevert "JAL-629 Add a --threads argument to allow a... commit | commitdiff | tree | snapshot
2023-05-15 James ProcterJAL-4182 failing test commit | commitdiff | tree | snapshot
2023-05-15 Ben SoaresJAL-629 Add a --threads argument to allow a limited... commit | commitdiff | tree | snapshot
2023-05-14 James ProcterJAL-2349 fix up tests for Java 11 compatibility and... commit | commitdiff | tree | snapshot
2023-05-14 James ProcterJAL-4134 add tree distance engine test to functional commit | commitdiff | tree | snapshot
2023-05-14 James ProcterJAL-2349 store/restore mappable contact matrix in proje... commit | commitdiff | tree | snapshot
2023-05-14 Ben SoaresJAL-629 add an {extension} substitution commit | commitdiff | tree | snapshot
2023-05-13 James ProcterJAL-2349 JAL-3855 PAE tests covers ContactListI.getMapp... commit | commitdiff | tree | snapshot
2023-05-13 James ProcterJAL-2349 JAL-3855 helper method to make it easy to... commit | commitdiff | tree | snapshot
2023-05-13 Ben SoaresJAL-629 launcher shell script uses jalview.bin.Launcher... commit | commitdiff | tree | snapshot
2023-05-12 Ben SoaresJAL-629 More docs commit | commitdiff | tree | snapshot
2023-05-12 James ProcterJAL-2349 allow PAE or other contact matrices to hold... commit | commitdiff | tree | snapshot
2023-05-12 Ben SoaresJAL-629 extra test for --output open*.ext when used... commit | commitdiff | tree | snapshot
2023-05-12 Ben SoaresJAL-629 Added --opened arg which is like limiting ... commit | commitdiff | tree | snapshot
2023-05-11 Ben SoaresJAL-629 Add some shortnames to args. Add Opt.OUTPUT... commit | commitdiff | tree | snapshot
2023-05-11 Ben SoaresJAL-629 Move clarguments documentation to default.... commit | commitdiff | tree | snapshot
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac... commit | commitdiff | tree | snapshot
2023-05-11 Ben SoaresJAL-629 Added linkedId to ArgValuesMap for reference... commit | commitdiff | tree | snapshot
2023-05-10 Ben SoaresJAL-629 Check Arg options for obtaining boolean or... commit | commitdiff | tree | snapshot
2023-05-10 Ben SoaresJAL-629 Catch a NPE, fix a test commit | commitdiff | tree | snapshot
2023-05-10 Ben SoaresJAL-629 More docs. Usage statement. Adjust some logging... commit | commitdiff | tree | snapshot
2023-05-09 Ben SoaresJAL-629 Add --seqid for non-subval use, make arg value... commit | commitdiff | tree | snapshot
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