2023-05-26 |
Ben Soares | Merge branch 'develop' into feature/JAL-3416_update_to_... feature/JAL-3416_update_to_flatlaf_3.1.1_with_unpacked_native_libraries |
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2023-05-25 |
Ben Soares | JAL-3416 JAL-3820 FlatLaf default for everyone, includi... |
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2023-05-25 |
James Procter | JAL-4134 popup menu and annotation row property to... |
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2023-05-25 |
Ben Soares | JAL-3820 JAL-3830 improvements to script launching... |
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2023-05-25 |
James Procter | JAL-2381 don’t need to set description, dbrefs etc... |
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2023-05-25 |
James Procter | JAL-2381 copy and paste sequence also copies contact... |
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2023-05-25 |
Ben Soares | JAL-3820 Create and use 'Jalview app' symblinks to... |
tree | commitdiff |
2023-05-25 |
Ben Soares | JAL-4186 Turn JvOptionPane Callable<Void> handlers... |
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2023-05-24 |
Ben Soares | JAL-4186 attempts to work in jalviewjs, still not working |
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2023-05-24 |
Ben Soares | JAL-4186 fix dialog. broken in JalviewJS |
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2023-05-24 |
Ben Soares | JAL-3416 slightly improved colours for tabber pane... |
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2023-05-23 |
Ben Soares | JAL-629 Updated help docs and fixed structure image... |
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2023-05-23 |
Ben Soares | JAL-629 Added --structureimage code and formatting... |
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2023-05-22 |
Ben Soares | JAL-629 --structureimage with formatting args. |
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2023-05-22 |
James Procter | JAL-4134 map between column and node selections better... |
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2023-05-22 |
James Procter | JAL-4134 efficiency improvement |
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2023-05-22 |
James Procter | JAL-629 javadoc on StructureSelectionManager.computeMapping |
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2023-05-22 |
James Procter | JAL-4134 only build tree when showing it in the tree... |
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2023-05-22 |
James Procter | JAL-4134 catch NPE - though in principle this should... |
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2023-05-22 |
James Procter | Merge branch 'JAL-1551_2_11_3_spotlett' into features... |
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2023-05-22 |
James Procter | JAL-1551 spotless |
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2023-05-21 |
Ben Soares | JAL-629 Clarify sections of arguments with --help-all... |
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2023-05-20 |
Ben Soares | JAL-4187 JAL-629 JAL-3830 small adjustments after furth... |
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2023-05-20 |
Ben Soares | JAL-3416 Ensure setFrameIcon(null) is set for remaining... |
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2023-05-20 |
Ben Soares | JAL-3416 Removed another internal Frame icon from title bar |
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2023-05-20 |
Ben Soares | JAL-4187 JAL-629 JAL-3830 adjustments to Cygwin and... |
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2023-05-20 |
Ben Soares | JAL-4160 JAL-3830 Improve jalview.bin.Launcher for... |
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2023-05-20 |
Ben Soares | JAL-4160 JAL-3830 Improve jalview.bin.Launcher for... |
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2023-05-19 |
James Procter | Merge branch 'develop' into features/JAL-4134_use_annot... |
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2023-05-19 |
Ben Soares | JAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for... |
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2023-05-19 |
James Procter | JAL-1551 spotlessApply |
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2023-05-19 |
James Procter | JAL-1551 spotlessApply |
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2023-05-19 |
Ben Soares | JAL-629 Added Arg.Types and additional --help-type... |
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2023-05-18 |
James Procter | JAL-4134 support recovery of mapped positions for raw... |
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2023-05-18 |
James Procter | JAL-4134 colour by annotation needs distinct annotation... |
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2023-05-18 |
Ben Soares | JAL-629 fixes to typed args |
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2023-05-18 |
James Procter | JAL-4134 column grouping model and methods moved to... |
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2023-05-18 |
Ben Soares | JAL-629 Added 'Type' to args and argvalues |
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2023-05-18 |
James Procter | JAL-4134 formatting |
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2023-05-18 |
James Procter | JAL-4134 properly specify BinaryNode as a typed generic... |
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2023-05-17 |
Ben Soares | JAL-629 Tidy up tests and replaced methods before merge... |
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2023-05-17 |
Ben Soares | Merge branch 'develop' into features/r2_11_2_alphafold... |
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2023-05-17 |
James Procter | JAL-4184 export description line in stockholm patch/JAL-4184_description_stockholm |
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2023-05-16 |
Ben Soares | JAL-629 Ensure precedence of named linked ID values... |
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2023-05-16 |
James Procter | JAL-4089 - if no centerViewOn commands are given, don... |
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2023-05-15 |
James Procter | JAL-4182 patch - map selection group onto sequence... |
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2023-05-15 |
Ben Soares | Revert "JAL-629 Add a --threads argument to allow a... |
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2023-05-15 |
Ben Soares | JAL-629 Add a --threads argument to allow a limited... |
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2023-05-14 |
James Procter | JAL-2349 fix up tests for Java 11 compatibility and... |
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2023-05-14 |
James Procter | JAL-2349 store/restore mappable contact matrix in proje... |
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2023-05-14 |
Ben Soares | JAL-629 add an {extension} substitution |
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2023-05-13 |
James Procter | JAL-2349 JAL-3855 PAE tests covers ContactListI.getMapp... |
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2023-05-13 |
James Procter | JAL-2349 JAL-3855 helper method to make it easy to... |
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2023-05-13 |
Ben Soares | JAL-629 launcher shell script uses jalview.bin.Launcher... |
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2023-05-12 |
James Procter | JAL-2349 allow PAE or other contact matrices to hold... |
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2023-05-12 |
Ben Soares | JAL-629 Added --opened arg which is like limiting ... |
tree | commitdiff |
2023-05-11 |
Ben Soares | JAL-629 Add some shortnames to args. Add Opt.OUTPUT... |
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2023-05-11 |
Ben Soares | JAL-629 Fix --tempfac. Hide non-working --notempfac... |
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2023-05-11 |
Ben Soares | JAL-629 Added linkedId to ArgValuesMap for reference... |
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2023-05-10 |
Ben Soares | JAL-629 Check Arg options for obtaining boolean or... |
tree | commitdiff |
2023-05-10 |
Ben Soares | JAL-629 Catch a NPE, fix a test |
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2023-05-10 |
Ben Soares | JAL-629 More docs. Usage statement. Adjust some logging... |
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2023-05-09 |
Ben Soares | JAL-629 Add --seqid for non-subval use, make arg value... |
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2023-05-09 |
Ben Soares | JAL-629 change --renderer to --textrenderer to be more... |
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2023-05-05 |
Ben Soares | JAL-629 test fixes |
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2023-05-04 |
Ben Soares | JAL-629 More NG arguments: --features, --annotations... |
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2023-05-03 |
Ben Soares | JAL-629 added eps and imagemap. Added --output and... |
tree | commitdiff |
2023-05-02 |
Ben Soares | JAL-629 Changed --newframe and --allframes to --new... |
tree | commitdiff |
2023-05-02 |
Ben Soares | JAL-629 Add --renderer arg/subval for vector output... |
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2023-05-01 |
James Procter | Merge branch 'features/JAL-4134_treeviewerforcolumns... |
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2023-05-01 |
James Procter | JAL-4177 disable ‘Cancel’ as well - since we as yet... features/JAL-4134_treeviewerforcolumns |
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2023-05-01 |
James Procter | JAL-4177 disable add/new view when an import is started. |
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2023-05-01 |
James Procter | JAL-4123 JAL-3914 JAL-3858 tweak wording and layout... |
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2023-05-01 |
James Procter | JAL-4134 double click to select column groups |
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2023-05-01 |
James Procter | JAL-3858 report errors when trying to parse JSON to... |
tree | commitdiff |
2023-04-30 |
Ben Soares | JAL-629 Change behaviour of --open GLOB to increment... |
tree | commitdiff |
2023-04-29 |
Ben Soares | JAL-629 Added --all arg, [*] linkedId and functionality... |
tree | commitdiff |
2023-04-28 |
Ben Soares | JAL-629 Change colour scheme shortnames to something... |
tree | commitdiff |
2023-04-27 |
Ben Soares | JAL-629 Fixed appending URLs |
tree | commitdiff |
2023-04-27 |
Ben Soares | JAL-629 Changed --increment to --newframe to make sense... |
tree | commitdiff |
2023-04-27 |
Ben Soares | JAL-629 allow opening URL as only argument(s) |
tree | commitdiff |
2023-04-26 |
Ben Soares | JAL-629 JAL-4167 Added args to tests. Fixed potential... |
tree | commitdiff |
2023-04-24 |
Ben Soares | JAL-629 Add --nowebdiscovery. Distinguish arg=="open... |
tree | commitdiff |
2023-04-23 |
Ben Soares | JAL-629 Change --open to --append and --opennew to... |
tree | commitdiff |
2023-04-22 |
Ben Soares | JAL-629 Test and fix --annotation --ssannotation args... |
tree | commitdiff |
2023-04-19 |
Ben Soares | JAL-629 Now showing temp fac and secondary structure... |
tree | commitdiff |
2023-04-14 |
Ben Soares | JAL-629 Adding PAE and TFType at structure loading... |
tree | commitdiff |
2023-04-12 |
Ben Soares | Merge branch 'develop' into features/r2_11_2_alphafold... |
tree | commitdiff |
2023-04-12 |
Ben Soares | JAL-629 Add substituteHomeDir to getDirname(). Tighten... |
tree | commitdiff |
2023-04-12 |
Ben Soares | JAL-629 Fix non-multi string bootstrap arg bug. |
tree | commitdiff |
2023-04-12 |
Ben Soares | JAL-629 parse SubVals once with ArgValue. Ensure SubVal... |
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2023-04-12 |
Ben Soares | JAL-629 allow argfiles in argfiles, but avoid looping... |
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2023-04-12 |
Ben Soares | JAL-629 allow comments in argfiles '#' |
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2023-04-05 |
Ben Soares | JAL-629 Tests for FileUtils. Tidying counter substituti... |
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2023-04-04 |
Ben Soares | JAL-629 more info in usage statement |
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2023-04-04 |
Ben Soares | JAL-629 Start of Usage statement |
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2023-04-04 |
Ben Soares | JAL-629 More consistent printing of --arguments. Exampl... |
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2023-04-04 |
Ben Soares | JAL-629 Remove debugging comment |
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2023-04-04 |
Ben Soares | JAL-629 --initsubstitutions as a bootstrap arg, new... |
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2023-04-03 |
Ben Soares | JAL-629 sort files from java glob for predictability... |
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