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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/ src
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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commitdiff
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 ...
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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...
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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...
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2023-05-02
Ben Soares
JAL-629 Changed --newframe and --allframes to --new...
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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...
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2023-04-30
Ben Soares
JAL-629 Change behaviour of --open GLOB to increment...
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2023-04-29
Ben Soares
JAL-629 Added --all arg, [*] linkedId and functionality...
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2023-04-28
Ben Soares
JAL-629 Change colour scheme shortnames to something...
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2023-04-27
Ben Soares
JAL-629 Fixed appending URLs
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2023-04-27
Ben Soares
JAL-629 Changed --increment to --newframe to make sense...
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2023-04-27
Ben Soares
JAL-629 allow opening URL as only argument(s)
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2023-04-26
Ben Soares
JAL-629 JAL-4167 Added args to tests. Fixed potential...
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2023-04-24
Ben Soares
JAL-629 Add --nowebdiscovery. Distinguish arg=="open...
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2023-04-23
Ben Soares
JAL-629 Change --open to --append and --opennew to...
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2023-04-22
Ben Soares
JAL-629 Test and fix --annotation --ssannotation args...
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2023-04-19
Ben Soares
JAL-629 Now showing temp fac and secondary structure...
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2023-04-14
Ben Soares
JAL-629 Adding PAE and TFType at structure loading...
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2023-04-12
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
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2023-04-12
Ben Soares
JAL-629 Add substituteHomeDir to getDirname(). Tighten...
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2023-04-12
Ben Soares
JAL-629 Fix non-multi string bootstrap arg bug.
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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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2023-04-03
Ben Soares
JAL-629 added setprop. More filename based substitution...
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2023-03-30
Ben Soares
JAL-629 More extensive tests with real files being...
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2023-03-30
Ben Soares
JAL-629 fix bug for opening single named file with...
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2023-03-30
Ben Soares
JAL-629 Don't use new ArgParser if there are no --args...
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2023-03-30
Ben Soares
JAL-629 fix SubVals npe
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2023-03-29
Ben Soares
JAL-629 Added --opennew --nonews --nosplash. Added...
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2023-03-28
Ben Soares
JAL-629 Opening files in new windows. not working yet
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2023-03-25
Ben Soares
JAL-629 open initial non-Arg arguments as files in...
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2023-03-25
Ben Soares
JAL-629 improvements to argparser toString. Improvement...
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2023-03-24
James Procter
JAL-4134 - store colours in annotation row, so colour...
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2023-03-24
James Procter
JAL-4158 first attempt at stashing colours for contact...
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2023-03-24
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
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2023-03-24
Ben Soares
JAL-629 Test tidyup
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2023-03-23
Ben Soares
JAL-629 refactor ArgParser and helper classes all to...
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2023-03-20
James Procter
JAL-4134 override default hasTree so PAE tree is saved!
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2023-03-20
James Procter
JAL-4134 - missing Jalview project JAXB class - st...
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2023-03-20
James Procter
Merge branch 'develop' into features/JAL-4134_treeviewe...
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2023-03-20
James Procter
JAL-4150 test and quick patch copying code from AlignFr...
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2023-03-20
James Procter
JAL-2349 JAL-4134 Console log messages for contact...
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2023-03-20
James Procter
JAL-4134 propagate column selection changes in tree...
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2023-03-20
James Procter
JAL-4134 fix off-by-one in selection
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2023-03-20
James Procter
JAL-4134 fix NPEs when matrix not resolved or alignment...
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2023-03-20
James Procter
JAL-4134 better popup menu name ‘Tree for Contact Matrix’
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