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JAL-4186 fixed a test
[jalview.git]
/
src
/
2023-05-25
Ben Soares
JAL-4186 Turn JvOptionPane Callable<Void> handlers...
tree
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commitdiff
2023-05-24
Ben Soares
JAL-4186 attempts to work in jalviewjs, still not working
tree
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commitdiff
2023-05-24
Ben Soares
JAL-4186 fix dialog. broken in JalviewJS
tree
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commitdiff
2023-05-23
Ben Soares
JAL-629 Updated help docs and fixed structure image...
tree
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commitdiff
2023-05-23
Ben Soares
JAL-629 Added --structureimage code and formatting...
tree
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commitdiff
2023-05-22
Ben Soares
JAL-629 --structureimage with formatting args.
tree
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commitdiff
2023-05-21
Ben Soares
JAL-629 Clarify sections of arguments with --help-all...
tree
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commitdiff
2023-05-20
Ben Soares
JAL-4187 JAL-629 JAL-3830 small adjustments after furth...
tree
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commitdiff
2023-05-20
Ben Soares
JAL-3416 Ensure setFrameIcon(null) is set for remaining...
tree
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commitdiff
2023-05-20
Ben Soares
JAL-3416 Removed another internal Frame icon from title bar
tree
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commitdiff
2023-05-20
Ben Soares
JAL-4187 JAL-629 JAL-3830 adjustments to Cygwin and...
tree
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commitdiff
2023-05-20
Ben Soares
JAL-4160 JAL-3830 Improve jalview.bin.Launcher for...
tree
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commitdiff
2023-05-20
Ben Soares
JAL-4160 JAL-3830 Improve jalview.bin.Launcher for...
tree
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commitdiff
2023-05-19
Ben Soares
JAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for...
tree
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commitdiff
2023-05-19
Ben Soares
JAL-629 Added Arg.Types and additional --help-type...
tree
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commitdiff
2023-05-18
Ben Soares
JAL-629 fixes to typed args
tree
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commitdiff
2023-05-18
Ben Soares
JAL-629 Added 'Type' to args and argvalues
tree
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commitdiff
2023-05-17
Ben Soares
JAL-629 Tidy up tests and replaced methods before merge...
tree
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commitdiff
2023-05-17
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-05-17
James Procter
JAL-4184 export description line in stockholm
patch/JAL-4184_description_stockholm
tree
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commitdiff
2023-05-16
Ben Soares
JAL-629 Ensure precedence of named linked ID values...
tree
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commitdiff
2023-05-15
Ben Soares
Revert "JAL-629 Add a --threads argument to allow a...
tree
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commitdiff
2023-05-15
Ben Soares
JAL-629 Add a --threads argument to allow a limited...
tree
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commitdiff
2023-05-14
Ben Soares
JAL-629 add an {extension} substitution
tree
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commitdiff
2023-05-13
Ben Soares
JAL-629 launcher shell script uses jalview.bin.Launcher...
tree
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commitdiff
2023-05-12
Ben Soares
JAL-629 Added --opened arg which is like limiting ...
tree
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commitdiff
2023-05-11
Ben Soares
JAL-629 Add some shortnames to args. Add Opt.OUTPUT...
tree
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commitdiff
2023-05-11
Ben Soares
JAL-629 Fix --tempfac. Hide non-working --notempfac...
tree
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commitdiff
2023-05-11
Ben Soares
JAL-629 Added linkedId to ArgValuesMap for reference...
tree
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commitdiff
2023-05-10
Ben Soares
JAL-629 Check Arg options for obtaining boolean or...
tree
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commitdiff
2023-05-10
Ben Soares
JAL-629 Catch a NPE, fix a test
tree
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commitdiff
2023-05-10
Ben Soares
JAL-629 More docs. Usage statement. Adjust some logging...
tree
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commitdiff
2023-05-09
Ben Soares
JAL-629 Add --seqid for non-subval use, make arg value...
tree
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commitdiff
2023-05-09
Ben Soares
JAL-629 change --renderer to --textrenderer to be more...
tree
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commitdiff
2023-05-05
Ben Soares
JAL-629 test fixes
tree
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commitdiff
2023-05-04
Ben Soares
JAL-629 More NG arguments: --features, --annotations...
tree
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commitdiff
2023-05-03
Ben Soares
JAL-629 added eps and imagemap. Added --output and...
tree
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commitdiff
2023-05-02
Ben Soares
JAL-629 Changed --newframe and --allframes to --new...
tree
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commitdiff
2023-05-02
Ben Soares
JAL-629 Add --renderer arg/subval for vector output...
tree
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commitdiff
2023-04-30
Ben Soares
JAL-629 Change behaviour of --open GLOB to increment...
tree
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commitdiff
2023-04-29
Ben Soares
JAL-629 Added --all arg, [*] linkedId and functionality...
tree
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commitdiff
2023-04-28
Ben Soares
JAL-629 Change colour scheme shortnames to something...
tree
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commitdiff
2023-04-27
Ben Soares
JAL-629 Fixed appending URLs
tree
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commitdiff
2023-04-27
Ben Soares
JAL-629 Changed --increment to --newframe to make sense...
tree
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commitdiff
2023-04-27
Ben Soares
JAL-629 allow opening URL as only argument(s)
tree
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commitdiff
2023-04-26
Ben Soares
JAL-629 JAL-4167 Added args to tests. Fixed potential...
tree
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commitdiff
2023-04-24
Ben Soares
JAL-629 Add --nowebdiscovery. Distinguish arg=="open...
tree
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commitdiff
2023-04-23
Ben Soares
JAL-629 Change --open to --append and --opennew to...
tree
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commitdiff
2023-04-22
Ben Soares
JAL-629 Test and fix --annotation --ssannotation args...
tree
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commitdiff
2023-04-19
Ben Soares
JAL-629 Now showing temp fac and secondary structure...
tree
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commitdiff
2023-04-14
Ben Soares
JAL-629 Adding PAE and TFType at structure loading...
tree
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commitdiff
2023-04-12
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-04-12
Ben Soares
JAL-629 Add substituteHomeDir to getDirname(). Tighten...
tree
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commitdiff
2023-04-12
Ben Soares
JAL-629 Fix non-multi string bootstrap arg bug.
tree
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commitdiff
2023-04-12
Ben Soares
JAL-629 parse SubVals once with ArgValue. Ensure SubVal...
tree
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commitdiff
2023-04-12
Ben Soares
JAL-629 allow argfiles in argfiles, but avoid looping...
tree
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commitdiff
2023-04-12
Ben Soares
JAL-629 allow comments in argfiles '#'
tree
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commitdiff
2023-04-05
Ben Soares
JAL-629 Tests for FileUtils. Tidying counter substituti...
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commitdiff
2023-04-04
Ben Soares
JAL-629 more info in usage statement
tree
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commitdiff
2023-04-04
Ben Soares
JAL-629 Start of Usage statement
tree
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commitdiff
2023-04-04
Ben Soares
JAL-629 More consistent printing of --arguments. Exampl...
tree
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commitdiff
2023-04-04
Ben Soares
JAL-629 Remove debugging comment
tree
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commitdiff
2023-04-04
Ben Soares
JAL-629 --initsubstitutions as a bootstrap arg, new...
tree
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commitdiff
2023-04-03
Ben Soares
JAL-629 sort files from java glob for predictability...
tree
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commitdiff
2023-04-03
Ben Soares
JAL-629 added setprop. More filename based substitution...
tree
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commitdiff
2023-03-30
Ben Soares
JAL-629 More extensive tests with real files being...
tree
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commitdiff
2023-03-30
Ben Soares
JAL-629 fix bug for opening single named file with...
tree
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commitdiff
2023-03-30
Ben Soares
JAL-629 Don't use new ArgParser if there are no --args...
tree
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commitdiff
2023-03-30
Ben Soares
JAL-629 fix SubVals npe
tree
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commitdiff
2023-03-29
Ben Soares
JAL-629 Added --opennew --nonews --nosplash. Added...
tree
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commitdiff
2023-03-28
Ben Soares
JAL-629 Opening files in new windows. not working yet
tree
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commitdiff
2023-03-25
Ben Soares
JAL-629 open initial non-Arg arguments as files in...
tree
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commitdiff
2023-03-25
Ben Soares
JAL-629 improvements to argparser toString. Improvement...
tree
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commitdiff
2023-03-24
James Procter
JAL-4158 first attempt at stashing colours for contact...
tree
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commitdiff
2023-03-24
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-03-24
Ben Soares
JAL-629 Test tidyup
tree
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commitdiff
2023-03-23
Ben Soares
JAL-629 refactor ArgParser and helper classes all to...
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 override default hasTree so PAE tree is saved!
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 - missing Jalview project JAXB class - st...
tree
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commitdiff
2023-03-20
James Procter
Merge branch 'develop' into features/JAL-4134_treeviewe...
tree
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commitdiff
2023-03-20
James Procter
JAL-4150 test and quick patch copying code from AlignFr...
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commitdiff
2023-03-20
James Procter
JAL-2349 JAL-4134 Console log messages for contact...
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 propagate column selection changes in tree...
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 fix off-by-one in selection
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 fix NPEs when matrix not resolved or alignment...
tree
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commitdiff
2023-03-20
James Procter
JAL-4134 better popup menu name ‘Tree for Contact Matrix’
tree
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commitdiff
2023-03-20
James Procter
JAL-2349 fix off by one when resolving columns for...
tree
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commitdiff
2023-03-18
Ben Soares
JAL-629 Check for new commandsSuccess before quit
tree
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commitdiff
2023-03-18
Ben Soares
JAL-629 move getdown update to earlier stage
tree
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commitdiff
2023-03-17
Ben Soares
JAL-629 All applications System.exits going through...
tree
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commitdiff
2023-03-17
James Procter
JAL-4134 fix up column selection when hidden regions...
tree
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commitdiff
2023-03-17
James Procter
JAL-4134 store/restore Newick tree for PAE annotation row
tree
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commitdiff
2023-03-16
Ben Soares
JAL-629 revert metal laf
tree
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commitdiff
2023-03-16
Ben Soares
JAL-629 Set Metal as default LAF for build server tests
tree
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commitdiff
2023-03-15
James Procter
JAL-4091 JAL-4147 - revised annotation label display...
tree
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commitdiff
2023-03-15
James Procter
JAL-4091 JAL-629 ‘Add Reference Annotations’ takes...
tree
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commitdiff
2023-03-15
James Procter
JAL-2349 don’t clobber existing label/description...
tree
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commitdiff
2023-03-15
James Procter
JAL-4134 JAL-3855 store/restore groups, tree and thresh...
tree
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commitdiff
2023-03-15
Ben Soares
JAL-629 Commands more objecty, less classy. FileLoader...
tree
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commitdiff
2023-03-12
Ben Soares
JAL-629 Allow substitutions of {} = defaultCounter...
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commitdiff
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