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JAL-4059 Revert libjs/MiGLayout as new miglayout transpile of 4.0 includes reference...
[jalview.git]
/
src
/
jalview
/
bin
/
2023-06-21
Ben Soares
JAL-4001 Change wording from google to plausible or...
tree
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commitdiff
2023-06-20
Ben Soares
JAL-4001 rename the init method
tree
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commitdiff
2023-06-20
Ben Soares
JAL-4001 Working Plausible analytics
tree
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commitdiff
2023-06-20
Ben Soares
JAL-4001 Added a genuine client_id (from gtag). Added...
task/JAL-4001_migrate_googleanalytics_to_GA4
tree
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commitdiff
2023-06-17
Ben Soares
JAL-4001 Check --nousagestats before doing analytics...
tree
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commitdiff
2023-06-16
Ben Soares
JAL-3830 Take account of --gui taking precedence over...
tree
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commitdiff
2023-06-16
Ben Soares
JAL-3830 Look for --headless mode and add -Djava.awt...
tree
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commitdiff
2023-06-16
Ben Soares
JAL-4001 Add a _geo=1 to query string and JSON. Add...
tree
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commitdiff
2023-06-16
Ben Soares
JAL-4001 Remove jgoogleanalytics code and jar
tree
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commitdiff
2023-06-16
Ben Soares
JAL-4001 make page_location the same encoding as the...
tree
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commitdiff
2023-06-08
Ben Soares
JAL-4001 Only send defaultParams for application_launch...
tree
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commitdiff
2023-06-08
Ben Soares
Merge branch 'develop' into task/JAL-4001_migrate_googl...
tree
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commitdiff
2023-06-08
James Procter
Merge branch 'develop' into patch/JAL-4196_structure_vi...
tree
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commitdiff
2023-06-08
James Procter
JAL-4196 report an error if structure view doesn’t...
tree
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commitdiff
2023-06-08
Ben Soares
JAL-3416 FlatLaf SystemInfo failing in JalviewJS. ...
tree
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commitdiff
2023-06-08
Ben Soares
Merge branch 'develop' into task/JAL-4001_migrate_googl...
tree
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commitdiff
2023-06-07
James Procter
JAL-4195 add exception handling for all image output...
tree
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commitdiff
2023-06-07
James Procter
Merge branch 'patch/JAL-4195_cli_eps_export_npe' into...
tree
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commitdiff
2023-06-07
James Procter
JAL-4195 catch thrown exceptions (if any) during image...
tree
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commitdiff
2023-06-07
Ben Soares
Merge branch 'develop' into task/JAL-4001_migrate_googl...
tree
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commitdiff
2023-06-07
Ben Soares
JAL-4001 GA4 tracking is now ENABLED. Currently loggin...
tree
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commitdiff
2023-06-06
James Procter
JAL-4160 --colour can now take user defined scheme...
tree
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commitdiff
2023-06-06
James Procter
JAL-4160 JAL-4195 wait around until alignFrame calculat...
tree
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commitdiff
2023-06-06
James Procter
JAL-1551 formatting and javadoc for ArgParser rather...
tree
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commitdiff
2023-06-06
James Procter
JAL-629 - remove TODO from jalview.bin.Jalview since...
tree
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commitdiff
2023-06-06
James Procter
JAL-4195 Debug message indicating creation of an image...
tree
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commitdiff
2023-06-06
James Procter
JAL-1551 a bit of javadoc for Jalview.testoutput methods
tree
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commitdiff
2023-06-05
Ben Soares
JAL-4001 untested GA4 client code
tree
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commitdiff
2023-06-02
Ben Soares
Merge branch 'develop' into task/JAL-4001_migrate_googl...
tree
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commitdiff
2023-06-01
Ben Soares
Merge branch 'develop' into improvement/JAL-4193_cl_arg...
tree
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commitdiff
2023-06-01
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-06-01
Ben Soares
JAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt...
tree
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commitdiff
2023-06-01
Ben Soares
JAL-4001 Changed title+message to MessageManager
tree
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commitdiff
2023-06-01
Ben Soares
JAL-4193 JAL-4194 sessionProperties layer in Cache...
tree
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commitdiff
2023-06-01
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
tree
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commitdiff
2023-05-30
Ben Soares
JAL-629 JAL-4121 Added documentation to Help docs and...
tree
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commitdiff
2023-05-30
Ben Soares
JAL-629 Better formatting of Arg.Opt options in usage...
tree
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commitdiff
2023-05-30
Ben Soares
JAL-4121 slight refactoring of method name and added...
tree
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commitdiff
2023-05-29
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
tree
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commitdiff
2023-05-27
Ben Soares
JAL-4121 Added a NPE check caught in tests. Added ...
tree
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commitdiff
2023-05-27
Ben Soares
JAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt...
tree
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commitdiff
2023-05-26
Ben Soares
JAL-4125 Fixed non-closing external viewers, also added...
tree
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commitdiff
2023-05-26
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
tree
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commitdiff
2023-05-25
Ben Soares
JAL-3416 JAL-3820 FlatLaf default for everyone, includi...
tree
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commitdiff
2023-05-25
Ben Soares
JAL-3820 JAL-3830 improvements to script launching...
tree
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commitdiff
2023-05-25
Ben Soares
JAL-3820 Create and use 'Jalview app' symblinks to...
tree
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commitdiff
2023-05-24
Ben Soares
JAL-3416 slightly improved colours for tabber pane...
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
2023-05-22
James Procter
JAL-1551 spotless
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-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
James Procter
JAL-1551 spotlessApply
tree
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
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
2023-05-16
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
2023-05-04
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
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...
tree
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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
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