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Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
[jalview.git] / src / jalview / bin /
2023-08-23 Ben SoaresJAL-4250 Fix one word bug for 'af.createEPS(file, rende... tree | commitdiff
2023-07-07 James ProcterJAL-4217 JAL-629 built in 25s time out waiting for... tree | commitdiff
2023-07-07 James ProcterJAL-629 even more console debug for --structureviewer... tree | commitdiff
2023-07-06 James ProcterJAL-629 liberal defensive coding, comments about refact... tree | commitdiff
2023-07-06 James ProcterJAL-4217 interruptedExceptions should also break any... tree | commitdiff
2023-06-28 Ben SoaresJAL-4001 remove headless code from analytics tree | commitdiff
2023-06-28 Ben SoaresJAL-4001 Remove analytics for --headless mode tree | commitdiff
2023-06-22 Ben SoaresMerge branch 'develop' into task/JAL-4001_Plausible_API tree | commitdiff
2023-06-21 James ProcterMerge branch 'patch/JAL-4196_structure_viewer_synchroni... patch/JAL-4196_structure_viewer_synchronising tree | commitdiff
2023-06-21 Ben SoaresJAL-4001 Rationalise user-agent string into HttpUtils tree | commitdiff
2023-06-21 Ben SoaresJAL-4001 Change wording from google to plausible or... tree | commitdiff
2023-06-20 Ben SoaresJAL-4001 rename the init method tree | commitdiff
2023-06-20 Ben SoaresJAL-4001 Working Plausible analytics tree | commitdiff
2023-06-20 Ben SoaresJAL-4001 Added a genuine client_id (from gtag). Added... task/JAL-4001_migrate_googleanalytics_to_GA4 tree | commitdiff
2023-06-17 Ben SoaresJAL-4001 Check --nousagestats before doing analytics... tree | commitdiff
2023-06-16 Ben SoaresJAL-4001 Add a _geo=1 to query string and JSON. Add... tree | commitdiff
2023-06-16 Ben SoaresJAL-4001 Remove jgoogleanalytics code and jar tree | commitdiff
2023-06-16 Ben SoaresJAL-4001 make page_location the same encoding as the... tree | commitdiff
2023-06-08 Ben SoaresJAL-4001 Only send defaultParams for application_launch... tree | commitdiff
2023-06-08 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl... tree | commitdiff
2023-06-08 James ProcterMerge branch 'develop' into patch/JAL-4196_structure_vi... tree | commitdiff
2023-06-08 James ProcterJAL-4196 report an error if structure view doesn’t... tree | commitdiff
2023-06-08 Ben SoaresJAL-3416 FlatLaf SystemInfo failing in JalviewJS. ... tree | commitdiff
2023-06-08 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl... tree | commitdiff
2023-06-07 James ProcterJAL-4195 add exception handling for all image output... tree | commitdiff
2023-06-07 James ProcterMerge branch 'patch/JAL-4195_cli_eps_export_npe' into... tree | commitdiff
2023-06-07 James ProcterJAL-4195 catch thrown exceptions (if any) during image... tree | commitdiff
2023-06-07 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl... tree | commitdiff
2023-06-07 Ben SoaresJAL-4001 GA4 tracking is now ENABLED. Currently loggin... tree | commitdiff
2023-06-06 James ProcterJAL-4160 --colour can now take user defined scheme... tree | commitdiff
2023-06-06 James ProcterJAL-4160 JAL-4195 wait around until alignFrame calculat... tree | commitdiff
2023-06-06 James ProcterJAL-1551 formatting and javadoc for ArgParser rather... tree | commitdiff
2023-06-06 James ProcterJAL-629 - remove TODO from jalview.bin.Jalview since... tree | commitdiff
2023-06-06 James ProcterJAL-4195 Debug message indicating creation of an image... tree | commitdiff
2023-06-06 James ProcterJAL-1551 a bit of javadoc for Jalview.testoutput methods tree | commitdiff
2023-06-05 Ben SoaresJAL-4001 untested GA4 client code tree | commitdiff
2023-06-02 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl... tree | commitdiff
2023-06-01 Ben SoaresMerge branch 'develop' into improvement/JAL-4193_cl_arg... tree | commitdiff
2023-06-01 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-06-01 Ben SoaresJAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt... tree | commitdiff
2023-06-01 Ben SoaresJAL-4001 Changed title+message to MessageManager tree | commitdiff
2023-06-01 Ben SoaresJAL-4193 JAL-4194 sessionProperties layer in Cache... tree | commitdiff
2023-06-01 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... tree | commitdiff
2023-05-30 Ben SoaresJAL-629 JAL-4121 Added documentation to Help docs and... tree | commitdiff
2023-05-30 Ben SoaresJAL-629 Better formatting of Arg.Opt options in usage... tree | commitdiff
2023-05-30 Ben SoaresJAL-4121 slight refactoring of method name and added... tree | commitdiff
2023-05-29 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... tree | commitdiff
2023-05-27 Ben SoaresJAL-4121 Added a NPE check caught in tests. Added ... tree | commitdiff
2023-05-27 Ben SoaresJAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt... tree | commitdiff
2023-05-26 Ben SoaresJAL-4125 Fixed non-closing external viewers, also added... tree | commitdiff
2023-05-26 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... tree | commitdiff
2023-05-25 Ben SoaresJAL-3416 JAL-3820 FlatLaf default for everyone, includi... tree | commitdiff
2023-05-25 Ben SoaresJAL-3820 JAL-3830 improvements to script launching... tree | commitdiff
2023-05-25 Ben SoaresJAL-3820 Create and use 'Jalview app' symblinks to... tree | commitdiff
2023-05-24 Ben SoaresJAL-3416 slightly improved colours for tabber pane... tree | commitdiff
2023-05-23 Ben SoaresJAL-629 Updated help docs and fixed structure image... tree | commitdiff
2023-05-23 Ben SoaresJAL-629 Added --structureimage code and formatting... tree | commitdiff
2023-05-22 Ben SoaresJAL-629 --structureimage with formatting args. tree | commitdiff
2023-05-22 James ProcterJAL-1551 spotless tree | commitdiff
2023-05-21 Ben SoaresJAL-629 Clarify sections of arguments with --help-all... tree | commitdiff
2023-05-20 Ben SoaresJAL-4187 JAL-629 JAL-3830 small adjustments after furth... tree | commitdiff
2023-05-20 Ben SoaresJAL-4187 JAL-629 JAL-3830 adjustments to Cygwin and... tree | commitdiff
2023-05-20 Ben SoaresJAL-4160 JAL-3830 Improve jalview.bin.Launcher for... tree | commitdiff
2023-05-20 Ben SoaresJAL-4160 JAL-3830 Improve jalview.bin.Launcher for... tree | commitdiff
2023-05-19 Ben SoaresJAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for... tree | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply tree | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply tree | commitdiff
2023-05-19 Ben SoaresJAL-629 Added Arg.Types and additional --help-type... tree | commitdiff
2023-05-18 Ben SoaresJAL-629 fixes to typed args tree | commitdiff
2023-05-18 Ben SoaresJAL-629 Added 'Type' to args and argvalues tree | commitdiff
2023-05-16 Ben SoaresJAL-629 Ensure precedence of named linked ID values... tree | commitdiff
2023-05-15 Ben SoaresRevert "JAL-629 Add a --threads argument to allow a... tree | commitdiff
2023-05-15 Ben SoaresJAL-629 Add a --threads argument to allow a limited... tree | commitdiff
2023-05-14 Ben SoaresJAL-629 add an {extension} substitution tree | commitdiff
2023-05-13 Ben SoaresJAL-629 launcher shell script uses jalview.bin.Launcher... tree | commitdiff
2023-05-12 Ben SoaresJAL-629 Added --opened arg which is like limiting ... tree | commitdiff
2023-05-11 Ben SoaresJAL-629 Add some shortnames to args. Add Opt.OUTPUT... tree | commitdiff
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac... tree | commitdiff
2023-05-11 Ben SoaresJAL-629 Added linkedId to ArgValuesMap for reference... tree | commitdiff
2023-05-10 Ben SoaresJAL-629 Check Arg options for obtaining boolean or... tree | commitdiff
2023-05-10 Ben SoaresJAL-629 Catch a NPE, fix a test tree | commitdiff
2023-05-10 Ben SoaresJAL-629 More docs. Usage statement. Adjust some logging... tree | commitdiff
2023-05-09 Ben SoaresJAL-629 Add --seqid for non-subval use, make arg value... tree | commitdiff
2023-05-09 Ben SoaresJAL-629 change --renderer to --textrenderer to be more... tree | commitdiff
2023-05-04 Ben SoaresJAL-629 More NG arguments: --features, --annotations... tree | commitdiff
2023-05-03 Ben SoaresJAL-629 added eps and imagemap. Added --output and... tree | commitdiff
2023-05-02 Ben SoaresJAL-629 Changed --newframe and --allframes to --new... tree | commitdiff
2023-05-02 Ben SoaresJAL-629 Add --renderer arg/subval for vector output... tree | commitdiff
2023-04-30 Ben SoaresJAL-629 Change behaviour of --open GLOB to increment... tree | commitdiff
2023-04-29 Ben SoaresJAL-629 Added --all arg, [*] linkedId and functionality... tree | commitdiff
2023-04-28 Ben SoaresJAL-629 Change colour scheme shortnames to something... tree | commitdiff
2023-04-27 Ben SoaresJAL-629 Fixed appending URLs tree | commitdiff
2023-04-27 Ben SoaresJAL-629 Changed --increment to --newframe to make sense... tree | commitdiff
2023-04-27 Ben SoaresJAL-629 allow opening URL as only argument(s) tree | commitdiff
2023-04-26 Ben SoaresJAL-629 JAL-4167 Added args to tests. Fixed potential... tree | commitdiff
2023-04-24 Ben SoaresJAL-629 Add --nowebdiscovery. Distinguish arg=="open... tree | commitdiff
2023-04-23 Ben SoaresJAL-629 Change --open to --append and --opennew to... tree | commitdiff
2023-04-22 Ben SoaresJAL-629 Test and fix --annotation --ssannotation args... tree | commitdiff
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... tree | commitdiff
2023-04-14 Ben SoaresJAL-629 Adding PAE and TFType at structure loading... tree | commitdiff
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