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Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID
[jalview.git] / src / jalview / bin /
2023-09-07 James ProcterJAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI tree | commitdiff
2023-09-07 James ProcterJAL-4279 move on if the file doesn't exist, or Identify... tree | commitdiff
2023-09-07 James ProcterJAL-4279 catch exceptions with fileLoader and report... tree | commitdiff
2023-09-07 James ProcterJAL-4090 JAL-4160 JAL-4274 image export dimensions... tree | commitdiff
2023-09-06 James ProcterJAL-629 javadoc tree | commitdiff
2023-09-02 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-09-02 Ben SoaresJAL-629 Add accessors for argParser and bootstrapArgs feature/JAL-629_--output_-_means_output_to_STDOUT tree | commitdiff
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options tree | commitdiff
2023-08-31 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-08-31 Ben SoaresJAL-629 Small buglet with getting --seqid features/r2_11_2_alphafold/JAL-629 tree | commitdiff
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-23 Ben SoaresJAL-4250 Fix one word bug for 'af.createEPS(file, rende... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'feature/JAL-244_Automatically_adjust_left... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_... tree | commitdiff
2023-08-18 Ben SoaresJAL-3416 Remove full height separators between new... improvement/JAL-3416_FlatLaf_3.2 tree | commitdiff
2023-08-17 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-08-17 Ben SoaresJAL-3830 JAL-4160 Remove --noheadless as --gui does... tree | commitdiff
2023-08-16 Ben SoaresJAL-3820 JAL-4189 Move checks for java executable symli... tree | commitdiff
2023-08-11 Ben SoaresJAL-629 Much better way of dealing with list of filenam... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 STDOUT documentation. Opt.STDOUT narrower... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Method to use for printStackTrace tree | commitdiff
2023-08-09 Ben SoaresJAL-629 Move more stdout messages to stderr when output... tree | commitdiff
2023-08-09 Ben SoaresJAL-629 Default to FASTA if no format given for output... tree | commitdiff
2023-08-09 Ben SoaresJAL-629 Enable output to STDOUT when specifying output... tree | commitdiff
2023-08-02 Ben SoaresJAL-244 Fix buglet with automatic change in id column... tree | commitdiff
2023-08-01 Ben SoaresJAL-244 More control of automatic idWidth adjustments... tree | commitdiff
2023-07-27 Ben SoaresJAL-244 Allow adjusting Id column width in wrap mode... tree | commitdiff
2023-07-21 Ben SoaresJAL-244 Fixed idWidth labels in headless mode for non... tree | commitdiff
2023-07-10 James ProcterMerge branch 'improvement/JAL-3830_remove_dock_icon_in_... 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 stray --headless mode analytic tree | commitdiff
2023-06-28 Ben SoaresMerge branch 'task/JAL-4001_Plausible_API' into improve... tree | commitdiff
2023-06-28 Ben SoaresJAL-3820 add java and java.exe from JAVAHOME to list... 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
2023-06-27 Ben SoaresJAL-3416 Don't forget java bin in the correct java... tree | commitdiff
2023-06-26 Ben SoaresMerge branch 'develop' into improvement/JAL-3830_remove... 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-3830 Take account of --gui taking precedence over... tree | commitdiff
2023-06-16 Ben SoaresJAL-3830 Look for --headless mode and add -Djava.awt... 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
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