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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / bin /
2023-12-01 James ProcterMerge branch 'releases/Release_2_11_3_Branch' master tree | commitdiff
2023-11-30 Ben SoaresJAL-4344 careful application of -Djava.awt.headless... tree | commitdiff
2023-11-16 James ProcterMerge branch 'releases/Release_2_11_3_Branch' tree | commitdiff
2023-11-13 James ProcterJAL-4090 JAL-1551 source license tree | commitdiff
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply tree | commitdiff
2023-11-02 James ProcterJAL-4217 wrap progress bar creation in an invokeLater... tree | commitdiff
2023-10-25 James ProcterJAL-4312 call AlignFrame.setAnnotationsVisibility on... tree | commitdiff
2023-10-20 James ProcterMerge branch 'improvement/JAL-3783_upgrade_to_groovy... tree | commitdiff
2023-10-20 Ben SoaresJAL-4298 Remove a stray return in the processGroovyScri... tree | commitdiff
2023-10-19 Ben SoaresJAL-629 Fix --nodebug turning off debug mode from prope... tree | commitdiff
2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from... tree | commitdiff
2023-10-18 Ben SoaresJAL-629 Run non-alignframe linked groovy scripts. ... tree | commitdiff
2023-10-11 Ben SoaresJAL-629 correct a timeout. Correct passing html flag. tree | commitdiff
2023-10-11 Ben SoaresJAL-629 Add a timeout to modal dialogs for command... tree | commitdiff
2023-10-11 Ben SoaresJAL-629 Remove argfiles from the hashset of used argfil... tree | commitdiff
2023-10-11 Ben SoaresJAL-4298 Added diagnostics and minor dimension changes... tree | commitdiff
2023-10-05 Ben SoaresJAL-4298 Fixed initial log level to see .jalview_proper... tree | commitdiff
2023-09-29 James ProcterJAL-629 JAL-4265 JAL-4286 report the filename for the... tree | commitdiff
2023-09-21 Ben SoaresJAL-4265 Use ColourUtils.parseColourString() for consis... merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285 tree | commitdiff
2023-09-21 Ben SoaresMerge branch 'develop' into merge/JAL-4262+JAL-4265... tree | commitdiff
2023-09-20 Ben SoaresJAL-4265 Use ColorUtils.parseColourString() and adjust... tree | commitdiff
2023-09-20 James ProcterJAL-4285 don’t say you are reporting warnings/errors... tree | commitdiff
2023-09-20 James ProcterJAL-4265 JAL-4286 reinstated explicit restoreSession... tree | commitdiff
2023-09-20 James ProcterJAL-4195 JAL-1069 JAL-4160 errors in Cache should go... tree | commitdiff
2023-09-20 James ProcterJAL-4265 bail early when attempting to export a view... tree | commitdiff
2023-09-19 Ben SoaresJAL-4265 Change to use JmolCommands tree | commitdiff
2023-09-19 Ben SoaresJAL-629 Allow multiple structure images for multiple... tree | commitdiff
2023-09-16 Ben SoaresJAL-629 Fix a test and omit an incorrect error message... improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters tree | commitdiff
2023-09-16 Ben SoaresJAL-4265 Added --bgcolour for --structureimage output... tree | commitdiff
2023-09-16 Ben SoaresJAL-4269 Now using --width, --height, --scale for both... tree | commitdiff
2023-09-14 Ben SoaresMerge branch 'develop' into feature/JAL-4274_configurab... tree | commitdiff
2023-09-13 Ben SoaresJAL-4274 Use Cache BITMAP_* if no other image restricti... tree | commitdiff
2023-09-13 Ben SoaresJAL-4262 Made deprecation warning properly modal bug/JAL-4277_dirname_substitution_always_absolute tree | commitdiff
2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI... tree | commitdiff
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog. tree | commitdiff
2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display... tree | commitdiff
2023-09-11 Ben SoaresJAL-4001 corrected analytics message labels tree | commitdiff
2023-09-11 Ben SoaresMerge branch 'improvement/JAL-4262_deprecation_warning_... tree | commitdiff
2023-09-11 Ben SoaresJAL-4277 --mkdirs with cautious refusal for paths with .. tree | commitdiff
2023-09-11 Ben SoaresJAL-4284 JAL-4285 Deal with output files/images consist... tree | commitdiff
2023-09-08 Ben SoaresJAL-4262 Make an excepetion for STDOUT filename in... improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed tree | commitdiff
2023-09-08 Ben SoaresMerge branch 'bug/JAL-4277_dirname_substitution_always_... tree | commitdiff
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style... tree | commitdiff
2023-09-07 Ben SoaresMerge branch 'develop' into bug/JAL-4277_dirname_substi... tree | commitdiff
2023-09-07 Ben SoaresJAL-4277 Corrected choice of all or last opened linkedI... tree | commitdiff
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
2023-09-07 Ben SoaresJAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTII... improvement/JAL-629_Apply_alignment_options_to_all_globbed_files 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 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
2023-06-22 Ben SoaresJAL-4001 Release_2_11_2 branch with Plausible analytics 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
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