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JAL-4366 hacked in a 1:1 mapping
[jalview.git]
/
src
/
jalview
/
bin
/
2023-12-12
Ben Soares
JAL-4353 helper method and test for primary/secondary...
tree
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commitdiff
2023-12-06
Ben Soares
JAL-4353 Preserve the user given 'linkedId' with ArgVal...
tree
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commitdiff
2023-12-05
Ben Soares
JAL-4353 Add secondary Types for Args, for STRUCTUREIMA...
tree
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commitdiff
2023-11-30
Ben Soares
JAL-4344 careful application of -Djava.awt.headless...
tree
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commitdiff
2023-11-13
James Procter
JAL-4090 JAL-1551 source license
tree
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commitdiff
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
tree
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commitdiff
2023-11-02
James Procter
JAL-4217 wrap progress bar creation in an invokeLater...
tree
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commitdiff
2023-10-25
James Procter
JAL-4312 call AlignFrame.setAnnotationsVisibility on...
tree
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commitdiff
2023-10-20
James Procter
Merge branch 'improvement/JAL-3783_upgrade_to_groovy...
tree
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commitdiff
2023-10-20
Ben Soares
JAL-4298 Remove a stray return in the processGroovyScri...
tree
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commitdiff
2023-10-19
Ben Soares
JAL-629 Fix --nodebug turning off debug mode from prope...
tree
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commitdiff
2023-10-19
Ben Soares
JAL-4305 Isolate and unify the Jalview object from...
tree
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commitdiff
2023-10-18
Ben Soares
JAL-629 Run non-alignframe linked groovy scripts. ...
tree
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commitdiff
2023-10-11
Ben Soares
JAL-629 correct a timeout. Correct passing html flag.
tree
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commitdiff
2023-10-11
Ben Soares
JAL-629 Add a timeout to modal dialogs for command...
tree
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commitdiff
2023-10-11
Ben Soares
JAL-629 Remove argfiles from the hashset of used argfil...
tree
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commitdiff
2023-10-11
Ben Soares
JAL-4298 Added diagnostics and minor dimension changes...
tree
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commitdiff
2023-10-05
Ben Soares
JAL-4298 Fixed initial log level to see .jalview_proper...
tree
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commitdiff
2023-09-29
James Procter
JAL-629 JAL-4265 JAL-4286 report the filename for the...
tree
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commitdiff
2023-09-21
Ben Soares
JAL-4265 Use ColourUtils.parseColourString() for consis...
merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285
tree
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commitdiff
2023-09-21
Ben Soares
Merge branch 'develop' into merge/JAL-4262+JAL-4265...
tree
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commitdiff
2023-09-20
Ben Soares
JAL-4265 Use ColorUtils.parseColourString() and adjust...
tree
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commitdiff
2023-09-20
James Procter
JAL-4285 don’t say you are reporting warnings/errors...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4286 reinstated explicit restoreSession...
tree
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commitdiff
2023-09-20
James Procter
JAL-4195 JAL-1069 JAL-4160 errors in Cache should go...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 bail early when attempting to export a view...
tree
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commitdiff
2023-09-19
Ben Soares
JAL-4265 Change to use JmolCommands
tree
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commitdiff
2023-09-19
Ben Soares
JAL-629 Allow multiple structure images for multiple...
tree
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commitdiff
2023-09-16
Ben Soares
JAL-629 Fix a test and omit an incorrect error message...
improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters
tree
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commitdiff
2023-09-16
Ben Soares
JAL-4265 Added --bgcolour for --structureimage output...
tree
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commitdiff
2023-09-16
Ben Soares
JAL-4269 Now using --width, --height, --scale for both...
tree
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commitdiff
2023-09-14
Ben Soares
Merge branch 'develop' into feature/JAL-4274_configurab...
tree
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commitdiff
2023-09-13
Ben Soares
JAL-4274 Use Cache BITMAP_* if no other image restricti...
tree
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commitdiff
2023-09-13
Ben Soares
JAL-4262 Made deprecation warning properly modal
bug/JAL-4277_dirname_substitution_always_absolute
tree
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commitdiff
2023-09-12
Ben Soares
JAL-4262 Allow HTML in the dialog box for link to CLI...
tree
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commitdiff
2023-09-12
Ben Soares
JAL-4285 Better checkFiles processing. Better dialog.
tree
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commitdiff
2023-09-12
Ben Soares
JAL-4285 JAL-4262 Added a scrollable dialog to display...
tree
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commitdiff
2023-09-11
Ben Soares
JAL-4001 corrected analytics message labels
tree
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commitdiff
2023-09-11
Ben Soares
Merge branch 'improvement/JAL-4262_deprecation_warning_...
tree
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commitdiff
2023-09-11
Ben Soares
JAL-4277 --mkdirs with cautious refusal for paths with ..
tree
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commitdiff
2023-09-11
Ben Soares
JAL-4284 JAL-4285 Deal with output files/images consist...
tree
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commitdiff
2023-09-08
Ben Soares
JAL-4262 Make an excepetion for STDOUT filename in...
improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed
tree
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commitdiff
2023-09-08
Ben Soares
Merge branch 'bug/JAL-4277_dirname_substitution_always_...
tree
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commitdiff
2023-09-08
Ben Soares
JAL-4262 Dialog for GUI and WARN for CLI of old style...
tree
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commitdiff
2023-09-07
Ben Soares
Merge branch 'develop' into bug/JAL-4277_dirname_substi...
tree
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commitdiff
2023-09-07
Ben Soares
JAL-4277 Corrected choice of all or last opened linkedI...
tree
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commitdiff
2023-09-07
James Procter
JAL-4279 suppress error dialogs raised by file loader...
improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI
tree
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commitdiff
2023-09-07
James Procter
JAL-4279 move on if the file doesn't exist, or Identify...
tree
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commitdiff
2023-09-07
James Procter
JAL-4279 catch exceptions with fileLoader and report...
tree
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commitdiff
2023-09-07
James Procter
JAL-4090 JAL-4160 JAL-4274 image export dimensions...
tree
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commitdiff
2023-09-07
Ben Soares
JAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTII...
improvement/JAL-629_Apply_alignment_options_to_all_globbed_files
tree
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commitdiff
2023-09-06
James Procter
JAL-629 javadoc
tree
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commitdiff
2023-09-02
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-09-02
Ben Soares
JAL-629 Add accessors for argParser and bootstrapArgs
feature/JAL-629_--output_-_means_output_to_STDOUT
tree
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commitdiff
2023-09-01
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-09-01
Ben Soares
JAL-629 Fix --structureimage and options
tree
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commitdiff
2023-08-31
Ben Soares
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
2023-08-31
Ben Soares
JAL-629 Small buglet with getting --seqid
features/r2_11_2_alphafold/JAL-629
tree
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commitdiff
2023-08-23
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
tree
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commitdiff
2023-08-23
Ben Soares
JAL-4250 Fix one word bug for 'af.createEPS(file, rende...
tree
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commitdiff
2023-08-18
Ben Soares
Merge branch 'feature/JAL-244_Automatically_adjust_left...
tree
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commitdiff
2023-08-18
Ben Soares
Merge branch 'improvement/JAL-3830_remove_dock_icon_in_...
tree
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commitdiff
2023-08-18
Ben Soares
JAL-3416 Remove full height separators between new...
improvement/JAL-3416_FlatLaf_3.2
tree
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commitdiff
2023-08-17
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-08-17
Ben Soares
JAL-3830 JAL-4160 Remove --noheadless as --gui does...
tree
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commitdiff
2023-08-16
Ben Soares
JAL-3820 JAL-4189 Move checks for java executable symli...
tree
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commitdiff
2023-08-11
Ben Soares
JAL-629 Much better way of dealing with list of filenam...
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 STDOUT documentation. Opt.STDOUT narrower...
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 Method to use for printStackTrace
tree
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commitdiff
2023-08-09
Ben Soares
JAL-629 Move more stdout messages to stderr when output...
tree
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commitdiff
2023-08-09
Ben Soares
JAL-629 Default to FASTA if no format given for output...
tree
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commitdiff
2023-08-09
Ben Soares
JAL-629 Enable output to STDOUT when specifying output...
tree
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commitdiff
2023-08-02
Ben Soares
JAL-244 Fix buglet with automatic change in id column...
tree
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commitdiff
2023-08-01
Ben Soares
JAL-244 More control of automatic idWidth adjustments...
tree
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commitdiff
2023-07-27
Ben Soares
JAL-244 Allow adjusting Id column width in wrap mode...
tree
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commitdiff
2023-07-21
Ben Soares
JAL-244 Fixed idWidth labels in headless mode for non...
tree
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commitdiff
2023-07-10
James Procter
Merge branch 'improvement/JAL-3830_remove_dock_icon_in_...
tree
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commitdiff
2023-07-07
James Procter
JAL-4217 JAL-629 built in 25s time out waiting for...
tree
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commitdiff
2023-07-07
James Procter
JAL-629 even more console debug for --structureviewer...
tree
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commitdiff
2023-07-06
James Procter
JAL-629 liberal defensive coding, comments about refact...
tree
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commitdiff
2023-07-06
James Procter
JAL-4217 interruptedExceptions should also break any...
tree
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commitdiff
2023-06-28
Ben Soares
JAL-4001 remove stray --headless mode analytic
tree
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commitdiff
2023-06-28
Ben Soares
Merge branch 'task/JAL-4001_Plausible_API' into improve...
tree
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commitdiff
2023-06-28
Ben Soares
JAL-3820 add java and java.exe from JAVAHOME to list...
tree
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commitdiff
2023-06-28
Ben Soares
JAL-4001 remove headless code from analytics
tree
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commitdiff
2023-06-28
Ben Soares
JAL-4001 Remove analytics for --headless mode
tree
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commitdiff
2023-06-27
Ben Soares
JAL-3416 Don't forget java bin in the correct java...
tree
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commitdiff
2023-06-26
Ben Soares
Merge branch 'develop' into improvement/JAL-3830_remove...
tree
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commitdiff
2023-06-22
Ben Soares
Merge branch 'develop' into task/JAL-4001_Plausible_API
tree
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commitdiff
2023-06-21
James Procter
Merge branch 'patch/JAL-4196_structure_viewer_synchroni...
patch/JAL-4196_structure_viewer_synchronising
tree
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commitdiff
2023-06-21
Ben Soares
JAL-4001 Rationalise user-agent string into HttpUtils
tree
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commitdiff
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
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