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JAL-4059 Revert libjs/MiGLayout as new miglayout transpile of 4.0 includes reference...
[jalview.git]
/
src
/
jalview
/
bin
/
Commands.java
2023-11-13
James Procter
Merge branch 'develop' into bug/JAL-4059_update_swingJS...
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2023-11-13
Ben Soares
Merge branch 'develop' into bug/JAL-4059_update_swingJS...
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2023-11-13
James Procter
JAL-4090 JAL-1551 source license
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2023-11-07
Ben Soares
Merge branch 'develop' into bug/JAL-4059_update_swingJS...
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2023-11-03
Ben Soares
JAL-4239 Using own id generation to avoid Random.nextLo...
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2023-11-02
James Procter
JAL-4217 wrap progress bar creation in an invokeLater...
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2023-10-25
James Procter
JAL-4312 call AlignFrame.setAnnotationsVisibility on...
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2023-10-20
Ben Soares
JAL-4298 Remove a stray return in the processGroovyScri...
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2023-10-18
Ben Soares
JAL-629 Run non-alignframe linked groovy scripts. ...
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2023-09-29
James Procter
JAL-629 JAL-4265 JAL-4286 report the filename for the...
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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
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2023-09-20
James Procter
JAL-4285 don’t say you are reporting warnings/errors...
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2023-09-20
James Procter
JAL-4265 JAL-4286 reinstated explicit restoreSession...
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2023-09-20
James Procter
JAL-4265 bail early when attempting to export a view...
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2023-09-19
Ben Soares
JAL-4265 Change to use JmolCommands
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2023-09-19
Ben Soares
JAL-629 Allow multiple structure images for multiple...
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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
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2023-09-16
Ben Soares
JAL-4265 Added --bgcolour for --structureimage output...
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2023-09-16
Ben Soares
JAL-4269 Now using --width, --height, --scale for both...
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2023-09-12
Ben Soares
JAL-4285 Better checkFiles processing. Better dialog.
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2023-09-12
Ben Soares
JAL-4285 JAL-4262 Added a scrollable dialog to display...
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2023-09-11
Ben Soares
Merge branch 'improvement/JAL-4262_deprecation_warning_...
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2023-09-11
Ben Soares
JAL-4284 JAL-4285 Deal with output files/images consist...
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2023-09-08
Ben Soares
JAL-4262 Dialog for GUI and WARN for CLI of old style...
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2023-09-07
James Procter
JAL-4279 move on if the file doesn't exist, or Identify...
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2023-09-07
James Procter
JAL-4279 catch exceptions with fileLoader and report...
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2023-09-01
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
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2023-09-01
Ben Soares
JAL-629 Fix --structureimage and options
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2023-08-31
Ben Soares
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
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2023-08-31
Ben Soares
JAL-629 Small buglet with getting --seqid
features/r2_11_2_alphafold/JAL-629
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2023-08-23
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
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2023-08-23
Ben Soares
JAL-4250 Fix one word bug for 'af.createEPS(file, rende...
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2023-08-18
Ben Soares
Merge branch 'feature/JAL-244_Automatically_adjust_left...
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2023-08-09
Ben Soares
JAL-629 Move more stdout messages to stderr when output...
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2023-08-09
Ben Soares
JAL-629 Default to FASTA if no format given for output...
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2023-08-09
Ben Soares
JAL-629 Enable output to STDOUT when specifying output...
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2023-08-02
Ben Soares
JAL-244 Fix buglet with automatic change in id column...
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2023-08-01
Ben Soares
JAL-244 More control of automatic idWidth adjustments...
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2023-07-27
Ben Soares
JAL-244 Allow adjusting Id column width in wrap mode...
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2023-07-21
Ben Soares
JAL-244 Fixed idWidth labels in headless mode for non...
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2023-07-07
James Procter
JAL-4217 JAL-629 built in 25s time out waiting for...
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2023-07-07
James Procter
JAL-629 even more console debug for --structureviewer...
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2023-07-06
James Procter
JAL-629 liberal defensive coding, comments about refact...
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2023-07-06
James Procter
JAL-4217 interruptedExceptions should also break any...
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2023-06-08
James Procter
JAL-4196 report an error if structure view doesn’t...
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2023-06-07
James Procter
JAL-4195 add exception handling for all image output...
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2023-06-07
James Procter
JAL-4195 catch thrown exceptions (if any) during image...
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2023-06-06
James Procter
JAL-4160 --colour can now take user defined scheme...
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2023-06-06
James Procter
JAL-4160 JAL-4195 wait around until alignFrame calculat...
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2023-06-06
James Procter
JAL-4195 Debug message indicating creation of an image...
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2023-06-01
Ben Soares
JAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt...
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2023-05-23
Ben Soares
JAL-629 Updated help docs and fixed structure image...
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2023-05-23
Ben Soares
JAL-629 Added --structureimage code and formatting...
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2023-05-22
Ben Soares
JAL-629 --structureimage with formatting args.
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2023-05-18
Ben Soares
JAL-629 Added 'Type' to args and argvalues
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2023-05-15
Ben Soares
Revert "JAL-629 Add a --threads argument to allow a...
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2023-05-15
Ben Soares
JAL-629 Add a --threads argument to allow a limited...
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2023-05-12
Ben Soares
JAL-629 Added --opened arg which is like limiting ...
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2023-05-11
Ben Soares
JAL-629 Fix --tempfac. Hide non-working --notempfac...
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2023-05-11
Ben Soares
JAL-629 Added linkedId to ArgValuesMap for reference...
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2023-05-10
Ben Soares
JAL-629 More docs. Usage statement. Adjust some logging...
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2023-05-09
Ben Soares
JAL-629 Add --seqid for non-subval use, make arg value...
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2023-05-09
Ben Soares
JAL-629 change --renderer to --textrenderer to be more...
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2023-05-04
Ben Soares
JAL-629 More NG arguments: --features, --annotations...
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2023-05-03
Ben Soares
JAL-629 added eps and imagemap. Added --output and...
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2023-05-02
Ben Soares
JAL-629 Changed --newframe and --allframes to --new...
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2023-05-02
Ben Soares
JAL-629 Add --renderer arg/subval for vector output...
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2023-04-30
Ben Soares
JAL-629 Change behaviour of --open GLOB to increment...
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2023-04-28
Ben Soares
JAL-629 Change colour scheme shortnames to something...
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2023-04-27
Ben Soares
JAL-629 Fixed appending URLs
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2023-04-23
Ben Soares
JAL-629 Change --open to --append and --opennew to...
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2023-04-22
Ben Soares
JAL-629 Test and fix --annotation --ssannotation args...
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2023-04-19
Ben Soares
JAL-629 Now showing temp fac and secondary structure...
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2023-04-14
Ben Soares
JAL-629 Adding PAE and TFType at structure loading...
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2023-04-12
Ben Soares
JAL-629 parse SubVals once with ArgValue. Ensure SubVal...
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2023-04-05
Ben Soares
JAL-629 Tests for FileUtils. Tidying counter substituti...
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2023-04-04
Ben Soares
JAL-629 More consistent printing of --arguments. Exampl...
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2023-03-29
Ben Soares
JAL-629 Added --opennew --nonews --nosplash. Added...
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2023-03-28
Ben Soares
JAL-629 Opening files in new windows. not working yet
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2023-03-25
Ben Soares
JAL-629 improvements to argparser toString. Improvement...
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2023-03-23
Ben Soares
JAL-629 refactor ArgParser and helper classes all to...
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2023-03-17
Ben Soares
JAL-629 All applications System.exits going through...
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2023-03-15
Ben Soares
JAL-629 Commands more objecty, less classy. FileLoader...
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2023-03-08
Ben Soares
JAL-629 --close individually for each AlignFrame opened...
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2023-03-08
Ben Soares
JAL-629 Fix --headless for new args. Fix progressbar...
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2023-03-03
Ben Soares
JAL-629 Improved consistency of ArgParser classes ...
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2023-03-02
Ben Soares
JAL-629 Some refactoring to allow more flexible use...
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2023-02-28
Ben Soares
JAL-629 Firm up bootstrapArgs. Correct '-colour' in...
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2023-02-27
Ben Soares
JAL-629 Fix Exceptions when running with CLI not headless
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2023-02-27
Ben Soares
JAL-629 removed debug prints. added .cif. added some...
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2023-02-24
Ben Soares
JAL-629 Made ArgValuesMap helper class, simplifies...
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2023-02-23
Ben Soares
JAL-629 bootstrap args and properties. Remember index...
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2023-02-03
Ben Soares
JAL-629 Fasta sequence id reading whitespace fix. Flexi...
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2023-01-26
Ben Soares
JAL-629 adjust arg type for tempfac-shading -- was...
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2023-01-24
James Procter
JAL-629 hacked in --tempfac-shading - hardcoded to...
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2023-01-24
James Procter
JAL-629 suggest not breaking out of the structure proce...
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2023-01-24
James Procter
JAL-629 don’t carry on Jalview.main if we’ve already...
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2023-01-24
James Procter
JAL-629 don’t trash user’s system property file when...
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2023-01-24
James Procter
JAL-629 labelled breaks are frowned upon by everyone
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2023-01-23
Ben Soares
JAL-629 Attempts to add PAE to structure. --headless...
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