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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / bin / Commands.java
2023-11-13 James ProcterJAL-4090 JAL-1551 source license commit | commitdiff
2023-11-02 James ProcterJAL-4217 wrap progress bar creation in an invokeLater... commit | commitdiff
2023-10-25 James ProcterJAL-4312 call AlignFrame.setAnnotationsVisibility on... commit | commitdiff
2023-10-20 Ben SoaresJAL-4298 Remove a stray return in the processGroovyScri... commit | commitdiff
2023-10-18 Ben SoaresJAL-629 Run non-alignframe linked groovy scripts. ... commit | commitdiff
2023-09-29 James ProcterJAL-629 JAL-4265 JAL-4286 report the filename for the... commit | 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 commit | commitdiff
2023-09-20 James ProcterJAL-4285 don’t say you are reporting warnings/errors... commit | commitdiff
2023-09-20 James ProcterJAL-4265 JAL-4286 reinstated explicit restoreSession... commit | commitdiff
2023-09-20 James ProcterJAL-4265 bail early when attempting to export a view... commit | commitdiff
2023-09-19 Ben SoaresJAL-4265 Change to use JmolCommands commit | commitdiff
2023-09-19 Ben SoaresJAL-629 Allow multiple structure images for multiple... commit | 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 commit | commitdiff
2023-09-16 Ben SoaresJAL-4265 Added --bgcolour for --structureimage output... commit | commitdiff
2023-09-16 Ben SoaresJAL-4269 Now using --width, --height, --scale for both... commit | commitdiff
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog. commit | commitdiff
2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display... commit | commitdiff
2023-09-11 Ben SoaresMerge branch 'improvement/JAL-4262_deprecation_warning_... commit | commitdiff
2023-09-11 Ben SoaresJAL-4284 JAL-4285 Deal with output files/images consist... commit | commitdiff
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style... commit | commitdiff
2023-09-07 James ProcterJAL-4279 move on if the file doesn't exist, or Identify... commit | commitdiff
2023-09-07 James ProcterJAL-4279 catch exceptions with fileLoader and report... commit | commitdiff
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... commit | commitdiff
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options commit | commitdiff
2023-08-31 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff
2023-08-31 Ben SoaresJAL-629 Small buglet with getting --seqid features/r2_11_2_alphafold/JAL-629 commit | commitdiff
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... commit | commitdiff
2023-08-23 Ben SoaresJAL-4250 Fix one word bug for 'af.createEPS(file, rende... commit | commitdiff
2023-08-18 Ben SoaresMerge branch 'feature/JAL-244_Automatically_adjust_left... commit | commitdiff
2023-08-09 Ben SoaresJAL-629 Move more stdout messages to stderr when output... commit | commitdiff
2023-08-09 Ben SoaresJAL-629 Default to FASTA if no format given for output... commit | commitdiff
2023-08-09 Ben SoaresJAL-629 Enable output to STDOUT when specifying output... commit | commitdiff
2023-08-02 Ben SoaresJAL-244 Fix buglet with automatic change in id column... commit | commitdiff
2023-08-01 Ben SoaresJAL-244 More control of automatic idWidth adjustments... commit | commitdiff
2023-07-27 Ben SoaresJAL-244 Allow adjusting Id column width in wrap mode... commit | commitdiff
2023-07-21 Ben SoaresJAL-244 Fixed idWidth labels in headless mode for non... commit | commitdiff
2023-07-07 James ProcterJAL-4217 JAL-629 built in 25s time out waiting for... commit | commitdiff
2023-07-07 James ProcterJAL-629 even more console debug for --structureviewer... commit | commitdiff
2023-07-06 James ProcterJAL-629 liberal defensive coding, comments about refact... commit | commitdiff
2023-07-06 James ProcterJAL-4217 interruptedExceptions should also break any... commit | commitdiff
2023-06-08 James ProcterJAL-4196 report an error if structure view doesn’t... commit | commitdiff
2023-06-07 James ProcterJAL-4195 add exception handling for all image output... commit | commitdiff
2023-06-07 James ProcterJAL-4195 catch thrown exceptions (if any) during image... commit | commitdiff
2023-06-06 James ProcterJAL-4160 --colour can now take user defined scheme... commit | commitdiff
2023-06-06 James ProcterJAL-4160 JAL-4195 wait around until alignFrame calculat... commit | commitdiff
2023-06-06 James ProcterJAL-4195 Debug message indicating creation of an image... commit | commitdiff
2023-06-01 Ben SoaresJAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt... commit | commitdiff
2023-05-23 Ben SoaresJAL-629 Updated help docs and fixed structure image... commit | commitdiff
2023-05-23 Ben SoaresJAL-629 Added --structureimage code and formatting... commit | commitdiff
2023-05-22 Ben SoaresJAL-629 --structureimage with formatting args. commit | commitdiff
2023-05-18 Ben SoaresJAL-629 Added 'Type' to args and argvalues commit | commitdiff
2023-05-15 Ben SoaresRevert "JAL-629 Add a --threads argument to allow a... commit | commitdiff
2023-05-15 Ben SoaresJAL-629 Add a --threads argument to allow a limited... commit | commitdiff
2023-05-12 Ben SoaresJAL-629 Added --opened arg which is like limiting ... commit | commitdiff
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac... commit | commitdiff
2023-05-11 Ben SoaresJAL-629 Added linkedId to ArgValuesMap for reference... commit | commitdiff
2023-05-10 Ben SoaresJAL-629 More docs. Usage statement. Adjust some logging... commit | commitdiff
2023-05-09 Ben SoaresJAL-629 Add --seqid for non-subval use, make arg value... commit | commitdiff
2023-05-09 Ben SoaresJAL-629 change --renderer to --textrenderer to be more... commit | commitdiff
2023-05-04 Ben SoaresJAL-629 More NG arguments: --features, --annotations... commit | commitdiff
2023-05-03 Ben SoaresJAL-629 added eps and imagemap. Added --output and... commit | commitdiff
2023-05-02 Ben SoaresJAL-629 Changed --newframe and --allframes to --new... commit | commitdiff
2023-05-02 Ben SoaresJAL-629 Add --renderer arg/subval for vector output... commit | commitdiff
2023-04-30 Ben SoaresJAL-629 Change behaviour of --open GLOB to increment... commit | commitdiff
2023-04-28 Ben SoaresJAL-629 Change colour scheme shortnames to something... commit | commitdiff
2023-04-27 Ben SoaresJAL-629 Fixed appending URLs commit | commitdiff
2023-04-23 Ben SoaresJAL-629 Change --open to --append and --opennew to... commit | commitdiff
2023-04-22 Ben SoaresJAL-629 Test and fix --annotation --ssannotation args... commit | commitdiff
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... commit | commitdiff
2023-04-14 Ben SoaresJAL-629 Adding PAE and TFType at structure loading... commit | commitdiff
2023-04-12 Ben SoaresJAL-629 parse SubVals once with ArgValue. Ensure SubVal... commit | commitdiff
2023-04-05 Ben SoaresJAL-629 Tests for FileUtils. Tidying counter substituti... commit | commitdiff
2023-04-04 Ben SoaresJAL-629 More consistent printing of --arguments. Exampl... commit | commitdiff
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added... commit | commitdiff
2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet commit | commitdiff
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement... commit | commitdiff
2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to... commit | commitdiff
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... commit | commitdiff
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader... commit | commitdiff
2023-03-08 Ben SoaresJAL-629 --close individually for each AlignFrame opened... commit | commitdiff
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar... commit | commitdiff
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ... commit | commitdiff
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... commit | commitdiff
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in... commit | commitdiff
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless commit | commitdiff
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some... commit | commitdiff
2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies... commit | commitdiff
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index... commit | commitdiff
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... commit | commitdiff
2023-01-26 Ben SoaresJAL-629 adjust arg type for tempfac-shading -- was... commit | commitdiff
2023-01-24 James ProcterJAL-629 hacked in --tempfac-shading - hardcoded to... commit | commitdiff
2023-01-24 James ProcterJAL-629 suggest not breaking out of the structure proce... commit | commitdiff
2023-01-24 James ProcterJAL-629 don’t carry on Jalview.main if we’ve already... commit | commitdiff
2023-01-24 James ProcterJAL-629 don’t trash user’s system property file when... commit | commitdiff
2023-01-24 James ProcterJAL-629 labelled breaks are frowned upon by everyone commit | commitdiff
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... commit | commitdiff
2023-01-18 Ben SoaresJAL-629 make sequence id key 'seqid' commit | commitdiff
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... commit | commitdiff
2022-12-19 Ben SoaresJAL-629 Add image output and quit commit | commitdiff
2022-12-15 Ben SoaresJAL-629 move SubId to more logical place. Attempt remov... commit | commitdiff
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