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Adapts PCA points to support rectangular selection
[jalview.git]
/
src
/
jalview
/
bin
/
Commands.java
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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2023-01-18
Ben Soares
JAL-629 make sequence id key 'seqid'
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2023-01-11
Ben Soares
JAL-629 refactoring TFType. Remove i18n identification...
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2022-12-19
Ben Soares
JAL-629 Add image output and quit
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2022-12-15
Ben Soares
JAL-629 move SubId to more logical place. Attempt remov...
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2022-12-14
Ben Soares
JAL-629 Open Structure Viewer from cmdline
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2022-12-09
Ben Soares
JAL-629 null check, fixed tests!
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2022-12-08
Ben Soares
JAL-629 stray code deleted
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2022-12-08
Ben Soares
JAL-629 Allow attachment of pAE file to a particular...
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2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
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2022-11-23
Ben Soares
JAL-629 Doing things with the command line arguments
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