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JAL-629 Move more stdout messages to stderr when outputting file to stdout
[jalview.git] / src / jalview / bin / Commands.java
2023-08-09 Ben SoaresJAL-629 Move more stdout messages to stderr when output... blob | commitdiff
2023-08-09 Ben SoaresJAL-629 Default to FASTA if no format given for output... blob | commitdiff | diff to current
2023-08-09 Ben SoaresJAL-629 Enable output to STDOUT when specifying output... blob | commitdiff | diff to current
2023-07-07 James ProcterJAL-4217 JAL-629 built in 25s time out waiting for... blob | commitdiff | diff to current
2023-07-07 James ProcterJAL-629 even more console debug for --structureviewer... blob | commitdiff | diff to current
2023-07-06 James ProcterJAL-629 liberal defensive coding, comments about refact... blob | commitdiff | diff to current
2023-07-06 James ProcterJAL-4217 interruptedExceptions should also break any... blob | commitdiff | diff to current
2023-06-08 James ProcterJAL-4196 report an error if structure view doesn’t... blob | commitdiff | diff to current
2023-06-07 James ProcterJAL-4195 add exception handling for all image output... blob | commitdiff | diff to current
2023-06-07 James ProcterJAL-4195 catch thrown exceptions (if any) during image... blob | commitdiff | diff to current
2023-06-06 James ProcterJAL-4160 --colour can now take user defined scheme... blob | commitdiff | diff to current
2023-06-06 James ProcterJAL-4160 JAL-4195 wait around until alignFrame calculat... blob | commitdiff | diff to current
2023-06-06 James ProcterJAL-4195 Debug message indicating creation of an image... blob | commitdiff | diff to current
2023-06-01 Ben SoaresJAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt... blob | commitdiff | diff to current
2023-05-23 Ben SoaresJAL-629 Updated help docs and fixed structure image... blob | commitdiff | diff to current
2023-05-23 Ben SoaresJAL-629 Added --structureimage code and formatting... blob | commitdiff | diff to current
2023-05-22 Ben SoaresJAL-629 --structureimage with formatting args. blob | commitdiff | diff to current
2023-05-18 Ben SoaresJAL-629 Added 'Type' to args and argvalues blob | commitdiff | diff to current
2023-05-15 Ben SoaresRevert "JAL-629 Add a --threads argument to allow a... blob | commitdiff | diff to current
2023-05-15 Ben SoaresJAL-629 Add a --threads argument to allow a limited... blob | commitdiff | diff to current
2023-05-12 Ben SoaresJAL-629 Added --opened arg which is like limiting ... blob | commitdiff | diff to current
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac... blob | commitdiff | diff to current
2023-05-11 Ben SoaresJAL-629 Added linkedId to ArgValuesMap for reference... blob | commitdiff | diff to current
2023-05-10 Ben SoaresJAL-629 More docs. Usage statement. Adjust some logging... blob | commitdiff | diff to current
2023-05-09 Ben SoaresJAL-629 Add --seqid for non-subval use, make arg value... blob | commitdiff | diff to current
2023-05-09 Ben SoaresJAL-629 change --renderer to --textrenderer to be more... blob | commitdiff | diff to current
2023-05-04 Ben SoaresJAL-629 More NG arguments: --features, --annotations... blob | commitdiff | diff to current
2023-05-03 Ben SoaresJAL-629 added eps and imagemap. Added --output and... blob | commitdiff | diff to current
2023-05-02 Ben SoaresJAL-629 Changed --newframe and --allframes to --new... blob | commitdiff | diff to current
2023-05-02 Ben SoaresJAL-629 Add --renderer arg/subval for vector output... blob | commitdiff | diff to current
2023-04-30 Ben SoaresJAL-629 Change behaviour of --open GLOB to increment... blob | commitdiff | diff to current
2023-04-28 Ben SoaresJAL-629 Change colour scheme shortnames to something... blob | commitdiff | diff to current
2023-04-27 Ben SoaresJAL-629 Fixed appending URLs blob | commitdiff | diff to current
2023-04-23 Ben SoaresJAL-629 Change --open to --append and --opennew to... blob | commitdiff | diff to current
2023-04-22 Ben SoaresJAL-629 Test and fix --annotation --ssannotation args... blob | commitdiff | diff to current
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... blob | commitdiff | diff to current
2023-04-14 Ben SoaresJAL-629 Adding PAE and TFType at structure loading... blob | commitdiff | diff to current
2023-04-12 Ben SoaresJAL-629 parse SubVals once with ArgValue. Ensure SubVal... blob | commitdiff | diff to current
2023-04-05 Ben SoaresJAL-629 Tests for FileUtils. Tidying counter substituti... blob | commitdiff | diff to current
2023-04-04 Ben SoaresJAL-629 More consistent printing of --arguments. Exampl... blob | commitdiff | diff to current
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added... blob | commitdiff | diff to current
2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet blob | commitdiff | diff to current
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement... blob | commitdiff | diff to current
2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to... blob | commitdiff | diff to current
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... blob | commitdiff | diff to current
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader... blob | commitdiff | diff to current
2023-03-08 Ben SoaresJAL-629 --close individually for each AlignFrame opened... blob | commitdiff | diff to current
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar... blob | commitdiff | diff to current
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ... blob | commitdiff | diff to current
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... blob | commitdiff | diff to current
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in... blob | commitdiff | diff to current
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless blob | commitdiff | diff to current
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some... blob | commitdiff | diff to current
2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies... blob | commitdiff | diff to current
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index... blob | commitdiff | diff to current
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... blob | commitdiff | diff to current
2023-01-26 Ben SoaresJAL-629 adjust arg type for tempfac-shading -- was... blob | commitdiff | diff to current
2023-01-24 James ProcterJAL-629 hacked in --tempfac-shading - hardcoded to... blob | commitdiff | diff to current
2023-01-24 James ProcterJAL-629 suggest not breaking out of the structure proce... blob | commitdiff | diff to current
2023-01-24 James ProcterJAL-629 don’t carry on Jalview.main if we’ve already... blob | commitdiff | diff to current
2023-01-24 James ProcterJAL-629 don’t trash user’s system property file when... blob | commitdiff | diff to current
2023-01-24 James ProcterJAL-629 labelled breaks are frowned upon by everyone blob | commitdiff | diff to current
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... blob | commitdiff | diff to current
2023-01-18 Ben SoaresJAL-629 make sequence id key 'seqid' blob | commitdiff | diff to current
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... blob | commitdiff | diff to current
2022-12-19 Ben SoaresJAL-629 Add image output and quit blob | commitdiff | diff to current
2022-12-15 Ben SoaresJAL-629 move SubId to more logical place. Attempt remov... blob | commitdiff | diff to current
2022-12-14 Ben SoaresJAL-629 Open Structure Viewer from cmdline blob | commitdiff | diff to current
2022-12-09 Ben SoaresJAL-629 null check, fixed tests! blob | commitdiff | diff to current
2022-12-08 Ben SoaresJAL-629 stray code deleted blob | commitdiff | diff to current
2022-12-08 Ben SoaresJAL-629 Allow attachment of pAE file to a particular... blob | commitdiff | diff to current
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options blob | commitdiff | diff to current
2022-11-23 Ben SoaresJAL-629 Doing things with the command line arguments blob | commitdiff | diff to current