Opt.UNARY, Opt.BOOTSTRAP),
HEADLESS(Type.CONFIG,
"Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed. "
- + "Headless mode is assumed if an output file is to be generated, this can be overridden with --noheadless or --gui.",
- Opt.BOOLEAN, Opt.BOOTSTRAP),
+ + "Headless mode is assumed if an output file is to be generated, this can be overridden with --gui.",
+ Opt.UNARY, Opt.BOOTSTRAP),
GUI(Type.CONFIG,
"Do not run Jalview in headless mode. This overrides the assumption of headless mode when an output file is to be generated.",
Opt.UNARY, Opt.BOOTSTRAP),
"Specifies the title for the open alignment window as string.",
Opt.STRING, Opt.LINKED),
COLOUR(Type.OPENING, "color", // being a bit soft on the Americans!
- "Applies the colour scheme to the open alignment window. Valid values are:\n"
+ "Applies the colour scheme to the open alignment window. Valid values include:\n"
+ "clustal,\n" + "blosum62,\n" + "pc-identity,\n"
+ "zappo,\n" + "taylor,\n" + "gecos-flower,\n"
+ "gecos-blossom,\n" + "gecos-sunset,\n"
+ "turn-propensity,\n" + "buried-index,\n"
+ "nucleotide,\n" + "nucleotide-ambiguity,\n"
+ "purine-pyrimidine,\n" + "rna-helices,\n"
- + "t-coffee-scores,\n" + "sequence-id.",
+ + "t-coffee-scores,\n" + "sequence-id.\n" + "\n"
+ + "Names of user defined colourschemes will also work,\n"
+ + "and jalview colourscheme specifications like\n"
+ + "--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"",
Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.",
Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ "clustal (aln),\n" + "phylip (phy),\n"
+ "jalview (jvp, jar).",
Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
- Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY),
+ Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.STDOUT, Opt.PRIMARY),
FORMAT(Type.OUTPUT,
"Sets the format for the preceding --output file. Valid formats are:\n"
+ "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n"
*/
OUTPUTFILE("output file --headless will be assumed unless --gui used"),
/*
+ * A STDOUT Arg can take an output filename that can be '-' to mean print to STDOUT.
+ */
+ STDOUT("allows the output filename '" + ArgParser.STDOUTFILENAME
+ + "' to mean output to STDOUT"),
+ /*
* A STORED Arg resets and creates a new set of "opened" linkedIds
*/
STORED(null),