{
// Initialising arguments (BOOTSTRAP)
- HELP("Display this help statement", Opt.UNARY, Opt.BOOTSTRAP),
- VERSION("Display the version of "
- + ChannelProperties.getProperty("app_name"), Opt.UNARY,
- Opt.BOOTSTRAP),
+ HELP("h", "Display this help statement", Opt.UNARY, Opt.BOOTSTRAP),
+ VERSION("v",
+ "Display the version of "
+ + ChannelProperties.getProperty("app_name"),
+ Opt.UNARY, Opt.BOOTSTRAP),
HEADLESS(
"Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.",
Opt.UNARY, Opt.BOOTSTRAP),
PROPS("Use a file as the preferences file instead of the usual ~/"
+ ChannelProperties.getProperty("preferences.filename")
+ " file.", Opt.STRING, Opt.BOOTSTRAP),
- DEBUG("Start Jalview in debug log level.", Opt.BOOLEAN, Opt.BOOTSTRAP),
+ DEBUG("d", "Start Jalview in debug log level.", Opt.BOOLEAN,
+ Opt.BOOTSTRAP),
TRACE("Start Jalview in trace log level.", Opt.BOOLEAN, Opt.BOOTSTRAP,
Opt.SECRET),
- QUIET("Stop all output to STDOUT (after the Java Virtual Machine has started). Use ‑‑quiet a second time to stop all output to STDERR.",
+ QUIET("q",
+ "Stop all output to STDOUT (after the Java Virtual Machine has started). Use ‑‑quiet a second time to stop all output to STDERR.",
Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP),
INITSUBSTITUTIONS(
"Set ‑‑substitutions to be initially enabled (or initially disabled).",
+ "turn-propensity,\n" + "buried-index,\n" + "nucleotide,\n"
+ "nucleotide-ambiguity,\n" + "purine-pyrimidine,\n"
+ "rna-helices,\n" + "t-coffee-scores,\n" + "sequence-id.",
- Opt.STRING, Opt.LINKED),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
FEATURES("Add a feature file or URL to the open alignment.", Opt.STRING,
Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
TREE("Add a tree file or URL to the open alignment.", Opt.STRING,
Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
SORTBYTREE(
"Enforces sorting (or not sorting) the open alignment in the order of an attached phylogenetic tree.",
- true, Opt.LINKED, Opt.BOOLEAN),
+ true, Opt.LINKED, Opt.BOOLEAN, Opt.ALLOWALL),
ANNOTATIONS("Add an annotations file or URL to the open alignment.",
Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
SHOWANNOTATIONS(
"Enforces showing (or not showing) alignment annotations.",
- Opt.BOOLEAN, Opt.LINKED),
+ Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
WRAP("Enforces wrapped (or not wrapped) alignment formatting.",
- Opt.BOOLEAN, Opt.LINKED),
+ Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
NOSTRUCTURE(
"Do not open or process any 3D structure in the ‑‑open or ‑‑append files.",
- Opt.UNARY, Opt.LINKED),
+ Opt.UNARY, Opt.LINKED, Opt.ALLOWALL),
// Adding a 3D structure
STRUCTURE(
Opt.STRING, Opt.LINKED, Opt.MULTI),
NOTEMPFAC(
"Do not show the temperature factor annotation for the preceding --structure.",
- Opt.UNARY, Opt.LINKED, Opt.SECRET), // keep this secret until it
- // works!
- SHOWSSANNOTATIONS(null, Opt.BOOLEAN, Opt.LINKED),
+ Opt.UNARY, Opt.LINKED, Opt.ALLOWALL, Opt.SECRET), // keep this secret
+ // until it
+ // works!
+ SHOWSSANNOTATIONS(null, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
// Outputting files
IMAGE("Output an image of the open alignment window. Format is specified by the subval modifier, a following --type argument or guessed from the file extension. Valid formats/extensions are:\n"
+ "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
- Opt.REQUIREINPUT),
+ Opt.REQUIREINPUT, Opt.OUTPUT),
TYPE("Set the image format for the preceding --image to name. Valid values for name are: svg,\n"
+ "png,\n" + "eps,\n" + "html,\n" + "biojs.", Opt.STRING,
Opt.LINKED, Opt.ALLOWALL),
+ "amsa (amsa),\n" + "json (json),\n" + "pileup (pileup),\n"
+ "msf (msf),\n" + "clustal (aln),\n" + "phylip (phy),\n"
+ "jalview (jvp, jar).", Opt.STRING, Opt.LINKED,
- Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL, Opt.REQUIREINPUT),
+ Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL, Opt.REQUIREINPUT,
+ Opt.OUTPUT),
FORMAT("Sets the format for the preceding --output file. Valid formats are:\n"
+ "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n" + "blc,\n"
+ "amsa,\n" + "json,\n" + "pileup,\n" + "msf,\n" + "clustal,\n"
+ "phylip,\n" + "jalview.", Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
GROOVY("Process a groovy script in the file for the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWALL),
BACKUPS("Enable (or disable) writing backup files when saving an ‑‑output file. This applies to the current open alignment. To apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
true, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
OVERWRITE(
+ "Note that if you use one or more --argfile arguments then all other non-initialising arguments will be ignored.",
Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB,
Opt.ALLOWSUBSTITUTIONS),
- NPP("Increase the index counter used in argument value substitutions.",
+ NPP("n++",
+ "Increase the index counter used in argument value substitutions.",
Opt.UNARY, Opt.MULTI, Opt.NOACTION),
ALL("Apply the following output arguments to all sets of linked arguments.",
Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
INPUT, // This Arg counts as an input for REQUIREINPUT
REQUIREINPUT, // This Arg can only be applied via --all if there is an
// input (i.e. --open or --append)
+ OUTPUT, // This Arg provides an output filename. With Opt.ALLOWALL *.ext is
+ // shorthand for --all --output={basename}.ext
}
private final String[] argNames;
git://source.jalview.org / jalview.git / blobdiff