+ "none,\n" + "jmol,\n" + "chimera,\n" + "chimerax,\n"
+ "pymol.",
Opt.STRING, Opt.LINKED, Opt.MULTI),
- STRUCTUREIMAGE(Type.STRUCTURE,
- "Export an image of a 3D structure opened in JMOL", Opt.STRING,
- Opt.LINKED, Opt.MULTI),
NOTEMPFAC(Type.STRUCTURE,
"Do not show the temperature factor annotation for the preceding --structure.",
Opt.UNARY, Opt.LINKED, Opt.ALLOWALL, Opt.SECRET), // keep this secret
- // until it
- // works!
+ // until it works!
SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
Opt.ALLOWALL),
Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
Opt.REQUIREINPUT, Opt.OUTPUT, Opt.PRIMARY),
TYPE(Type.IMAGE,
- "Set the image format for the preceding --image to name. Valid values for name are: svg,\n"
- + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
+ "Set the image format for the preceding --image. Valid values are:\n"
+ + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
TEXTRENDERER(Type.IMAGE,
- "Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values for name are:\n"
+ "Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values are:\n"
+ "text,\n" + "lineart.",
Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
SCALE(Type.IMAGE,
HEIGHT(Type.IMAGE,
"Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --scale and --width then the smallest scaling will be used (scale, width and height provide bounds for the image).",
Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ STRUCTUREIMAGE(Type.STRUCTUREIMAGE,
+ "Export an image of a 3D structure opened in JMOL", Opt.STRING,
+ Opt.LINKED, Opt.MULTI),
+ STRUCTUREIMAGETYPE(Type.STRUCTUREIMAGE,
+ "Set the structure image format for the preceding --structureimage. Valid values are:\n"
+ + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ STRUCTUREIMAGETEXTRENDERER(Type.STRUCTUREIMAGE,
+ "Sets whether text in a vector structure image format (SVG, EPS) should be rendered as text or vector line-art. Possible values are:\n"
+ + "text,\n" + "lineart.",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ STRUCTUREIMAGESCALE(Type.STRUCTUREIMAGE,
+ "Sets a scaling for bitmap structure image format (PNG). Should be given as a floating point number. If used in conjunction with --structureimagewidth and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ STRUCTUREIMAGEWIDTH(Type.STRUCTUREIMAGE,
+ "Sets a width for bitmap structure image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ STRUCTUREIMAGEHEIGHT(Type.STRUCTUREIMAGE,
+ "Sets a height for bitmap structure image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimagewidth then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+
OUTPUT(Type.OUTPUT,
"Export the open alignment to file filename. The format name is specified by the subval modifier format=name, a following --format name argument or guessed from the file extension. Valid format names (and file extensions) are:\n"
+ "fasta (fa, fasta, mfa, fastq),\n" + "pfam (pfam),\n"
QUIT(Type.FLOW,
"After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.",
Opt.UNARY),
+ NOQUIT(Type.FLOW,
+ "Secret arg to not quit after --headless mode for tests",
+ Opt.UNARY, Opt.SECRET),
+ ALLSTRUCTURES(Type.FLOW,
+ "Apply the following 3D structure formatting arguments to all structures within the open alignment.",
+ Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
// secret options
TESTOUTPUT(Type.CONFIG,
PROCESS("arguments used to process an alignment once opened"),
OUTPUT("arguments used to save data from a processed alignment"),
IMAGE("arguments used to export an image of an alignment"),
+ STRUCTUREIMAGE("arguments used to export an image of an structure"),
FLOW("arguments that control processing of the other arguments"), //
ALL("all arguments"), // mostly just a place-holder for --help-all
NONE, // mostly a place-holder for --help
{
StringBuilder sb = new StringBuilder();
- sb.append("usage: jalview [" + Arg.HEADLESS.argString() + "] ["
+ sb.append("usage: jalview [" + Arg.HEADLESS.argString() + "] [["
+ Arg.OPEN.argString() + "/" + Arg.APPEND.argString()
- + " file(s)] [args]");
+ + "] file(s)] [args]");
sb.append(System.lineSeparator());
sb.append(System.lineSeparator());
}
Iterator<Arg> argsI = args.iterator();
+ Type typeSection = null;
while (argsI.hasNext())
{
Arg a = argsI.next();
continue;
}
+ if (a.getType() != typeSection)
+ {
+ typeSection = a.getType();
+ String typeDescription = a.getType().description();
+ if (typeDescription != null && typeDescription.length() > 0)
+ {
+ // typeDescription = typeDescription.substring(0,
+ // 1).toUpperCase(Locale.ROOT) + typeDescription.substring(1);
+ typeDescription = typeDescription.toUpperCase(Locale.ROOT);
+ sb.append(typeDescription);
+ sb.append(System.lineSeparator());
+ sb.append(System.lineSeparator());
+ }
+ }
+
appendArgUsage(sb, a, maxArgLength);
if (argsI.hasNext())
+ {
sb.append(System.lineSeparator());
+ }
}
}
return sb.toString();
git://source.jalview.org / jalview.git / blobdiff