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),
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.IMAGE,
+ STRUCTUREIMAGE(Type.STRUCTUREIMAGE,
"Export an image of a 3D structure opened in JMOL", Opt.STRING,
Opt.LINKED, Opt.MULTI),
-
- STRUCTUREIMAGETYPE(Type.IMAGE,
+ 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.IMAGE,
- "Sets whether text in a vector structure image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values are:\n"
+ 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.IMAGE,
+ 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.IMAGE,
+ 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.IMAGE,
+ 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),
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