TEMPFAC(Type.STRUCTURE,
"Set the type of temperature factor. Possible values are:\n"
+ "default,\n" + "plddt.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
STRUCTUREVIEWER(Type.STRUCTURE,
"Set the structure viewer to use to open the 3D structure file specified in previous --structure to name. Possible values of name are:\n"
+ "none,\n" + "jmol,\n" + "chimera,\n" + "chimerax,\n"
NOTEMPFAC(Type.STRUCTURE,
"Do not show the temperature factor annotation for the preceding --structure.",
Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.SECRET), // keep this
- // secret
- // until it works!
+ // secret until
+ // it works!
SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
Opt.ALLOWMULTIID),
IMAGE(Type.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.ALLOWMULTIID,
- Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.MULTIVALUE,
+ Opt.ALLOWMULTIID, Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY),
+ STRUCTUREIMAGE(Type.IMAGE,
+ "Export an image of a 3D structure opened in JMOL", Opt.STRING,
+ Opt.LINKED, Opt.MULTIVALUE, Opt.OUTPUTFILE, Opt.ALLOWMULTIID,
+ Opt.PRIMARY),
TYPE(Type.IMAGE,
- "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.ALLOWMULTIID),
+ "Set the image format for the preceding " + Arg.IMAGE.argString()
+ + " or " + Arg.STRUCTUREIMAGE.argString()
+ + ". Valid values are:\n" + "svg,\n" + "png,\n" + "eps,\n"
+ + "html,\n" + "biojs.",
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
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 are:\n"
+ "text,\n" + "lineart.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
SCALE(Type.IMAGE,
"Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. If used in conjunction with --width and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
WIDTH(Type.IMAGE,
"Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --scale and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
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.ALLOWMULTIID),
- STRUCTUREIMAGE(Type.STRUCTUREIMAGE,
- "Export an image of a 3D structure opened in JMOL", Opt.STRING,
- Opt.LINKED, Opt.MULTIVALUE, Opt.OUTPUTFILE, Opt.ALLOWMULTIID),
- STRUCTUREIMAGETYPE(Type.STRUCTUREIMAGE,
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
+ IMAGECOLOUR(Type.IMAGE, "imagecolor", // being a bit soft on the Americans!
+ "Applies the colour scheme to the open alignment window for this image, otherwise the value of "
+ + Arg.COLOUR.argString()
+ + " (or none) will apply. Valid values are the same as "
+ + Arg.COLOUR.argString() + ".",
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
+ BGCOLOUR(Type.IMAGE, "bgcolor", // being a bit soft on the Americans!
+ "Applies a background colour to the structure image. Valid values are named colours or #RRGGBB.",
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
+ /*
+ STRUCTUREIMAGETYPE(Type.IMAGE,
"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.ALLOWMULTIID),
- STRUCTUREIMAGETEXTRENDERER(Type.STRUCTUREIMAGE,
+ STRUCTUREIMAGETEXTRENDERER(Type.IMAGE,
"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.ALLOWMULTIID),
- STRUCTUREIMAGESCALE(Type.STRUCTUREIMAGE,
+ STRUCTUREIMAGESCALE(Type.IMAGE,
"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.ALLOWMULTIID),
- STRUCTUREIMAGEWIDTH(Type.STRUCTUREIMAGE,
+ STRUCTUREIMAGEWIDTH(Type.IMAGE,
"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.ALLOWMULTIID),
- STRUCTUREIMAGEHEIGHT(Type.STRUCTUREIMAGE,
+ STRUCTUREIMAGEHEIGHT(Type.IMAGE,
"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.ALLOWMULTIID),
+ */
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"
STRUCTURE("arguments used to add and format 3D structure data"),
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"),
+ IMAGE("arguments used to export an image of an alignment or structure"),
+ // 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
git://source.jalview.org / jalview.git / blobdiff