true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION, Opt.SECRET),
P(Type.CONFIG, "Set a Jalview preference value for this session.",
Opt.PREFIXKEV, Opt.PRESERVECASE, Opt.STRING, Opt.BOOTSTRAP,
true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION, Opt.SECRET),
P(Type.CONFIG, "Set a Jalview preference value for this session.",
Opt.PREFIXKEV, Opt.PRESERVECASE, Opt.STRING, Opt.BOOTSTRAP,
- Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET), // keep this secret for now.
+ Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET), // keep this secret for
+ // now.
- Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER, Opt.MULTIVALUE,
- Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT, Opt.STORED,
- Opt.PRIMARY),
+ Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER,
+ Opt.MULTIVALUE, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT,
+ Opt.STORED, Opt.PRIMARY),
APPEND(Type.OPENING,
"Appends one or more alignment files or URLs to the open alignment window (or opens a new alignment if none already open).",
Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.GLOB,
APPEND(Type.OPENING,
"Appends one or more alignment files or URLs to the open alignment window (or opens a new alignment if none already open).",
Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.GLOB,
Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
NOTEMPFAC(Type.STRUCTURE,
"Do not show the temperature factor annotation for the preceding --structure.",
Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
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!
+ Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.SECRET), // keep this
+ // secret
+ // until it works!
SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
Opt.ALLOWMULTIID),
SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
Opt.ALLOWMULTIID),
CLOSE(Type.OPENING,
"Close the current open alignment window. This occurs after other output arguments. This applies to the current open alignment. To apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID),
CLOSE(Type.OPENING,
"Close the current open alignment window. This occurs after other output arguments. This applies to the current open alignment. To apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID),
// controlling flow of arguments
NEW(Type.FLOW,
"Move on to a new alignment window. This will ensure --append will start a new alignment window and other linked arguments will apply to the new alignment window.",
// controlling flow of arguments
NEW(Type.FLOW,
"Move on to a new alignment window. This will ensure --append will start a new alignment window and other linked arguments will apply to the new alignment window.",
- Opt.UNARY, Opt.MULTIVALUE, Opt.NOACTION, Opt.INCREMENTDEFAULTCOUNTER),
+ Opt.UNARY, Opt.MULTIVALUE, Opt.NOACTION,
+ Opt.INCREMENTDEFAULTCOUNTER),
SUBSTITUTIONS(Type.FLOW,
"The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are:\n"
+ "{basename} - the filename-without-extension of the currently --opened file (or first --appended file),\n"
SUBSTITUTIONS(Type.FLOW,
"The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are:\n"
+ "{basename} - the filename-without-extension of the currently --opened file (or first --appended file),\n"
"Allow specific stdout information. For testing purposes only.",
Opt.UNARY, Opt.BOOTSTRAP, Opt.SECRET), // do not show this to the user
SETPROP(Type.CONFIG, "Set an individual Java System property.",
"Allow specific stdout information. For testing purposes only.",
Opt.UNARY, Opt.BOOTSTRAP, Opt.SECRET), // do not show this to the user
SETPROP(Type.CONFIG, "Set an individual Java System property.",
- Opt.STRING, Opt.MULTIVALUE, Opt.BOOTSTRAP, Opt.SECRET), // not in use yet
+ Opt.STRING, Opt.MULTIVALUE, Opt.BOOTSTRAP, Opt.SECRET), // not in use
+ // yet
NIL(Type.FLOW,
"This argument does nothing on its own, but can be used with linkedIds.",
Opt.UNARY, Opt.LINKED, Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET),
NIL(Type.FLOW,
"This argument does nothing on its own, but can be used with linkedIds.",
Opt.UNARY, Opt.LINKED, Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET),