// Initialising arguments (BOOTSTRAP)
HELP(Type.HELP, "h", "Display basic help", Opt.UNARY, Opt.BOOTSTRAP,
- Opt.HASTYPE, Opt.MULTI),
+ Opt.HASTYPE, Opt.MULTIVALUE),
/*
* Other --help-type Args will be added by the static block.
*/
Opt.BOOTSTRAP, Opt.SECRET),
QUIET(Type.CONFIG, "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),
+ Opt.UNARY, Opt.MULTIVALUE, Opt.BOOTSTRAP),
INITSUBSTITUTIONS(Type.CONFIG,
"Set ‑‑substitutions to be initially enabled (or initially disabled).",
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.MULTI, Opt.NOACTION, Opt.SECRET), // keep this secret for now.
+ Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET), // keep this secret for now.
// Opening an alignment
OPEN(Type.OPENING,
"Opens one or more alignment files or URLs in new alignment windows.",
- Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER, Opt.MULTI,
+ 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.MULTI, Opt.GLOB,
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.GLOB,
Opt.ALLOWSUBSTITUTIONS, Opt.INPUT, Opt.PRIMARY),
TITLE(Type.OPENING,
"Specifies the title for the open alignment window as string.",
- Opt.STRING, Opt.LINKED),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
COLOUR(Type.OPENING, "color", // being a bit soft on the Americans!
"Applies the colour scheme to the open alignment window. Valid values include:\n"
+ "clustal,\n" + "blosum62,\n" + "pc-identity,\n"
+ "Names of user defined colourschemes will also work,\n"
+ "and jalview colourscheme specifications like\n"
+ "--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"",
- Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
TREE(Type.OPENING, "Add a tree file or URL to the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
SORTBYTREE(Type.OPENING,
"Enforces sorting (or not sorting) the open alignment in the order of an attached phylogenetic tree.",
- true, Opt.LINKED, Opt.BOOLEAN, Opt.ALLOWALL),
+ true, Opt.LINKED, Opt.BOOLEAN, Opt.ALLOWMULTIID),
ANNOTATIONS(Type.OPENING,
"Add an annotations file or URL to the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
SHOWANNOTATIONS(Type.OPENING,
"Enforces showing (or not showing) alignment annotations.",
- Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
+ Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID, Opt.ALLOWMULTIID),
WRAP(Type.OPENING,
"Enforces wrapped (or not wrapped) alignment formatting.",
- Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
+ Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID, Opt.ALLOWMULTIID),
NOSTRUCTURE(Type.OPENING,
"Do not open or process any 3D structure in the ‑‑open or ‑‑append files.",
- Opt.UNARY, Opt.LINKED, Opt.ALLOWALL),
+ Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.ALLOWMULTIID),
// Adding a 3D structure
STRUCTURE(Type.STRUCTURE,
"Load a structure file or URL associated with a sequence in the open alignment.\n"
+ "The sequence to be associated with can be specified with a following --seqid argument, or the subval modifier seqid=ID can be used. A subval INDEX can also be used to specify the INDEX-th sequence in the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS,
- Opt.PRIMARY),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.PRIMARY, Opt.ALLOWMULTIID),
SEQID(Type.STRUCTURE,
"Specify the sequence name for the preceding --structure to be associated with.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
PAEMATRIX(Type.STRUCTURE,
"Add a PAE json matrix file to the preceding --structure.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
TEMPFAC(Type.STRUCTURE,
"Set the type of temperature factor. Possible values are:\n"
+ "default,\n" + "plddt.",
- Opt.STRING, Opt.LINKED),
+ Opt.STRING, Opt.LINKED, 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"
+ "pymol.",
- Opt.STRING, Opt.LINKED, Opt.MULTI),
+ 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.ALLOWALL, Opt.SECRET), // keep this secret
+ Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.SECRET), // keep this secret
// until it works!
SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
- Opt.ALLOWALL),
+ Opt.ALLOWMULTIID),
// Outputting files
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.ALLOWALL,
+ Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWMULTIID,
Opt.REQUIREINPUT, Opt.OUTPUTFILE, 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.ALLOWALL),
+ Opt.STRING, Opt.LINKED, 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.ALLOWALL),
+ Opt.STRING, Opt.LINKED, 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.ALLOWALL),
+ Opt.STRING, Opt.LINKED, 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.ALLOWALL),
+ Opt.STRING, Opt.LINKED, 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.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
STRUCTUREIMAGE(Type.STRUCTUREIMAGE,
"Export an image of a 3D structure opened in JMOL", Opt.STRING,
- Opt.LINKED, Opt.MULTI, Opt.OUTPUTFILE),
+ Opt.LINKED, Opt.MULTIVALUE, Opt.OUTPUTFILE, Opt.ALLOWMULTIID),
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),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
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),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
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),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
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),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
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),
+ 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"
+ "pileup (pileup),\n" + "msf (msf),\n"
+ "clustal (aln),\n" + "phylip (phy),\n"
+ "jalview (jvp, jar).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
+ Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWMULTIID,
Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.STDOUT, Opt.PRIMARY),
FORMAT(Type.OUTPUT,
"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),
+ Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
GROOVY(Type.PROCESS,
"Process a groovy script in the file for the open alignment.",
- Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS,
- Opt.ALLOWALL),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWMULTIID),
BACKUPS(Type.OUTPUT,
"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),
+ true, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID),
OVERWRITE(Type.OUTPUT,
"Enable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment. To apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
- Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
+ 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.ALLOWALL),
+ 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.",
- Opt.UNARY, Opt.MULTI, 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"
+ "{n} - the value of the index counter (starting at 0).\n"
+ "{++n} - increase and substitute the value of the index counter,\n"
+ "{} - the value of the current alignment window default index.",
- true, Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
+ true, Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION),
ARGFILE(Type.FLOW,
"Open one or more files filename and read, line-by-line, as arguments to Jalview.\n"
+ "Values in an argfile should be given with an equals sign (\"=\") separator with no spaces.\n"
+ "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.STRING, Opt.MULTIVALUE, Opt.BOOTSTRAP, Opt.GLOB,
Opt.ALLOWSUBSTITUTIONS),
NPP(Type.FLOW, "n++",
"Increase the index counter used in argument value substitutions.",
- Opt.UNARY, Opt.MULTI, Opt.NOACTION),
+ Opt.UNARY, Opt.MULTIVALUE, Opt.NOACTION),
ALL(Type.FLOW,
"Apply the following output arguments to all sets of linked arguments.",
- Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
+ Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION),
OPENED(Type.FLOW,
"Apply the following output arguments to all of the last --open'ed set of linked arguments.",
- Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
+ Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION),
QUIT(Type.FLOW,
"After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.",
Opt.UNARY),
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),
+ Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION),
// secret options
TESTOUTPUT(Type.CONFIG,
"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.MULTI, 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.MULTI, Opt.NOACTION, Opt.SECRET),
+ Opt.UNARY, Opt.LINKED, Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET),
// private options (inserted during arg processing)
SETARGFILE(Type.FLOW,
"Sets the current value of the argfilename. Inserted before argfilecontents.",
- Opt.UNARY, Opt.LINKED, Opt.STRING, Opt.MULTI, Opt.PRIVATE,
+ Opt.UNARY, Opt.LINKED, Opt.STRING, Opt.MULTIVALUE, Opt.PRIVATE,
Opt.NOACTION),
UNSETARGFILE(Type.FLOW,
"Unsets the current value of the argfilename. Inserted after argfile contents.",
- Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION),
+ Opt.UNARY, Opt.LINKED, Opt.MULTIVALUE, Opt.PRIVATE, Opt.NOACTION),
// these last two have no purpose in the normal Jalview application but are
// used by jalview.bin.Launcher to set memory settings. They are not used by
* A MULTI Arg can be specified multiple times.
* Multiple values are stored in the ArgValuesMap (along with their positional index) for each linkedId.
*/
- MULTI("can be specified multiple times"),
+ MULTIVALUE("can be specified multiple times"),
/*
* A Linked Arg can be linked to others through a --arg[linkedId] or --arg[linkedId]=value.
* If no linkedId is specified then the current default linkedId will be used.
/*
* An ALLOWALL Arg can use the '*' linkedId to apply to all known linkedIds
*/
- ALLOWALL("can be used with " + ArgParser.DOUBLEDASH + "all"),
+ ALLOWMULTIID("can be used with " + ArgParser.DOUBLEDASH + "all"),
/*
* If an Arg has the INCREMENTDEFAULTCOUNTER option and the default linkedId is used,
* the defaultLinkedIdCounter is incremented *first*.
git://source.jalview.org / jalview.git / blobdiff