public enum Arg
{
- HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
- COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
- SORTBYTREE, USAGESTATS, OPEN, OPENNEW, PROPS, QUESTIONNAIRE, SETPROP,
- TREE, VDOC, VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATIONS, NOTEMPFAC, TEMPFAC,
+ HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, SHOWANNOTATIONS,
+ COLOUR("color"), FEATURES, ANNOTATIONS, GROOVY, GROUPS, HEADLESS, JABAWS,
+ DISPLAY, NEWS, SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE,
+ SETPROP, TREE, VDOC, VSESS, OUTPUT, SSANNOTATIONS, NOTEMPFAC, TEMPFAC,
TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE,
- QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
- SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
+ TYPE, FORMAT, OVERWRITE, TEXTRENDERER, QUIT, CLOSE, DEBUG("d"), TRACE,
+ QUIET("q"), ARGFILE, NEW, NPP("n++"), SUBSTITUTIONS, INITSUBSTITUTIONS,
+ NIL, SPLASH, SETARGFILE, UNSETARGFILE, WEBSERVICEDISCOVERY, ALL, BACKUPS,
+ TESTOUTPUT;
- protected static enum Opt
+ public static enum Opt
{
- BOOLEAN, STRING, UNARY, MULTI, LINKED, NODUPLICATEVALUES, BOOTSTRAP,
- GLOB, NOACTION, ALLOWSUBSTITUTIONS, PRIVATE
+ BOOLEAN, // This Arg can be specified as --arg or --noarg to give true or
+ // false. A default can be given with setOptions(bool, Opt....).
+ // Use ArgParser.isSet(Arg) to see if this arg was not specified.
+ STRING, // This Arg can accept a value either through --arg=value or --arg
+ // value.
+ UNARY, // This Arg is a boolean value, true if present, false if not. Like
+ // BOOLEAN but without the --noarg option.
+ MULTI, // This Arg can be specified multiple times. Multiple values are
+ // stored in the ArgValuesMap (along with their positional index) for
+ // each linkedId.
+ LINKED, // This 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.
+ NODUPLICATEVALUES, // This Arg can only have one value (per linkedId). The
+ // first value will be used and subsequent values ignored
+ // with a warning.
+ BOOTSTRAP, // This Arg value(s) can be determined at an earlier stage than
+ // non-BOOTSTRAP Args. Substitutions do not happen in BOOTSTRAP
+ // Args and they cannot be linked or contain SubVals. See
+ // jalview.bin.argparser.BootstrapArgs.
+ GLOB, // This Arg can expand wildcard filename "globs" (e.g.
+ // path/*/filename*). If the Arg value is given as --arg filename*
+ // then the shell will have expanded the glob already, but if
+ // specified as --arg=filename* then the Java glob expansion method
+ // will be used (see FileUtils.getFilenamesFromGlob()). Note that this
+ // might be different from the shell expansion rules.
+ NOACTION, // This Arg does not perform a data task, usually used to control
+ // flow in ArgParser.parse(args).
+ ALLOWSUBSTITUTIONS, // This Arg allows substitutions in its linkedId,
+ // SubVals and values.
+ PRIVATE, // This Arg is used internally, and cannot be specified by the
+ // user.
+ ALLOWALL, // This Arg can use the '*' linkedId to apply to all known
+ // linkedIds
+ INCREMENTDEFAULTCOUNTER, // If an Arg has this option and the default
+ // linkedId is used, the defaultLinkedIdCounter is
+ // incremented *first*.
+ INPUT, // This Arg counts as an input for REQUIREINPUT
+ REQUIREINPUT, // This Arg can only be applied via --all if there is an
+ // input (i.e. --open or --append)
}
static
MENUBAR.setOptions(true, Opt.BOOLEAN);
STATUS.setOptions(true, Opt.BOOLEAN);
SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
- ANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
+ SHOWANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
COLOUR.setOptions(Opt.STRING, Opt.LINKED);
FEATURES.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
Opt.ALLOWSUBSTITUTIONS);
+ ANNOTATIONS.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+ Opt.ALLOWSUBSTITUTIONS);
+ TREE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+ Opt.ALLOWSUBSTITUTIONS);
GROOVY.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
Opt.ALLOWSUBSTITUTIONS);
GROUPS.setOptions(Opt.STRING, Opt.LINKED);
HEADLESS.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
- JABAWS.setOptions(Opt.STRING);
+ TESTOUTPUT.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
+ JABAWS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
DISPLAY.setOptions(true, Opt.BOOLEAN);
- GUI.setOptions(true, Opt.BOOLEAN);
NEWS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
SPLASH.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
- // expects a string value
- SORTBYTREE.setOptions(true, Opt.BOOLEAN);
- USAGESTATS.setOptions(true, Opt.BOOLEAN);
- OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
- Opt.ALLOWSUBSTITUTIONS);
- OPENNEW.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
- Opt.ALLOWSUBSTITUTIONS);
+ SORTBYTREE.setOptions(true, Opt.LINKED, Opt.BOOLEAN);
+ QUESTIONNAIRE.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+ USAGESTATS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+ WEBSERVICEDISCOVERY.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+ APPEND.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
+ Opt.ALLOWSUBSTITUTIONS, Opt.INPUT);
+ OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER,
+ Opt.MULTI, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT);
PROPS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
- QUESTIONNAIRE.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
SETPROP.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP);
- TREE.setOptions(Opt.STRING);
VDOC.setOptions(Opt.UNARY);
VSESS.setOptions(Opt.UNARY);
- OUTPUT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS);
- OUTPUTTYPE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
+ OUTPUT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWALL, Opt.REQUIREINPUT);
SSANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
NOTEMPFAC.setOptions(Opt.UNARY, Opt.LINKED);
Opt.ALLOWSUBSTITUTIONS);
STRUCTUREVIEWER.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
- IMAGE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS);
+ IMAGE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS,
+ Opt.ALLOWALL, Opt.REQUIREINPUT);
+ TYPE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWALL);
+ FORMAT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWALL);
+ TEXTRENDERER.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWALL);
QUIT.setOptions(Opt.UNARY);
- CLOSE.setOptions(Opt.UNARY, Opt.LINKED);
+ OVERWRITE.setOptions(Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL);
+ BACKUPS.setOptions(true, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL);
+ CLOSE.setOptions(Opt.UNARY, Opt.LINKED, Opt.ALLOWALL);
DEBUG.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
+ TRACE.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
QUIET.setOptions(Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP);
ARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB,
Opt.ALLOWSUBSTITUTIONS);
- INCREMENT.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
+ NEW.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION,
+ Opt.INCREMENTDEFAULTCOUNTER);
NPP.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
SUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
- INITSUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION);
+ INITSUBSTITUTIONS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP,
+ Opt.NOACTION); // defaulting substitutions to true
NIL.setOptions(Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION);
SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
- // Opt.BOOTSTRAP args are parsed (not linked with no SubVals so using a
- // simplified parser, see jalview.bin.argparser.BootstrapArgs)
- // before a full parse of arguments and so can be accessible at an earlier
- // stage to (e.g.) set debug log level, provide a props file (that might set
- // log level), run headlessly, read an argfile instead of other args.
+ ALL.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
+
}
private final String[] argNames;
git://source.jalview.org / jalview.git / blobdiff