- 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.
- SECRET, // This Arg is used by development processes and although it can be
- // set by the user, it is not displayed to 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)
- OUTPUTFILE, // This Arg provides an output filename. With Opt.ALLOWALL *.ext
- // is
- // shorthand for --all --output={basename}.ext
- STORED, // This Arg resets and creates a new set of "opened" linkedIds
- HELP, // This Arg is a --help type arg
- PRIMARY, // This Arg is the main Arg for its type
- HASTYPE, // This Arg can have an Arg.Type assigned to it (and no value)
- FIRST, // Move this arg to the first in usage statement (within type)
- LAST, // Move this arg to the end in usage statement (within type)
+ /*
+ * A BOOLEAN 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.
+ */
+ BOOLEAN("can be negated with " + ArgParser.DOUBLEDASH
+ + ArgParser.NEGATESTRING + "..."),
+
+ /*
+ * A STRING Arg will take a value either through --arg=value or --arg value.
+ */
+ STRING("expects a value"),
+ /*
+ * A UNARY Arg is a boolean value, true if present, false if not.
+ * Like BOOLEAN but without the --noarg option.
+ */
+ UNARY(null),
+ /*
+ * A MULTI Arg can be specified multiple times.
+ * Multiple values are stored in the ArgValuesMap (along with their positional index) for each linkedId.
+ */
+ 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.
+ */
+ LINKED("is linked to an alignment"),
+ /*
+ * A NODUPLICATES Arg can only have one value (per linkedId).
+ * The first value will be used and subsequent values ignored with a warning.
+ */
+ NODUPLICATEVALUES("cannot have the same value more than once"),
+ /*
+ * A BOOTSTRAP 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.
+ */
+ BOOTSTRAP("a configuration argument"),
+ /*
+ * A GLOB 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.
+ */
+ GLOB("can take multiple filenames with wildcards"),
+ /*
+ * A NOACTION Arg does not perform a data task,
+ * usually used to control flow in ArgParser.parse(args).
+ */
+ NOACTION(null),
+ /*
+ * An ALLOWSUBSTITUTIONS Arg allows substitutions in its linkedId,
+ * SubVals and values.
+ */
+ ALLOWSUBSTITUTIONS("values can use substitutions"),
+ /*
+ * A PRIVATE Arg is used internally, and cannot be specified by the user.
+ */
+ PRIVATE(null),
+ /*
+ * A SECRET Arg is used by development processes and although it can be set by the user,
+ * it is not displayed to the user.
+ */
+ SECRET(null),
+ /*
+ * An ALLOWALL Arg can use the '*' linkedId to apply to all known linkedIds
+ */
+ 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*.
+ */
+ INCREMENTDEFAULTCOUNTER("starts a new default alignment"),
+ /*
+ * An INPUT Arg counts as an input for REQUIREINPUT
+ */
+ INPUT(null),
+ /*
+ * A REQUIREINPUT Arg can only be applied via --all if there is an input
+ * (i.e. --open or --append)
+ */
+ REQUIREINPUT(null),
+ /*
+ * An OUTPUTFILE Arg provides an output filename. With Opt.ALLOWALL *.ext is shorthand for
+ * --all --output={basename}.ext
+ */
+ OUTPUTFILE("output file --headless will be assumed unless --gui used"),
+ /*
+ * A STDOUT Arg can take an output filename that can be '-' to mean print to STDOUT.
+ */
+ STDOUT("allows the output filename '" + ArgParser.STDOUTFILENAME
+ + "' to mean output to STDOUT"),
+ /*
+ * A STORED Arg resets and creates a new set of "opened" linkedIds
+ */
+ STORED(null),
+ /*
+ * A HELP Arg is a --help type arg
+ */
+ HELP("provides a help statement"),
+ /*
+ * A PRIMARY Arg is the main Arg for its type
+ */
+ PRIMARY("is a primary argument for its type"),
+ /*
+ * A HASTYPE Arg can have an Arg.Type assigned to its ArgValue
+ */
+ HASTYPE(null),
+ /*
+ * A FIRST arg gets moved to appear first in the usage statement (within type)
+ */
+ FIRST(null),
+ /*
+ * A LAST arg gets moved to appear last in the usage statement (within type)
+ */
+ LAST(null),
+ /*
+ * After other args are checked, the following args can prefix a KEY=VALUE argument
+ */
+ PREFIXKEV("prefixes key=value"),
+ /*
+ * do not lowercase the name when getting the arg name or arg string
+ */
+ PRESERVECASE(null),
+ //
+ ;
+
+ private String description;
+
+ private Opt()
+ {
+ description = null;
+ }
+
+ private Opt(String description)
+ {
+ this.description = description;
+ }
+
+ public String description()
+ {
+ return description;
+ }
+
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