package jalview.bin.argparser;
+import java.util.ArrayList;
import java.util.Arrays;
+import java.util.EnumSet;
import java.util.List;
import java.util.Locale;
import java.util.stream.Collectors;
public enum Arg
{
HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
- COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, ANNOTATION,
- ANNOTATION2, DISPLAY, GUI, NEWS, SORTBYTREE, USAGESTATS, OPEN, OPENNEW,
- PROPS, QUESTIONNAIRE, SETPROP, TREE, VDOC, VSESS, OUTPUT, OUTPUTTYPE,
- SSANNOTATION, NOTEMPFAC, TEMPFAC, TEMPFAC_LABEL, TEMPFAC_DESC,
- TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, IMAGE,
- QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
- SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
+ COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
+ SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE, SETPROP, TREE,
+ VDOC, VSESS, OUTPUT, SSANNOTATIONS, NOTEMPFAC, TEMPFAC, TITLE, PAEMATRIX,
+ WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE, TYPE, RENDERER,
+ QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, NEW, NPP("n++"),
+ SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE,
+ WEBSERVICEDISCOVERY, ALL;
protected 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
{
- HELP.setOptions(Opt.UNARY);
+ HELP.setOptions("Display this help message", Opt.UNARY, Opt.BOOTSTRAP);
CALCULATION.setOptions(true, Opt.BOOLEAN); // default "true" implies only
// expecting "--nocalculation"
MENUBAR.setOptions(true, Opt.BOOLEAN);
STATUS.setOptions(true, Opt.BOOLEAN);
SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
- ANNOTATIONS.setOptions(Opt.STRING, Opt.LINKED);
+ ANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
COLOUR.setOptions(Opt.STRING, Opt.LINKED);
FEATURES.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);
- ANNOTATION.setOptions(true, Opt.BOOLEAN, Opt.LINKED);
- ANNOTATION2.setOptions(true, Opt.BOOLEAN, Opt.LINKED);
DISPLAY.setOptions(true, Opt.BOOLEAN);
GUI.setOptions(true, Opt.BOOLEAN);
NEWS.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);
+ 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);
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);
- SSANNOTATION.setOptions(Opt.BOOLEAN, Opt.LINKED);
+ SSANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
NOTEMPFAC.setOptions(Opt.UNARY, Opt.LINKED);
TEMPFAC.setOptions(Opt.STRING, Opt.LINKED);
- TEMPFAC_LABEL.setOptions(Opt.STRING, Opt.LINKED);
- TEMPFAC_DESC.setOptions(Opt.STRING, Opt.LINKED);
- TEMPFAC_SHADING.setOptions(Opt.BOOLEAN, Opt.LINKED);
TITLE.setOptions(Opt.STRING, Opt.LINKED);
PAEMATRIX.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
Opt.ALLOWSUBSTITUTIONS);
NOSTRUCTURE.setOptions(Opt.UNARY, Opt.LINKED);
STRUCTURE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
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);
+ RENDERER.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWALL);
QUIT.setOptions(Opt.UNARY);
- CLOSE.setOptions(Opt.UNARY, Opt.LINKED);
+ CLOSE.setOptions(Opt.UNARY, Opt.LINKED, Opt.ALLOWALL);
DEBUG.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);
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.
+ WEBSERVICEDISCOVERY.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
+ ALL.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
+
}
private final String[] argNames;
private boolean defaultBoolValue = false;
+ private String description = null;
+
private Arg()
{
this(new String[0]);
System.arraycopy(names, 0, this.argNames, 1, names.length);
}
+ public String argString()
+ {
+ return argString(false);
+ }
+
+ public String negateArgString()
+ {
+ return argString(true);
+ }
+
+ private String argString(boolean negate)
+ {
+ StringBuilder sb = new StringBuilder(ArgParser.DOUBLEDASH);
+ if (negate && hasOption(Opt.BOOLEAN))
+ sb.append(ArgParser.NEGATESTRING);
+ sb.append(getName());
+ return sb.toString();
+ }
+
public String toLongString()
{
StringBuilder sb = new StringBuilder();
protected void setOptions(Opt... options)
{
- setOptions(false, options);
+ setOptions("", false, options);
+ }
+
+ protected void setOptions(String desc, Opt... options)
+ {
+ setOptions(desc, false, options);
}
protected void setOptions(boolean defaultBoolValue, Opt... options)
{
+ setOptions("", defaultBoolValue, options);
+ }
+
+ protected void setOptions(String desc, boolean defaultBoolValue,
+ Opt... options)
+ {
+ this.description = desc;
this.defaultBoolValue = defaultBoolValue;
- argOptions = options;
+ this.argOptions = options;
}
protected boolean getDefaultBoolValue()
{
return defaultBoolValue;
}
-}
+
+ private void setDescription(String d)
+ {
+ description = d;
+ }
+
+ protected String getDescription()
+ {
+ return description;
+ }
+
+ public static String booleanArgString(Arg a)
+ {
+ StringBuilder sb = new StringBuilder(a.argString());
+ if (a.hasOption(Opt.BOOLEAN))
+ {
+ sb.append('/');
+ sb.append(a.negateArgString());
+ }
+ return sb.toString();
+ }
+
+ public static final String usage()
+ {
+ StringBuilder sb = new StringBuilder();
+
+ sb.append("Usage: jalview [args]");
+ sb.append(System.lineSeparator());
+
+ int maxArgLength = 0;
+ for (Arg a : EnumSet.allOf(Arg.class))
+ {
+ if (a.hasOption(Opt.PRIVATE))
+ continue;
+ StringBuilder argSb = new StringBuilder();
+ argSb.append(a.hasOption(Opt.BOOLEAN) ? booleanArgString(a)
+ : a.argString());
+ if (a.hasOption(Opt.STRING))
+ argSb.append("=value");
+ if (argSb.length() > maxArgLength)
+ maxArgLength = argSb.length();
+ }
+
+ // might want to sort these
+ for (Arg a : EnumSet.allOf(Arg.class))
+ {
+ if (a.hasOption(Opt.PRIVATE))
+ continue;
+ StringBuilder argSb = new StringBuilder();
+ argSb.append(a.hasOption(Opt.BOOLEAN) ? booleanArgString(a)
+ : a.argString());
+ if (a.hasOption(Opt.STRING))
+ argSb.append("=value");
+ sb.append(String.format("%-" + maxArgLength + "s - %s",
+ argSb.toString(), a.getDescription()));
+
+ List<String> options = new ArrayList<>();
+
+ if (a.hasOption(Opt.BOOLEAN))
+ {
+ options.add("default " + (a.getDefaultBoolValue() ? a.argString()
+ : a.negateArgString()));
+ }
+
+ if (a.hasOption(Opt.MULTI))
+ {
+ options.add("multiple");
+ }
+
+ if (a.hasOption(Opt.LINKED))
+ {
+ options.add("can be linked");
+ }
+
+ if (a.hasOption(Opt.GLOB))
+ {
+ options.add("allows file globs");
+ }
+
+ if (a.hasOption(Opt.ALLOWSUBSTITUTIONS))
+ {
+ options.add("allows substitutions");
+ }
+
+ if (options.size() > 0)
+ {
+ sb.append(" (");
+ sb.append(String.join("; ", options));
+ sb.append(')');
+ }
+ sb.append(System.lineSeparator());
+ }
+ return sb.toString();
+ }
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff