private static final String ARGFILEDIRNAME = "{argfiledirname}";
// flag to say whether {n} subtitutions in output filenames should be made.
- // Turn on and off with --subs and --nosubs
- private boolean substitutions = false;
+ // Turn on and off with --substitutions and --nosubstitutions
+ // Start with it on
+ private boolean substitutions = true;
// flag to say whether the default linkedId is the current default linked id
// or ALL linkedIds
private int argIndex = 0;
+ private BootstrapArgs bootstrapArgs = null;
+
static
{
argMap = new HashMap<>();
public ArgParser(String[] args)
{
- this(args, false);
+ this(args, false, null);
}
- public ArgParser(String[] args, boolean initsubstitutions)
+ public ArgParser(String[] args, boolean initsubstitutions,
+ BootstrapArgs bsa)
{
// Make a mutable new ArrayList so that shell globbing parser works.
// (When shell file globbing is used, there are a sequence of non-Arg
// consumed by the --append/--argfile/etc Arg which is most easily done by
// removing these filenames from the list one at a time. This can't be done
// with an ArrayList made with only Arrays.asList(String[] args). )
- this(new ArrayList<>(Arrays.asList(args)), initsubstitutions);
+ this(new ArrayList<>(Arrays.asList(args)), initsubstitutions, false,
+ bsa);
}
public ArgParser(List<String> args, boolean initsubstitutions)
{
- this(args, initsubstitutions, false);
+ this(args, initsubstitutions, false, null);
}
public ArgParser(List<String> args, boolean initsubstitutions,
- boolean allowPrivate)
+ boolean allowPrivate, BootstrapArgs bsa)
{
// do nothing if there are no "--" args and (some "-" args || >0 arg is
// "open")
parse(new ArrayList<String>(), false, false);
return;
}
+ if (bsa != null)
+ this.bootstrapArgs = bsa;
+ else
+ this.bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
parse(args, initsubstitutions, allowPrivate);
}
{
// arg not found
Console.error("Argument '" + arg + "' not recognised. Exiting.");
- Jalview.exit("Unrecognised command line argument '" + arg + "'",
- 13);
+ Jalview.exit("Invalid argument used." + System.lineSeparator()
+ + "Use" + System.lineSeparator() + "jalview "
+ + Arg.HELP.argString() + System.lineSeparator()
+ + "for a usage statement.", 13);
continue;
}
if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
// make NOACTION adjustments
// default and auto counter increments
- if (a == Arg.NEWFRAME)
- {
- defaultLinkedIdCounter++;
- }
- else if (a == Arg.NPP)
+ if (a == Arg.NPP)
{
linkedIdAutoCounter++;
}
{
argFile = null;
}
- else if (a == Arg.ALLFRAMES)
+ else if (a == Arg.ALL)
{
allLinkedIds = !negated;
}
+ // this is probably only Arg.NEW and Arg.OPEN
+ if (a.hasOption(Opt.INCREMENTDEFAULTCOUNTER))
+ {
+ // use the next default prefixed OPENLINKEDID
+ defaultLinkedId(true);
+ }
+
String autoCounterString = null;
boolean usingAutoCounterLinkedId = false;
String defaultLinkedId = defaultLinkedId(false);
{
if (linkedId == null)
{
- if (a.hasOption(Opt.INCREMENTDEFAULTCOUNTER))
- {
- // use the next default prefixed OPENLINKEDID
- defaultLinkedId = defaultLinkedId(true);
- }
if (allLinkedIds && a.hasOption(Opt.ALLOWALL))
{
linkedId = MATCHALLLINKEDIDS;
}
}
- // do not continue for NOACTION args
+ // do not continue in this block for NOACTION args
if (a.hasOption(Opt.NOACTION))
continue;
- if (!linkedArgs.containsKey(linkedId))
- linkedArgs.put(linkedId, new ArgValuesMap());
-
- ArgValuesMap avm = linkedArgs.get(linkedId);
+ ArgValuesMap avm = getOrCreateLinkedArgValuesMap(linkedId);
// not dealing with both NODUPLICATEVALUES and GLOB
if (a.hasOption(Opt.NODUPLICATEVALUES) && avm.hasValue(a, val))
.toString();
}
}
- if (!linkedArgs.containsKey(defaultLinkedId))
- linkedArgs.put(defaultLinkedId, new ArgValuesMap());
+ getOrCreateLinkedArgValuesMap(defaultLinkedId);
return defaultLinkedId;
}
return vals;
}
+ public BootstrapArgs getBootstrapArgs()
+ {
+ return bootstrapArgs;
+ }
+
public boolean isSet(Arg a)
{
- return a.hasOption(Opt.LINKED) ? isSet("", a) : isSet(null, a);
+ return a.hasOption(Opt.LINKED) ? isSetAtAll(a) : isSet(null, a);
+ }
+
+ public boolean isSetAtAll(Arg a)
+ {
+ for (String linkedId : linkedOrder)
+ {
+ if (isSet(linkedId, a))
+ return true;
+ }
+ return false;
}
public boolean isSet(String linkedId, Arg a)
return avm == null ? false : avm.containsArg(a);
}
- public boolean getBool(Arg a)
+ public boolean getBoolean(Arg a)
{
if (!a.hasOption(Opt.BOOLEAN) && !a.hasOption(Opt.UNARY))
{
}
public static ArgParser parseArgFiles(List<String> argFilenameGlobs,
- boolean initsubstitutions)
+ boolean initsubstitutions, BootstrapArgs bsa)
{
List<File> argFiles = new ArrayList<>();
argFiles.addAll(FileUtils.getFilesFromGlob(pattern));
}
- return parseArgFileList(argFiles, initsubstitutions);
+ return parseArgFileList(argFiles, initsubstitutions, bsa);
}
public static ArgParser parseArgFileList(List<File> argFiles,
- boolean initsubstitutions)
+ boolean initsubstitutions, BootstrapArgs bsa)
{
List<String> argsList = new ArrayList<>();
for (File argFile : argFiles)
}
// Third param "true" uses Opt.PRIVATE args --setargile=argfile and
// --unsetargfile
- return new ArgParser(argsList, initsubstitutions, true);
+ return new ArgParser(argsList, initsubstitutions, true, bsa);
}
protected static List<String> readArgFile(File argFile)
FIRST, BEFORE, AFTER
}
- public static String getValueFromSubValOrArg(ArgValuesMap avm, Arg a,
- SubVals sv)
+ // get from following Arg of type a or subval of same name (lowercase)
+ public static String getValueFromSubValOrArg(ArgValuesMap avm,
+ ArgValue av, Arg a, SubVals sv)
{
- return getFromSubValArgOrPref(avm, a, sv, null, null, null);
+ return getFromSubValArgOrPref(avm, av, a, sv, null, null, null);
}
- public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
- SubVals sv, String key, String pref, String def)
+ // get from following Arg of type a or subval key or preference pref or
+ // default def
+ public static String getFromSubValArgOrPref(ArgValuesMap avm, ArgValue av,
+ Arg a, SubVals sv, String key, String pref, String def)
{
- return getFromSubValArgOrPref(avm, a, Position.FIRST, null, sv, key,
- pref, def);
+ return getFromSubValArgOrPref(avm, a, Position.AFTER, av, sv, key, pref,
+ def);
}
+ // get from following(AFTER), first occurence of (FIRST) or previous (BEFORE)
+ // Arg of type a or subval key or preference pref or default def
public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
Position pos, ArgValue av, SubVals sv, String key, String pref,
String def)
{
+ return getFromSubValArgOrPrefWithSubstitutions(null, avm, a, pos, av,
+ sv, key, pref, def);
+ }
+
+ public static String getFromSubValArgOrPrefWithSubstitutions(ArgParser ap,
+ ArgValuesMap avm, Arg a, Position pos, ArgValue av, SubVals sv,
+ String key, String pref, String def)
+ {
if (key == null)
key = a.getName();
+ String value = null;
if (sv != null && sv.has(key) && sv.get(key) != null)
- return sv.get(key);
- if (avm != null && avm.containsArg(a))
{
- String val = null;
+ value = ap == null ? sv.get(key)
+ : sv.getWithSubstitutions(ap, avm.getLinkedId(), key);
+ }
+ else if (avm != null && avm.containsArg(a))
+ {
if (pos == Position.FIRST && avm.getValue(a) != null)
- return avm.getValue(a);
+ value = avm.getValue(a);
else if (pos == Position.BEFORE
&& avm.getClosestPreviousArgValueOfArg(av, a) != null)
- return avm.getClosestPreviousArgValueOfArg(av, a).getValue();
+ value = avm.getClosestPreviousArgValueOfArg(av, a).getValue();
else if (pos == Position.AFTER
&& avm.getClosestNextArgValueOfArg(av, a) != null)
- return avm.getClosestNextArgValueOfArg(av, a).getValue();
+ value = avm.getClosestNextArgValueOfArg(av, a).getValue();
}
- return pref != null ? Cache.getDefault(pref, def) : def;
+ else
+ {
+ value = pref != null ? Cache.getDefault(pref, def) : def;
+ }
+ return value;
}
public static boolean getBoolFromSubValOrArg(ArgValuesMap avm, Arg a,
public static boolean getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
SubVals sv, String key, String pref, boolean def)
{
+ if ((key == null && a == null) || (sv == null && a == null))
+ return false;
+
+ boolean usingArgKey = false;
if (key == null)
+ {
key = a.getName();
- if (sv != null && sv.has(key) && sv.get(key) != null)
- return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
+ usingArgKey = true;
+ }
+
+ String nokey = ArgParser.NEGATESTRING + key;
+
+ // look for key or nokey in subvals first (if using Arg check options)
+ if (sv != null)
+ {
+ // check for true boolean
+ if (sv.has(key) && sv.get(key) != null)
+ {
+ if (usingArgKey)
+ {
+ if (!(a.hasOption(Opt.BOOLEAN) || a.hasOption(Opt.UNARY)))
+ {
+ Console.debug(
+ "Looking for boolean in subval from non-boolean/non-unary Arg "
+ + a.getName());
+ return false;
+ }
+ }
+ return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
+ }
+
+ // check for negative boolean (subval "no..." will be "true")
+ if (sv.has(nokey) && sv.get(nokey) != null)
+ {
+ if (usingArgKey)
+ {
+ if (!(a.hasOption(Opt.BOOLEAN)))
+ {
+ Console.debug(
+ "Looking for negative boolean in subval from non-boolean Arg "
+ + a.getName());
+ return false;
+ }
+ }
+ return !sv.get(nokey).toLowerCase(Locale.ROOT).equals("true");
+ }
+ }
+
+ // check argvalues
if (avm != null && avm.containsArg(a))
return avm.getBoolean(a);
+
+ // return preference or default
return pref != null ? Cache.getDefault(pref, def) : def;
}
}
}
+ private ArgValuesMap getOrCreateLinkedArgValuesMap(String linkedId)
+ {
+ if (linkedArgs.containsKey(linkedId)
+ && linkedArgs.get(linkedId) != null)
+ return linkedArgs.get(linkedId);
+
+ linkedArgs.put(linkedId, new ArgValuesMap(linkedId));
+ return linkedArgs.get(linkedId);
+ }
+
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff