// the counter added to the default linked id prefix
private int defaultLinkedIdCounter = 0;
+ // the linked id prefix used for --opennew files
+ protected static final String OPENNEWLINKEDIDPREFIX = "OPENNEW:";
+
+ // the counter added to the default linked id prefix
+ private int opennewLinkedIdCounter = 0;
+
// the linked id used to increment the idCounter (and use the incremented
// value)
private static final String INCREMENTAUTOCOUNTERLINKEDID = "{++n}";
// the linked id used to use the idCounter
private static final String AUTOCOUNTERLINKEDID = "{n}";
- private int idCounter = 0;
+ private int linkedIdAutoCounter = 0;
// flag to say whether {n} subtitutions in output filenames should be made.
// Turn on and off with --subs and --nosubs
public ArgParser(String[] args)
{
- // make a mutable new ArrayList so that shell globbing parser works
+ // Make a mutable new ArrayList so that shell globbing parser works.
+ // (When shell file globbing is used, there are a sequence of non-Arg
+ // arguments (which are the expanded globbed filenames) that need to be
+ // consumed by the --open/--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)));
}
public ArgParser(List<String> args)
{
- init(args);
+ // do nothing if there are no "--" args and some "-" args
+ boolean d = false;
+ boolean dd = false;
+ for (String arg : args)
+ {
+ if (arg.startsWith(DOUBLEDASH))
+ {
+ dd = true;
+ break;
+ }
+ else if (arg.startsWith("-"))
+ {
+ d = true;
+ }
+ }
+ if (d && !dd)
+ {
+ // leave it to the old style -- parse an empty list
+ parse(new ArrayList<String>());
+ return;
+ }
+ parse(args);
}
- private void init(List<String> args)
+ private void parse(List<String> args)
{
- // Enumeration<String> argE = Collections.enumeration(args);
int argIndex = 0;
- // while (argE.hasMoreElements())
+ boolean openEachInitialFilenames = true;
for (int i = 0; i < args.size(); i++)
{
- // String arg = argE.nextElement();
String arg = args.get(i);
+
+ // If the first arguments do not start with "--" or "-" or is "open" and
+ // is a filename that exists it is probably a file/list of files to open
+ // so we fake an Arg.OPEN argument and when adding files only add the
+ // single arg[i] and increment the defaultLinkedIdCounter so that each of
+ // these files is opened separately.
+ if (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH)
+ && !arg.startsWith("-") && new File(arg).exists())
+ {
+ arg = DOUBLEDASH + Arg.OPENNEW.getName();
+ }
+ else
+ {
+ openEachInitialFilenames = false;
+ }
+
String argName = null;
String val = null;
- List<String> vals = null; // for Opt.GLOB only
+ List<String> globVals = null; // for Opt.GLOB only
+ SubVals globSubVals = null; // also for use by Opt.GLOB only
String linkedId = null;
if (arg.startsWith(DOUBLEDASH))
{
continue;
}
- if (a.hasOption(Opt.STRING) && equalPos == -1)
+ // String value(s)
+ if (a.hasOption(Opt.STRING))
{
- // take next arg as value if required, and '=' was not found
- // if (!argE.hasMoreElements())
- if (i + 1 >= args.size())
- {
- // no value to take for arg, which wants a value
- Console.error("Argument '" + a.getName()
- + "' requires a value, none given. Ignoring.");
- continue;
- }
- // deal with bash globs here (--arg val* is expanded before reaching
- // the JVM). Note that SubVals cannot be used in this case.
- // If using the --arg=val then the glob is preserved and Java globs
- // will be used later. SubVals can be used.
- if (a.hasOption(Opt.GLOB))
+ if (equalPos >= 0)
{
- vals.addAll(getShellGlobbedFilenameValues(a, args, i + 1));
+ if (a.hasOption(Opt.GLOB))
+ {
+ // strip off and save the SubVals to be added individually later
+ globSubVals = ArgParser.getSubVals(val);
+ globVals = FileUtils
+ .getFilenamesFromGlob(globSubVals.getContent());
+ }
+ else
+ {
+ // val is already set -- will be saved in the ArgValue later in
+ // the normal way
+ }
}
else
{
- val = args.get(i + 1);
+ // There is no "=" so value is next arg or args (possibly shell
+ // glob-expanded)
+ if (i + 1 >= args.size())
+ {
+ // no value to take for arg, which wants a value
+ Console.error("Argument '" + a.getName()
+ + "' requires a value, none given. Ignoring.");
+ continue;
+ }
+ // deal with bash globs here (--arg val* is expanded before reaching
+ // the JVM). Note that SubVals cannot be used in this case.
+ // If using the --arg=val then the glob is preserved and Java globs
+ // will be used later. SubVals can be used.
+ if (a.hasOption(Opt.GLOB))
+ {
+ // if this is the first argument with a file list at the start of
+ // the args we add filenames from index i instead of i+1
+ globVals = getShellGlobbedFilenameValues(a, args,
+ openEachInitialFilenames ? i : i + 1);
+ }
+ else
+ {
+ val = args.get(i + 1);
+ }
}
}
}
else if (a == Arg.NPP)
{
- idCounter++;
+ linkedIdAutoCounter++;
}
else if (a == Arg.SUBSTITUTIONS)
{
{
if (linkedId == null)
{
- // use default linkedId for linked arguments
- linkedId = defaultLinkedId;
- usingDefaultLinkedId = true;
- Console.debug(
- "Changing linkedId to '" + linkedId + "' from " + arg);
+ if (a == Arg.OPENNEW)
+ {
+ // use the next default prefixed OPENNEWLINKEDID
+ linkedId = new StringBuilder(OPENNEWLINKEDIDPREFIX)
+ .append(Integer.toString(opennewLinkedIdCounter))
+ .toString();
+ opennewLinkedIdCounter++;
+ }
+ else
+ {
+ // use default linkedId for linked arguments
+ linkedId = defaultLinkedId;
+ usingDefaultLinkedId = true;
+ Console.debug("Changing linkedId to '" + linkedId + "' from "
+ + arg);
+ }
}
- else if (linkedId.equals(AUTOCOUNTERLINKEDID))
+ else if (linkedId.contains(AUTOCOUNTERLINKEDID))
{
// turn {n} to the autoCounter
- autoCounterString = Integer.toString(idCounter);
- linkedId = autoCounterString;
+ autoCounterString = Integer.toString(linkedIdAutoCounter);
+ linkedId = linkedId.replace(AUTOCOUNTERLINKEDID,
+ autoCounterString);
usingAutoCounterLinkedId = true;
Console.debug(
"Changing linkedId to '" + linkedId + "' from " + arg);
}
- else if (linkedId.equals(INCREMENTAUTOCOUNTERLINKEDID))
+ else if (linkedId.contains(INCREMENTAUTOCOUNTERLINKEDID))
{
// turn {++n} to the incremented autoCounter
- autoCounterString = Integer.toString(++idCounter);
- linkedId = autoCounterString;
+ autoCounterString = Integer.toString(++linkedIdAutoCounter);
+ linkedId = linkedId.replace(INCREMENTAUTOCOUNTERLINKEDID,
+ autoCounterString);
usingAutoCounterLinkedId = true;
Console.debug(
"Changing linkedId to '" + linkedId + "' from " + arg);
}
// check for unique id
- SubVals sv = ArgParser.getSubVals(val);
- String id = sv.get(ArgValues.ID);
+ SubVals idsv = ArgParser.getSubVals(val);
+ String id = idsv.get(ArgValues.ID);
if (id != null && avm.hasId(a, id))
{
Console.error("Argument '--" + argName + "' has a duplicate id ('"
continue;
}
+ boolean argIndexIncremented = false;
ArgValues avs = avm.getOrCreateArgValues(a);
- if (avs == null)
- {
- avs = new ArgValues(a);
- }
- // store appropriate value
+
+ // store appropriate String value(s)
if (a.hasOption(Opt.STRING))
{
- if (a.hasOption(Opt.GLOB) && vals != null && vals.size() > 0)
+ if (a.hasOption(Opt.GLOB) && globVals != null
+ && globVals.size() > 0)
{
- for (String v : vals)
+ for (String v : globVals)
{
- avs.addValue(makeSubstitutions(v), argIndex++);
+ v = makeSubstitutions(v);
+ SubVals vsv = new SubVals(globSubVals, v);
+ avs.addValue(vsv, v, argIndex++);
+ argIndexIncremented = true;
}
}
else
avs.setBoolean(true, argIndex);
}
avs.incrementCount();
+ if (!argIndexIncremented)
+ argIndex++;
// store in appropriate place
if (a.hasOption(Opt.LINKED))
{
- // allow a default linked id for single usage
- if (linkedId == null)
- linkedId = defaultLinkedId;
// store the order of linkedIds
if (linkedOrder == null)
linkedOrder = new ArrayList<>();
argList = new ArrayList<>();
if (!argList.contains(a))
argList.add(a);
+
}
}
}
subvals = "";
rest = val;
}
- rest.replace(AUTOCOUNTERLINKEDID, String.valueOf(idCounter));
- rest.replace(INCREMENTAUTOCOUNTERLINKEDID, String.valueOf(++idCounter));
- rest.replace("{}", String.valueOf(defaultLinkedIdCounter));
+ if ((rest.contains(AUTOCOUNTERLINKEDID)))
+ rest = rest.replace(AUTOCOUNTERLINKEDID,
+ String.valueOf(linkedIdAutoCounter));
+ if ((rest.contains(INCREMENTAUTOCOUNTERLINKEDID)))
+ rest = rest.replace(INCREMENTAUTOCOUNTERLINKEDID,
+ String.valueOf(++linkedIdAutoCounter));
+ if ((rest.contains("{}")))
+ rest = rest.replace("{}", String.valueOf(defaultLinkedIdCounter));
return new StringBuilder(subvals).append(rest).toString();
}
List<String> vals = new ArrayList<>();
while (i < args.size() && !args.get(i).startsWith(DOUBLEDASH))
{
- vals.add(args.remove(i));
+ vals.add(FileUtils.substituteHomeDir(args.remove(i)));
if (!a.hasOption(Opt.GLOB))
break;
}
git://source.jalview.org / jalview.git / blobdiff