import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
import jalview.bin.argparser.Arg.Opt;
import jalview.bin.argparser.Arg.Type;
import jalview.util.FileUtils;
private boolean allLinkedIds = false;
/**
- * flag to say whether the default linkedId is the current default linked id
- * or OPENED linkedIds
- */
- private boolean openedLinkedIds = false;
-
- /**
* flag to say whether the structure arguments should be applied to all
* structures with this linked id
*/
private BootstrapArgs bootstrapArgs = null;
+ private boolean oldArguments = false;
+
+ private boolean mixedArguments = false;
+
+ /**
+ * saved examples of mixed arguments
+ */
+ private String[] mixedExamples = new String[] { null, null };
+
static
{
argMap = new HashMap<>();
if (arg.startsWith(DOUBLEDASH))
{
dd = true;
- break;
+ if (mixedExamples[1] == null)
+ {
+ mixedExamples[1] = arg;
+ }
}
- else if (arg.startsWith("-") || arg.equals("open"))
+ else if ((arg.startsWith("-") && !arg.equals(STDOUTFILENAME))
+ || arg.equals("open"))
{
d = true;
+ if (mixedExamples[0] == null)
+ {
+ mixedExamples[0] = arg;
+ }
+ }
+ }
+ if (d)
+ {
+ if (dd)
+ {
+ mixedArguments = true;
+ }
+ else
+ {
+ oldArguments = true;
}
}
- if (d && !dd)
+
+ if (oldArguments || mixedArguments)
{
// leave it to the old style -- parse an empty list
parse(new ArrayList<String>(), false, false);
return;
}
+
if (bsa != null)
this.bootstrapArgs = bsa;
else
{
// arg not found
Console.error("Argument '" + arg + "' not recognised. Exiting.");
- Jalview.exit("Invalid argument used." + System.lineSeparator()
- + "Use" + System.lineSeparator() + "jalview "
- + Arg.HELP.argString() + System.lineSeparator()
- + "for a usage statement.", 13);
+ Jalview.exit(
+ "Invalid argument used." + System.lineSeparator() + "Use"
+ + System.lineSeparator() + "jalview "
+ + Arg.HELP.argString() + System.lineSeparator()
+ + "for a usage statement.",
+ ExitCode.INVALID_ARGUMENT);
continue;
}
if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
else if (a == Arg.ALL)
{
allLinkedIds = !negated;
- openedLinkedIds = false;
- }
- else if (a == Arg.OPENED)
- {
- openedLinkedIds = !negated;
- allLinkedIds = false;
}
else if (a == Arg.ALLSTRUCTURES)
{
{
if (linkedId == null)
{
- if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWALL)
- && val.startsWith(MATCHALLLINKEDIDS))
+ if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWMULTIID)
+ && val.contains(MATCHALLLINKEDIDS))
{
- // --output=*.ext is shorthand for --all --output {basename}.ext
+ // --output=*.ext is shorthand for --output {basename}.ext
+ // --output=*/*.ext is shorthand for
+ // --output {dirname}/{basename}.ext
// (or --image=*.ext)
- allLinkedIds = true;
- openedLinkedIds = false;
- linkedId = MATCHALLLINKEDIDS;
- val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
- + val.substring(MATCHALLLINKEDIDS.length());
+ linkedId = allLinkedIds ? MATCHALLLINKEDIDS
+ : MATCHOPENEDLINKEDIDS;
+ val = FileUtils.convertWildcardsToPath(val, MATCHALLLINKEDIDS,
+ LINKEDIDDIRNAME, LINKEDIDBASENAME);
}
- else if (a.hasOption(Opt.OUTPUTFILE)
- && a.hasOption(Opt.ALLOWALL)
- && val.startsWith(MATCHOPENEDLINKEDIDS))
- {
- // --output=open*.ext is shorthand for --opened --output
- // {basename}.ext
- // (or --image=open*.ext)
- openedLinkedIds = true;
- allLinkedIds = false;
- linkedId = MATCHOPENEDLINKEDIDS;
- val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
- + val.substring(MATCHOPENEDLINKEDIDS.length());
- }
- else if (allLinkedIds && a.hasOption(Opt.ALLOWALL))
+ else if (allLinkedIds && a.hasOption(Opt.ALLOWMULTIID))
{
linkedId = MATCHALLLINKEDIDS;
}
- else if (openedLinkedIds && a.hasOption(Opt.ALLOWALL))
+ else if (a.hasOption(Opt.ALLOWMULTIID)
+ && this.storedLinkedIds != null
+ && this.storedLinkedIds.size() > 0)
{
linkedId = MATCHOPENEDLINKEDIDS;
}
// remove the '*' or 'open*' linkedId that should be empty if it was
// created
if ((MATCHALLLINKEDIDS.equals(linkedId)
+ || MATCHOPENEDLINKEDIDS.equals(linkedId))
&& linkedArgs.containsKey(linkedId))
- || (MATCHOPENEDLINKEDIDS.equals(linkedId)
- && linkedArgs.containsKey(linkedId)))
{
linkedArgs.remove(linkedId);
}
{
String message = Arg.ARGFILE.argString() + EQUALS + "\""
+ argFile.getPath() + "\": File does not exist.";
- Jalview.exit(message, 2);
+ Jalview.exit(message, ExitCode.FILE_NOT_FOUND);
}
try
{
{
String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
+ "\": File could not be read.";
- Jalview.exit(message, 3);
+ Jalview.exit(message, ExitCode.FILE_NOT_READABLE);
}
}
// Third param "true" uses Opt.PRIVATE args --setargile=argfile and
String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
+ "\": File could not be read.";
Console.debug(message, e);
- Jalview.exit(message, 3);
+ Jalview.exit(message, ExitCode.FILE_NOT_READABLE);
}
}
return args;
Arg a = avs.arg();
List<String> wildcardLinkedIds = null;
- if (a.hasOption(Opt.ALLOWALL))
+ if (a.hasOption(Opt.ALLOWMULTIID))
{
switch (linkedId)
{
// skip incorrectly stored wildcard ids!
if (id == null || MATCHALLLINKEDIDS.equals(id)
|| MATCHOPENEDLINKEDIDS.equals(id))
+ {
continue;
+ }
ArgValuesMap avm = linkedArgs.get(id);
// don't set an output if there isn't an input
if (a.hasOption(Opt.REQUIREINPUT)
return linkedArgs.get(linkedId);
}
+ public boolean isOldStyle()
+ {
+ return oldArguments;
+ }
+
+ public boolean isMixedStyle()
+ {
+ return mixedArguments;
+ }
+
+ public String[] getMixedExamples()
+ {
+ return mixedExamples;
+ }
}
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