import java.util.Enumeration;
import java.util.HashMap;
import java.util.List;
-import java.util.Locale;
import java.util.Map;
-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 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)
if (linkedId == null)
{
if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWMULTIID)
- && val.startsWith(MATCHALLLINKEDIDS))
+ && 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;
- linkedId = MATCHALLLINKEDIDS;
- val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
- + val.substring(MATCHALLLINKEDIDS.length());
+ linkedId = allLinkedIds ? MATCHALLLINKEDIDS
+ : MATCHOPENEDLINKEDIDS;
+ val = FileUtils.convertWildcardsToPath(val, MATCHALLLINKEDIDS,
+ LINKEDIDDIRNAME, LINKEDIDBASENAME);
}
else if (allLinkedIds && a.hasOption(Opt.ALLOWMULTIID))
{
// set allstructures to all non-primary structure options in this linked
// id if --allstructures has been set
- if (allStructures
- && (a.getType() == Type.STRUCTURE
- || a.getType() == Type.STRUCTUREIMAGE)
- && !a.hasOption(Opt.PRIMARY))
+ if (allStructures && (a.getType() == Type.STRUCTURE
+ // || a.getType() == Type.STRUCTUREIMAGE)
+ ) && !a.hasOption(Opt.PRIMARY))
{
if (!subvals.has(Arg.ALLSTRUCTURES.getName()))
// && !subvals.has("structureid"))
{
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;
}
- public static enum Position
- {
- FIRST, BEFORE, AFTER
- }
-
- /**
- * 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, av, a, sv, null, null, null);
- }
-
- /**
- * 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.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)
- {
- 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)
- value = avm.getValue(a);
- else if (pos == Position.BEFORE
- && avm.getClosestPreviousArgValueOfArg(av, a) != null)
- value = avm.getClosestPreviousArgValueOfArg(av, a).getValue();
- else if (pos == Position.AFTER
- && avm.getClosestNextArgValueOfArg(av, a) != null)
- value = avm.getClosestNextArgValueOfArg(av, a).getValue();
-
- // look for allstructures subval for Type.STRUCTURE*
- Arg arg = av.getArg();
- if (value == null && arg.hasOption(Opt.PRIMARY)
- && arg.getType() == Type.STRUCTURE
- && !a.hasOption(Opt.PRIMARY) && (a.getType() == Type.STRUCTURE
- || a.getType() == Type.STRUCTUREIMAGE))
- {
- ArgValue av2 = avm.getArgValueOfArgWithSubValKey(a,
- Arg.ALLSTRUCTURES.getName());
- if (av2 != null)
- {
- value = av2.getValue();
- }
- }
- }
- if (value == null)
- {
- value = pref != null ? Cache.getDefault(pref, def) : def;
- }
- return value;
- }
-
- public static boolean getBoolFromSubValOrArg(ArgValuesMap avm, Arg a,
- SubVals sv)
- {
- return getFromSubValArgOrPref(avm, a, sv, null, null, false);
- }
-
- public static boolean getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
- SubVals sv, String key, String pref, boolean def)
- {
- return getFromSubValArgOrPref(avm, a, sv, key, pref, def, false);
- }
-
- public static boolean getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
- SubVals sv, String key, String pref, boolean def,
- boolean invertPref)
- {
- if ((key == null && a == null) || (sv == null && a == null))
- return false;
-
- boolean usingArgKey = false;
- if (key == null)
- {
- key = a.getName();
- 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
- boolean prefVal = pref != null ? Cache.getDefault(pref, def) : false;
- return pref != null ? (invertPref ? !prefVal : prefVal) : def;
- }
-
// the following methods look for the "*" linkedId and add the argvalue to all
// linkedId ArgValues if it does.
/**
argIndex, doSubs);
}
- private void addValue(String linkedId, Type type, ArgValues avs, String v,
- int argIndex, boolean doSubs)
- {
- this.argValueOperation(Op.ADDVALUE, linkedId, type, avs, null, v, false,
- argIndex, doSubs);
- }
-
private void setBoolean(String linkedId, Type type, ArgValues avs,
boolean b, int argIndex)
{
return linkedArgs.get(linkedId);
}
+ public boolean isOldStyle()
+ {
+ return oldArguments;
+ }
+
+ public boolean isMixedStyle()
+ {
+ return mixedArguments;
+ }
+
+ public String[] getMixedExamples()
+ {
+ return mixedExamples;
+ }
+
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff