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;
import jalview.util.HttpUtils;
public class ArgParser
{
+ protected static final String SINGLEDASH = "-";
+
protected static final String DOUBLEDASH = "--";
- protected static final char EQUALS = '=';
+ public static final char EQUALS = '=';
+
+ public static final String STDOUTFILENAME = "-";
protected static final String NEGATESTRING = "no";
- // the default linked id prefix used for no id (not even square braces)
+ /**
+ * the default linked id prefix used for no id (ie when not even square braces
+ * are provided)
+ */
protected static final String DEFAULTLINKEDIDPREFIX = "JALVIEW:";
- // the linkedId string used to match all linkedIds seen so far
+ /**
+ * the linkedId string used to match all linkedIds seen so far
+ */
protected static final String MATCHALLLINKEDIDS = "*";
- // the linkedId string used to match all of the last --open'ed linkedIds
+ /**
+ * the linkedId string used to match all of the last --open'ed linkedIds
+ */
protected static final String MATCHOPENEDLINKEDIDS = "open*";
- // the counter added to the default linked id prefix
+ /**
+ * the counter added to the default linked id prefix
+ */
private int defaultLinkedIdCounter = 0;
- // the substitution string used to use the defaultLinkedIdCounter
+ /**
+ * the substitution string used to use the defaultLinkedIdCounter
+ */
private static final String DEFAULTLINKEDIDCOUNTER = "{}";
- // the counter added to the default linked id prefix. NOW using
- // linkedIdAutoCounter
- // private int openLinkedIdCounter = 0;
-
- // the linked id prefix used for --open files. NOW the same as DEFAULT
+ /**
+ * the linked id prefix used for --open files. NOW the same as DEFAULT
+ */
protected static final String OPENLINKEDIDPREFIX = DEFAULTLINKEDIDPREFIX;
- // the counter used for {n} substitutions
+ /**
+ * the counter used for {n} substitutions
+ */
private int linkedIdAutoCounter = 0;
- // the linked id substitution string used to increment the idCounter (and use
- // the incremented value)
+ /**
+ * the linked id substitution string used to increment the idCounter (and use
+ * the incremented value)
+ */
private static final String INCREMENTLINKEDIDAUTOCOUNTER = "{++n}";
- // the linked id substitution string used to use the idCounter
+ /**
+ * the linked id substitution string used to use the idCounter
+ */
private static final String LINKEDIDAUTOCOUNTER = "{n}";
- // the linked id substitution string used to use the base filename of --append
- // or --open
+ /**
+ * the linked id substitution string used to use the filename extension of
+ * --append or --open
+ */
+ private static final String LINKEDIDEXTENSION = "{extension}";
+
+ /**
+ * the linked id substitution string used to use the base filename of --append
+ */
+ /** or --open */
private static final String LINKEDIDBASENAME = "{basename}";
- // the linked id substitution string used to use the dir path of --append
- // or --open
+ /**
+ * the linked id substitution string used to use the dir path of --append or
+ * --open
+ */
private static final String LINKEDIDDIRNAME = "{dirname}";
- // the current argfile
+ /**
+ * the current argfile
+ */
private String argFile = null;
- // the linked id substitution string used to use the dir path of the latest
- // --argfile name
+ /**
+ * the linked id substitution string used to use the dir path of the latest
+ */
+ /** --argfile name */
private static final String ARGFILEBASENAME = "{argfilebasename}";
- // the linked id substitution string used to use the dir path of the latest
- // --argfile name
+ /**
+ * the linked id substitution string used to use the dir path of the latest
+ * --argfile name
+ */
private static final String ARGFILEDIRNAME = "{argfiledirname}";
- // an output file wildcard to signify --output=*.ext is really --all --output
- // {basename}.ext
- private static final String OUTPUTWILDCARD = "*.";
-
- // flag to say whether {n} subtitutions in output filenames should be made.
- // Turn on and off with --substitutions and --nosubstitutions
- // Start with it on
+ /**
+ * flag to say whether {n} subtitutions in output filenames should be made.
+ * 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
+ /**
+ * flag to say whether the default linkedId is the current default linked id
+ *
+ * or ALL linkedIds
+ */
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 boolean allStructures = false;
protected static final Map<String, Arg> argMap;
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 (argMap.containsKey(argName))
{
Console.warn("Trying to add argument name multiple times: '"
- + argName + "'"); // RESTORE THIS WHEN
- // MERGED
+ + argName + "'");
if (argMap.get(argName) != a)
{
Console.error(
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
- // arguments (which are the expanded globbed filenames) that need to be
- // 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). )
+ /*
+ * 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 --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) as
+ * that is not mutable. )
+ */
this(new ArrayList<>(Arrays.asList(args)), initsubstitutions, false,
bsa);
}
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 && !dd)
+ if (d)
+ {
+ if (dd)
+ {
+ mixedArguments = true;
+ }
+ else
+ {
+ oldArguments = true;
+ }
+ }
+
+ 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
boolean allowPrivate)
{
this.substitutions = initsubstitutions;
- boolean openEachInitialFilenames = true;
- for (int i = 0; i < args.size(); i++)
- {
- String arg = args.get(i);
- // If the first arguments do not start with "--" or "-" or is not "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("-") && !arg.equals("open")
- && (new File(arg).exists()
- || HttpUtils.startsWithHttpOrHttps(arg)))
- {
- arg = Arg.OPEN.argString();
- }
- else
+ /*
+ * If the first argument does not start with "--" or "-" or is not "open",
+ * and is a filename that exists or a URL, it is probably a file/list of
+ * files to open so we insert an Arg.OPEN argument before it. This will
+ * mean the list of files at the start of the arguments are all opened
+ * separately.
+ */
+ if (args.size() > 0)
+ {
+ String arg0 = args.get(0);
+ if (arg0 != null
+ && (!arg0.startsWith(DOUBLEDASH) && !arg0.startsWith("-")
+ && !arg0.equals("open") && (new File(arg0).exists()
+ || HttpUtils.startsWithHttpOrHttps(arg0))))
{
- openEachInitialFilenames = false;
+ // insert "--open" at the start
+ args.add(0, Arg.OPEN.argString());
}
+ }
+
+ for (int i = 0; i < args.size(); i++)
+ {
+ String arg = args.get(i);
- String argName = null;
- String val = null;
- List<String> globVals = null; // for Opt.GLOB only
- SubVals globSubVals = null; // also for use by Opt.GLOB only
- String linkedId = null;
+ // look for double-dash, e.g. --arg
if (arg.startsWith(DOUBLEDASH))
{
+ String argName = null;
+ String val = null;
+ List<String> globVals = null; // for Opt.GLOB only
+ SubVals globSubVals = null; // also for use by Opt.GLOB only
+ String linkedId = null;
+ Type type = null;
+
+ // look for equals e.g. --arg=value
int equalPos = arg.indexOf(EQUALS);
if (equalPos > -1)
{
{
argName = arg.substring(DOUBLEDASH.length());
}
+
+ // look for linked ID e.g. --arg[linkedID]
int idOpen = argName.indexOf('[');
int idClose = argName.indexOf(']');
-
if (idOpen > -1 && idClose == argName.length() - 1)
{
linkedId = argName.substring(idOpen + 1, idClose);
argName = argName.substring(0, idOpen);
}
+ // look for type modification e.g. --help-opening
+ int dashPos = argName.indexOf(SINGLEDASH);
+ if (dashPos > -1)
+ {
+ String potentialArgName = argName.substring(0, dashPos);
+ Arg potentialArg = argMap.get(potentialArgName);
+ if (potentialArg != null && potentialArg.hasOption(Opt.HASTYPE))
+ {
+ String typeName = argName.substring(dashPos + 1);
+ try
+ {
+ type = Type.valueOf(typeName);
+ } catch (IllegalArgumentException e)
+ {
+ type = Type.INVALID;
+ }
+ argName = argName.substring(0, dashPos);
+ }
+ }
+
Arg a = argMap.get(argName);
- // check for boolean prepended by "no"
+ // check for boolean prepended by "no" e.g. --nowrap
boolean negated = false;
- if (a == null && argName.startsWith(NEGATESTRING) && argMap
- .containsKey(argName.substring(NEGATESTRING.length())))
+ if (a == null)
{
- argName = argName.substring(NEGATESTRING.length());
- a = argMap.get(argName);
- negated = true;
+ if (argName.startsWith(NEGATESTRING) && argMap
+ .containsKey(argName.substring(NEGATESTRING.length())))
+ {
+ argName = argName.substring(NEGATESTRING.length());
+ a = argMap.get(argName);
+ negated = true;
+ }
+ else
+ {
+ // after all other args, look for Opt.PREFIXKEV args if still not
+ // found
+ for (Arg potentialArg : EnumSet.allOf(Arg.class))
+ {
+ if (potentialArg.hasOption(Opt.PREFIXKEV) && argName != null
+ && argName.startsWith(potentialArg.getName())
+ && equalPos > -1)
+ {
+ val = argName.substring(potentialArg.getName().length())
+ + EQUALS + val;
+ argName = argName.substring(0,
+ potentialArg.getName().length());
+ a = potentialArg;
+ break;
+ }
+ }
+ }
}
// check for config errors
{
// 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)
{
// There is no "=" so value is next arg or args (possibly shell
// glob-expanded)
- if ((openEachInitialFilenames ? i : i + 1) >= args.size())
+ if (i + 1 >= args.size())
{
// no value to take for arg, which wants a value
Console.error("Argument '" + a.getName()
{
// 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);
+ globVals = getShellGlobbedFilenameValues(a, args, i + 1);
}
else
{
else if (a == Arg.ALL)
{
allLinkedIds = !negated;
- openedLinkedIds = false;
}
- else if (a == Arg.OPENED)
+ else if (a == Arg.ALLSTRUCTURES)
{
- openedLinkedIds = !negated;
- allLinkedIds = false;
+ allStructures = !negated;
}
if (a.hasOption(Opt.STORED))
}
String autoCounterString = null;
- boolean usingAutoCounterLinkedId = false;
String defaultLinkedId = defaultLinkedId(false);
boolean usingDefaultLinkedId = false;
if (a.hasOption(Opt.LINKED))
{
if (linkedId == null)
{
- if (a.hasOption(Opt.OUTPUT) && 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.OUTPUT) && 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;
}
+ arg);
}
}
- else if (linkedId.contains(LINKEDIDAUTOCOUNTER))
- {
- // turn {n} to the autoCounter
- autoCounterString = Integer.toString(linkedIdAutoCounter);
- linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER,
- autoCounterString);
- usingAutoCounterLinkedId = true;
- Console.debug(
- "Changing linkedId to '" + linkedId + "' from " + arg);
- }
- else if (linkedId.contains(INCREMENTLINKEDIDAUTOCOUNTER))
+ else
{
- // turn {++n} to the incremented autoCounter
- autoCounterString = Integer.toString(++linkedIdAutoCounter);
- linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER,
- autoCounterString);
- usingAutoCounterLinkedId = true;
- Console.debug(
- "Changing linkedId to '" + linkedId + "' from " + arg);
+ if (linkedId.contains(LINKEDIDAUTOCOUNTER))
+ {
+ // turn {n} to the autoCounter
+ autoCounterString = Integer.toString(linkedIdAutoCounter);
+ linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER,
+ autoCounterString);
+ Console.debug("Changing linkedId to '" + linkedId + "' from "
+ + arg);
+ }
+ if (linkedId.contains(INCREMENTLINKEDIDAUTOCOUNTER))
+ {
+ // turn {++n} to the incremented autoCounter
+ autoCounterString = Integer.toString(++linkedIdAutoCounter);
+ linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER,
+ autoCounterString);
+ Console.debug("Changing linkedId to '" + linkedId + "' from "
+ + arg);
+ }
}
}
}
// check for unique id
- SubVals idsv = new SubVals(val);
- String id = idsv.get(ArgValues.ID);
+ SubVals subvals = new SubVals(val);
+ boolean addNewSubVals = false;
+ String id = subvals.get(ArgValues.ID);
if (id != null && avm.hasId(a, id))
{
Console.error("Argument '" + a.argString()
continue;
}
- /* TODO
- * Change all avs.addValue() avs.setBoolean avs.setNegated() avs.incrementCount calls to checkfor linkedId == "*"
- * DONE, need to check
- */
+ // 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 (!subvals.has(Arg.ALLSTRUCTURES.getName()))
+ // && !subvals.has("structureid"))
+ {
+ subvals.put(Arg.ALLSTRUCTURES.getName(), "true");
+ addNewSubVals = true;
+ }
+ }
+
ArgValues avs = avm.getOrCreateArgValues(a);
// store appropriate String value(s)
{
String v = gve.nextElement();
SubVals vsv = new SubVals(globSubVals, v);
- addValue(linkedId, avs, vsv, v, argIndex++, true);
+ addValue(linkedId, type, avs, vsv, v, argIndex++, true);
// if we're using defaultLinkedId and the arg increments the
// counter:
if (gve.hasMoreElements() && usingDefaultLinkedId
}
else
{
- addValue(linkedId, avs, val, argIndex, true);
+ // addValue(linkedId, type, avs, val, argIndex, true);
+ addValue(linkedId, type, avs, addNewSubVals ? subvals : null,
+ val, argIndex, true);
}
}
else if (a.hasOption(Opt.BOOLEAN))
{
- setBoolean(linkedId, avs, !negated, argIndex);
+ setBoolean(linkedId, type, avs, !negated, argIndex);
setNegated(linkedId, avs, negated);
}
else if (a.hasOption(Opt.UNARY))
{
- setBoolean(linkedId, avs, true, argIndex);
+ setBoolean(linkedId, type, avs, true, argIndex);
}
// 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);
}
{
rest = rest.replace(LINKEDIDBASENAME, avm.getBasename());
}
+ if (rest.contains(LINKEDIDEXTENSION))
+ {
+ rest = rest.replace(LINKEDIDEXTENSION, avm.getExtension());
+ }
if (rest.contains(LINKEDIDDIRNAME))
{
rest = rest.replace(LINKEDIDDIRNAME, avm.getDirname());
{
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();
- }
- else
- {
- 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)
- {
- 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
- return pref != null ? Cache.getDefault(pref, def) : def;
- }
-
// the following methods look for the "*" linkedId and add the argvalue to all
// linkedId ArgValues if it does.
- // This version inserts the subvals sv into all created values
- private void addValue(String linkedId, ArgValues avs, SubVals sv,
- String v, int argIndex, boolean doSubs)
- {
- this.argValueOperation(Op.ADDVALUE, linkedId, avs, sv, v, false,
- argIndex, doSubs);
- }
-
- private void NOTaddValue(String linkedId, ArgValues avs, SubVals sv,
- String v, int argIndex, boolean doSubs)
- {
- Arg a = avs.arg();
-
- List<String> wildcardLinkedIds = null;
- if (a.hasOption(Opt.ALLOWALL))
- {
- switch (linkedId)
- {
- case MATCHALLLINKEDIDS:
- wildcardLinkedIds = getLinkedIds();
- break;
- case MATCHOPENEDLINKEDIDS:
- wildcardLinkedIds = this.storedLinkedIds;
- break;
- }
- }
-
- // if we're not a wildcard linkedId and the arg is marked to be stored, add
- // to storedLinkedIds
- if (linkedId != null && wildcardLinkedIds == null
- && a.hasOption(Opt.STORED)
- && !storedLinkedIds.contains(linkedId))
- {
- storedLinkedIds.add(linkedId);
- }
-
- // if we are a wildcard linkedId, apply the arg and value to all appropriate
- // linkedIds
- if (wildcardLinkedIds != null)
- {
- for (String id : wildcardLinkedIds)
- {
- // skip incorrectly stored wildcard ids!
- if (id == null || MATCHALLLINKEDIDS.equals(id)
- || MATCHOPENEDLINKEDIDS.equals(id))
- continue;
- ArgValuesMap avm = linkedArgs.get(id);
- if (a.hasOption(Opt.REQUIREINPUT)
- && !avm.hasArgWithOption(Opt.INPUT))
- continue;
- ArgValues tavs = avm.getOrCreateArgValues(a);
- String val = v;
- if (doSubs)
- {
- val = makeSubstitutions(v, id);
- sv = new SubVals(sv, val);
- }
- tavs.addValue(sv, val, argIndex);
- finaliseStoringArgValue(id, tavs);
- }
- }
- else
- {
- String val = v;
- if (doSubs)
- {
- val = makeSubstitutions(v, linkedId);
- sv = new SubVals(sv, val);
- }
- avs.addValue(sv, val, argIndex);
- finaliseStoringArgValue(linkedId, avs);
- }
- }
-
- private void addValue(String linkedId, ArgValues avs, String v,
- int argIndex, boolean doSubs)
+ /**
+ * This version inserts the subvals sv into all created values
+ */
+ private void addValue(String linkedId, Type type, ArgValues avs,
+ SubVals sv, String v, int argIndex, boolean doSubs)
{
- this.argValueOperation(Op.ADDVALUE, linkedId, avs, null, v, false,
+ this.argValueOperation(Op.ADDVALUE, linkedId, type, avs, sv, v, false,
argIndex, doSubs);
}
- // the following methods look for the "*" linkedId and add the argvalue to all
- // linkedId ArgValues if it does.
- private void NOTaddValue(String linkedId, ArgValues avs, String v,
- int argIndex, boolean doSubs)
- {
- Arg a = avs.arg();
- if (linkedId != null && a.hasOption(Opt.STORED)
- && !storedLinkedIds.contains(linkedId))
- {
- storedLinkedIds.add(linkedId);
- }
-
- List<String> wildcardLinkedIds = null;
- if (a.hasOption(Opt.ALLOWALL))
- {
- switch (linkedId)
- {
- case MATCHALLLINKEDIDS:
- wildcardLinkedIds = getLinkedIds();
- break;
- case MATCHOPENEDLINKEDIDS:
- wildcardLinkedIds = this.storedLinkedIds;
- break;
- }
- }
-
- // if we're not a wildcard linkedId and the arg is marked to be stored, add
- // to storedLinkedIds
- if (linkedId != null && wildcardLinkedIds == null
- && a.hasOption(Opt.STORED)
- && !storedLinkedIds.contains(linkedId))
- {
- storedLinkedIds.add(linkedId);
- }
-
- // if we are a wildcard linkedId, apply the arg and value to all appropriate
- // linkedIds
- if (wildcardLinkedIds != null)
- {
- for (String id : wildcardLinkedIds)
- {
- // 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)
- && !avm.hasArgWithOption(Opt.INPUT))
- continue;
- ArgValues tavs = avm.getOrCreateArgValues(a);
- String val = doSubs ? makeSubstitutions(v, id) : v;
- tavs.addValue(val, argIndex);
- finaliseStoringArgValue(id, tavs);
- }
- }
- else
- {
- String val = doSubs ? makeSubstitutions(v, linkedId) : v;
- avs.addValue(val, argIndex);
- finaliseStoringArgValue(linkedId, avs);
- }
- }
-
- private void setBoolean(String linkedId, ArgValues avs, boolean b,
- int argIndex)
+ private void setBoolean(String linkedId, Type type, ArgValues avs,
+ boolean b, int argIndex)
{
- this.argValueOperation(Op.SETBOOLEAN, linkedId, avs, null, null, b,
- argIndex, false);
- }
-
- private void NOTsetBoolean(String linkedId, ArgValues avs, boolean b,
- int argIndex)
- {
- Arg a = avs.arg();
- if (linkedId != null && a.hasOption(Opt.STORED)
- && !storedLinkedIds.contains(linkedId))
- {
- storedLinkedIds.add(linkedId);
- }
-
- List<String> wildcardLinkedIds = null;
- if (a.hasOption(Opt.ALLOWALL))
- {
- switch (linkedId)
- {
- case MATCHALLLINKEDIDS:
- wildcardLinkedIds = getLinkedIds();
- break;
- case MATCHOPENEDLINKEDIDS:
- wildcardLinkedIds = this.storedLinkedIds;
- break;
- }
- }
-
- // if we're not a wildcard linkedId and the arg is marked to be stored, add
- // to storedLinkedIds
- if (linkedId != null && wildcardLinkedIds == null
- && a.hasOption(Opt.STORED)
- && !storedLinkedIds.contains(linkedId))
- {
- storedLinkedIds.add(linkedId);
- }
-
- // if we are a wildcard linkedId, apply the arg and value to all appropriate
- // linkedIds
- if (wildcardLinkedIds != null)
- {
- for (String id : wildcardLinkedIds)
- {
- // skip incorrectly stored wildcard ids!
- if (id == null || MATCHALLLINKEDIDS.equals(id)
- || MATCHOPENEDLINKEDIDS.equals(id))
- continue;
- ArgValuesMap avm = linkedArgs.get(id);
- if (a.hasOption(Opt.REQUIREINPUT)
- && !avm.hasArgWithOption(Opt.INPUT))
- continue;
- ArgValues tavs = avm.getOrCreateArgValues(a);
- tavs.setBoolean(b, argIndex);
- finaliseStoringArgValue(id, tavs);
- }
- }
- else
- {
- avs.setBoolean(b, argIndex);
- finaliseStoringArgValue(linkedId, avs);
- }
+ this.argValueOperation(Op.SETBOOLEAN, linkedId, type, avs, null, null,
+ b, argIndex, false);
}
private void setNegated(String linkedId, ArgValues avs, boolean b)
{
- this.argValueOperation(Op.SETNEGATED, linkedId, avs, null, null, b, 0,
- false);
- }
-
- private void NOTsetNegated(String linkedId, ArgValues avs, boolean b)
- {
- Arg a = avs.arg();
- if (linkedId != null && a.hasOption(Opt.STORED)
- && !storedLinkedIds.contains(linkedId))
- {
- storedLinkedIds.add(linkedId);
- }
-
- List<String> wildcardLinkedIds = null;
- if (a.hasOption(Opt.ALLOWALL))
- {
- switch (linkedId)
- {
- case MATCHALLLINKEDIDS:
- wildcardLinkedIds = getLinkedIds();
- break;
- case MATCHOPENEDLINKEDIDS:
- wildcardLinkedIds = this.storedLinkedIds;
- break;
- }
- }
-
- // if we're not a wildcard linkedId and the arg is marked to be stored, add
- // to storedLinkedIds
- if (linkedId != null && wildcardLinkedIds == null
- && a.hasOption(Opt.STORED)
- && !storedLinkedIds.contains(linkedId))
- {
- storedLinkedIds.add(linkedId);
- }
-
- // if we are a wildcard linkedId, apply the arg and value to all appropriate
- // linkedIds
- if (wildcardLinkedIds != null)
- {
- for (String id : wildcardLinkedIds)
- {
- // skip incorrectly stored wildcard ids!
- if (id == null || MATCHALLLINKEDIDS.equals(id)
- || MATCHOPENEDLINKEDIDS.equals(id))
- continue;
- ArgValuesMap avm = linkedArgs.get(id);
- if (a.hasOption(Opt.REQUIREINPUT)
- && !avm.hasArgWithOption(Opt.INPUT))
- continue;
- ArgValues tavs = avm.getOrCreateArgValues(a);
- tavs.setNegated(b);
- }
- }
- else
- {
- avs.setNegated(b);
- }
+ this.argValueOperation(Op.SETNEGATED, linkedId, null, avs, null, null,
+ b, 0, false);
}
private void incrementCount(String linkedId, ArgValues avs)
{
- this.argValueOperation(Op.INCREMENTCOUNT, linkedId, avs, null, null,
- false, 0, false);
+ this.argValueOperation(Op.INCREMENTCOUNT, linkedId, null, avs, null,
+ null, false, 0, false);
}
- private void NOTincrementCount(String linkedId, ArgValues avs)
+ private enum Op
{
- Arg a = avs.arg();
-
- List<String> wildcardLinkedIds = null;
- if (a.hasOption(Opt.ALLOWALL))
- {
- switch (linkedId)
- {
- case MATCHALLLINKEDIDS:
- wildcardLinkedIds = getLinkedIds();
- break;
- case MATCHOPENEDLINKEDIDS:
- wildcardLinkedIds = this.storedLinkedIds;
- break;
- }
- }
-
- // if we're not a wildcard linkedId and the arg is marked to be stored, add
- // to storedLinkedIds
- if (linkedId != null && wildcardLinkedIds == null
- && a.hasOption(Opt.STORED)
- && !storedLinkedIds.contains(linkedId))
- {
- storedLinkedIds.add(linkedId);
- }
-
- // if we are a wildcard linkedId, apply the arg and value to all appropriate
- // linkedIds
- if (wildcardLinkedIds != null)
- {
- for (String id : wildcardLinkedIds)
- {
- // skip incorrectly stored wildcard ids!
- if (id == null || MATCHALLLINKEDIDS.equals(id)
- || MATCHOPENEDLINKEDIDS.equals(id))
- continue;
- ArgValuesMap avm = linkedArgs.get(id);
- if (a.hasOption(Opt.REQUIREINPUT)
- && !avm.hasArgWithOption(Opt.INPUT))
- continue;
- ArgValues tavs = avm.getOrCreateArgValues(a);
- tavs.incrementCount();
- }
- }
- else
- {
- avs.incrementCount();
- }
+ ADDVALUE, SETBOOLEAN, SETNEGATED, INCREMENTCOUNT
}
- private enum Op
+ private void argValueOperation(Op op, String linkedId, Type type,
+ ArgValues avs, SubVals sv, String v, boolean b, int argIndex,
+ boolean doSubs)
{
- ADDVALUE, SETBOOLEAN, SETNEGATED, INCREMENTCOUNT
+ // default to merge subvals if subvals are provided
+ argValueOperation(op, linkedId, type, avs, sv, true, v, b, argIndex,
+ doSubs);
}
- // The following operations look for the "*" and "open*" linkedIds and add the
- // argvalue to all appropriate linkedId ArgValues if it does.
- // If subvals are supplied, they are inserted into all new set values.
- private void argValueOperation(Op op, String linkedId, ArgValues avs,
- SubVals sv, String v, boolean b, int argIndex, boolean doSubs)
+ /**
+ * The following operations look for the "*" and "open*" linkedIds and add the
+ * argvalue to all appropriate linkedId ArgValues if it does. If subvals are
+ * supplied, they are inserted into all new set values.
+ *
+ * @param op
+ * The ArgParser.Op operation
+ * @param linkedId
+ * The String linkedId from the ArgValuesMap
+ * @param type
+ * The Arg.Type to attach to this ArgValue
+ * @param avs
+ * The ArgValues for this linkedId
+ * @param sv
+ * Use these SubVals on the ArgValue
+ * @param merge
+ * Merge the SubVals with any existing on the value. False will
+ * replace unless sv is null
+ * @param v
+ * The value of the ArgValue (may contain subvals).
+ * @param b
+ * The boolean value of the ArgValue.
+ * @param argIndex
+ * The argIndex for the ArgValue.
+ * @param doSubs
+ * Whether to perform substitutions on the subvals and value.
+ */
+ private void argValueOperation(Op op, String linkedId, Type type,
+ ArgValues avs, SubVals sv, boolean merge, String v, boolean b,
+ int argIndex, boolean doSubs)
{
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)
{
if (doSubs)
{
- val = makeSubstitutions(v, id);
- sv = new SubVals(sv, val);
+ sv = new SubVals(sv, val, merge);
+ val = makeSubstitutions(sv.getContent(), id);
}
- tavs.addValue(sv, val, argIndex);
+ tavs.addValue(sv, type, val, argIndex, true);
}
else
{
{
val = makeSubstitutions(v, id);
}
- tavs.addValue(val, argIndex);
+ tavs.addValue(type, val, argIndex, true);
}
finaliseStoringArgValue(id, tavs);
break;
case SETBOOLEAN:
- tavs.setBoolean(b, argIndex);
+ tavs.setBoolean(type, b, argIndex, true);
finaliseStoringArgValue(id, tavs);
break;
case SETNEGATED:
- tavs.setNegated(b);
+ tavs.setNegated(b, true);
break;
case INCREMENTCOUNT:
val = makeSubstitutions(v, linkedId);
sv = new SubVals(sv, val);
}
- avs.addValue(sv, val, argIndex);
+ avs.addValue(sv, type, val, argIndex, false);
}
else
{
{
val = makeSubstitutions(v, linkedId);
}
- avs.addValue(val, argIndex);
+ avs.addValue(type, val, argIndex, false);
}
finaliseStoringArgValue(linkedId, avs);
break;
case SETBOOLEAN:
- avs.setBoolean(b, argIndex);
+ avs.setBoolean(type, b, argIndex, false);
finaliseStoringArgValue(linkedId, avs);
break;
case SETNEGATED:
- avs.setNegated(b);
+ avs.setNegated(b, false);
break;
case INCREMENTCOUNT:
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