import jalview.bin.Console;
import jalview.bin.Jalview;
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 = '=';
// 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
+ protected static final String MATCHOPENEDLINKEDIDS = "open*";
+
// the counter added to the default linked id prefix
private int defaultLinkedIdCounter = 0;
// 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 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}";
// 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;
+
protected static final Map<String, Arg> argMap;
protected Map<String, ArgValuesMap> linkedArgs = new HashMap<>();
protected List<String> linkedOrder = new ArrayList<>();
+ protected List<String> storedLinkedIds = new ArrayList<>();
+
protected List<Arg> argList = new ArrayList<>();
private static final char ARGFILECOMMENT = '#';
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(
openEachInitialFilenames = false;
}
- 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())))
{
// 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)
else if (a == Arg.ALL)
{
allLinkedIds = !negated;
+ openedLinkedIds = false;
+ }
+ else if (a == Arg.OPENED)
+ {
+ openedLinkedIds = !negated;
+ allLinkedIds = false;
+ }
+
+ if (a.hasOption(Opt.STORED))
+ {
+ // reset the lastOpenedLinkedIds list
+ this.storedLinkedIds = new ArrayList<>();
}
// this is probably only Arg.NEW and Arg.OPEN
}
String autoCounterString = null;
- boolean usingAutoCounterLinkedId = false;
String defaultLinkedId = defaultLinkedId(false);
boolean usingDefaultLinkedId = false;
if (a.hasOption(Opt.LINKED))
{
if (linkedId == null)
{
- if (allLinkedIds && a.hasOption(Opt.ALLOWALL))
+ if (a.hasOption(Opt.OUTPUT) && a.hasOption(Opt.ALLOWALL)
+ && val.startsWith(MATCHALLLINKEDIDS))
+ {
+ // --output=*.ext is shorthand for --all --output {basename}.ext
+ // (or --image=*.ext)
+ allLinkedIds = true;
+ openedLinkedIds = false;
+ linkedId = MATCHALLLINKEDIDS;
+ val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
+ + val.substring(MATCHALLLINKEDIDS.length());
+ }
+ 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))
{
linkedId = MATCHALLLINKEDIDS;
}
+ else if (openedLinkedIds && a.hasOption(Opt.ALLOWALL))
+ {
+ linkedId = MATCHOPENEDLINKEDIDS;
+ }
else
{
// use default linkedId for linked arguments
autoCounterString = Integer.toString(linkedIdAutoCounter);
linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER,
autoCounterString);
- usingAutoCounterLinkedId = true;
Console.debug(
"Changing linkedId to '" + linkedId + "' from " + arg);
}
autoCounterString = Integer.toString(++linkedIdAutoCounter);
linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER,
autoCounterString);
- usingAutoCounterLinkedId = true;
Console.debug(
"Changing linkedId to '" + linkedId + "' from " + arg);
}
{
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);
}
}
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 '*' linkedId that should be empty if it was created
- if (MATCHALLLINKEDIDS.equals(linkedId)
+ // remove the '*' or 'open*' linkedId that should be empty if it was
+ // created
+ if ((MATCHALLLINKEDIDS.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());
}
// the following methods look for the "*" linkedId and add the argvalue to all
- // linkedId ArgValues if it does
- private void addValue(String linkedId, ArgValues avs, SubVals sv,
- String v, int argIndex, boolean doSubs)
+ // linkedId ArgValues if it does.
+ // 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)
{
- Arg a = avs.arg();
- if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
- {
- for (String id : getLinkedIds())
- {
- if (id == null || MATCHALLLINKEDIDS.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);
- }
+ this.argValueOperation(Op.ADDVALUE, linkedId, type, avs, sv, v, false,
+ argIndex, doSubs);
}
- private void addValue(String linkedId, ArgValues avs, String v,
+ private void addValue(String linkedId, Type type, ArgValues avs, String v,
int argIndex, boolean doSubs)
{
- Arg a = avs.arg();
- if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
- {
- for (String id : getLinkedIds())
- {
- if (id == null || MATCHALLLINKEDIDS.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);
- }
+ this.argValueOperation(Op.ADDVALUE, linkedId, type, avs, null, v, false,
+ argIndex, doSubs);
}
- private void setBoolean(String linkedId, ArgValues avs, boolean b,
- int argIndex)
+ private void setBoolean(String linkedId, Type type, ArgValues avs,
+ boolean b, int argIndex)
{
- Arg a = avs.arg();
- if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
- {
- for (String id : getLinkedIds())
- {
- if (id == null || MATCHALLLINKEDIDS.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, null, avs, null, null,
+ b, 0, false);
+ }
+
+ private void incrementCount(String linkedId, ArgValues avs)
+ {
+ this.argValueOperation(Op.INCREMENTCOUNT, linkedId, null, avs, null,
+ null, false, 0, false);
+ }
+
+ private enum Op
+ {
+ ADDVALUE, SETBOOLEAN, SETNEGATED, INCREMENTCOUNT
+ }
+
+ // 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, Type type,
+ ArgValues avs, SubVals sv, String v, boolean b, int argIndex,
+ boolean doSubs)
+ {
Arg a = avs.arg();
- if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
+
+ List<String> wildcardLinkedIds = null;
+ if (a.hasOption(Opt.ALLOWALL))
{
- for (String id : getLinkedIds())
+ switch (linkedId)
{
- if (id == null || MATCHALLLINKEDIDS.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);
+ case MATCHALLLINKEDIDS:
+ wildcardLinkedIds = getLinkedIds();
+ break;
+ case MATCHOPENEDLINKEDIDS:
+ wildcardLinkedIds = this.storedLinkedIds;
+ break;
}
}
- else
+
+ // 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))
{
- avs.setNegated(b);
+ storedLinkedIds.add(linkedId);
}
- }
- private void incrementCount(String linkedId, ArgValues avs)
- {
- Arg a = avs.arg();
- if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
+ // if we are a wildcard linkedId, apply the arg and value to all appropriate
+ // linkedIds
+ if (wildcardLinkedIds != null)
{
- for (String id : getLinkedIds())
+ for (String id : wildcardLinkedIds)
{
- if (id == null || MATCHALLLINKEDIDS.equals(id))
+ // 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);
- tavs.incrementCount();
+ switch (op)
+ {
+
+ case ADDVALUE:
+ String val = v;
+ if (sv != null)
+ {
+ if (doSubs)
+ {
+ val = makeSubstitutions(v, id);
+ sv = new SubVals(sv, val);
+ }
+ tavs.addValue(sv, type, val, argIndex, true);
+ }
+ else
+ {
+ if (doSubs)
+ {
+ val = makeSubstitutions(v, id);
+ }
+ tavs.addValue(type, val, argIndex, true);
+ }
+ finaliseStoringArgValue(id, tavs);
+ break;
+
+ case SETBOOLEAN:
+ tavs.setBoolean(type, b, argIndex, true);
+ finaliseStoringArgValue(id, tavs);
+ break;
+
+ case SETNEGATED:
+ tavs.setNegated(b, true);
+ break;
+
+ case INCREMENTCOUNT:
+ tavs.incrementCount();
+ break;
+
+ default:
+ break;
+
+ }
+
}
}
- else
+ else // no wildcard linkedId -- do it simpler
{
- avs.incrementCount();
+ switch (op)
+ {
+ case ADDVALUE:
+ String val = v;
+ if (sv != null)
+ {
+ if (doSubs)
+ {
+ val = makeSubstitutions(v, linkedId);
+ sv = new SubVals(sv, val);
+ }
+ avs.addValue(sv, type, val, argIndex, false);
+ }
+ else
+ {
+ if (doSubs)
+ {
+ val = makeSubstitutions(v, linkedId);
+ }
+ avs.addValue(type, val, argIndex, false);
+ }
+ finaliseStoringArgValue(linkedId, avs);
+ break;
+
+ case SETBOOLEAN:
+ avs.setBoolean(type, b, argIndex, false);
+ finaliseStoringArgValue(linkedId, avs);
+ break;
+
+ case SETNEGATED:
+ avs.setNegated(b, false);
+ break;
+
+ case INCREMENTCOUNT:
+ avs.incrementCount();
+ break;
+
+ default:
+ break;
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff