JAL-629 Added linkedId to ArgValuesMap for reference. Updated Arg descriptions. Made...

[jalview.git] / src / jalview / bin / argparser / ArgParser.java

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index d551b26..38cb2d4 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -430,10 +430,7 @@ public class ArgParser
         if (a.hasOption(Opt.NOACTION))
           continue;
 
-        if (!linkedArgs.containsKey(linkedId))
-          linkedArgs.put(linkedId, new ArgValuesMap());
-
-        ArgValuesMap avm = linkedArgs.get(linkedId);
+        ArgValuesMap avm = getOrCreateLinkedArgValuesMap(linkedId);
 
         // not dealing with both NODUPLICATEVALUES and GLOB
         if (a.hasOption(Opt.NODUPLICATEVALUES) && avm.hasValue(a, val))
@@ -543,8 +540,7 @@ public class ArgParser
                 .toString();
       }
     }
-    if (!linkedArgs.containsKey(defaultLinkedId))
-      linkedArgs.put(defaultLinkedId, new ArgValuesMap());
+    getOrCreateLinkedArgValuesMap(defaultLinkedId);
     return defaultLinkedId;
   }
 
@@ -817,22 +813,38 @@ public class ArgParser
           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)
-      return sv.get(key);
-    if (avm != null && avm.containsArg(a))
+    {
+      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)
-        return avm.getValue(a);
+        value = avm.getValue(a);
       else if (pos == Position.BEFORE
               && avm.getClosestPreviousArgValueOfArg(av, a) != null)
-        return avm.getClosestPreviousArgValueOfArg(av, a).getValue();
+        value = avm.getClosestPreviousArgValueOfArg(av, a).getValue();
       else if (pos == Position.AFTER
               && avm.getClosestNextArgValueOfArg(av, a) != null)
-        return avm.getClosestNextArgValueOfArg(av, a).getValue();
+        value = avm.getClosestNextArgValueOfArg(av, a).getValue();
     }
-    return pref != null ? Cache.getDefault(pref, def) : def;
+    else
+    {
+      value = pref != null ? Cache.getDefault(pref, def) : def;
+    }
+    return value;
   }
 
   public static boolean getBoolFromSubValOrArg(ArgValuesMap avm, Arg a,
@@ -844,22 +856,59 @@ public class ArgParser
   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;
-    if (sv != null && sv.has(key) && sv.get(key) != null)
-      return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
 
-    if (sv != null && sv.has(key) && sv.get(key) != null)
-      return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
+    // 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 != null && sv.has(nokey) && sv.get(nokey) != null)
-      return !sv.get(nokey).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;
   }
 
@@ -1004,4 +1053,14 @@ public class ArgParser
     }
   }
 
+  private ArgValuesMap getOrCreateLinkedArgValuesMap(String linkedId)
+  {
+    if (linkedArgs.containsKey(linkedId)
+            && linkedArgs.get(linkedId) != null)
+      return linkedArgs.get(linkedId);
+
+    linkedArgs.put(linkedId, new ArgValuesMap(linkedId));
+    return linkedArgs.get(linkedId);
+  }
+
 }
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