X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FSubVals.java;h=4d146d9e8e029c63d9a72db70848a9677c585e5b;hb=fbdb24c3c8ad23e3966a8295bed2de3b05f60119;hp=6708cf9267700371a3220d2502adfbd9d1b1524c;hpb=f52d881ba992cf5d4570d487f6319666f13263a9;p=jalview.git

diff --git a/src/jalview/bin/argparser/SubVals.java b/src/jalview/bin/argparser/SubVals.java
index 6708cf9..4d146d9 100644
--- a/src/jalview/bin/argparser/SubVals.java
+++ b/src/jalview/bin/argparser/SubVals.java
@@ -21,7 +21,7 @@ public class SubVals
 
   private Map<String, String> subValMap;
 
-  private static char SEPARATOR = ';';
+  private static char SEPARATOR = ',';
 
   private static char EQUALS = '=';
 
@@ -29,14 +29,42 @@ public class SubVals
 
   protected SubVals(SubVals sv, String c)
   {
-    if (sv == null)
+    this(sv, c, true);
+  }
+
+  protected SubVals(SubVals sv, String c, boolean merge)
+  {
+    SubVals subvals;
+    if (merge)
+    {
+      SubVals vsv = new SubVals(c);
+      if (sv != null && sv.getSubValMap() != null)
+      {
+        for (String key : sv.getSubValMap().keySet())
+        {
+          vsv.put(key, sv.get(key));
+        }
+      }
+      if (sv != null && sv.getIndex() > 0)
+      {
+        vsv.index = sv.getIndex();
+      }
+      subvals = vsv;
+    }
+    else
+    {
+      // replace
+      subvals = sv;
+    }
+    if (subvals == null)
     {
       this.subValMap = new HashMap<>();
     }
     else
     {
-      this.subValMap = sv == null ? new HashMap<>() : sv.getSubValMap();
-      this.index = sv.getIndex();
+      this.subValMap = subvals == null ? new HashMap<>()
+              : subvals.getSubValMap();
+      this.index = subvals.getIndex();
     }
     this.content = c;
   }
@@ -104,6 +132,11 @@ public class SubVals
     return index == NOTSET && (subValMap == null || subValMap.size() == 0);
   }
 
+  public String getWithSubstitutions(ArgParser ap, String id, String key)
+  {
+    return ap.makeSubstitutions(subValMap.get(key), id);
+  }
+
   public String get(String key)
   {
     return subValMap.get(key);