X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FSubVals.java;h=9723c9adc784d14ceae668fff5bf7e2636af7b7d;hb=bc1a3842b31a35a7794f4afec4911ad421c7c3e4;hp=196cd24522b7e5420b7e6bcc7f03399450225e82;hpb=03968fce3d428957aced82b7f051527fa66e762f;p=jalview.git

diff --git a/src/jalview/bin/argparser/SubVals.java b/src/jalview/bin/argparser/SubVals.java
index 196cd24..9723c9a 100644
--- a/src/jalview/bin/argparser/SubVals.java
+++ b/src/jalview/bin/argparser/SubVals.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.bin.argparser;
 
 import java.util.ArrayList;
@@ -21,7 +41,7 @@ public class SubVals
 
   private Map<String, String> subValMap;
 
-  private static char SEPARATOR = ';';
+  private static char SEPARATOR = ',';
 
   private static char EQUALS = '=';
 
@@ -29,14 +49,42 @@ 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;
   }