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diff --git a/src/jalview/util/SetUtils.java b/src/jalview/util/SetUtils.java
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+++ b/src/jalview/util/SetUtils.java
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+/*
+ * 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.util;
+
+import java.util.Set;
+
+public class SetUtils
+{
+  /**
+   * Returns the count of things that are in one or other of two sets but not in
+   * both. The sets are not modified.
+   * 
+   * @param set1
+   * @param set2
+   * @return
+   */
+  public static int countDisjunction(Set<? extends Object> set1,
+          Set<? extends Object> set2)
+  {
+    if (set1 == null)
+    {
+      return set2 == null ? 0 : set2.size();
+    }
+    if (set2 == null)
+    {
+      return set1.size();
+    }
+
+    int size1 = set1.size();
+    int size2 = set2.size();
+    Set<? extends Object> smallerSet = size1 < size2 ? set1 : set2;
+    Set<? extends Object> largerSet = (smallerSet == set1 ? set2 : set1);
+    int inCommon = 0;
+    for (Object k : smallerSet)
+    {
+      if (largerSet.contains(k))
+      {
+        inCommon++;
+      }
+    }
+
+    int notInCommon = (size1 - inCommon) + (size2 - inCommon);
+    return notInCommon;
+  }
+}