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diff --git a/test/jalview/util/SparseCountTest.java b/test/jalview/util/SparseCountTest.java
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+++ b/test/jalview/util/SparseCountTest.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 static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+public class SparseCountTest
+{
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = "Functional")
+  public void testAdd()
+  {
+    SparseCount p = new SparseCount(8);
+    p.add('a', 1);
+    p.add('b', 2);
+    p.add('a', 3);
+    p.add('b', -4);
+    assertEquals(p.size(), 2);
+    assertEquals(p.get('a'), 4);
+    assertEquals(p.get('b'), -2);
+  }
+
+  @Test(groups = "Functional")
+  public void testPut()
+  {
+    SparseCount p = new SparseCount(8);
+    p.put('a', 3);
+    p.add('b', 2);
+    p.put('b', 4);
+    assertEquals(p.size(), 2);
+    assertEquals(p.get('a'), 3);
+    assertEquals(p.get('b'), 4);
+  }
+
+  /**
+   * Test handling overflow of short by switching to counting ints
+   */
+  @Test(groups = "Functional")
+  public void testOverflow()
+  {
+    SparseCount p = new SparseCount(8);
+    p.put('a', Short.MAX_VALUE - 1);
+    p.add('a', 1);
+    assertFalse(p.isUsingInt());
+    p.add('a', 1);
+    assertTrue(p.isUsingInt());
+  }
+
+  /**
+   * Test handling underflow of short by switching to counting ints
+   */
+  @Test(groups = "Functional")
+  public void testUnderflow()
+  {
+    SparseCount p = new SparseCount(8);
+    p.put('a', Short.MIN_VALUE + 1);
+    p.add('a', -1);
+    assertFalse(p.isUsingInt());
+    p.add('a', -1);
+    assertTrue(p.isUsingInt());
+  }
+
+  @Test(groups = "Functional")
+  public void testKeyAt_ValueAt()
+  {
+    SparseCount p = new SparseCount(8);
+    p.put('W', 12);
+    p.put('K', 9);
+    p.put('R', 6);
+    assertEquals(p.size(), 3);
+    assertEquals(p.keyAt(0), 'K');
+    assertEquals(p.valueAt(0), 9);
+    assertEquals(p.keyAt(1), 'R');
+    assertEquals(p.valueAt(1), 6);
+    assertEquals(p.keyAt(2), 'W');
+    assertEquals(p.valueAt(2), 12);
+  }
+
+}