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diff --git a/src/jalview/util/SparseCount.java b/src/jalview/util/SparseCount.java
new file mode 100644
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+++ b/src/jalview/util/SparseCount.java
@@ -0,0 +1,154 @@
+package jalview.util;
+
+import jalview.ext.android.SparseIntArray;
+import jalview.ext.android.SparseShortArray;
+
+/**
+ * A class to count occurrences of characters with minimal memory footprint.
+ * Sparse arrays of short values are used to hold the counts, with automatic
+ * promotion to arrays of int if any count exceeds the maximum value for a
+ * short.
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class SparseCount
+{
+  private static final int DEFAULT_PROFILE_SIZE = 2;
+
+  /*
+   * array of keys (chars) and values (counts)
+   * held either as shorts or (if shorts overflow) as ints 
+   */
+  private SparseShortArray shortProfile;
+
+  private SparseIntArray intProfile;
+
+  /*
+   * flag is set true after short overflow occurs
+   */
+  private boolean useInts;
+
+  /**
+   * Constructor which initially creates a new sparse array of short values to
+   * hold counts.
+   * 
+   * @param profileSize
+   */
+  public SparseCount(int profileSize)
+  {
+    this.shortProfile = new SparseShortArray(profileSize);
+  }
+
+  /**
+   * Constructor which allocates an initial count array for only two distinct
+   * values (the array will grow if needed)
+   */
+  public SparseCount()
+  {
+    this(DEFAULT_PROFILE_SIZE);
+  }
+
+  /**
+   * Adds the given value for the given key (or sets the initial value), and
+   * returns the new value
+   * 
+   * @param key
+   * @param value
+   */
+  public int add(int key, int value)
+  {
+    int newValue = 0;
+    if (useInts)
+    {
+      newValue = intProfile.add(key, value);
+    }
+    else
+    {
+      try {
+        newValue = shortProfile.add(key, value);
+      } catch (ArithmeticException e) {
+        handleOverflow();
+        newValue = intProfile.add(key, value);
+      }
+    }
+    return newValue;
+  }
+
+  /**
+   * Switch from counting shorts to counting ints
+   */
+  synchronized void handleOverflow()
+  {
+    int size = shortProfile.size();
+    intProfile = new SparseIntArray(size);
+    for (int i = 0; i < size; i++)
+    {
+      short key = shortProfile.keyAt(i);
+      short value = shortProfile.valueAt(i);
+      intProfile.put(key, value);
+    }
+    shortProfile = null;
+    useInts = true;
+  }
+
+  /**
+   * Returns the size of the profile (number of distinct items counted)
+   * 
+   * @return
+   */
+  public int size()
+  {
+    return useInts ? intProfile.size() : shortProfile.size();
+  }
+
+  /**
+   * Returns the value for the key (zero if no such key)
+   * 
+   * @param key
+   * @return
+   */
+  public int get(int key)
+  {
+    return useInts ? intProfile.get(key) : shortProfile.get(key);
+  }
+
+  /**
+   * Sets the value for the given key
+   * 
+   * @param key
+   * @param value
+   */
+  public void put(int key, int value)
+  {
+    if (useInts)
+    {
+      intProfile.put(key, value);
+    }
+    else
+    {
+      shortProfile.put(key, value);
+    }
+  }
+
+  public int keyAt(int k)
+  {
+    return useInts ? intProfile.keyAt(k) : shortProfile.keyAt(k);
+  }
+
+  public int valueAt(int k)
+  {
+    return useInts ? intProfile.valueAt(k) : shortProfile.valueAt(k);
+  }
+
+  /**
+   * Answers true if this object wraps arrays of int values, false if using
+   * short values
+   * 
+   * @return
+   */
+  boolean isUsingInt()
+  {
+    return useInts;
+  }
+}