fix for JAL-3765

[jalview.git] / src / jalview / ext / android / SparseIntArray.java

diff --git a/src/jalview/ext/android/SparseIntArray.java b/src/jalview/ext/android/SparseIntArray.java
index 0e05803..d67121b 100644 (file)
--- a/src/jalview/ext/android/SparseIntArray.java
+++ b/src/jalview/ext/android/SparseIntArray.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.ext.android;
 
 /*
@@ -40,6 +60,13 @@ package jalview.ext.android;
  * order in the case of <code>valueAt(int)<code>.
  * </p>
  */
+
+/*
+ * Imported into Jalview September 2016
+ * Change log:
+ *   Sep 2016 method add(int, int) added for more efficient increment of counts
+ *            (a single binary search, rather than one on read and one on write)
+ */
 public class SparseIntArray implements Cloneable
 {
   private int[] mKeys;
@@ -348,21 +375,78 @@ public class SparseIntArray implements Cloneable
   }
 
   /**
-   * Method added for Jalview to increment a key's value if present, else add it
-   * with the value 1
+   * Method (copied from put) added for Jalview to efficiently increment a key's
+   * value if present, else add it with the given value. This avoids a double
+   * binary search (once to get the value, again to put the updated value).
    * 
    * @param key
+   * @oparam toAdd
+   * @return the new value of the count for the key
+   * @throw ArithmeticException if the result would exceed the maximum value of
+   *        an int
    */
-  public void increment(int key)
+  public int add(int key, int toAdd)
   {
+    int newValue = toAdd;
     int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
     if (i >= 0)
     {
-      mValues[i]++;
+      checkOverflow(mValues[i], toAdd);
+      mValues[i] += toAdd;
+      newValue = mValues[i];
     }
     else
     {
-      put(key, 1);
+      i = ~i;
+      if (mSize >= mKeys.length)
+      {
+        int n = idealIntArraySize(mSize + 1);
+        int[] nkeys = new int[n];
+        int[] nvalues = new int[n];
+        System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length);
+        System.arraycopy(mValues, 0, nvalues, 0, mValues.length);
+        mKeys = nkeys;
+        mValues = nvalues;
+      }
+      if (mSize - i != 0)
+      {
+        System.arraycopy(mKeys, i, mKeys, i + 1, mSize - i);
+        System.arraycopy(mValues, i, mValues, i + 1, mSize - i);
+      }
+      mKeys[i] = key;
+      mValues[i] = toAdd;
+      mSize++;
+    }
+    return newValue;
+  }
+
+  /**
+   * Throws ArithmeticException if adding addend to value would exceed the range
+   * of int
+   * 
+   * @param value
+   * @param addend
+   */
+  static void checkOverflow(int value, int addend)
+  {
+    /*
+     * test cases being careful to avoid overflow while testing!
+     */
+    if (addend > 0)
+    {
+      if (value > 0 && Integer.MAX_VALUE - value < addend)
+      {
+        throw new ArithmeticException("Integer overflow adding " + addend
+                + " to  " + value);
+      }
+    }
+    else if (addend < 0)
+    {
+      if (value < 0 && Integer.MIN_VALUE - value > addend)
+      {
+        throw new ArithmeticException("Integer underflow adding " + addend
+                + " to  " + value);
+      }
     }
   }
 }