Merge branch 'develop' into merge/big_merge_of_bens_stuff_before_2_11_3_0

[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 e286cb4..6344092 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;
@@ -139,8 +166,8 @@ public class SparseIntArray implements Cloneable
   public void removeAt(int index)
   {
     System.arraycopy(mKeys, index + 1, mKeys, index, mSize - (index + 1));
-    System.arraycopy(mValues, index + 1, mValues, index, mSize
-            - (index + 1));
+    System.arraycopy(mValues, index + 1, mValues, index,
+            mSize - (index + 1));
     mSize--;
   }
 
@@ -355,6 +382,8 @@ public class SparseIntArray implements Cloneable
    * @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 int add(int key, int toAdd)
   {
@@ -362,6 +391,7 @@ public class SparseIntArray implements Cloneable
     int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
     if (i >= 0)
     {
+      checkOverflow(mValues[i], toAdd);
       mValues[i] += toAdd;
       newValue = mValues[i];
     }
@@ -389,4 +419,34 @@ public class SparseIntArray implements Cloneable
     }
     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);
+      }
+    }
+  }
 }