JAL-2403 ensure array held in Matrix is immutable

[jalview.git] / src / jalview / math / Matrix.java

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 821fc66..b39d3c9 100755 (executable)
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -65,7 +65,8 @@ public class Matrix implements MatrixI
   }
   
   /**
-   * Creates a new Matrix object. For example
+   * Creates a new Matrix object containing a copy of the supplied array values.
+   * For example
    * 
    * <pre>
    *   new Matrix(new double[][] {{2, 3, 4}, {5, 6, 7})
@@ -85,13 +86,27 @@ public class Matrix implements MatrixI
   {
     this.rows = values.length;
     this.cols = this.rows == 0 ? 0 : values[0].length;
-    this.value = values;
+
+    /*
+     * make a copy of the values array, for immutability
+     */
+    this.value = new double[rows][];
+    int i = 0;
+    for (double[] row : values)
+    {
+      if (row != null)
+      {
+        value[i] = new double[row.length];
+        System.arraycopy(row, 0, value[i], 0, row.length);
+      }
+      i++;
+    }
   }
 
   /**
    * Returns a new matrix which is the transpose of this one
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   @Override
   public MatrixI transpose()
@@ -959,11 +974,12 @@ public class Matrix implements MatrixI
   }
 
   /**
-   * Multiply every entry in the matrix by the given value. This method is not
-   * thread-safe.
+   * Multiplies every entry in the matrix by the given value.
+   * 
+   * @param
    */
   @Override
-  public void multiply(double d)
+  public void multiply(double by)
   {
     for (double[] row : value)
     {
@@ -971,7 +987,7 @@ public class Matrix implements MatrixI
       {
         for (int i = 0; i < row.length; i++)
         {
-          row[i] *= d;
+          row[i] *= by;
         }
       }
     }