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 3f0bae4..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()
@@ -891,37 +906,58 @@ public class Matrix implements MatrixI
     return row;
   }
 
-  @Override
-  public double getMaxValue()
+  /**
+   * Returns a length 2 array of {minValue, maxValue} of all values in the
+   * matrix. Returns null if the matrix is null or empty.
+   * 
+   * @return
+   */
+  double[] findMinMax()
   {
     if (value == null)
     {
-      return 0;
+      return null;
     }
+    double min = Double.MAX_VALUE;
     double max = -Double.MAX_VALUE;
+    boolean empty = true;
     for (double[] row : value)
     {
       if (row != null)
       {
         for (double x : row)
         {
+          empty = false;
           if (x > max)
           {
             max = x;
           }
+          if (x < min)
+          {
+            min = x;
+          }
         }
       }
     }
-    return max;
+    return empty ? null : new double[] { min, max };
   }
 
+  /**
+   * {@inheritDoc}
+   */
   @Override
-  public void subtractAllFrom(double val)
+  public void reverseRange(boolean maxToZero)
   {
     if (value == null)
     {
       return;
     }
+    double[] minMax = findMinMax();
+    if (minMax == null)
+    {
+      return; // empty matrix
+    }
+    double subtractFrom = maxToZero ? minMax[1] : minMax[0] + minMax[1];
 
     for (double[] row : value)
     {
@@ -930,10 +966,30 @@ public class Matrix implements MatrixI
         int j = 0;
         for (double x : row)
         {
-          row[j] = val - x;
+          row[j] = subtractFrom - x;
           j++;
         }
       }
     }
   }
+
+  /**
+   * Multiplies every entry in the matrix by the given value.
+   * 
+   * @param
+   */
+  @Override
+  public void multiply(double by)
+  {
+    for (double[] row : value)
+    {
+      if (row != null)
+      {
+        for (int i = 0; i < row.length; i++)
+        {
+          row[i] *= by;
+        }
+      }
+    }
+  }
 }