X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrixI.java;h=94b933349d2352474331b8d0961a394909ae5e49;hb=7733b7433ee8771d85ccfe2ed32119feac8056e0;hp=05fe22ffa887fee646501d628d81d1764fbc7614;hpb=d6a30c6516e8e2f923c8c2f6dce7592cb3b7d974;p=jalview.git

diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index 05fe22f..94b9333 100644
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.java
@@ -65,12 +65,33 @@ public interface MatrixI
 
   void tred();
 
-  double getMaxValue();
+  /**
+   * Reverses the range of the matrix values, so that the smallest values become
+   * the largest, and the largest become the smallest. This operation supports
+   * using a distance measure as a similarity measure, or vice versa.
+   * <p>
+   * If parameter <code>maxToZero</code> is true, then the maximum value becomes
+   * zero, i.e. all values are subtracted from the maximum. This is consistent
+   * with converting an identity similarity score to a distance score - the most
+   * similar (identity) corresponds to zero distance. However note that the
+   * operation is not reversible (unless the original minimum value is zero).
+   * For example a range of 10-40 would become 30-0, which would reverse a
+   * second time to 0-30. Also note that a general similarity measure (such as
+   * BLOSUM) may give different 'identity' scores for different sequences, so
+   * they cannot all convert to zero distance.
+   * <p>
+   * If parameter <code>maxToZero</code> is false, then the values are reflected
+   * about the average of {min, max} (effectively swapping min and max). This
+   * operation <em>is</em> reversible.
+   * 
+   * @param maxToZero
+   */
+  void reverseRange(boolean maxToZero);
 
   /**
-   * Update each value in the matrix by subtracting it from the given value
+   * Multiply all entries by the given value
    * 
-   * @param val
+   * @param d
    */
-  void subtractAllFrom(double val);
+  void multiply(double d);
 }