JAL-2418 add GPL to main sources

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

diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index 05fe22f..5b93c76 100644 (file)
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.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.math;
 
 import java.io.PrintStream;
@@ -42,7 +62,7 @@ public interface MatrixI
    * @return
    */
   double[] getRow(int i);
-  
+
   MatrixI copy();
 
   MatrixI transpose();
@@ -65,12 +85,33 @@ 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);
 }