JAL-2418 add GPL to main sources

[jalview.git] / src / jalview / analysis / scoremodels / SimilarityScoreModel.java

diff --git a/src/jalview/analysis/scoremodels/SimilarityScoreModel.java b/src/jalview/analysis/scoremodels/SimilarityScoreModel.java
index d41e0ba..e702340 100644 (file)
--- a/src/jalview/analysis/scoremodels/SimilarityScoreModel.java
+++ b/src/jalview/analysis/scoremodels/SimilarityScoreModel.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.analysis.scoremodels;
 
 import jalview.api.analysis.ScoreModelI;
@@ -17,14 +37,27 @@ public abstract class SimilarityScoreModel implements ScoreModelI
   public MatrixI findDistances(AlignmentView seqData,
           SimilarityParamsI options)
   {
-    MatrixI result = findSimilarities(seqData, options);
+    MatrixI similarities = findSimilarities(seqData, options);
 
-    /*
-     * reverse the range of the scores mapping the maximum to zero
-     */
-    result.reverseRange(true);
+    MatrixI distances = similarityToDistance(similarities);
 
-    return result;
+    return distances;
+  }
+
+  /**
+   * Converts a matrix of similarity scores to distance scores, by reversing the
+   * range of the scores, mapping the maximum to zero. The input matrix is not
+   * modified.
+   * 
+   * @param similarities
+   */
+  public static MatrixI similarityToDistance(MatrixI similarities)
+  {
+    MatrixI distances = similarities.copy();
+
+    distances.reverseRange(true);
+
+    return distances;
   }
 
 }