JAL-2418 add GPL to main sources

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

diff --git a/src/jalview/analysis/scoremodels/DistanceScoreModel.java b/src/jalview/analysis/scoremodels/DistanceScoreModel.java
index 14c9667..3521757 100644 (file)
--- a/src/jalview/analysis/scoremodels/DistanceScoreModel.java
+++ b/src/jalview/analysis/scoremodels/DistanceScoreModel.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;
@@ -15,14 +35,26 @@ public abstract class DistanceScoreModel implements ScoreModelI
   public MatrixI findSimilarities(AlignmentView seqData,
           SimilarityParamsI options)
   {
-    MatrixI result = findDistances(seqData, options);
+    MatrixI distances = findDistances(seqData, options);
 
-    /*
-     * reverse the range of score values so that 
-     * max becomes min and vice versa
-     */
-    result.reverseRange(false);
+    MatrixI similarities = distanceToSimilarity(distances);
 
-    return result;
+    return similarities;
+  }
+
+  /**
+   * Converts distance scores to similarity scores, by reversing the range of
+   * score values so that max becomes min and vice versa. The input matrix is
+   * not modified.
+   * 
+   * @param distances
+   */
+  public static MatrixI distanceToSimilarity(MatrixI distances)
+  {
+    MatrixI similarities = distances.copy();
+
+    similarities.reverseRange(false);
+
+    return similarities;
   }
 }