JAL-2526 correct boundary conditions for sequence left/right of cursor

[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..dae1f62 100644 (file)
--- a/src/jalview/analysis/scoremodels/SimilarityScoreModel.java
+++ b/src/jalview/analysis/scoremodels/SimilarityScoreModel.java
@@ -17,14 +17,27 @@ 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;
   }
 
 }