From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 12 Apr 2017 13:41:45 +0000 (+0100)
Subject: JAL-2403 public static methods to convert distance/similarity matrices
X-Git-Tag: Release_2_10_2~3^2~105^2~2^2~21
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a581eb571426fb19c6b3421eebaedd90c63bb630;p=jalview.git

JAL-2403 public static methods to convert distance/similarity matrices
---

diff --git a/src/jalview/analysis/scoremodels/DistanceScoreModel.java b/src/jalview/analysis/scoremodels/DistanceScoreModel.java
index 14c9667..0dd7617 100644
--- a/src/jalview/analysis/scoremodels/DistanceScoreModel.java
+++ b/src/jalview/analysis/scoremodels/DistanceScoreModel.java
@@ -15,14 +15,26 @@ 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;
   }
 }
diff --git a/src/jalview/analysis/scoremodels/SimilarityScoreModel.java b/src/jalview/analysis/scoremodels/SimilarityScoreModel.java
index d41e0ba..dae1f62 100644
--- 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;
   }
 
 }