Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

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

diff --git a/src/jalview/analysis/scoremodels/SimilarityScoreModel.java b/src/jalview/analysis/scoremodels/SimilarityScoreModel.java
new file mode 100644 (file)
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+++ b/src/jalview/analysis/scoremodels/SimilarityScoreModel.java
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+package jalview.analysis.scoremodels;
+
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.datamodel.AlignmentView;
+import jalview.math.MatrixI;
+
+public abstract class SimilarityScoreModel implements ScoreModelI
+{
+
+  /**
+   * Computed similarity scores are converted to distance scores by subtracting
+   * every value from the maximum value. That is, maximum similarity corresponds
+   * to zero distance, and smaller similarities to larger distances.
+   */
+  @Override
+  public MatrixI findDistances(AlignmentView seqData,
+          SimilarityParamsI options)
+  {
+    MatrixI similarities = findSimilarities(seqData, options);
+
+    MatrixI distances = similarityToDistance(similarities);
+
+    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;
+  }
+
+}