X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=e2c14e91e590cff8a69b98a08ff588702a228b31;hb=ae783be4cfa1df7fd59a4d0895df8bd1534d334c;hp=84e91aebc3c555aba5efc0dad30cb6533b4c9b27;hpb=2a9d6da50bb346c1f8cd38f104c958b7e8e6eff0;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 84e91ae..e2c14e9 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -38,6 +38,13 @@ public class ScoreMatrix implements SimilarityScoreModelI,
         PairwiseScoreModelI
 {
   /*
+   * an arbitrary score to assign for identity of an unknown symbol
+   * (this is the value on the diagonal in the * column of the NCBI matrix)
+   * (though a case could be made for using the minimum diagonal value)
+   */
+  private static final int UNKNOWN_IDENTITY_SCORE = 1;
+
+  /*
    * this fields records which gap character (if any) is used in the alphabet;
    * space, dash or dot are recognised as gap symbols
    */
@@ -289,8 +296,9 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   }
 
   /**
-   * Returns the pairwise score for substituting c with d, or zero if c or d is
-   * an unscored or unexpected character
+   * Returns the pairwise score for substituting c with d. If either c or d is
+   * an unexpected character, returns 1 for identity (c == d), else the minimum
+   * score value in the matrix.
    */
   @Override
   public float getPairwiseScore(char c, char d)
@@ -315,10 +323,11 @@ public class ScoreMatrix implements SimilarityScoreModelI,
 
     /*
      * one or both symbols not found in the matrix
-     * note: a possible strategy here would be to return the minimum
-     * matrix value if c != d
+     * currently scoring as 1 (for identity) or the minimum
+     * matrix score value (otherwise)
+     * (a case could be made for using minimum row/column value instead)
      */
-    return 0;
+    return c == d ? UNKNOWN_IDENTITY_SCORE : getMinimumScore();
   }
 
   /**