From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 29 Mar 2017 08:20:13 +0000 (+0100)
Subject: JAL-2416 explicit constant for unknown/unknown identity score (*
X-Git-Tag: Release_2_10_2~3^2~105^2~2^2~35
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ae783be4cfa1df7fd59a4d0895df8bd1534d334c;p=jalview.git

JAL-2416 explicit constant for unknown/unknown identity score (*
diagonal), comments
---

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 7e07b9f..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
    */
@@ -316,8 +323,11 @@ public class ScoreMatrix implements SimilarityScoreModelI,
 
     /*
      * one or both symbols not found in the matrix
+     * 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 c == d ? 1 : getMinimumScore();
+    return c == d ? UNKNOWN_IDENTITY_SCORE : getMinimumScore();
   }
 
   /**