X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=d82f54c68dad59cfac976a86ec2c9f6ed2e1eb1b;hb=7d123b6259738869c16529b8c28cfd8931da4205;hp=b5e3ef1a28d4bb412f56579fe5d80d7c6a87f805;hpb=53efd00e5fe4b886ede8ec0a6eaa36bc7c8a781e;p=jalview.git

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index b5e3ef1..d82f54c 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -93,7 +93,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel
   @Override
   public int getPairwiseScore(char c, char d)
   {
-    int pog = 0;
+    int score = 0;
 
     try
     {
@@ -101,45 +101,13 @@ public class ScoreMatrix extends PairwiseSeqScoreModel
               : ResidueProperties.nucleotideIndex[c];
       int b = (type == 0) ? ResidueProperties.aaIndex[d]
               : ResidueProperties.nucleotideIndex[d];
-
-      /*
-       * FIXME: 2.10.1 PCA treats gap as [22] or 'X', but Tree
-       * calculation treats as [23]; which is correct?
-       */
-      /*
-       * hack to convert unassigned / unknown (including gap)
-       * to index of unknown (X for amino acids, N for nucleotide)
-       * TODO: statically assign gap characters to this index?
-       */
-//      if (type == 0)
-//      {
-//        if (a == ResidueProperties.maxProteinIndex)
-//        {
-//          a = ResidueProperties.aaIndex['X'];
-//        }
-//        if (b == ResidueProperties.maxProteinIndex)
-//        {
-//          b = ResidueProperties.aaIndex['X'];
-//        }
-//      }
-//      if (type != 0)
-//      {
-//        if (a == ResidueProperties.maxNucleotideIndex)
-//        {
-//          a = ResidueProperties.nucleotideIndex['N'];
-//        }
-//        if (b == ResidueProperties.maxNucleotideIndex)
-//        {
-//          b = ResidueProperties.nucleotideIndex['N'];
-//        }
-//      }
-      pog = matrix[a][b];
+      score = matrix[a][b];
     } catch (Exception e)
     {
       // System.out.println("Unknown residue in " + A1 + " " + A2);
     }
 
-    return pog;
+    return score;
   }
 
   /**