JAL-2416 better encapsulated 'constants' for BLOSUM62, PAM250

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 61ff012..ed4e3bc 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -118,8 +118,7 @@ public class AlignSeq
 
   int gapExtend = 20;
 
-  float[][] lookup = ((ScoreMatrix) ScoreModels.getInstance().forName(
-          ScoreModels.BLOSUM62)).getMatrix();
+  float[][] lookup = ScoreModels.getInstance().getBlosum62().getMatrix();
 
   // ResidueProperties.getBLOSUM62();
 
@@ -604,8 +603,7 @@ public class AlignSeq
             .append(String.valueOf(s2str.length())).append(")")
             .append(NEWLINE).append(NEWLINE);
 
-    PairwiseSeqScoreModel pam250 = (PairwiseSeqScoreModel) ScoreModels
-            .getInstance().forName(ScoreModels.PAM250);
+    PairwiseSeqScoreModel pam250 = ScoreModels.getInstance().getPam250();
 
     for (int j = 0; j < nochunks; j++)
     {