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JAL-2416 score matrix gap symbol (if any) dynamically determined
[jalview.git] / src / jalview / analysis / AlignSeq.java
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 1a6826d..d04e897 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -352,7 +352,7 @@ public class AlignSeq
     scoreModel = ScoreModels.getInstance().getDefaultModel(
             PEP.equals(type));
     lookup = scoreModel.getMatrix();
-    gapIndex = scoreModel.getMatrixIndex(' ');
+    gapIndex = scoreModel.getGapIndex();
   }
 
   /**