Merge branch 'feature/JAL-3187linkedFeatures' into

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 7a082be..0d2e002 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2425,7 +2425,8 @@ public class AlignmentUtils
   static int computePeptideVariants(SequenceI peptide, int peptidePos,
           List<DnaVariant>[] codonVariants)
   {
-    String residue = String.valueOf(peptide.getCharAt(peptidePos - 1));
+    String residue = String
+            .valueOf(peptide.getCharAt(peptidePos - peptide.getStart()));
     int count = 0;
     String base1 = codonVariants[0].get(0).base;
     String base2 = codonVariants[1].get(0).base;