X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=14096cfb72f2f3493af31d02eaaad928c765d47f;hb=8ff6ad0a4030c6e8d816cb086aababfce4eaeb17;hp=d1217bfa2d67c2303c777e532b642c360ea5cc65;hpb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index d1217bf..14096cf 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2434,11 +2434,11 @@ public class AlignmentUtils
     /*
      * variants in first codon base
      */
-    for (DnaVariant var : codonVariants[0])
+    for (DnaVariant dnavar : codonVariants[0])
     {
-      if (var.variant != null)
+      if (dnavar.variant != null)
       {
-        String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
+        String alleles = (String) dnavar.variant.getValue(Gff3Helper.ALLELES);
         if (alleles != null)
         {
           for (String base : alleles.split(","))
@@ -2449,7 +2449,7 @@ public class AlignmentUtils
                       + base3.toLowerCase();
               String canonical = base1.toUpperCase() + base2.toLowerCase()
                       + base3.toLowerCase();
-              if (addPeptideVariant(peptide, peptidePos, residue, var,
+              if (addPeptideVariant(peptide, peptidePos, residue, dnavar,
                       codon, canonical))
               {
                 count++;