JAL-3032 for (var var

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index d1217bf..14096cf 100644 (file)
--- 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++;