From: hansonr <hansonr@stolaf.edu>
Date: Wed, 20 Jun 2018 23:38:30 +0000 (+0100)
Subject: JAL-3032 for (var var
X-Git-Tag: Release_2_11_4_0~45^2~18^2~673
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=10175089b98fdbbf2407b7787174e86a003b13b1;p=jalview.git

JAL-3032 for (var var
---

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++;