From 10175089b98fdbbf2407b7787174e86a003b13b1 Mon Sep 17 00:00:00 2001 From: hansonr Date: Thu, 21 Jun 2018 00:38:30 +0100 Subject: [PATCH] JAL-3032 for (var var --- src/jalview/analysis/AlignmentUtils.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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++; -- 1.7.10.2