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JalviewJS pre-configured entry point for demos
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
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
*/
/*
* 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(","))
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();
+ 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++;
codon, canonical))
{
count++;