JAL-2738 one constant in codebase for "alleles" attribute of

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 41fe77e..6acac01 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -36,6 +36,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.SequenceFeatures;
+import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
@@ -2374,7 +2375,7 @@ public class AlignmentUtils
     {
       if (var.variant != null)
       {
-        String alleles = (String) var.variant.getValue("alleles");
+        String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
         if (alleles != null)
         {
           for (String base : alleles.split(","))
@@ -2396,7 +2397,7 @@ public class AlignmentUtils
     {
       if (var.variant != null)
       {
-        String alleles = (String) var.variant.getValue("alleles");
+        String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
         if (alleles != null)
         {
           for (String base : alleles.split(","))
@@ -2418,7 +2419,7 @@ public class AlignmentUtils
     {
       if (var.variant != null)
       {
-        String alleles = (String) var.variant.getValue("alleles");
+        String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
         if (alleles != null)
         {
           for (String base : alleles.split(","))
@@ -2555,7 +2556,7 @@ public class AlignmentUtils
       /*
        * extract dna variants to a string array
        */
-      String alls = (String) sf.getValue("alleles");
+      String alls = (String) sf.getValue(Gff3Helper.ALLELES);
       if (alls == null)
       {
         continue; // non-SNP VCF variant perhaps - can't process this