Merge branch 'develop' into features/JAL-1793VCF

[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.java

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index b2ebb1a..9229379 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -34,6 +34,7 @@ import jalview.datamodel.features.SequenceFeatures;
 import jalview.exceptions.JalviewException;
 import jalview.io.FastaFile;
 import jalview.io.FileParse;
+import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.Comparison;
@@ -57,8 +58,6 @@ import java.util.List;
  */
 public abstract class EnsemblSeqProxy extends EnsemblRestClient
 {
-  private static final String ALLELES = "alleles";
-
   protected static final String NAME = "Name";
 
   protected static final String DESCRIPTION = "description";
@@ -708,7 +707,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
    */
   static void reverseComplementAlleles(SequenceFeature sf)
   {
-    final String alleles = (String) sf.getValue(ALLELES);
+    final String alleles = (String) sf.getValue(Gff3Helper.ALLELES);
     if (alleles == null)
     {
       return;
@@ -719,7 +718,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       reverseComplementAllele(complement, allele);
     }
     String comp = complement.toString();
-    sf.setValue(ALLELES, comp);
+    sf.setValue(Gff3Helper.ALLELES, comp);
     sf.setDescription(comp);
 
     /*
@@ -729,7 +728,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     String atts = sf.getAttributes();
     if (atts != null)
     {
-      atts = atts.replace(ALLELES + "=" + alleles, ALLELES + "=" + comp);
+      atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
+              Gff3Helper.ALLELES + "=" + comp);
       sf.setAttributes(atts);
     }
   }