X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;fp=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=9c7ce638fdf95fca1caca1a5347c0d27115dbb55;hb=6a05eb3f55d97e685f0c723822384633d5636778;hp=7648536487ea8ceb99a6fdf1f1044b3b80b78600;hpb=d113749a183a3ea8f3f7e22c725511f59f1d833f;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 7648536..9c7ce63 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -23,7 +23,6 @@ package jalview.ext.ensembl;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLociI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -62,6 +61,8 @@ public class EnsemblGene extends EnsemblSeqProxy
       EnsemblFeatureType.exon, EnsemblFeatureType.cds,
       EnsemblFeatureType.variation };
 
+  private static final String CHROMOSOME = "chromosome";
+
   /**
    * Default constructor (to use rest.ensembl.org)
    */
@@ -187,7 +188,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     if (geneLoci != null)
     {
       seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
-              geneLoci.getChromosomeId(), geneLoci.getMap());
+              geneLoci.getChromosomeId(), geneLoci.getMapping());
     }
     else
     {
@@ -209,7 +210,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       return false;
     }
     String[] tokens = description.split(":");
-    if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME))
+    if (tokens.length == 6 && tokens[0].startsWith(CHROMOSOME))
     {
       String ref = tokens[1];
       String chrom = tokens[2];
@@ -460,7 +461,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       return;
     }
 
-    MapList geneMapping = loci.getMap();
+    MapList geneMapping = loci.getMapping();
 
     List<int[]> exons = mapping.getFromRanges();
     List<int[]> transcriptLoci = new ArrayList<>();