Merge branch 'develop' into features/JAL-2094_colourInterface

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

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index b320e83..6f3c062 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -119,7 +119,10 @@ public class EnsemblGene extends EnsemblSeqProxy
        * fetch the gene sequence(s) with features and xrefs
        */
       AlignmentI geneAlignment = super.getSequenceRecords(geneId);
-
+      if (geneAlignment == null)
+      {
+        continue;
+      }
       if (geneAlignment.getHeight() == 1)
       {
         getTranscripts(geneAlignment, geneId);
@@ -175,7 +178,8 @@ public class EnsemblGene extends EnsemblSeqProxy
        */
       else
       {
-        List<String> ids = new EnsemblSymbol(getDomain()).getIds(acc);
+        List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
+                getDbVersion()).getIds(acc);
         for (String geneId : ids)
         {
           if (!geneIds.contains(geneId))
@@ -197,7 +201,8 @@ public class EnsemblGene extends EnsemblSeqProxy
    */
   protected String getGeneIdentifiersForName(String query)
   {
-    List<String> ids = new EnsemblSymbol(getDomain()).getIds(query);
+    List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
+            getDbVersion()).getIds(query);
     if (ids != null)
     {
       for (String id : ids)