X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblFeatures.java;h=cb6f54896d66a85e01819df5ba48e402e530b2de;hb=10dd3a771da0085ead2318b7385211c7b675d7f4;hp=b28a37f636c7b8836d63da4163d5788aa70d7f5e;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index b28a37f..cb6f548 100644
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -82,9 +82,13 @@ class EnsemblFeatures extends EnsemblRestClient
   public AlignmentI getSequenceRecords(String query) throws IOException
   {
     // TODO: use a vararg String... for getSequenceRecords instead?
-    List<String> queries = new ArrayList<String>();
+    List<String> queries = new ArrayList<>();
     queries.add(query);
     FileParse fp = getSequenceReader(queries);
+    if (fp == null || !fp.isValid())
+    {
+      return null;
+    }
     FeaturesFile fr = new FeaturesFile(fp);
     return new Alignment(fr.getSeqsAsArray());
   }
@@ -105,9 +109,17 @@ class EnsemblFeatures extends EnsemblRestClient
     urlstring.append("?content-type=text/x-gff3");
 
     /*
+     * specify object_type=gene in case is shared by transcript and/or protein;
+     * currently only fetching features for gene sequences;
+     * refactor in future if needed to fetch for transcripts
+     */
+    urlstring.append("&").append(OBJECT_TYPE).append("=")
+            .append(OBJECT_TYPE_GENE);
+
+    /*
      * specify  features to retrieve
      * @see http://rest.ensembl.org/documentation/info/overlap_id
-     * could make the list a configurable entry in jalview.properties
+     * could make the list a configurable entry in .jalview_properties
      */
     for (EnsemblFeatureType feature : featuresWanted)
     {