From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 11 Apr 2016 15:37:04 +0000 (+0100)
Subject: JAL-2051 fetch Ensembl Gene accessions one at a time
X-Git-Tag: Release_2_10_0~263^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=70ad0f1ae40759c435ead9d732983aeb091dfd0e;p=jalview.git

JAL-2051 fetch Ensembl Gene accessions one at a time
---

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 0bc6a74..84b5dcf 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -101,23 +101,18 @@ public class EnsemblGene extends EnsemblSeqProxy
    * </ul>
    * 
    * @param query
-   *          one or more identifiers separated by a space
-   * @return an alignment containing one or more genes, and possibly
-   *         transcripts, or null
+   *          a single gene or transcript identifier or gene name
+   * @return an alignment containing a gene, and possibly transcripts, or null
    */
   @Override
   public AlignmentI getSequenceRecords(String query) throws Exception
   {
-    // todo: tidy up handling of one or multiple accession ids
-    String[] queries = query.split(getAccessionSeparator());
-
     /*
      * if given a transcript id, look up its gene parent
      */
     if (isTranscriptIdentifier(query))
     {
-      // we are assuming all transcripts have the same gene parent here
-      query = new EnsemblLookup(getDomain()).getParent(queries[0]);
+      query = new EnsemblLookup(getDomain()).getParent(query);
       if (query == null)
       {
         return null;
@@ -556,4 +551,10 @@ public class EnsemblGene extends EnsemblSeqProxy
     };
   }
 
+  @Override
+  public int getMaximumQueryCount()
+  {
+    return 1;
+  }
+
 }
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index b6ee041..a5f218e 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -554,7 +554,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                             proxy.getDbName() }), Thread.currentThread()
                         .hashCode());
         isAliSource = proxy.isAlignmentSource();
-        if (proxy.getAccessionSeparator() == null)
+        if (proxy.getMaximumQueryCount() == 1)
         {
           while (en.hasNext())
           {