From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 25 Oct 2017 14:37:53 +0000 (+0100)
Subject: JAL-2743 fall back to parsing description if chromosome lookup fails;
X-Git-Tag: Release_2_11_0~183
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=329b71c12ee91c57d83df128e6447d6ef0583b17;p=jalview.git

JAL-2743 fall back to parsing description if chromosome lookup fails;
code formatting
---

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 11322c8..cdcfa96 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -166,25 +166,25 @@ public class EnsemblGene extends EnsemblSeqProxy
 
   /**
    * Calls the /lookup/id REST service, parses the response for gene
-   * coordinates, and if successful, adds these to the sequence
+   * coordinates, and if successful, adds these to the sequence. If this fails,
+   * fall back on trying to parse the sequence description in case it is in
+   * Ensembl-gene format e.g. chromosome:GRCh38:17:45051610:45109016:1.
    * 
    * @param seq
    * @param geneId
    */
   void findGeneLoci(SequenceI seq, String geneId)
   {
-    /*
-     * if sequence description is in gene loci format, parse this
-     * - but try remote lookup anyway as 'better' if available
-     */
-    parseChromosomeLocations(seq);
-
     GeneLociI geneLoci = new EnsemblLookup(getDomain()).getGeneLoci(geneId);
     if (geneLoci != null)
     {
       seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
               geneLoci.getChromosomeId(), geneLoci.getMap());
     }
+    else
+    {
+      parseChromosomeLocations(seq);
+    }
   }
 
   /**
diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index af7bb0b..85bf7ef 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -895,8 +895,7 @@ public class VCFLoader
      */
     EnsemblMap mapper = new EnsemblMap();
     int[] mapping = mapper.getAssemblyMapping(species, chromosome, fromRef,
-            toRef,
-            queryRange);
+            toRef, queryRange);
 
     if (mapping == null)
     {