X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblFeatures.java;h=bc94619b55a00b89b3d7348c4e2f3e37fb4e5075;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=ab358295f800f3a1efef8ad06ec7c4e6c5393b8c;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index ab35829..bc94619 100644
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -89,12 +89,12 @@ class EnsemblFeatures extends EnsemblRestClient
   public AlignmentI getSequenceRecords(String query) throws IOException
   {
     // TODO: use a vararg String... for getSequenceRecords instead?
-	  
+
     List<String> queries = new ArrayList<>();
     queries.add(query);
     SequenceI seq = parseFeaturesJson(queries);
     if (seq == null)
-    	return null;
+      return null;
     return new Alignment(new SequenceI[] { seq });
 
   }
@@ -112,13 +112,14 @@ class EnsemblFeatures extends EnsemblRestClient
     SequenceI seq = new Sequence("Dummy", "");
     try
     {
-      Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1, MODE_ITERATOR, null);
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1,
+              MODE_ITERATOR, null);
       if (rvals == null)
       {
-    	  return null;
+        return null;
       }
       while (rvals.hasNext())
-      {    	  
+      {
         try
         {
           Map<String, Object> obj = (Map<String, Object>) rvals.next();
@@ -130,9 +131,8 @@ class EnsemblFeatures extends EnsemblRestClient
           Object phase = obj.get("phase");
           String alleles = JSONUtils
                   .arrayToStringList((List<Object>) obj.get("alleles"));
-          String clinSig = JSONUtils
-                  .arrayToStringList(
-                          (List<Object>) obj.get("clinical_significance"));
+          String clinSig = JSONUtils.arrayToStringList(
+                  (List<Object>) obj.get("clinical_significance"));
 
           /*
            * convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
@@ -164,7 +164,7 @@ class EnsemblFeatures extends EnsemblRestClient
           sf.setValue("clinical_significance", clinSig);
 
           seq.addSequenceFeature(sf);
-          
+
         } catch (Throwable t)
         {
           // ignore - keep trying other features
@@ -172,7 +172,7 @@ class EnsemblFeatures extends EnsemblRestClient
       }
     } catch (ParseException | IOException e)
     {
-    	e.printStackTrace();
+      e.printStackTrace();
       // ignore
     }
 
@@ -216,8 +216,8 @@ class EnsemblFeatures extends EnsemblRestClient
    * @param obj
    * @param key
    */
-  protected void setFeatureAttribute(SequenceFeature sf, Map<String, Object> obj,
-          String key)
+  protected void setFeatureAttribute(SequenceFeature sf,
+          Map<String, Object> obj, String key)
   {
     Object object = obj.get(key);
     if (object != null)