X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblFeatures.java;h=56498590928b507ac15f510d9b18fd68d875b4a6;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=e28cc7f0b4a4fdf9828ad89eaca14c35ed9e2d19;hpb=e7338a61f3ce96dadf44ac80b2b32cc5ba4b94c8;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index e28cc7f..5649859 100644
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -91,12 +91,12 @@ 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 });
 
   }
@@ -114,13 +114,14 @@ 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();
@@ -132,9 +133,8 @@ 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'
@@ -166,7 +166,7 @@ class EnsemblFeatures extends EnsemblRestClient
           sf.setValue("clinical_significance", clinSig);
 
           seq.addSequenceFeature(sf);
-          
+
         } catch (Throwable t)
         {
           // ignore - keep trying other features
@@ -174,7 +174,7 @@ class EnsemblFeatures extends EnsemblRestClient
       }
     } catch (ParseException | IOException e)
     {
-    	e.printStackTrace();
+      e.printStackTrace();
       // ignore
     }
 
@@ -218,8 +218,8 @@ 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)