Jalview.isJS() --> Platform.isJS(), DBRefEntry[] --> List<DBRefEntry>

[jalview.git] / src / jalview / ext / ensembl / EnsemblFeatures.java

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index 6a0d67c..2772498 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -27,6 +27,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.JSONUtils;
+import jalview.util.Platform;
 
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -90,12 +91,14 @@ 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 new Alignment(new SequenceI[] { seq });
+
   }
 
   /**
@@ -119,7 +122,7 @@ private SequenceI parseFeaturesJson(List<String> queries)
       if (rvals == null)
          return null;
       while (rvals.hasNext())
-      {
+      {          
         try
         {
           Map<String, Object> obj = (Map<String, Object>) rvals.next();
@@ -147,7 +150,7 @@ private SequenceI parseFeaturesJson(List<String> queries)
           {
             type = SequenceOntologyI.CDS;
           }
-          
+
           String desc = getFirstNotNull(obj, "alleles", "external_name",
                   JSON_ID);
           SequenceFeature sf = new SequenceFeature(type, desc, start, end,
@@ -160,6 +163,7 @@ private SequenceI parseFeaturesJson(List<String> queries)
           sf.setValue("clinical_significance", clinSig);
 
           seq.addSequenceFeature(sf);
+          
         } catch (Throwable t)
         {
           // ignore - keep trying other features