Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[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 e28cc7f..bc94619 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -20,16 +20,6 @@
  */
 package jalview.ext.ensembl;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-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;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -40,6 +30,14 @@ import java.util.Map;
 
 import org.json.simple.parser.ParseException;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.JSONUtils;
+
 /**
  * A client for fetching and processing Ensembl feature data in GFF format by
  * calling the overlap REST service
@@ -91,12 +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 });
 
   }
@@ -114,13 +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();
@@ -132,9 +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'
@@ -166,7 +164,7 @@ class EnsemblFeatures extends EnsemblRestClient
           sf.setValue("clinical_significance", clinSig);
 
           seq.addSequenceFeature(sf);
-          
+
         } catch (Throwable t)
         {
           // ignore - keep trying other features
@@ -174,7 +172,7 @@ class EnsemblFeatures extends EnsemblRestClient
       }
     } catch (ParseException | IOException e)
     {
-       e.printStackTrace();
+      e.printStackTrace();
       // ignore
     }
 
@@ -218,8 +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)