X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;fp=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=0813ba88ba37041533070729ff491b1aa4d88016;hb=5e20c0116864d77705d951e35c41a13197791156;hp=9b56d6bfe91560cacb1cbb8e9997cfe8a79de196;hpb=1bad3c3f74b2e204e0d7ba93a745f5ec775c8a3e;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 9b56d6b..0813ba8 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -20,7 +20,7 @@
  */
 package jalview.ext.ensembl;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.GeneLociI;
 import jalview.datamodel.GeneLocus;
@@ -202,8 +202,8 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * Calls the /lookup/id rest service and returns the response as a Map<String, Object>,
-   * or null if any error
+   * Calls the /lookup/id rest service and returns the response as a Map<String,
+   * Object>, or null if any error
    * 
    * @param identifier
    * @param objectType
@@ -211,15 +211,16 @@ public class EnsemblLookup extends EnsemblRestClient
    * @return
    */
   @SuppressWarnings("unchecked")
-  protected Map<String, Object> getResult(String identifier, String objectType)
+  protected Map<String, Object> getResult(String identifier,
+          String objectType)
   {
     List<String> ids = Arrays.asList(new String[] { identifier });
 
     try
     {
-      return (Map<String, Object>) getJSON(getUrl(identifier, objectType), ids, -1, MODE_MAP, null);
-    } 
-    catch (IOException | ParseException e)
+      return (Map<String, Object>) getJSON(getUrl(identifier, objectType),
+              ids, -1, MODE_MAP, null);
+    } catch (IOException | ParseException e)
     {
       System.err.println("Error parsing " + identifier + " lookup response "
               + e.getMessage());
@@ -266,17 +267,19 @@ public class EnsemblLookup extends EnsemblRestClient
       boolean reverseStrand = "-1".equals(strand);
       int toStart = reverseStrand ? end : start;
       int toEnd = reverseStrand ? start : end;
-      List<int[]> fromRange = Collections.singletonList(new int[] { 1,
-          fromEnd });
-      List<int[]> toRange = Collections.singletonList(new int[] { toStart,
-          toEnd });
+      List<int[]> fromRange = Collections
+              .singletonList(new int[]
+              { 1, fromEnd });
+      List<int[]> toRange = Collections
+              .singletonList(new int[]
+              { toStart, toEnd });
       final Mapping map = new Mapping(
               new MapList(fromRange, toRange, 1, 1));
       return new GeneLocus(species == null ? "" : species, assembly,
               chromosome, map);
     } catch (NullPointerException | NumberFormatException e)
     {
-      Cache.log.error("Error looking up gene loci: " + e.getMessage());
+      Console.error("Error looking up gene loci: " + e.getMessage());
       e.printStackTrace();
     }
     return null;