X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=bdaef0b23a9fb6b77d72eb4d4a82b94314d3a9ca;hb=be94287924736b46264674a189fd1719d38273ad;hp=fb017087fba3f049241eef851dd05fb040016638;hpb=9e5d1bced16aa9975692115a964c661cd7897a7c;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index fb01708..bdaef0b 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -423,7 +423,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     List<SequenceI> seqs = parseSequenceJson(ids);
     if (seqs == null)
-    	return alignment;
+    {
+      return alignment;
+    }
 
     if (seqs.isEmpty())
     {
@@ -490,7 +492,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     	Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK);
       Map<String, Object> val = (Map<String, Object>) getJSON(null, ids, -1, MODE_MAP, null);
       if (val == null)
-    	  return null;
+      {
+        return null;
+      }
       Object s = val.get("desc");
       String desc = s == null ? null : s.toString();
       s = val.get("id");
@@ -736,7 +740,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
        * for sequence_variant on reverse strand, have to convert the allele
        * values to their complements
        */
-      if (!forwardStrand && SequenceOntologyFactory.getInstance()
+      if (!forwardStrand && SequenceOntologyFactory.getSequenceOntology()
               .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
       {
         reverseComplementAlleles(copy);
@@ -879,10 +883,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     for (int i = 0, n = sfs.size(); i < n; i++)
     {
 
-    	if ((i%1000) == 0) {
-//    	    Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET);
-	Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n, Platform.TIME_MARK);	  
-    	}
+//    	if ((i%1000) == 0) {
+////    	    Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET);
+//	Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n, Platform.TIME_MARK);	  
+//    	}
 
       SequenceFeature sf = sfs.get(i);
       if (retainFeature(sf, parentId))
@@ -984,7 +988,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   public static boolean isTranscript(String featureType)
   {
     return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
-            || SequenceOntologyFactory.getInstance().isA(featureType,
+            || SequenceOntologyFactory.getSequenceOntology().isA(featureType,
                     SequenceOntologyI.TRANSCRIPT);
   }
 }