Jalview-JS/JAL-3253-applet adds shell JalviewJSApi methods to Jalview

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

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index fb01708..bdaef0b 100644 (file)
--- 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);
   }
 }