X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=104480253703d868a8edffd30614fec6e7d2e519;hb=48e68905336d8ee17ee6b3903d80b36bac8c56cf;hp=00bb63ac01bb6d1dd5a791060384876065bd5301;hpb=beff7ac7ab7be2c24ccb179be16b8816d2c18610;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 00bb63a..1044802 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -20,6 +20,10 @@
  */
 package jalview.analysis;
 
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -31,12 +35,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
-import jalview.ws.SequenceFetcherFactory;
-import jalview.ws.seqfetcher.ASequenceFetcher;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
+import jalview.ws.SequenceFetcher;
 
 /**
  * Functions for cross-referencing sequence databases.
@@ -402,7 +401,6 @@ public class CrossRef
   private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
           List<DBRefEntry> xrfs, boolean fromDna, AlignedCodonFrame cf)
   {
-    ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
     SequenceI[] retrieved = null;
     SequenceI dss = seq.getDatasetSequence() == null ? seq
             : seq.getDatasetSequence();
@@ -418,7 +416,7 @@ public class CrossRef
     }
     try
     {
-      retrieved = sftch.getSequences(sourceRefs, !fromDna);
+      retrieved = SequenceFetcher.getInstance().getSequences(sourceRefs, !fromDna);
     } catch (Exception e)
     {
       System.err.println(
@@ -483,7 +481,7 @@ public class CrossRef
   private void removeAlreadyRetrievedSeqs(List<DBRefEntry> sourceRefs,
           boolean fromDna)
   {
-    List<DBRefEntry> dbrSourceSet = new ArrayList<DBRefEntry>(sourceRefs);
+    List<DBRefEntry> dbrSourceSet = new ArrayList<>(sourceRefs);
     List<SequenceI> dsSeqs = dataset.getSequences();
     for (int ids = 0, nds = dsSeqs.size(); ids < nds; ids++)
     {
@@ -929,7 +927,7 @@ public class CrossRef
 
     if (fromDna)
     {
-      AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
+      // AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
       mappings.addMap(mapFrom, mapTo, mapping);
     }
     else