3253-omnibus save

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index ecdd11e..61add1e 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -32,6 +32,7 @@ import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.ws.SequenceFetcher;
+import jalview.ws.seqfetcher.ASequenceFetcher;
 
 import java.util.ArrayList;
 import java.util.Iterator;
@@ -401,6 +402,7 @@ public class CrossRef
   private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
           List<DBRefEntry> xrfs, boolean fromDna, AlignedCodonFrame cf)
   {
+    ASequenceFetcher sftch = SequenceFetcher.getInstance();// Factory.getSequenceFetcher();
     SequenceI[] retrieved = null;
     SequenceI dss = seq.getDatasetSequence() == null ? seq
             : seq.getDatasetSequence();
@@ -416,8 +418,7 @@ public class CrossRef
     }
     try
     {
-      retrieved = SequenceFetcher.getInstance()
-              .getSequences(sourceRefs, !fromDna);
+      retrieved = sftch.getSequences(sourceRefs, !fromDna);
     } catch (Exception e)
     {
       System.err.println(
@@ -640,7 +641,7 @@ public class CrossRef
                     @Override
                     public boolean equals(Object o)
                     {
-                      return equals((SequenceFeature) o, true);
+                      return super.equals(o, true);
                     }
                   };
                   matched.addSequenceFeature(newFeature);
@@ -928,7 +929,7 @@ public class CrossRef
 
     if (fromDna)
     {
-      AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
+      // AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
       mappings.addMap(mapFrom, mapTo, mapping);
     }
     else