JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index c69858f..00bb63a 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -31,7 +31,8 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
-import jalview.ws.SequenceFetcher;
+import jalview.ws.SequenceFetcherFactory;
+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 = SequenceFetcherFactory.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(
@@ -482,7 +483,7 @@ public class CrossRef
   private void removeAlreadyRetrievedSeqs(List<DBRefEntry> sourceRefs,
           boolean fromDna)
   {
-    List<DBRefEntry> dbrSourceSet = new ArrayList<>(sourceRefs);
+    List<DBRefEntry> dbrSourceSet = new ArrayList<DBRefEntry>(sourceRefs);
     List<SequenceI> dsSeqs = dataset.getSequences();
     for (int ids = 0, nds = dsSeqs.size(); ids < nds; ids++)
     {