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 dbad53e..00bb63a 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -31,14 +31,13 @@ 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;
 import java.util.List;
 
-import intervalstore.api.IntervalI;
-
 /**
  * Functions for cross-referencing sequence databases.
  * 
@@ -403,6 +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();
@@ -418,8 +418,7 @@ public class CrossRef
     }
     try
     {
-      retrieved = SequenceFetcher.getInstance()
-              .getSequences(sourceRefs, !fromDna);
+      retrieved = sftch.getSequences(sourceRefs, !fromDna);
     } catch (Exception e)
     {
       System.err.println(
@@ -484,7 +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++)
     {
@@ -639,23 +638,12 @@ public class CrossRef
                    */
                   SequenceFeature newFeature = new SequenceFeature(feat)
                   {
-                    // BH 2019.08.15 We must override equalsInterval, not
-                    // equals, because that is part of the IntervalI interface,
-                    // and IntervalStore may need that for proper, faster
-                    // processing.
-                    // @Override
-                    // public boolean equals(Object o)
-                    // {
-                    // return super.equals(o, true);
-                    // }
-                    //
                     @Override
-                    public boolean equalsInterval(IntervalI sf)
+                    public boolean equals(Object o)
                     {
-                      return equals((SequenceFeature) sf, true);
+                      return super.equals(o, true);
                     }
                   };
-
                   matched.addSequenceFeature(newFeature);
                 }
               }