JAL-3397 final update

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index c69858f..1ab8a24 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -37,6 +37,8 @@ import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 
+import intervalstore.api.IntervalI;
+
 /**
  * Functions for cross-referencing sequence databases.
  * 
@@ -637,12 +639,24 @@ 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 equals(Object o)
+                    public boolean equalsInterval(IntervalI sf)
                     {
-                      return super.equals(o, true);
+                      return sf != null
+                              && equals((SequenceFeature) sf, true);
                     }
                   };
+
                   matched.addSequenceFeature(newFeature);
                 }
               }