JAL-3253-applet JAL-3397 JAL-3383 fast IntervalStore for JavaScript

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index c69858f..dbad53e 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 +639,23 @@ 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 equals((SequenceFeature) sf, true);
                     }
                   };
+
                   matched.addSequenceFeature(newFeature);
                 }
               }