From bda14302200fc3bcfe66dc513bd030cba10a3681 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Fri, 2 Jun 2017 14:10:57 +0100
Subject: [PATCH 1/1] JAL-2576 Proposed fix

---
 src/jalview/datamodel/Alignment.java        |    9 +++------
 src/jalview/util/LinkedIdentityHashSet.java |    4 ++--
 2 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 5d91b36..f5e6fc7 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1067,21 +1067,18 @@ public class Alignment implements AlignmentI
         currentSeq = currentSeq.createDatasetSequence();
       }
     }
-    if (seqs.contains(currentSeq))
-    {
-      return;
-    }
+
     List<SequenceI> toProcess = new ArrayList<>();
     toProcess.add(currentSeq);
     while (toProcess.size() > 0)
     {
       // use a queue ?
       SequenceI curDs = toProcess.remove(0);
-      if (seqs.contains(curDs))
+
+      if (!seqs.add(curDs))
       {
         continue;
       }
-      seqs.add(curDs);
       // iterate over database references, making sure we add forward referenced
       // sequences
       if (curDs.getDBRefs() != null)
diff --git a/src/jalview/util/LinkedIdentityHashSet.java b/src/jalview/util/LinkedIdentityHashSet.java
index bce540f..7f109ec 100644
--- a/src/jalview/util/LinkedIdentityHashSet.java
+++ b/src/jalview/util/LinkedIdentityHashSet.java
@@ -34,7 +34,7 @@ import java.util.LinkedHashMap;
  */
 public class LinkedIdentityHashSet<E> extends AbstractSet<E>
 {
-  LinkedHashMap<IdentityWrapper, IdentityWrapper> set = new LinkedHashMap<IdentityWrapper, IdentityWrapper>();
+  LinkedHashMap<IdentityWrapper, IdentityWrapper> set = new LinkedHashMap<>();
 
   static class IdentityWrapper
   {
@@ -51,7 +51,7 @@ public class LinkedIdentityHashSet<E> extends AbstractSet<E>
     @Override
     public boolean equals(Object obj)
     {
-      return this.obj == obj;
+      return this.obj == ((IdentityWrapper) obj).obj;
     }
 
     @Override
-- 
1.7.10.2