From 86f6122c4537264ac1a6203aaf589f08d725e648 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 7 Aug 2016 16:13:43 +0100
Subject: [PATCH] JAL-2154 add in missing class for createDatasetAlignment(),
 and add support for recovering position for an object in
 the set.

---
 src/jalview/datamodel/Alignment.java        |    2 +-
 src/jalview/util/LinkedIdentityHashSet.java |  109 +++++++++++++++++++++++++++
 2 files changed, 110 insertions(+), 1 deletion(-)
 create mode 100644 src/jalview/util/LinkedIdentityHashSet.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index e9c0b4c..dcfbaad 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1095,7 +1095,7 @@ public class Alignment implements AlignmentI
     {
       return;
     }
-    // try to avoid using equals at this stage, it will be expensive
+    // try to avoid using SequenceI.equals at this stage, it will be expensive
     Set<SequenceI> seqs = new jalview.util.LinkedIdentityHashSet<SequenceI>();
 
     for (int i = 0; i < getHeight(); i++)
diff --git a/src/jalview/util/LinkedIdentityHashSet.java b/src/jalview/util/LinkedIdentityHashSet.java
new file mode 100644
index 0000000..5cdbeb1
--- /dev/null
+++ b/src/jalview/util/LinkedIdentityHashSet.java
@@ -0,0 +1,109 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import java.util.AbstractSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+
+/**
+ * Order preserving Set based on System.identityHashCode() for an object, which
+ * also supports Object->index lookup.
+ * 
+ * @author Jim Procter (2016) based on Evgeniy Dorofeev's response: via
+ *         https://stackoverflow.com/questions/17276658/linkedidentityhashset
+ * 
+ */
+public class LinkedIdentityHashSet<E> extends AbstractSet<E>
+{
+  LinkedHashMap<IdentityWrapper, IdentityWrapper> set = new LinkedHashMap<IdentityWrapper, IdentityWrapper>();
+
+  static class IdentityWrapper
+  {
+    Object obj;
+
+    public int p;
+
+    IdentityWrapper(Object obj, int p)
+    {
+      this.obj = obj;
+      this.p = p;
+    }
+
+    @Override
+    public boolean equals(Object obj)
+    {
+      return this.obj == obj;
+    }
+
+    @Override
+    public int hashCode()
+    {
+      return System.identityHashCode(obj);
+    }
+  }
+
+  @Override
+  public boolean add(E e)
+  {
+    IdentityWrapper el = (new IdentityWrapper(e, set.size()));
+    return set.putIfAbsent(el, el) == null;
+  }
+
+  @Override
+  public Iterator<E> iterator()
+  {
+    return new Iterator<E>()
+    {
+      final Iterator<IdentityWrapper> se = set.keySet().iterator();
+
+      @Override
+      public boolean hasNext()
+      {
+        return se.hasNext();
+      }
+
+      @SuppressWarnings("unchecked")
+      @Override
+      public E next()
+      {
+        return (E) se.next().obj;
+      }
+    };
+  }
+
+  @Override
+  public int size()
+  {
+    return set.size();
+  }
+
+  /**
+   * Lookup the index for e in the set
+   * 
+   * @param e
+   * @return position of e in the set when it was added.
+   */
+  public int indexOf(E e)
+  {
+    return set.get(e).p;
+  }
+}
-- 
1.7.10.2