From f2a83f0360d406859b80cc798099a9d270461bb3 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 5 Feb 2018 13:41:52 +0000
Subject: [PATCH] JAL-2788 possible adjustments to sequence accesses

---
 src/jalview/datamodel/Alignment.java |   44 ++++++++++++++++++++++++++++------
 1 file changed, 37 insertions(+), 7 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index baa8e83..c564618 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -49,7 +49,7 @@ public class Alignment implements AlignmentI
 {
   private Alignment dataset;
 
-  protected List<SequenceI> sequences;
+  private List<SequenceI> sequences;
 
   protected List<SequenceGroup> groups;
 
@@ -191,10 +191,12 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceI getSequenceAt(int i)
   {
-    // don't need to synchronise here as sequences is a synchronizedList
-    if (i > -1 && i < sequences.size())
+    synchronized (sequences)
     {
-      return sequences.get(i);
+      if (i > -1 && i < sequences.size())
+      {
+        return sequences.get(i);
+      }
     }
 
     return null;
@@ -705,7 +707,7 @@ public class Alignment implements AlignmentI
   public int getWidth()
   {
     int maxLength = -1;
-
+  
     for (int i = 0; i < sequences.size(); i++)
     {
       if (getSequenceAt(i).getLength() > maxLength)
@@ -713,9 +715,34 @@ public class Alignment implements AlignmentI
         maxLength = getSequenceAt(i).getLength();
       }
     }
-
+  
     return maxLength;
   }
+  /*
+  @Override
+  public int getWidth()
+  {
+    final Wrapper temp = new Wrapper();
+  
+    forEachSequence(new Consumer<SequenceI>()
+    {
+      @Override
+      public void accept(SequenceI s)
+      {
+        if (s.getLength() > temp.inner)
+        {
+          temp.inner = s.getLength();
+        }
+      }
+    }, 0, sequences.size() - 1);
+  
+    return temp.inner;
+  }
+  
+  public static class Wrapper
+  {
+    public int inner;
+  }*/
 
   /**
    * DOCUMENT ME!
@@ -1917,7 +1944,10 @@ public class Alignment implements AlignmentI
   @Override
   public void forEachSequence(Consumer<SequenceI> c, int start, int end)
   {
-    sequences.subList(start, end).forEach(c);
+    synchronized (sequences)
+    {
+      sequences.subList(start, end).forEach(c);
+    }
   }
 
 }
-- 
1.7.10.2