JAL-1115 refactor base collection for Alignment from Vector to locally synchronized...

[jalview.git] / src / jalview / io / vamsas / Tree.java

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 5fdd0c9..ae53074 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -20,6 +20,7 @@ package jalview.io.vamsas;
 import java.io.IOException;
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 import jalview.analysis.NJTree;
@@ -264,10 +265,10 @@ public class Tree extends DatastoreItem
     SeqCigar[] tseqs = new SeqCigar[sequences.length];
     System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
     Vector alsq = new Vector();
-    Enumeration as = jal.getSequences().elements();
-    while (as.hasMoreElements())
+    List<SequenceI> jalsqs;
+    synchronized (jalsqs=jal.getSequences())
+    {for (SequenceI asq:jalsqs)
     {
-      SequenceI asq = (SequenceI) as.nextElement();
       for (int t = 0; t < sequences.length; t++)
       {
         if (tseqs[t] != null