X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;fp=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=300c950bdb28e09c2a504545e51a6ecc04693724;hb=2f87d72ea4f1bbf768918a253be05771f9c430cb;hp=93ad332d24f13d9babd3c7d253a151c745d971d1;hpb=17d607a60a36a0711021bec7492266cd57cf02a7;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 93ad332..300c950 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -195,6 +195,7 @@ public class Alignment implements AlignmentI
   {
     synchronized (sequences)
     {
+    
       if (i > -1 && i < sequences.size())
       {
         return sequences.get(i);
@@ -589,11 +590,12 @@ public class Alignment implements AlignmentI
     int i = 0;
     SequenceI sq = null;
     String sqname = null;
+    int nseq = sequences.size();
     if (startAfter != null)
     {
       // try to find the sequence in the alignment
       boolean matched = false;
-      while (i < sequences.size())
+      while (i < nseq)
       {
         if (getSequenceAt(i++) == startAfter)
         {
@@ -606,7 +608,7 @@ public class Alignment implements AlignmentI
         i = 0;
       }
     }
-    while (i < sequences.size())
+    while (i < nseq)
     {
       sq = getSequenceAt(i);
       sqname = sq.getName();