From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Tue, 29 Jan 2019 03:03:15 +0000 (-0600)
Subject: iterators
X-Git-Tag: Release_2_11_4_0~45^2~18^2~278
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2f87d72ea4f1bbf768918a253be05771f9c430cb;p=jalview.git

iterators
---

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();