X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;fp=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=c4098e26594753f3caa175ca4ae6922e41e0856f;hb=65740880573a48adc758bec3939ece9d9ae104dd;hp=3b0ca46f83e01ac83aae1e3c7116fc5b1a09f71a;hpb=71aa78b8a7d54e5aeb6b278310dfd735efb77477;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3b0ca46..c4098e2 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -195,6 +195,7 @@ public class Alignment implements AlignmentI, AutoCloseable
   {
     synchronized (sequences)
     {
+    
       if (i > -1 && i < sequences.size())
       {
         return sequences.get(i);
@@ -594,11 +595,12 @@ public class Alignment implements AlignmentI, AutoCloseable
     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)
         {
@@ -611,7 +613,7 @@ public class Alignment implements AlignmentI, AutoCloseable
         i = 0;
       }
     }
-    while (i < sequences.size())
+    while (i < nseq)
     {
       sq = getSequenceAt(i);
       sqname = sq.getName();
@@ -1193,7 +1195,8 @@ public class Alignment implements AlignmentI, AutoCloseable
     int maxLength = -1;
 
     SequenceI current;
-    for (int i = 0; i < sequences.size(); i++)
+    int nseq = sequences.size();
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       for (int j = current.getLength(); j > maxLength; j--)
@@ -1210,7 +1213,7 @@ public class Alignment implements AlignmentI, AutoCloseable
     maxLength++;
 
     int cLength;
-    for (int i = 0; i < sequences.size(); i++)
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       cLength = current.getLength();