X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;fp=src%2Fjalview%2Fio%2FFormatAdapter.java;h=63a14d71502b5099a23eec46b25648108c119237;hb=f06554784411ddbf871d642e66c8dcb7f147d4a8;hp=8a563faa80df880eeaed89d9f078a258a3df7be3;hpb=cf06ee5d732af6cc874115aece1138adafca8ad7;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 8a563fa..63a14d7 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -108,11 +108,11 @@ public class FormatAdapter extends AppletFormatAdapter
         startRes = seqs[i].getStart();
         endRes = seqs[i].getEnd();
 
-        startIndex = startEnd[0];
-        endIndex = startEnd[1];
 
         if (startEnd != null)
         {
+          startIndex = startEnd[0];
+          endIndex = startEnd[1];
           // get first non-gaped residue start position
           while (jalview.util.Comparison.isGap(seqs[i]
                   .getCharAt(startIndex)) && startIndex < endIndex)