merge from develop

[jalview.git] / src / jalview / io / FormatAdapter.java

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 8a563fa..63a14d7 100755 (executable)
--- 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)