X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=63a14d71502b5099a23eec46b25648108c119237;hb=d131f05c68757d57e5e4a1f440196ae1b70f3b8a;hp=e7959250112bfdf572b42ed20dbf4aa1f3ed35c4;hpb=6dd554fdbf34db6b79595d5027159d20225f4894;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index e795925..63a14d7 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -29,7 +29,6 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignmentPanel;
 
 /**
  * Additional formatting methods used by the application in a number of places.
@@ -51,7 +50,7 @@ public class FormatAdapter extends AppletFormatAdapter
     init();
   }
 
-  public FormatAdapter(AlignmentPanel alignPanel,
+  public FormatAdapter(AlignmentViewPanel alignPanel,
           AlignExportSettingI settings)
   {
     super(alignPanel, settings);
@@ -109,11 +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)