JAL-1486 fixed flatfile output of visible region for consensus sequence

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index e795925..63a14d7 100755 (executable)
--- 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)