X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=079645fd3596fb69ba0fffc62cdf2c3640a9d398;hb=983d1a8699629252cde6bf5eb47f74064049884e;hp=f4a4f4da57663fb82ed5f019ade540b2c25ef856;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index f4a4f4d..079645f 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.RnaViewerModel;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -400,7 +401,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
 
   @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-          SelectionSource source)
+          HiddenColumns hidden, SelectionSource source)
   {
     if (source != ap.av)
     {
@@ -621,11 +622,10 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     ShiftList offset = new ShiftList();
     int ofstart = -1;
     int sleng = seq.getLength();
-    char[] seqChars = seq.getSequence();
 
     for (int i = 0; i < sleng; i++)
     {
-      if (Comparison.isGap(seqChars[i]))
+      if (Comparison.isGap(seq.getCharAt(i)))
       {
         if (ofstart == -1)
         {