X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=8ca1a4e844079893d1fd469f2e5a540fff3df7cf;hb=42498abb930c08393b09fc7af2564b7f210ac294;hp=c9535d038db8c17cc5d6985e4139ae8b2d0120db;hpb=734d0e761fda32cebaae59c370c5d64e1e8c99e8;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index c9535d0..8ca1a4e 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -947,12 +947,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     Alignment ds = new Alignment(dseqs);
     if (av.hasHiddenColumns())
     {
-      omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
+      omitHidden = av.getAlignment().getHiddenColumns()
+              .getVisibleSequenceStrings(0,
               sq.getLength(), seqs);
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
-    List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
+    List<int[]> hiddenCols = av.getAlignment().getHiddenColumns()
+            .getHiddenRegions();
     if (hiddenCols != null)
     {
       alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
@@ -968,7 +970,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     if (av.hasHiddenColumns())
     {
       hiddenColumns = new ArrayList<int[]>();
-      for (int[] region : av.getColumnSelection().getHiddenColumns())
+      for (int[] region : av.getAlignment().getHiddenColumns()
+              .getHiddenRegions())
       {
         hiddenColumns.add(new int[] { region[0], region[1] });
       }