JAL-2388 Hidden cols separated from column selection (almost complete)

[jalview.git] / src / jalview / gui / AnnotationLabels.java

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index c9535d0..3e4ec98 100755 (executable)
--- 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()
+            .getListOfCols();
     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()
+              .getListOfCols())
       {
         hiddenColumns.add(new int[] { region[0], region[1] });
       }