X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=e16867a4c0d9389ee6614cc6ec625068a1a235dd;hb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;hp=8ca1a4e844079893d1fd469f2e5a540fff3df7cf;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 8ca1a4e..e16867a 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -52,7 +52,6 @@ import java.awt.image.BufferedImage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.List;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -953,13 +952,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
-    List<int[]> hiddenCols = av.getAlignment().getHiddenColumns()
-            .getHiddenRegions();
-    if (hiddenCols != null)
+    if (av.hasHiddenColumns())
     {
-      alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
-              hiddenCols);
+      alignmentStartEnd = av.getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
     }
+
     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
             seqs, omitHidden, alignmentStartEnd);
 
@@ -967,14 +965,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             .setContents(new StringSelection(output), Desktop.instance);
 
     ArrayList<int[]> hiddenColumns = null;
+
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = new ArrayList<int[]>();
-      for (int[] region : av.getAlignment().getHiddenColumns()
-              .getHiddenRegions())
-      {
-        hiddenColumns.add(new int[] { region[0], region[1] });
-      }
+      hiddenColumns = av.getAlignment().getHiddenColumns()
+              .getHiddenColumnsCopy();
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset