JAL-2591 simplifying hidden columns usage

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 3e4ec98..07a5ad9 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -954,7 +954,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
     List<int[]> hiddenCols = av.getAlignment().getHiddenColumns()
-            .getListOfCols();
+            .getHiddenRegions();
     if (hiddenCols != null)
     {
       alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
@@ -967,14 +967,11 @@ 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()
-              .getListOfCols())
-      {
-        hiddenColumns.add(new int[] { region[0], region[1] });
-      }
+      av.getAlignment().getHiddenColumns()
+              .getHiddenColumnsCopy(hiddenColumns);
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset