JAL-2591 More refactoring (incomplete)

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 07a5ad9..7741956 100755 (executable)
--- 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);
 
@@ -970,8 +968,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     if (av.hasHiddenColumns())
     {
-      av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy(hiddenColumns);
+      hiddenColumns = av.getAlignment().getHiddenColumns()
+              .getHiddenColumnsCopyAsList();
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset