X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=b58269d10aa1823f76092eddd5b1aaf074291976;hb=aad3640b07f836362df7ea025fa09127a0a06145;hp=15f1fe059a9d3c1165e79091913c584b385f01ba;hpb=783c351b9a8aed11ea41c9db193e8ae3be20b017;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 15f1fe0..b58269d 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -25,6 +25,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -50,9 +51,11 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -934,8 +937,9 @@ public class AnnotationLabels extends JPanel
     Alignment ds = new Alignment(dseqs);
     if (av.hasHiddenColumns())
     {
-      omitHidden = av.getAlignment().getHiddenColumns()
-              .getVisibleSequenceStrings(0, sq.getLength(), seqs);
+      Iterator<int[]> it = av.getAlignment().getHiddenColumns()
+              .getVisContigsIterator(0, sq.getLength(), false);
+      omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
@@ -951,12 +955,12 @@ public class AnnotationLabels extends JPanel
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
 
-    ArrayList<int[]> hiddenColumns = null;
+    HiddenColumns hiddenColumns = null;
 
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy();
+      hiddenColumns = new HiddenColumns(
+              av.getAlignment().getHiddenColumns());
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset