X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=82b97a51b9fe52e88a78b7fe79ca427f1db0e370;hb=a6cd54c46366acd8bc3350a79374b18f9eb0b240;hp=38013d1a0804a379dd864484bfb1bef1389edfad;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 38013d1..82b97a5 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -75,7 +75,7 @@ public class AnnotationLabels
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame,
@@ -121,7 +121,26 @@ public class AnnotationLabels
     item = new MenuItem(OUTPUT_TEXT);
     item.addActionListener(this);
     pop.add(item);
-    pop.show(this, evt.getX(), evt.getY());
+
+    if (aa[selectedRow].label.equals("Consensus"))
+    {
+      pop.addSeparator();
+      final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+          "Ignore Gaps In Consensus",
+          ap.av.getIgnoreGapsConsensus());
+
+      cbmi.addItemListener(new ItemListener()
+      {
+        public void itemStateChanged(ItemEvent e)
+        {
+          ap.av.setIgnoreGapsConsensus(cbmi.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cbmi);
+    }
+
+     pop.show(this, evt.getX(), evt.getY());
 
   }