X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=7c8850df957c6486d1ce6a965a495e12136dd7f4;hb=a6359c6eb746b06030b22135ed20417b971f580f;hp=2a972eaacc08205318c8e4c135eed541589054e3;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 2a972ea..7c8850d 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -171,6 +171,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             cap.setText(aa[selectedRow].toString());
         }
 
+
         ap.annotationPanel.adjustPanelHeight();
 
         Dimension d = ap.annotationScroller.getPreferredSize();
@@ -319,6 +320,24 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         item = new JMenuItem(OUTPUT_TEXT);
         item.addActionListener(this);
         pop.add(item);
+
+        if (aa[selectedRow].label.equals("Consensus"))
+        {
+          pop.addSeparator();
+          final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+              "Ignore Gaps In Consensus",
+              ap.av.getIgnoreGapsConsensus());
+          cbmi.addActionListener(new ActionListener()
+              {public void actionPerformed(ActionEvent e)
+               {
+                 ap.av.setIgnoreGapsConsensus(cbmi.getState());
+                 ap.repaint();
+               }
+              });
+          pop.add(cbmi);
+
+        }
+
         pop.show(this, evt.getX(), evt.getY());
     }