JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to align...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 910ab63..90a3532 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -907,6 +907,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     padGapsMenuitem.setSelected(av.isPadGaps());
     colourTextMenuItem.setSelected(av.isShowColourText());
+    colourGapsMenuItem.setSelected(av.getColourGaps());
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
     modifyPID.setEnabled(abovePIDThreshold.isSelected());
     conservationMenuItem.setSelected(av.getConservationSelected());
@@ -3001,6 +3002,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          DOCUMENT ME!
    */
   @Override
+  protected void colourGapsMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setColourGaps(colourGapsMenuItem.isSelected());
+    alignPanel.paintAlignment(false, false);
+  }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
     scaleAbove.setVisible(wrapMenuItem.isSelected());