Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index 7456e18..5b77dfc 100644 (file)
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
@@ -674,7 +675,7 @@ public class FeatureTypeSettings extends JalviewDialog
          */
         if (ap != null)
         {
-          ap.paintAlignment(true, true);
+          refreshDisplay(true);
         }
       }
     });
@@ -875,7 +876,7 @@ public class FeatureTypeSettings extends JalviewDialog
      * save the colour, and repaint stuff
      */
     fr.setColour(featureType, acg);
-    ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
+    refreshDisplay(updateStructsAndOverview);
 
     updateColoursTab();
   }
@@ -1014,7 +1015,7 @@ public class FeatureTypeSettings extends JalviewDialog
   {
     fr.setColour(featureType, originalColour);
     fr.setFeatureFilter(featureType, originalFilter);
-    ap.paintAlignment(true, true);
+    refreshDisplay(true);
   }
 
   /**
@@ -1753,8 +1754,26 @@ public class FeatureTypeSettings extends JalviewDialog
      * (note this might now be an empty filter with no conditions)
      */
     fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
-    ap.paintAlignment(true, true);
+    refreshDisplay(true);
 
     updateFiltersTab();
   }
+
+  /**
+   * Repaints alignment, structure and overview (if shown). If there is a
+   * complementary view which is showing this view's features, then also
+   * repaints that.
+   * 
+   * @param updateStructsAndOverview
+   */
+  void refreshDisplay(boolean updateStructsAndOverview)
+  {
+    ap.paintAlignment(true, updateStructsAndOverview);
+    AlignViewportI complement = ap.getAlignViewport().getCodingComplement();
+    if (complement != null && complement.isShowComplementFeatures())
+    {
+      AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+      af2.alignPanel.paintAlignment(true, updateStructsAndOverview);
+    }
+  }
 }