X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=9f7326fe04e49b7c1d5c80db256c6628b02094c3;hb=6a0443ac38398913712bcece37a672d0f33e8d81;hp=35215b44f7f74d7993440b2a4529c940c7edcb78;hpb=3740241b6d0dfa109dc81847afe58f17497c39e8;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 35215b4..9f7326f 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.datamodel.AlignmentI;
@@ -520,7 +521,7 @@ public class FeatureSettings extends JPanel
       {
         fr.setGroupVisibility(check.getText(), check.isSelected());
         resetTable(new String[] { grp });
-        af.alignPanel.paintAlignment(true, true);
+        refreshDisplay();
       }
     });
     groupPanel.add(check);
@@ -1078,7 +1079,7 @@ public class FeatureSettings extends JPanel
 
     if (fr.setFeaturePriority(rowData, visibleNew))
     {
-      af.alignPanel.paintAlignment(true, true);
+      refreshDisplay();
     }
   }
 
@@ -1253,7 +1254,7 @@ public class FeatureSettings extends JPanel
         if (!inConstruction)
         {
           fr.setTransparency((100 - transparency.getValue()) / 100f);
-          af.alignPanel.paintAlignment(true, true);
+          refreshDisplay();
         }
       }
     });
@@ -1272,6 +1273,7 @@ public class FeatureSettings extends JPanel
       {
         af.getViewport()
                 .setShowComplementFeatures(showComplement.isSelected());
+        refreshDisplay();
       }
     });
 
@@ -1307,6 +1309,22 @@ public class FeatureSettings extends JPanel
     this.add(settingsPane);
   }
 
+  /**
+   * Repaints alignment, structure and overview (if shown). If there is a
+   * complementary view which is showing this view's features, then also
+   * repaints that.
+   */
+  void refreshDisplay()
+  {
+    af.alignPanel.paintAlignment(true, true);
+    AlignViewportI complement = af.getViewport().getCodingComplement();
+    if (complement != null && complement.isShowComplementFeatures())
+    {
+      AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+      af2.alignPanel.paintAlignment(true, true);
+    }
+  }
+
   // ///////////////////////////////////////////////////////////////////////
   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
   // ///////////////////////////////////////////////////////////////////////