X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=681fc7d954cce827d451bcbb89161036f9f2f505;hb=a5e22141bc3185284588761a69f023d527e7f18e;hp=22c467de1e7b5ec4adacae45ceaef109d4b2b952;hpb=3207f84e04c66fc89da22ed04876e50b66e94649;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 22c467d..681fc7d 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -528,7 +528,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
   private void setColourScheme(ColourSchemeI cs) 
   {
-    jmb.setJalviewColourScheme(cs, ap);
+    jmb.setJalviewColourScheme(cs, ap, ap.av.isShowSequenceFeatures());
   }
 
 /**
@@ -555,7 +555,7 @@ public class AppletJmol extends EmbmenuFrame implements
     else if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap);
+      jmb.colourBySequence(ap, ap.av.isShowSequenceFeatures());
     }
     else if (!allChainsSelected)
     {
@@ -588,7 +588,7 @@ public class AppletJmol extends EmbmenuFrame implements
   public void updateColours(Object source)
   {
     AlignmentPanel panel = (AlignmentPanel) source;
-    jmb.colourBySequence(panel);
+    jmb.colourBySequence(panel, ap.av.isShowSequenceFeatures());
   }
 
   public void updateTitleAndMenus()
@@ -599,7 +599,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.getChainNames());
-    jmb.colourBySequence(ap);
+    jmb.colourBySequence(ap, ap.av.isShowSequenceFeatures());
 
     setTitle(jmb.getViewerTitle());
   }