X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=95aafab1c2056f1bc76a32d7f4aa84ae11169fd9;hb=a822fc744dcc06e6a8d2399218da0d0dfd56cf2b;hp=ab9a25d66ae1886f5e07c98391ae279c4cf36dd9;hpb=209d11e9f68d26ae195e48627a9364aca9e0ee27;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index ab9a25d..95aafab 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -280,6 +280,14 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
 
           alignment.addAnnotation(quality);
         }
+      } else {
+        if (alignment.hasRNAStructure())
+        {
+          strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+                  new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+          strucConsensus.hasText = true;
+          strucConsensus.autoCalculated = true;
+        }
       }
 
       consensus = new AlignmentAnnotation("Consensus", "PID",
@@ -290,6 +298,10 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
       if (showConsensus)
       {
         alignment.addAnnotation(consensus);
+        if (strucConsensus!=null)
+        {
+          alignment.addAnnotation(strucConsensus);
+        }
       }
     }