transferred the storage position of the HMM to annotations

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 60cee46..f86282f 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -95,6 +95,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   protected Deque<CommandI> historyList = new ArrayDeque<>();
 
   protected Deque<CommandI> redoList = new ArrayDeque<>();
+  
 
   /**
    * alignment displayed in the viewport. Please use get/setter
@@ -696,6 +697,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected AlignmentAnnotation[] groupConservation;
 
+  protected AlignmentAnnotation hmmConsensus;
+
   /**
    * results of alignment consensus analysis for visible portion of view
    */
@@ -1913,6 +1916,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
               MessageManager.getString("label.consensus_descr"),
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
+
       initGapCounts();
 
       initComplementConsensus();
@@ -2870,4 +2874,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return searchResults;
   }
+  
+
 }