X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=cbc218987ff4b54217b00f423d4438a548a59943;hb=97fd3b7a62963b882bf14ca7ec352b5f6f7325e7;hp=2c430dbe6dcbe73c12b55acf68ec3de1f8cba1ab;hpb=eccc204bba7aab9101c16df03cc5f740241d9184;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 2c430db..cbc2189 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -959,6 +959,7 @@ public abstract class AlignmentViewport
     ranges = null;
     currentTree = null;
     selectionGroup = null;
+    colSel = null;
     setAlignment(null);
   }
 
@@ -1693,11 +1694,29 @@ public abstract class AlignmentViewport
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
   {
-    return new AlignmentView(alignment, alignment.getHiddenColumns(),
-            selectionGroup,
+    return getAlignmentViewWithComplement(selectedOnly,markGroups,true);
+  }
+  
+  @Override
+  public jalview.datamodel.AlignmentView getAlignmentViewWithComplement(
+          boolean selectedOnly, boolean markGroups,boolean withComplment)
+  {
+    AlignmentView complementView = null;
+    if (withComplment)
+    {
+      if (codingComplement != null)
+      {
+        complementView = codingComplement.getAlignmentViewWithComplement(
+                selectedOnly, markGroups, false);
+      }
+    }
+    AlignmentView thisView = new AlignmentView(alignment,
+            alignment.getHiddenColumns(), selectionGroup,
             alignment.getHiddenColumns() != null
                     && alignment.getHiddenColumns().hasHiddenColumns(),
             selectedOnly, markGroups);
+    thisView.setComplement(complementView);
+    return thisView;
   }
 
   @Override