JAL-3748 store an AlignmentView for the complement within an viewport’s AlignView...

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index c9a3a80..cbc2189 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1694,11 +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