X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=75cb45b718e84224215197065fcc87b84c990d79;hb=69344c80b438aa373e041540d368da1d7f74d2cb;hp=4f399f0d2aee44c3c5479464b17568d7a7accb8e;hpb=0b573ed90b14079f7326281f50c0c9cffdace586;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 4f399f0..75cb45b 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -963,6 +963,7 @@ public abstract class AlignmentViewport
     ranges = null;
     currentTree = null;
     selectionGroup = null;
+    colSel = null;
     setAlignment(null);
   }
 
@@ -3078,4 +3079,22 @@ public abstract class AlignmentViewport
       codingComplement.setUpdateStructures(needToUpdateStructureViews);
     }
   }
+
+  @Override
+  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+  {
+    int start = 0;
+    int end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
+    {
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
+    }
+    else
+    {
+      end = alignment.getWidth();
+    }
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
+  }
 }