X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=75cb45b718e84224215197065fcc87b84c990d79;hb=caa5930cf71ef14a4af891f2c17aa4a6e0f72bcf;hp=5a99c3db974ca32a2c5acff2ae499d3e6338e4c8;hpb=042832306c7e7aa0484079f3bab1e141b2944de5;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 5a99c3d..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);
   }
 
@@ -2267,7 +2268,7 @@ public abstract class AlignmentViewport
   public void clearSequenceColours()
   {
     sequenceColours.clear();
-  };
+  }
 
   @Override
   public AlignViewportI getCodingComplement()
@@ -2720,6 +2721,30 @@ public abstract class AlignmentViewport
     viewStyle.setProteinFontAsCdna(b);
   }
 
+  @Override
+  public void setShowComplementFeatures(boolean b)
+  {
+    viewStyle.setShowComplementFeatures(b);
+  }
+
+  @Override
+  public boolean isShowComplementFeatures()
+  {
+    return viewStyle.isShowComplementFeatures();
+  }
+
+  @Override
+  public void setShowComplementFeaturesOnTop(boolean b)
+  {
+    viewStyle.setShowComplementFeaturesOnTop(b);
+  }
+
+  @Override
+  public boolean isShowComplementFeaturesOnTop()
+  {
+    return viewStyle.isShowComplementFeaturesOnTop();
+  }
+
   /**
    * @return true if view should scroll to show the highlighted region of a
    *         sequence
@@ -3054,4 +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));
+  }
 }