X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=eb5ef20372ec2396af208c5bdd0421b179f6e58c;hb=ea7870f9bf9ae81876afbe3fdd4d9bd9022b4014;hp=88a6e37fab493ce38f6f9506039fd0ce4f24c705;hpb=1b5ee75e7538b6229da397b28a91296e612d23e8;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 88a6e37..eb5ef20 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -29,6 +29,7 @@ import jalview.bin.*;
 import jalview.datamodel.*;
 
 import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
 
 /**
  * DOCUMENT ME!
@@ -300,7 +301,7 @@ public class AlignViewport
             {
               if (ap != null)
               {
-              ap.paintAlignment(true);
+                ap.paintAlignment(false);
               }
               Thread.sleep(200);
             }
@@ -496,7 +497,7 @@ public class AlignViewport
           {
             if (ap != null)
             {
-            ap.paintAlignment(true);
+            ap.paintAlignment(false);
             }
 
             Thread.sleep(200);
@@ -916,7 +917,15 @@ public class AlignViewport
      */
     public void setAlignment(AlignmentI align)
     {
+      if (alignment!=null && alignment.getCodonFrames()!=null)
+      {
+        StructureSelectionManager.getStructureSelectionManager().removeMappings(alignment.getCodonFrames());
+      }
         this.alignment = align;
+        if (alignment.getCodonFrames()!=null)
+        {
+          StructureSelectionManager.getStructureSelectionManager().addMappings(alignment.getCodonFrames());
+        }
     }
 
     /**
@@ -1466,7 +1475,7 @@ public class AlignViewport
     }
 
     /**
-     * This method returns an array of new SequenceI objects 
+     * This method returns an array of new SequenceI objects
      * derived from the whole alignment or just the current
      * selection with start and end points adjusted
      * @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
@@ -1479,9 +1488,10 @@ public class AlignViewport
       if (selectionGroup == null)
     {
         sequences = alignment.getSequencesArray();
+        AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
         for (int i=0; i<sequences.length; i++)
         {
-          sequences[i] = new Sequence(sequences[i]); // construct new sequence
+          sequences[i] = new Sequence(sequences[i], annots); // construct new sequence with subset of visible annotation
         }
     }
       else