X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=e89f978aa4b144e2189e6b9a4b50c843d4c2a48e;hb=9673231c870387fffa4516124d802ee47bbdaf45;hp=28d0ae3028864c008df3168389e8dde6de2f3dbb;hpb=b0e44267b1b9686573c2fd0eb8ef1e14814106c8;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 28d0ae3..e89f978 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -548,10 +548,16 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         if ( phy == null || phy.getNumberOfExternalNodes() < 2 ) {
             return;
         }
-        List<PhylogenyNode> nodes = null;
+        List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
-            nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
+            final List<PhylogenyNode>  all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
+            for( final PhylogenyNode n : all_selected_nodes ) {
+                if ( n.isExternal() ) {
+                    nodes.add( n );
+                }
+            }
         }
+        
         String function = "Retain";
         if ( delete ) {
             function = "Delete";