X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=e89f978aa4b144e2189e6b9a4b50c843d4c2a48e;hb=aaac4312b5a1356278bad15c79d0e97de8823c72;hp=8bbedf1e28edbeaae8c000de4aaab55eb242038f;hpb=6ebad4e2283f33540c6ed4a9b1c8efc839d62637;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 8bbedf1..e89f978 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -165,8 +165,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _annotate_item;
     JMenuItem                   _remove_branch_color_item;
     JMenuItem                   _remove_visual_styles_item;
-    JMenuItem                   _deleted_selected_nodes_item;
-    JMenuItem                   _deleted_not_selected_nodes_item;
+    JMenuItem                   _delete_selected_nodes_item;
+    JMenuItem                   _delete_not_selected_nodes_item;
     // font size menu:
     JMenuItem                   _super_tiny_fonts_item;
     JMenuItem                   _tiny_fonts_item;
@@ -325,13 +325,13 @@ public abstract class MainFrame extends JFrame implements ActionListener {
             }
             midpointRoot();
         }
-        else if ( o == _deleted_selected_nodes_item ) {
+        else if ( o == _delete_selected_nodes_item ) {
             if ( isSubtreeDisplayed() ) {
                 return;
             }
             deleteSelectedNodes( true );
         }
-        else if ( o == _deleted_not_selected_nodes_item ) {
+        else if ( o == _delete_not_selected_nodes_item ) {
             if ( isSubtreeDisplayed() ) {
                 return;
             }
@@ -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";
@@ -570,7 +576,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         if ( delete ) {
             res = ext - todo;
         }
-        
         if ( res < 1 ) {
             JOptionPane.showMessageDialog( this,
                                            "Cannot delete all nodes",
@@ -578,9 +583,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                                            JOptionPane.ERROR_MESSAGE );
             return;
         }
-        final int result = JOptionPane.showConfirmDialog( null, "OK to " + function.toLowerCase() + " " + todo
+        final int result = JOptionPane.showConfirmDialog( null, function + " " + todo
                 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res
-                + " nodes", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
+                + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );
         if ( result == JOptionPane.OK_OPTION ) {
             if ( !delete ) {
                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();