X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=aab7b78af16ca538bc9e49803e325ef923ecb094;hb=05157d0ba7145aebb34f4d3b6d4c38c380626b2b;hp=eaf7536dbf02ee73c90a666b877e55ad2902d50d;hpb=733f051a048f64b6850314a08880f1f77a633db8;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index eaf7536..aab7b78 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -36,6 +36,7 @@ import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.data.SequenceRelation;
 import org.forester.sdi.GSDI;
 import org.forester.sdi.GSDIR;
@@ -261,6 +262,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         else if ( o == _label_direction_cbmi ) {
             updateOptions( getOptions() );
         }
+        else if ( o == _abbreviate_scientific_names ) {
+            updateOptions( getOptions() );
+        }
         else if ( o == _show_overview_cbmi ) {
             updateOptions( getOptions() );
             if ( getCurrentTreePanel() != null ) {
@@ -811,7 +815,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
 
     void buildViewMenu() {
         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
-        _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+        _view_jmenu
+                .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
         _view_jmenu.addSeparator();
         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
@@ -891,7 +896,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         GSDI gsdi = null;
         final Phylogeny species_tree = _species_tree.copy();
         try {
-            gsdi = new GSDI( gene_tree, species_tree, false, true, true );
+            gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
         }
         catch ( final SDIException e ) {
             JOptionPane.showMessageDialog( this,
@@ -964,7 +969,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         GSDIR gsdir = null;
         final Phylogeny species_tree = _species_tree.copy();
         try {
-            gsdir = new GSDIR( gene_tree, species_tree, true, true );
+            gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
         }
         catch ( final SDIException e ) {
             JOptionPane.showMessageDialog( this,
@@ -981,6 +986,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         result_gene_tree.setRerootable( false );
         result_gene_tree.clearHashIdToNodeMap();
         result_gene_tree.recalculateNumberOfExternalDescendants( true );
+        PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
         getMainPanel().getControlPanel().setShowEvents( true );
         showWhole();