X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=bc565ac748cb980faf30b54e1511273a2bc44222;hb=6062dfb954cafb6af22e01af89222888d9d5ba66;hp=3c319d3e88067fd31a55f723dae401e88bb9c0b8;hpb=733f051a048f64b6850314a08880f1f77a633db8;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 3c319d3..bc565ac 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -60,6 +60,7 @@ import org.forester.archaeopteryx.tools.ProcessRunning;
 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.PhylogenyNode;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Annotation;
@@ -119,6 +120,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         SHOW_CONF_STDDEV_LABEL                  = "Show Confidence Standard Deviations";
     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";
     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
+    static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Show Basic Tree Information";
     JMenuBar                    _jmenubar;
     JMenu                       _file_jmenu;
     JMenu                       _tools_menu;
@@ -199,8 +201,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     // _  parsing
     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;
     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;
-    JRadioButtonMenuItem        _extract_taxonomy_yes_rbmi;
-    JRadioButtonMenuItem        _extract_taxonomy_pfam_rbmi;
+    JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;
+    JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;
+    JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;
     JCheckBoxMenuItem           _replace_underscores_cbmi;
     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;
     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;
@@ -650,7 +653,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
 
     void buildViewMenu() {
         _view_jmenu = createMenu( "View", getConfiguration() );
-        _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+        _view_jmenu.add( _display_basic_information_item = new JMenuItem( 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" ) );
@@ -799,7 +802,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         GSDI gsdi = null;
         final Phylogeny species_tree = getSpeciesTree().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,
@@ -872,7 +875,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         GSDIR gsdir = null;
         final Phylogeny species_tree = getSpeciesTree().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,
@@ -889,6 +892,7 @@ public abstract class MainFrame extends JFrame 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();
@@ -1314,14 +1318,17 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 && _print_black_and_white_cbmi.isSelected() );
         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
-        if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.AGRESSIVE );
+        if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
         }
-        else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+        else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+        }
+        else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
         }
         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
         }
         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
                 && _replace_underscores_cbmi.isSelected() );