inprogress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrame.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 8689bd4..bc565ac 100644 (file)
--- 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;
@@ -239,7 +242,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     Configuration               _configuration;
     JMenuItem                   _remove_branch_color_item;
     Options                     _options;
-    Phylogeny                   _species_tree;
+    private Phylogeny           _species_tree;
     InferenceManager            _inference_manager;
     final ProcessPool           _process_pool;
     private String              _previous_node_annotation_ref;
@@ -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" ) );
@@ -797,9 +800,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         gene_tree.setAllNodesToNotCollapse();
         gene_tree.recalculateNumberOfExternalDescendants( false );
         GSDI gsdi = null;
-        final Phylogeny species_tree = _species_tree.copy();
+        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,
@@ -870,9 +873,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         gene_tree.setAllNodesToNotCollapse();
         gene_tree.recalculateNumberOfExternalDescendants( false );
         GSDIR gsdir = null;
-        final Phylogeny species_tree = _species_tree.copy();
+        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();
@@ -959,6 +963,10 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         return _jmenubar;
     }
 
+    final Phylogeny getSpeciesTree() {
+        return _species_tree;
+    }
+
     void help() {
         final StringBuilder sb = new StringBuilder();
         sb.append( "Display options\n" );
@@ -1083,14 +1091,14 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
             return false;
         }
-        else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
+        else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
             JOptionPane.showMessageDialog( this,
                                            "No species tree loaded",
                                            "Cannot execute GSDI",
                                            JOptionPane.ERROR_MESSAGE );
             return false;
         }
-        else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
+        else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
             JOptionPane.showMessageDialog( this,
                                            "Species tree is not completely binary",
                                            "Cannot execute GSDI",
@@ -1189,6 +1197,10 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
     }
 
+    final void setSpeciesTree( final Phylogeny species_tree ) {
+        _species_tree = species_tree;
+    }
+
     void setTypeMenuToAllUnselected() {
         _convex_type_cbmi.setSelected( false );
         _curved_type_cbmi.setSelected( false );
@@ -1306,14 +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_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
         }
-        else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+        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() );