compactor work
[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrame.java
index cc2c9eb..505918e 100644 (file)
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2010 Christian M. Zmasek
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
-
-package org.forester.archaeopteryx;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Font;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.IOException;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Locale;
-import java.util.NoSuchElementException;
-import java.util.Set;
-
-import javax.swing.Box;
-import javax.swing.JApplet;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JMenu;
-import javax.swing.JMenuBar;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.JTextField;
-import javax.swing.SwingUtilities;
-
-import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
-import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
-import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
-import org.forester.archaeopteryx.tools.InferenceManager;
-import org.forester.archaeopteryx.tools.ProcessPool;
-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;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
-import org.forester.sdi.GSDI;
-import org.forester.sdi.GSDIR;
-import org.forester.sdi.SDIException;
-import org.forester.util.ForesterConstants;
-import org.forester.util.ForesterUtil;
-
-public abstract class MainFrame extends JFrame implements ActionListener {
-
-    static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";
-    static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME
-    static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;
-    private static final long   serialVersionUID                        = 3655000897845508358L;
-    final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),
-                                                                                    Font.PLAIN,
-                                                                                    10 );
-    static final String         TYPE_MENU_HEADER                        = "Type";
-    static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";
-    static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";
-    static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";
-    static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";
-    static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";
-    static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";
-    static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO
-    static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO
-    static final String         OPTIONS_HEADER                          = "Options";
-    static final String         SEARCH_SUBHEADER                        = "Search:";
-    static final String         DISPLAY_SUBHEADER                       = "Display:";
-    static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";
-    static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";
-    static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";
-    static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Display Branch Length Values";
-    static final String         DISPLAY_SCALE_LABEL                     = "Display Scale";
-    static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";
-    static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";
-    static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";
-    static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";
-    static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";
-    static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";
-    static final String         BG_GRAD_LABEL                           = "Background Color Gradient";
-    static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Show External Node Shapes";
-    static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Show Internal Node Shapes";
-    static final String         SHOW_OVERVIEW_LABEL                     = "Show Overview";
-    static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";
-    static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";
-    static final String         SHOW_DOMAIN_LABELS_LABEL                = "Show Domain Labels";
-    static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Show Seq Annotation Ref Sources";
-    static final String         COLOR_LABELS_TIP                        = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
-    static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";
-    static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";
-    static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";
-    static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";
-    static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";
-    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;
-    JMenu                       _view_jmenu;
-    JMenu                       _options_jmenu;
-    JMenu                       _font_size_menu;
-    JMenu                       _help_jmenu;
-    JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;
-    // Analysis menu
-    JMenu                       _analysis_menu;
-    JMenuItem                   _load_species_tree_item;
-    JMenuItem                   _gsdi_item;
-    JMenuItem                   _gsdir_item;
-    JMenuItem                   _lineage_inference;
-    // file menu:
-    JMenuItem                   _open_item;
-    JMenuItem                   _open_url_item;
-    JMenuItem                   _save_item;
-    JMenuItem                   _save_all_item;
-    JMenuItem                   _close_item;
-    JMenuItem                   _exit_item;
-    JMenuItem                   _new_item;
-    // tools menu:
-    JMenuItem                   _midpoint_root_item;
-    JMenuItem                   _taxcolor_item;
-    JMenuItem                   _confcolor_item;
-    JMenuItem                   _color_rank_jmi;
-    JMenuItem                   _collapse_species_specific_subtrees;
-    JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me
-    JMenuItem                   _obtain_detailed_taxonomic_information_jmi;
-    JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;
-    JMenuItem                   _obtain_seq_information_jmi;
-    JMenuItem                   _move_node_names_to_tax_sn_jmi;
-    JMenuItem                   _move_node_names_to_seq_names_jmi;
-    JMenuItem                   _extract_tax_code_from_node_names_jmi;
-    JMenuItem                   _annotate_item;
-    // font size menu:
-    JMenuItem                   _super_tiny_fonts_item;
-    JMenuItem                   _tiny_fonts_item;
-    JMenuItem                   _small_fonts_item;
-    JMenuItem                   _medium_fonts_item;
-    JMenuItem                   _large_fonts_item;
-    // options menu:
-    // _  screen and print
-    JMenuItem                   _choose_font_mi;
-    JMenuItem                   _switch_colors_mi;
-    JCheckBoxMenuItem           _label_direction_cbmi;
-    // _  screen display
-    JCheckBoxMenuItem           _screen_antialias_cbmi;
-    JCheckBoxMenuItem           _background_gradient_cbmi;
-    JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
-    JRadioButtonMenuItem        _uniform_cladograms_rbmi;
-    JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
-    JCheckBoxMenuItem           _show_branch_length_values_cbmi;
-    JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me
-    JCheckBoxMenuItem           _show_overview_cbmi;
-    JCheckBoxMenuItem           _show_domain_labels;
-    JCheckBoxMenuItem           _show_annotation_ref_source;
-    JCheckBoxMenuItem           _abbreviate_scientific_names;
-    JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
-    JMenuItem                   _overview_placment_mi;
-    JMenuItem                   _choose_minimal_confidence_mi;
-    JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
-    JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
-    JMenuItem                   _cycle_node_shape_mi;
-    JMenuItem                   _cycle_node_fill_mi;
-    JMenuItem                   _choose_node_size_mi;
-    JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
-    JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
-    // _  print
-    JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;
-    JCheckBoxMenuItem           _antialias_print_cbmi;
-    JCheckBoxMenuItem           _print_black_and_white_cbmi;
-    JCheckBoxMenuItem           _print_using_actual_size_cbmi;
-    JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;
-    JMenuItem                   _print_size_mi;
-    JMenuItem                   _choose_pdf_width_mi;
-    // _  parsing
-    JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;
-    JRadioButtonMenuItem        _extract_taxonomy_no_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;
-    // _  search
-    JCheckBoxMenuItem           _search_case_senstive_cbmi;
-    JCheckBoxMenuItem           _search_whole_words_only_cbmi;
-    JCheckBoxMenuItem           _inverse_search_result_cbmi;
-    // type menu:
-    JMenu                       _type_menu;
-    JCheckBoxMenuItem           _rectangular_type_cbmi;
-    JCheckBoxMenuItem           _triangular_type_cbmi;
-    JCheckBoxMenuItem           _curved_type_cbmi;
-    JCheckBoxMenuItem           _convex_type_cbmi;
-    JCheckBoxMenuItem           _euro_type_cbmi;
-    JCheckBoxMenuItem           _rounded_type_cbmi;
-    JCheckBoxMenuItem           _unrooted_type_cbmi;
-    JCheckBoxMenuItem           _circular_type_cbmi;
-    // view as text menu:
-    JMenuItem                   _view_as_NH_item;
-    JMenuItem                   _view_as_XML_item;
-    JMenuItem                   _view_as_nexus_item;
-    JMenuItem                   _display_basic_information_item;
-    // help menu:
-    JMenuItem                   _about_item;
-    JMenuItem                   _help_item;
-    JMenuItem                   _website_item;
-    JMenuItem                   _phyloxml_website_item;
-    JMenuItem                   _phyloxml_ref_item;
-    JMenuItem                   _aptx_ref_item;
-    // process menu:
-    JMenu                       _process_menu;
-    // Handy pointers to child components:
-    MainPanel                   _mainpanel;
-    Container                   _contentpane;
-    final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;
-    Configuration               _configuration;
-    JMenuItem                   _remove_branch_color_item;
-    Options                     _options;
-    private Phylogeny           _species_tree;
-    InferenceManager            _inference_manager;
-    final ProcessPool           _process_pool;
-    private String              _previous_node_annotation_ref;
-
-    MainFrame() {
-        _process_pool = ProcessPool.createInstance();
-    }
-
-    /**
-     * Action performed.
-     */
-    @Override
-    public void actionPerformed( final ActionEvent e ) {
-        final Object o = e.getSource();
-        boolean is_applet = false;
-        JApplet applet = null;
-        if ( getCurrentTreePanel() != null ) {
-            is_applet = getCurrentTreePanel().isApplet();
-            if ( is_applet ) {
-                applet = getCurrentTreePanel().obtainApplet();
-            }
-        }
-        if ( o == _open_url_item ) {
-            readPhylogeniesFromURL();
-        }
-        else if ( o == _exit_item ) {
-            close();
-        }
-        else if ( o == _gsdi_item ) {
-            if ( isSubtreeDisplayed() ) {
-                return;
-            }
-            executeGSDI();
-        }
-        else if ( o == _gsdir_item ) {
-            if ( isSubtreeDisplayed() ) {
-                return;
-            }
-            executeGSDIR();
-        }
-        else if ( o == _taxcolor_item ) {
-            taxColor();
-        }
-        else if ( o == _confcolor_item ) {
-            confColor();
-        }
-        else if ( o == _color_rank_jmi ) {
-            colorRank();
-        }
-        else if ( o == _collapse_species_specific_subtrees ) {
-            if ( isSubtreeDisplayed() ) {
-                return;
-            }
-            if ( getCurrentTreePanel() != null ) {
-                getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
-            }
-        }
-        else if ( o == _remove_branch_color_item ) {
-            if ( isSubtreeDisplayed() ) {
-                return;
-            }
-            removeBranchColors();
-        }
-        else if ( o == _midpoint_root_item ) {
-            if ( isSubtreeDisplayed() ) {
-                return;
-            }
-            midpointRoot();
-        }
-        else if ( o == _annotate_item ) {
-            annotateSequences();
-        }
-        else if ( o == _switch_colors_mi ) {
-            switchColors();
-        }
-        else if ( o == _display_basic_information_item ) {
-            displayBasicInformation();
-        }
-        else if ( o == _view_as_NH_item ) {
-            viewAsNH();
-        }
-        else if ( o == _view_as_XML_item ) {
-            viewAsXML();
-        }
-        else if ( o == _view_as_nexus_item ) {
-            viewAsNexus();
-        }
-        else if ( o == _super_tiny_fonts_item ) {
-            if ( getCurrentTreePanel() != null ) {
-                getCurrentTreePanel().setSuperTinyFonts();
-                getCurrentTreePanel().repaint();
-            }
-        }
-        else if ( o == _tiny_fonts_item ) {
-            if ( getCurrentTreePanel() != null ) {
-                getCurrentTreePanel().setTinyFonts();
-                getCurrentTreePanel().repaint();
-            }
-        }
-        else if ( o == _small_fonts_item ) {
-            if ( getCurrentTreePanel() != null ) {
-                getCurrentTreePanel().setSmallFonts();
-                getCurrentTreePanel().repaint();
-            }
-        }
-        else if ( o == _medium_fonts_item ) {
-            if ( getCurrentTreePanel() != null ) {
-                getCurrentTreePanel().setMediumFonts();
-                getCurrentTreePanel().repaint();
-            }
-        }
-        else if ( o == _large_fonts_item ) {
-            if ( getCurrentTreePanel() != null ) {
-                getCurrentTreePanel().setLargeFonts();
-                getCurrentTreePanel().repaint();
-            }
-        }
-        else if ( o == _choose_font_mi ) {
-            chooseFont();
-        }
-        else if ( o == _choose_minimal_confidence_mi ) {
-            chooseMinimalConfidence();
-        }
-        else if ( o == _choose_node_size_mi ) {
-            chooseNodeSize( getOptions(), this );
-        }
-        else if ( o == _overview_placment_mi ) {
-            MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
-        }
-        else if ( o == _cycle_node_fill_mi ) {
-            MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
-        }
-        else if ( o == _cycle_node_shape_mi ) {
-            MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
-        }
-        else if ( o == _screen_antialias_cbmi ) {
-            updateOptions( getOptions() );
-            updateScreenTextAntialias( getMainPanel().getTreePanels() );
-        }
-        else if ( o == _background_gradient_cbmi ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _show_domain_labels ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _show_annotation_ref_source ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _abbreviate_scientific_names ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _color_labels_same_as_parent_branch ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _show_default_node_shapes_internal_cbmi ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _show_default_node_shapes_external_cbmi ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _non_lined_up_cladograms_rbmi ) {
-            updateOptions( getOptions() );
-            showWhole();
-        }
-        else if ( o == _uniform_cladograms_rbmi ) {
-            updateOptions( getOptions() );
-            showWhole();
-        }
-        else if ( o == _ext_node_dependent_cladogram_rbmi ) {
-            updateOptions( getOptions() );
-            showWhole();
-        }
-        else if ( o == _search_case_senstive_cbmi ) {
-            updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
-        }
-        else if ( o == _search_whole_words_only_cbmi ) {
-            updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
-        }
-        else if ( o == _inverse_search_result_cbmi ) {
-            updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
-        }
-        else if ( o == _show_scale_cbmi ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _show_branch_length_values_cbmi ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _show_confidence_stddev_cbmi ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
-            if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
-                _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
-            }
-            updateOptions( getOptions() );
-        }
-        else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
-            if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
-                _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
-            }
-            updateOptions( getOptions() );
-        }
-        else if ( o == _label_direction_cbmi ) {
-            updateOptions( getOptions() );
-        }
-        else if ( o == _show_overview_cbmi ) {
-            updateOptions( getOptions() );
-            if ( getCurrentTreePanel() != null ) {
-                getCurrentTreePanel().updateOvSizes();
-            }
-        }
-        else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
-                || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
-                || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
-            typeChanged( o );
-        }
-        else if ( o == _about_item ) {
-            about();
-        }
-        else if ( o == _help_item ) {
-            help();
-        }
-        else if ( o == _website_item ) {
-            try {
-                AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
-            }
-            catch ( final IOException e1 ) {
-                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
-            }
-        }
-        else if ( o == _phyloxml_website_item ) {
-            try {
-                AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
-            }
-            catch ( final IOException e1 ) {
-                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
-            }
-        }
-        else if ( o == _aptx_ref_item ) {
-            try {
-                AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
-            }
-            catch ( final IOException e1 ) {
-                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
-            }
-        }
-        else if ( o == _phyloxml_ref_item ) {
-            try {
-                AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
-            }
-            catch ( final IOException e1 ) {
-                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
-            }
-        }
-        else {
-            if ( _load_phylogeny_from_webservice_menu_items != null ) {
-                for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
-                    if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
-                        readPhylogeniesFromWebservice( i );
-                    }
-                }
-            }
-        }
-        _contentpane.repaint();
-    }
-
-    public Configuration getConfiguration() {
-        return _configuration;
-    }
-
-    /**
-     * This method returns the current external node data which
-     * has been selected by the user by clicking the "Return ..."
-     * menu item. This method is expected to be called from Javascript or
-     * something like it.
-     * 
-     * @return current external node data as String
-     */
-    public String getCurrentExternalNodesDataBuffer() {
-        return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
-    }
-
-    public int getCurrentExternalNodesDataBufferChangeCounter() {
-        return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
-    }
-
-    public int getCurrentExternalNodesDataBufferLength() {
-        return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
-    }
-
-    public InferenceManager getInferenceManager() {
-        return _inference_manager;
-    }
-
-    public MainPanel getMainPanel() {
-        return _mainpanel;
-    }
-
-    public Options getOptions() {
-        return _options;
-    }
-
-    public ProcessPool getProcessPool() {
-        return _process_pool;
-    }
-
-    public void showTextFrame( final String s, final String title ) {
-        checkTextFrames();
-        _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
-    }
-
-    public void showWhole() {
-        _mainpanel.getControlPanel().showWhole();
-    }
-
-    public void updateProcessMenu() {
-        // In general Swing is not thread safe.
-        // See "Swing's Threading Policy".
-        SwingUtilities.invokeLater( new Runnable() {
-
-            @Override
-            public void run() {
-                doUpdateProcessMenu();
-            }
-        } );
-    }
-
-    void activateSaveAllIfNeeded() {
-        if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
-            _save_all_item.setEnabled( true );
-        }
-        else {
-            _save_all_item.setEnabled( false );
-        }
-    }
-
-    void buildFileMenu() {
-        _file_jmenu = createMenu( "File", getConfiguration() );
-        _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
-        _file_jmenu.addSeparator();
-        _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
-        customizeJMenuItem( _open_url_item );
-        customizeJMenuItem( _exit_item );
-        _jmenubar.add( _file_jmenu );
-    }
-
-    void buildFontSizeMenu() {
-        _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
-        _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
-        _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
-        _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
-        _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
-        _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
-        customizeJMenuItem( _super_tiny_fonts_item );
-        customizeJMenuItem( _tiny_fonts_item );
-        customizeJMenuItem( _small_fonts_item );
-        customizeJMenuItem( _medium_fonts_item );
-        customizeJMenuItem( _large_fonts_item );
-        _jmenubar.add( _font_size_menu );
-    }
-
-    void buildHelpMenu() {
-        _help_jmenu = createMenu( "Help", getConfiguration() );
-        _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
-        _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
-        _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
-        _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
-        _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
-        _help_jmenu.addSeparator();
-        _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
-        customizeJMenuItem( _help_item );
-        customizeJMenuItem( _website_item );
-        customizeJMenuItem( _phyloxml_website_item );
-        customizeJMenuItem( _aptx_ref_item );
-        customizeJMenuItem( _phyloxml_ref_item );
-        customizeJMenuItem( _about_item );
-        _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
-        _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
-        _jmenubar.add( _help_jmenu );
-    }
-
-    void buildTypeMenu() {
-        _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
-        _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
-        _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
-        _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
-        _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
-        _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
-        _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
-        _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
-        _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
-        customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
-        customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
-        customizeCheckBoxMenuItem( _euro_type_cbmi, false );
-        customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
-        customizeCheckBoxMenuItem( _curved_type_cbmi, false );
-        customizeCheckBoxMenuItem( _convex_type_cbmi, false );
-        customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
-        customizeCheckBoxMenuItem( _circular_type_cbmi, false );
-        _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
-        _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
-        initializeTypeMenu( getOptions() );
-        _jmenubar.add( _type_menu );
-    }
-
-    void buildViewMenu() {
-        _view_jmenu = createMenu( "View", getConfiguration() );
-        _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" ) );
-        _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
-        customizeJMenuItem( _display_basic_information_item );
-        customizeJMenuItem( _view_as_NH_item );
-        customizeJMenuItem( _view_as_XML_item );
-        customizeJMenuItem( _view_as_nexus_item );
-        _jmenubar.add( _view_jmenu );
-    }
-
-    void checkTextFrames() {
-        if ( _textframes.size() > 5 ) {
-            try {
-                if ( _textframes.getFirst() != null ) {
-                    _textframes.getFirst().removeMe();
-                }
-                else {
-                    _textframes.removeFirst();
-                }
-            }
-            catch ( final NoSuchElementException e ) {
-                // Ignore.
-            }
-        }
-    }
-
-    void close() {
-        removeAllTextFrames();
-        if ( _mainpanel != null ) {
-            _mainpanel.terminate();
-        }
-        if ( _contentpane != null ) {
-            _contentpane.removeAll();
-        }
-        setVisible( false );
-        dispose();
-    }
-
-    void colorRank() {
-        if ( _mainpanel.getCurrentTreePanel() != null ) {
-            final String[] ranks = AptxUtil.getAllPossibleRanks();
-            final String rank = ( String ) JOptionPane
-                    .showInputDialog( this,
-                                      "What rank should the colorization be based on",
-                                      "Rank Selection",
-                                      JOptionPane.QUESTION_MESSAGE,
-                                      null,
-                                      ranks,
-                                      null );
-            if ( !ForesterUtil.isEmpty( rank ) ) {
-                _mainpanel.getCurrentTreePanel().colorRank( rank );
-            }
-        }
-    }
-
-    void confColor() {
-        if ( _mainpanel.getCurrentTreePanel() != null ) {
-            _mainpanel.getCurrentTreePanel().confColor();
-        }
-    }
-
-    void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
-        if ( item != null ) {
-            item.setFont( MainFrame.menu_font );
-            if ( !getConfiguration().isUseNativeUI() ) {
-                item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
-                item.setForeground( getConfiguration().getGuiMenuTextColor() );
-            }
-            item.setSelected( is_selected );
-            item.addActionListener( this );
-        }
-    }
-
-    JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
-        if ( jmi != null ) {
-            jmi.setFont( MainFrame.menu_font );
-            if ( !getConfiguration().isUseNativeUI() ) {
-                jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
-                jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
-            }
-            jmi.addActionListener( this );
-        }
-        return jmi;
-    }
-
-    void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
-        if ( item != null ) {
-            item.setFont( MainFrame.menu_font );
-            if ( !getConfiguration().isUseNativeUI() ) {
-                item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
-                item.setForeground( getConfiguration().getGuiMenuTextColor() );
-            }
-            item.setSelected( is_selected );
-            item.addActionListener( this );
-        }
-    }
-
-    void displayBasicInformation() {
-        if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
-            String title = "Basic Information";
-            if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
-                title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
-            }
-            showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
-        }
-    }
-
-    void exceptionOccuredDuringOpenFile( final Exception e ) {
-        try {
-            _mainpanel.getCurrentTreePanel().setArrowCursor();
-        }
-        catch ( final Exception ex ) {
-            // Do nothing.
-        }
-        JOptionPane.showMessageDialog( this,
-                                       ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
-                                       "Error during File|Open",
-                                       JOptionPane.ERROR_MESSAGE );
-    }
-
-    void exceptionOccuredDuringSaveAs( final Exception e ) {
-        try {
-            _mainpanel.getCurrentTreePanel().setArrowCursor();
-        }
-        catch ( final Exception ex ) {
-            // Do nothing.
-        }
-        JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
-    }
-
-    void executeGSDI() {
-        if ( !isOKforSDI( false, true ) ) {
-            return;
-        }
-        if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
-            JOptionPane.showMessageDialog( this,
-                                           "Gene tree is not rooted.",
-                                           "Cannot execute GSDI",
-                                           JOptionPane.ERROR_MESSAGE );
-            return;
-        }
-        final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
-        gene_tree.setAllNodesToNotCollapse();
-        gene_tree.recalculateNumberOfExternalDescendants( false );
-        GSDI gsdi = null;
-        final Phylogeny species_tree = getSpeciesTree().copy();
-        try {
-            gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
-        }
-        catch ( final SDIException e ) {
-            JOptionPane.showMessageDialog( this,
-                                           e.getLocalizedMessage(),
-                                           "Error during GSDI",
-                                           JOptionPane.ERROR_MESSAGE );
-            return;
-        }
-        catch ( final Exception e ) {
-            AptxUtil.unexpectedException( e );
-            return;
-        }
-        gene_tree.setRerootable( false );
-        gene_tree.clearHashIdToNodeMap();
-        gene_tree.recalculateNumberOfExternalDescendants( true );
-        _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
-        getMainPanel().getControlPanel().setShowEvents( true );
-        showWhole();
-        final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
-        _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
-        showWhole();
-        _mainpanel.getTabbedPane().setSelectedIndex( selected );
-        showWhole();
-        _mainpanel.getCurrentTreePanel().setEdited( true );
-        final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
-        if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
-            JOptionPane.showMessageDialog( this,
-                                           "Duplications: " + gsdi.getDuplicationsSum() + "\n"
-                                                   + "Potential duplications: "
-                                                   + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
-                                                   + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
-                                                   + "Stripped gene tree nodes: "
-                                                   + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
-                                                   + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
-                                                   + "Number of polytomies in species tree used: " + poly + "\n",
-                                           "GSDI successfully completed",
-                                           JOptionPane.WARNING_MESSAGE );
-        }
-        else {
-            JOptionPane.showMessageDialog( this,
-                                           "Duplications: " + gsdi.getDuplicationsSum() + "\n"
-                                                   + "Potential duplications: "
-                                                   + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
-                                                   + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
-                                                   + "Stripped gene tree nodes: "
-                                                   + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
-                                                   + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
-                                                   + "Number of polytomies in species tree used: " + poly + "\n",
-                                           "GSDI successfully completed",
-                                           JOptionPane.INFORMATION_MESSAGE );
-        }
-    }
-
-    void executeGSDIR() {
-        if ( !isOKforSDI( false, false ) ) {
-            return;
-        }
-        final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
-        if ( ( p > 0 )
-                && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
-            JOptionPane.showMessageDialog( this,
-                                           "Gene tree is not completely binary",
-                                           "Cannot execute GSDI",
-                                           JOptionPane.ERROR_MESSAGE );
-            return;
-        }
-        final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
-        gene_tree.setAllNodesToNotCollapse();
-        gene_tree.recalculateNumberOfExternalDescendants( false );
-        GSDIR gsdir = null;
-        final Phylogeny species_tree = getSpeciesTree().copy();
-        try {
-            gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
-        }
-        catch ( final SDIException e ) {
-            JOptionPane.showMessageDialog( this,
-                                           e.getLocalizedMessage(),
-                                           "Error during GSDIR",
-                                           JOptionPane.ERROR_MESSAGE );
-            return;
-        }
-        catch ( final Exception e ) {
-            AptxUtil.unexpectedException( e );
-            return;
-        }
-        final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
-        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();
-        final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
-        _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
-        showWhole();
-        _mainpanel.getTabbedPane().setSelectedIndex( selected );
-        showWhole();
-        _mainpanel.getCurrentTreePanel().setEdited( true );
-        final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
-        if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
-            JOptionPane.showMessageDialog( this,
-                                           "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
-                                                   + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
-                                                   + "Stripped gene tree nodes: "
-                                                   + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
-                                                   + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
-                                                   + "Number of polytomies in species tree used: " + poly + "\n",
-                                           "GSDIR successfully completed",
-                                           JOptionPane.WARNING_MESSAGE );
-        }
-        else {
-            JOptionPane.showMessageDialog( this,
-                                           "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
-                                                   + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
-                                                   + "Stripped gene tree nodes: "
-                                                   + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
-                                                   + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
-                                                   + "Number of polytomies in species tree used: " + poly + "\n",
-                                           "GSDIR successfully completed",
-                                           JOptionPane.INFORMATION_MESSAGE );
-        }
-    }
-
-    boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
-        if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
-            JOptionPane.showMessageDialog( this,
-                                           "Gene tree and species tree have no species in common.",
-                                           "Error during SDI",
-                                           JOptionPane.ERROR_MESSAGE );
-            return false;
-        }
-        else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
-            JOptionPane.showMessageDialog( this,
-                                           "Gene tree and species tree have only one species in common.",
-                                           "Error during SDI",
-                                           JOptionPane.ERROR_MESSAGE );
-            return false;
-        }
-        else {
-            return true;
-        }
-    }
-
-    TreePanel getCurrentTreePanel() {
-        return getMainPanel().getCurrentTreePanel();
-    }
-
-    JMenu getHelpMenu() {
-        return _help_jmenu;
-    }
-
-    JCheckBoxMenuItem getlabelDirectionCbmi() {
-        return _label_direction_cbmi;
-    }
-
-    JMenuBar getMenuBarOfMainFrame() {
-        return _jmenubar;
-    }
-
-    final Phylogeny getSpeciesTree() {
-        return _species_tree;
-    }
-
-    void help() {
-        final StringBuilder sb = new StringBuilder();
-        sb.append( "Display options\n" );
-        sb.append( "-------------------\n" );
-        sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
-        sb.append( "Clickable tree nodes\n" );
-        sb.append( "--------------------\n" );
-        sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
-        sb.append( "or by right clicking:\n" );
-        sb.append( "o  Display Node Data -- display information for a node\n" );
-        sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
-        sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
-        sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
-        sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
-        sb.append( "o  Colorize Subtree -- color a subtree\n" );
-        sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
-        sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
-        sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
-        sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
-        sb.append( "Zooming\n" );
-        sb.append( "---------\n" );
-        sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
-        sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
-        sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
-        sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
-        sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
-        sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
-        sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
-        sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
-        sb.append( "Quick tree manipulation:\n" );
-        sb.append( "------------------------\n" );
-        sb.append( "Order Subtrees -- order the tree by branch length\n" );
-        sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
-        sb.append( "Memory problems (Java heap space error)\n" );
-        sb.append( "---------------------------------------\n" );
-        sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
-        sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
-        sb.append( "the '-Xmx' Java command line option. For example:\n" );
-        sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
-        // + "General remarks\n"
-        // + "---------------\n"
-        // +
-        // "o  The application version permits copying to the clipboard \n"
-        // +
-        // "    in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
-        // +
-        // "o  Changes made to a subtree affect this subtree and its subtrees,\n"
-        // + "    but not any of its parent tree(s).\n"
-        // +
-        // "o  Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
-        // +
-        // "    are likely to be bootstrap values instead of branch length values.\n\n"
-        // +
-        // " Remarks regarding SDI (Speciation Duplication Inference):\n"
-        // +
-        // "o  Each external node of the gene tree (in display) needs to be associated with\n"
-        // +
-        // "    a species: either directly through the \"Species\" field, or the species\n"
-        // +
-        // "    is part of the sequence name in the form \"XXXX_SPECIES\"\n"
-        // +
-        // "    (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
-        // +
-        // "o  A species tree for each species of the gene tree needs to be loaded with\n"
-        // +
-        // "   \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
-        // +
-        // "o  !External nodes of the gene tree associated with species not present in\n"
-        // +
-        // "    the species tree are REMOVED prior to SDI execution!\n"
-        // +
-        // "o  Both the gene tree and the species tree must be completely binary.\n"
-        // +
-        // "o  Duplications and speciations are a function of the position of the root.\n"
-        // +
-        // "    Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
-        // + "    incorrect and need to be inferred again\n"
-        // +
-        // "    with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
-        sb.append( "phyloXML\n" );
-        sb.append( "-------------------\n" );
-        sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
-        sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
-        sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
-        sb.append( "\n" );
-        sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
-        sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
-        TextFrame.instantiate( sb.toString(), "Help", _textframes );
-    }
-
-    void initializeTypeMenu( final Options options ) {
-        setTypeMenuToAllUnselected();
-        switch ( options.getPhylogenyGraphicsType() ) {
-            case CONVEX:
-                _convex_type_cbmi.setSelected( true );
-                break;
-            case CURVED:
-                _curved_type_cbmi.setSelected( true );
-                break;
-            case EURO_STYLE:
-                _euro_type_cbmi.setSelected( true );
-                break;
-            case ROUNDED:
-                _rounded_type_cbmi.setSelected( true );
-                break;
-            case TRIANGULAR:
-                _triangular_type_cbmi.setSelected( true );
-                break;
-            case UNROOTED:
-                _unrooted_type_cbmi.setSelected( true );
-                break;
-            case CIRCULAR:
-                _circular_type_cbmi.setSelected( true );
-                break;
-            default:
-                _rectangular_type_cbmi.setSelected( true );
-                break;
-        }
-    }
-
-    boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
-        if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
-            return false;
-        }
-        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 && !getSpeciesTree().isCompletelyBinary() ) {
-            JOptionPane.showMessageDialog( this,
-                                           "Species tree is not completely binary",
-                                           "Cannot execute GSDI",
-                                           JOptionPane.ERROR_MESSAGE );
-            return false;
-        }
-        else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
-            JOptionPane.showMessageDialog( this,
-                                           "Gene tree is not completely binary",
-                                           "Cannot execute GSDI",
-                                           JOptionPane.ERROR_MESSAGE );
-            return false;
-        }
-        else {
-            return true;
-        }
-    }
-
-    boolean isSubtreeDisplayed() {
-        if ( getCurrentTreePanel() != null ) {
-            if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
-                JOptionPane
-                        .showMessageDialog( this,
-                                            "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
-                                            "Operation can not be exectuted on a sub-tree",
-                                            JOptionPane.WARNING_MESSAGE );
-                return true;
-            }
-        }
-        return false;
-    }
-
-    void midpointRoot() {
-        if ( _mainpanel.getCurrentTreePanel() != null ) {
-            _mainpanel.getCurrentTreePanel().midpointRoot();
-        }
-    }
-
-    abstract void readPhylogeniesFromURL();
-
-    void readPhylogeniesFromWebservice( final int i ) {
-        final UrlTreeReader reader = new UrlTreeReader( this, i );
-        new Thread( reader ).start();
-    }
-
-    void removeAllTextFrames() {
-        for( final TextFrame tf : _textframes ) {
-            if ( tf != null ) {
-                tf.close();
-            }
-        }
-        _textframes.clear();
-    }
-
-    void setConfiguration( final Configuration configuration ) {
-        _configuration = configuration;
-    }
-
-    void setInferenceManager( final InferenceManager i ) {
-        _inference_manager = i;
-    }
-
-    void setOptions( final Options options ) {
-        _options = options;
-    }
-
-    void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
-        setTypeMenuToAllUnselected();
-        switch ( type ) {
-            case CIRCULAR:
-                _circular_type_cbmi.setSelected( true );
-                break;
-            case CONVEX:
-                _convex_type_cbmi.setSelected( true );
-                break;
-            case CURVED:
-                _curved_type_cbmi.setSelected( true );
-                break;
-            case EURO_STYLE:
-                _euro_type_cbmi.setSelected( true );
-                break;
-            case ROUNDED:
-                _rounded_type_cbmi.setSelected( true );
-                break;
-            case RECTANGULAR:
-                _rectangular_type_cbmi.setSelected( true );
-                break;
-            case TRIANGULAR:
-                _triangular_type_cbmi.setSelected( true );
-                break;
-            case UNROOTED:
-                _unrooted_type_cbmi.setSelected( true );
-                break;
-            default:
-                throw new IllegalArgumentException( "unknown type: " + type );
-        }
-    }
-
-    final void setSpeciesTree( final Phylogeny species_tree ) {
-        _species_tree = species_tree;
-    }
-
-    void setTypeMenuToAllUnselected() {
-        _convex_type_cbmi.setSelected( false );
-        _curved_type_cbmi.setSelected( false );
-        _euro_type_cbmi.setSelected( false );
-        _rounded_type_cbmi.setSelected( false );
-        _triangular_type_cbmi.setSelected( false );
-        _rectangular_type_cbmi.setSelected( false );
-        _unrooted_type_cbmi.setSelected( false );
-        _circular_type_cbmi.setSelected( false );
-    }
-
-    void switchColors() {
-        final TreeColorSet colorset = _mainpanel.getTreeColorSet();
-        final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
-        csc.setVisible( true );
-    }
-
-    void taxColor() {
-        if ( _mainpanel.getCurrentTreePanel() != null ) {
-            _mainpanel.getCurrentTreePanel().taxColor();
-        }
-    }
-
-    void typeChanged( final Object o ) {
-        updateTypeCheckboxes( getOptions(), o );
-        updateOptions( getOptions() );
-        if ( getCurrentTreePanel() != null ) {
-            final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
-            final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
-            if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
-                    || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
-                    || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
-                    || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
-                getCurrentTreePanel().getControlPanel().showWhole();
-            }
-            if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
-                getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
-            }
-            else {
-                getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
-            }
-            getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
-            updateScreenTextAntialias( getMainPanel().getTreePanels() );
-            if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
-                if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
-                    getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
-                }
-                else {
-                    getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
-                }
-            }
-        }
-    }
-
-    void updateOptions( final Options options ) {
-        options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
-        options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
-                && _background_gradient_cbmi.isSelected() );
-        options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
-        options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
-                && _show_annotation_ref_source.isSelected() );
-        options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
-                && _abbreviate_scientific_names.isSelected() );
-        options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
-                && _color_labels_same_as_parent_branch.isSelected() );
-        options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
-                && _show_default_node_shapes_internal_cbmi.isSelected() );
-        options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
-                && _show_default_node_shapes_external_cbmi.isSelected() );
-        options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
-                && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
-        if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
-            options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
-        }
-        else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
-            options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
-        }
-        else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
-            options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
-        }
-        options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
-                && _search_case_senstive_cbmi.isSelected() );
-        if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
-            options.setShowScale( _show_scale_cbmi.isSelected() );
-        }
-        if ( _label_direction_cbmi != null ) {
-            if ( _label_direction_cbmi.isSelected() ) {
-                options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
-            }
-            else {
-                options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
-            }
-        }
-        options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
-        options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
-                && _show_confidence_stddev_cbmi.isSelected() );
-        if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
-            options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
-        }
-        options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
-                && ( _print_using_actual_size_cbmi.isSelected() ) );
-        options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
-                && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
-        options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
-        if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
-                && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
-            options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
-        }
-        else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
-                && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
-            options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
-        }
-        else {
-            options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
-        }
-        options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
-                && _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_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_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.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
-        }
-        options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
-                && _replace_underscores_cbmi.isSelected() );
-        options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
-                && _search_whole_words_only_cbmi.isSelected() );
-        options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
-                && _inverse_search_result_cbmi.isSelected() );
-        if ( _graphics_export_visible_only_cbmi != null ) {
-            options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
-            if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
-                _graphics_export_using_actual_size_cbmi.setSelected( true );
-                _graphics_export_using_actual_size_cbmi.setEnabled( false );
-            }
-            else {
-                _graphics_export_using_actual_size_cbmi.setEnabled( true );
-            }
-        }
-        if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
-            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
-        }
-        else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
-            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
-        }
-        else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
-            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
-        }
-        else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
-            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
-        }
-        else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
-            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
-        }
-        else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
-            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
-        }
-        else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
-            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
-        }
-        else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
-            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
-        }
-    }
-
-    void updateTypeCheckboxes( final Options options, final Object o ) {
-        setTypeMenuToAllUnselected();
-        ( ( JCheckBoxMenuItem ) o ).setSelected( true );
-    }
-
-    void viewAsNexus() {
-        if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
-            String title = "Nexus";
-            if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
-                title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
-            }
-            showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
-                           title );
-        }
-    }
-
-    void viewAsNH() {
-        if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
-            String title = "New Hampshire";
-            if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
-                title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
-            }
-            showTextFrame( _mainpanel.getCurrentPhylogeny()
-                                   .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
-                           title );
-        }
-    }
-
-    void viewAsXML() {
-        if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
-            String title = "phyloXML";
-            if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
-                title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
-            }
-            showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
-        }
-    }
-
-    private void annotateSequences() {
-        if ( getCurrentTreePanel() != null ) {
-            final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
-            if ( ( nodes == null ) || nodes.isEmpty() ) {
-                JOptionPane
-                        .showMessageDialog( this,
-                                            "Need to select nodes, either via direct selection or via the \"Search\" function",
-                                            "No nodes selected for annotation",
-                                            JOptionPane.ERROR_MESSAGE );
-                return;
-            }
-            final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
-            if ( ( phy != null ) && !phy.isEmpty() ) {
-                final JTextField ref_field = new JTextField( 10 );
-                final JTextField desc_filed = new JTextField( 20 );
-                ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
-                        : getPreviousNodeAnnotationReference() );
-                final JPanel my_panel = new JPanel();
-                my_panel.add( new JLabel( "Reference " ) );
-                my_panel.add( ref_field );
-                my_panel.add( Box.createHorizontalStrut( 15 ) );
-                my_panel.add( new JLabel( "Description " ) );
-                my_panel.add( desc_filed );
-                final int result = JOptionPane.showConfirmDialog( null,
-                                                                  my_panel,
-                                                                  "Enter the sequence annotation(s) for the "
-                                                                          + nodes.size() + " selected nodes",
-                                                                  JOptionPane.OK_CANCEL_OPTION );
-                if ( result == JOptionPane.OK_OPTION ) {
-                    String ref = ref_field.getText();
-                    String desc = desc_filed.getText();
-                    if ( !ForesterUtil.isEmpty( ref ) ) {
-                        ref = ref.trim();
-                        ref = ref.replaceAll( "\\s+", " " );
-                        if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 )
-                                || ( ref.length() < 3 ) ) {
-                            JOptionPane.showMessageDialog( this,
-                                                           "Reference needs to be in the form of \"GO:1234567\"",
-                                                           "Illegal Format for Annotation Reference",
-                                                           JOptionPane.ERROR_MESSAGE );
-                            return;
-                        }
-                    }
-                    if ( ref != null ) {
-                        setPreviousNodeAnnotationReference( ref );
-                    }
-                    if ( desc != null ) {
-                        desc = desc.trim();
-                        desc = desc.replaceAll( "\\s+", " " );
-                    }
-                    if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
-                        for( final Long id : nodes ) {
-                            final PhylogenyNode n = phy.getNode( id );
-                            ForesterUtil.ensurePresenceOfSequence( n );
-                            final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
-                                    : new Annotation( ref );
-                            if ( !ForesterUtil.isEmpty( desc ) ) {
-                                ann.setDesc( desc );
-                            }
-                            n.getNodeData().getSequence().addAnnotation( ann );
-                        }
-                    }
-                    getMainPanel().getControlPanel().showAnnotations();
-                }
-            }
-        }
-    }
-
-    private void chooseFont() {
-        final FontChooser fc = new FontChooser();
-        fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
-        fc.showDialog( this, "Select the Base Font" );
-        getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
-    }
-
-    private void chooseMinimalConfidence() {
-        final String s = ( String ) JOptionPane
-                .showInputDialog( this,
-                                  "Please enter the minimum for confidence values to be displayed.\n"
-                                          + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
-                                  "Minimal Confidence Value",
-                                  JOptionPane.QUESTION_MESSAGE,
-                                  null,
-                                  null,
-                                  getOptions().getMinConfidenceValue() );
-        if ( !ForesterUtil.isEmpty( s ) ) {
-            boolean success = true;
-            double m = 0.0;
-            final String m_str = s.trim();
-            if ( !ForesterUtil.isEmpty( m_str ) ) {
-                try {
-                    m = Double.parseDouble( m_str );
-                }
-                catch ( final Exception ex ) {
-                    success = false;
-                }
-            }
-            else {
-                success = false;
-            }
-            if ( success && ( m >= 0.0 ) ) {
-                getOptions().setMinConfidenceValue( m );
-            }
-        }
-    }
-
-    private void doUpdateProcessMenu() {
-        if ( _process_pool.size() > 0 ) {
-            if ( _process_menu == null ) {
-                _process_menu = createMenu( "", getConfiguration() );
-                _process_menu.setForeground( Color.RED );
-            }
-            _process_menu.removeAll();
-            final String text = "processes running: " + _process_pool.size();
-            _process_menu.setText( text );
-            _jmenubar.add( _process_menu );
-            for( int i = 0; i < _process_pool.size(); ++i ) {
-                final ProcessRunning p = _process_pool.getProcessByIndex( i );
-                _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
-            }
-        }
-        else {
-            if ( _process_menu != null ) {
-                _process_menu.removeAll();
-                _jmenubar.remove( _process_menu );
-            }
-        }
-        _jmenubar.validate();
-        _jmenubar.repaint();
-        repaint();
-    }
-
-    private String getPreviousNodeAnnotationReference() {
-        return _previous_node_annotation_ref;
-    }
-
-    private void removeBranchColors() {
-        if ( getMainPanel().getCurrentPhylogeny() != null ) {
-            AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
-        }
-    }
-
-    private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
-        _previous_node_annotation_ref = previous_node_annotation_ref;
-    }
-
-    /**
-     * Display the about box.
-     */
-    static void about() {
-        final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
-        about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
-        about.append( "All Rights Reserved\n" );
-        about.append( "License: GNU Lesser General Public License (LGPL)\n" );
-        about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
-        about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
-        about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
-        about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
-        if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
-            about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
-        }
-        if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
-                && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
-            about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
-                    + ForesterUtil.OS_VERSION + "]\n" );
-        }
-        final Runtime rt = java.lang.Runtime.getRuntime();
-        final long free_memory = rt.freeMemory() / 1000000;
-        final long total_memory = rt.totalMemory() / 1000000;
-        about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
-        about.append( "[locale: " + Locale.getDefault() + "]\n" );
-        about.append( "References:\n" );
-        about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
-        about.append( "For more information & download:\n" );
-        about.append( Constants.APTX_WEB_SITE + "\n" );
-        about.append( "Comments: " + Constants.AUTHOR_EMAIL );
-        JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
-    }
-
-    static void chooseNodeSize( final Options options, final Component parent ) {
-        final String s = ( String ) JOptionPane.showInputDialog( parent,
-                                                                 "Please enter the default size for node shapes.\n"
-                                                                         + "[current value: "
-                                                                         + options.getDefaultNodeShapeSize() + "]\n",
-                                                                 "Node Shape Size",
-                                                                 JOptionPane.QUESTION_MESSAGE,
-                                                                 null,
-                                                                 null,
-                                                                 options.getDefaultNodeShapeSize() );
-        if ( !ForesterUtil.isEmpty( s ) ) {
-            boolean success = true;
-            double m = 0.0;
-            final String m_str = s.trim();
-            if ( !ForesterUtil.isEmpty( m_str ) ) {
-                try {
-                    m = Double.parseDouble( m_str );
-                }
-                catch ( final Exception ex ) {
-                    success = false;
-                }
-            }
-            else {
-                success = false;
-            }
-            if ( success && ( m >= 0.0 ) ) {
-                final short size = ForesterUtil.roundToShort( m );
-                if ( size >= 0.0 ) {
-                    options.setDefaultNodeShapeSize( size );
-                }
-            }
-        }
-    }
-
-    static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
-        return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
-    }
-
-    static JMenu createMenu( final String title, final Configuration conf ) {
-        final JMenu jmenu = new JMenu( title );
-        if ( !conf.isUseNativeUI() ) {
-            jmenu.setFont( MainFrame.menu_font );
-            jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
-            jmenu.setForeground( conf.getGuiMenuTextColor() );
-        }
-        return jmenu;
-    }
-
-    static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
-        label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
-        if ( !configuration.isUseNativeUI() ) {
-            label.setBackground( configuration.getGuiMenuBackgroundColor() );
-            label.setForeground( configuration.getGuiMenuTextColor() );
-            label.setOpaque( true );
-        }
-        label.setSelected( false );
-        label.setEnabled( false );
-        return label;
-    }
-
-    static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
-        switch ( op.getDefaultNodeFill() ) {
-            case GRADIENT:
-                op.setDefaultNodeFill( NodeFill.SOLID );
-                break;
-            case NONE:
-                op.setDefaultNodeFill( NodeFill.GRADIENT );
-                break;
-            case SOLID:
-                op.setDefaultNodeFill( NodeFill.NONE );
-                break;
-            default:
-                throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
-        }
-    }
-
-    static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
-        switch ( op.getDefaultNodeShape() ) {
-            case CIRCLE:
-                op.setDefaultNodeShape( NodeShape.RECTANGLE );
-                break;
-            case RECTANGLE:
-                op.setDefaultNodeShape( NodeShape.CIRCLE );
-                break;
-            default:
-                throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
-        }
-    }
-
-    static void cycleOverview( final Options op, final TreePanel tree_panel ) {
-        switch ( op.getOvPlacement() ) {
-            case LOWER_LEFT:
-                op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
-                break;
-            case LOWER_RIGHT:
-                op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
-                break;
-            case UPPER_LEFT:
-                op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
-                break;
-            case UPPER_RIGHT:
-                op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
-                break;
-            default:
-                throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
-        }
-        if ( tree_panel != null ) {
-            tree_panel.updateOvSettings();
-        }
-    }
-
-    static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
-        if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
-            mi.setText( "Cycle Node Shape Fill Type... (current: "
-                    + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
-        }
-        else {
-            mi.setText( "Cycle Node Shape Fill Type..." );
-        }
-    }
-
-    static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
-        if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
-            mi.setText( "Cycle Node Shape Fill Type... (current: "
-                    + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
-        }
-        else {
-            mi.setText( "Cycle Node Shape Fill Type..." );
-        }
-    }
-
-    static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
-        if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
-            mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
-        }
-        else {
-            mi.setText( "Cycle Overview Placement..." );
-        }
-    }
-
-    static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
-        if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
-            mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
-        }
-        else {
-            mi.setText( "Select Colors..." );
-        }
-    }
-
-    static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
-        mi.setText( "Select Font... (current: " + font_desc + ")" );
-    }
-
-    static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
-        if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
-            mi.setEnabled( true );
-        }
-        else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
-            mi.setEnabled( true );
-        }
-        else {
-            mi.setEnabled( false );
-        }
-        mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
-    }
-
-    static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
-        mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
-    }
-
-    static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
-                                                           final JCheckBoxMenuItem scale,
-                                                           final JCheckBoxMenuItem branch_lengths,
-                                                           final JRadioButtonMenuItem non_lined_up,
-                                                           final JRadioButtonMenuItem uniform_clado,
-                                                           final JRadioButtonMenuItem nonuniform_clado,
-                                                           final JCheckBoxMenuItem label_direction_cbmi ) {
-        final TreePanel tree_panel = main_panel.getCurrentTreePanel();
-        final ControlPanel control = main_panel.getControlPanel();
-        final Options options = main_panel.getOptions();
-        scale.setSelected( options.isShowScale() );
-        branch_lengths.setSelected( options.isShowBranchLengthValues() );
-        // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
-        if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
-            scale.setSelected( false );
-            scale.setEnabled( false );
-            branch_lengths.setSelected( false );
-            branch_lengths.setEnabled( false );
-        }
-        else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
-            scale.setSelected( false );
-            scale.setEnabled( false );
-            branch_lengths.setEnabled( true );
-        }
-        else {
-            scale.setEnabled( true );
-            branch_lengths.setEnabled( true );
-        }
-        if ( ( tree_panel != null )
-                && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
-                        && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
-                        .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
-            branch_lengths.setSelected( false );
-            branch_lengths.setEnabled( false );
-        }
-        if ( tree_panel != null ) {
-            if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
-                    || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
-                non_lined_up.setEnabled( false );
-                uniform_clado.setEnabled( false );
-                nonuniform_clado.setEnabled( false );
-            }
-            else {
-                non_lined_up.setEnabled( true );
-                uniform_clado.setEnabled( true );
-                nonuniform_clado.setEnabled( true );
-            }
-        }
-        else {
-            if ( ( tree_panel != null )
-                    && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
-                            .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
-                branch_lengths.setSelected( false );
-                branch_lengths.setEnabled( false );
-            }
-            if ( ( tree_panel != null )
-                    && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
-                            .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
-                non_lined_up.setEnabled( false );
-            }
-            else {
-                // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
-                non_lined_up.setEnabled( true );
-            }
-        }
-        label_direction_cbmi.setEnabled( true );
-        if ( tree_panel != null ) {
-            if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
-                    && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
-                label_direction_cbmi.setEnabled( false );
-            }
-            if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
-                scale.setSelected( false );
-                scale.setEnabled( false );
-            }
-        }
-    }
-
-    static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
-        for( final TreePanel tree_panel : treepanels ) {
-            tree_panel.setTextAntialias();
-        }
-    }
-}
+// $Id:\r
+// FORESTER -- software libraries and applications\r
+// for evolutionary biology research and applications.\r
+//\r
+// Copyright (C) 2008-2010 Christian M. Zmasek\r
+// All rights reserved\r
+//\r
+// This library is free software; you can redistribute it and/or\r
+// modify it under the terms of the GNU Lesser General Public\r
+// License as published by the Free Software Foundation; either\r
+// version 2.1 of the License, or (at your option) any later version.\r
+//\r
+// This library is distributed in the hope that it will be useful,\r
+// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+// Lesser General Public License for more details.\r
+//\r
+// You should have received a copy of the GNU Lesser General Public\r
+// License along with this library; if not, write to the Free Software\r
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+//\r
+// Contact: phylosoft @ gmail . com\r
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
+\r
+package org.forester.archaeopteryx;\r
+\r
+import java.awt.Color;\r
+import java.awt.Component;\r
+import java.awt.Container;\r
+import java.awt.Font;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.io.File;\r
+import java.io.IOException;\r
+import java.util.ArrayList;\r
+import java.util.LinkedList;\r
+import java.util.List;\r
+import java.util.Locale;\r
+import java.util.NoSuchElementException;\r
+\r
+import javax.swing.Box;\r
+import javax.swing.JApplet;\r
+import javax.swing.JCheckBoxMenuItem;\r
+import javax.swing.JFrame;\r
+import javax.swing.JLabel;\r
+import javax.swing.JMenu;\r
+import javax.swing.JMenuBar;\r
+import javax.swing.JMenuItem;\r
+import javax.swing.JOptionPane;\r
+import javax.swing.JPanel;\r
+import javax.swing.JRadioButtonMenuItem;\r
+import javax.swing.JTextField;\r
+import javax.swing.SwingUtilities;\r
+\r
+import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
+import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
+import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
+import org.forester.archaeopteryx.tools.InferenceManager;\r
+import org.forester.archaeopteryx.tools.ProcessPool;\r
+import org.forester.archaeopteryx.tools.ProcessRunning;\r
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
+import org.forester.phylogeny.Phylogeny;\r
+import org.forester.phylogeny.PhylogenyMethods;\r
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
+import org.forester.phylogeny.PhylogenyNode;\r
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
+import org.forester.phylogeny.data.Annotation;\r
+import org.forester.phylogeny.data.NodeDataField;\r
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
+import org.forester.sdi.GSDI;\r
+import org.forester.sdi.GSDIR;\r
+import org.forester.sdi.SDIException;\r
+import org.forester.util.ForesterConstants;\r
+import org.forester.util.ForesterUtil;\r
+\r
+public abstract class MainFrame extends JFrame implements ActionListener {\r
+\r
+    static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
+    static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                                //TODO //FIXME\r
+    static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
+    private static final long   serialVersionUID                        = 3655000897845508358L;\r
+    final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
+                                                                                    Font.PLAIN,\r
+                                                                                    10 );\r
+    static final String         TYPE_MENU_HEADER                        = "Type";\r
+    static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
+    static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
+    static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
+    static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
+    static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
+    static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
+    static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                          //TODO\r
+    static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                          //TODO\r
+    static final String         OPTIONS_HEADER                          = "Options";\r
+    static final String         SEARCH_SUBHEADER                        = "Search:";\r
+    static final String         DISPLAY_SUBHEADER                       = "Display:";\r
+    static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
+    static final String         SEARCH_REGEX_LABEL                      = "Search with Regular Expressions";\r
+    static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
+    static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
+    static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
+    static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
+    static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
+    static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
+    static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
+    static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
+    static final String         SEARCH_WITH_REGEX_TIP                   = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";\r
+    static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
+    static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
+    static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
+    static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Shapes for External Nodes";\r
+    static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Shapes for Internal Nodes";\r
+    static final String         DISPLAY_NODE_BOXES_LABEL_MARKED         = "Shapes for Nodes with Visual Data";\r
+    static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
+    static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
+    static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
+    static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
+    static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
+    static final String         COLOR_LABELS_TIP                        = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";\r
+    static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
+    static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
+    static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
+    static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
+    static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
+    static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
+    static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
+    static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
+    static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
+    static final String         RIGHT_LINE_UP_DOMAINS                   = "Right-align Domain Architectures";\r
+    static final String         LINE_UP_RENDERABLE_DATA                 = "Line Up Diagrams (such as Domain Architectures)";\r
+    JMenuBar                    _jmenubar;\r
+    JMenu                       _file_jmenu;\r
+    JMenu                       _tools_menu;\r
+    JMenu                       _view_jmenu;\r
+    JMenu                       _options_jmenu;\r
+    JMenu                       _font_size_menu;\r
+    JMenu                       _help_jmenu;\r
+    JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
+    // Analysis menu\r
+    JMenu                       _analysis_menu;\r
+    JMenuItem                   _load_species_tree_item;\r
+    JMenuItem                   _gsdi_item;\r
+    JMenuItem                   _gsdir_item;\r
+    JMenuItem                   _lineage_inference;\r
+    // file menu:\r
+    JMenuItem                   _open_item;\r
+    JMenuItem                   _open_url_item;\r
+    JMenuItem                   _save_item;\r
+    JMenuItem                   _save_all_item;\r
+    JMenuItem                   _close_item;\r
+    JMenuItem                   _exit_item;\r
+    JMenuItem                   _new_item;\r
+    // tools menu:\r
+    JMenuItem                   _midpoint_root_item;\r
+    JMenuItem                   _taxcolor_item;\r
+    JMenuItem                   _confcolor_item;\r
+    JMenuItem                   _color_rank_jmi;\r
+    JMenuItem                   _collapse_species_specific_subtrees;\r
+    JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
+    JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
+    JMenuItem                   _obtain_seq_information_jmi;\r
+    JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
+    JMenuItem                   _move_node_names_to_seq_names_jmi;\r
+    JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
+    JMenuItem                   _annotate_item;\r
+    JMenuItem                   _remove_branch_color_item;\r
+    JMenuItem                   _remove_visual_styles_item;\r
+    JMenuItem                   _delete_selected_nodes_item;\r
+    JMenuItem                   _delete_not_selected_nodes_item;\r
+    // font size menu:\r
+    JMenuItem                   _super_tiny_fonts_item;\r
+    JMenuItem                   _tiny_fonts_item;\r
+    JMenuItem                   _small_fonts_item;\r
+    JMenuItem                   _medium_fonts_item;\r
+    JMenuItem                   _large_fonts_item;\r
+    // options menu:\r
+    // _  screen and print\r
+    JMenuItem                   _choose_font_mi;\r
+    JMenuItem                   _switch_colors_mi;\r
+    JCheckBoxMenuItem           _label_direction_cbmi;\r
+    // _  screen display\r
+    JCheckBoxMenuItem           _screen_antialias_cbmi;\r
+    JCheckBoxMenuItem           _background_gradient_cbmi;\r
+    JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
+    JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
+    JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
+    JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
+    JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                                      //TODO fix me\r
+    JCheckBoxMenuItem           _show_overview_cbmi;\r
+    JCheckBoxMenuItem           _show_domain_labels;\r
+    JCheckBoxMenuItem           _show_annotation_ref_source;\r
+    JCheckBoxMenuItem           _abbreviate_scientific_names;\r
+    JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
+    JMenuItem                   _overview_placment_mi;\r
+    JMenuItem                   _choose_minimal_confidence_mi;\r
+    JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
+    JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
+    JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;\r
+    JMenuItem                   _cycle_node_shape_mi;\r
+    JMenuItem                   _cycle_node_fill_mi;\r
+    JMenuItem                   _choose_node_size_mi;\r
+    JMenuItem                   _cycle_data_return;\r
+    JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
+    JCheckBoxMenuItem           _right_line_up_domains_cbmi;\r
+    JCheckBoxMenuItem           _line_up_renderable_data_cbmi;\r
+    // _  print\r
+    JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
+    JCheckBoxMenuItem           _antialias_print_cbmi;\r
+    JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
+    JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
+    JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
+    JMenuItem                   _print_size_mi;\r
+    JMenuItem                   _choose_pdf_width_mi;\r
+    // _  parsing\r
+    JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
+    JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
+    JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
+    JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
+    JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
+    JCheckBoxMenuItem           _replace_underscores_cbmi;\r
+    JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
+    JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
+    JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
+    // _  search\r
+    JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
+    JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
+    JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
+    JCheckBoxMenuItem           _search_with_regex_cbmi;\r
+    // type menu:\r
+    JMenu                       _type_menu;\r
+    JCheckBoxMenuItem           _rectangular_type_cbmi;\r
+    JCheckBoxMenuItem           _triangular_type_cbmi;\r
+    JCheckBoxMenuItem           _curved_type_cbmi;\r
+    JCheckBoxMenuItem           _convex_type_cbmi;\r
+    JCheckBoxMenuItem           _euro_type_cbmi;\r
+    JCheckBoxMenuItem           _rounded_type_cbmi;\r
+    JCheckBoxMenuItem           _unrooted_type_cbmi;\r
+    JCheckBoxMenuItem           _circular_type_cbmi;\r
+    // view as text menu:\r
+    JMenuItem                   _view_as_NH_item;\r
+    JMenuItem                   _view_as_XML_item;\r
+    JMenuItem                   _view_as_nexus_item;\r
+    JMenuItem                   _display_basic_information_item;\r
+    // help menu:\r
+    JMenuItem                   _about_item;\r
+    JMenuItem                   _help_item;\r
+    JMenuItem                   _website_item;\r
+    JMenuItem                   _phyloxml_website_item;\r
+    JMenuItem                   _phyloxml_ref_item;\r
+    JMenuItem                   _aptx_ref_item;\r
+    // process menu:\r
+    JMenu                       _process_menu;\r
+    // Handy pointers to child components:\r
+    MainPanel                   _mainpanel;\r
+    Container                   _contentpane;\r
+    final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                                  ;\r
+    Configuration               _configuration;\r
+    Options                     _options;\r
+    private Phylogeny           _species_tree;\r
+    InferenceManager            _inference_manager;\r
+    final ProcessPool           _process_pool;\r
+    private String              _previous_node_annotation_ref;\r
+\r
+    MainFrame() {\r
+        _process_pool = ProcessPool.createInstance();\r
+    }\r
+\r
+    /**\r
+     * Action performed.\r
+     */\r
+    @Override\r
+    public void actionPerformed( final ActionEvent e ) {\r
+        final Object o = e.getSource();\r
+        boolean is_applet = false;\r
+        JApplet applet = null;\r
+        if ( getCurrentTreePanel() != null ) {\r
+            is_applet = getCurrentTreePanel().isApplet();\r
+            if ( is_applet ) {\r
+                applet = getCurrentTreePanel().obtainApplet();\r
+            }\r
+        }\r
+        if ( o == _exit_item ) {\r
+            close();\r
+        }\r
+        else if ( o == _gsdi_item ) {\r
+            if ( isSubtreeDisplayed() ) {\r
+                return;\r
+            }\r
+            executeGSDI();\r
+        }\r
+        else if ( o == _gsdir_item ) {\r
+            if ( isSubtreeDisplayed() ) {\r
+                return;\r
+            }\r
+            executeGSDIR();\r
+        }\r
+        else if ( o == _taxcolor_item ) {\r
+            taxColor();\r
+        }\r
+        else if ( o == _confcolor_item ) {\r
+            confColor();\r
+        }\r
+        else if ( o == _color_rank_jmi ) {\r
+            colorRank();\r
+        }\r
+        else if ( o == _collapse_species_specific_subtrees ) {\r
+            if ( isSubtreeDisplayed() ) {\r
+                return;\r
+            }\r
+            if ( getCurrentTreePanel() != null ) {\r
+                getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
+            }\r
+        }\r
+        else if ( o == _remove_branch_color_item ) {\r
+            if ( isSubtreeDisplayed() ) {\r
+                return;\r
+            }\r
+            removeBranchColors();\r
+        }\r
+        else if ( o == _remove_visual_styles_item ) {\r
+            if ( isSubtreeDisplayed() ) {\r
+                return;\r
+            }\r
+            removeVisualStyles();\r
+        }\r
+        else if ( o == _midpoint_root_item ) {\r
+            if ( isSubtreeDisplayed() ) {\r
+                return;\r
+            }\r
+            midpointRoot();\r
+        }\r
+        else if ( o == _delete_selected_nodes_item ) {\r
+            if ( isSubtreeDisplayed() ) {\r
+                return;\r
+            }\r
+            deleteSelectedNodes( true );\r
+        }\r
+        else if ( o == _delete_not_selected_nodes_item ) {\r
+            if ( isSubtreeDisplayed() ) {\r
+                return;\r
+            }\r
+            deleteSelectedNodes( false );\r
+        }\r
+        else if ( o == _annotate_item ) {\r
+            annotateSequences();\r
+        }\r
+        else if ( o == _switch_colors_mi ) {\r
+            switchColors();\r
+        }\r
+        else if ( o == _display_basic_information_item ) {\r
+            if ( getCurrentTreePanel() != null ) {\r
+                displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
+            }\r
+        }\r
+        else if ( o == _view_as_NH_item ) {\r
+            viewAsNH();\r
+        }\r
+        else if ( o == _view_as_XML_item ) {\r
+            viewAsXML();\r
+        }\r
+        else if ( o == _view_as_nexus_item ) {\r
+            viewAsNexus();\r
+        }\r
+        else if ( o == _super_tiny_fonts_item ) {\r
+            if ( getCurrentTreePanel() != null ) {\r
+                getCurrentTreePanel().setSuperTinyFonts();\r
+                getCurrentTreePanel().repaint();\r
+            }\r
+        }\r
+        else if ( o == _tiny_fonts_item ) {\r
+            if ( getCurrentTreePanel() != null ) {\r
+                getCurrentTreePanel().setTinyFonts();\r
+                getCurrentTreePanel().repaint();\r
+            }\r
+        }\r
+        else if ( o == _small_fonts_item ) {\r
+            if ( getCurrentTreePanel() != null ) {\r
+                getCurrentTreePanel().setSmallFonts();\r
+                getCurrentTreePanel().repaint();\r
+            }\r
+        }\r
+        else if ( o == _medium_fonts_item ) {\r
+            if ( getCurrentTreePanel() != null ) {\r
+                getCurrentTreePanel().setMediumFonts();\r
+                getCurrentTreePanel().repaint();\r
+            }\r
+        }\r
+        else if ( o == _large_fonts_item ) {\r
+            if ( getCurrentTreePanel() != null ) {\r
+                getCurrentTreePanel().setLargeFonts();\r
+                getCurrentTreePanel().repaint();\r
+            }\r
+        }\r
+        else if ( o == _choose_font_mi ) {\r
+            chooseFont();\r
+        }\r
+        else if ( o == _choose_minimal_confidence_mi ) {\r
+            chooseMinimalConfidence();\r
+        }\r
+        else if ( o == _choose_node_size_mi ) {\r
+            chooseNodeSize( getOptions(), this );\r
+        }\r
+        else if ( o == _overview_placment_mi ) {\r
+            MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
+        }\r
+        else if ( o == _cycle_node_fill_mi ) {\r
+            MainFrame.cycleNodeFill( getOptions() );\r
+        }\r
+        else if ( o == _cycle_node_shape_mi ) {\r
+            MainFrame.cycleNodeShape( getOptions() );\r
+        }\r
+        else if ( o == _cycle_data_return ) {\r
+            MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );\r
+        }\r
+        else if ( o == _screen_antialias_cbmi ) {\r
+            updateOptions( getOptions() );\r
+            updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
+        }\r
+        else if ( o == _background_gradient_cbmi ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _show_domain_labels ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _show_annotation_ref_source ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _abbreviate_scientific_names ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _color_labels_same_as_parent_branch ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _show_default_node_shapes_external_cbmi ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _non_lined_up_cladograms_rbmi ) {\r
+            updateOptions( getOptions() );\r
+            showWhole();\r
+        }\r
+        else if ( o == _uniform_cladograms_rbmi ) {\r
+            updateOptions( getOptions() );\r
+            showWhole();\r
+        }\r
+        else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
+            updateOptions( getOptions() );\r
+            showWhole();\r
+        }\r
+        else if ( o == _search_case_senstive_cbmi ) {\r
+            updateOptions( getOptions() );\r
+            getMainPanel().getControlPanel().search0();\r
+            getMainPanel().getControlPanel().search1();\r
+        }\r
+        else if ( o == _search_whole_words_only_cbmi ) {\r
+            if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
+                _search_with_regex_cbmi.setSelected( false );\r
+            }\r
+            updateOptions( getOptions() );\r
+            getMainPanel().getControlPanel().search0();\r
+            getMainPanel().getControlPanel().search1();\r
+        }\r
+        else if ( o == _inverse_search_result_cbmi ) {\r
+            updateOptions( getOptions() );\r
+            getMainPanel().getControlPanel().search0();\r
+            getMainPanel().getControlPanel().search1();\r
+        }\r
+        else if ( o == _search_with_regex_cbmi ) {\r
+            if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
+                _search_whole_words_only_cbmi.setSelected( false );\r
+            }\r
+            if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
+                _search_case_senstive_cbmi.setSelected( true );\r
+            }\r
+            updateOptions( getOptions() );\r
+            getMainPanel().getControlPanel().search0();\r
+            getMainPanel().getControlPanel().search1();\r
+        }\r
+        else if ( o == _show_scale_cbmi ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _color_by_taxonomic_group_cbmi ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _show_confidence_stddev_cbmi ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
+            if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+                _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
+            }\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
+            if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+                _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
+            }\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _label_direction_cbmi ) {\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _show_overview_cbmi ) {\r
+            updateOptions( getOptions() );\r
+            if ( getCurrentTreePanel() != null ) {\r
+                getCurrentTreePanel().updateOvSizes();\r
+            }\r
+        }\r
+        else if ( o == _line_up_renderable_data_cbmi ) {\r
+            if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
+                _right_line_up_domains_cbmi.setSelected( false );\r
+            }\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( o == _right_line_up_domains_cbmi ) {\r
+            if ( _right_line_up_domains_cbmi.isSelected() ) {\r
+                _line_up_renderable_data_cbmi.setSelected( true );\r
+            }\r
+            updateOptions( getOptions() );\r
+        }\r
+        else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
+                || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
+                || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
+            typeChanged( o );\r
+        }\r
+        else if ( o == _about_item ) {\r
+            about();\r
+        }\r
+        else if ( o == _help_item ) {\r
+            try {\r
+                AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
+            }\r
+            catch ( final IOException e1 ) {\r
+                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+            }\r
+        }\r
+        else if ( o == _website_item ) {\r
+            try {\r
+                AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
+            }\r
+            catch ( final IOException e1 ) {\r
+                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+            }\r
+        }\r
+        else if ( o == _phyloxml_website_item ) {\r
+            try {\r
+                AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
+            }\r
+            catch ( final IOException e1 ) {\r
+                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+            }\r
+        }\r
+        else if ( o == _aptx_ref_item ) {\r
+            try {\r
+                AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
+            }\r
+            catch ( final IOException e1 ) {\r
+                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+            }\r
+        }\r
+        else if ( o == _phyloxml_ref_item ) {\r
+            try {\r
+                AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
+            }\r
+            catch ( final IOException e1 ) {\r
+                ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+            }\r
+        }\r
+        else {\r
+            if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
+                for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
+                    if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
+                        readPhylogeniesFromWebservice( i );\r
+                    }\r
+                }\r
+            }\r
+        }\r
+        _contentpane.repaint();\r
+    }\r
+\r
+    private void deleteSelectedNodes( final boolean delete ) {\r
+        final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+        if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
+            return;\r
+        }\r
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+        if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+            final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+            for( final PhylogenyNode n : all_selected_nodes ) {\r
+                if ( n.isExternal() ) {\r
+                    nodes.add( n );\r
+                }\r
+            }\r
+        }\r
+        String function = "Retain";\r
+        if ( delete ) {\r
+            function = "Delete";\r
+        }\r
+        if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+            JOptionPane\r
+            .showMessageDialog( this,\r
+                                "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
+                                "No external nodes selected to " + function.toLowerCase(),\r
+                                JOptionPane.ERROR_MESSAGE );\r
+            return;\r
+        }\r
+        final int todo = nodes.size();\r
+        final int ext = phy.getNumberOfExternalNodes();\r
+        int res = todo;\r
+        if ( delete ) {\r
+            res = ext - todo;\r
+        }\r
+        if ( res < 1 ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Cannot delete all nodes",\r
+                                           "Attempt to delete all nodes ",\r
+                                           JOptionPane.ERROR_MESSAGE );\r
+            return;\r
+        }\r
+        final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
+                                                          + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
+                                                          + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
+        if ( result == JOptionPane.OK_OPTION ) {\r
+            if ( !delete ) {\r
+                final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
+                for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+                    final PhylogenyNode n = it.next();\r
+                    if ( !nodes.contains( n ) ) {\r
+                        to_delete.add( n );\r
+                    }\r
+                }\r
+                for( final PhylogenyNode n : to_delete ) {\r
+                    phy.deleteSubtree( n, true );\r
+                }\r
+            }\r
+            else {\r
+                for( final PhylogenyNode n : nodes ) {\r
+                    phy.deleteSubtree( n, true );\r
+                }\r
+            }\r
+            resetSearch();\r
+            getCurrentTreePanel().setNodeInPreorderToNull();\r
+            phy.externalNodesHaveChanged();\r
+            phy.clearHashIdToNodeMap();\r
+            phy.recalculateNumberOfExternalDescendants( true );\r
+            getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+            getCurrentTreePanel().setEdited( true );\r
+            repaint();\r
+        }\r
+    }\r
+\r
+    void resetSearch() {\r
+        getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
+        getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
+        getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
+        getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
+        getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
+        getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
+        getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
+        getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
+        getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
+        getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
+        getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
+        getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
+    }\r
+\r
+    public Configuration getConfiguration() {\r
+        return _configuration;\r
+    }\r
+\r
+    /**\r
+     * This method returns the current external node data which\r
+     * has been selected by the user by clicking the "Return ..."\r
+     * menu item. This method is expected to be called from Javascript or\r
+     * something like it.\r
+     *\r
+     * @return current external node data as String\r
+     */\r
+    public String getCurrentExternalNodesDataBuffer() {\r
+        return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
+    }\r
+\r
+    public int getCurrentExternalNodesDataBufferChangeCounter() {\r
+        return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
+    }\r
+\r
+    public int getCurrentExternalNodesDataBufferLength() {\r
+        return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
+    }\r
+\r
+    public InferenceManager getInferenceManager() {\r
+        return _inference_manager;\r
+    }\r
+\r
+    public MainPanel getMainPanel() {\r
+        return _mainpanel;\r
+    }\r
+\r
+    public Options getOptions() {\r
+        return _options;\r
+    }\r
+\r
+    public ProcessPool getProcessPool() {\r
+        return _process_pool;\r
+    }\r
+\r
+    public void showTextFrame( final String s, final String title ) {\r
+        checkTextFrames();\r
+        _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
+    }\r
+\r
+    public void showWhole() {\r
+        _mainpanel.getControlPanel().showWhole();\r
+    }\r
+\r
+    public void updateProcessMenu() {\r
+        // In general Swing is not thread safe.\r
+        // See "Swing's Threading Policy".\r
+        SwingUtilities.invokeLater( new Runnable() {\r
+\r
+            @Override\r
+            public void run() {\r
+                doUpdateProcessMenu();\r
+            }\r
+        } );\r
+    }\r
+\r
+    void activateSaveAllIfNeeded() {\r
+        if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
+            _save_all_item.setEnabled( true );\r
+        }\r
+        else {\r
+            _save_all_item.setEnabled( false );\r
+        }\r
+    }\r
+\r
+    void buildFileMenu() {\r
+        _file_jmenu = createMenu( "File", getConfiguration() );\r
+        _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+        customizeJMenuItem( _exit_item );\r
+        _jmenubar.add( _file_jmenu );\r
+    }\r
+\r
+    void buildFontSizeMenu() {\r
+        _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
+        _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
+        _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
+        _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
+        _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
+        _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
+        customizeJMenuItem( _super_tiny_fonts_item );\r
+        customizeJMenuItem( _tiny_fonts_item );\r
+        customizeJMenuItem( _small_fonts_item );\r
+        customizeJMenuItem( _medium_fonts_item );\r
+        customizeJMenuItem( _large_fonts_item );\r
+        _jmenubar.add( _font_size_menu );\r
+    }\r
+\r
+    void buildHelpMenu() {\r
+        _help_jmenu = createMenu( "Help", getConfiguration() );\r
+        _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
+        _help_jmenu.addSeparator();\r
+        _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
+        _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
+        _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
+        _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
+        _help_jmenu.addSeparator();\r
+        _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
+        customizeJMenuItem( _help_item );\r
+        customizeJMenuItem( _website_item );\r
+        customizeJMenuItem( _phyloxml_website_item );\r
+        customizeJMenuItem( _aptx_ref_item );\r
+        customizeJMenuItem( _phyloxml_ref_item );\r
+        customizeJMenuItem( _about_item );\r
+        _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
+        _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
+        _jmenubar.add( _help_jmenu );\r
+    }\r
+\r
+    void buildTypeMenu() {\r
+        _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
+        _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
+        _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
+        _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
+        _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
+        _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
+        _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
+        _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
+        _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
+        customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
+        customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
+        customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
+        customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
+        customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
+        customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
+        customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
+        customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
+        _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+        _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+        initializeTypeMenu( getOptions() );\r
+        _jmenubar.add( _type_menu );\r
+    }\r
+\r
+    void buildViewMenu() {\r
+        _view_jmenu = createMenu( "View", getConfiguration() );\r
+        _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
+        _view_jmenu.addSeparator();\r
+        _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
+        _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
+        _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
+        customizeJMenuItem( _display_basic_information_item );\r
+        customizeJMenuItem( _view_as_NH_item );\r
+        customizeJMenuItem( _view_as_XML_item );\r
+        customizeJMenuItem( _view_as_nexus_item );\r
+        _jmenubar.add( _view_jmenu );\r
+    }\r
+\r
+    void checkTextFrames() {\r
+        if ( _textframes.size() > 5 ) {\r
+            try {\r
+                if ( _textframes.getFirst() != null ) {\r
+                    _textframes.getFirst().removeMe();\r
+                }\r
+                else {\r
+                    _textframes.removeFirst();\r
+                }\r
+            }\r
+            catch ( final NoSuchElementException e ) {\r
+                // Ignore.\r
+            }\r
+        }\r
+    }\r
+\r
+    void close() {\r
+        removeAllTextFrames();\r
+        if ( _mainpanel != null ) {\r
+            _mainpanel.terminate();\r
+        }\r
+        if ( _contentpane != null ) {\r
+            _contentpane.removeAll();\r
+        }\r
+        setVisible( false );\r
+        dispose();\r
+    }\r
+\r
+    void colorRank() {\r
+        if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+            final String[] ranks = AptxUtil.getAllPossibleRanks();\r
+            final String rank = ( String ) JOptionPane\r
+                    .showInputDialog( this,\r
+                                      "What rank should the colorization be based on",\r
+                                      "Rank Selection",\r
+                                      JOptionPane.QUESTION_MESSAGE,\r
+                                      null,\r
+                                      ranks,\r
+                                      null );\r
+            if ( !ForesterUtil.isEmpty( rank ) ) {\r
+                _mainpanel.getCurrentTreePanel().colorRank( rank );\r
+            }\r
+        }\r
+    }\r
+\r
+    void confColor() {\r
+        if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+            _mainpanel.getCurrentTreePanel().confColor();\r
+        }\r
+    }\r
+\r
+    void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
+        if ( item != null ) {\r
+            item.setFont( MainFrame.menu_font );\r
+            if ( !getConfiguration().isUseNativeUI() ) {\r
+                item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+                item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+            }\r
+            item.setSelected( is_selected );\r
+            item.addActionListener( this );\r
+        }\r
+    }\r
+\r
+    JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
+        if ( jmi != null ) {\r
+            jmi.setFont( MainFrame.menu_font );\r
+            if ( !getConfiguration().isUseNativeUI() ) {\r
+                jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+                jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+            }\r
+            jmi.addActionListener( this );\r
+        }\r
+        return jmi;\r
+    }\r
+\r
+    void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
+        if ( item != null ) {\r
+            item.setFont( MainFrame.menu_font );\r
+            if ( !getConfiguration().isUseNativeUI() ) {\r
+                item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+                item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+            }\r
+            item.setSelected( is_selected );\r
+            item.addActionListener( this );\r
+        }\r
+    }\r
+\r
+    void displayBasicInformation( final File treefile ) {\r
+        if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+            String title = "Basic Information";\r
+            if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+                title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
+            }\r
+            showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
+        }\r
+    }\r
+\r
+    void exceptionOccuredDuringOpenFile( final Exception e ) {\r
+        try {\r
+            _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+        }\r
+        catch ( final Exception ex ) {\r
+            // Do nothing.\r
+        }\r
+        JOptionPane.showMessageDialog( this,\r
+                                       ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+                                       "Error during File|Open",\r
+                                       JOptionPane.ERROR_MESSAGE );\r
+    }\r
+\r
+    void exceptionOccuredDuringSaveAs( final Exception e ) {\r
+        try {\r
+            _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+        }\r
+        catch ( final Exception ex ) {\r
+            // Do nothing.\r
+        }\r
+        JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
+    }\r
+\r
+    void executeGSDI() {\r
+        if ( !isOKforSDI( false, true ) ) {\r
+            return;\r
+        }\r
+        if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Gene tree is not rooted.",\r
+                                           "Cannot execute GSDI",\r
+                                           JOptionPane.ERROR_MESSAGE );\r
+            return;\r
+        }\r
+        final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+        gene_tree.setAllNodesToNotCollapse();\r
+        gene_tree.recalculateNumberOfExternalDescendants( false );\r
+        GSDI gsdi = null;\r
+        final Phylogeny species_tree = getSpeciesTree().copy();\r
+        try {\r
+            gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
+        }\r
+        catch ( final SDIException e ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           e.getLocalizedMessage(),\r
+                                           "Error during GSDI",\r
+                                           JOptionPane.ERROR_MESSAGE );\r
+            return;\r
+        }\r
+        catch ( final Exception e ) {\r
+            AptxUtil.unexpectedException( e );\r
+            return;\r
+        }\r
+        gene_tree.setRerootable( false );\r
+        gene_tree.clearHashIdToNodeMap();\r
+        gene_tree.recalculateNumberOfExternalDescendants( true );\r
+        _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
+        getMainPanel().getControlPanel().setShowEvents( true );\r
+        showWhole();\r
+        final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
+        _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
+        showWhole();\r
+        _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
+        showWhole();\r
+        _mainpanel.getCurrentTreePanel().setEdited( true );\r
+        final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
+        if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
+                                                   + "Potential duplications: "\r
+                                                   + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
+                                                   + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
+                                                   + "Stripped gene tree nodes: "\r
+                                                   + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+                                                   + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+                                                   + "Number of polytomies in species tree used: " + poly + "\n",\r
+                                                   "GSDI successfully completed",\r
+                                                   JOptionPane.WARNING_MESSAGE );\r
+        }\r
+        else {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
+                                                   + "Potential duplications: "\r
+                                                   + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
+                                                   + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
+                                                   + "Stripped gene tree nodes: "\r
+                                                   + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+                                                   + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+                                                   + "Number of polytomies in species tree used: " + poly + "\n",\r
+                                                   "GSDI successfully completed",\r
+                                                   JOptionPane.INFORMATION_MESSAGE );\r
+        }\r
+    }\r
+\r
+    void executeGSDIR() {\r
+        if ( !isOKforSDI( false, false ) ) {\r
+            return;\r
+        }\r
+        final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
+        if ( ( p > 0 )\r
+                && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Gene tree is not completely binary",\r
+                                           "Cannot execute GSDI",\r
+                                           JOptionPane.ERROR_MESSAGE );\r
+            return;\r
+        }\r
+        final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+        gene_tree.setAllNodesToNotCollapse();\r
+        gene_tree.recalculateNumberOfExternalDescendants( false );\r
+        GSDIR gsdir = null;\r
+        final Phylogeny species_tree = getSpeciesTree().copy();\r
+        try {\r
+            gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
+        }\r
+        catch ( final SDIException e ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           e.getLocalizedMessage(),\r
+                                           "Error during GSDIR",\r
+                                           JOptionPane.ERROR_MESSAGE );\r
+            return;\r
+        }\r
+        catch ( final Exception e ) {\r
+            AptxUtil.unexpectedException( e );\r
+            return;\r
+        }\r
+        final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
+        result_gene_tree.setRerootable( false );\r
+        result_gene_tree.clearHashIdToNodeMap();\r
+        result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
+        PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
+        _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
+        getMainPanel().getControlPanel().setShowEvents( true );\r
+        showWhole();\r
+        final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
+        _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
+        showWhole();\r
+        _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
+        showWhole();\r
+        _mainpanel.getCurrentTreePanel().setEdited( true );\r
+        final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
+        if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
+                                                   + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
+                                                   + "Stripped gene tree nodes: "\r
+                                                   + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+                                                   + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+                                                   + "Number of polytomies in species tree used: " + poly + "\n",\r
+                                                   "GSDIR successfully completed",\r
+                                                   JOptionPane.WARNING_MESSAGE );\r
+        }\r
+        else {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
+                                                   + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
+                                                   + "Stripped gene tree nodes: "\r
+                                                   + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+                                                   + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+                                                   + "Number of polytomies in species tree used: " + poly + "\n",\r
+                                                   "GSDIR successfully completed",\r
+                                                   JOptionPane.INFORMATION_MESSAGE );\r
+        }\r
+    }\r
+\r
+    boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
+        if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Gene tree and species tree have no species in common.",\r
+                                           "Error during SDI",\r
+                                           JOptionPane.ERROR_MESSAGE );\r
+            return false;\r
+        }\r
+        else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Gene tree and species tree have only one species in common.",\r
+                                           "Error during SDI",\r
+                                           JOptionPane.ERROR_MESSAGE );\r
+            return false;\r
+        }\r
+        else {\r
+            return true;\r
+        }\r
+    }\r
+\r
+    TreePanel getCurrentTreePanel() {\r
+        return getMainPanel().getCurrentTreePanel();\r
+    }\r
+\r
+    JMenu getHelpMenu() {\r
+        return _help_jmenu;\r
+    }\r
+\r
+    JCheckBoxMenuItem getlabelDirectionCbmi() {\r
+        return _label_direction_cbmi;\r
+    }\r
+\r
+    JMenuBar getMenuBarOfMainFrame() {\r
+        return _jmenubar;\r
+    }\r
+\r
+    final Phylogeny getSpeciesTree() {\r
+        return _species_tree;\r
+    }\r
+\r
+    void initializeTypeMenu( final Options options ) {\r
+        setTypeMenuToAllUnselected();\r
+        switch ( options.getPhylogenyGraphicsType() ) {\r
+            case CONVEX:\r
+                _convex_type_cbmi.setSelected( true );\r
+                break;\r
+            case CURVED:\r
+                _curved_type_cbmi.setSelected( true );\r
+                break;\r
+            case EURO_STYLE:\r
+                _euro_type_cbmi.setSelected( true );\r
+                break;\r
+            case ROUNDED:\r
+                _rounded_type_cbmi.setSelected( true );\r
+                break;\r
+            case TRIANGULAR:\r
+                _triangular_type_cbmi.setSelected( true );\r
+                break;\r
+            case UNROOTED:\r
+                _unrooted_type_cbmi.setSelected( true );\r
+                break;\r
+            case CIRCULAR:\r
+                _circular_type_cbmi.setSelected( true );\r
+                break;\r
+            default:\r
+                _rectangular_type_cbmi.setSelected( true );\r
+                break;\r
+        }\r
+    }\r
+\r
+    boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
+        if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+            return false;\r
+        }\r
+        else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "No species tree loaded",\r
+                                           "Cannot execute GSDI",\r
+                                           JOptionPane.ERROR_MESSAGE );\r
+            return false;\r
+        }\r
+        else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Species tree is not completely binary",\r
+                                           "Cannot execute GSDI",\r
+                                           JOptionPane.ERROR_MESSAGE );\r
+            return false;\r
+        }\r
+        else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
+            JOptionPane.showMessageDialog( this,\r
+                                           "Gene tree is not completely binary",\r
+                                           "Cannot execute GSDI",\r
+                                           JOptionPane.ERROR_MESSAGE );\r
+            return false;\r
+        }\r
+        else {\r
+            return true;\r
+        }\r
+    }\r
+\r
+    boolean isSubtreeDisplayed() {\r
+        if ( getCurrentTreePanel() != null ) {\r
+            if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
+                JOptionPane\r
+                .showMessageDialog( this,\r
+                                    "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
+                                    "Operation can not be exectuted on a sub-tree",\r
+                                    JOptionPane.WARNING_MESSAGE );\r
+                return true;\r
+            }\r
+        }\r
+        return false;\r
+    }\r
+\r
+    void midpointRoot() {\r
+        if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+            _mainpanel.getCurrentTreePanel().midpointRoot();\r
+        }\r
+    }\r
+\r
+    void readPhylogeniesFromWebservice( final int i ) {\r
+        final UrlTreeReader reader = new UrlTreeReader( this, i );\r
+        new Thread( reader ).start();\r
+    }\r
+\r
+    void removeAllTextFrames() {\r
+        for( final TextFrame tf : _textframes ) {\r
+            if ( tf != null ) {\r
+                tf.close();\r
+            }\r
+        }\r
+        _textframes.clear();\r
+    }\r
+\r
+    void setConfiguration( final Configuration configuration ) {\r
+        _configuration = configuration;\r
+    }\r
+\r
+    void setInferenceManager( final InferenceManager i ) {\r
+        _inference_manager = i;\r
+    }\r
+\r
+    void setOptions( final Options options ) {\r
+        _options = options;\r
+    }\r
+\r
+    void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
+        setTypeMenuToAllUnselected();\r
+        switch ( type ) {\r
+            case CIRCULAR:\r
+                _circular_type_cbmi.setSelected( true );\r
+                break;\r
+            case CONVEX:\r
+                _convex_type_cbmi.setSelected( true );\r
+                break;\r
+            case CURVED:\r
+                _curved_type_cbmi.setSelected( true );\r
+                break;\r
+            case EURO_STYLE:\r
+                _euro_type_cbmi.setSelected( true );\r
+                break;\r
+            case ROUNDED:\r
+                _rounded_type_cbmi.setSelected( true );\r
+                break;\r
+            case RECTANGULAR:\r
+                _rectangular_type_cbmi.setSelected( true );\r
+                break;\r
+            case TRIANGULAR:\r
+                _triangular_type_cbmi.setSelected( true );\r
+                break;\r
+            case UNROOTED:\r
+                _unrooted_type_cbmi.setSelected( true );\r
+                break;\r
+            default:\r
+                throw new IllegalArgumentException( "unknown type: " + type );\r
+        }\r
+    }\r
+\r
+    final void setSpeciesTree( final Phylogeny species_tree ) {\r
+        _species_tree = species_tree;\r
+    }\r
+\r
+    void setTypeMenuToAllUnselected() {\r
+        _convex_type_cbmi.setSelected( false );\r
+        _curved_type_cbmi.setSelected( false );\r
+        _euro_type_cbmi.setSelected( false );\r
+        _rounded_type_cbmi.setSelected( false );\r
+        _triangular_type_cbmi.setSelected( false );\r
+        _rectangular_type_cbmi.setSelected( false );\r
+        _unrooted_type_cbmi.setSelected( false );\r
+        _circular_type_cbmi.setSelected( false );\r
+    }\r
+\r
+    void switchColors() {\r
+        final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
+        final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
+        csc.setVisible( true );\r
+    }\r
+\r
+    void taxColor() {\r
+        if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+            _mainpanel.getCurrentTreePanel().taxColor();\r
+        }\r
+    }\r
+\r
+    void typeChanged( final Object o ) {\r
+        updateTypeCheckboxes( getOptions(), o );\r
+        updateOptions( getOptions() );\r
+        if ( getCurrentTreePanel() != null ) {\r
+            final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
+            final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
+            if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+                    || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
+                    || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+                    || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
+                getCurrentTreePanel().getControlPanel().showWhole();\r
+            }\r
+            if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
+                getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
+            }\r
+            else {\r
+                getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
+            }\r
+            getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
+            updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
+            if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
+                if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
+                    getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
+                }\r
+                else {\r
+                    getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
+                }\r
+            }\r
+        }\r
+    }\r
+\r
+    void updateOptions( final Options options ) {\r
+        options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
+        options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
+                                            && _background_gradient_cbmi.isSelected() );\r
+        options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
+        options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
+                                            && _show_annotation_ref_source.isSelected() );\r
+        options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
+                                                   && _abbreviate_scientific_names.isSelected() );\r
+        options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
+                                                  && _color_labels_same_as_parent_branch.isSelected() );\r
+        options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
+                                                  && _show_default_node_shapes_internal_cbmi.isSelected() );\r
+        options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
+                                                  && _show_default_node_shapes_external_cbmi.isSelected() );\r
+        options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
+                                                        && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
+        if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
+            options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
+        }\r
+        else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
+            options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
+        }\r
+        else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
+            options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
+        }\r
+        options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
+                                        && _search_case_senstive_cbmi.isSelected() );\r
+        if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
+            options.setShowScale( _show_scale_cbmi.isSelected() );\r
+        }\r
+        if ( _label_direction_cbmi != null ) {\r
+            if ( _label_direction_cbmi.isSelected() ) {\r
+                options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
+            }\r
+            else {\r
+                options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
+            }\r
+        }\r
+        options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
+        options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
+                                         && _show_confidence_stddev_cbmi.isSelected() );\r
+        if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
+            options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
+        }\r
+        options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
+                                         && ( _print_using_actual_size_cbmi.isSelected() ) );\r
+        options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
+                                                  && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
+        options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
+        if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
+                && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+            options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
+        }\r
+        else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
+                && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+            options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+        }\r
+        else {\r
+            options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
+        }\r
+        options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
+                                       && _print_black_and_white_cbmi.isSelected() );\r
+        options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
+                                                            && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
+        if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
+        }\r
+        else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
+        }\r
+        else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
+        }\r
+        else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
+            options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
+        }\r
+        options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
+                                                  && _replace_underscores_cbmi.isSelected() );\r
+        options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
+                                                  && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
+        options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
+                                        && _search_whole_words_only_cbmi.isSelected() );\r
+        options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
+        options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
+                                        && _inverse_search_result_cbmi.isSelected() );\r
+        if ( _graphics_export_visible_only_cbmi != null ) {\r
+            options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
+            if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
+                _graphics_export_using_actual_size_cbmi.setSelected( true );\r
+                _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
+            }\r
+            else {\r
+                _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
+            }\r
+        }\r
+        if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
+            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+        }\r
+        else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
+            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
+        }\r
+        else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
+            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
+        }\r
+        else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
+            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
+        }\r
+        else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
+            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
+        }\r
+        else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
+            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
+        }\r
+        else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
+            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
+        }\r
+        else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
+            options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
+        }\r
+        if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
+            options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
+        }\r
+        if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
+            options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
+        }\r
+    }\r
+\r
+    void updateTypeCheckboxes( final Options options, final Object o ) {\r
+        setTypeMenuToAllUnselected();\r
+        ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
+    }\r
+\r
+    void viewAsNexus() {\r
+        if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+            String title = "Nexus";\r
+            if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+                title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+            }\r
+            showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
+                           title );\r
+        }\r
+    }\r
+\r
+    void viewAsNH() {\r
+        if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+            String title = "New Hampshire";\r
+            if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+                title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+            }\r
+            showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
+                                                                            .getNhConversionSupportValueStyle() ),\r
+                                                                            title );\r
+        }\r
+    }\r
+\r
+    void viewAsXML() {\r
+        if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+            String title = "phyloXML";\r
+            if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+                title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+            }\r
+            showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
+        }\r
+    }\r
+\r
+    private void annotateSequences() {\r
+        if ( getCurrentTreePanel() != null ) {\r
+            List<PhylogenyNode> nodes = null;\r
+            if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
+                    || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+                nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+            }\r
+            if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+                JOptionPane\r
+                .showMessageDialog( this,\r
+                                    "Need to select nodes, either via direct selection or via the \"Search\" function",\r
+                                    "No nodes selected for annotation",\r
+                                    JOptionPane.ERROR_MESSAGE );\r
+                return;\r
+            }\r
+            final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+            if ( ( phy != null ) && !phy.isEmpty() ) {\r
+                final JTextField ref_field = new JTextField( 10 );\r
+                final JTextField desc_filed = new JTextField( 20 );\r
+                ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
+                        : getPreviousNodeAnnotationReference() );\r
+                final JPanel my_panel = new JPanel();\r
+                my_panel.add( new JLabel( "Reference " ) );\r
+                my_panel.add( ref_field );\r
+                my_panel.add( Box.createHorizontalStrut( 15 ) );\r
+                my_panel.add( new JLabel( "Description " ) );\r
+                my_panel.add( desc_filed );\r
+                final int result = JOptionPane.showConfirmDialog( null,\r
+                                                                  my_panel,\r
+                                                                  "Enter the sequence annotation(s) for the "\r
+                                                                          + nodes.size() + " selected nodes",\r
+                                                                          JOptionPane.OK_CANCEL_OPTION );\r
+                if ( result == JOptionPane.OK_OPTION ) {\r
+                    String ref = ref_field.getText();\r
+                    String desc = desc_filed.getText();\r
+                    if ( !ForesterUtil.isEmpty( ref ) ) {\r
+                        ref = ref.trim();\r
+                        ref = ref.replaceAll( "\\s+", " " );\r
+                        if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
+                                || ( ref.length() < 3 ) ) {\r
+                            JOptionPane.showMessageDialog( this,\r
+                                                           "Reference needs to be in the form of \"GO:1234567\"",\r
+                                                           "Illegal Format for Annotation Reference",\r
+                                                           JOptionPane.ERROR_MESSAGE );\r
+                            return;\r
+                        }\r
+                    }\r
+                    if ( ref != null ) {\r
+                        setPreviousNodeAnnotationReference( ref );\r
+                    }\r
+                    if ( desc != null ) {\r
+                        desc = desc.trim();\r
+                        desc = desc.replaceAll( "\\s+", " " );\r
+                    }\r
+                    if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
+                        for( final PhylogenyNode n : nodes ) {\r
+                            ForesterUtil.ensurePresenceOfSequence( n );\r
+                            final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
+                            : new Annotation( ref );\r
+                            if ( !ForesterUtil.isEmpty( desc ) ) {\r
+                                ann.setDesc( desc );\r
+                            }\r
+                            n.getNodeData().getSequence().addAnnotation( ann );\r
+                        }\r
+                    }\r
+                    getMainPanel().getControlPanel().showAnnotations();\r
+                }\r
+            }\r
+        }\r
+    }\r
+\r
+    private void chooseFont() {\r
+        final FontChooser fc = new FontChooser();\r
+        fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
+        fc.showDialog( this, "Select the Base Font" );\r
+        getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
+    }\r
+\r
+    private void chooseMinimalConfidence() {\r
+        final String s = ( String ) JOptionPane\r
+                .showInputDialog( this,\r
+                                  "Please enter the minimum for confidence values to be displayed.\n"\r
+                                          + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
+                                          "Minimal Confidence Value",\r
+                                          JOptionPane.QUESTION_MESSAGE,\r
+                                          null,\r
+                                          null,\r
+                                          getOptions().getMinConfidenceValue() );\r
+        if ( !ForesterUtil.isEmpty( s ) ) {\r
+            boolean success = true;\r
+            double m = 0.0;\r
+            final String m_str = s.trim();\r
+            if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+                try {\r
+                    m = Double.parseDouble( m_str );\r
+                }\r
+                catch ( final Exception ex ) {\r
+                    success = false;\r
+                }\r
+            }\r
+            else {\r
+                success = false;\r
+            }\r
+            if ( success && ( m >= 0.0 ) ) {\r
+                getOptions().setMinConfidenceValue( m );\r
+            }\r
+        }\r
+    }\r
+\r
+    private void doUpdateProcessMenu() {\r
+        if ( _process_pool.size() > 0 ) {\r
+            if ( _process_menu == null ) {\r
+                _process_menu = createMenu( "", getConfiguration() );\r
+                _process_menu.setForeground( Color.RED );\r
+            }\r
+            _process_menu.removeAll();\r
+            final String text = "processes running: " + _process_pool.size();\r
+            _process_menu.setText( text );\r
+            _jmenubar.add( _process_menu );\r
+            for( int i = 0; i < _process_pool.size(); ++i ) {\r
+                final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
+                _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
+            }\r
+        }\r
+        else {\r
+            if ( _process_menu != null ) {\r
+                _process_menu.removeAll();\r
+                _jmenubar.remove( _process_menu );\r
+            }\r
+        }\r
+        _jmenubar.validate();\r
+        _jmenubar.repaint();\r
+        repaint();\r
+    }\r
+\r
+    private String getPreviousNodeAnnotationReference() {\r
+        return _previous_node_annotation_ref;\r
+    }\r
+\r
+    private void removeBranchColors() {\r
+        if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+            AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
+        }\r
+    }\r
+\r
+    private void removeVisualStyles() {\r
+        if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+            AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
+        }\r
+    }\r
+\r
+    private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
+        _previous_node_annotation_ref = previous_node_annotation_ref;\r
+    }\r
+\r
+    /**\r
+     * Display the about box.\r
+     */\r
+    static void about() {\r
+        final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
+        about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
+        about.append( "All Rights Reserved\n" );\r
+        about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
+        about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
+        about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
+        about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
+        about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
+        if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
+            about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
+        }\r
+        if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
+                && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
+            about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
+                    + ForesterUtil.OS_VERSION + "]\n" );\r
+        }\r
+        final Runtime rt = java.lang.Runtime.getRuntime();\r
+        final long free_memory = rt.freeMemory() / 1000000;\r
+        final long total_memory = rt.totalMemory() / 1000000;\r
+        about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
+        about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
+        about.append( "References:\n" );\r
+        about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
+        about.append( "For more information & download:\n" );\r
+        about.append( Constants.APTX_WEB_SITE + "\n" );\r
+        about.append( "Documentation:\n" );\r
+        about.append( Constants.APTX_DOC_SITE + "\n" );\r
+        about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
+        JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
+    }\r
+\r
+    static void chooseNodeSize( final Options options, final Component parent ) {\r
+        final String s = ( String ) JOptionPane.showInputDialog( parent,\r
+                                                                 "Please enter the default size for node shapes.\n"\r
+                                                                         + "[current value: "\r
+                                                                         + options.getDefaultNodeShapeSize() + "]\n",\r
+                                                                         "Node Shape Size",\r
+                                                                         JOptionPane.QUESTION_MESSAGE,\r
+                                                                         null,\r
+                                                                         null,\r
+                                                                         options.getDefaultNodeShapeSize() );\r
+        if ( !ForesterUtil.isEmpty( s ) ) {\r
+            boolean success = true;\r
+            double m = 0.0;\r
+            final String m_str = s.trim();\r
+            if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+                try {\r
+                    m = Double.parseDouble( m_str );\r
+                }\r
+                catch ( final Exception ex ) {\r
+                    success = false;\r
+                }\r
+            }\r
+            else {\r
+                success = false;\r
+            }\r
+            if ( success && ( m >= 0.0 ) ) {\r
+                final short size = ForesterUtil.roundToShort( m );\r
+                if ( size >= 0.0 ) {\r
+                    options.setDefaultNodeShapeSize( size );\r
+                }\r
+            }\r
+        }\r
+    }\r
+\r
+    static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
+        return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
+    }\r
+\r
+    static JMenu createMenu( final String title, final Configuration conf ) {\r
+        final JMenu jmenu = new JMenu( title );\r
+        if ( !conf.isUseNativeUI() ) {\r
+            jmenu.setFont( MainFrame.menu_font );\r
+            jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
+            jmenu.setForeground( conf.getGuiMenuTextColor() );\r
+        }\r
+        return jmenu;\r
+    }\r
+\r
+    static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
+        label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
+        if ( !configuration.isUseNativeUI() ) {\r
+            label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
+            label.setForeground( configuration.getGuiMenuTextColor() );\r
+            label.setOpaque( true );\r
+        }\r
+        label.setSelected( false );\r
+        label.setEnabled( false );\r
+        return label;\r
+    }\r
+\r
+    static void cycleNodeFill( final Options op ) {\r
+        switch ( op.getDefaultNodeFill() ) {\r
+            case GRADIENT:\r
+                op.setDefaultNodeFill( NodeFill.SOLID );\r
+                break;\r
+            case NONE:\r
+                op.setDefaultNodeFill( NodeFill.GRADIENT );\r
+                break;\r
+            case SOLID:\r
+                op.setDefaultNodeFill( NodeFill.NONE );\r
+                break;\r
+            default:\r
+                throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
+        }\r
+    }\r
+\r
+    static void cycleNodeShape( final Options op ) {\r
+        switch ( op.getDefaultNodeShape() ) {\r
+            case CIRCLE:\r
+                op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
+                break;\r
+            case RECTANGLE:\r
+                op.setDefaultNodeShape( NodeShape.CIRCLE );\r
+                break;\r
+            default:\r
+                throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
+        }\r
+    }\r
+\r
+    private static void cycleNodeDataReturn( final Options op, Configuration conf ) {\r
+        switch ( op.getExtDescNodeDataToReturn() ) {\r
+            case UNKNOWN:\r
+                op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
+                break;\r
+            case DOMAINS_ALL:\r
+                op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
+                break;\r
+            case DOMAINS_COLLAPSED_PER_PROTEIN:\r
+                op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
+                break;\r
+            case SEQ_ANNOTATIONS:\r
+                op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
+                break;\r
+            case GO_TERM_IDS:\r
+                op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
+                break;\r
+            case SEQUENCE_MOL_SEQ_FASTA:\r
+                if ( conf != null && conf.getExtDescNodeDataToReturn() != null\r
+                   &&      conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL\r
+                   &&      conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN\r
+                   &&       conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS\r
+                   &&      conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS\r
+                   &&       conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA\r
+                        ) {\r
+                    op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
+                }\r
+                else {\r
+                    op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+                }\r
+                break;  \r
+            default:\r
+                op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+        }\r
+    }\r
+\r
+    static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
+        switch ( op.getOvPlacement() ) {\r
+            case LOWER_LEFT:\r
+                op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
+                break;\r
+            case LOWER_RIGHT:\r
+                op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
+                break;\r
+            case UPPER_LEFT:\r
+                op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
+                break;\r
+            case UPPER_RIGHT:\r
+                op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
+                break;\r
+            default:\r
+                throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
+        }\r
+        if ( tree_panel != null ) {\r
+            tree_panel.updateOvSettings();\r
+        }\r
+    }\r
+\r
+    static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
+        if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
+            mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+                    + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
+        }\r
+        else {\r
+            mi.setText( "Cycle Node Shape Fill Type..." );\r
+        }\r
+    }\r
+\r
+    static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
+        if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
+            mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+                    + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
+        }\r
+        else {\r
+            mi.setText( "Cycle Node Shape Fill Type..." );\r
+        }\r
+    }\r
+\r
+    static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
+        if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
+            mi.setText( "Cycle Node Return Data... (current: "\r
+                    + options.getExtDescNodeDataToReturn().toString() + ")" );\r
+        }\r
+        else {\r
+            mi.setText( "Cycle Node Return Data..." );\r
+        }\r
+    }\r
+\r
+    static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
+        if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
+            mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
+        }\r
+        else {\r
+            mi.setText( "Cycle Overview Placement..." );\r
+        }\r
+    }\r
+\r
+    static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
+        if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
+            mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
+                        + ")" );\r
+        }\r
+        else {\r
+            mi.setText( "Select Color Scheme..." );\r
+        }\r
+    }\r
+\r
+    static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
+        mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
+    }\r
+\r
+    static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
+        if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
+            mi.setEnabled( true );\r
+        }\r
+        else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
+            mi.setEnabled( true );\r
+        }\r
+        else {\r
+            mi.setEnabled( false );\r
+        }\r
+        mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
+    }\r
+\r
+    static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
+        mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
+    }\r
+\r
+    static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
+        for( final TreePanel tree_panel : treepanels ) {\r
+            tree_panel.setTextAntialias();\r
+        }\r
+    }\r
+}\r