forester/java/src/org/forester/archaeopteryx/MainFrame.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2010 Christian M. Zmasek
   6 // All rights reserved
   7 //
   8 // This library is free software; you can redistribute it and/or
   9 // modify it under the terms of the GNU Lesser General Public
  10 // License as published by the Free Software Foundation; either
  11 // version 2.1 of the License, or (at your option) any later version.
  12 //
  13 // This library is distributed in the hope that it will be useful,
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  16 // Lesser General Public License for more details.
  17 //
  18 // You should have received a copy of the GNU Lesser General Public
  19 // License along with this library; if not, write to the Free Software
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  21 //
  22 // Contact: phylosoft @ gmail . com
  23 // WWW: www.phylosoft.org/forester
  24
  25 package org.forester.archaeopteryx;
  26
  27 import java.awt.Color;
  28 import java.awt.Component;
  29 import java.awt.Container;
  30 import java.awt.Font;
  31 import java.awt.event.ActionEvent;
  32 import java.awt.event.ActionListener;
  33 import java.io.IOException;
  34 import java.util.LinkedList;
  35 import java.util.List;
  36 import java.util.Locale;
  37 import java.util.Map;
  38 import java.util.NoSuchElementException;
  39
  40 import javax.swing.JApplet;
  41 import javax.swing.JCheckBoxMenuItem;
  42 import javax.swing.JFrame;
  43 import javax.swing.JMenu;
  44 import javax.swing.JMenuBar;
  45 import javax.swing.JMenuItem;
  46 import javax.swing.JOptionPane;
  47 import javax.swing.JRadioButtonMenuItem;
  48 import javax.swing.SwingUtilities;
  49
  50 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  51 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  52 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  53 import org.forester.archaeopteryx.tools.InferenceManager;
  54 import org.forester.archaeopteryx.tools.ProcessPool;
  55 import org.forester.archaeopteryx.tools.ProcessRunning;
  56 import org.forester.phylogeny.Phylogeny;
  57 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  58 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
  59 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
  60 import org.forester.util.ForesterConstants;
  61 import org.forester.util.ForesterUtil;
  62
  63 public abstract class MainFrame extends JFrame implements ActionListener {
  64
  65     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";
  66     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME
  67     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;
  68     private static final long   serialVersionUID                        = 3655000897845508358L;
  69     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),
  70                                                                                     Font.PLAIN,
  71                                                                                     10 );
  72     static final String         TYPE_MENU_HEADER                        = "Type";
  73     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";
  74     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";
  75     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";
  76     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";
  77     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";
  78     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";
  79     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO
  80     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO
  81     static final String         OPTIONS_HEADER                          = "Options";
  82     static final String         SEARCH_SUBHEADER                        = "Search:";
  83     static final String         DISPLAY_SUBHEADER                       = "Display:";
  84     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";
  85     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";
  86     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";
  87     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Display Branch Length Values";
  88     static final String         DISPLAY_SCALE_LABEL                     = "Display Scale";
  89     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";
  90     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";
  91     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";
  92     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";
  93     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";
  94     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";
  95     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";
  96     static final String         DISPLAY_NODE_BOXES_LABEL                = "Show Node Shapes";
  97     static final String         SHOW_OVERVIEW_LABEL                     = "Show Overview";
  98     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";
  99     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";
 100     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Show Domain Labels";
 101     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";
 102     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";
 103     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";
 104     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";
 105     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";
 106     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";
 107     static final String         SHOW_CONF_STDDEV_LABEL                  = "Show Confidence Standard Deviations";
 108     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";
 109     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
 110     JMenuBar                    _jmenubar;
 111     JMenu                       _file_jmenu;
 112     JMenu                       _tools_menu;
 113     JMenu                       _view_jmenu;
 114     JMenu                       _options_jmenu;
 115     JMenu                       _font_size_menu;
 116     JMenu                       _help_jmenu;
 117     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;
 118     // file menu:
 119     JMenuItem                   _open_item;
 120     JMenuItem                   _open_url_item;
 121     JMenuItem                   _save_item;
 122     JMenuItem                   _save_all_item;
 123     JMenuItem                   _close_item;
 124     JMenuItem                   _exit_item;
 125     JMenuItem                   _new_item;
 126     // tools menu:
 127     JMenuItem                   _midpoint_root_item;
 128     JMenuItem                   _taxcolor_item;
 129     JMenuItem                   _confcolor_item;
 130     JMenuItem                   _color_rank_jmi;
 131     JMenuItem                   _infer_common_sn_names_item;
 132     JMenuItem                   _collapse_species_specific_subtrees;
 133     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me
 134     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;
 135     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;
 136     JMenuItem                   _obtain_uniprot_seq_information_jmi;
 137     JMenuItem                   _move_node_names_to_tax_sn_jmi;
 138     JMenuItem                   _move_node_names_to_seq_names_jmi;
 139     JMenuItem                   _extract_tax_code_from_node_names_jmi;
 140     // font size menu:
 141     JMenuItem                   _super_tiny_fonts_item;
 142     JMenuItem                   _tiny_fonts_item;
 143     JMenuItem                   _small_fonts_item;
 144     JMenuItem                   _medium_fonts_item;
 145     JMenuItem                   _large_fonts_item;
 146     // options menu:
 147     // _  screen and print
 148     JMenuItem                   _choose_font_mi;
 149     JMenuItem                   _switch_colors_mi;
 150     JCheckBoxMenuItem           _label_direction_cbmi;
 151     // _  screen display
 152     JCheckBoxMenuItem           _screen_antialias_cbmi;
 153     JCheckBoxMenuItem           _background_gradient_cbmi;
 154     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 155     JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 156     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 157     JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 158     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me
 159     JCheckBoxMenuItem           _show_overview_cbmi;
 160     JCheckBoxMenuItem           _show_domain_labels;
 161     JCheckBoxMenuItem           _abbreviate_scientific_names;
 162     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 163     JMenuItem                   _overview_placment_mi;
 164     JMenuItem                   _choose_minimal_confidence_mi;
 165     JCheckBoxMenuItem           _show_default_node_shapes_cbmi;
 166     JMenuItem                   _cycle_node_shape_mi;
 167     JMenuItem                   _cycle_node_fill_mi;
 168     JMenuItem                   _choose_node_size_mi;
 169     JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
 170     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 171     // _  print
 172     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;
 173     JCheckBoxMenuItem           _antialias_print_cbmi;
 174     JCheckBoxMenuItem           _print_black_and_white_cbmi;
 175     JCheckBoxMenuItem           _print_using_actual_size_cbmi;
 176     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;
 177     JMenuItem                   _print_size_mi;
 178     JMenuItem                   _choose_pdf_width_mi;
 179     // _  parsing
 180     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;
 181     JCheckBoxMenuItem           _extract_pfam_style_tax_codes_cbmi;
 182     JCheckBoxMenuItem           _replace_underscores_cbmi;
 183     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;
 184     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;
 185     // _  search
 186     JCheckBoxMenuItem           _search_case_senstive_cbmi;
 187     JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 188     JCheckBoxMenuItem           _inverse_search_result_cbmi;
 189     // type menu:
 190     JMenu                       _type_menu;
 191     JCheckBoxMenuItem           _rectangular_type_cbmi;
 192     JCheckBoxMenuItem           _triangular_type_cbmi;
 193     JCheckBoxMenuItem           _curved_type_cbmi;
 194     JCheckBoxMenuItem           _convex_type_cbmi;
 195     JCheckBoxMenuItem           _euro_type_cbmi;
 196     JCheckBoxMenuItem           _rounded_type_cbmi;
 197     JCheckBoxMenuItem           _unrooted_type_cbmi;
 198     JCheckBoxMenuItem           _circular_type_cbmi;
 199     // view as text menu:
 200     JMenuItem                   _view_as_NH_item;
 201     JMenuItem                   _view_as_NHX_item;
 202     JMenuItem                   _view_as_XML_item;
 203     JMenuItem                   _view_as_nexus_item;
 204     JMenuItem                   _display_basic_information_item;
 205     // help menu:
 206     JMenuItem                   _about_item;
 207     JMenuItem                   _help_item;
 208     JMenuItem                   _website_item;
 209     JMenuItem                   _phyloxml_website_item;
 210     JMenuItem                   _phyloxml_ref_item;
 211     JMenuItem                   _aptx_ref_item;
 212     // process menu:
 213     JMenu                       _process_menu;
 214     // Handy pointers to child components:
 215     MainPanel                   _mainpanel;
 216     Container                   _contentpane;
 217     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;
 218     Configuration               _configuration;
 219     JMenuItem                   _remove_branch_color_item;
 220     Options                     _options;
 221     InferenceManager            _inference_manager;
 222     final ProcessPool           _process_pool;
 223
 224     MainFrame() {
 225         _process_pool = ProcessPool.createInstance();
 226     }
 227
 228     public ProcessPool getProcessPool() {
 229         return _process_pool;
 230     }
 231
 232     /**
 233      * Action performed.
 234      */
 235     @Override
 236     public void actionPerformed( final ActionEvent e ) {
 237         final Object o = e.getSource();
 238         boolean is_applet = false;
 239         JApplet applet = null;
 240         if ( getCurrentTreePanel() != null ) {
 241             is_applet = getCurrentTreePanel().isApplet();
 242             if ( is_applet ) {
 243                 applet = getCurrentTreePanel().obtainApplet();
 244             }
 245         }
 246         if ( o == _open_url_item ) {
 247             readPhylogeniesFromURL();
 248         }
 249         else if ( o == _exit_item ) {
 250             close();
 251         }
 252         else if ( o == _taxcolor_item ) {
 253             taxColor();
 254         }
 255         else if ( o == _confcolor_item ) {
 256             confColor();
 257         }
 258         else if ( o == _color_rank_jmi ) {
 259             colorRank();
 260         }
 261         else if ( o == _infer_common_sn_names_item ) {
 262             if ( isSubtreeDisplayed() ) {
 263                 return;
 264             }
 265             if ( getCurrentTreePanel() != null ) {
 266                 getCurrentTreePanel().inferCommonPartOfScientificNames();
 267             }
 268         }
 269         else if ( o == _collapse_species_specific_subtrees ) {
 270             if ( isSubtreeDisplayed() ) {
 271                 return;
 272             }
 273             if ( getCurrentTreePanel() != null ) {
 274                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 275             }
 276         }
 277         else if ( o == _remove_branch_color_item ) {
 278             if ( isSubtreeDisplayed() ) {
 279                 return;
 280             }
 281             removeBranchColors();
 282         }
 283         else if ( o == _midpoint_root_item ) {
 284             if ( isSubtreeDisplayed() ) {
 285                 return;
 286             }
 287             midpointRoot();
 288         }
 289         else if ( o == _switch_colors_mi ) {
 290             switchColors();
 291         }
 292         else if ( o == _display_basic_information_item ) {
 293             displayBasicInformation();
 294         }
 295         else if ( o == _view_as_NH_item ) {
 296             viewAsNH();
 297         }
 298         else if ( o == _view_as_NHX_item ) {
 299             viewAsNHX();
 300         }
 301         else if ( o == _view_as_XML_item ) {
 302             viewAsXML();
 303         }
 304         else if ( o == _view_as_nexus_item ) {
 305             viewAsNexus();
 306         }
 307         else if ( o == _super_tiny_fonts_item ) {
 308             if ( getCurrentTreePanel() != null ) {
 309                 getCurrentTreePanel().setSuperTinyFonts();
 310                 getCurrentTreePanel().repaint();
 311             }
 312         }
 313         else if ( o == _tiny_fonts_item ) {
 314             if ( getCurrentTreePanel() != null ) {
 315                 getCurrentTreePanel().setTinyFonts();
 316                 getCurrentTreePanel().repaint();
 317             }
 318         }
 319         else if ( o == _small_fonts_item ) {
 320             if ( getCurrentTreePanel() != null ) {
 321                 getCurrentTreePanel().setSmallFonts();
 322                 getCurrentTreePanel().repaint();
 323             }
 324         }
 325         else if ( o == _medium_fonts_item ) {
 326             if ( getCurrentTreePanel() != null ) {
 327                 getCurrentTreePanel().setMediumFonts();
 328                 getCurrentTreePanel().repaint();
 329             }
 330         }
 331         else if ( o == _large_fonts_item ) {
 332             if ( getCurrentTreePanel() != null ) {
 333                 getCurrentTreePanel().setLargeFonts();
 334                 getCurrentTreePanel().repaint();
 335             }
 336         }
 337         else if ( o == _choose_font_mi ) {
 338             chooseFont();
 339         }
 340         else if ( o == _choose_minimal_confidence_mi ) {
 341             chooseMinimalConfidence();
 342         }
 343         else if ( o == _choose_node_size_mi ) {
 344             chooseNodeSize( getOptions(), this );
 345         }
 346         else if ( o == _overview_placment_mi ) {
 347             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 348         }
 349         else if ( o == _cycle_node_fill_mi ) {
 350             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 351         }
 352         else if ( o == _cycle_node_shape_mi ) {
 353             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 354         }
 355         else if ( o == _screen_antialias_cbmi ) {
 356             updateOptions( getOptions() );
 357             updateScreenTextAntialias( getMainPanel().getTreePanels() );
 358         }
 359         else if ( o == _background_gradient_cbmi ) {
 360             updateOptions( getOptions() );
 361         }
 362         else if ( o == _show_domain_labels ) {
 363             updateOptions( getOptions() );
 364         }
 365         else if ( o == _abbreviate_scientific_names ) {
 366             updateOptions( getOptions() );
 367         }
 368         else if ( o == _color_labels_same_as_parent_branch ) {
 369             updateOptions( getOptions() );
 370         }
 371         else if ( o == _show_default_node_shapes_cbmi ) {
 372             updateOptions( getOptions() );
 373         }
 374         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 375             updateOptions( getOptions() );
 376         }
 377         else if ( o == _non_lined_up_cladograms_rbmi ) {
 378             updateOptions( getOptions() );
 379             showWhole();
 380         }
 381         else if ( o == _uniform_cladograms_rbmi ) {
 382             updateOptions( getOptions() );
 383             showWhole();
 384         }
 385         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 386             updateOptions( getOptions() );
 387             showWhole();
 388         }
 389         else if ( o == _search_case_senstive_cbmi ) {
 390             updateOptions( getOptions() );
 391             getMainPanel().getControlPanel().search();
 392         }
 393         else if ( o == _search_whole_words_only_cbmi ) {
 394             updateOptions( getOptions() );
 395             getMainPanel().getControlPanel().search();
 396         }
 397         else if ( o == _inverse_search_result_cbmi ) {
 398             updateOptions( getOptions() );
 399             getMainPanel().getControlPanel().search();
 400         }
 401         else if ( o == _show_scale_cbmi ) {
 402             updateOptions( getOptions() );
 403         }
 404         else if ( o == _show_branch_length_values_cbmi ) {
 405             updateOptions( getOptions() );
 406         }
 407         else if ( o == _show_confidence_stddev_cbmi ) {
 408             updateOptions( getOptions() );
 409         }
 410         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
 411             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
 412                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
 413             }
 414             updateOptions( getOptions() );
 415         }
 416         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
 417             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
 418                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
 419             }
 420             updateOptions( getOptions() );
 421         }
 422         else if ( o == _label_direction_cbmi ) {
 423             updateOptions( getOptions() );
 424         }
 425         else if ( o == _show_overview_cbmi ) {
 426             updateOptions( getOptions() );
 427             if ( getCurrentTreePanel() != null ) {
 428                 getCurrentTreePanel().updateOvSizes();
 429             }
 430         }
 431         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 432                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
 433                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 434             typeChanged( o );
 435         }
 436         else if ( o == _about_item ) {
 437             about();
 438         }
 439         else if ( o == _help_item ) {
 440             help( getConfiguration().getWebLinks() );
 441         }
 442         else if ( o == _website_item ) {
 443             try {
 444                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
 445             }
 446             catch ( final IOException e1 ) {
 447                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 448             }
 449         }
 450         else if ( o == _phyloxml_website_item ) {
 451             try {
 452                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
 453             }
 454             catch ( final IOException e1 ) {
 455                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 456             }
 457         }
 458         else if ( o == _aptx_ref_item ) {
 459             try {
 460                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
 461             }
 462             catch ( final IOException e1 ) {
 463                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 464             }
 465         }
 466         else if ( o == _phyloxml_ref_item ) {
 467             try {
 468                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
 469             }
 470             catch ( final IOException e1 ) {
 471                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 472             }
 473         }
 474         else {
 475             if ( _load_phylogeny_from_webservice_menu_items != null ) {
 476                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
 477                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
 478                         readPhylogeniesFromWebservice( i );
 479                     }
 480                 }
 481             }
 482         }
 483         _contentpane.repaint();
 484     }
 485
 486     boolean isSubtreeDisplayed() {
 487         if ( getCurrentTreePanel() != null ) {
 488             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
 489                 JOptionPane
 490                         .showMessageDialog( this,
 491                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
 492                                             "Operation can not be exectuted on a sub-tree",
 493                                             JOptionPane.WARNING_MESSAGE );
 494                 return true;
 495             }
 496         }
 497         return false;
 498     }
 499
 500     void activateSaveAllIfNeeded() {
 501         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
 502             _save_all_item.setEnabled( true );
 503         }
 504         else {
 505             _save_all_item.setEnabled( false );
 506         }
 507     }
 508
 509     void buildFileMenu() {
 510         _file_jmenu = createMenu( "File", getConfiguration() );
 511         _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
 512         _file_jmenu.addSeparator();
 513         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 514         customizeJMenuItem( _open_url_item );
 515         customizeJMenuItem( _exit_item );
 516         _jmenubar.add( _file_jmenu );
 517     }
 518
 519     void buildFontSizeMenu() {
 520         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
 521         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
 522         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
 523         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
 524         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
 525         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
 526         customizeJMenuItem( _super_tiny_fonts_item );
 527         customizeJMenuItem( _tiny_fonts_item );
 528         customizeJMenuItem( _small_fonts_item );
 529         customizeJMenuItem( _medium_fonts_item );
 530         customizeJMenuItem( _large_fonts_item );
 531         _jmenubar.add( _font_size_menu );
 532     }
 533
 534     void buildHelpMenu() {
 535         _help_jmenu = createMenu( "Help", getConfiguration() );
 536         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 537         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 538         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 539         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 540         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 541         _help_jmenu.addSeparator();
 542         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 543         customizeJMenuItem( _help_item );
 544         customizeJMenuItem( _website_item );
 545         customizeJMenuItem( _phyloxml_website_item );
 546         customizeJMenuItem( _aptx_ref_item );
 547         customizeJMenuItem( _phyloxml_ref_item );
 548         customizeJMenuItem( _about_item );
 549         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
 550         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
 551         _jmenubar.add( _help_jmenu );
 552     }
 553
 554     public void updateProcessMenu() {
 555         // In general Swing is not thread safe.
 556         // See "Swing's Threading Policy".
 557         SwingUtilities.invokeLater( new Runnable() {
 558
 559             @Override
 560             public void run() {
 561                 doUpdateProcessMenu();
 562             }
 563         } );
 564     }
 565
 566     private void doUpdateProcessMenu() {
 567         if ( _process_pool.size() > 0 ) {
 568             if ( _process_menu == null ) {
 569                 _process_menu = createMenu( "", getConfiguration() );
 570                 _process_menu.setForeground( Color.RED );
 571             }
 572             _process_menu.removeAll();
 573             final String text = "processes running: " + _process_pool.size();
 574             _process_menu.setText( text );
 575             _jmenubar.add( _process_menu );
 576             for( int i = 0; i < _process_pool.size(); ++i ) {
 577                 final ProcessRunning p = _process_pool.getProcessByIndex( i );
 578                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
 579             }
 580         }
 581         else {
 582             if ( _process_menu != null ) {
 583                 _process_menu.removeAll();
 584                 _jmenubar.remove( _process_menu );
 585             }
 586         }
 587         _jmenubar.validate();
 588         _jmenubar.repaint();
 589         repaint();
 590     }
 591
 592     void buildTypeMenu() {
 593         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
 594         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 595         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 596         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 597         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 598         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 599         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 600         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 601         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 602         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 603         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 604         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 605         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 606         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 607         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 608         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 609         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 610         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 611         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 612         initializeTypeMenu( getOptions() );
 613         _jmenubar.add( _type_menu );
 614     }
 615
 616     void buildViewMenu() {
 617         _view_jmenu = createMenu( "View", getConfiguration() );
 618         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 619         _view_jmenu.addSeparator();
 620         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 621         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 622         _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
 623         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 624         customizeJMenuItem( _display_basic_information_item );
 625         customizeJMenuItem( _view_as_NH_item );
 626         customizeJMenuItem( _view_as_NHX_item );
 627         customizeJMenuItem( _view_as_XML_item );
 628         customizeJMenuItem( _view_as_nexus_item );
 629         _jmenubar.add( _view_jmenu );
 630     }
 631
 632     private void chooseFont() {
 633         final FontChooser fc = new FontChooser();
 634         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
 635         fc.showDialog( this, "Select the Base Font" );
 636         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
 637     }
 638
 639     private void chooseMinimalConfidence() {
 640         final String s = ( String ) JOptionPane
 641                 .showInputDialog( this,
 642                                   "Please enter the minimum for confidence values to be displayed.\n"
 643                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
 644                                   "Minimal Confidence Value",
 645                                   JOptionPane.QUESTION_MESSAGE,
 646                                   null,
 647                                   null,
 648                                   getOptions().getMinConfidenceValue() );
 649         if ( !ForesterUtil.isEmpty( s ) ) {
 650             boolean success = true;
 651             double m = 0.0;
 652             final String m_str = s.trim();
 653             if ( !ForesterUtil.isEmpty( m_str ) ) {
 654                 try {
 655                     m = Double.parseDouble( m_str );
 656                 }
 657                 catch ( final Exception ex ) {
 658                     success = false;
 659                 }
 660             }
 661             else {
 662                 success = false;
 663             }
 664             if ( success && ( m >= 0.0 ) ) {
 665                 getOptions().setMinConfidenceValue( m );
 666             }
 667         }
 668     }
 669
 670     static void chooseNodeSize( final Options options, final Component parent ) {
 671         final String s = ( String ) JOptionPane.showInputDialog( parent,
 672                                                                  "Please enter the default size for node shapes.\n"
 673                                                                          + "[current value: "
 674                                                                          + options.getDefaultNodeShapeSize() + "]\n",
 675                                                                  "Node Shape Size",
 676                                                                  JOptionPane.QUESTION_MESSAGE,
 677                                                                  null,
 678                                                                  null,
 679                                                                  options.getDefaultNodeShapeSize() );
 680         if ( !ForesterUtil.isEmpty( s ) ) {
 681             boolean success = true;
 682             double m = 0.0;
 683             final String m_str = s.trim();
 684             if ( !ForesterUtil.isEmpty( m_str ) ) {
 685                 try {
 686                     m = Double.parseDouble( m_str );
 687                 }
 688                 catch ( final Exception ex ) {
 689                     success = false;
 690                 }
 691             }
 692             else {
 693                 success = false;
 694             }
 695             if ( success && ( m >= 0.0 ) ) {
 696                 final short size = ForesterUtil.roundToShort( m );
 697                 if ( size >= 0.0 ) {
 698                     options.setDefaultNodeShapeSize( size );
 699                 }
 700             }
 701         }
 702     }
 703
 704     void close() {
 705         removeAllTextFrames();
 706         if ( _mainpanel != null ) {
 707             _mainpanel.terminate();
 708         }
 709         if ( _contentpane != null ) {
 710             _contentpane.removeAll();
 711         }
 712         setVisible( false );
 713         dispose();
 714     }
 715
 716     void confColor() {
 717         if ( _mainpanel.getCurrentTreePanel() != null ) {
 718             _mainpanel.getCurrentTreePanel().confColor();
 719         }
 720     }
 721
 722     void colorRank() {
 723         if ( _mainpanel.getCurrentTreePanel() != null ) {
 724             final String[] ranks = AptxUtil.getAllPossibleRanks();
 725             final String rank = ( String ) JOptionPane
 726                     .showInputDialog( this,
 727                                       "What rank should the colorization be based on",
 728                                       "Rank Selection",
 729                                       JOptionPane.QUESTION_MESSAGE,
 730                                       null,
 731                                       ranks,
 732                                       null );
 733             if ( !ForesterUtil.isEmpty( rank ) ) {
 734                 _mainpanel.getCurrentTreePanel().colorRank( rank );
 735             }
 736         }
 737     }
 738
 739     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 740         if ( item != null ) {
 741             item.setFont( MainFrame.menu_font );
 742             if ( !getConfiguration().isUseNativeUI() ) {
 743                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 744                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 745             }
 746             item.setSelected( is_selected );
 747             item.addActionListener( this );
 748         }
 749     }
 750
 751     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
 752         if ( jmi != null ) {
 753             jmi.setFont( MainFrame.menu_font );
 754             if ( !getConfiguration().isUseNativeUI() ) {
 755                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 756                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 757             }
 758             jmi.addActionListener( this );
 759         }
 760         return jmi;
 761     }
 762
 763     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 764         if ( item != null ) {
 765             item.setFont( MainFrame.menu_font );
 766             if ( !getConfiguration().isUseNativeUI() ) {
 767                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 768                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 769             }
 770             item.setSelected( is_selected );
 771             item.addActionListener( this );
 772         }
 773     }
 774
 775     void exceptionOccuredDuringOpenFile( final Exception e ) {
 776         try {
 777             _mainpanel.getCurrentTreePanel().setArrowCursor();
 778         }
 779         catch ( final Exception ex ) {
 780             // Do nothing.
 781         }
 782         JOptionPane.showMessageDialog( this,
 783                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
 784                                        "Error during File|Open",
 785                                        JOptionPane.ERROR_MESSAGE );
 786     }
 787
 788     void exceptionOccuredDuringSaveAs( final Exception e ) {
 789         try {
 790             _mainpanel.getCurrentTreePanel().setArrowCursor();
 791         }
 792         catch ( final Exception ex ) {
 793             // Do nothing.
 794         }
 795         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
 796     }
 797
 798     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
 799         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
 800             JOptionPane.showMessageDialog( this,
 801                                            "Gene tree and species tree have no species in common.",
 802                                            "Error during SDI",
 803                                            JOptionPane.ERROR_MESSAGE );
 804             return false;
 805         }
 806         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
 807             JOptionPane.showMessageDialog( this,
 808                                            "Gene tree and species tree have only one species in common.",
 809                                            "Error during SDI",
 810                                            JOptionPane.ERROR_MESSAGE );
 811             return false;
 812         }
 813         else {
 814             return true;
 815         }
 816     }
 817
 818     public Configuration getConfiguration() {
 819         return _configuration;
 820     }
 821
 822     TreePanel getCurrentTreePanel() {
 823         return getMainPanel().getCurrentTreePanel();
 824     }
 825
 826     JMenu getHelpMenu() {
 827         return _help_jmenu;
 828     }
 829
 830     JCheckBoxMenuItem getlabelDirectionCbmi() {
 831         return _label_direction_cbmi;
 832     }
 833
 834     public MainPanel getMainPanel() {
 835         return _mainpanel;
 836     }
 837
 838     JMenuBar getMenuBarOfMainFrame() {
 839         return _jmenubar;
 840     }
 841
 842     public Options getOptions() {
 843         return _options;
 844     }
 845
 846     void initializeTypeMenu( final Options options ) {
 847         setTypeMenuToAllUnselected();
 848         switch ( options.getPhylogenyGraphicsType() ) {
 849             case CONVEX:
 850                 _convex_type_cbmi.setSelected( true );
 851                 break;
 852             case CURVED:
 853                 _curved_type_cbmi.setSelected( true );
 854                 break;
 855             case EURO_STYLE:
 856                 _euro_type_cbmi.setSelected( true );
 857                 break;
 858             case ROUNDED:
 859                 _rounded_type_cbmi.setSelected( true );
 860                 break;
 861             case TRIANGULAR:
 862                 _triangular_type_cbmi.setSelected( true );
 863                 break;
 864             case UNROOTED:
 865                 _unrooted_type_cbmi.setSelected( true );
 866                 break;
 867             case CIRCULAR:
 868                 _circular_type_cbmi.setSelected( true );
 869                 break;
 870             default:
 871                 _rectangular_type_cbmi.setSelected( true );
 872                 break;
 873         }
 874     }
 875
 876     void midpointRoot() {
 877         if ( _mainpanel.getCurrentTreePanel() != null ) {
 878             _mainpanel.getCurrentTreePanel().midpointRoot();
 879         }
 880     }
 881
 882     abstract void readPhylogeniesFromURL();
 883
 884     void readPhylogeniesFromWebservice( final int i ) {
 885         final UrlTreeReader reader = new UrlTreeReader( this, i );
 886         new Thread( reader ).start();
 887     }
 888
 889     private void removeBranchColors() {
 890         if ( getMainPanel().getCurrentPhylogeny() != null ) {
 891             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
 892         }
 893     }
 894
 895     void checkTextFrames() {
 896         if ( _textframes.size() > 5 ) {
 897             try {
 898                 if ( _textframes.getFirst() != null ) {
 899                     _textframes.getFirst().removeMe();
 900                 }
 901                 else {
 902                     _textframes.removeFirst();
 903                 }
 904             }
 905             catch ( final NoSuchElementException e ) {
 906                 // Ignore.
 907             }
 908         }
 909     }
 910
 911     void removeAllTextFrames() {
 912         for( final TextFrame tf : _textframes ) {
 913             if ( tf != null ) {
 914                 tf.close();
 915             }
 916         }
 917         _textframes.clear();
 918     }
 919
 920     void setConfiguration( final Configuration configuration ) {
 921         _configuration = configuration;
 922     }
 923
 924     void setOptions( final Options options ) {
 925         _options = options;
 926     }
 927
 928     void setInferenceManager( final InferenceManager i ) {
 929         _inference_manager = i;
 930     }
 931
 932     public InferenceManager getInferenceManager() {
 933         return _inference_manager;
 934     }
 935
 936     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 937         setTypeMenuToAllUnselected();
 938         switch ( type ) {
 939             case CIRCULAR:
 940                 _circular_type_cbmi.setSelected( true );
 941                 break;
 942             case CONVEX:
 943                 _convex_type_cbmi.setSelected( true );
 944                 break;
 945             case CURVED:
 946                 _curved_type_cbmi.setSelected( true );
 947                 break;
 948             case EURO_STYLE:
 949                 _euro_type_cbmi.setSelected( true );
 950                 break;
 951             case ROUNDED:
 952                 _rounded_type_cbmi.setSelected( true );
 953                 break;
 954             case RECTANGULAR:
 955                 _rectangular_type_cbmi.setSelected( true );
 956                 break;
 957             case TRIANGULAR:
 958                 _triangular_type_cbmi.setSelected( true );
 959                 break;
 960             case UNROOTED:
 961                 _unrooted_type_cbmi.setSelected( true );
 962                 break;
 963             default:
 964                 throw new IllegalArgumentException( "unknown type: " + type );
 965         }
 966     }
 967
 968     void setTypeMenuToAllUnselected() {
 969         _convex_type_cbmi.setSelected( false );
 970         _curved_type_cbmi.setSelected( false );
 971         _euro_type_cbmi.setSelected( false );
 972         _rounded_type_cbmi.setSelected( false );
 973         _triangular_type_cbmi.setSelected( false );
 974         _rectangular_type_cbmi.setSelected( false );
 975         _unrooted_type_cbmi.setSelected( false );
 976         _circular_type_cbmi.setSelected( false );
 977     }
 978
 979     public void showWhole() {
 980         _mainpanel.getControlPanel().showWhole();
 981     }
 982
 983     void switchColors() {
 984         final TreeColorSet colorset = _mainpanel.getTreeColorSet();
 985         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
 986         csc.setVisible( true );
 987     }
 988
 989     void taxColor() {
 990         if ( _mainpanel.getCurrentTreePanel() != null ) {
 991             _mainpanel.getCurrentTreePanel().taxColor();
 992         }
 993     }
 994
 995     void typeChanged( final Object o ) {
 996         updateTypeCheckboxes( getOptions(), o );
 997         updateOptions( getOptions() );
 998         if ( getCurrentTreePanel() != null ) {
 999             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1000             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1001             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1002                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1003                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1004                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1005                 getCurrentTreePanel().getControlPanel().showWhole();
1006             }
1007             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1008                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1009             }
1010             else {
1011                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1012             }
1013             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1014             updateScreenTextAntialias( getMainPanel().getTreePanels() );
1015             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
1016                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1017                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
1018                 }
1019                 else {
1020                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
1021                 }
1022             }
1023         }
1024     }
1025
1026     void updateOptions( final Options options ) {
1027         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1028         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1029                 && _background_gradient_cbmi.isSelected() );
1030         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1031         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1032                 && _abbreviate_scientific_names.isSelected() );
1033         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1034                 && _color_labels_same_as_parent_branch.isSelected() );
1035         options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1036                 && _show_default_node_shapes_cbmi.isSelected() );
1037         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1038                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1039         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1040             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1041         }
1042         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1043             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1044         }
1045         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1046             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1047         }
1048         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1049                 && _search_case_senstive_cbmi.isSelected() );
1050         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1051             options.setShowScale( _show_scale_cbmi.isSelected() );
1052         }
1053         if ( _label_direction_cbmi != null ) {
1054             if ( _label_direction_cbmi.isSelected() ) {
1055                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1056             }
1057             else {
1058                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1059             }
1060         }
1061         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1062         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1063                 && _show_confidence_stddev_cbmi.isSelected() );
1064         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1065             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1066         }
1067         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1068                 && ( _print_using_actual_size_cbmi.isSelected() ) );
1069         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1070                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1071         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1072         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1073                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1074             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1075         }
1076         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1077                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1078             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1079         }
1080         else {
1081             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1082         }
1083         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1084                 && _print_black_and_white_cbmi.isSelected() );
1085         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1086                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1087         options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
1088                 && _extract_pfam_style_tax_codes_cbmi.isSelected() );
1089         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1090                 && _replace_underscores_cbmi.isSelected() );
1091         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1092                 && _search_whole_words_only_cbmi.isSelected() );
1093         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1094                 && _inverse_search_result_cbmi.isSelected() );
1095         if ( _graphics_export_visible_only_cbmi != null ) {
1096             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1097             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1098                 _graphics_export_using_actual_size_cbmi.setSelected( true );
1099                 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1100             }
1101             else {
1102                 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1103             }
1104         }
1105         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1106             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1107         }
1108         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1109             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1110         }
1111         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1112             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1113         }
1114         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1115             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1116         }
1117         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1118             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1119         }
1120         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1121             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1122         }
1123         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1124             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1125         }
1126         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1127             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1128         }
1129     }
1130
1131     void updateTypeCheckboxes( final Options options, final Object o ) {
1132         setTypeMenuToAllUnselected();
1133         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1134     }
1135
1136     void displayBasicInformation() {
1137         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1138             String title = "Basic Information";
1139             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1140                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1141             }
1142             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
1143         }
1144     }
1145
1146     void viewAsNexus() {
1147         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1148             String title = "Nexus";
1149             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1150                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1151             }
1152             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
1153                            title );
1154         }
1155     }
1156
1157     void viewAsNH() {
1158         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1159             String title = "New Hampshire";
1160             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1161                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1162             }
1163             showTextFrame( _mainpanel.getCurrentPhylogeny()
1164                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1165                            title );
1166         }
1167     }
1168
1169     void viewAsNHX() {
1170         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1171             String title = "NHX";
1172             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1173                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1174             }
1175             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title );
1176         }
1177     }
1178
1179     void viewAsXML() {
1180         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1181             String title = "phyloXML";
1182             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1183                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1184             }
1185             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
1186         }
1187     }
1188
1189     public void showTextFrame( final String s, final String title ) {
1190         checkTextFrames();
1191         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
1192     }
1193
1194     /**
1195      * Display the about box.
1196      */
1197     static void about() {
1198         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1199         about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
1200         about.append( "All Rights Reserved\n" );
1201         about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1202         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1203         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
1204         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1205         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1206         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1207             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1208         }
1209         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1210                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1211             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1212                     + ForesterUtil.OS_VERSION + "]\n" );
1213         }
1214         final Runtime rt = java.lang.Runtime.getRuntime();
1215         final long free_memory = rt.freeMemory() / 1000000;
1216         final long total_memory = rt.totalMemory() / 1000000;
1217         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1218         about.append( "[locale: " + Locale.getDefault() + "]\n" );
1219         about.append( "References:\n" );
1220         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1221         about.append( "For more information & download:\n" );
1222         about.append( Constants.APTX_WEB_SITE + "\n" );
1223         about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1224         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1225     }
1226
1227     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1228         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1229     }
1230
1231     static JMenu createMenu( final String title, final Configuration conf ) {
1232         final JMenu jmenu = new JMenu( title );
1233         if ( !conf.isUseNativeUI() ) {
1234             jmenu.setFont( MainFrame.menu_font );
1235             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1236             jmenu.setForeground( conf.getGuiMenuTextColor() );
1237         }
1238         return jmenu;
1239     }
1240
1241     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1242         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1243         if ( !configuration.isUseNativeUI() ) {
1244             label.setBackground( configuration.getGuiMenuBackgroundColor() );
1245             label.setForeground( configuration.getGuiMenuTextColor() );
1246             label.setOpaque( true );
1247         }
1248         label.setSelected( false );
1249         label.setEnabled( false );
1250         return label;
1251     }
1252
1253     static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1254         switch ( op.getOvPlacement() ) {
1255             case LOWER_LEFT:
1256                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1257                 break;
1258             case LOWER_RIGHT:
1259                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1260                 break;
1261             case UPPER_LEFT:
1262                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1263                 break;
1264             case UPPER_RIGHT:
1265                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1266                 break;
1267             default:
1268                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1269         }
1270         if ( tree_panel != null ) {
1271             tree_panel.updateOvSettings();
1272         }
1273     }
1274
1275     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1276         switch ( op.getDefaultNodeFill() ) {
1277             case GRADIENT:
1278                 op.setDefaultNodeFill( NodeFill.SOLID );
1279                 break;
1280             case NONE:
1281                 op.setDefaultNodeFill( NodeFill.GRADIENT );
1282                 break;
1283             case SOLID:
1284                 op.setDefaultNodeFill( NodeFill.NONE );
1285                 break;
1286             default:
1287                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1288         }
1289     }
1290
1291     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1292         switch ( op.getDefaultNodeShape() ) {
1293             case CIRCLE:
1294                 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1295                 break;
1296             case RECTANGLE:
1297                 op.setDefaultNodeShape( NodeShape.CIRCLE );
1298                 break;
1299             default:
1300                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1301         }
1302     }
1303
1304     void help( final Map<String, WebLink> weblinks ) {
1305         final StringBuilder sb = new StringBuilder();
1306         sb.append( "Display options\n" );
1307         sb.append( "-------------------\n" );
1308         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1309         sb.append( "Clickable tree nodes\n" );
1310         sb.append( "--------------------\n" );
1311         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1312         sb.append( "or by right clicking:\n" );
1313         sb.append( "o  Display Node Data -- display information for a node\n" );
1314         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1315         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
1316         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1317         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
1318         sb.append( "o  Colorize Subtree -- color a subtree\n" );
1319         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
1320         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1321         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
1322         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1323         sb.append( "Zooming\n" );
1324         sb.append( "---------\n" );
1325         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1326         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1327         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1328         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1329         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1330         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1331         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1332         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1333         sb.append( "Quick tree manipulation:\n" );
1334         sb.append( "------------------------\n" );
1335         sb.append( "Order Subtrees -- order the tree by branch length\n" );
1336         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1337         sb.append( "Memory problems (Java heap space error)\n" );
1338         sb.append( "---------------------------------------\n" );
1339         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1340         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1341         sb.append( "the '-Xmx' Java command line option. For example:\n" );
1342         sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1343         if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
1344             sb.append( "Active web links\n" );
1345             sb.append( "--------------------\n" );
1346             for( final String key : weblinks.keySet() ) {
1347                 sb.append( " " + weblinks.get( key ).toString() + "\n" );
1348             }
1349         }
1350         // + "General remarks\n"
1351         // + "---------------\n"
1352         // +
1353         // "o  The application version permits copying to the clipboard \n"
1354         // +
1355         // "    in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1356         // +
1357         // "o  Changes made to a subtree affect this subtree and its subtrees,\n"
1358         // + "    but not any of its parent tree(s).\n"
1359         // +
1360         // "o  Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1361         // +
1362         // "    are likely to be bootstrap values instead of branch length values.\n\n"
1363         // +
1364         // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1365         // +
1366         // "o  Each external node of the gene tree (in display) needs to be associated with\n"
1367         // +
1368         // "    a species: either directly through the \"Species\" field, or the species\n"
1369         // +
1370         // "    is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1371         // +
1372         // "    (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1373         // +
1374         // "o  A species tree for each species of the gene tree needs to be loaded with\n"
1375         // +
1376         // "   \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1377         // +
1378         // "o  !External nodes of the gene tree associated with species not present in\n"
1379         // +
1380         // "    the species tree are REMOVED prior to SDI execution!\n"
1381         // +
1382         // "o  Both the gene tree and the species tree must be completely binary.\n"
1383         // +
1384         // "o  Duplications and speciations are a function of the position of the root.\n"
1385         // +
1386         // "    Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1387         // + "    incorrect and need to be inferred again\n"
1388         // +
1389         // "    with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1390         sb.append( "\n" );
1391         sb.append( "phyloXML\n" );
1392         sb.append( "-------------------\n" );
1393         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1394         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1395         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1396         sb.append( "\n" );
1397         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1398         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1399         TextFrame.instantiate( sb.toString(), "Help", _textframes );
1400     }
1401
1402     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1403         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1404             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1405         }
1406         else {
1407             mi.setText( "Cycle Overview Placement..." );
1408         }
1409     }
1410
1411     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1412         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1413             mi.setText( "Cycle Node Shape Fill Type... (current: "
1414                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1415         }
1416         else {
1417             mi.setText( "Cycle Node Shape Fill Type..." );
1418         }
1419     }
1420
1421     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1422         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1423             mi.setText( "Cycle Node Shape Fill Type... (current: "
1424                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1425         }
1426         else {
1427             mi.setText( "Cycle Node Shape Fill Type..." );
1428         }
1429     }
1430
1431     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1432         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1433             mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1434         }
1435         else {
1436             mi.setText( "Select Colors..." );
1437         }
1438     }
1439
1440     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1441         mi.setText( "Select Font... (current: " + font_desc + ")" );
1442     }
1443
1444     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1445         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1446             mi.setEnabled( true );
1447         }
1448         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1449             mi.setEnabled( true );
1450         }
1451         else {
1452             mi.setEnabled( false );
1453         }
1454         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1455     }
1456
1457     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1458         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1459     }
1460
1461     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1462                                                            final JCheckBoxMenuItem scale,
1463                                                            final JCheckBoxMenuItem branch_lengths,
1464                                                            final JRadioButtonMenuItem non_lined_up,
1465                                                            final JRadioButtonMenuItem uniform_clado,
1466                                                            final JRadioButtonMenuItem nonuniform_clado,
1467                                                            final JCheckBoxMenuItem label_direction_cbmi ) {
1468         final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1469         final ControlPanel control = main_panel.getControlPanel();
1470         final Options options = main_panel.getOptions();
1471         scale.setSelected( options.isShowScale() );
1472         branch_lengths.setSelected( options.isShowBranchLengthValues() );
1473         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1474         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1475             scale.setSelected( false );
1476             scale.setEnabled( false );
1477             branch_lengths.setSelected( false );
1478             branch_lengths.setEnabled( false );
1479         }
1480         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1481             scale.setSelected( false );
1482             scale.setEnabled( false );
1483             branch_lengths.setEnabled( true );
1484         }
1485         else {
1486             scale.setEnabled( true );
1487             branch_lengths.setEnabled( true );
1488         }
1489         if ( ( tree_panel != null )
1490                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1491                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1492                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1493             branch_lengths.setSelected( false );
1494             branch_lengths.setEnabled( false );
1495         }
1496         if ( tree_panel != null ) {
1497             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1498                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1499                 non_lined_up.setEnabled( false );
1500                 uniform_clado.setEnabled( false );
1501                 nonuniform_clado.setEnabled( false );
1502             }
1503             else {
1504                 non_lined_up.setEnabled( true );
1505                 uniform_clado.setEnabled( true );
1506                 nonuniform_clado.setEnabled( true );
1507             }
1508         }
1509         else {
1510             if ( ( tree_panel != null )
1511                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1512                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1513                 branch_lengths.setSelected( false );
1514                 branch_lengths.setEnabled( false );
1515             }
1516             if ( ( tree_panel != null )
1517                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1518                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1519                 non_lined_up.setEnabled( false );
1520             }
1521             else {
1522                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1523                 non_lined_up.setEnabled( true );
1524             }
1525         }
1526         label_direction_cbmi.setEnabled( true );
1527         if ( tree_panel != null ) {
1528             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1529                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1530                 label_direction_cbmi.setEnabled( false );
1531             }
1532             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1533                 scale.setSelected( false );
1534                 scale.setEnabled( false );
1535             }
1536         }
1537     }
1538
1539     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1540         for( final TreePanel tree_panel : treepanels ) {
1541             tree_panel.setTextAntialias();
1542         }
1543     }
1544 }