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