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 import java.util.Set;
  40
  41 import javax.swing.Box;
  42 import javax.swing.JApplet;
  43 import javax.swing.JCheckBoxMenuItem;
  44 import javax.swing.JFrame;
  45 import javax.swing.JLabel;
  46 import javax.swing.JMenu;
  47 import javax.swing.JMenuBar;
  48 import javax.swing.JMenuItem;
  49 import javax.swing.JOptionPane;
  50 import javax.swing.JPanel;
  51 import javax.swing.JRadioButtonMenuItem;
  52 import javax.swing.JTextField;
  53 import javax.swing.SwingUtilities;
  54
  55 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  56 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  57 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  58 import org.forester.archaeopteryx.tools.InferenceManager;
  59 import org.forester.archaeopteryx.tools.ProcessPool;
  60 import org.forester.archaeopteryx.tools.ProcessRunning;
  61 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  62 import org.forester.phylogeny.Phylogeny;
  63 import org.forester.phylogeny.PhylogenyNode;
  64 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  65 import org.forester.phylogeny.data.Annotation;
  66 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
  67 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
  68 import org.forester.util.ForesterConstants;
  69 import org.forester.util.ForesterUtil;
  70
  71 public abstract class MainFrame extends JFrame implements ActionListener {
  72
  73     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";
  74     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME
  75     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;
  76     private static final long   serialVersionUID                        = 3655000897845508358L;
  77     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),
  78                                                                                     Font.PLAIN,
  79                                                                                     10 );
  80     static final String         TYPE_MENU_HEADER                        = "Type";
  81     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";
  82     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";
  83     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";
  84     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";
  85     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";
  86     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";
  87     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO
  88     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO
  89     static final String         OPTIONS_HEADER                          = "Options";
  90     static final String         SEARCH_SUBHEADER                        = "Search:";
  91     static final String         DISPLAY_SUBHEADER                       = "Display:";
  92     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";
  93     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";
  94     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";
  95     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Display Branch Length Values";
  96     static final String         DISPLAY_SCALE_LABEL                     = "Display Scale";
  97     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";
  98     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";
  99     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";
 100     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";
 101     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";
 102     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";
 103     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";
 104     static final String         DISPLAY_NODE_BOXES_LABEL                = "Show Node Shapes";
 105     static final String         SHOW_OVERVIEW_LABEL                     = "Show Overview";
 106     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";
 107     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";
 108     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Show Domain Labels";
 109     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";
 110     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";
 111     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";
 112     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";
 113     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";
 114     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";
 115     static final String         SHOW_CONF_STDDEV_LABEL                  = "Show Confidence Standard Deviations";
 116     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";
 117     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
 118     JMenuBar                    _jmenubar;
 119     JMenu                       _file_jmenu;
 120     JMenu                       _tools_menu;
 121     JMenu                       _view_jmenu;
 122     JMenu                       _options_jmenu;
 123     JMenu                       _font_size_menu;
 124     JMenu                       _help_jmenu;
 125     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;
 126     // file menu:
 127     JMenuItem                   _open_item;
 128     JMenuItem                   _open_url_item;
 129     JMenuItem                   _save_item;
 130     JMenuItem                   _save_all_item;
 131     JMenuItem                   _close_item;
 132     JMenuItem                   _exit_item;
 133     JMenuItem                   _new_item;
 134     // tools menu:
 135     JMenuItem                   _midpoint_root_item;
 136     JMenuItem                   _taxcolor_item;
 137     JMenuItem                   _confcolor_item;
 138     JMenuItem                   _color_rank_jmi;
 139     JMenuItem                   _collapse_species_specific_subtrees;
 140     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me
 141     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;
 142     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;
 143     JMenuItem                   _obtain_seq_information_jmi;
 144     JMenuItem                   _move_node_names_to_tax_sn_jmi;
 145     JMenuItem                   _move_node_names_to_seq_names_jmi;
 146     JMenuItem                   _extract_tax_code_from_node_names_jmi;
 147     JMenuItem                   _annotate_item;
 148     // font size menu:
 149     JMenuItem                   _super_tiny_fonts_item;
 150     JMenuItem                   _tiny_fonts_item;
 151     JMenuItem                   _small_fonts_item;
 152     JMenuItem                   _medium_fonts_item;
 153     JMenuItem                   _large_fonts_item;
 154     // options menu:
 155     // _  screen and print
 156     JMenuItem                   _choose_font_mi;
 157     JMenuItem                   _switch_colors_mi;
 158     JCheckBoxMenuItem           _label_direction_cbmi;
 159     // _  screen display
 160     JCheckBoxMenuItem           _screen_antialias_cbmi;
 161     JCheckBoxMenuItem           _background_gradient_cbmi;
 162     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 163     JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 164     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 165     JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 166     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me
 167     JCheckBoxMenuItem           _show_overview_cbmi;
 168     JCheckBoxMenuItem           _show_domain_labels;
 169     JCheckBoxMenuItem           _abbreviate_scientific_names;
 170     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 171     JMenuItem                   _overview_placment_mi;
 172     JMenuItem                   _choose_minimal_confidence_mi;
 173     JCheckBoxMenuItem           _show_default_node_shapes_cbmi;
 174     JMenuItem                   _cycle_node_shape_mi;
 175     JMenuItem                   _cycle_node_fill_mi;
 176     JMenuItem                   _choose_node_size_mi;
 177     JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
 178     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 179     // _  print
 180     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;
 181     JCheckBoxMenuItem           _antialias_print_cbmi;
 182     JCheckBoxMenuItem           _print_black_and_white_cbmi;
 183     JCheckBoxMenuItem           _print_using_actual_size_cbmi;
 184     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;
 185     JMenuItem                   _print_size_mi;
 186     JMenuItem                   _choose_pdf_width_mi;
 187     // _  parsing
 188     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;
 189     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;
 190     JRadioButtonMenuItem        _extract_taxonomy_yes_rbmi;
 191     JRadioButtonMenuItem        _extract_taxonomy_pfam_rbmi;
 192     JCheckBoxMenuItem           _replace_underscores_cbmi;
 193     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;
 194     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;
 195     // _  search
 196     JCheckBoxMenuItem           _search_case_senstive_cbmi;
 197     JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 198     JCheckBoxMenuItem           _inverse_search_result_cbmi;
 199     // type menu:
 200     JMenu                       _type_menu;
 201     JCheckBoxMenuItem           _rectangular_type_cbmi;
 202     JCheckBoxMenuItem           _triangular_type_cbmi;
 203     JCheckBoxMenuItem           _curved_type_cbmi;
 204     JCheckBoxMenuItem           _convex_type_cbmi;
 205     JCheckBoxMenuItem           _euro_type_cbmi;
 206     JCheckBoxMenuItem           _rounded_type_cbmi;
 207     JCheckBoxMenuItem           _unrooted_type_cbmi;
 208     JCheckBoxMenuItem           _circular_type_cbmi;
 209     // view as text menu:
 210     JMenuItem                   _view_as_NH_item;
 211     JMenuItem                   _view_as_NHX_item;
 212     JMenuItem                   _view_as_XML_item;
 213     JMenuItem                   _view_as_nexus_item;
 214     JMenuItem                   _display_basic_information_item;
 215     // help menu:
 216     JMenuItem                   _about_item;
 217     JMenuItem                   _help_item;
 218     JMenuItem                   _website_item;
 219     JMenuItem                   _phyloxml_website_item;
 220     JMenuItem                   _phyloxml_ref_item;
 221     JMenuItem                   _aptx_ref_item;
 222     // process menu:
 223     JMenu                       _process_menu;
 224     // Handy pointers to child components:
 225     MainPanel                   _mainpanel;
 226     Container                   _contentpane;
 227     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;
 228     Configuration               _configuration;
 229     JMenuItem                   _remove_branch_color_item;
 230     Options                     _options;
 231     InferenceManager            _inference_manager;
 232     final ProcessPool           _process_pool;
 233     private String              _previous_node_annotation_ref;
 234     private String              _ext_node_data_buffer                   = "";
 235     private int                 _ext_node_data_buffer_change_counter    = 0;
 236
 237     MainFrame() {
 238         _process_pool = ProcessPool.createInstance();
 239     }
 240
 241     /**
 242      * Action performed.
 243      */
 244     @Override
 245     public void actionPerformed( final ActionEvent e ) {
 246         final Object o = e.getSource();
 247         boolean is_applet = false;
 248         JApplet applet = null;
 249         if ( getCurrentTreePanel() != null ) {
 250             is_applet = getCurrentTreePanel().isApplet();
 251             if ( is_applet ) {
 252                 applet = getCurrentTreePanel().obtainApplet();
 253             }
 254         }
 255         if ( o == _open_url_item ) {
 256             readPhylogeniesFromURL();
 257         }
 258         else if ( o == _exit_item ) {
 259             close();
 260         }
 261         else if ( o == _taxcolor_item ) {
 262             taxColor();
 263         }
 264         else if ( o == _confcolor_item ) {
 265             confColor();
 266         }
 267         else if ( o == _color_rank_jmi ) {
 268             colorRank();
 269         }
 270         else if ( o == _collapse_species_specific_subtrees ) {
 271             if ( isSubtreeDisplayed() ) {
 272                 return;
 273             }
 274             if ( getCurrentTreePanel() != null ) {
 275                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 276             }
 277         }
 278         else if ( o == _remove_branch_color_item ) {
 279             if ( isSubtreeDisplayed() ) {
 280                 return;
 281             }
 282             removeBranchColors();
 283         }
 284         else if ( o == _midpoint_root_item ) {
 285             if ( isSubtreeDisplayed() ) {
 286                 return;
 287             }
 288             midpointRoot();
 289         }
 290         else if ( o == _annotate_item ) {
 291             annotateSequences();
 292         }
 293         else if ( o == _switch_colors_mi ) {
 294             switchColors();
 295         }
 296         else if ( o == _display_basic_information_item ) {
 297             displayBasicInformation();
 298         }
 299         else if ( o == _view_as_NH_item ) {
 300             viewAsNH();
 301         }
 302         else if ( o == _view_as_NHX_item ) {
 303             viewAsNHX();
 304         }
 305         else if ( o == _view_as_XML_item ) {
 306             viewAsXML();
 307         }
 308         else if ( o == _view_as_nexus_item ) {
 309             viewAsNexus();
 310         }
 311         else if ( o == _super_tiny_fonts_item ) {
 312             if ( getCurrentTreePanel() != null ) {
 313                 getCurrentTreePanel().setSuperTinyFonts();
 314                 getCurrentTreePanel().repaint();
 315             }
 316         }
 317         else if ( o == _tiny_fonts_item ) {
 318             if ( getCurrentTreePanel() != null ) {
 319                 getCurrentTreePanel().setTinyFonts();
 320                 getCurrentTreePanel().repaint();
 321             }
 322         }
 323         else if ( o == _small_fonts_item ) {
 324             if ( getCurrentTreePanel() != null ) {
 325                 getCurrentTreePanel().setSmallFonts();
 326                 getCurrentTreePanel().repaint();
 327             }
 328         }
 329         else if ( o == _medium_fonts_item ) {
 330             if ( getCurrentTreePanel() != null ) {
 331                 getCurrentTreePanel().setMediumFonts();
 332                 getCurrentTreePanel().repaint();
 333             }
 334         }
 335         else if ( o == _large_fonts_item ) {
 336             if ( getCurrentTreePanel() != null ) {
 337                 getCurrentTreePanel().setLargeFonts();
 338                 getCurrentTreePanel().repaint();
 339             }
 340         }
 341         else if ( o == _choose_font_mi ) {
 342             chooseFont();
 343         }
 344         else if ( o == _choose_minimal_confidence_mi ) {
 345             chooseMinimalConfidence();
 346         }
 347         else if ( o == _choose_node_size_mi ) {
 348             chooseNodeSize( getOptions(), this );
 349         }
 350         else if ( o == _overview_placment_mi ) {
 351             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 352         }
 353         else if ( o == _cycle_node_fill_mi ) {
 354             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 355         }
 356         else if ( o == _cycle_node_shape_mi ) {
 357             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 358         }
 359         else if ( o == _screen_antialias_cbmi ) {
 360             updateOptions( getOptions() );
 361             updateScreenTextAntialias( getMainPanel().getTreePanels() );
 362         }
 363         else if ( o == _background_gradient_cbmi ) {
 364             updateOptions( getOptions() );
 365         }
 366         else if ( o == _show_domain_labels ) {
 367             updateOptions( getOptions() );
 368         }
 369         else if ( o == _abbreviate_scientific_names ) {
 370             updateOptions( getOptions() );
 371         }
 372         else if ( o == _color_labels_same_as_parent_branch ) {
 373             updateOptions( getOptions() );
 374         }
 375         else if ( o == _show_default_node_shapes_cbmi ) {
 376             updateOptions( getOptions() );
 377         }
 378         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 379             updateOptions( getOptions() );
 380         }
 381         else if ( o == _non_lined_up_cladograms_rbmi ) {
 382             updateOptions( getOptions() );
 383             showWhole();
 384         }
 385         else if ( o == _uniform_cladograms_rbmi ) {
 386             updateOptions( getOptions() );
 387             showWhole();
 388         }
 389         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 390             updateOptions( getOptions() );
 391             showWhole();
 392         }
 393         else if ( o == _search_case_senstive_cbmi ) {
 394             updateOptions( getOptions() );
 395             getMainPanel().getControlPanel().search();
 396         }
 397         else if ( o == _search_whole_words_only_cbmi ) {
 398             updateOptions( getOptions() );
 399             getMainPanel().getControlPanel().search();
 400         }
 401         else if ( o == _inverse_search_result_cbmi ) {
 402             updateOptions( getOptions() );
 403             getMainPanel().getControlPanel().search();
 404         }
 405         else if ( o == _show_scale_cbmi ) {
 406             updateOptions( getOptions() );
 407         }
 408         else if ( o == _show_branch_length_values_cbmi ) {
 409             updateOptions( getOptions() );
 410         }
 411         else if ( o == _show_confidence_stddev_cbmi ) {
 412             updateOptions( getOptions() );
 413         }
 414         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
 415             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
 416                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
 417             }
 418             updateOptions( getOptions() );
 419         }
 420         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
 421             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
 422                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
 423             }
 424             updateOptions( getOptions() );
 425         }
 426         else if ( o == _label_direction_cbmi ) {
 427             updateOptions( getOptions() );
 428         }
 429         else if ( o == _show_overview_cbmi ) {
 430             updateOptions( getOptions() );
 431             if ( getCurrentTreePanel() != null ) {
 432                 getCurrentTreePanel().updateOvSizes();
 433             }
 434         }
 435         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 436                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
 437                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 438             typeChanged( o );
 439         }
 440         else if ( o == _about_item ) {
 441             about();
 442         }
 443         else if ( o == _help_item ) {
 444             help( getConfiguration().getWebLinks() );
 445         }
 446         else if ( o == _website_item ) {
 447             try {
 448                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
 449             }
 450             catch ( final IOException e1 ) {
 451                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 452             }
 453         }
 454         else if ( o == _phyloxml_website_item ) {
 455             try {
 456                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
 457             }
 458             catch ( final IOException e1 ) {
 459                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 460             }
 461         }
 462         else if ( o == _aptx_ref_item ) {
 463             try {
 464                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
 465             }
 466             catch ( final IOException e1 ) {
 467                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 468             }
 469         }
 470         else if ( o == _phyloxml_ref_item ) {
 471             try {
 472                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
 473             }
 474             catch ( final IOException e1 ) {
 475                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 476             }
 477         }
 478         else {
 479             if ( _load_phylogeny_from_webservice_menu_items != null ) {
 480                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
 481                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
 482                         readPhylogeniesFromWebservice( i );
 483                     }
 484                 }
 485             }
 486         }
 487         _contentpane.repaint();
 488     }
 489
 490     public Configuration getConfiguration() {
 491         return _configuration;
 492     }
 493
 494     /**
 495      * This method returns the current external node data which
 496      * has been selected by the user by clicking the "Return ..."
 497      * menu item. This method is expected to be called from Javascript or
 498      * something like it.
 499      *
 500      * @return current external node data as String
 501      */
 502     public String getCurrentExternalNodesDataBuffer() {
 503         return _ext_node_data_buffer;
 504     }
 505
 506     public int getExtNodeDataBufferChangeCounter() {
 507         return _ext_node_data_buffer_change_counter;
 508     }
 509
 510     public InferenceManager getInferenceManager() {
 511         return _inference_manager;
 512     }
 513
 514     public MainPanel getMainPanel() {
 515         return _mainpanel;
 516     }
 517
 518     public Options getOptions() {
 519         return _options;
 520     }
 521
 522     public ProcessPool getProcessPool() {
 523         return _process_pool;
 524     }
 525
 526     public void increaseExtNodeDataBufferChangeCounter() {
 527         _ext_node_data_buffer_change_counter++;
 528     }
 529
 530     public void showTextFrame( final String s, final String title ) {
 531         checkTextFrames();
 532         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 533     }
 534
 535     public void showWhole() {
 536         _mainpanel.getControlPanel().showWhole();
 537     }
 538
 539     public void updateProcessMenu() {
 540         // In general Swing is not thread safe.
 541         // See "Swing's Threading Policy".
 542         SwingUtilities.invokeLater( new Runnable() {
 543
 544             @Override
 545             public void run() {
 546                 doUpdateProcessMenu();
 547             }
 548         } );
 549     }
 550
 551     void activateSaveAllIfNeeded() {
 552         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
 553             _save_all_item.setEnabled( true );
 554         }
 555         else {
 556             _save_all_item.setEnabled( false );
 557         }
 558     }
 559
 560     void buildFileMenu() {
 561         _file_jmenu = createMenu( "File", getConfiguration() );
 562         _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
 563         _file_jmenu.addSeparator();
 564         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 565         customizeJMenuItem( _open_url_item );
 566         customizeJMenuItem( _exit_item );
 567         _jmenubar.add( _file_jmenu );
 568     }
 569
 570     void buildFontSizeMenu() {
 571         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
 572         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
 573         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
 574         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
 575         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
 576         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
 577         customizeJMenuItem( _super_tiny_fonts_item );
 578         customizeJMenuItem( _tiny_fonts_item );
 579         customizeJMenuItem( _small_fonts_item );
 580         customizeJMenuItem( _medium_fonts_item );
 581         customizeJMenuItem( _large_fonts_item );
 582         _jmenubar.add( _font_size_menu );
 583     }
 584
 585     void buildHelpMenu() {
 586         _help_jmenu = createMenu( "Help", getConfiguration() );
 587         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 588         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 589         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 590         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 591         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 592         _help_jmenu.addSeparator();
 593         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 594         customizeJMenuItem( _help_item );
 595         customizeJMenuItem( _website_item );
 596         customizeJMenuItem( _phyloxml_website_item );
 597         customizeJMenuItem( _aptx_ref_item );
 598         customizeJMenuItem( _phyloxml_ref_item );
 599         customizeJMenuItem( _about_item );
 600         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
 601         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
 602         _jmenubar.add( _help_jmenu );
 603     }
 604
 605     void buildTypeMenu() {
 606         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
 607         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 608         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 609         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 610         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 611         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 612         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 613         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 614         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 615         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 616         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 617         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 618         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 619         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 620         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 621         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 622         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 623         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 624         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 625         initializeTypeMenu( getOptions() );
 626         _jmenubar.add( _type_menu );
 627     }
 628
 629     void buildViewMenu() {
 630         _view_jmenu = createMenu( "View", getConfiguration() );
 631         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 632         _view_jmenu.addSeparator();
 633         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 634         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 635         _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
 636         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 637         customizeJMenuItem( _display_basic_information_item );
 638         customizeJMenuItem( _view_as_NH_item );
 639         customizeJMenuItem( _view_as_NHX_item );
 640         customizeJMenuItem( _view_as_XML_item );
 641         customizeJMenuItem( _view_as_nexus_item );
 642         _jmenubar.add( _view_jmenu );
 643     }
 644
 645     void checkTextFrames() {
 646         if ( _textframes.size() > 5 ) {
 647             try {
 648                 if ( _textframes.getFirst() != null ) {
 649                     _textframes.getFirst().removeMe();
 650                 }
 651                 else {
 652                     _textframes.removeFirst();
 653                 }
 654             }
 655             catch ( final NoSuchElementException e ) {
 656                 // Ignore.
 657             }
 658         }
 659     }
 660
 661     void close() {
 662         removeAllTextFrames();
 663         if ( _mainpanel != null ) {
 664             _mainpanel.terminate();
 665         }
 666         if ( _contentpane != null ) {
 667             _contentpane.removeAll();
 668         }
 669         setVisible( false );
 670         dispose();
 671     }
 672
 673     void colorRank() {
 674         if ( _mainpanel.getCurrentTreePanel() != null ) {
 675             final String[] ranks = AptxUtil.getAllPossibleRanks();
 676             final String rank = ( String ) JOptionPane
 677                     .showInputDialog( this,
 678                                       "What rank should the colorization be based on",
 679                                       "Rank Selection",
 680                                       JOptionPane.QUESTION_MESSAGE,
 681                                       null,
 682                                       ranks,
 683                                       null );
 684             if ( !ForesterUtil.isEmpty( rank ) ) {
 685                 _mainpanel.getCurrentTreePanel().colorRank( rank );
 686             }
 687         }
 688     }
 689
 690     void confColor() {
 691         if ( _mainpanel.getCurrentTreePanel() != null ) {
 692             _mainpanel.getCurrentTreePanel().confColor();
 693         }
 694     }
 695
 696     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 697         if ( item != null ) {
 698             item.setFont( MainFrame.menu_font );
 699             if ( !getConfiguration().isUseNativeUI() ) {
 700                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 701                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 702             }
 703             item.setSelected( is_selected );
 704             item.addActionListener( this );
 705         }
 706     }
 707
 708     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
 709         if ( jmi != null ) {
 710             jmi.setFont( MainFrame.menu_font );
 711             if ( !getConfiguration().isUseNativeUI() ) {
 712                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 713                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 714             }
 715             jmi.addActionListener( this );
 716         }
 717         return jmi;
 718     }
 719
 720     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 721         if ( item != null ) {
 722             item.setFont( MainFrame.menu_font );
 723             if ( !getConfiguration().isUseNativeUI() ) {
 724                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 725                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 726             }
 727             item.setSelected( is_selected );
 728             item.addActionListener( this );
 729         }
 730     }
 731
 732     void displayBasicInformation() {
 733         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
 734             String title = "Basic Information";
 735             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
 736                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
 737             }
 738             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
 739         }
 740     }
 741
 742     void exceptionOccuredDuringOpenFile( final Exception e ) {
 743         try {
 744             _mainpanel.getCurrentTreePanel().setArrowCursor();
 745         }
 746         catch ( final Exception ex ) {
 747             // Do nothing.
 748         }
 749         JOptionPane.showMessageDialog( this,
 750                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
 751                                        "Error during File|Open",
 752                                        JOptionPane.ERROR_MESSAGE );
 753     }
 754
 755     void exceptionOccuredDuringSaveAs( final Exception e ) {
 756         try {
 757             _mainpanel.getCurrentTreePanel().setArrowCursor();
 758         }
 759         catch ( final Exception ex ) {
 760             // Do nothing.
 761         }
 762         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
 763     }
 764
 765     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
 766         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
 767             JOptionPane.showMessageDialog( this,
 768                                            "Gene tree and species tree have no species in common.",
 769                                            "Error during SDI",
 770                                            JOptionPane.ERROR_MESSAGE );
 771             return false;
 772         }
 773         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
 774             JOptionPane.showMessageDialog( this,
 775                                            "Gene tree and species tree have only one species in common.",
 776                                            "Error during SDI",
 777                                            JOptionPane.ERROR_MESSAGE );
 778             return false;
 779         }
 780         else {
 781             return true;
 782         }
 783     }
 784
 785     TreePanel getCurrentTreePanel() {
 786         return getMainPanel().getCurrentTreePanel();
 787     }
 788
 789     JMenu getHelpMenu() {
 790         return _help_jmenu;
 791     }
 792
 793     JCheckBoxMenuItem getlabelDirectionCbmi() {
 794         return _label_direction_cbmi;
 795     }
 796
 797     JMenuBar getMenuBarOfMainFrame() {
 798         return _jmenubar;
 799     }
 800
 801     void help( final Map<String, WebLink> weblinks ) {
 802         final StringBuilder sb = new StringBuilder();
 803         sb.append( "Display options\n" );
 804         sb.append( "-------------------\n" );
 805         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 806         sb.append( "Clickable tree nodes\n" );
 807         sb.append( "--------------------\n" );
 808         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 809         sb.append( "or by right clicking:\n" );
 810         sb.append( "o  Display Node Data -- display information for a node\n" );
 811         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 812         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 813         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 814         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 815         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 816         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 817         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
 818         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
 819         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
 820         sb.append( "Zooming\n" );
 821         sb.append( "---------\n" );
 822         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
 823         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
 824         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
 825         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
 826         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
 827         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
 828         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
 829         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
 830         sb.append( "Quick tree manipulation:\n" );
 831         sb.append( "------------------------\n" );
 832         sb.append( "Order Subtrees -- order the tree by branch length\n" );
 833         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
 834         sb.append( "Memory problems (Java heap space error)\n" );
 835         sb.append( "---------------------------------------\n" );
 836         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
 837         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
 838         sb.append( "the '-Xmx' Java command line option. For example:\n" );
 839         sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
 840         if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
 841             sb.append( "Active web links\n" );
 842             sb.append( "--------------------\n" );
 843             for( final String key : weblinks.keySet() ) {
 844                 sb.append( " " + weblinks.get( key ).toString() + "\n" );
 845             }
 846         }
 847         // + "General remarks\n"
 848         // + "---------------\n"
 849         // +
 850         // "o  The application version permits copying to the clipboard \n"
 851         // +
 852         // "    in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
 853         // +
 854         // "o  Changes made to a subtree affect this subtree and its subtrees,\n"
 855         // + "    but not any of its parent tree(s).\n"
 856         // +
 857         // "o  Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
 858         // +
 859         // "    are likely to be bootstrap values instead of branch length values.\n\n"
 860         // +
 861         // " Remarks regarding SDI (Speciation Duplication Inference):\n"
 862         // +
 863         // "o  Each external node of the gene tree (in display) needs to be associated with\n"
 864         // +
 865         // "    a species: either directly through the \"Species\" field, or the species\n"
 866         // +
 867         // "    is part of the sequence name in the form \"XXXX_SPECIES\"\n"
 868         // +
 869         // "    (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
 870         // +
 871         // "o  A species tree for each species of the gene tree needs to be loaded with\n"
 872         // +
 873         // "   \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
 874         // +
 875         // "o  !External nodes of the gene tree associated with species not present in\n"
 876         // +
 877         // "    the species tree are REMOVED prior to SDI execution!\n"
 878         // +
 879         // "o  Both the gene tree and the species tree must be completely binary.\n"
 880         // +
 881         // "o  Duplications and speciations are a function of the position of the root.\n"
 882         // +
 883         // "    Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
 884         // + "    incorrect and need to be inferred again\n"
 885         // +
 886         // "    with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
 887         sb.append( "\n" );
 888         sb.append( "phyloXML\n" );
 889         sb.append( "-------------------\n" );
 890         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
 891         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
 892         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
 893         sb.append( "\n" );
 894         sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
 895         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
 896         TextFrame.instantiate( sb.toString(), "Help", _textframes );
 897     }
 898
 899     void initializeTypeMenu( final Options options ) {
 900         setTypeMenuToAllUnselected();
 901         switch ( options.getPhylogenyGraphicsType() ) {
 902             case CONVEX:
 903                 _convex_type_cbmi.setSelected( true );
 904                 break;
 905             case CURVED:
 906                 _curved_type_cbmi.setSelected( true );
 907                 break;
 908             case EURO_STYLE:
 909                 _euro_type_cbmi.setSelected( true );
 910                 break;
 911             case ROUNDED:
 912                 _rounded_type_cbmi.setSelected( true );
 913                 break;
 914             case TRIANGULAR:
 915                 _triangular_type_cbmi.setSelected( true );
 916                 break;
 917             case UNROOTED:
 918                 _unrooted_type_cbmi.setSelected( true );
 919                 break;
 920             case CIRCULAR:
 921                 _circular_type_cbmi.setSelected( true );
 922                 break;
 923             default:
 924                 _rectangular_type_cbmi.setSelected( true );
 925                 break;
 926         }
 927     }
 928
 929     boolean isSubtreeDisplayed() {
 930         if ( getCurrentTreePanel() != null ) {
 931             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
 932                 JOptionPane
 933                         .showMessageDialog( this,
 934                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
 935                                             "Operation can not be exectuted on a sub-tree",
 936                                             JOptionPane.WARNING_MESSAGE );
 937                 return true;
 938             }
 939         }
 940         return false;
 941     }
 942
 943     void midpointRoot() {
 944         if ( _mainpanel.getCurrentTreePanel() != null ) {
 945             _mainpanel.getCurrentTreePanel().midpointRoot();
 946         }
 947     }
 948
 949     abstract void readPhylogeniesFromURL();
 950
 951     void readPhylogeniesFromWebservice( final int i ) {
 952         final UrlTreeReader reader = new UrlTreeReader( this, i );
 953         new Thread( reader ).start();
 954     }
 955
 956     void removeAllTextFrames() {
 957         for( final TextFrame tf : _textframes ) {
 958             if ( tf != null ) {
 959                 tf.close();
 960             }
 961         }
 962         _textframes.clear();
 963     }
 964
 965     void setConfiguration( final Configuration configuration ) {
 966         _configuration = configuration;
 967     }
 968
 969     void setCurrentExternalNodesDataBuffer( final String s ) {
 970         increaseExtNodeDataBufferChangeCounter();
 971         if ( !ForesterUtil.isEmpty( s ) ) {
 972             _ext_node_data_buffer = s.trim();
 973         }
 974         else {
 975             _ext_node_data_buffer = "";
 976         }
 977     }
 978
 979     void setInferenceManager( final InferenceManager i ) {
 980         _inference_manager = i;
 981     }
 982
 983     void setOptions( final Options options ) {
 984         _options = options;
 985     }
 986
 987     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 988         setTypeMenuToAllUnselected();
 989         switch ( type ) {
 990             case CIRCULAR:
 991                 _circular_type_cbmi.setSelected( true );
 992                 break;
 993             case CONVEX:
 994                 _convex_type_cbmi.setSelected( true );
 995                 break;
 996             case CURVED:
 997                 _curved_type_cbmi.setSelected( true );
 998                 break;
 999             case EURO_STYLE:
1000                 _euro_type_cbmi.setSelected( true );
1001                 break;
1002             case ROUNDED:
1003                 _rounded_type_cbmi.setSelected( true );
1004                 break;
1005             case RECTANGULAR:
1006                 _rectangular_type_cbmi.setSelected( true );
1007                 break;
1008             case TRIANGULAR:
1009                 _triangular_type_cbmi.setSelected( true );
1010                 break;
1011             case UNROOTED:
1012                 _unrooted_type_cbmi.setSelected( true );
1013                 break;
1014             default:
1015                 throw new IllegalArgumentException( "unknown type: " + type );
1016         }
1017     }
1018
1019     void setTypeMenuToAllUnselected() {
1020         _convex_type_cbmi.setSelected( false );
1021         _curved_type_cbmi.setSelected( false );
1022         _euro_type_cbmi.setSelected( false );
1023         _rounded_type_cbmi.setSelected( false );
1024         _triangular_type_cbmi.setSelected( false );
1025         _rectangular_type_cbmi.setSelected( false );
1026         _unrooted_type_cbmi.setSelected( false );
1027         _circular_type_cbmi.setSelected( false );
1028     }
1029
1030     void switchColors() {
1031         final TreeColorSet colorset = _mainpanel.getTreeColorSet();
1032         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1033         csc.setVisible( true );
1034     }
1035
1036     void taxColor() {
1037         if ( _mainpanel.getCurrentTreePanel() != null ) {
1038             _mainpanel.getCurrentTreePanel().taxColor();
1039         }
1040     }
1041
1042     void typeChanged( final Object o ) {
1043         updateTypeCheckboxes( getOptions(), o );
1044         updateOptions( getOptions() );
1045         if ( getCurrentTreePanel() != null ) {
1046             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1047             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1048             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1049                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1050                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1051                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1052                 getCurrentTreePanel().getControlPanel().showWhole();
1053             }
1054             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1055                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1056             }
1057             else {
1058                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1059             }
1060             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1061             updateScreenTextAntialias( getMainPanel().getTreePanels() );
1062             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
1063                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1064                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
1065                 }
1066                 else {
1067                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
1068                 }
1069             }
1070         }
1071     }
1072
1073     void updateOptions( final Options options ) {
1074         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1075         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1076                 && _background_gradient_cbmi.isSelected() );
1077         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1078         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1079                 && _abbreviate_scientific_names.isSelected() );
1080         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1081                 && _color_labels_same_as_parent_branch.isSelected() );
1082         options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
1083                 && _show_default_node_shapes_cbmi.isSelected() );
1084         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1085                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1086         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1087             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1088         }
1089         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1090             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1091         }
1092         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1093             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1094         }
1095         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1096                 && _search_case_senstive_cbmi.isSelected() );
1097         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1098             options.setShowScale( _show_scale_cbmi.isSelected() );
1099         }
1100         if ( _label_direction_cbmi != null ) {
1101             if ( _label_direction_cbmi.isSelected() ) {
1102                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1103             }
1104             else {
1105                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1106             }
1107         }
1108         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1109         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1110                 && _show_confidence_stddev_cbmi.isSelected() );
1111         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1112             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1113         }
1114         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1115                 && ( _print_using_actual_size_cbmi.isSelected() ) );
1116         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1117                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1118         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1119         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1120                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1121             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1122         }
1123         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1124                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1125             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1126         }
1127         else {
1128             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1129         }
1130         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1131                 && _print_black_and_white_cbmi.isSelected() );
1132         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1133                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1134         if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
1135             options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.YES );
1136         }
1137         else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
1138             options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
1139         }
1140         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
1141             options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );
1142         }
1143         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1144                 && _replace_underscores_cbmi.isSelected() );
1145         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1146                 && _search_whole_words_only_cbmi.isSelected() );
1147         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1148                 && _inverse_search_result_cbmi.isSelected() );
1149         if ( _graphics_export_visible_only_cbmi != null ) {
1150             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1151             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1152                 _graphics_export_using_actual_size_cbmi.setSelected( true );
1153                 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1154             }
1155             else {
1156                 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1157             }
1158         }
1159         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1160             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1161         }
1162         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1163             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1164         }
1165         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1166             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1167         }
1168         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1169             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1170         }
1171         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1172             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1173         }
1174         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1175             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1176         }
1177         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1178             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1179         }
1180         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1181             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1182         }
1183     }
1184
1185     void updateTypeCheckboxes( final Options options, final Object o ) {
1186         setTypeMenuToAllUnselected();
1187         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1188     }
1189
1190     void viewAsNexus() {
1191         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1192             String title = "Nexus";
1193             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1194                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1195             }
1196             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
1197                            title );
1198         }
1199     }
1200
1201     void viewAsNH() {
1202         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1203             String title = "New Hampshire";
1204             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1205                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1206             }
1207             showTextFrame( _mainpanel.getCurrentPhylogeny()
1208                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1209                            title );
1210         }
1211     }
1212
1213     void viewAsNHX() {
1214         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1215             String title = "NHX";
1216             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1217                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1218             }
1219             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title );
1220         }
1221     }
1222
1223     void viewAsXML() {
1224         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1225             String title = "phyloXML";
1226             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1227                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1228             }
1229             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
1230         }
1231     }
1232
1233     private void annotateSequences() {
1234         if ( getCurrentTreePanel() != null ) {
1235             final Set<Integer> nodes = getCurrentTreePanel().getFoundNodes();
1236             if ( ( nodes == null ) || nodes.isEmpty() ) {
1237                 JOptionPane
1238                         .showMessageDialog( this,
1239                                             "Need to select nodes, either via direct selection or via the \"Search\" function",
1240                                             "No nodes selected for annotation",
1241                                             JOptionPane.ERROR_MESSAGE );
1242                 return;
1243             }
1244             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
1245             if ( ( phy != null ) && !phy.isEmpty() ) {
1246                 final JTextField ref_field = new JTextField( 10 );
1247                 final JTextField desc_filed = new JTextField( 20 );
1248                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
1249                         : getPreviousNodeAnnotationReference() );
1250                 final JPanel my_panel = new JPanel();
1251                 my_panel.add( new JLabel( "Reference " ) );
1252                 my_panel.add( ref_field );
1253                 my_panel.add( Box.createHorizontalStrut( 15 ) );
1254                 my_panel.add( new JLabel( "Description " ) );
1255                 my_panel.add( desc_filed );
1256                 final int result = JOptionPane.showConfirmDialog( null,
1257                                                                   my_panel,
1258                                                                   "Enter the sequence annotation(s) for the "
1259                                                                           + nodes.size() + " selected nodes",
1260                                                                   JOptionPane.OK_CANCEL_OPTION );
1261                 if ( result == JOptionPane.OK_OPTION ) {
1262                     String ref = ref_field.getText();
1263                     String desc = desc_filed.getText();
1264                     if ( !ForesterUtil.isEmpty( ref ) ) {
1265                         ref = ref.trim();
1266                         ref = ref.replaceAll( "\\s+", " " );
1267                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 )
1268                                 || ( ref.length() < 3 ) ) {
1269                             JOptionPane.showMessageDialog( this,
1270                                                            "Reference needs to be in the form of \"GO:1234567\"",
1271                                                            "Illegal Format for Annotation Reference",
1272                                                            JOptionPane.ERROR_MESSAGE );
1273                             return;
1274                         }
1275                     }
1276                     if ( ref != null ) {
1277                         setPreviousNodeAnnotationReference( ref );
1278                     }
1279                     if ( desc != null ) {
1280                         desc = desc.trim();
1281                         desc = desc.replaceAll( "\\s+", " " );
1282                     }
1283                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
1284                         for( final Integer id : nodes ) {
1285                             final PhylogenyNode n = phy.getNode( id );
1286                             ForesterUtil.ensurePresenceOfSequence( n );
1287                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
1288                                     : new Annotation( ref );
1289                             if ( !ForesterUtil.isEmpty( desc ) ) {
1290                                 ann.setDesc( desc );
1291                             }
1292                             n.getNodeData().getSequence().addAnnotation( ann );
1293                         }
1294                     }
1295                     getMainPanel().getControlPanel().showAnnotations();
1296                 }
1297             }
1298         }
1299     }
1300
1301     private void chooseFont() {
1302         final FontChooser fc = new FontChooser();
1303         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1304         fc.showDialog( this, "Select the Base Font" );
1305         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1306     }
1307
1308     private void chooseMinimalConfidence() {
1309         final String s = ( String ) JOptionPane
1310                 .showInputDialog( this,
1311                                   "Please enter the minimum for confidence values to be displayed.\n"
1312                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
1313                                   "Minimal Confidence Value",
1314                                   JOptionPane.QUESTION_MESSAGE,
1315                                   null,
1316                                   null,
1317                                   getOptions().getMinConfidenceValue() );
1318         if ( !ForesterUtil.isEmpty( s ) ) {
1319             boolean success = true;
1320             double m = 0.0;
1321             final String m_str = s.trim();
1322             if ( !ForesterUtil.isEmpty( m_str ) ) {
1323                 try {
1324                     m = Double.parseDouble( m_str );
1325                 }
1326                 catch ( final Exception ex ) {
1327                     success = false;
1328                 }
1329             }
1330             else {
1331                 success = false;
1332             }
1333             if ( success && ( m >= 0.0 ) ) {
1334                 getOptions().setMinConfidenceValue( m );
1335             }
1336         }
1337     }
1338
1339     private void doUpdateProcessMenu() {
1340         if ( _process_pool.size() > 0 ) {
1341             if ( _process_menu == null ) {
1342                 _process_menu = createMenu( "", getConfiguration() );
1343                 _process_menu.setForeground( Color.RED );
1344             }
1345             _process_menu.removeAll();
1346             final String text = "processes running: " + _process_pool.size();
1347             _process_menu.setText( text );
1348             _jmenubar.add( _process_menu );
1349             for( int i = 0; i < _process_pool.size(); ++i ) {
1350                 final ProcessRunning p = _process_pool.getProcessByIndex( i );
1351                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
1352             }
1353         }
1354         else {
1355             if ( _process_menu != null ) {
1356                 _process_menu.removeAll();
1357                 _jmenubar.remove( _process_menu );
1358             }
1359         }
1360         _jmenubar.validate();
1361         _jmenubar.repaint();
1362         repaint();
1363     }
1364
1365     private String getPreviousNodeAnnotationReference() {
1366         return _previous_node_annotation_ref;
1367     }
1368
1369     private void removeBranchColors() {
1370         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1371             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1372         }
1373     }
1374
1375     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
1376         _previous_node_annotation_ref = previous_node_annotation_ref;
1377     }
1378
1379     /**
1380      * Display the about box.
1381      */
1382     static void about() {
1383         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1384         about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
1385         about.append( "All Rights Reserved\n" );
1386         about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1387         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1388         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
1389         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1390         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1391         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1392             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1393         }
1394         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1395                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1396             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1397                     + ForesterUtil.OS_VERSION + "]\n" );
1398         }
1399         final Runtime rt = java.lang.Runtime.getRuntime();
1400         final long free_memory = rt.freeMemory() / 1000000;
1401         final long total_memory = rt.totalMemory() / 1000000;
1402         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1403         about.append( "[locale: " + Locale.getDefault() + "]\n" );
1404         about.append( "References:\n" );
1405         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1406         about.append( "For more information & download:\n" );
1407         about.append( Constants.APTX_WEB_SITE + "\n" );
1408         about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1409         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1410     }
1411
1412     static void chooseNodeSize( final Options options, final Component parent ) {
1413         final String s = ( String ) JOptionPane.showInputDialog( parent,
1414                                                                  "Please enter the default size for node shapes.\n"
1415                                                                          + "[current value: "
1416                                                                          + options.getDefaultNodeShapeSize() + "]\n",
1417                                                                  "Node Shape Size",
1418                                                                  JOptionPane.QUESTION_MESSAGE,
1419                                                                  null,
1420                                                                  null,
1421                                                                  options.getDefaultNodeShapeSize() );
1422         if ( !ForesterUtil.isEmpty( s ) ) {
1423             boolean success = true;
1424             double m = 0.0;
1425             final String m_str = s.trim();
1426             if ( !ForesterUtil.isEmpty( m_str ) ) {
1427                 try {
1428                     m = Double.parseDouble( m_str );
1429                 }
1430                 catch ( final Exception ex ) {
1431                     success = false;
1432                 }
1433             }
1434             else {
1435                 success = false;
1436             }
1437             if ( success && ( m >= 0.0 ) ) {
1438                 final short size = ForesterUtil.roundToShort( m );
1439                 if ( size >= 0.0 ) {
1440                     options.setDefaultNodeShapeSize( size );
1441                 }
1442             }
1443         }
1444     }
1445
1446     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1447         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1448     }
1449
1450     static JMenu createMenu( final String title, final Configuration conf ) {
1451         final JMenu jmenu = new JMenu( title );
1452         if ( !conf.isUseNativeUI() ) {
1453             jmenu.setFont( MainFrame.menu_font );
1454             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1455             jmenu.setForeground( conf.getGuiMenuTextColor() );
1456         }
1457         return jmenu;
1458     }
1459
1460     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1461         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1462         if ( !configuration.isUseNativeUI() ) {
1463             label.setBackground( configuration.getGuiMenuBackgroundColor() );
1464             label.setForeground( configuration.getGuiMenuTextColor() );
1465             label.setOpaque( true );
1466         }
1467         label.setSelected( false );
1468         label.setEnabled( false );
1469         return label;
1470     }
1471
1472     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1473         switch ( op.getDefaultNodeFill() ) {
1474             case GRADIENT:
1475                 op.setDefaultNodeFill( NodeFill.SOLID );
1476                 break;
1477             case NONE:
1478                 op.setDefaultNodeFill( NodeFill.GRADIENT );
1479                 break;
1480             case SOLID:
1481                 op.setDefaultNodeFill( NodeFill.NONE );
1482                 break;
1483             default:
1484                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1485         }
1486     }
1487
1488     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1489         switch ( op.getDefaultNodeShape() ) {
1490             case CIRCLE:
1491                 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1492                 break;
1493             case RECTANGLE:
1494                 op.setDefaultNodeShape( NodeShape.CIRCLE );
1495                 break;
1496             default:
1497                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1498         }
1499     }
1500
1501     static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1502         switch ( op.getOvPlacement() ) {
1503             case LOWER_LEFT:
1504                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1505                 break;
1506             case LOWER_RIGHT:
1507                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1508                 break;
1509             case UPPER_LEFT:
1510                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1511                 break;
1512             case UPPER_RIGHT:
1513                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1514                 break;
1515             default:
1516                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1517         }
1518         if ( tree_panel != null ) {
1519             tree_panel.updateOvSettings();
1520         }
1521     }
1522
1523     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1524         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1525             mi.setText( "Cycle Node Shape Fill Type... (current: "
1526                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1527         }
1528         else {
1529             mi.setText( "Cycle Node Shape Fill Type..." );
1530         }
1531     }
1532
1533     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1534         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1535             mi.setText( "Cycle Node Shape Fill Type... (current: "
1536                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1537         }
1538         else {
1539             mi.setText( "Cycle Node Shape Fill Type..." );
1540         }
1541     }
1542
1543     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1544         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1545             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1546         }
1547         else {
1548             mi.setText( "Cycle Overview Placement..." );
1549         }
1550     }
1551
1552     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1553         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1554             mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1555         }
1556         else {
1557             mi.setText( "Select Colors..." );
1558         }
1559     }
1560
1561     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1562         mi.setText( "Select Font... (current: " + font_desc + ")" );
1563     }
1564
1565     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1566         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1567             mi.setEnabled( true );
1568         }
1569         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1570             mi.setEnabled( true );
1571         }
1572         else {
1573             mi.setEnabled( false );
1574         }
1575         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1576     }
1577
1578     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1579         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1580     }
1581
1582     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1583                                                            final JCheckBoxMenuItem scale,
1584                                                            final JCheckBoxMenuItem branch_lengths,
1585                                                            final JRadioButtonMenuItem non_lined_up,
1586                                                            final JRadioButtonMenuItem uniform_clado,
1587                                                            final JRadioButtonMenuItem nonuniform_clado,
1588                                                            final JCheckBoxMenuItem label_direction_cbmi ) {
1589         final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1590         final ControlPanel control = main_panel.getControlPanel();
1591         final Options options = main_panel.getOptions();
1592         scale.setSelected( options.isShowScale() );
1593         branch_lengths.setSelected( options.isShowBranchLengthValues() );
1594         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1595         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1596             scale.setSelected( false );
1597             scale.setEnabled( false );
1598             branch_lengths.setSelected( false );
1599             branch_lengths.setEnabled( false );
1600         }
1601         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1602             scale.setSelected( false );
1603             scale.setEnabled( false );
1604             branch_lengths.setEnabled( true );
1605         }
1606         else {
1607             scale.setEnabled( true );
1608             branch_lengths.setEnabled( true );
1609         }
1610         if ( ( tree_panel != null )
1611                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1612                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1613                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1614             branch_lengths.setSelected( false );
1615             branch_lengths.setEnabled( false );
1616         }
1617         if ( tree_panel != null ) {
1618             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1619                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1620                 non_lined_up.setEnabled( false );
1621                 uniform_clado.setEnabled( false );
1622                 nonuniform_clado.setEnabled( false );
1623             }
1624             else {
1625                 non_lined_up.setEnabled( true );
1626                 uniform_clado.setEnabled( true );
1627                 nonuniform_clado.setEnabled( true );
1628             }
1629         }
1630         else {
1631             if ( ( tree_panel != null )
1632                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1633                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1634                 branch_lengths.setSelected( false );
1635                 branch_lengths.setEnabled( false );
1636             }
1637             if ( ( tree_panel != null )
1638                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1639                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1640                 non_lined_up.setEnabled( false );
1641             }
1642             else {
1643                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1644                 non_lined_up.setEnabled( true );
1645             }
1646         }
1647         label_direction_cbmi.setEnabled( true );
1648         if ( tree_panel != null ) {
1649             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1650                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1651                 label_direction_cbmi.setEnabled( false );
1652             }
1653             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1654                 scale.setSelected( false );
1655                 scale.setEnabled( false );
1656             }
1657         }
1658     }
1659
1660     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1661         for( final TreePanel tree_panel : treepanels ) {
1662             tree_panel.setTextAntialias();
1663         }
1664     }
1665 }