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