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