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