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_EXT            = "Show External Node Shapes";
 105     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Show Internal Node Shapes";
 106     static final String         SHOW_OVERVIEW_LABEL                     = "Show Overview";
 107     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";
 108     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";
 109     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Show Domain Labels";
 110     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";
 111     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";
 112     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";
 113     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";
 114     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";
 115     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";
 116     static final String         SHOW_CONF_STDDEV_LABEL                  = "Show Confidence Standard Deviations";
 117     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";
 118     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
 119     JMenuBar                    _jmenubar;
 120     JMenu                       _file_jmenu;
 121     JMenu                       _tools_menu;
 122     JMenu                       _view_jmenu;
 123     JMenu                       _options_jmenu;
 124     JMenu                       _font_size_menu;
 125     JMenu                       _help_jmenu;
 126     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;
 127     // Analysis menu
 128     JMenu                       _analysis_menu;
 129     JMenuItem                   _load_species_tree_item;
 130     JMenuItem                   _gsdi_item;
 131     JMenuItem                   _gsdir_item;
 132     JMenuItem                   _lineage_inference;
 133     JMenuItem                   _function_analysis;
 134     // file menu:
 135     JMenuItem                   _open_item;
 136     JMenuItem                   _open_url_item;
 137     JMenuItem                   _save_item;
 138     JMenuItem                   _save_all_item;
 139     JMenuItem                   _close_item;
 140     JMenuItem                   _exit_item;
 141     JMenuItem                   _new_item;
 142     // tools menu:
 143     JMenuItem                   _midpoint_root_item;
 144     JMenuItem                   _taxcolor_item;
 145     JMenuItem                   _confcolor_item;
 146     JMenuItem                   _color_rank_jmi;
 147     JMenuItem                   _collapse_species_specific_subtrees;
 148     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me
 149     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;
 150     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;
 151     JMenuItem                   _obtain_seq_information_jmi;
 152     JMenuItem                   _move_node_names_to_tax_sn_jmi;
 153     JMenuItem                   _move_node_names_to_seq_names_jmi;
 154     JMenuItem                   _extract_tax_code_from_node_names_jmi;
 155     JMenuItem                   _annotate_item;
 156     // font size menu:
 157     JMenuItem                   _super_tiny_fonts_item;
 158     JMenuItem                   _tiny_fonts_item;
 159     JMenuItem                   _small_fonts_item;
 160     JMenuItem                   _medium_fonts_item;
 161     JMenuItem                   _large_fonts_item;
 162     // options menu:
 163     // _  screen and print
 164     JMenuItem                   _choose_font_mi;
 165     JMenuItem                   _switch_colors_mi;
 166     JCheckBoxMenuItem           _label_direction_cbmi;
 167     // _  screen display
 168     JCheckBoxMenuItem           _screen_antialias_cbmi;
 169     JCheckBoxMenuItem           _background_gradient_cbmi;
 170     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 171     JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 172     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 173     JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 174     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me
 175     JCheckBoxMenuItem           _show_overview_cbmi;
 176     JCheckBoxMenuItem           _show_domain_labels;
 177     JCheckBoxMenuItem           _abbreviate_scientific_names;
 178     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 179     JMenuItem                   _overview_placment_mi;
 180     JMenuItem                   _choose_minimal_confidence_mi;
 181     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 182     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 183     JMenuItem                   _cycle_node_shape_mi;
 184     JMenuItem                   _cycle_node_fill_mi;
 185     JMenuItem                   _choose_node_size_mi;
 186     JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
 187     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 188     // _  print
 189     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;
 190     JCheckBoxMenuItem           _antialias_print_cbmi;
 191     JCheckBoxMenuItem           _print_black_and_white_cbmi;
 192     JCheckBoxMenuItem           _print_using_actual_size_cbmi;
 193     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;
 194     JMenuItem                   _print_size_mi;
 195     JMenuItem                   _choose_pdf_width_mi;
 196     // _  parsing
 197     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;
 198     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;
 199     JRadioButtonMenuItem        _extract_taxonomy_yes_rbmi;
 200     JRadioButtonMenuItem        _extract_taxonomy_pfam_rbmi;
 201     JCheckBoxMenuItem           _replace_underscores_cbmi;
 202     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;
 203     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;
 204     // _  search
 205     JCheckBoxMenuItem           _search_case_senstive_cbmi;
 206     JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 207     JCheckBoxMenuItem           _inverse_search_result_cbmi;
 208     // type menu:
 209     JMenu                       _type_menu;
 210     JCheckBoxMenuItem           _rectangular_type_cbmi;
 211     JCheckBoxMenuItem           _triangular_type_cbmi;
 212     JCheckBoxMenuItem           _curved_type_cbmi;
 213     JCheckBoxMenuItem           _convex_type_cbmi;
 214     JCheckBoxMenuItem           _euro_type_cbmi;
 215     JCheckBoxMenuItem           _rounded_type_cbmi;
 216     JCheckBoxMenuItem           _unrooted_type_cbmi;
 217     JCheckBoxMenuItem           _circular_type_cbmi;
 218     // view as text menu:
 219     JMenuItem                   _view_as_NH_item;
 220     JMenuItem                   _view_as_XML_item;
 221     JMenuItem                   _view_as_nexus_item;
 222     JMenuItem                   _display_basic_information_item;
 223     // help menu:
 224     JMenuItem                   _about_item;
 225     JMenuItem                   _help_item;
 226     JMenuItem                   _website_item;
 227     JMenuItem                   _phyloxml_website_item;
 228     JMenuItem                   _phyloxml_ref_item;
 229     JMenuItem                   _aptx_ref_item;
 230     // process menu:
 231     JMenu                       _process_menu;
 232     // Handy pointers to child components:
 233     MainPanel                   _mainpanel;
 234     Container                   _contentpane;
 235     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;
 236     Configuration               _configuration;
 237     JMenuItem                   _remove_branch_color_item;
 238     Options                     _options;
 239     Phylogeny                   _species_tree;
 240     InferenceManager            _inference_manager;
 241     final ProcessPool           _process_pool;
 242     private String              _previous_node_annotation_ref;
 243
 244     MainFrame() {
 245         _process_pool = ProcessPool.createInstance();
 246     }
 247
 248     /**
 249      * Action performed.
 250      */
 251     @Override
 252     public void actionPerformed( final ActionEvent e ) {
 253         final Object o = e.getSource();
 254         boolean is_applet = false;
 255         JApplet applet = null;
 256         if ( getCurrentTreePanel() != null ) {
 257             is_applet = getCurrentTreePanel().isApplet();
 258             if ( is_applet ) {
 259                 applet = getCurrentTreePanel().obtainApplet();
 260             }
 261         }
 262         if ( o == _open_url_item ) {
 263             readPhylogeniesFromURL();
 264         }
 265         else if ( o == _exit_item ) {
 266             close();
 267         }
 268         else if ( o == _taxcolor_item ) {
 269             taxColor();
 270         }
 271         else if ( o == _confcolor_item ) {
 272             confColor();
 273         }
 274         else if ( o == _color_rank_jmi ) {
 275             colorRank();
 276         }
 277         else if ( o == _collapse_species_specific_subtrees ) {
 278             if ( isSubtreeDisplayed() ) {
 279                 return;
 280             }
 281             if ( getCurrentTreePanel() != null ) {
 282                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 283             }
 284         }
 285         else if ( o == _remove_branch_color_item ) {
 286             if ( isSubtreeDisplayed() ) {
 287                 return;
 288             }
 289             removeBranchColors();
 290         }
 291         else if ( o == _midpoint_root_item ) {
 292             if ( isSubtreeDisplayed() ) {
 293                 return;
 294             }
 295             midpointRoot();
 296         }
 297         else if ( o == _annotate_item ) {
 298             annotateSequences();
 299         }
 300         else if ( o == _switch_colors_mi ) {
 301             switchColors();
 302         }
 303         else if ( o == _display_basic_information_item ) {
 304             displayBasicInformation();
 305         }
 306         else if ( o == _view_as_NH_item ) {
 307             viewAsNH();
 308         }
 309         else if ( o == _view_as_XML_item ) {
 310             viewAsXML();
 311         }
 312         else if ( o == _view_as_nexus_item ) {
 313             viewAsNexus();
 314         }
 315         else if ( o == _super_tiny_fonts_item ) {
 316             if ( getCurrentTreePanel() != null ) {
 317                 getCurrentTreePanel().setSuperTinyFonts();
 318                 getCurrentTreePanel().repaint();
 319             }
 320         }
 321         else if ( o == _tiny_fonts_item ) {
 322             if ( getCurrentTreePanel() != null ) {
 323                 getCurrentTreePanel().setTinyFonts();
 324                 getCurrentTreePanel().repaint();
 325             }
 326         }
 327         else if ( o == _small_fonts_item ) {
 328             if ( getCurrentTreePanel() != null ) {
 329                 getCurrentTreePanel().setSmallFonts();
 330                 getCurrentTreePanel().repaint();
 331             }
 332         }
 333         else if ( o == _medium_fonts_item ) {
 334             if ( getCurrentTreePanel() != null ) {
 335                 getCurrentTreePanel().setMediumFonts();
 336                 getCurrentTreePanel().repaint();
 337             }
 338         }
 339         else if ( o == _large_fonts_item ) {
 340             if ( getCurrentTreePanel() != null ) {
 341                 getCurrentTreePanel().setLargeFonts();
 342                 getCurrentTreePanel().repaint();
 343             }
 344         }
 345         else if ( o == _choose_font_mi ) {
 346             chooseFont();
 347         }
 348         else if ( o == _choose_minimal_confidence_mi ) {
 349             chooseMinimalConfidence();
 350         }
 351         else if ( o == _choose_node_size_mi ) {
 352             chooseNodeSize( getOptions(), this );
 353         }
 354         else if ( o == _overview_placment_mi ) {
 355             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 356         }
 357         else if ( o == _cycle_node_fill_mi ) {
 358             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 359         }
 360         else if ( o == _cycle_node_shape_mi ) {
 361             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 362         }
 363         else if ( o == _screen_antialias_cbmi ) {
 364             updateOptions( getOptions() );
 365             updateScreenTextAntialias( getMainPanel().getTreePanels() );
 366         }
 367         else if ( o == _background_gradient_cbmi ) {
 368             updateOptions( getOptions() );
 369         }
 370         else if ( o == _show_domain_labels ) {
 371             updateOptions( getOptions() );
 372         }
 373         else if ( o == _abbreviate_scientific_names ) {
 374             updateOptions( getOptions() );
 375         }
 376         else if ( o == _color_labels_same_as_parent_branch ) {
 377             updateOptions( getOptions() );
 378         }
 379         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 380             updateOptions( getOptions() );
 381         }
 382         else if ( o == _show_default_node_shapes_external_cbmi ) {
 383             updateOptions( getOptions() );
 384         }
 385         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 386             updateOptions( getOptions() );
 387         }
 388         else if ( o == _non_lined_up_cladograms_rbmi ) {
 389             updateOptions( getOptions() );
 390             showWhole();
 391         }
 392         else if ( o == _uniform_cladograms_rbmi ) {
 393             updateOptions( getOptions() );
 394             showWhole();
 395         }
 396         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 397             updateOptions( getOptions() );
 398             showWhole();
 399         }
 400         else if ( o == _search_case_senstive_cbmi ) {
 401             updateOptions( getOptions() );
 402             getMainPanel().getControlPanel().search();
 403         }
 404         else if ( o == _search_whole_words_only_cbmi ) {
 405             updateOptions( getOptions() );
 406             getMainPanel().getControlPanel().search();
 407         }
 408         else if ( o == _inverse_search_result_cbmi ) {
 409             updateOptions( getOptions() );
 410             getMainPanel().getControlPanel().search();
 411         }
 412         else if ( o == _show_scale_cbmi ) {
 413             updateOptions( getOptions() );
 414         }
 415         else if ( o == _show_branch_length_values_cbmi ) {
 416             updateOptions( getOptions() );
 417         }
 418         else if ( o == _show_confidence_stddev_cbmi ) {
 419             updateOptions( getOptions() );
 420         }
 421         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
 422             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
 423                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
 424             }
 425             updateOptions( getOptions() );
 426         }
 427         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
 428             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
 429                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
 430             }
 431             updateOptions( getOptions() );
 432         }
 433         else if ( o == _label_direction_cbmi ) {
 434             updateOptions( getOptions() );
 435         }
 436         else if ( o == _show_overview_cbmi ) {
 437             updateOptions( getOptions() );
 438             if ( getCurrentTreePanel() != null ) {
 439                 getCurrentTreePanel().updateOvSizes();
 440             }
 441         }
 442         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 443                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
 444                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 445             typeChanged( o );
 446         }
 447         else if ( o == _about_item ) {
 448             about();
 449         }
 450         else if ( o == _help_item ) {
 451             help( getConfiguration().getWebLinks() );
 452         }
 453         else if ( o == _website_item ) {
 454             try {
 455                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
 456             }
 457             catch ( final IOException e1 ) {
 458                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 459             }
 460         }
 461         else if ( o == _phyloxml_website_item ) {
 462             try {
 463                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
 464             }
 465             catch ( final IOException e1 ) {
 466                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 467             }
 468         }
 469         else if ( o == _aptx_ref_item ) {
 470             try {
 471                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
 472             }
 473             catch ( final IOException e1 ) {
 474                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 475             }
 476         }
 477         else if ( o == _phyloxml_ref_item ) {
 478             try {
 479                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
 480             }
 481             catch ( final IOException e1 ) {
 482                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 483             }
 484         }
 485         else {
 486             if ( _load_phylogeny_from_webservice_menu_items != null ) {
 487                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
 488                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
 489                         readPhylogeniesFromWebservice( i );
 490                     }
 491                 }
 492             }
 493         }
 494         _contentpane.repaint();
 495     }
 496
 497     public Configuration getConfiguration() {
 498         return _configuration;
 499     }
 500
 501     /**
 502      * This method returns the current external node data which
 503      * has been selected by the user by clicking the "Return ..."
 504      * menu item. This method is expected to be called from Javascript or
 505      * something like it.
 506      *
 507      * @return current external node data as String
 508      */
 509     public String getCurrentExternalNodesDataBuffer() {
 510         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 511     }
 512
 513     public int getCurrentExternalNodesDataBufferChangeCounter() {
 514         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 515     }
 516
 517     public int getCurrentExternalNodesDataBufferLength() {
 518         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 519     }
 520
 521     public InferenceManager getInferenceManager() {
 522         return _inference_manager;
 523     }
 524
 525     public MainPanel getMainPanel() {
 526         return _mainpanel;
 527     }
 528
 529     public Options getOptions() {
 530         return _options;
 531     }
 532
 533     public ProcessPool getProcessPool() {
 534         return _process_pool;
 535     }
 536
 537     public void showTextFrame( final String s, final String title ) {
 538         checkTextFrames();
 539         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 540     }
 541
 542     public void showWhole() {
 543         _mainpanel.getControlPanel().showWhole();
 544     }
 545
 546     public void updateProcessMenu() {
 547         // In general Swing is not thread safe.
 548         // See "Swing's Threading Policy".
 549         SwingUtilities.invokeLater( new Runnable() {
 550
 551             @Override
 552             public void run() {
 553                 doUpdateProcessMenu();
 554             }
 555         } );
 556     }
 557
 558     void activateSaveAllIfNeeded() {
 559         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
 560             _save_all_item.setEnabled( true );
 561         }
 562         else {
 563             _save_all_item.setEnabled( false );
 564         }
 565     }
 566
 567     void buildFileMenu() {
 568         _file_jmenu = createMenu( "File", getConfiguration() );
 569         _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
 570         _file_jmenu.addSeparator();
 571         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 572         customizeJMenuItem( _open_url_item );
 573         customizeJMenuItem( _exit_item );
 574         _jmenubar.add( _file_jmenu );
 575     }
 576
 577     void buildFontSizeMenu() {
 578         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
 579         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
 580         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
 581         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
 582         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
 583         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
 584         customizeJMenuItem( _super_tiny_fonts_item );
 585         customizeJMenuItem( _tiny_fonts_item );
 586         customizeJMenuItem( _small_fonts_item );
 587         customizeJMenuItem( _medium_fonts_item );
 588         customizeJMenuItem( _large_fonts_item );
 589         _jmenubar.add( _font_size_menu );
 590     }
 591
 592     void buildHelpMenu() {
 593         _help_jmenu = createMenu( "Help", getConfiguration() );
 594         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 595         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 596         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 597         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 598         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 599         _help_jmenu.addSeparator();
 600         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 601         customizeJMenuItem( _help_item );
 602         customizeJMenuItem( _website_item );
 603         customizeJMenuItem( _phyloxml_website_item );
 604         customizeJMenuItem( _aptx_ref_item );
 605         customizeJMenuItem( _phyloxml_ref_item );
 606         customizeJMenuItem( _about_item );
 607         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
 608         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
 609         _jmenubar.add( _help_jmenu );
 610     }
 611
 612     void buildTypeMenu() {
 613         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
 614         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 615         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 616         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 617         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 618         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 619         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 620         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 621         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 622         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 623         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 624         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 625         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 626         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 627         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 628         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 629         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 630         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 631         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 632         initializeTypeMenu( getOptions() );
 633         _jmenubar.add( _type_menu );
 634     }
 635
 636     void buildViewMenu() {
 637         _view_jmenu = createMenu( "View", getConfiguration() );
 638         _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
 639         _view_jmenu.addSeparator();
 640         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 641         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 642         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 643         customizeJMenuItem( _display_basic_information_item );
 644         customizeJMenuItem( _view_as_NH_item );
 645         customizeJMenuItem( _view_as_XML_item );
 646         customizeJMenuItem( _view_as_nexus_item );
 647         _jmenubar.add( _view_jmenu );
 648     }
 649
 650     void checkTextFrames() {
 651         if ( _textframes.size() > 5 ) {
 652             try {
 653                 if ( _textframes.getFirst() != null ) {
 654                     _textframes.getFirst().removeMe();
 655                 }
 656                 else {
 657                     _textframes.removeFirst();
 658                 }
 659             }
 660             catch ( final NoSuchElementException e ) {
 661                 // Ignore.
 662             }
 663         }
 664     }
 665
 666     void close() {
 667         removeAllTextFrames();
 668         if ( _mainpanel != null ) {
 669             _mainpanel.terminate();
 670         }
 671         if ( _contentpane != null ) {
 672             _contentpane.removeAll();
 673         }
 674         setVisible( false );
 675         dispose();
 676     }
 677
 678     void colorRank() {
 679         if ( _mainpanel.getCurrentTreePanel() != null ) {
 680             final String[] ranks = AptxUtil.getAllPossibleRanks();
 681             final String rank = ( String ) JOptionPane
 682                     .showInputDialog( this,
 683                                       "What rank should the colorization be based on",
 684                                       "Rank Selection",
 685                                       JOptionPane.QUESTION_MESSAGE,
 686                                       null,
 687                                       ranks,
 688                                       null );
 689             if ( !ForesterUtil.isEmpty( rank ) ) {
 690                 _mainpanel.getCurrentTreePanel().colorRank( rank );
 691             }
 692         }
 693     }
 694
 695     void confColor() {
 696         if ( _mainpanel.getCurrentTreePanel() != null ) {
 697             _mainpanel.getCurrentTreePanel().confColor();
 698         }
 699     }
 700
 701     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 702         if ( item != null ) {
 703             item.setFont( MainFrame.menu_font );
 704             if ( !getConfiguration().isUseNativeUI() ) {
 705                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 706                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 707             }
 708             item.setSelected( is_selected );
 709             item.addActionListener( this );
 710         }
 711     }
 712
 713     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
 714         if ( jmi != null ) {
 715             jmi.setFont( MainFrame.menu_font );
 716             if ( !getConfiguration().isUseNativeUI() ) {
 717                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 718                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 719             }
 720             jmi.addActionListener( this );
 721         }
 722         return jmi;
 723     }
 724
 725     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 726         if ( item != null ) {
 727             item.setFont( MainFrame.menu_font );
 728             if ( !getConfiguration().isUseNativeUI() ) {
 729                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 730                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 731             }
 732             item.setSelected( is_selected );
 733             item.addActionListener( this );
 734         }
 735     }
 736
 737     void displayBasicInformation() {
 738         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
 739             String title = "Basic Information";
 740             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
 741                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
 742             }
 743             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
 744         }
 745     }
 746
 747     void exceptionOccuredDuringOpenFile( final Exception e ) {
 748         try {
 749             _mainpanel.getCurrentTreePanel().setArrowCursor();
 750         }
 751         catch ( final Exception ex ) {
 752             // Do nothing.
 753         }
 754         JOptionPane.showMessageDialog( this,
 755                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
 756                                        "Error during File|Open",
 757                                        JOptionPane.ERROR_MESSAGE );
 758     }
 759
 760     void exceptionOccuredDuringSaveAs( final Exception e ) {
 761         try {
 762             _mainpanel.getCurrentTreePanel().setArrowCursor();
 763         }
 764         catch ( final Exception ex ) {
 765             // Do nothing.
 766         }
 767         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
 768     }
 769
 770     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
 771         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
 772             JOptionPane.showMessageDialog( this,
 773                                            "Gene tree and species tree have no species in common.",
 774                                            "Error during SDI",
 775                                            JOptionPane.ERROR_MESSAGE );
 776             return false;
 777         }
 778         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
 779             JOptionPane.showMessageDialog( this,
 780                                            "Gene tree and species tree have only one species in common.",
 781                                            "Error during SDI",
 782                                            JOptionPane.ERROR_MESSAGE );
 783             return false;
 784         }
 785         else {
 786             return true;
 787         }
 788     }
 789
 790     TreePanel getCurrentTreePanel() {
 791         return getMainPanel().getCurrentTreePanel();
 792     }
 793
 794     JMenu getHelpMenu() {
 795         return _help_jmenu;
 796     }
 797
 798     JCheckBoxMenuItem getlabelDirectionCbmi() {
 799         return _label_direction_cbmi;
 800     }
 801
 802     JMenuBar getMenuBarOfMainFrame() {
 803         return _jmenubar;
 804     }
 805
 806     void help( final Map<String, WebLink> weblinks ) {
 807         final StringBuilder sb = new StringBuilder();
 808         sb.append( "Display options\n" );
 809         sb.append( "-------------------\n" );
 810         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 811         sb.append( "Clickable tree nodes\n" );
 812         sb.append( "--------------------\n" );
 813         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 814         sb.append( "or by right clicking:\n" );
 815         sb.append( "o  Display Node Data -- display information for a node\n" );
 816         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 817         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 818         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 819         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 820         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 821         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 822         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
 823         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
 824         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
 825         sb.append( "Zooming\n" );
 826         sb.append( "---------\n" );
 827         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
 828         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
 829         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
 830         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
 831         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
 832         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
 833         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
 834         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
 835         sb.append( "Quick tree manipulation:\n" );
 836         sb.append( "------------------------\n" );
 837         sb.append( "Order Subtrees -- order the tree by branch length\n" );
 838         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
 839         sb.append( "Memory problems (Java heap space error)\n" );
 840         sb.append( "---------------------------------------\n" );
 841         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
 842         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
 843         sb.append( "the '-Xmx' Java command line option. For example:\n" );
 844         sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
 845         if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
 846             sb.append( "Active web links\n" );
 847             sb.append( "--------------------\n" );
 848             for( final String key : weblinks.keySet() ) {
 849                 sb.append( " " + weblinks.get( key ).toString() + "\n" );
 850             }
 851         }
 852         // + "General remarks\n"
 853         // + "---------------\n"
 854         // +
 855         // "o  The application version permits copying to the clipboard \n"
 856         // +
 857         // "    in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
 858         // +
 859         // "o  Changes made to a subtree affect this subtree and its subtrees,\n"
 860         // + "    but not any of its parent tree(s).\n"
 861         // +
 862         // "o  Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
 863         // +
 864         // "    are likely to be bootstrap values instead of branch length values.\n\n"
 865         // +
 866         // " Remarks regarding SDI (Speciation Duplication Inference):\n"
 867         // +
 868         // "o  Each external node of the gene tree (in display) needs to be associated with\n"
 869         // +
 870         // "    a species: either directly through the \"Species\" field, or the species\n"
 871         // +
 872         // "    is part of the sequence name in the form \"XXXX_SPECIES\"\n"
 873         // +
 874         // "    (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
 875         // +
 876         // "o  A species tree for each species of the gene tree needs to be loaded with\n"
 877         // +
 878         // "   \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
 879         // +
 880         // "o  !External nodes of the gene tree associated with species not present in\n"
 881         // +
 882         // "    the species tree are REMOVED prior to SDI execution!\n"
 883         // +
 884         // "o  Both the gene tree and the species tree must be completely binary.\n"
 885         // +
 886         // "o  Duplications and speciations are a function of the position of the root.\n"
 887         // +
 888         // "    Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
 889         // + "    incorrect and need to be inferred again\n"
 890         // +
 891         // "    with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
 892         sb.append( "\n" );
 893         sb.append( "phyloXML\n" );
 894         sb.append( "-------------------\n" );
 895         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
 896         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
 897         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
 898         sb.append( "\n" );
 899         sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
 900         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
 901         TextFrame.instantiate( sb.toString(), "Help", _textframes );
 902     }
 903
 904     void initializeTypeMenu( final Options options ) {
 905         setTypeMenuToAllUnselected();
 906         switch ( options.getPhylogenyGraphicsType() ) {
 907             case CONVEX:
 908                 _convex_type_cbmi.setSelected( true );
 909                 break;
 910             case CURVED:
 911                 _curved_type_cbmi.setSelected( true );
 912                 break;
 913             case EURO_STYLE:
 914                 _euro_type_cbmi.setSelected( true );
 915                 break;
 916             case ROUNDED:
 917                 _rounded_type_cbmi.setSelected( true );
 918                 break;
 919             case TRIANGULAR:
 920                 _triangular_type_cbmi.setSelected( true );
 921                 break;
 922             case UNROOTED:
 923                 _unrooted_type_cbmi.setSelected( true );
 924                 break;
 925             case CIRCULAR:
 926                 _circular_type_cbmi.setSelected( true );
 927                 break;
 928             default:
 929                 _rectangular_type_cbmi.setSelected( true );
 930                 break;
 931         }
 932     }
 933
 934     boolean isSubtreeDisplayed() {
 935         if ( getCurrentTreePanel() != null ) {
 936             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
 937                 JOptionPane
 938                         .showMessageDialog( this,
 939                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
 940                                             "Operation can not be exectuted on a sub-tree",
 941                                             JOptionPane.WARNING_MESSAGE );
 942                 return true;
 943             }
 944         }
 945         return false;
 946     }
 947
 948     void midpointRoot() {
 949         if ( _mainpanel.getCurrentTreePanel() != null ) {
 950             _mainpanel.getCurrentTreePanel().midpointRoot();
 951         }
 952     }
 953
 954     abstract void readPhylogeniesFromURL();
 955
 956     void readPhylogeniesFromWebservice( final int i ) {
 957         final UrlTreeReader reader = new UrlTreeReader( this, i );
 958         new Thread( reader ).start();
 959     }
 960
 961     void removeAllTextFrames() {
 962         for( final TextFrame tf : _textframes ) {
 963             if ( tf != null ) {
 964                 tf.close();
 965             }
 966         }
 967         _textframes.clear();
 968     }
 969
 970     void setConfiguration( final Configuration configuration ) {
 971         _configuration = configuration;
 972     }
 973
 974     void setInferenceManager( final InferenceManager i ) {
 975         _inference_manager = i;
 976     }
 977
 978     void setOptions( final Options options ) {
 979         _options = options;
 980     }
 981
 982     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
 983         setTypeMenuToAllUnselected();
 984         switch ( type ) {
 985             case CIRCULAR:
 986                 _circular_type_cbmi.setSelected( true );
 987                 break;
 988             case CONVEX:
 989                 _convex_type_cbmi.setSelected( true );
 990                 break;
 991             case CURVED:
 992                 _curved_type_cbmi.setSelected( true );
 993                 break;
 994             case EURO_STYLE:
 995                 _euro_type_cbmi.setSelected( true );
 996                 break;
 997             case ROUNDED:
 998                 _rounded_type_cbmi.setSelected( true );
 999                 break;
1000             case RECTANGULAR:
1001                 _rectangular_type_cbmi.setSelected( true );
1002                 break;
1003             case TRIANGULAR:
1004                 _triangular_type_cbmi.setSelected( true );
1005                 break;
1006             case UNROOTED:
1007                 _unrooted_type_cbmi.setSelected( true );
1008                 break;
1009             default:
1010                 throw new IllegalArgumentException( "unknown type: " + type );
1011         }
1012     }
1013
1014     void setTypeMenuToAllUnselected() {
1015         _convex_type_cbmi.setSelected( false );
1016         _curved_type_cbmi.setSelected( false );
1017         _euro_type_cbmi.setSelected( false );
1018         _rounded_type_cbmi.setSelected( false );
1019         _triangular_type_cbmi.setSelected( false );
1020         _rectangular_type_cbmi.setSelected( false );
1021         _unrooted_type_cbmi.setSelected( false );
1022         _circular_type_cbmi.setSelected( false );
1023     }
1024
1025     void switchColors() {
1026         final TreeColorSet colorset = _mainpanel.getTreeColorSet();
1027         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1028         csc.setVisible( true );
1029     }
1030
1031     void taxColor() {
1032         if ( _mainpanel.getCurrentTreePanel() != null ) {
1033             _mainpanel.getCurrentTreePanel().taxColor();
1034         }
1035     }
1036
1037     void typeChanged( final Object o ) {
1038         updateTypeCheckboxes( getOptions(), o );
1039         updateOptions( getOptions() );
1040         if ( getCurrentTreePanel() != null ) {
1041             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1042             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1043             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1044                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1045                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1046                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1047                 getCurrentTreePanel().getControlPanel().showWhole();
1048             }
1049             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1050                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1051             }
1052             else {
1053                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1054             }
1055             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1056             updateScreenTextAntialias( getMainPanel().getTreePanels() );
1057             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
1058                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1059                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
1060                 }
1061                 else {
1062                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
1063                 }
1064             }
1065         }
1066     }
1067
1068     void updateOptions( final Options options ) {
1069         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1070         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1071                 && _background_gradient_cbmi.isSelected() );
1072         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1073         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1074                 && _abbreviate_scientific_names.isSelected() );
1075         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1076                 && _color_labels_same_as_parent_branch.isSelected() );
1077         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1078                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1079         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1080                 && _show_default_node_shapes_external_cbmi.isSelected() );
1081         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1082                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1083         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1084             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1085         }
1086         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1087             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1088         }
1089         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1090             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1091         }
1092         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1093                 && _search_case_senstive_cbmi.isSelected() );
1094         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1095             options.setShowScale( _show_scale_cbmi.isSelected() );
1096         }
1097         if ( _label_direction_cbmi != null ) {
1098             if ( _label_direction_cbmi.isSelected() ) {
1099                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1100             }
1101             else {
1102                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1103             }
1104         }
1105         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1106         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1107                 && _show_confidence_stddev_cbmi.isSelected() );
1108         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1109             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1110         }
1111         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1112                 && ( _print_using_actual_size_cbmi.isSelected() ) );
1113         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1114                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1115         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1116         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1117                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1118             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1119         }
1120         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1121                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1122             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1123         }
1124         else {
1125             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1126         }
1127         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1128                 && _print_black_and_white_cbmi.isSelected() );
1129         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1130                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1131         if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
1132             options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.AGRESSIVE );
1133         }
1134         else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
1135             options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1136         }
1137         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
1138             options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );
1139         }
1140         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1141                 && _replace_underscores_cbmi.isSelected() );
1142         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1143                 && _search_whole_words_only_cbmi.isSelected() );
1144         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1145                 && _inverse_search_result_cbmi.isSelected() );
1146         if ( _graphics_export_visible_only_cbmi != null ) {
1147             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1148             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1149                 _graphics_export_using_actual_size_cbmi.setSelected( true );
1150                 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1151             }
1152             else {
1153                 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1154             }
1155         }
1156         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1157             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1158         }
1159         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1160             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1161         }
1162         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1163             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1164         }
1165         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1166             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1167         }
1168         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1169             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1170         }
1171         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1172             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1173         }
1174         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1175             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1176         }
1177         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1178             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1179         }
1180     }
1181
1182     void updateTypeCheckboxes( final Options options, final Object o ) {
1183         setTypeMenuToAllUnselected();
1184         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1185     }
1186
1187     void viewAsNexus() {
1188         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1189             String title = "Nexus";
1190             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1191                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1192             }
1193             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
1194                            title );
1195         }
1196     }
1197
1198     void viewAsNH() {
1199         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1200             String title = "New Hampshire";
1201             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1202                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1203             }
1204             showTextFrame( _mainpanel.getCurrentPhylogeny()
1205                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1206                            title );
1207         }
1208     }
1209
1210     void viewAsXML() {
1211         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1212             String title = "phyloXML";
1213             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1214                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1215             }
1216             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
1217         }
1218     }
1219
1220     private void annotateSequences() {
1221         if ( getCurrentTreePanel() != null ) {
1222             final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
1223             if ( ( nodes == null ) || nodes.isEmpty() ) {
1224                 JOptionPane
1225                         .showMessageDialog( this,
1226                                             "Need to select nodes, either via direct selection or via the \"Search\" function",
1227                                             "No nodes selected for annotation",
1228                                             JOptionPane.ERROR_MESSAGE );
1229                 return;
1230             }
1231             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
1232             if ( ( phy != null ) && !phy.isEmpty() ) {
1233                 final JTextField ref_field = new JTextField( 10 );
1234                 final JTextField desc_filed = new JTextField( 20 );
1235                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
1236                         : getPreviousNodeAnnotationReference() );
1237                 final JPanel my_panel = new JPanel();
1238                 my_panel.add( new JLabel( "Reference " ) );
1239                 my_panel.add( ref_field );
1240                 my_panel.add( Box.createHorizontalStrut( 15 ) );
1241                 my_panel.add( new JLabel( "Description " ) );
1242                 my_panel.add( desc_filed );
1243                 final int result = JOptionPane.showConfirmDialog( null,
1244                                                                   my_panel,
1245                                                                   "Enter the sequence annotation(s) for the "
1246                                                                           + nodes.size() + " selected nodes",
1247                                                                   JOptionPane.OK_CANCEL_OPTION );
1248                 if ( result == JOptionPane.OK_OPTION ) {
1249                     String ref = ref_field.getText();
1250                     String desc = desc_filed.getText();
1251                     if ( !ForesterUtil.isEmpty( ref ) ) {
1252                         ref = ref.trim();
1253                         ref = ref.replaceAll( "\\s+", " " );
1254                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 )
1255                                 || ( ref.length() < 3 ) ) {
1256                             JOptionPane.showMessageDialog( this,
1257                                                            "Reference needs to be in the form of \"GO:1234567\"",
1258                                                            "Illegal Format for Annotation Reference",
1259                                                            JOptionPane.ERROR_MESSAGE );
1260                             return;
1261                         }
1262                     }
1263                     if ( ref != null ) {
1264                         setPreviousNodeAnnotationReference( ref );
1265                     }
1266                     if ( desc != null ) {
1267                         desc = desc.trim();
1268                         desc = desc.replaceAll( "\\s+", " " );
1269                     }
1270                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
1271                         for( final Long id : nodes ) {
1272                             final PhylogenyNode n = phy.getNode( id );
1273                             ForesterUtil.ensurePresenceOfSequence( n );
1274                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
1275                                     : new Annotation( ref );
1276                             if ( !ForesterUtil.isEmpty( desc ) ) {
1277                                 ann.setDesc( desc );
1278                             }
1279                             n.getNodeData().getSequence().addAnnotation( ann );
1280                         }
1281                     }
1282                     getMainPanel().getControlPanel().showAnnotations();
1283                 }
1284             }
1285         }
1286     }
1287
1288     private void chooseFont() {
1289         final FontChooser fc = new FontChooser();
1290         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1291         fc.showDialog( this, "Select the Base Font" );
1292         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1293     }
1294
1295     private void chooseMinimalConfidence() {
1296         final String s = ( String ) JOptionPane
1297                 .showInputDialog( this,
1298                                   "Please enter the minimum for confidence values to be displayed.\n"
1299                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
1300                                   "Minimal Confidence Value",
1301                                   JOptionPane.QUESTION_MESSAGE,
1302                                   null,
1303                                   null,
1304                                   getOptions().getMinConfidenceValue() );
1305         if ( !ForesterUtil.isEmpty( s ) ) {
1306             boolean success = true;
1307             double m = 0.0;
1308             final String m_str = s.trim();
1309             if ( !ForesterUtil.isEmpty( m_str ) ) {
1310                 try {
1311                     m = Double.parseDouble( m_str );
1312                 }
1313                 catch ( final Exception ex ) {
1314                     success = false;
1315                 }
1316             }
1317             else {
1318                 success = false;
1319             }
1320             if ( success && ( m >= 0.0 ) ) {
1321                 getOptions().setMinConfidenceValue( m );
1322             }
1323         }
1324     }
1325
1326     private void doUpdateProcessMenu() {
1327         if ( _process_pool.size() > 0 ) {
1328             if ( _process_menu == null ) {
1329                 _process_menu = createMenu( "", getConfiguration() );
1330                 _process_menu.setForeground( Color.RED );
1331             }
1332             _process_menu.removeAll();
1333             final String text = "processes running: " + _process_pool.size();
1334             _process_menu.setText( text );
1335             _jmenubar.add( _process_menu );
1336             for( int i = 0; i < _process_pool.size(); ++i ) {
1337                 final ProcessRunning p = _process_pool.getProcessByIndex( i );
1338                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
1339             }
1340         }
1341         else {
1342             if ( _process_menu != null ) {
1343                 _process_menu.removeAll();
1344                 _jmenubar.remove( _process_menu );
1345             }
1346         }
1347         _jmenubar.validate();
1348         _jmenubar.repaint();
1349         repaint();
1350     }
1351
1352     private String getPreviousNodeAnnotationReference() {
1353         return _previous_node_annotation_ref;
1354     }
1355
1356     private void removeBranchColors() {
1357         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1358             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1359         }
1360     }
1361
1362     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
1363         _previous_node_annotation_ref = previous_node_annotation_ref;
1364     }
1365
1366     /**
1367      * Display the about box.
1368      */
1369     static void about() {
1370         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1371         about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
1372         about.append( "All Rights Reserved\n" );
1373         about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1374         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1375         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
1376         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1377         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1378         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1379             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1380         }
1381         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1382                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1383             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1384                     + ForesterUtil.OS_VERSION + "]\n" );
1385         }
1386         final Runtime rt = java.lang.Runtime.getRuntime();
1387         final long free_memory = rt.freeMemory() / 1000000;
1388         final long total_memory = rt.totalMemory() / 1000000;
1389         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1390         about.append( "[locale: " + Locale.getDefault() + "]\n" );
1391         about.append( "References:\n" );
1392         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1393         about.append( "For more information & download:\n" );
1394         about.append( Constants.APTX_WEB_SITE + "\n" );
1395         about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1396         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1397     }
1398
1399     static void chooseNodeSize( final Options options, final Component parent ) {
1400         final String s = ( String ) JOptionPane.showInputDialog( parent,
1401                                                                  "Please enter the default size for node shapes.\n"
1402                                                                          + "[current value: "
1403                                                                          + options.getDefaultNodeShapeSize() + "]\n",
1404                                                                  "Node Shape Size",
1405                                                                  JOptionPane.QUESTION_MESSAGE,
1406                                                                  null,
1407                                                                  null,
1408                                                                  options.getDefaultNodeShapeSize() );
1409         if ( !ForesterUtil.isEmpty( s ) ) {
1410             boolean success = true;
1411             double m = 0.0;
1412             final String m_str = s.trim();
1413             if ( !ForesterUtil.isEmpty( m_str ) ) {
1414                 try {
1415                     m = Double.parseDouble( m_str );
1416                 }
1417                 catch ( final Exception ex ) {
1418                     success = false;
1419                 }
1420             }
1421             else {
1422                 success = false;
1423             }
1424             if ( success && ( m >= 0.0 ) ) {
1425                 final short size = ForesterUtil.roundToShort( m );
1426                 if ( size >= 0.0 ) {
1427                     options.setDefaultNodeShapeSize( size );
1428                 }
1429             }
1430         }
1431     }
1432
1433     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1434         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1435     }
1436
1437     static JMenu createMenu( final String title, final Configuration conf ) {
1438         final JMenu jmenu = new JMenu( title );
1439         if ( !conf.isUseNativeUI() ) {
1440             jmenu.setFont( MainFrame.menu_font );
1441             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1442             jmenu.setForeground( conf.getGuiMenuTextColor() );
1443         }
1444         return jmenu;
1445     }
1446
1447     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1448         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1449         if ( !configuration.isUseNativeUI() ) {
1450             label.setBackground( configuration.getGuiMenuBackgroundColor() );
1451             label.setForeground( configuration.getGuiMenuTextColor() );
1452             label.setOpaque( true );
1453         }
1454         label.setSelected( false );
1455         label.setEnabled( false );
1456         return label;
1457     }
1458
1459     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1460         switch ( op.getDefaultNodeFill() ) {
1461             case GRADIENT:
1462                 op.setDefaultNodeFill( NodeFill.SOLID );
1463                 break;
1464             case NONE:
1465                 op.setDefaultNodeFill( NodeFill.GRADIENT );
1466                 break;
1467             case SOLID:
1468                 op.setDefaultNodeFill( NodeFill.NONE );
1469                 break;
1470             default:
1471                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1472         }
1473     }
1474
1475     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1476         switch ( op.getDefaultNodeShape() ) {
1477             case CIRCLE:
1478                 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1479                 break;
1480             case RECTANGLE:
1481                 op.setDefaultNodeShape( NodeShape.CIRCLE );
1482                 break;
1483             default:
1484                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1485         }
1486     }
1487
1488     static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1489         switch ( op.getOvPlacement() ) {
1490             case LOWER_LEFT:
1491                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1492                 break;
1493             case LOWER_RIGHT:
1494                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1495                 break;
1496             case UPPER_LEFT:
1497                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1498                 break;
1499             case UPPER_RIGHT:
1500                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1501                 break;
1502             default:
1503                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1504         }
1505         if ( tree_panel != null ) {
1506             tree_panel.updateOvSettings();
1507         }
1508     }
1509
1510     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1511         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1512             mi.setText( "Cycle Node Shape Fill Type... (current: "
1513                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1514         }
1515         else {
1516             mi.setText( "Cycle Node Shape Fill Type..." );
1517         }
1518     }
1519
1520     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1521         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1522             mi.setText( "Cycle Node Shape Fill Type... (current: "
1523                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1524         }
1525         else {
1526             mi.setText( "Cycle Node Shape Fill Type..." );
1527         }
1528     }
1529
1530     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1531         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1532             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1533         }
1534         else {
1535             mi.setText( "Cycle Overview Placement..." );
1536         }
1537     }
1538
1539     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1540         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1541             mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1542         }
1543         else {
1544             mi.setText( "Select Colors..." );
1545         }
1546     }
1547
1548     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1549         mi.setText( "Select Font... (current: " + font_desc + ")" );
1550     }
1551
1552     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1553         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1554             mi.setEnabled( true );
1555         }
1556         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1557             mi.setEnabled( true );
1558         }
1559         else {
1560             mi.setEnabled( false );
1561         }
1562         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1563     }
1564
1565     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1566         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1567     }
1568
1569     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1570                                                            final JCheckBoxMenuItem scale,
1571                                                            final JCheckBoxMenuItem branch_lengths,
1572                                                            final JRadioButtonMenuItem non_lined_up,
1573                                                            final JRadioButtonMenuItem uniform_clado,
1574                                                            final JRadioButtonMenuItem nonuniform_clado,
1575                                                            final JCheckBoxMenuItem label_direction_cbmi ) {
1576         final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1577         final ControlPanel control = main_panel.getControlPanel();
1578         final Options options = main_panel.getOptions();
1579         scale.setSelected( options.isShowScale() );
1580         branch_lengths.setSelected( options.isShowBranchLengthValues() );
1581         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1582         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1583             scale.setSelected( false );
1584             scale.setEnabled( false );
1585             branch_lengths.setSelected( false );
1586             branch_lengths.setEnabled( false );
1587         }
1588         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1589             scale.setSelected( false );
1590             scale.setEnabled( false );
1591             branch_lengths.setEnabled( true );
1592         }
1593         else {
1594             scale.setEnabled( true );
1595             branch_lengths.setEnabled( true );
1596         }
1597         if ( ( tree_panel != null )
1598                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1599                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1600                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1601             branch_lengths.setSelected( false );
1602             branch_lengths.setEnabled( false );
1603         }
1604         if ( tree_panel != null ) {
1605             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1606                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1607                 non_lined_up.setEnabled( false );
1608                 uniform_clado.setEnabled( false );
1609                 nonuniform_clado.setEnabled( false );
1610             }
1611             else {
1612                 non_lined_up.setEnabled( true );
1613                 uniform_clado.setEnabled( true );
1614                 nonuniform_clado.setEnabled( true );
1615             }
1616         }
1617         else {
1618             if ( ( tree_panel != null )
1619                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1620                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1621                 branch_lengths.setSelected( false );
1622                 branch_lengths.setEnabled( false );
1623             }
1624             if ( ( tree_panel != null )
1625                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1626                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1627                 non_lined_up.setEnabled( false );
1628             }
1629             else {
1630                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1631                 non_lined_up.setEnabled( true );
1632             }
1633         }
1634         label_direction_cbmi.setEnabled( true );
1635         if ( tree_panel != null ) {
1636             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1637                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1638                 label_direction_cbmi.setEnabled( false );
1639             }
1640             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1641                 scale.setSelected( false );
1642                 scale.setEnabled( false );
1643             }
1644         }
1645     }
1646
1647     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1648         for( final TreePanel tree_panel : treepanels ) {
1649             tree_panel.setTextAntialias();
1650         }
1651     }
1652 }