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