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.NoSuchElementException;
  38 import java.util.Set;
  39
  40 import javax.swing.Box;
  41 import javax.swing.JApplet;
  42 import javax.swing.JCheckBoxMenuItem;
  43 import javax.swing.JFrame;
  44 import javax.swing.JLabel;
  45 import javax.swing.JMenu;
  46 import javax.swing.JMenuBar;
  47 import javax.swing.JMenuItem;
  48 import javax.swing.JOptionPane;
  49 import javax.swing.JPanel;
  50 import javax.swing.JRadioButtonMenuItem;
  51 import javax.swing.JTextField;
  52 import javax.swing.SwingUtilities;
  53
  54 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  55 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  56 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  57 import org.forester.archaeopteryx.tools.InferenceManager;
  58 import org.forester.archaeopteryx.tools.ProcessPool;
  59 import org.forester.archaeopteryx.tools.ProcessRunning;
  60 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  61 import org.forester.phylogeny.Phylogeny;
  62 import org.forester.phylogeny.PhylogenyMethods;
  63 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  64 import org.forester.phylogeny.PhylogenyNode;
  65 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  66 import org.forester.phylogeny.data.Annotation;
  67 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
  68 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
  69 import org.forester.sdi.GSDI;
  70 import org.forester.sdi.GSDIR;
  71 import org.forester.sdi.SDIException;
  72 import org.forester.util.ForesterConstants;
  73 import org.forester.util.ForesterUtil;
  74
  75 public abstract class MainFrame extends JFrame implements ActionListener {
  76
  77     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";
  78     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME
  79     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;
  80     private static final long   serialVersionUID                        = 3655000897845508358L;
  81     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),
  82                                                                                     Font.PLAIN,
  83                                                                                     10 );
  84     static final String         TYPE_MENU_HEADER                        = "Type";
  85     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";
  86     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";
  87     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";
  88     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";
  89     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";
  90     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";
  91     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO
  92     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO
  93     static final String         OPTIONS_HEADER                          = "Options";
  94     static final String         SEARCH_SUBHEADER                        = "Search:";
  95     static final String         DISPLAY_SUBHEADER                       = "Display:";
  96     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";
  97     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";
  98     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";
  99     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Display Branch Length Values";
 100     static final String         DISPLAY_SCALE_LABEL                     = "Display Scale";
 101     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";
 102     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";
 103     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";
 104     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";
 105     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";
 106     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";
 107     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";
 108     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Show External Node Shapes";
 109     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Show Internal Node Shapes";
 110     static final String         SHOW_OVERVIEW_LABEL                     = "Show Overview";
 111     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";
 112     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";
 113     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Show Domain Labels";
 114     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Show Seq Annotation Ref Sources";
 115     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";
 116     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";
 117     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";
 118     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";
 119     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";
 120     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";
 121     static final String         SHOW_CONF_STDDEV_LABEL                  = "Show Confidence Standard Deviations";
 122     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";
 123     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
 124     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Show Basic Tree Information";
 125     JMenuBar                    _jmenubar;
 126     JMenu                       _file_jmenu;
 127     JMenu                       _tools_menu;
 128     JMenu                       _view_jmenu;
 129     JMenu                       _options_jmenu;
 130     JMenu                       _font_size_menu;
 131     JMenu                       _help_jmenu;
 132     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;
 133     // Analysis menu
 134     JMenu                       _analysis_menu;
 135     JMenuItem                   _load_species_tree_item;
 136     JMenuItem                   _gsdi_item;
 137     JMenuItem                   _gsdir_item;
 138     JMenuItem                   _lineage_inference;
 139     // file menu:
 140     JMenuItem                   _open_item;
 141     JMenuItem                   _open_url_item;
 142     JMenuItem                   _save_item;
 143     JMenuItem                   _save_all_item;
 144     JMenuItem                   _close_item;
 145     JMenuItem                   _exit_item;
 146     JMenuItem                   _new_item;
 147     // tools menu:
 148     JMenuItem                   _midpoint_root_item;
 149     JMenuItem                   _taxcolor_item;
 150     JMenuItem                   _confcolor_item;
 151     JMenuItem                   _color_rank_jmi;
 152     JMenuItem                   _collapse_species_specific_subtrees;
 153     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me
 154     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;
 155     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;
 156     JMenuItem                   _obtain_seq_information_jmi;
 157     JMenuItem                   _move_node_names_to_tax_sn_jmi;
 158     JMenuItem                   _move_node_names_to_seq_names_jmi;
 159     JMenuItem                   _extract_tax_code_from_node_names_jmi;
 160     JMenuItem                   _annotate_item;
 161     // font size menu:
 162     JMenuItem                   _super_tiny_fonts_item;
 163     JMenuItem                   _tiny_fonts_item;
 164     JMenuItem                   _small_fonts_item;
 165     JMenuItem                   _medium_fonts_item;
 166     JMenuItem                   _large_fonts_item;
 167     // options menu:
 168     // _  screen and print
 169     JMenuItem                   _choose_font_mi;
 170     JMenuItem                   _switch_colors_mi;
 171     JCheckBoxMenuItem           _label_direction_cbmi;
 172     // _  screen display
 173     JCheckBoxMenuItem           _screen_antialias_cbmi;
 174     JCheckBoxMenuItem           _background_gradient_cbmi;
 175     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 176     JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 177     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 178     JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 179     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me
 180     JCheckBoxMenuItem           _show_overview_cbmi;
 181     JCheckBoxMenuItem           _show_domain_labels;
 182     JCheckBoxMenuItem           _show_annotation_ref_source;
 183     JCheckBoxMenuItem           _abbreviate_scientific_names;
 184     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 185     JMenuItem                   _overview_placment_mi;
 186     JMenuItem                   _choose_minimal_confidence_mi;
 187     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 188     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 189     JMenuItem                   _cycle_node_shape_mi;
 190     JMenuItem                   _cycle_node_fill_mi;
 191     JMenuItem                   _choose_node_size_mi;
 192     JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
 193     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 194     // _  print
 195     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;
 196     JCheckBoxMenuItem           _antialias_print_cbmi;
 197     JCheckBoxMenuItem           _print_black_and_white_cbmi;
 198     JCheckBoxMenuItem           _print_using_actual_size_cbmi;
 199     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;
 200     JMenuItem                   _print_size_mi;
 201     JMenuItem                   _choose_pdf_width_mi;
 202     // _  parsing
 203     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;
 204     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;
 205     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;
 206     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;
 207     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;
 208     JCheckBoxMenuItem           _replace_underscores_cbmi;
 209     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;
 210     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;
 211     // _  search
 212     JCheckBoxMenuItem           _search_case_senstive_cbmi;
 213     JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 214     JCheckBoxMenuItem           _inverse_search_result_cbmi;
 215     // type menu:
 216     JMenu                       _type_menu;
 217     JCheckBoxMenuItem           _rectangular_type_cbmi;
 218     JCheckBoxMenuItem           _triangular_type_cbmi;
 219     JCheckBoxMenuItem           _curved_type_cbmi;
 220     JCheckBoxMenuItem           _convex_type_cbmi;
 221     JCheckBoxMenuItem           _euro_type_cbmi;
 222     JCheckBoxMenuItem           _rounded_type_cbmi;
 223     JCheckBoxMenuItem           _unrooted_type_cbmi;
 224     JCheckBoxMenuItem           _circular_type_cbmi;
 225     // view as text menu:
 226     JMenuItem                   _view_as_NH_item;
 227     JMenuItem                   _view_as_XML_item;
 228     JMenuItem                   _view_as_nexus_item;
 229     JMenuItem                   _display_basic_information_item;
 230     // help menu:
 231     JMenuItem                   _about_item;
 232     JMenuItem                   _help_item;
 233     JMenuItem                   _website_item;
 234     JMenuItem                   _phyloxml_website_item;
 235     JMenuItem                   _phyloxml_ref_item;
 236     JMenuItem                   _aptx_ref_item;
 237     // process menu:
 238     JMenu                       _process_menu;
 239     // Handy pointers to child components:
 240     MainPanel                   _mainpanel;
 241     Container                   _contentpane;
 242     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;
 243     Configuration               _configuration;
 244     JMenuItem                   _remove_branch_color_item;
 245     Options                     _options;
 246     private Phylogeny           _species_tree;
 247     InferenceManager            _inference_manager;
 248     final ProcessPool           _process_pool;
 249     private String              _previous_node_annotation_ref;
 250
 251     MainFrame() {
 252         _process_pool = ProcessPool.createInstance();
 253     }
 254
 255     /**
 256      * Action performed.
 257      */
 258     @Override
 259     public void actionPerformed( final ActionEvent e ) {
 260         final Object o = e.getSource();
 261         boolean is_applet = false;
 262         JApplet applet = null;
 263         if ( getCurrentTreePanel() != null ) {
 264             is_applet = getCurrentTreePanel().isApplet();
 265             if ( is_applet ) {
 266                 applet = getCurrentTreePanel().obtainApplet();
 267             }
 268         }
 269         if ( o == _open_url_item ) {
 270             readPhylogeniesFromURL();
 271         }
 272         else if ( o == _exit_item ) {
 273             close();
 274         }
 275         else if ( o == _gsdi_item ) {
 276             if ( isSubtreeDisplayed() ) {
 277                 return;
 278             }
 279             executeGSDI();
 280         }
 281         else if ( o == _gsdir_item ) {
 282             if ( isSubtreeDisplayed() ) {
 283                 return;
 284             }
 285             executeGSDIR();
 286         }
 287         else if ( o == _taxcolor_item ) {
 288             taxColor();
 289         }
 290         else if ( o == _confcolor_item ) {
 291             confColor();
 292         }
 293         else if ( o == _color_rank_jmi ) {
 294             colorRank();
 295         }
 296         else if ( o == _collapse_species_specific_subtrees ) {
 297             if ( isSubtreeDisplayed() ) {
 298                 return;
 299             }
 300             if ( getCurrentTreePanel() != null ) {
 301                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 302             }
 303         }
 304         else if ( o == _remove_branch_color_item ) {
 305             if ( isSubtreeDisplayed() ) {
 306                 return;
 307             }
 308             removeBranchColors();
 309         }
 310         else if ( o == _midpoint_root_item ) {
 311             if ( isSubtreeDisplayed() ) {
 312                 return;
 313             }
 314             midpointRoot();
 315         }
 316         else if ( o == _annotate_item ) {
 317             annotateSequences();
 318         }
 319         else if ( o == _switch_colors_mi ) {
 320             switchColors();
 321         }
 322         else if ( o == _display_basic_information_item ) {
 323             displayBasicInformation();
 324         }
 325         else if ( o == _view_as_NH_item ) {
 326             viewAsNH();
 327         }
 328         else if ( o == _view_as_XML_item ) {
 329             viewAsXML();
 330         }
 331         else if ( o == _view_as_nexus_item ) {
 332             viewAsNexus();
 333         }
 334         else if ( o == _super_tiny_fonts_item ) {
 335             if ( getCurrentTreePanel() != null ) {
 336                 getCurrentTreePanel().setSuperTinyFonts();
 337                 getCurrentTreePanel().repaint();
 338             }
 339         }
 340         else if ( o == _tiny_fonts_item ) {
 341             if ( getCurrentTreePanel() != null ) {
 342                 getCurrentTreePanel().setTinyFonts();
 343                 getCurrentTreePanel().repaint();
 344             }
 345         }
 346         else if ( o == _small_fonts_item ) {
 347             if ( getCurrentTreePanel() != null ) {
 348                 getCurrentTreePanel().setSmallFonts();
 349                 getCurrentTreePanel().repaint();
 350             }
 351         }
 352         else if ( o == _medium_fonts_item ) {
 353             if ( getCurrentTreePanel() != null ) {
 354                 getCurrentTreePanel().setMediumFonts();
 355                 getCurrentTreePanel().repaint();
 356             }
 357         }
 358         else if ( o == _large_fonts_item ) {
 359             if ( getCurrentTreePanel() != null ) {
 360                 getCurrentTreePanel().setLargeFonts();
 361                 getCurrentTreePanel().repaint();
 362             }
 363         }
 364         else if ( o == _choose_font_mi ) {
 365             chooseFont();
 366         }
 367         else if ( o == _choose_minimal_confidence_mi ) {
 368             chooseMinimalConfidence();
 369         }
 370         else if ( o == _choose_node_size_mi ) {
 371             chooseNodeSize( getOptions(), this );
 372         }
 373         else if ( o == _overview_placment_mi ) {
 374             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 375         }
 376         else if ( o == _cycle_node_fill_mi ) {
 377             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 378         }
 379         else if ( o == _cycle_node_shape_mi ) {
 380             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 381         }
 382         else if ( o == _screen_antialias_cbmi ) {
 383             updateOptions( getOptions() );
 384             updateScreenTextAntialias( getMainPanel().getTreePanels() );
 385         }
 386         else if ( o == _background_gradient_cbmi ) {
 387             updateOptions( getOptions() );
 388         }
 389         else if ( o == _show_domain_labels ) {
 390             updateOptions( getOptions() );
 391         }
 392         else if ( o == _show_annotation_ref_source ) {
 393             updateOptions( getOptions() );
 394         }
 395         else if ( o == _abbreviate_scientific_names ) {
 396             updateOptions( getOptions() );
 397         }
 398         else if ( o == _color_labels_same_as_parent_branch ) {
 399             updateOptions( getOptions() );
 400         }
 401         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 402             updateOptions( getOptions() );
 403         }
 404         else if ( o == _show_default_node_shapes_external_cbmi ) {
 405             updateOptions( getOptions() );
 406         }
 407         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 408             updateOptions( getOptions() );
 409         }
 410         else if ( o == _non_lined_up_cladograms_rbmi ) {
 411             updateOptions( getOptions() );
 412             showWhole();
 413         }
 414         else if ( o == _uniform_cladograms_rbmi ) {
 415             updateOptions( getOptions() );
 416             showWhole();
 417         }
 418         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 419             updateOptions( getOptions() );
 420             showWhole();
 421         }
 422         else if ( o == _search_case_senstive_cbmi ) {
 423             updateOptions( getOptions() );
 424             getMainPanel().getControlPanel().search();
 425         }
 426         else if ( o == _search_whole_words_only_cbmi ) {
 427             updateOptions( getOptions() );
 428             getMainPanel().getControlPanel().search();
 429         }
 430         else if ( o == _inverse_search_result_cbmi ) {
 431             updateOptions( getOptions() );
 432             getMainPanel().getControlPanel().search();
 433         }
 434         else if ( o == _show_scale_cbmi ) {
 435             updateOptions( getOptions() );
 436         }
 437         else if ( o == _show_branch_length_values_cbmi ) {
 438             updateOptions( getOptions() );
 439         }
 440         else if ( o == _show_confidence_stddev_cbmi ) {
 441             updateOptions( getOptions() );
 442         }
 443         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
 444             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
 445                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
 446             }
 447             updateOptions( getOptions() );
 448         }
 449         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
 450             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
 451                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
 452             }
 453             updateOptions( getOptions() );
 454         }
 455         else if ( o == _label_direction_cbmi ) {
 456             updateOptions( getOptions() );
 457         }
 458         else if ( o == _show_overview_cbmi ) {
 459             updateOptions( getOptions() );
 460             if ( getCurrentTreePanel() != null ) {
 461                 getCurrentTreePanel().updateOvSizes();
 462             }
 463         }
 464         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 465                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
 466                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 467             typeChanged( o );
 468         }
 469         else if ( o == _about_item ) {
 470             about();
 471         }
 472         else if ( o == _help_item ) {
 473             help();
 474         }
 475         else if ( o == _website_item ) {
 476             try {
 477                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
 478             }
 479             catch ( final IOException e1 ) {
 480                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 481             }
 482         }
 483         else if ( o == _phyloxml_website_item ) {
 484             try {
 485                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
 486             }
 487             catch ( final IOException e1 ) {
 488                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 489             }
 490         }
 491         else if ( o == _aptx_ref_item ) {
 492             try {
 493                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
 494             }
 495             catch ( final IOException e1 ) {
 496                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 497             }
 498         }
 499         else if ( o == _phyloxml_ref_item ) {
 500             try {
 501                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
 502             }
 503             catch ( final IOException e1 ) {
 504                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 505             }
 506         }
 507         else {
 508             if ( _load_phylogeny_from_webservice_menu_items != null ) {
 509                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
 510                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
 511                         readPhylogeniesFromWebservice( i );
 512                     }
 513                 }
 514             }
 515         }
 516         _contentpane.repaint();
 517     }
 518
 519     public Configuration getConfiguration() {
 520         return _configuration;
 521     }
 522
 523     /**
 524      * This method returns the current external node data which
 525      * has been selected by the user by clicking the "Return ..."
 526      * menu item. This method is expected to be called from Javascript or
 527      * something like it.
 528      *
 529      * @return current external node data as String
 530      */
 531     public String getCurrentExternalNodesDataBuffer() {
 532         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 533     }
 534
 535     public int getCurrentExternalNodesDataBufferChangeCounter() {
 536         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 537     }
 538
 539     public int getCurrentExternalNodesDataBufferLength() {
 540         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 541     }
 542
 543     public InferenceManager getInferenceManager() {
 544         return _inference_manager;
 545     }
 546
 547     public MainPanel getMainPanel() {
 548         return _mainpanel;
 549     }
 550
 551     public Options getOptions() {
 552         return _options;
 553     }
 554
 555     public ProcessPool getProcessPool() {
 556         return _process_pool;
 557     }
 558
 559     public void showTextFrame( final String s, final String title ) {
 560         checkTextFrames();
 561         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 562     }
 563
 564     public void showWhole() {
 565         _mainpanel.getControlPanel().showWhole();
 566     }
 567
 568     public void updateProcessMenu() {
 569         // In general Swing is not thread safe.
 570         // See "Swing's Threading Policy".
 571         SwingUtilities.invokeLater( new Runnable() {
 572
 573             @Override
 574             public void run() {
 575                 doUpdateProcessMenu();
 576             }
 577         } );
 578     }
 579
 580     void activateSaveAllIfNeeded() {
 581         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
 582             _save_all_item.setEnabled( true );
 583         }
 584         else {
 585             _save_all_item.setEnabled( false );
 586         }
 587     }
 588
 589     void buildFileMenu() {
 590         _file_jmenu = createMenu( "File", getConfiguration() );
 591         _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
 592         _file_jmenu.addSeparator();
 593         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 594         customizeJMenuItem( _open_url_item );
 595         customizeJMenuItem( _exit_item );
 596         _jmenubar.add( _file_jmenu );
 597     }
 598
 599     void buildFontSizeMenu() {
 600         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
 601         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
 602         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
 603         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
 604         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
 605         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
 606         customizeJMenuItem( _super_tiny_fonts_item );
 607         customizeJMenuItem( _tiny_fonts_item );
 608         customizeJMenuItem( _small_fonts_item );
 609         customizeJMenuItem( _medium_fonts_item );
 610         customizeJMenuItem( _large_fonts_item );
 611         _jmenubar.add( _font_size_menu );
 612     }
 613
 614     void buildHelpMenu() {
 615         _help_jmenu = createMenu( "Help", getConfiguration() );
 616         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 617         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 618         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 619         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 620         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 621         _help_jmenu.addSeparator();
 622         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 623         customizeJMenuItem( _help_item );
 624         customizeJMenuItem( _website_item );
 625         customizeJMenuItem( _phyloxml_website_item );
 626         customizeJMenuItem( _aptx_ref_item );
 627         customizeJMenuItem( _phyloxml_ref_item );
 628         customizeJMenuItem( _about_item );
 629         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
 630         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
 631         _jmenubar.add( _help_jmenu );
 632     }
 633
 634     void buildTypeMenu() {
 635         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
 636         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 637         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 638         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 639         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 640         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 641         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 642         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 643         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 644         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 645         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 646         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 647         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 648         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 649         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 650         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 651         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 652         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 653         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 654         initializeTypeMenu( getOptions() );
 655         _jmenubar.add( _type_menu );
 656     }
 657
 658     void buildViewMenu() {
 659         _view_jmenu = createMenu( "View", getConfiguration() );
 660         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 661         _view_jmenu.addSeparator();
 662         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
 663         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
 664         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
 665         customizeJMenuItem( _display_basic_information_item );
 666         customizeJMenuItem( _view_as_NH_item );
 667         customizeJMenuItem( _view_as_XML_item );
 668         customizeJMenuItem( _view_as_nexus_item );
 669         _jmenubar.add( _view_jmenu );
 670     }
 671
 672     void checkTextFrames() {
 673         if ( _textframes.size() > 5 ) {
 674             try {
 675                 if ( _textframes.getFirst() != null ) {
 676                     _textframes.getFirst().removeMe();
 677                 }
 678                 else {
 679                     _textframes.removeFirst();
 680                 }
 681             }
 682             catch ( final NoSuchElementException e ) {
 683                 // Ignore.
 684             }
 685         }
 686     }
 687
 688     void close() {
 689         removeAllTextFrames();
 690         if ( _mainpanel != null ) {
 691             _mainpanel.terminate();
 692         }
 693         if ( _contentpane != null ) {
 694             _contentpane.removeAll();
 695         }
 696         setVisible( false );
 697         dispose();
 698     }
 699
 700     void colorRank() {
 701         if ( _mainpanel.getCurrentTreePanel() != null ) {
 702             final String[] ranks = AptxUtil.getAllPossibleRanks();
 703             final String rank = ( String ) JOptionPane
 704                     .showInputDialog( this,
 705                                       "What rank should the colorization be based on",
 706                                       "Rank Selection",
 707                                       JOptionPane.QUESTION_MESSAGE,
 708                                       null,
 709                                       ranks,
 710                                       null );
 711             if ( !ForesterUtil.isEmpty( rank ) ) {
 712                 _mainpanel.getCurrentTreePanel().colorRank( rank );
 713             }
 714         }
 715     }
 716
 717     void confColor() {
 718         if ( _mainpanel.getCurrentTreePanel() != null ) {
 719             _mainpanel.getCurrentTreePanel().confColor();
 720         }
 721     }
 722
 723     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 724         if ( item != null ) {
 725             item.setFont( MainFrame.menu_font );
 726             if ( !getConfiguration().isUseNativeUI() ) {
 727                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 728                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 729             }
 730             item.setSelected( is_selected );
 731             item.addActionListener( this );
 732         }
 733     }
 734
 735     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
 736         if ( jmi != null ) {
 737             jmi.setFont( MainFrame.menu_font );
 738             if ( !getConfiguration().isUseNativeUI() ) {
 739                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 740                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 741             }
 742             jmi.addActionListener( this );
 743         }
 744         return jmi;
 745     }
 746
 747     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 748         if ( item != null ) {
 749             item.setFont( MainFrame.menu_font );
 750             if ( !getConfiguration().isUseNativeUI() ) {
 751                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 752                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 753             }
 754             item.setSelected( is_selected );
 755             item.addActionListener( this );
 756         }
 757     }
 758
 759     void displayBasicInformation() {
 760         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
 761             String title = "Basic Information";
 762             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
 763                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
 764             }
 765             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
 766         }
 767     }
 768
 769     void exceptionOccuredDuringOpenFile( final Exception e ) {
 770         try {
 771             _mainpanel.getCurrentTreePanel().setArrowCursor();
 772         }
 773         catch ( final Exception ex ) {
 774             // Do nothing.
 775         }
 776         JOptionPane.showMessageDialog( this,
 777                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
 778                                        "Error during File|Open",
 779                                        JOptionPane.ERROR_MESSAGE );
 780     }
 781
 782     void exceptionOccuredDuringSaveAs( final Exception e ) {
 783         try {
 784             _mainpanel.getCurrentTreePanel().setArrowCursor();
 785         }
 786         catch ( final Exception ex ) {
 787             // Do nothing.
 788         }
 789         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
 790     }
 791
 792     void executeGSDI() {
 793         if ( !isOKforSDI( false, true ) ) {
 794             return;
 795         }
 796         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 797             JOptionPane.showMessageDialog( this,
 798                                            "Gene tree is not rooted.",
 799                                            "Cannot execute GSDI",
 800                                            JOptionPane.ERROR_MESSAGE );
 801             return;
 802         }
 803         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 804         gene_tree.setAllNodesToNotCollapse();
 805         gene_tree.recalculateNumberOfExternalDescendants( false );
 806         GSDI gsdi = null;
 807         final Phylogeny species_tree = getSpeciesTree().copy();
 808         try {
 809             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 810         }
 811         catch ( final SDIException e ) {
 812             JOptionPane.showMessageDialog( this,
 813                                            e.getLocalizedMessage(),
 814                                            "Error during GSDI",
 815                                            JOptionPane.ERROR_MESSAGE );
 816             return;
 817         }
 818         catch ( final Exception e ) {
 819             AptxUtil.unexpectedException( e );
 820             return;
 821         }
 822         gene_tree.setRerootable( false );
 823         gene_tree.clearHashIdToNodeMap();
 824         gene_tree.recalculateNumberOfExternalDescendants( true );
 825         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 826         getMainPanel().getControlPanel().setShowEvents( true );
 827         showWhole();
 828         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 829         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 830         showWhole();
 831         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 832         showWhole();
 833         _mainpanel.getCurrentTreePanel().setEdited( true );
 834         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 835         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 836             JOptionPane.showMessageDialog( this,
 837                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 838                                                    + "Potential duplications: "
 839                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 840                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 841                                                    + "Stripped gene tree nodes: "
 842                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 843                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 844                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 845                                            "GSDI successfully completed",
 846                                            JOptionPane.WARNING_MESSAGE );
 847         }
 848         else {
 849             JOptionPane.showMessageDialog( this,
 850                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 851                                                    + "Potential duplications: "
 852                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 853                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 854                                                    + "Stripped gene tree nodes: "
 855                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 856                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 857                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 858                                            "GSDI successfully completed",
 859                                            JOptionPane.INFORMATION_MESSAGE );
 860         }
 861     }
 862
 863     void executeGSDIR() {
 864         if ( !isOKforSDI( false, false ) ) {
 865             return;
 866         }
 867         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
 868         if ( ( p > 0 )
 869                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
 870             JOptionPane.showMessageDialog( this,
 871                                            "Gene tree is not completely binary",
 872                                            "Cannot execute GSDI",
 873                                            JOptionPane.ERROR_MESSAGE );
 874             return;
 875         }
 876         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 877         gene_tree.setAllNodesToNotCollapse();
 878         gene_tree.recalculateNumberOfExternalDescendants( false );
 879         GSDIR gsdir = null;
 880         final Phylogeny species_tree = getSpeciesTree().copy();
 881         try {
 882             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
 883         }
 884         catch ( final SDIException e ) {
 885             JOptionPane.showMessageDialog( this,
 886                                            e.getLocalizedMessage(),
 887                                            "Error during GSDIR",
 888                                            JOptionPane.ERROR_MESSAGE );
 889             return;
 890         }
 891         catch ( final Exception e ) {
 892             AptxUtil.unexpectedException( e );
 893             return;
 894         }
 895         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
 896         result_gene_tree.setRerootable( false );
 897         result_gene_tree.clearHashIdToNodeMap();
 898         result_gene_tree.recalculateNumberOfExternalDescendants( true );
 899         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
 900         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
 901         getMainPanel().getControlPanel().setShowEvents( true );
 902         showWhole();
 903         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 904         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 905         showWhole();
 906         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 907         showWhole();
 908         _mainpanel.getCurrentTreePanel().setEdited( true );
 909         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 910         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 911             JOptionPane.showMessageDialog( this,
 912                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
 913                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
 914                                                    + "Stripped gene tree nodes: "
 915                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
 916                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
 917                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 918                                            "GSDIR successfully completed",
 919                                            JOptionPane.WARNING_MESSAGE );
 920         }
 921         else {
 922             JOptionPane.showMessageDialog( this,
 923                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
 924                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
 925                                                    + "Stripped gene tree nodes: "
 926                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
 927                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
 928                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 929                                            "GSDIR successfully completed",
 930                                            JOptionPane.INFORMATION_MESSAGE );
 931         }
 932     }
 933
 934     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
 935         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
 936             JOptionPane.showMessageDialog( this,
 937                                            "Gene tree and species tree have no species in common.",
 938                                            "Error during SDI",
 939                                            JOptionPane.ERROR_MESSAGE );
 940             return false;
 941         }
 942         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
 943             JOptionPane.showMessageDialog( this,
 944                                            "Gene tree and species tree have only one species in common.",
 945                                            "Error during SDI",
 946                                            JOptionPane.ERROR_MESSAGE );
 947             return false;
 948         }
 949         else {
 950             return true;
 951         }
 952     }
 953
 954     TreePanel getCurrentTreePanel() {
 955         return getMainPanel().getCurrentTreePanel();
 956     }
 957
 958     JMenu getHelpMenu() {
 959         return _help_jmenu;
 960     }
 961
 962     JCheckBoxMenuItem getlabelDirectionCbmi() {
 963         return _label_direction_cbmi;
 964     }
 965
 966     JMenuBar getMenuBarOfMainFrame() {
 967         return _jmenubar;
 968     }
 969
 970     final Phylogeny getSpeciesTree() {
 971         return _species_tree;
 972     }
 973
 974     void help() {
 975         final StringBuilder sb = new StringBuilder();
 976         sb.append( "Display options\n" );
 977         sb.append( "-------------------\n" );
 978         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 979         sb.append( "Clickable tree nodes\n" );
 980         sb.append( "--------------------\n" );
 981         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 982         sb.append( "or by right clicking:\n" );
 983         sb.append( "o  Display Node Data -- display information for a node\n" );
 984         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 985         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 986         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 987         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 988         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 989         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 990         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
 991         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
 992         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
 993         sb.append( "Zooming\n" );
 994         sb.append( "---------\n" );
 995         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
 996         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
 997         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
 998         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
 999         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1000         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1001         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1002         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1003         sb.append( "Quick tree manipulation:\n" );
1004         sb.append( "------------------------\n" );
1005         sb.append( "Order Subtrees -- order the tree by branch length\n" );
1006         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1007         sb.append( "Memory problems (Java heap space error)\n" );
1008         sb.append( "---------------------------------------\n" );
1009         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1010         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1011         sb.append( "the '-Xmx' Java command line option. For example:\n" );
1012         sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1013         // + "General remarks\n"
1014         // + "---------------\n"
1015         // +
1016         // "o  The application version permits copying to the clipboard \n"
1017         // +
1018         // "    in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1019         // +
1020         // "o  Changes made to a subtree affect this subtree and its subtrees,\n"
1021         // + "    but not any of its parent tree(s).\n"
1022         // +
1023         // "o  Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1024         // +
1025         // "    are likely to be bootstrap values instead of branch length values.\n\n"
1026         // +
1027         // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1028         // +
1029         // "o  Each external node of the gene tree (in display) needs to be associated with\n"
1030         // +
1031         // "    a species: either directly through the \"Species\" field, or the species\n"
1032         // +
1033         // "    is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1034         // +
1035         // "    (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1036         // +
1037         // "o  A species tree for each species of the gene tree needs to be loaded with\n"
1038         // +
1039         // "   \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1040         // +
1041         // "o  !External nodes of the gene tree associated with species not present in\n"
1042         // +
1043         // "    the species tree are REMOVED prior to SDI execution!\n"
1044         // +
1045         // "o  Both the gene tree and the species tree must be completely binary.\n"
1046         // +
1047         // "o  Duplications and speciations are a function of the position of the root.\n"
1048         // +
1049         // "    Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1050         // + "    incorrect and need to be inferred again\n"
1051         // +
1052         // "    with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1053         sb.append( "phyloXML\n" );
1054         sb.append( "-------------------\n" );
1055         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1056         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1057         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1058         sb.append( "\n" );
1059         sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
1060         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1061         TextFrame.instantiate( sb.toString(), "Help", _textframes );
1062     }
1063
1064     void initializeTypeMenu( final Options options ) {
1065         setTypeMenuToAllUnselected();
1066         switch ( options.getPhylogenyGraphicsType() ) {
1067             case CONVEX:
1068                 _convex_type_cbmi.setSelected( true );
1069                 break;
1070             case CURVED:
1071                 _curved_type_cbmi.setSelected( true );
1072                 break;
1073             case EURO_STYLE:
1074                 _euro_type_cbmi.setSelected( true );
1075                 break;
1076             case ROUNDED:
1077                 _rounded_type_cbmi.setSelected( true );
1078                 break;
1079             case TRIANGULAR:
1080                 _triangular_type_cbmi.setSelected( true );
1081                 break;
1082             case UNROOTED:
1083                 _unrooted_type_cbmi.setSelected( true );
1084                 break;
1085             case CIRCULAR:
1086                 _circular_type_cbmi.setSelected( true );
1087                 break;
1088             default:
1089                 _rectangular_type_cbmi.setSelected( true );
1090                 break;
1091         }
1092     }
1093
1094     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1095         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1096             return false;
1097         }
1098         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
1099             JOptionPane.showMessageDialog( this,
1100                                            "No species tree loaded",
1101                                            "Cannot execute GSDI",
1102                                            JOptionPane.ERROR_MESSAGE );
1103             return false;
1104         }
1105         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
1106             JOptionPane.showMessageDialog( this,
1107                                            "Species tree is not completely binary",
1108                                            "Cannot execute GSDI",
1109                                            JOptionPane.ERROR_MESSAGE );
1110             return false;
1111         }
1112         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1113             JOptionPane.showMessageDialog( this,
1114                                            "Gene tree is not completely binary",
1115                                            "Cannot execute GSDI",
1116                                            JOptionPane.ERROR_MESSAGE );
1117             return false;
1118         }
1119         else {
1120             return true;
1121         }
1122     }
1123
1124     boolean isSubtreeDisplayed() {
1125         if ( getCurrentTreePanel() != null ) {
1126             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1127                 JOptionPane
1128                         .showMessageDialog( this,
1129                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1130                                             "Operation can not be exectuted on a sub-tree",
1131                                             JOptionPane.WARNING_MESSAGE );
1132                 return true;
1133             }
1134         }
1135         return false;
1136     }
1137
1138     void midpointRoot() {
1139         if ( _mainpanel.getCurrentTreePanel() != null ) {
1140             _mainpanel.getCurrentTreePanel().midpointRoot();
1141         }
1142     }
1143
1144     abstract void readPhylogeniesFromURL();
1145
1146     void readPhylogeniesFromWebservice( final int i ) {
1147         final UrlTreeReader reader = new UrlTreeReader( this, i );
1148         new Thread( reader ).start();
1149     }
1150
1151     void removeAllTextFrames() {
1152         for( final TextFrame tf : _textframes ) {
1153             if ( tf != null ) {
1154                 tf.close();
1155             }
1156         }
1157         _textframes.clear();
1158     }
1159
1160     void setConfiguration( final Configuration configuration ) {
1161         _configuration = configuration;
1162     }
1163
1164     void setInferenceManager( final InferenceManager i ) {
1165         _inference_manager = i;
1166     }
1167
1168     void setOptions( final Options options ) {
1169         _options = options;
1170     }
1171
1172     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1173         setTypeMenuToAllUnselected();
1174         switch ( type ) {
1175             case CIRCULAR:
1176                 _circular_type_cbmi.setSelected( true );
1177                 break;
1178             case CONVEX:
1179                 _convex_type_cbmi.setSelected( true );
1180                 break;
1181             case CURVED:
1182                 _curved_type_cbmi.setSelected( true );
1183                 break;
1184             case EURO_STYLE:
1185                 _euro_type_cbmi.setSelected( true );
1186                 break;
1187             case ROUNDED:
1188                 _rounded_type_cbmi.setSelected( true );
1189                 break;
1190             case RECTANGULAR:
1191                 _rectangular_type_cbmi.setSelected( true );
1192                 break;
1193             case TRIANGULAR:
1194                 _triangular_type_cbmi.setSelected( true );
1195                 break;
1196             case UNROOTED:
1197                 _unrooted_type_cbmi.setSelected( true );
1198                 break;
1199             default:
1200                 throw new IllegalArgumentException( "unknown type: " + type );
1201         }
1202     }
1203
1204     final void setSpeciesTree( final Phylogeny species_tree ) {
1205         _species_tree = species_tree;
1206     }
1207
1208     void setTypeMenuToAllUnselected() {
1209         _convex_type_cbmi.setSelected( false );
1210         _curved_type_cbmi.setSelected( false );
1211         _euro_type_cbmi.setSelected( false );
1212         _rounded_type_cbmi.setSelected( false );
1213         _triangular_type_cbmi.setSelected( false );
1214         _rectangular_type_cbmi.setSelected( false );
1215         _unrooted_type_cbmi.setSelected( false );
1216         _circular_type_cbmi.setSelected( false );
1217     }
1218
1219     void switchColors() {
1220         final TreeColorSet colorset = _mainpanel.getTreeColorSet();
1221         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1222         csc.setVisible( true );
1223     }
1224
1225     void taxColor() {
1226         if ( _mainpanel.getCurrentTreePanel() != null ) {
1227             _mainpanel.getCurrentTreePanel().taxColor();
1228         }
1229     }
1230
1231     void typeChanged( final Object o ) {
1232         updateTypeCheckboxes( getOptions(), o );
1233         updateOptions( getOptions() );
1234         if ( getCurrentTreePanel() != null ) {
1235             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1236             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1237             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1238                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1239                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1240                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1241                 getCurrentTreePanel().getControlPanel().showWhole();
1242             }
1243             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1244                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1245             }
1246             else {
1247                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1248             }
1249             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1250             updateScreenTextAntialias( getMainPanel().getTreePanels() );
1251             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
1252                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1253                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
1254                 }
1255                 else {
1256                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
1257                 }
1258             }
1259         }
1260     }
1261
1262     void updateOptions( final Options options ) {
1263         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1264         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1265                 && _background_gradient_cbmi.isSelected() );
1266         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1267         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1268                 && _show_annotation_ref_source.isSelected() );
1269         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1270                 && _abbreviate_scientific_names.isSelected() );
1271         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1272                 && _color_labels_same_as_parent_branch.isSelected() );
1273         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1274                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1275         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1276                 && _show_default_node_shapes_external_cbmi.isSelected() );
1277         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1278                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1279         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1280             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1281         }
1282         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1283             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1284         }
1285         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1286             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1287         }
1288         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1289                 && _search_case_senstive_cbmi.isSelected() );
1290         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1291             options.setShowScale( _show_scale_cbmi.isSelected() );
1292         }
1293         if ( _label_direction_cbmi != null ) {
1294             if ( _label_direction_cbmi.isSelected() ) {
1295                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1296             }
1297             else {
1298                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1299             }
1300         }
1301         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1302         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1303                 && _show_confidence_stddev_cbmi.isSelected() );
1304         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1305             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1306         }
1307         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1308                 && ( _print_using_actual_size_cbmi.isSelected() ) );
1309         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1310                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1311         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1312         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1313                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1314             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1315         }
1316         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1317                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1318             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1319         }
1320         else {
1321             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1322         }
1323         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1324                 && _print_black_and_white_cbmi.isSelected() );
1325         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1326                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1327         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
1328             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1329         }
1330         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
1331             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1332         }
1333         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
1334             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1335         }
1336         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
1337             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1338         }
1339         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1340                 && _replace_underscores_cbmi.isSelected() );
1341         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1342                 && _search_whole_words_only_cbmi.isSelected() );
1343         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1344                 && _inverse_search_result_cbmi.isSelected() );
1345         if ( _graphics_export_visible_only_cbmi != null ) {
1346             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1347             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1348                 _graphics_export_using_actual_size_cbmi.setSelected( true );
1349                 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1350             }
1351             else {
1352                 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1353             }
1354         }
1355         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1356             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1357         }
1358         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1359             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1360         }
1361         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1362             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1363         }
1364         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1365             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1366         }
1367         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1368             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1369         }
1370         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1371             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1372         }
1373         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1374             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1375         }
1376         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1377             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1378         }
1379     }
1380
1381     void updateTypeCheckboxes( final Options options, final Object o ) {
1382         setTypeMenuToAllUnselected();
1383         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1384     }
1385
1386     void viewAsNexus() {
1387         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1388             String title = "Nexus";
1389             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1390                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1391             }
1392             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
1393                            title );
1394         }
1395     }
1396
1397     void viewAsNH() {
1398         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1399             String title = "New Hampshire";
1400             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1401                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1402             }
1403             showTextFrame( _mainpanel.getCurrentPhylogeny()
1404                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1405                            title );
1406         }
1407     }
1408
1409     void viewAsXML() {
1410         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1411             String title = "phyloXML";
1412             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1413                 title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
1414             }
1415             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
1416         }
1417     }
1418
1419     private void annotateSequences() {
1420         if ( getCurrentTreePanel() != null ) {
1421             final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
1422             if ( ( nodes == null ) || nodes.isEmpty() ) {
1423                 JOptionPane
1424                         .showMessageDialog( this,
1425                                             "Need to select nodes, either via direct selection or via the \"Search\" function",
1426                                             "No nodes selected for annotation",
1427                                             JOptionPane.ERROR_MESSAGE );
1428                 return;
1429             }
1430             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
1431             if ( ( phy != null ) && !phy.isEmpty() ) {
1432                 final JTextField ref_field = new JTextField( 10 );
1433                 final JTextField desc_filed = new JTextField( 20 );
1434                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
1435                         : getPreviousNodeAnnotationReference() );
1436                 final JPanel my_panel = new JPanel();
1437                 my_panel.add( new JLabel( "Reference " ) );
1438                 my_panel.add( ref_field );
1439                 my_panel.add( Box.createHorizontalStrut( 15 ) );
1440                 my_panel.add( new JLabel( "Description " ) );
1441                 my_panel.add( desc_filed );
1442                 final int result = JOptionPane.showConfirmDialog( null,
1443                                                                   my_panel,
1444                                                                   "Enter the sequence annotation(s) for the "
1445                                                                           + nodes.size() + " selected nodes",
1446                                                                   JOptionPane.OK_CANCEL_OPTION );
1447                 if ( result == JOptionPane.OK_OPTION ) {
1448                     String ref = ref_field.getText();
1449                     String desc = desc_filed.getText();
1450                     if ( !ForesterUtil.isEmpty( ref ) ) {
1451                         ref = ref.trim();
1452                         ref = ref.replaceAll( "\\s+", " " );
1453                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 )
1454                                 || ( ref.length() < 3 ) ) {
1455                             JOptionPane.showMessageDialog( this,
1456                                                            "Reference needs to be in the form of \"GO:1234567\"",
1457                                                            "Illegal Format for Annotation Reference",
1458                                                            JOptionPane.ERROR_MESSAGE );
1459                             return;
1460                         }
1461                     }
1462                     if ( ref != null ) {
1463                         setPreviousNodeAnnotationReference( ref );
1464                     }
1465                     if ( desc != null ) {
1466                         desc = desc.trim();
1467                         desc = desc.replaceAll( "\\s+", " " );
1468                     }
1469                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
1470                         for( final Long id : nodes ) {
1471                             final PhylogenyNode n = phy.getNode( id );
1472                             ForesterUtil.ensurePresenceOfSequence( n );
1473                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
1474                                     : new Annotation( ref );
1475                             if ( !ForesterUtil.isEmpty( desc ) ) {
1476                                 ann.setDesc( desc );
1477                             }
1478                             n.getNodeData().getSequence().addAnnotation( ann );
1479                         }
1480                     }
1481                     getMainPanel().getControlPanel().showAnnotations();
1482                 }
1483             }
1484         }
1485     }
1486
1487     private void chooseFont() {
1488         final FontChooser fc = new FontChooser();
1489         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1490         fc.showDialog( this, "Select the Base Font" );
1491         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1492     }
1493
1494     private void chooseMinimalConfidence() {
1495         final String s = ( String ) JOptionPane
1496                 .showInputDialog( this,
1497                                   "Please enter the minimum for confidence values to be displayed.\n"
1498                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
1499                                   "Minimal Confidence Value",
1500                                   JOptionPane.QUESTION_MESSAGE,
1501                                   null,
1502                                   null,
1503                                   getOptions().getMinConfidenceValue() );
1504         if ( !ForesterUtil.isEmpty( s ) ) {
1505             boolean success = true;
1506             double m = 0.0;
1507             final String m_str = s.trim();
1508             if ( !ForesterUtil.isEmpty( m_str ) ) {
1509                 try {
1510                     m = Double.parseDouble( m_str );
1511                 }
1512                 catch ( final Exception ex ) {
1513                     success = false;
1514                 }
1515             }
1516             else {
1517                 success = false;
1518             }
1519             if ( success && ( m >= 0.0 ) ) {
1520                 getOptions().setMinConfidenceValue( m );
1521             }
1522         }
1523     }
1524
1525     private void doUpdateProcessMenu() {
1526         if ( _process_pool.size() > 0 ) {
1527             if ( _process_menu == null ) {
1528                 _process_menu = createMenu( "", getConfiguration() );
1529                 _process_menu.setForeground( Color.RED );
1530             }
1531             _process_menu.removeAll();
1532             final String text = "processes running: " + _process_pool.size();
1533             _process_menu.setText( text );
1534             _jmenubar.add( _process_menu );
1535             for( int i = 0; i < _process_pool.size(); ++i ) {
1536                 final ProcessRunning p = _process_pool.getProcessByIndex( i );
1537                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
1538             }
1539         }
1540         else {
1541             if ( _process_menu != null ) {
1542                 _process_menu.removeAll();
1543                 _jmenubar.remove( _process_menu );
1544             }
1545         }
1546         _jmenubar.validate();
1547         _jmenubar.repaint();
1548         repaint();
1549     }
1550
1551     private String getPreviousNodeAnnotationReference() {
1552         return _previous_node_annotation_ref;
1553     }
1554
1555     private void removeBranchColors() {
1556         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1557             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1558         }
1559     }
1560
1561     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
1562         _previous_node_annotation_ref = previous_node_annotation_ref;
1563     }
1564
1565     /**
1566      * Display the about box.
1567      */
1568     static void about() {
1569         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1570         about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
1571         about.append( "All Rights Reserved\n" );
1572         about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1573         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1574         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
1575         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1576         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1577         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1578             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1579         }
1580         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1581                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1582             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1583                     + ForesterUtil.OS_VERSION + "]\n" );
1584         }
1585         final Runtime rt = java.lang.Runtime.getRuntime();
1586         final long free_memory = rt.freeMemory() / 1000000;
1587         final long total_memory = rt.totalMemory() / 1000000;
1588         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1589         about.append( "[locale: " + Locale.getDefault() + "]\n" );
1590         about.append( "References:\n" );
1591         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1592         about.append( "For more information & download:\n" );
1593         about.append( Constants.APTX_WEB_SITE + "\n" );
1594         about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1595         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1596     }
1597
1598     static void chooseNodeSize( final Options options, final Component parent ) {
1599         final String s = ( String ) JOptionPane.showInputDialog( parent,
1600                                                                  "Please enter the default size for node shapes.\n"
1601                                                                          + "[current value: "
1602                                                                          + options.getDefaultNodeShapeSize() + "]\n",
1603                                                                  "Node Shape Size",
1604                                                                  JOptionPane.QUESTION_MESSAGE,
1605                                                                  null,
1606                                                                  null,
1607                                                                  options.getDefaultNodeShapeSize() );
1608         if ( !ForesterUtil.isEmpty( s ) ) {
1609             boolean success = true;
1610             double m = 0.0;
1611             final String m_str = s.trim();
1612             if ( !ForesterUtil.isEmpty( m_str ) ) {
1613                 try {
1614                     m = Double.parseDouble( m_str );
1615                 }
1616                 catch ( final Exception ex ) {
1617                     success = false;
1618                 }
1619             }
1620             else {
1621                 success = false;
1622             }
1623             if ( success && ( m >= 0.0 ) ) {
1624                 final short size = ForesterUtil.roundToShort( m );
1625                 if ( size >= 0.0 ) {
1626                     options.setDefaultNodeShapeSize( size );
1627                 }
1628             }
1629         }
1630     }
1631
1632     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1633         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1634     }
1635
1636     static JMenu createMenu( final String title, final Configuration conf ) {
1637         final JMenu jmenu = new JMenu( title );
1638         if ( !conf.isUseNativeUI() ) {
1639             jmenu.setFont( MainFrame.menu_font );
1640             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1641             jmenu.setForeground( conf.getGuiMenuTextColor() );
1642         }
1643         return jmenu;
1644     }
1645
1646     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1647         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1648         if ( !configuration.isUseNativeUI() ) {
1649             label.setBackground( configuration.getGuiMenuBackgroundColor() );
1650             label.setForeground( configuration.getGuiMenuTextColor() );
1651             label.setOpaque( true );
1652         }
1653         label.setSelected( false );
1654         label.setEnabled( false );
1655         return label;
1656     }
1657
1658     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1659         switch ( op.getDefaultNodeFill() ) {
1660             case GRADIENT:
1661                 op.setDefaultNodeFill( NodeFill.SOLID );
1662                 break;
1663             case NONE:
1664                 op.setDefaultNodeFill( NodeFill.GRADIENT );
1665                 break;
1666             case SOLID:
1667                 op.setDefaultNodeFill( NodeFill.NONE );
1668                 break;
1669             default:
1670                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1671         }
1672     }
1673
1674     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1675         switch ( op.getDefaultNodeShape() ) {
1676             case CIRCLE:
1677                 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1678                 break;
1679             case RECTANGLE:
1680                 op.setDefaultNodeShape( NodeShape.CIRCLE );
1681                 break;
1682             default:
1683                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1684         }
1685     }
1686
1687     static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1688         switch ( op.getOvPlacement() ) {
1689             case LOWER_LEFT:
1690                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1691                 break;
1692             case LOWER_RIGHT:
1693                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1694                 break;
1695             case UPPER_LEFT:
1696                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1697                 break;
1698             case UPPER_RIGHT:
1699                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1700                 break;
1701             default:
1702                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1703         }
1704         if ( tree_panel != null ) {
1705             tree_panel.updateOvSettings();
1706         }
1707     }
1708
1709     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1710         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1711             mi.setText( "Cycle Node Shape Fill Type... (current: "
1712                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1713         }
1714         else {
1715             mi.setText( "Cycle Node Shape Fill Type..." );
1716         }
1717     }
1718
1719     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1720         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1721             mi.setText( "Cycle Node Shape Fill Type... (current: "
1722                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1723         }
1724         else {
1725             mi.setText( "Cycle Node Shape Fill Type..." );
1726         }
1727     }
1728
1729     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1730         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1731             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1732         }
1733         else {
1734             mi.setText( "Cycle Overview Placement..." );
1735         }
1736     }
1737
1738     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1739         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1740             mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1741         }
1742         else {
1743             mi.setText( "Select Colors..." );
1744         }
1745     }
1746
1747     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1748         mi.setText( "Select Font... (current: " + font_desc + ")" );
1749     }
1750
1751     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1752         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1753             mi.setEnabled( true );
1754         }
1755         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1756             mi.setEnabled( true );
1757         }
1758         else {
1759             mi.setEnabled( false );
1760         }
1761         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1762     }
1763
1764     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1765         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1766     }
1767
1768     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1769                                                            final JCheckBoxMenuItem scale,
1770                                                            final JCheckBoxMenuItem branch_lengths,
1771                                                            final JRadioButtonMenuItem non_lined_up,
1772                                                            final JRadioButtonMenuItem uniform_clado,
1773                                                            final JRadioButtonMenuItem nonuniform_clado,
1774                                                            final JCheckBoxMenuItem label_direction_cbmi ) {
1775         final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1776         final ControlPanel control = main_panel.getControlPanel();
1777         final Options options = main_panel.getOptions();
1778         scale.setSelected( options.isShowScale() );
1779         branch_lengths.setSelected( options.isShowBranchLengthValues() );
1780         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1781         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1782             scale.setSelected( false );
1783             scale.setEnabled( false );
1784             branch_lengths.setSelected( false );
1785             branch_lengths.setEnabled( false );
1786         }
1787         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1788             scale.setSelected( false );
1789             scale.setEnabled( false );
1790             branch_lengths.setEnabled( true );
1791         }
1792         else {
1793             scale.setEnabled( true );
1794             branch_lengths.setEnabled( true );
1795         }
1796         if ( ( tree_panel != null )
1797                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1798                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1799                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1800             branch_lengths.setSelected( false );
1801             branch_lengths.setEnabled( false );
1802         }
1803         if ( tree_panel != null ) {
1804             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1805                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1806                 non_lined_up.setEnabled( false );
1807                 uniform_clado.setEnabled( false );
1808                 nonuniform_clado.setEnabled( false );
1809             }
1810             else {
1811                 non_lined_up.setEnabled( true );
1812                 uniform_clado.setEnabled( true );
1813                 nonuniform_clado.setEnabled( true );
1814             }
1815         }
1816         else {
1817             if ( ( tree_panel != null )
1818                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1819                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1820                 branch_lengths.setSelected( false );
1821                 branch_lengths.setEnabled( false );
1822             }
1823             if ( ( tree_panel != null )
1824                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1825                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1826                 non_lined_up.setEnabled( false );
1827             }
1828             else {
1829                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1830                 non_lined_up.setEnabled( true );
1831             }
1832         }
1833         label_direction_cbmi.setEnabled( true );
1834         if ( tree_panel != null ) {
1835             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1836                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1837                 label_direction_cbmi.setEnabled( false );
1838             }
1839             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1840                 scale.setSelected( false );
1841                 scale.setEnabled( false );
1842             }
1843         }
1844     }
1845
1846     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1847         for( final TreePanel tree_panel : treepanels ) {
1848             tree_panel.setTextAntialias();
1849         }
1850     }
1851 }