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.File;
  34 import java.io.IOException;
  35 import java.util.LinkedList;
  36 import java.util.List;
  37 import java.util.Locale;
  38 import java.util.NoSuchElementException;
  39 import java.util.Set;
  40
  41 import javax.swing.Box;
  42 import javax.swing.JApplet;
  43 import javax.swing.JCheckBoxMenuItem;
  44 import javax.swing.JFrame;
  45 import javax.swing.JLabel;
  46 import javax.swing.JMenu;
  47 import javax.swing.JMenuBar;
  48 import javax.swing.JMenuItem;
  49 import javax.swing.JOptionPane;
  50 import javax.swing.JPanel;
  51 import javax.swing.JRadioButtonMenuItem;
  52 import javax.swing.JTextField;
  53 import javax.swing.SwingUtilities;
  54
  55 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  56 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  57 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  58 import org.forester.archaeopteryx.tools.InferenceManager;
  59 import org.forester.archaeopteryx.tools.ProcessPool;
  60 import org.forester.archaeopteryx.tools.ProcessRunning;
  61 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  62 import org.forester.phylogeny.Phylogeny;
  63 import org.forester.phylogeny.PhylogenyMethods;
  64 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  65 import org.forester.phylogeny.PhylogenyNode;
  66 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  67 import org.forester.phylogeny.data.Annotation;
  68 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
  69 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
  70 import org.forester.sdi.GSDI;
  71 import org.forester.sdi.GSDIR;
  72 import org.forester.sdi.SDIException;
  73 import org.forester.util.ForesterConstants;
  74 import org.forester.util.ForesterUtil;
  75
  76 public abstract class MainFrame extends JFrame implements ActionListener {
  77
  78     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";
  79     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME
  80     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;
  81     private static final long   serialVersionUID                        = 3655000897845508358L;
  82     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),
  83                                                                                     Font.PLAIN,
  84                                                                                     10 );
  85     static final String         TYPE_MENU_HEADER                        = "Type";
  86     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";
  87     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";
  88     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";
  89     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";
  90     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";
  91     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";
  92     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO
  93     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO
  94     static final String         OPTIONS_HEADER                          = "Options";
  95     static final String         SEARCH_SUBHEADER                        = "Search:";
  96     static final String         DISPLAY_SUBHEADER                       = "Display:";
  97     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";
  98     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";
  99     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";
 100     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Branch Length Values";
 101     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";
 102     static final String         DISPLAY_SCALE_LABEL                     = "Scale";
 103     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";
 104     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";
 105     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";
 106     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";
 107     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";
 108     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";
 109     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";
 110     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "External Node Shapes";
 111     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Internal Node Shapes";
 112     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";
 113     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";
 114     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";
 115     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";
 116     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";
 117     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";
 118     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";
 119     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";
 120     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";
 121     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";
 122     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";
 123     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";
 124     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";
 125     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
 126     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";
 127     JMenuBar                    _jmenubar;
 128     JMenu                       _file_jmenu;
 129     JMenu                       _tools_menu;
 130     JMenu                       _view_jmenu;
 131     JMenu                       _options_jmenu;
 132     JMenu                       _font_size_menu;
 133     JMenu                       _help_jmenu;
 134     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;
 135     // Analysis menu
 136     JMenu                       _analysis_menu;
 137     JMenuItem                   _load_species_tree_item;
 138     JMenuItem                   _gsdi_item;
 139     JMenuItem                   _gsdir_item;
 140     JMenuItem                   _lineage_inference;
 141     // file menu:
 142     JMenuItem                   _open_item;
 143     JMenuItem                   _open_url_item;
 144     JMenuItem                   _save_item;
 145     JMenuItem                   _save_all_item;
 146     JMenuItem                   _close_item;
 147     JMenuItem                   _exit_item;
 148     JMenuItem                   _new_item;
 149     // tools menu:
 150     JMenuItem                   _midpoint_root_item;
 151     JMenuItem                   _taxcolor_item;
 152     JMenuItem                   _confcolor_item;
 153     JMenuItem                   _color_rank_jmi;
 154     JMenuItem                   _collapse_species_specific_subtrees;
 155     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me
 156     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;
 157     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;
 158     JMenuItem                   _obtain_seq_information_jmi;
 159     JMenuItem                   _move_node_names_to_tax_sn_jmi;
 160     JMenuItem                   _move_node_names_to_seq_names_jmi;
 161     JMenuItem                   _extract_tax_code_from_node_names_jmi;
 162     JMenuItem                   _annotate_item;
 163     // font size menu:
 164     JMenuItem                   _super_tiny_fonts_item;
 165     JMenuItem                   _tiny_fonts_item;
 166     JMenuItem                   _small_fonts_item;
 167     JMenuItem                   _medium_fonts_item;
 168     JMenuItem                   _large_fonts_item;
 169     // options menu:
 170     // _  screen and print
 171     JMenuItem                   _choose_font_mi;
 172     JMenuItem                   _switch_colors_mi;
 173     JCheckBoxMenuItem           _label_direction_cbmi;
 174     // _  screen display
 175     JCheckBoxMenuItem           _screen_antialias_cbmi;
 176     JCheckBoxMenuItem           _background_gradient_cbmi;
 177     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 178     JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 179     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 180     JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 181     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;
 182     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me
 183     JCheckBoxMenuItem           _show_overview_cbmi;
 184     JCheckBoxMenuItem           _show_domain_labels;
 185     JCheckBoxMenuItem           _show_annotation_ref_source;
 186     JCheckBoxMenuItem           _abbreviate_scientific_names;
 187     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 188     JMenuItem                   _overview_placment_mi;
 189     JMenuItem                   _choose_minimal_confidence_mi;
 190     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 191     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 192     JMenuItem                   _cycle_node_shape_mi;
 193     JMenuItem                   _cycle_node_fill_mi;
 194     JMenuItem                   _choose_node_size_mi;
 195     JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
 196     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 197     // _  print
 198     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;
 199     JCheckBoxMenuItem           _antialias_print_cbmi;
 200     JCheckBoxMenuItem           _print_black_and_white_cbmi;
 201     JCheckBoxMenuItem           _print_using_actual_size_cbmi;
 202     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;
 203     JMenuItem                   _print_size_mi;
 204     JMenuItem                   _choose_pdf_width_mi;
 205     // _  parsing
 206     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;
 207     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;
 208     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;
 209     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;
 210     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;
 211     JCheckBoxMenuItem           _replace_underscores_cbmi;
 212     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;
 213     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;
 214     // _  search
 215     JCheckBoxMenuItem           _search_case_senstive_cbmi;
 216     JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 217     JCheckBoxMenuItem           _inverse_search_result_cbmi;
 218     // type menu:
 219     JMenu                       _type_menu;
 220     JCheckBoxMenuItem           _rectangular_type_cbmi;
 221     JCheckBoxMenuItem           _triangular_type_cbmi;
 222     JCheckBoxMenuItem           _curved_type_cbmi;
 223     JCheckBoxMenuItem           _convex_type_cbmi;
 224     JCheckBoxMenuItem           _euro_type_cbmi;
 225     JCheckBoxMenuItem           _rounded_type_cbmi;
 226     JCheckBoxMenuItem           _unrooted_type_cbmi;
 227     JCheckBoxMenuItem           _circular_type_cbmi;
 228     // view as text menu:
 229     JMenuItem                   _view_as_NH_item;
 230     JMenuItem                   _view_as_XML_item;
 231     JMenuItem                   _view_as_nexus_item;
 232     JMenuItem                   _display_basic_information_item;
 233     // help menu:
 234     JMenuItem                   _about_item;
 235     JMenuItem                   _help_item;
 236     JMenuItem                   _website_item;
 237     JMenuItem                   _phyloxml_website_item;
 238     JMenuItem                   _phyloxml_ref_item;
 239     JMenuItem                   _aptx_ref_item;
 240     // process menu:
 241     JMenu                       _process_menu;
 242     // Handy pointers to child components:
 243     MainPanel                   _mainpanel;
 244     Container                   _contentpane;
 245     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;
 246     Configuration               _configuration;
 247     JMenuItem                   _remove_branch_color_item;
 248     Options                     _options;
 249     private Phylogeny           _species_tree;
 250     InferenceManager            _inference_manager;
 251     final ProcessPool           _process_pool;
 252     private String              _previous_node_annotation_ref;
 253
 254     MainFrame() {
 255         _process_pool = ProcessPool.createInstance();
 256     }
 257
 258     /**
 259      * Action performed.
 260      */
 261     @Override
 262     public void actionPerformed( final ActionEvent e ) {
 263         final Object o = e.getSource();
 264         boolean is_applet = false;
 265         JApplet applet = null;
 266         if ( getCurrentTreePanel() != null ) {
 267             is_applet = getCurrentTreePanel().isApplet();
 268             if ( is_applet ) {
 269                 applet = getCurrentTreePanel().obtainApplet();
 270             }
 271         }
 272         if ( o == _open_url_item ) {
 273             readPhylogeniesFromURL();
 274         }
 275         else if ( o == _exit_item ) {
 276             close();
 277         }
 278         else if ( o == _gsdi_item ) {
 279             if ( isSubtreeDisplayed() ) {
 280                 return;
 281             }
 282             executeGSDI();
 283         }
 284         else if ( o == _gsdir_item ) {
 285             if ( isSubtreeDisplayed() ) {
 286                 return;
 287             }
 288             executeGSDIR();
 289         }
 290         else if ( o == _taxcolor_item ) {
 291             taxColor();
 292         }
 293         else if ( o == _confcolor_item ) {
 294             confColor();
 295         }
 296         else if ( o == _color_rank_jmi ) {
 297             colorRank();
 298         }
 299         else if ( o == _collapse_species_specific_subtrees ) {
 300             if ( isSubtreeDisplayed() ) {
 301                 return;
 302             }
 303             if ( getCurrentTreePanel() != null ) {
 304                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 305             }
 306         }
 307         else if ( o == _remove_branch_color_item ) {
 308             if ( isSubtreeDisplayed() ) {
 309                 return;
 310             }
 311             removeBranchColors();
 312         }
 313         else if ( o == _midpoint_root_item ) {
 314             if ( isSubtreeDisplayed() ) {
 315                 return;
 316             }
 317             midpointRoot();
 318         }
 319         else if ( o == _annotate_item ) {
 320             annotateSequences();
 321         }
 322         else if ( o == _switch_colors_mi ) {
 323             switchColors();
 324         }
 325         else if ( o == _display_basic_information_item ) {
 326             displayBasicInformation( getCurrentTreePanel().getTreeFile() );
 327         }
 328         else if ( o == _view_as_NH_item ) {
 329             viewAsNH();
 330         }
 331         else if ( o == _view_as_XML_item ) {
 332             viewAsXML();
 333         }
 334         else if ( o == _view_as_nexus_item ) {
 335             viewAsNexus();
 336         }
 337         else if ( o == _super_tiny_fonts_item ) {
 338             if ( getCurrentTreePanel() != null ) {
 339                 getCurrentTreePanel().setSuperTinyFonts();
 340                 getCurrentTreePanel().repaint();
 341             }
 342         }
 343         else if ( o == _tiny_fonts_item ) {
 344             if ( getCurrentTreePanel() != null ) {
 345                 getCurrentTreePanel().setTinyFonts();
 346                 getCurrentTreePanel().repaint();
 347             }
 348         }
 349         else if ( o == _small_fonts_item ) {
 350             if ( getCurrentTreePanel() != null ) {
 351                 getCurrentTreePanel().setSmallFonts();
 352                 getCurrentTreePanel().repaint();
 353             }
 354         }
 355         else if ( o == _medium_fonts_item ) {
 356             if ( getCurrentTreePanel() != null ) {
 357                 getCurrentTreePanel().setMediumFonts();
 358                 getCurrentTreePanel().repaint();
 359             }
 360         }
 361         else if ( o == _large_fonts_item ) {
 362             if ( getCurrentTreePanel() != null ) {
 363                 getCurrentTreePanel().setLargeFonts();
 364                 getCurrentTreePanel().repaint();
 365             }
 366         }
 367         else if ( o == _choose_font_mi ) {
 368             chooseFont();
 369         }
 370         else if ( o == _choose_minimal_confidence_mi ) {
 371             chooseMinimalConfidence();
 372         }
 373         else if ( o == _choose_node_size_mi ) {
 374             chooseNodeSize( getOptions(), this );
 375         }
 376         else if ( o == _overview_placment_mi ) {
 377             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 378         }
 379         else if ( o == _cycle_node_fill_mi ) {
 380             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 381         }
 382         else if ( o == _cycle_node_shape_mi ) {
 383             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 384         }
 385         else if ( o == _screen_antialias_cbmi ) {
 386             updateOptions( getOptions() );
 387             updateScreenTextAntialias( getMainPanel().getTreePanels() );
 388         }
 389         else if ( o == _background_gradient_cbmi ) {
 390             updateOptions( getOptions() );
 391         }
 392         else if ( o == _show_domain_labels ) {
 393             updateOptions( getOptions() );
 394         }
 395         else if ( o == _show_annotation_ref_source ) {
 396             updateOptions( getOptions() );
 397         }
 398         else if ( o == _abbreviate_scientific_names ) {
 399             updateOptions( getOptions() );
 400         }
 401         else if ( o == _color_labels_same_as_parent_branch ) {
 402             updateOptions( getOptions() );
 403         }
 404         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 405             updateOptions( getOptions() );
 406         }
 407         else if ( o == _show_default_node_shapes_external_cbmi ) {
 408             updateOptions( getOptions() );
 409         }
 410         else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
 411             updateOptions( getOptions() );
 412         }
 413         else if ( o == _non_lined_up_cladograms_rbmi ) {
 414             updateOptions( getOptions() );
 415             showWhole();
 416         }
 417         else if ( o == _uniform_cladograms_rbmi ) {
 418             updateOptions( getOptions() );
 419             showWhole();
 420         }
 421         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 422             updateOptions( getOptions() );
 423             showWhole();
 424         }
 425         else if ( o == _search_case_senstive_cbmi ) {
 426             updateOptions( getOptions() );
 427             getMainPanel().getControlPanel().search0();
 428             getMainPanel().getControlPanel().search1();
 429         }
 430         else if ( o == _search_whole_words_only_cbmi ) {
 431             updateOptions( getOptions() );
 432             getMainPanel().getControlPanel().search0();
 433             getMainPanel().getControlPanel().search1();
 434         }
 435         else if ( o == _inverse_search_result_cbmi ) {
 436             updateOptions( getOptions() );
 437             getMainPanel().getControlPanel().search0();
 438             getMainPanel().getControlPanel().search1();
 439         }
 440         else if ( o == _show_scale_cbmi ) {
 441             updateOptions( getOptions() );
 442         }
 443         else if ( o == _show_branch_length_values_cbmi ) {
 444             updateOptions( getOptions() );
 445         }
 446         else if ( o == _color_by_taxonomic_group_cbmi ) {
 447             updateOptions( getOptions() );
 448         }
 449         else if ( o == _show_confidence_stddev_cbmi ) {
 450             updateOptions( getOptions() );
 451         }
 452         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {
 453             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
 454                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );
 455             }
 456             updateOptions( getOptions() );
 457         }
 458         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {
 459             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
 460                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );
 461             }
 462             updateOptions( getOptions() );
 463         }
 464         else if ( o == _label_direction_cbmi ) {
 465             updateOptions( getOptions() );
 466         }
 467         else if ( o == _show_overview_cbmi ) {
 468             updateOptions( getOptions() );
 469             if ( getCurrentTreePanel() != null ) {
 470                 getCurrentTreePanel().updateOvSizes();
 471             }
 472         }
 473         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 474                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
 475                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 476             typeChanged( o );
 477         }
 478         else if ( o == _about_item ) {
 479             about();
 480         }
 481         else if ( o == _help_item ) {
 482             help();
 483         }
 484         else if ( o == _website_item ) {
 485             try {
 486                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
 487             }
 488             catch ( final IOException e1 ) {
 489                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 490             }
 491         }
 492         else if ( o == _phyloxml_website_item ) {
 493             try {
 494                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
 495             }
 496             catch ( final IOException e1 ) {
 497                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 498             }
 499         }
 500         else if ( o == _aptx_ref_item ) {
 501             try {
 502                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
 503             }
 504             catch ( final IOException e1 ) {
 505                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 506             }
 507         }
 508         else if ( o == _phyloxml_ref_item ) {
 509             try {
 510                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
 511             }
 512             catch ( final IOException e1 ) {
 513                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 514             }
 515         }
 516         else {
 517             if ( _load_phylogeny_from_webservice_menu_items != null ) {
 518                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
 519                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
 520                         readPhylogeniesFromWebservice( i );
 521                     }
 522                 }
 523             }
 524         }
 525         _contentpane.repaint();
 526     }
 527
 528     public Configuration getConfiguration() {
 529         return _configuration;
 530     }
 531
 532     /**
 533      * This method returns the current external node data which
 534      * has been selected by the user by clicking the "Return ..."
 535      * menu item. This method is expected to be called from Javascript or
 536      * something like it.
 537      *
 538      * @return current external node data as String
 539      */
 540     public String getCurrentExternalNodesDataBuffer() {
 541         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 542     }
 543
 544     public int getCurrentExternalNodesDataBufferChangeCounter() {
 545         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 546     }
 547
 548     public int getCurrentExternalNodesDataBufferLength() {
 549         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 550     }
 551
 552     public InferenceManager getInferenceManager() {
 553         return _inference_manager;
 554     }
 555
 556     public MainPanel getMainPanel() {
 557         return _mainpanel;
 558     }
 559
 560     public Options getOptions() {
 561         return _options;
 562     }
 563
 564     public ProcessPool getProcessPool() {
 565         return _process_pool;
 566     }
 567
 568     public void showTextFrame( final String s, final String title ) {
 569         checkTextFrames();
 570         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 571     }
 572
 573     public void showWhole() {
 574         _mainpanel.getControlPanel().showWhole();
 575     }
 576
 577     public void updateProcessMenu() {
 578         // In general Swing is not thread safe.
 579         // See "Swing's Threading Policy".
 580         SwingUtilities.invokeLater( new Runnable() {
 581
 582             @Override
 583             public void run() {
 584                 doUpdateProcessMenu();
 585             }
 586         } );
 587     }
 588
 589     void activateSaveAllIfNeeded() {
 590         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
 591             _save_all_item.setEnabled( true );
 592         }
 593         else {
 594             _save_all_item.setEnabled( false );
 595         }
 596     }
 597
 598     void buildFileMenu() {
 599         _file_jmenu = createMenu( "File", getConfiguration() );
 600         _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
 601         _file_jmenu.addSeparator();
 602         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
 603         customizeJMenuItem( _open_url_item );
 604         customizeJMenuItem( _exit_item );
 605         _jmenubar.add( _file_jmenu );
 606     }
 607
 608     void buildFontSizeMenu() {
 609         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
 610         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
 611         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
 612         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
 613         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
 614         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
 615         customizeJMenuItem( _super_tiny_fonts_item );
 616         customizeJMenuItem( _tiny_fonts_item );
 617         customizeJMenuItem( _small_fonts_item );
 618         customizeJMenuItem( _medium_fonts_item );
 619         customizeJMenuItem( _large_fonts_item );
 620         _jmenubar.add( _font_size_menu );
 621     }
 622
 623     void buildHelpMenu() {
 624         _help_jmenu = createMenu( "Help", getConfiguration() );
 625         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
 626         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 627         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 628         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 629         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 630         _help_jmenu.addSeparator();
 631         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 632         customizeJMenuItem( _help_item );
 633         customizeJMenuItem( _website_item );
 634         customizeJMenuItem( _phyloxml_website_item );
 635         customizeJMenuItem( _aptx_ref_item );
 636         customizeJMenuItem( _phyloxml_ref_item );
 637         customizeJMenuItem( _about_item );
 638         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
 639         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
 640         _jmenubar.add( _help_jmenu );
 641     }
 642
 643     void buildTypeMenu() {
 644         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
 645         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 646         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 647         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 648         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 649         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 650         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 651         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 652         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 653         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 654         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 655         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 656         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 657         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 658         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 659         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 660         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 661         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 662         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 663         initializeTypeMenu( getOptions() );
 664         _jmenubar.add( _type_menu );
 665     }
 666
 667     void buildViewMenu() {
 668         _view_jmenu = createMenu( "View", getConfiguration() );
 669         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 670         _view_jmenu.addSeparator();
 671         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
 672         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
 673         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
 674         customizeJMenuItem( _display_basic_information_item );
 675         customizeJMenuItem( _view_as_NH_item );
 676         customizeJMenuItem( _view_as_XML_item );
 677         customizeJMenuItem( _view_as_nexus_item );
 678         _jmenubar.add( _view_jmenu );
 679     }
 680
 681     void checkTextFrames() {
 682         if ( _textframes.size() > 5 ) {
 683             try {
 684                 if ( _textframes.getFirst() != null ) {
 685                     _textframes.getFirst().removeMe();
 686                 }
 687                 else {
 688                     _textframes.removeFirst();
 689                 }
 690             }
 691             catch ( final NoSuchElementException e ) {
 692                 // Ignore.
 693             }
 694         }
 695     }
 696
 697     void close() {
 698         removeAllTextFrames();
 699         if ( _mainpanel != null ) {
 700             _mainpanel.terminate();
 701         }
 702         if ( _contentpane != null ) {
 703             _contentpane.removeAll();
 704         }
 705         setVisible( false );
 706         dispose();
 707     }
 708
 709     void colorRank() {
 710         if ( _mainpanel.getCurrentTreePanel() != null ) {
 711             final String[] ranks = AptxUtil.getAllPossibleRanks();
 712             final String rank = ( String ) JOptionPane
 713                     .showInputDialog( this,
 714                                       "What rank should the colorization be based on",
 715                                       "Rank Selection",
 716                                       JOptionPane.QUESTION_MESSAGE,
 717                                       null,
 718                                       ranks,
 719                                       null );
 720             if ( !ForesterUtil.isEmpty( rank ) ) {
 721                 _mainpanel.getCurrentTreePanel().colorRank( rank );
 722             }
 723         }
 724     }
 725
 726     void confColor() {
 727         if ( _mainpanel.getCurrentTreePanel() != null ) {
 728             _mainpanel.getCurrentTreePanel().confColor();
 729         }
 730     }
 731
 732     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 733         if ( item != null ) {
 734             item.setFont( MainFrame.menu_font );
 735             if ( !getConfiguration().isUseNativeUI() ) {
 736                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 737                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 738             }
 739             item.setSelected( is_selected );
 740             item.addActionListener( this );
 741         }
 742     }
 743
 744     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {
 745         if ( jmi != null ) {
 746             jmi.setFont( MainFrame.menu_font );
 747             if ( !getConfiguration().isUseNativeUI() ) {
 748                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 749                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 750             }
 751             jmi.addActionListener( this );
 752         }
 753         return jmi;
 754     }
 755
 756     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
 757         if ( item != null ) {
 758             item.setFont( MainFrame.menu_font );
 759             if ( !getConfiguration().isUseNativeUI() ) {
 760                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 761                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 762             }
 763             item.setSelected( is_selected );
 764             item.addActionListener( this );
 765         }
 766     }
 767
 768     void displayBasicInformation( final File treefile ) {
 769         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
 770             String title = "Basic Information";
 771             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
 772                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
 773             }
 774             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
 775         }
 776     }
 777
 778     void exceptionOccuredDuringOpenFile( final Exception e ) {
 779         try {
 780             _mainpanel.getCurrentTreePanel().setArrowCursor();
 781         }
 782         catch ( final Exception ex ) {
 783             // Do nothing.
 784         }
 785         JOptionPane.showMessageDialog( this,
 786                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
 787                                        "Error during File|Open",
 788                                        JOptionPane.ERROR_MESSAGE );
 789     }
 790
 791     void exceptionOccuredDuringSaveAs( final Exception e ) {
 792         try {
 793             _mainpanel.getCurrentTreePanel().setArrowCursor();
 794         }
 795         catch ( final Exception ex ) {
 796             // Do nothing.
 797         }
 798         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
 799     }
 800
 801     void executeGSDI() {
 802         if ( !isOKforSDI( false, true ) ) {
 803             return;
 804         }
 805         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 806             JOptionPane.showMessageDialog( this,
 807                                            "Gene tree is not rooted.",
 808                                            "Cannot execute GSDI",
 809                                            JOptionPane.ERROR_MESSAGE );
 810             return;
 811         }
 812         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 813         gene_tree.setAllNodesToNotCollapse();
 814         gene_tree.recalculateNumberOfExternalDescendants( false );
 815         GSDI gsdi = null;
 816         final Phylogeny species_tree = getSpeciesTree().copy();
 817         try {
 818             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 819         }
 820         catch ( final SDIException e ) {
 821             JOptionPane.showMessageDialog( this,
 822                                            e.getLocalizedMessage(),
 823                                            "Error during GSDI",
 824                                            JOptionPane.ERROR_MESSAGE );
 825             return;
 826         }
 827         catch ( final Exception e ) {
 828             AptxUtil.unexpectedException( e );
 829             return;
 830         }
 831         gene_tree.setRerootable( false );
 832         gene_tree.clearHashIdToNodeMap();
 833         gene_tree.recalculateNumberOfExternalDescendants( true );
 834         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 835         getMainPanel().getControlPanel().setShowEvents( true );
 836         showWhole();
 837         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 838         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 839         showWhole();
 840         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 841         showWhole();
 842         _mainpanel.getCurrentTreePanel().setEdited( true );
 843         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 844         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 845             JOptionPane.showMessageDialog( this,
 846                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 847                                                    + "Potential duplications: "
 848                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 849                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 850                                                    + "Stripped gene tree nodes: "
 851                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 852                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 853                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 854                                            "GSDI successfully completed",
 855                                            JOptionPane.WARNING_MESSAGE );
 856         }
 857         else {
 858             JOptionPane.showMessageDialog( this,
 859                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
 860                                                    + "Potential duplications: "
 861                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
 862                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
 863                                                    + "Stripped gene tree nodes: "
 864                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
 865                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
 866                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 867                                            "GSDI successfully completed",
 868                                            JOptionPane.INFORMATION_MESSAGE );
 869         }
 870     }
 871
 872     void executeGSDIR() {
 873         if ( !isOKforSDI( false, false ) ) {
 874             return;
 875         }
 876         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
 877         if ( ( p > 0 )
 878                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
 879             JOptionPane.showMessageDialog( this,
 880                                            "Gene tree is not completely binary",
 881                                            "Cannot execute GSDI",
 882                                            JOptionPane.ERROR_MESSAGE );
 883             return;
 884         }
 885         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 886         gene_tree.setAllNodesToNotCollapse();
 887         gene_tree.recalculateNumberOfExternalDescendants( false );
 888         GSDIR gsdir = null;
 889         final Phylogeny species_tree = getSpeciesTree().copy();
 890         try {
 891             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
 892         }
 893         catch ( final SDIException e ) {
 894             JOptionPane.showMessageDialog( this,
 895                                            e.getLocalizedMessage(),
 896                                            "Error during GSDIR",
 897                                            JOptionPane.ERROR_MESSAGE );
 898             return;
 899         }
 900         catch ( final Exception e ) {
 901             AptxUtil.unexpectedException( e );
 902             return;
 903         }
 904         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
 905         result_gene_tree.setRerootable( false );
 906         result_gene_tree.clearHashIdToNodeMap();
 907         result_gene_tree.recalculateNumberOfExternalDescendants( true );
 908         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
 909         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
 910         getMainPanel().getControlPanel().setShowEvents( true );
 911         showWhole();
 912         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 913         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 914         showWhole();
 915         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 916         showWhole();
 917         _mainpanel.getCurrentTreePanel().setEdited( true );
 918         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 919         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 920             JOptionPane.showMessageDialog( this,
 921                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
 922                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
 923                                                    + "Stripped gene tree nodes: "
 924                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
 925                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
 926                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 927                                            "GSDIR successfully completed",
 928                                            JOptionPane.WARNING_MESSAGE );
 929         }
 930         else {
 931             JOptionPane.showMessageDialog( this,
 932                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
 933                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
 934                                                    + "Stripped gene tree nodes: "
 935                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
 936                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
 937                                                    + "Number of polytomies in species tree used: " + poly + "\n",
 938                                            "GSDIR successfully completed",
 939                                            JOptionPane.INFORMATION_MESSAGE );
 940         }
 941     }
 942
 943     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
 944         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
 945             JOptionPane.showMessageDialog( this,
 946                                            "Gene tree and species tree have no species in common.",
 947                                            "Error during SDI",
 948                                            JOptionPane.ERROR_MESSAGE );
 949             return false;
 950         }
 951         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
 952             JOptionPane.showMessageDialog( this,
 953                                            "Gene tree and species tree have only one species in common.",
 954                                            "Error during SDI",
 955                                            JOptionPane.ERROR_MESSAGE );
 956             return false;
 957         }
 958         else {
 959             return true;
 960         }
 961     }
 962
 963     TreePanel getCurrentTreePanel() {
 964         return getMainPanel().getCurrentTreePanel();
 965     }
 966
 967     JMenu getHelpMenu() {
 968         return _help_jmenu;
 969     }
 970
 971     JCheckBoxMenuItem getlabelDirectionCbmi() {
 972         return _label_direction_cbmi;
 973     }
 974
 975     JMenuBar getMenuBarOfMainFrame() {
 976         return _jmenubar;
 977     }
 978
 979     final Phylogeny getSpeciesTree() {
 980         return _species_tree;
 981     }
 982
 983     void help() {
 984         final StringBuilder sb = new StringBuilder();
 985         sb.append( "Display options\n" );
 986         sb.append( "-------------------\n" );
 987         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
 988         sb.append( "Clickable tree nodes\n" );
 989         sb.append( "--------------------\n" );
 990         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
 991         sb.append( "or by right clicking:\n" );
 992         sb.append( "o  Display Node Data -- display information for a node\n" );
 993         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
 994         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );
 995         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
 996         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );
 997         sb.append( "o  Colorize Subtree -- color a subtree\n" );
 998         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );
 999         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1000         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );
1001         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1002         sb.append( "Zooming\n" );
1003         sb.append( "---------\n" );
1004         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1005         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1006         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1007         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1008         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1009         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1010         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1011         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1012         sb.append( "Quick tree manipulation:\n" );
1013         sb.append( "------------------------\n" );
1014         sb.append( "Order Subtrees -- order the tree by branch length\n" );
1015         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1016         sb.append( "Memory problems (Java heap space error)\n" );
1017         sb.append( "---------------------------------------\n" );
1018         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1019         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1020         sb.append( "the '-Xmx' Java command line option. For example:\n" );
1021         sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1022         // + "General remarks\n"
1023         // + "---------------\n"
1024         // +
1025         // "o  The application version permits copying to the clipboard \n"
1026         // +
1027         // "    in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1028         // +
1029         // "o  Changes made to a subtree affect this subtree and its subtrees,\n"
1030         // + "    but not any of its parent tree(s).\n"
1031         // +
1032         // "o  Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1033         // +
1034         // "    are likely to be bootstrap values instead of branch length values.\n\n"
1035         // +
1036         // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1037         // +
1038         // "o  Each external node of the gene tree (in display) needs to be associated with\n"
1039         // +
1040         // "    a species: either directly through the \"Species\" field, or the species\n"
1041         // +
1042         // "    is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1043         // +
1044         // "    (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1045         // +
1046         // "o  A species tree for each species of the gene tree needs to be loaded with\n"
1047         // +
1048         // "   \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1049         // +
1050         // "o  !External nodes of the gene tree associated with species not present in\n"
1051         // +
1052         // "    the species tree are REMOVED prior to SDI execution!\n"
1053         // +
1054         // "o  Both the gene tree and the species tree must be completely binary.\n"
1055         // +
1056         // "o  Duplications and speciations are a function of the position of the root.\n"
1057         // +
1058         // "    Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1059         // + "    incorrect and need to be inferred again\n"
1060         // +
1061         // "    with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1062         sb.append( "phyloXML\n" );
1063         sb.append( "-------------------\n" );
1064         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1065         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1066         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1067         sb.append( "\n" );
1068         sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
1069         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1070         TextFrame.instantiate( sb.toString(), "Help", _textframes );
1071     }
1072
1073     void initializeTypeMenu( final Options options ) {
1074         setTypeMenuToAllUnselected();
1075         switch ( options.getPhylogenyGraphicsType() ) {
1076             case CONVEX:
1077                 _convex_type_cbmi.setSelected( true );
1078                 break;
1079             case CURVED:
1080                 _curved_type_cbmi.setSelected( true );
1081                 break;
1082             case EURO_STYLE:
1083                 _euro_type_cbmi.setSelected( true );
1084                 break;
1085             case ROUNDED:
1086                 _rounded_type_cbmi.setSelected( true );
1087                 break;
1088             case TRIANGULAR:
1089                 _triangular_type_cbmi.setSelected( true );
1090                 break;
1091             case UNROOTED:
1092                 _unrooted_type_cbmi.setSelected( true );
1093                 break;
1094             case CIRCULAR:
1095                 _circular_type_cbmi.setSelected( true );
1096                 break;
1097             default:
1098                 _rectangular_type_cbmi.setSelected( true );
1099                 break;
1100         }
1101     }
1102
1103     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1104         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1105             return false;
1106         }
1107         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
1108             JOptionPane.showMessageDialog( this,
1109                                            "No species tree loaded",
1110                                            "Cannot execute GSDI",
1111                                            JOptionPane.ERROR_MESSAGE );
1112             return false;
1113         }
1114         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
1115             JOptionPane.showMessageDialog( this,
1116                                            "Species tree is not completely binary",
1117                                            "Cannot execute GSDI",
1118                                            JOptionPane.ERROR_MESSAGE );
1119             return false;
1120         }
1121         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1122             JOptionPane.showMessageDialog( this,
1123                                            "Gene tree is not completely binary",
1124                                            "Cannot execute GSDI",
1125                                            JOptionPane.ERROR_MESSAGE );
1126             return false;
1127         }
1128         else {
1129             return true;
1130         }
1131     }
1132
1133     boolean isSubtreeDisplayed() {
1134         if ( getCurrentTreePanel() != null ) {
1135             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1136                 JOptionPane
1137                         .showMessageDialog( this,
1138                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1139                                             "Operation can not be exectuted on a sub-tree",
1140                                             JOptionPane.WARNING_MESSAGE );
1141                 return true;
1142             }
1143         }
1144         return false;
1145     }
1146
1147     void midpointRoot() {
1148         if ( _mainpanel.getCurrentTreePanel() != null ) {
1149             _mainpanel.getCurrentTreePanel().midpointRoot();
1150         }
1151     }
1152
1153     abstract void readPhylogeniesFromURL();
1154
1155     void readPhylogeniesFromWebservice( final int i ) {
1156         final UrlTreeReader reader = new UrlTreeReader( this, i );
1157         new Thread( reader ).start();
1158     }
1159
1160     void removeAllTextFrames() {
1161         for( final TextFrame tf : _textframes ) {
1162             if ( tf != null ) {
1163                 tf.close();
1164             }
1165         }
1166         _textframes.clear();
1167     }
1168
1169     void setConfiguration( final Configuration configuration ) {
1170         _configuration = configuration;
1171     }
1172
1173     void setInferenceManager( final InferenceManager i ) {
1174         _inference_manager = i;
1175     }
1176
1177     void setOptions( final Options options ) {
1178         _options = options;
1179     }
1180
1181     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1182         setTypeMenuToAllUnselected();
1183         switch ( type ) {
1184             case CIRCULAR:
1185                 _circular_type_cbmi.setSelected( true );
1186                 break;
1187             case CONVEX:
1188                 _convex_type_cbmi.setSelected( true );
1189                 break;
1190             case CURVED:
1191                 _curved_type_cbmi.setSelected( true );
1192                 break;
1193             case EURO_STYLE:
1194                 _euro_type_cbmi.setSelected( true );
1195                 break;
1196             case ROUNDED:
1197                 _rounded_type_cbmi.setSelected( true );
1198                 break;
1199             case RECTANGULAR:
1200                 _rectangular_type_cbmi.setSelected( true );
1201                 break;
1202             case TRIANGULAR:
1203                 _triangular_type_cbmi.setSelected( true );
1204                 break;
1205             case UNROOTED:
1206                 _unrooted_type_cbmi.setSelected( true );
1207                 break;
1208             default:
1209                 throw new IllegalArgumentException( "unknown type: " + type );
1210         }
1211     }
1212
1213     final void setSpeciesTree( final Phylogeny species_tree ) {
1214         _species_tree = species_tree;
1215     }
1216
1217     void setTypeMenuToAllUnselected() {
1218         _convex_type_cbmi.setSelected( false );
1219         _curved_type_cbmi.setSelected( false );
1220         _euro_type_cbmi.setSelected( false );
1221         _rounded_type_cbmi.setSelected( false );
1222         _triangular_type_cbmi.setSelected( false );
1223         _rectangular_type_cbmi.setSelected( false );
1224         _unrooted_type_cbmi.setSelected( false );
1225         _circular_type_cbmi.setSelected( false );
1226     }
1227
1228     void switchColors() {
1229         final TreeColorSet colorset = _mainpanel.getTreeColorSet();
1230         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1231         csc.setVisible( true );
1232     }
1233
1234     void taxColor() {
1235         if ( _mainpanel.getCurrentTreePanel() != null ) {
1236             _mainpanel.getCurrentTreePanel().taxColor();
1237         }
1238     }
1239
1240     void typeChanged( final Object o ) {
1241         updateTypeCheckboxes( getOptions(), o );
1242         updateOptions( getOptions() );
1243         if ( getCurrentTreePanel() != null ) {
1244             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1245             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1246             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1247                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1248                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1249                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1250                 getCurrentTreePanel().getControlPanel().showWhole();
1251             }
1252             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1253                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1254             }
1255             else {
1256                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1257             }
1258             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1259             updateScreenTextAntialias( getMainPanel().getTreePanels() );
1260             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
1261                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1262                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
1263                 }
1264                 else {
1265                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
1266                 }
1267             }
1268         }
1269     }
1270
1271     void updateOptions( final Options options ) {
1272         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1273         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1274                 && _background_gradient_cbmi.isSelected() );
1275         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1276         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1277                 && _show_annotation_ref_source.isSelected() );
1278         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1279                 && _abbreviate_scientific_names.isSelected() );
1280         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1281                 && _color_labels_same_as_parent_branch.isSelected() );
1282         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1283                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1284         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1285                 && _show_default_node_shapes_external_cbmi.isSelected() );
1286         options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
1287                 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
1288         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1289             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1290         }
1291         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1292             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1293         }
1294         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1295             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1296         }
1297         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1298                 && _search_case_senstive_cbmi.isSelected() );
1299         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1300             options.setShowScale( _show_scale_cbmi.isSelected() );
1301         }
1302         if ( _label_direction_cbmi != null ) {
1303             if ( _label_direction_cbmi.isSelected() ) {
1304                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1305             }
1306             else {
1307                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1308             }
1309         }
1310         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1311         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1312                 && _show_confidence_stddev_cbmi.isSelected() );
1313         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1314             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1315         }
1316         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1317             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1318         }
1319         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
1320                 && ( _print_using_actual_size_cbmi.isSelected() ) );
1321         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
1322                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
1323         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
1324         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
1325                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {
1326             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1327         }
1328         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )
1329                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {
1330             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1331         }
1332         else {
1333             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1334         }
1335         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
1336                 && _print_black_and_white_cbmi.isSelected() );
1337         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
1338                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
1339         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
1340             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1341         }
1342         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
1343             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1344         }
1345         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
1346             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
1347         }
1348         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
1349             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
1350         }
1351         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
1352                 && _replace_underscores_cbmi.isSelected() );
1353         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1354                 && _search_whole_words_only_cbmi.isSelected() );
1355         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1356                 && _inverse_search_result_cbmi.isSelected() );
1357         if ( _graphics_export_visible_only_cbmi != null ) {
1358             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
1359             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
1360                 _graphics_export_using_actual_size_cbmi.setSelected( true );
1361                 _graphics_export_using_actual_size_cbmi.setEnabled( false );
1362             }
1363             else {
1364                 _graphics_export_using_actual_size_cbmi.setEnabled( true );
1365             }
1366         }
1367         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1368             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1369         }
1370         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1371             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1372         }
1373         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1374             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1375         }
1376         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1377             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1378         }
1379         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1380             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1381         }
1382         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1383             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1384         }
1385         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1386             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1387         }
1388         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1389             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1390         }
1391     }
1392
1393     void updateTypeCheckboxes( final Options options, final Object o ) {
1394         setTypeMenuToAllUnselected();
1395         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1396     }
1397
1398     void viewAsNexus() {
1399         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1400             String title = "Nexus";
1401             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1402                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1403             }
1404             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
1405                            title );
1406         }
1407     }
1408
1409     void viewAsNH() {
1410         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1411             String title = "New Hampshire";
1412             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1413                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1414             }
1415             showTextFrame( _mainpanel.getCurrentPhylogeny()
1416                                    .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
1417                            title );
1418         }
1419     }
1420
1421     void viewAsXML() {
1422         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
1423             String title = "phyloXML";
1424             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
1425                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1426             }
1427             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
1428         }
1429     }
1430
1431     private void annotateSequences() {
1432         if ( getCurrentTreePanel() != null ) {
1433             final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();
1434             if ( ( nodes == null ) || nodes.isEmpty() ) {
1435                 JOptionPane
1436                         .showMessageDialog( this,
1437                                             "Need to select nodes, either via direct selection or via the \"Search\" function",
1438                                             "No nodes selected for annotation",
1439                                             JOptionPane.ERROR_MESSAGE );
1440                 return;
1441             }
1442             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
1443             if ( ( phy != null ) && !phy.isEmpty() ) {
1444                 final JTextField ref_field = new JTextField( 10 );
1445                 final JTextField desc_filed = new JTextField( 20 );
1446                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
1447                         : getPreviousNodeAnnotationReference() );
1448                 final JPanel my_panel = new JPanel();
1449                 my_panel.add( new JLabel( "Reference " ) );
1450                 my_panel.add( ref_field );
1451                 my_panel.add( Box.createHorizontalStrut( 15 ) );
1452                 my_panel.add( new JLabel( "Description " ) );
1453                 my_panel.add( desc_filed );
1454                 final int result = JOptionPane.showConfirmDialog( null,
1455                                                                   my_panel,
1456                                                                   "Enter the sequence annotation(s) for the "
1457                                                                           + nodes.size() + " selected nodes",
1458                                                                   JOptionPane.OK_CANCEL_OPTION );
1459                 if ( result == JOptionPane.OK_OPTION ) {
1460                     String ref = ref_field.getText();
1461                     String desc = desc_filed.getText();
1462                     if ( !ForesterUtil.isEmpty( ref ) ) {
1463                         ref = ref.trim();
1464                         ref = ref.replaceAll( "\\s+", " " );
1465                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 )
1466                                 || ( ref.length() < 3 ) ) {
1467                             JOptionPane.showMessageDialog( this,
1468                                                            "Reference needs to be in the form of \"GO:1234567\"",
1469                                                            "Illegal Format for Annotation Reference",
1470                                                            JOptionPane.ERROR_MESSAGE );
1471                             return;
1472                         }
1473                     }
1474                     if ( ref != null ) {
1475                         setPreviousNodeAnnotationReference( ref );
1476                     }
1477                     if ( desc != null ) {
1478                         desc = desc.trim();
1479                         desc = desc.replaceAll( "\\s+", " " );
1480                     }
1481                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
1482                         for( final Long id : nodes ) {
1483                             final PhylogenyNode n = phy.getNode( id );
1484                             ForesterUtil.ensurePresenceOfSequence( n );
1485                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
1486                                     : new Annotation( ref );
1487                             if ( !ForesterUtil.isEmpty( desc ) ) {
1488                                 ann.setDesc( desc );
1489                             }
1490                             n.getNodeData().getSequence().addAnnotation( ann );
1491                         }
1492                     }
1493                     getMainPanel().getControlPanel().showAnnotations();
1494                 }
1495             }
1496         }
1497     }
1498
1499     private void chooseFont() {
1500         final FontChooser fc = new FontChooser();
1501         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1502         fc.showDialog( this, "Select the Base Font" );
1503         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1504     }
1505
1506     private void chooseMinimalConfidence() {
1507         final String s = ( String ) JOptionPane
1508                 .showInputDialog( this,
1509                                   "Please enter the minimum for confidence values to be displayed.\n"
1510                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
1511                                   "Minimal Confidence Value",
1512                                   JOptionPane.QUESTION_MESSAGE,
1513                                   null,
1514                                   null,
1515                                   getOptions().getMinConfidenceValue() );
1516         if ( !ForesterUtil.isEmpty( s ) ) {
1517             boolean success = true;
1518             double m = 0.0;
1519             final String m_str = s.trim();
1520             if ( !ForesterUtil.isEmpty( m_str ) ) {
1521                 try {
1522                     m = Double.parseDouble( m_str );
1523                 }
1524                 catch ( final Exception ex ) {
1525                     success = false;
1526                 }
1527             }
1528             else {
1529                 success = false;
1530             }
1531             if ( success && ( m >= 0.0 ) ) {
1532                 getOptions().setMinConfidenceValue( m );
1533             }
1534         }
1535     }
1536
1537     private void doUpdateProcessMenu() {
1538         if ( _process_pool.size() > 0 ) {
1539             if ( _process_menu == null ) {
1540                 _process_menu = createMenu( "", getConfiguration() );
1541                 _process_menu.setForeground( Color.RED );
1542             }
1543             _process_menu.removeAll();
1544             final String text = "processes running: " + _process_pool.size();
1545             _process_menu.setText( text );
1546             _jmenubar.add( _process_menu );
1547             for( int i = 0; i < _process_pool.size(); ++i ) {
1548                 final ProcessRunning p = _process_pool.getProcessByIndex( i );
1549                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
1550             }
1551         }
1552         else {
1553             if ( _process_menu != null ) {
1554                 _process_menu.removeAll();
1555                 _jmenubar.remove( _process_menu );
1556             }
1557         }
1558         _jmenubar.validate();
1559         _jmenubar.repaint();
1560         repaint();
1561     }
1562
1563     private String getPreviousNodeAnnotationReference() {
1564         return _previous_node_annotation_ref;
1565     }
1566
1567     private void removeBranchColors() {
1568         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1569             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1570         }
1571     }
1572
1573     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
1574         _previous_node_annotation_ref = previous_node_annotation_ref;
1575     }
1576
1577     /**
1578      * Display the about box.
1579      */
1580     static void about() {
1581         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1582         about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
1583         about.append( "All Rights Reserved\n" );
1584         about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1585         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1586         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
1587         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1588         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1589         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1590             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1591         }
1592         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1593                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1594             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1595                     + ForesterUtil.OS_VERSION + "]\n" );
1596         }
1597         final Runtime rt = java.lang.Runtime.getRuntime();
1598         final long free_memory = rt.freeMemory() / 1000000;
1599         final long total_memory = rt.totalMemory() / 1000000;
1600         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1601         about.append( "[locale: " + Locale.getDefault() + "]\n" );
1602         about.append( "References:\n" );
1603         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1604         about.append( "For more information & download:\n" );
1605         about.append( Constants.APTX_WEB_SITE + "\n" );
1606         about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1607         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1608     }
1609
1610     static void chooseNodeSize( final Options options, final Component parent ) {
1611         final String s = ( String ) JOptionPane.showInputDialog( parent,
1612                                                                  "Please enter the default size for node shapes.\n"
1613                                                                          + "[current value: "
1614                                                                          + options.getDefaultNodeShapeSize() + "]\n",
1615                                                                  "Node Shape Size",
1616                                                                  JOptionPane.QUESTION_MESSAGE,
1617                                                                  null,
1618                                                                  null,
1619                                                                  options.getDefaultNodeShapeSize() );
1620         if ( !ForesterUtil.isEmpty( s ) ) {
1621             boolean success = true;
1622             double m = 0.0;
1623             final String m_str = s.trim();
1624             if ( !ForesterUtil.isEmpty( m_str ) ) {
1625                 try {
1626                     m = Double.parseDouble( m_str );
1627                 }
1628                 catch ( final Exception ex ) {
1629                     success = false;
1630                 }
1631             }
1632             else {
1633                 success = false;
1634             }
1635             if ( success && ( m >= 0.0 ) ) {
1636                 final short size = ForesterUtil.roundToShort( m );
1637                 if ( size >= 0.0 ) {
1638                     options.setDefaultNodeShapeSize( size );
1639                 }
1640             }
1641         }
1642     }
1643
1644     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1645         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1646     }
1647
1648     static JMenu createMenu( final String title, final Configuration conf ) {
1649         final JMenu jmenu = new JMenu( title );
1650         if ( !conf.isUseNativeUI() ) {
1651             jmenu.setFont( MainFrame.menu_font );
1652             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1653             jmenu.setForeground( conf.getGuiMenuTextColor() );
1654         }
1655         return jmenu;
1656     }
1657
1658     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1659         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1660         if ( !configuration.isUseNativeUI() ) {
1661             label.setBackground( configuration.getGuiMenuBackgroundColor() );
1662             label.setForeground( configuration.getGuiMenuTextColor() );
1663             label.setOpaque( true );
1664         }
1665         label.setSelected( false );
1666         label.setEnabled( false );
1667         return label;
1668     }
1669
1670     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1671         switch ( op.getDefaultNodeFill() ) {
1672             case GRADIENT:
1673                 op.setDefaultNodeFill( NodeFill.SOLID );
1674                 break;
1675             case NONE:
1676                 op.setDefaultNodeFill( NodeFill.GRADIENT );
1677                 break;
1678             case SOLID:
1679                 op.setDefaultNodeFill( NodeFill.NONE );
1680                 break;
1681             default:
1682                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1683         }
1684     }
1685
1686     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1687         switch ( op.getDefaultNodeShape() ) {
1688             case CIRCLE:
1689                 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1690                 break;
1691             case RECTANGLE:
1692                 op.setDefaultNodeShape( NodeShape.CIRCLE );
1693                 break;
1694             default:
1695                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1696         }
1697     }
1698
1699     static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1700         switch ( op.getOvPlacement() ) {
1701             case LOWER_LEFT:
1702                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1703                 break;
1704             case LOWER_RIGHT:
1705                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1706                 break;
1707             case UPPER_LEFT:
1708                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1709                 break;
1710             case UPPER_RIGHT:
1711                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1712                 break;
1713             default:
1714                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1715         }
1716         if ( tree_panel != null ) {
1717             tree_panel.updateOvSettings();
1718         }
1719     }
1720
1721     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1722         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1723             mi.setText( "Cycle Node Shape Fill Type... (current: "
1724                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1725         }
1726         else {
1727             mi.setText( "Cycle Node Shape Fill Type..." );
1728         }
1729     }
1730
1731     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1732         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1733             mi.setText( "Cycle Node Shape Fill Type... (current: "
1734                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1735         }
1736         else {
1737             mi.setText( "Cycle Node Shape Fill Type..." );
1738         }
1739     }
1740
1741     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1742         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1743             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1744         }
1745         else {
1746             mi.setText( "Cycle Overview Placement..." );
1747         }
1748     }
1749
1750     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1751         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1752             mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1753         }
1754         else {
1755             mi.setText( "Select Colors..." );
1756         }
1757     }
1758
1759     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1760         mi.setText( "Select Font... (current: " + font_desc + ")" );
1761     }
1762
1763     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1764         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1765             mi.setEnabled( true );
1766         }
1767         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1768             mi.setEnabled( true );
1769         }
1770         else {
1771             mi.setEnabled( false );
1772         }
1773         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1774     }
1775
1776     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1777         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1778     }
1779
1780     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1781                                                            final JCheckBoxMenuItem scale,
1782                                                            final JCheckBoxMenuItem branch_lengths,
1783                                                            final JRadioButtonMenuItem non_lined_up,
1784                                                            final JRadioButtonMenuItem uniform_clado,
1785                                                            final JRadioButtonMenuItem nonuniform_clado,
1786                                                            final JCheckBoxMenuItem label_direction_cbmi ) {
1787         final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1788         final ControlPanel control = main_panel.getControlPanel();
1789         final Options options = main_panel.getOptions();
1790         scale.setSelected( options.isShowScale() );
1791         branch_lengths.setSelected( options.isShowBranchLengthValues() );
1792         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1793         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1794             scale.setSelected( false );
1795             scale.setEnabled( false );
1796             branch_lengths.setSelected( false );
1797             branch_lengths.setEnabled( false );
1798         }
1799         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1800             scale.setSelected( false );
1801             scale.setEnabled( false );
1802             branch_lengths.setEnabled( true );
1803         }
1804         else {
1805             scale.setEnabled( true );
1806             branch_lengths.setEnabled( true );
1807         }
1808         if ( ( tree_panel != null )
1809                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1810                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1811                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1812             branch_lengths.setSelected( false );
1813             branch_lengths.setEnabled( false );
1814         }
1815         if ( tree_panel != null ) {
1816             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1817                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1818                 non_lined_up.setEnabled( false );
1819                 uniform_clado.setEnabled( false );
1820                 nonuniform_clado.setEnabled( false );
1821             }
1822             else {
1823                 non_lined_up.setEnabled( true );
1824                 uniform_clado.setEnabled( true );
1825                 nonuniform_clado.setEnabled( true );
1826             }
1827         }
1828         else {
1829             if ( ( tree_panel != null )
1830                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1831                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1832                 branch_lengths.setSelected( false );
1833                 branch_lengths.setEnabled( false );
1834             }
1835             if ( ( tree_panel != null )
1836                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1837                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1838                 non_lined_up.setEnabled( false );
1839             }
1840             else {
1841                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1842                 non_lined_up.setEnabled( true );
1843             }
1844         }
1845         label_direction_cbmi.setEnabled( true );
1846         if ( tree_panel != null ) {
1847             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1848                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1849                 label_direction_cbmi.setEnabled( false );
1850             }
1851             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1852                 scale.setSelected( false );
1853                 scale.setEnabled( false );
1854             }
1855         }
1856     }
1857
1858     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1859         for( final TreePanel tree_panel : treepanels ) {
1860             tree_panel.setTextAntialias();
1861         }
1862     }
1863 }