forester/java/src/org/forester/archaeopteryx/MainFrame.java

   1 // $Id:\r
   2 // FORESTER -- software libraries and applications\r
   3 // for evolutionary biology research and applications.\r
   4 //\r
   5 // Copyright (C) 2008-2010 Christian M. Zmasek\r
   6 // All rights reserved\r
   7 //\r
   8 // This library is free software; you can redistribute it and/or\r
   9 // modify it under the terms of the GNU Lesser General Public\r
  10 // License as published by the Free Software Foundation; either\r
  11 // version 2.1 of the License, or (at your option) any later version.\r
  12 //\r
  13 // This library is distributed in the hope that it will be useful,\r
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
  16 // Lesser General Public License for more details.\r
  17 //\r
  18 // You should have received a copy of the GNU Lesser General Public\r
  19 // License along with this library; if not, write to the Free Software\r
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
  21 //\r
  22 // Contact: phylosoft @ gmail . com\r
  23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
  24 \r
  25 package org.forester.archaeopteryx;\r
  26 \r
  27 import java.awt.Color;\r
  28 import java.awt.Component;\r
  29 import java.awt.Container;\r
  30 import java.awt.Font;\r
  31 import java.awt.event.ActionEvent;\r
  32 import java.awt.event.ActionListener;\r
  33 import java.io.File;\r
  34 import java.io.IOException;\r
  35 import java.util.ArrayList;\r
  36 import java.util.LinkedList;\r
  37 import java.util.List;\r
  38 import java.util.Locale;\r
  39 import java.util.NoSuchElementException;\r
  40 \r
  41 import javax.swing.Box;\r
  42 import javax.swing.JApplet;\r
  43 import javax.swing.JCheckBoxMenuItem;\r
  44 import javax.swing.JFrame;\r
  45 import javax.swing.JLabel;\r
  46 import javax.swing.JMenu;\r
  47 import javax.swing.JMenuBar;\r
  48 import javax.swing.JMenuItem;\r
  49 import javax.swing.JOptionPane;\r
  50 import javax.swing.JPanel;\r
  51 import javax.swing.JRadioButtonMenuItem;\r
  52 import javax.swing.JTextField;\r
  53 import javax.swing.SwingUtilities;\r
  54 \r
  55 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
  56 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
  57 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
  58 import org.forester.archaeopteryx.tools.InferenceManager;\r
  59 import org.forester.archaeopteryx.tools.ProcessPool;\r
  60 import org.forester.archaeopteryx.tools.ProcessRunning;\r
  61 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
  62 import org.forester.phylogeny.Phylogeny;\r
  63 import org.forester.phylogeny.PhylogenyMethods;\r
  64 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
  65 import org.forester.phylogeny.PhylogenyNode;\r
  66 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
  67 import org.forester.phylogeny.data.Annotation;\r
  68 import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
  69 import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
  70 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
  71 import org.forester.sdi.GSDI;\r
  72 import org.forester.sdi.GSDIR;\r
  73 import org.forester.sdi.SDIException;\r
  74 import org.forester.util.ForesterConstants;\r
  75 import org.forester.util.ForesterUtil;\r
  76 \r
  77 public abstract class MainFrame extends JFrame implements ActionListener {\r
  78 \r
  79     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
  80     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME\r
  81     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
  82     private static final long   serialVersionUID                        = 3655000897845508358L;\r
  83     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
  84                                                                                     Font.PLAIN,\r
  85                                                                                     10 );\r
  86     static final String         TYPE_MENU_HEADER                        = "Type";\r
  87     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
  88     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
  89     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
  90     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
  91     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
  92     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
  93     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO\r
  94     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO\r
  95     static final String         OPTIONS_HEADER                          = "Options";\r
  96     static final String         SEARCH_SUBHEADER                        = "Search:";\r
  97     static final String         DISPLAY_SUBHEADER                       = "Display:";\r
  98     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
  99     static final String         SEARCH_REGEX_LABEL                       = "Search with Regular Expressions";\r
 100     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
 101     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
 102     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
 103     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
 104     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
 105     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
 106     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
 107     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
 108     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 109     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 110     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 111     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Shapes for External Nodes";\r
 112     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Shapes for Internal Nodes";\r
 113     static final String         DISPLAY_NODE_BOXES_LABEL_MARKED         = "Shapes for Nodes with Visual Data";\r
 114     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 115     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 116     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 117     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 118     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 119     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";\r
 120     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 121     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 122     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 123     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 124     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 125     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 126     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 127     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 128     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 129     static final String         RIGHT_LINE_UP_DOMAINS                   = "Right-align Domain Architectures";\r
 130     static final String         LINE_UP_RENDERABLE_DATA                 = "Line Up Diagrams (such as Domain Architectures)";\r
 131     JMenuBar                    _jmenubar;\r
 132     JMenu                       _file_jmenu;\r
 133     JMenu                       _tools_menu;\r
 134     JMenu                       _view_jmenu;\r
 135     JMenu                       _options_jmenu;\r
 136     JMenu                       _font_size_menu;\r
 137     JMenu                       _help_jmenu;\r
 138     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 139     // Analysis menu\r
 140     JMenu                       _analysis_menu;\r
 141     JMenuItem                   _load_species_tree_item;\r
 142     JMenuItem                   _gsdi_item;\r
 143     JMenuItem                   _gsdir_item;\r
 144     JMenuItem                   _lineage_inference;\r
 145     // file menu:\r
 146     JMenuItem                   _open_item;\r
 147     JMenuItem                   _open_url_item;\r
 148     JMenuItem                   _save_item;\r
 149     JMenuItem                   _save_all_item;\r
 150     JMenuItem                   _close_item;\r
 151     JMenuItem                   _exit_item;\r
 152     JMenuItem                   _new_item;\r
 153     // tools menu:\r
 154     JMenuItem                   _midpoint_root_item;\r
 155     JMenuItem                   _taxcolor_item;\r
 156     JMenuItem                   _confcolor_item;\r
 157     JMenuItem                   _color_rank_jmi;\r
 158     JMenuItem                   _collapse_species_specific_subtrees;\r
 159     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 160     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 161     JMenuItem                   _obtain_seq_information_jmi;\r
 162     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 163     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 164     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 165     JMenuItem                   _annotate_item;\r
 166     JMenuItem                   _remove_branch_color_item;\r
 167     JMenuItem                   _remove_visual_styles_item;\r
 168     JMenuItem                   _delete_selected_nodes_item;\r
 169     JMenuItem                   _delete_not_selected_nodes_item;\r
 170     // font size menu:\r
 171     JMenuItem                   _super_tiny_fonts_item;\r
 172     JMenuItem                   _tiny_fonts_item;\r
 173     JMenuItem                   _small_fonts_item;\r
 174     JMenuItem                   _medium_fonts_item;\r
 175     JMenuItem                   _large_fonts_item;\r
 176     // options menu:\r
 177     // _  screen and print\r
 178     JMenuItem                   _choose_font_mi;\r
 179     JMenuItem                   _switch_colors_mi;\r
 180     JCheckBoxMenuItem           _label_direction_cbmi;\r
 181     // _  screen display\r
 182     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 183     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 184     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 185     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 186     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 187     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 188     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me\r
 189     JCheckBoxMenuItem           _show_overview_cbmi;\r
 190     JCheckBoxMenuItem           _show_domain_labels;\r
 191     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 192     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 193     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 194     JMenuItem                   _overview_placment_mi;\r
 195     JMenuItem                   _choose_minimal_confidence_mi;\r
 196     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 197     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 198     JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;\r
 199     JMenuItem                   _cycle_node_shape_mi;\r
 200     JMenuItem                   _cycle_node_fill_mi;\r
 201     JMenuItem                   _choose_node_size_mi;\r
 202     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 203     JCheckBoxMenuItem           _right_line_up_domains_cbmi;\r
 204     JCheckBoxMenuItem           _line_up_renderable_data_cbmi;\r
 205     // _  print\r
 206     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 207     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 208     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 209     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 210     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 211     JMenuItem                   _print_size_mi;\r
 212     JMenuItem                   _choose_pdf_width_mi;\r
 213     // _  parsing\r
 214     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 215     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 216     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 217     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 218     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 219     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 220     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 221     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 222     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 223     // _  search\r
 224     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 225     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 226     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 227     JCheckBoxMenuItem           _search_with_regex_cbmi;\r
 228     // type menu:\r
 229     JMenu                       _type_menu;\r
 230     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 231     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 232     JCheckBoxMenuItem           _curved_type_cbmi;\r
 233     JCheckBoxMenuItem           _convex_type_cbmi;\r
 234     JCheckBoxMenuItem           _euro_type_cbmi;\r
 235     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 236     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 237     JCheckBoxMenuItem           _circular_type_cbmi;\r
 238     // view as text menu:\r
 239     JMenuItem                   _view_as_NH_item;\r
 240     JMenuItem                   _view_as_XML_item;\r
 241     JMenuItem                   _view_as_nexus_item;\r
 242     JMenuItem                   _display_basic_information_item;\r
 243     // help menu:\r
 244     JMenuItem                   _about_item;\r
 245     JMenuItem                   _help_item;\r
 246     JMenuItem                   _website_item;\r
 247     JMenuItem                   _phyloxml_website_item;\r
 248     JMenuItem                   _phyloxml_ref_item;\r
 249     JMenuItem                   _aptx_ref_item;\r
 250     // process menu:\r
 251     JMenu                       _process_menu;\r
 252     // Handy pointers to child components:\r
 253     MainPanel                   _mainpanel;\r
 254     Container                   _contentpane;\r
 255     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;\r
 256     Configuration               _configuration;\r
 257     Options                     _options;\r
 258     private Phylogeny           _species_tree;\r
 259     InferenceManager            _inference_manager;\r
 260     final ProcessPool           _process_pool;\r
 261     private String              _previous_node_annotation_ref;\r
 262 \r
 263     MainFrame() {\r
 264         _process_pool = ProcessPool.createInstance();\r
 265     }\r
 266 \r
 267     /**\r
 268      * Action performed.\r
 269      */\r
 270     @Override\r
 271     public void actionPerformed( final ActionEvent e ) {\r
 272         final Object o = e.getSource();\r
 273         boolean is_applet = false;\r
 274         JApplet applet = null;\r
 275         if ( getCurrentTreePanel() != null ) {\r
 276             is_applet = getCurrentTreePanel().isApplet();\r
 277             if ( is_applet ) {\r
 278                 applet = getCurrentTreePanel().obtainApplet();\r
 279             }\r
 280         }\r
 281         if ( o == _exit_item ) {\r
 282             close();\r
 283         }\r
 284         else if ( o == _gsdi_item ) {\r
 285             if ( isSubtreeDisplayed() ) {\r
 286                 return;\r
 287             }\r
 288             executeGSDI();\r
 289         }\r
 290         else if ( o == _gsdir_item ) {\r
 291             if ( isSubtreeDisplayed() ) {\r
 292                 return;\r
 293             }\r
 294             executeGSDIR();\r
 295         }\r
 296         else if ( o == _taxcolor_item ) {\r
 297             taxColor();\r
 298         }\r
 299         else if ( o == _confcolor_item ) {\r
 300             confColor();\r
 301         }\r
 302         else if ( o == _color_rank_jmi ) {\r
 303             colorRank();\r
 304         }\r
 305         else if ( o == _collapse_species_specific_subtrees ) {\r
 306             if ( isSubtreeDisplayed() ) {\r
 307                 return;\r
 308             }\r
 309             if ( getCurrentTreePanel() != null ) {\r
 310                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 311             }\r
 312         }\r
 313         else if ( o == _remove_branch_color_item ) {\r
 314             if ( isSubtreeDisplayed() ) {\r
 315                 return;\r
 316             }\r
 317             removeBranchColors();\r
 318         }\r
 319         else if ( o == _remove_visual_styles_item ) {\r
 320             if ( isSubtreeDisplayed() ) {\r
 321                 return;\r
 322             }\r
 323             removeVisualStyles();\r
 324         }\r
 325         else if ( o == _midpoint_root_item ) {\r
 326             if ( isSubtreeDisplayed() ) {\r
 327                 return;\r
 328             }\r
 329             midpointRoot();\r
 330         }\r
 331         else if ( o == _delete_selected_nodes_item ) {\r
 332             if ( isSubtreeDisplayed() ) {\r
 333                 return;\r
 334             }\r
 335             deleteSelectedNodes( true );\r
 336         }\r
 337         else if ( o == _delete_not_selected_nodes_item ) {\r
 338             if ( isSubtreeDisplayed() ) {\r
 339                 return;\r
 340             }\r
 341             deleteSelectedNodes( false );\r
 342         }\r
 343         else if ( o == _annotate_item ) {\r
 344             annotateSequences();\r
 345         }\r
 346         else if ( o == _switch_colors_mi ) {\r
 347             switchColors();\r
 348         }\r
 349         else if ( o == _display_basic_information_item ) {\r
 350             if ( getCurrentTreePanel() != null ) {\r
 351                 displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 352             }\r
 353         }\r
 354         else if ( o == _view_as_NH_item ) {\r
 355             viewAsNH();\r
 356         }\r
 357         else if ( o == _view_as_XML_item ) {\r
 358             viewAsXML();\r
 359         }\r
 360         else if ( o == _view_as_nexus_item ) {\r
 361             viewAsNexus();\r
 362         }\r
 363         else if ( o == _super_tiny_fonts_item ) {\r
 364             if ( getCurrentTreePanel() != null ) {\r
 365                 getCurrentTreePanel().setSuperTinyFonts();\r
 366                 getCurrentTreePanel().repaint();\r
 367             }\r
 368         }\r
 369         else if ( o == _tiny_fonts_item ) {\r
 370             if ( getCurrentTreePanel() != null ) {\r
 371                 getCurrentTreePanel().setTinyFonts();\r
 372                 getCurrentTreePanel().repaint();\r
 373             }\r
 374         }\r
 375         else if ( o == _small_fonts_item ) {\r
 376             if ( getCurrentTreePanel() != null ) {\r
 377                 getCurrentTreePanel().setSmallFonts();\r
 378                 getCurrentTreePanel().repaint();\r
 379             }\r
 380         }\r
 381         else if ( o == _medium_fonts_item ) {\r
 382             if ( getCurrentTreePanel() != null ) {\r
 383                 getCurrentTreePanel().setMediumFonts();\r
 384                 getCurrentTreePanel().repaint();\r
 385             }\r
 386         }\r
 387         else if ( o == _large_fonts_item ) {\r
 388             if ( getCurrentTreePanel() != null ) {\r
 389                 getCurrentTreePanel().setLargeFonts();\r
 390                 getCurrentTreePanel().repaint();\r
 391             }\r
 392         }\r
 393         else if ( o == _choose_font_mi ) {\r
 394             chooseFont();\r
 395         }\r
 396         else if ( o == _choose_minimal_confidence_mi ) {\r
 397             chooseMinimalConfidence();\r
 398         }\r
 399         else if ( o == _choose_node_size_mi ) {\r
 400             chooseNodeSize( getOptions(), this );\r
 401         }\r
 402         else if ( o == _overview_placment_mi ) {\r
 403             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 404         }\r
 405         else if ( o == _cycle_node_fill_mi ) {\r
 406             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
 407         }\r
 408         else if ( o == _cycle_node_shape_mi ) {\r
 409             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
 410         }\r
 411         else if ( o == _screen_antialias_cbmi ) {\r
 412             updateOptions( getOptions() );\r
 413             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 414         }\r
 415         else if ( o == _background_gradient_cbmi ) {\r
 416             updateOptions( getOptions() );\r
 417         }\r
 418         else if ( o == _show_domain_labels ) {\r
 419             updateOptions( getOptions() );\r
 420         }\r
 421         else if ( o == _show_annotation_ref_source ) {\r
 422             updateOptions( getOptions() );\r
 423         }\r
 424         else if ( o == _abbreviate_scientific_names ) {\r
 425             updateOptions( getOptions() );\r
 426         }\r
 427         else if ( o == _color_labels_same_as_parent_branch ) {\r
 428             updateOptions( getOptions() );\r
 429         }\r
 430         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 431             updateOptions( getOptions() );\r
 432         }\r
 433         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 434             updateOptions( getOptions() );\r
 435         }\r
 436         else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
 437             updateOptions( getOptions() );\r
 438         }\r
 439         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 440             updateOptions( getOptions() );\r
 441             showWhole();\r
 442         }\r
 443         else if ( o == _uniform_cladograms_rbmi ) {\r
 444             updateOptions( getOptions() );\r
 445             showWhole();\r
 446         }\r
 447         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 448             updateOptions( getOptions() );\r
 449             showWhole();\r
 450         }\r
 451         else if ( o == _search_case_senstive_cbmi ) {\r
 452             updateOptions( getOptions() );\r
 453             getMainPanel().getControlPanel().search0();\r
 454             getMainPanel().getControlPanel().search1();\r
 455         }\r
 456         else if ( o == _search_whole_words_only_cbmi ) {\r
 457             updateOptions( getOptions() );\r
 458             getMainPanel().getControlPanel().search0();\r
 459             getMainPanel().getControlPanel().search1();\r
 460         }\r
 461         else if ( o == _inverse_search_result_cbmi ) {\r
 462             updateOptions( getOptions() );\r
 463             getMainPanel().getControlPanel().search0();\r
 464             getMainPanel().getControlPanel().search1();\r
 465         }\r
 466         else if ( o == _search_with_regex_cbmi ) {\r
 467             updateOptions( getOptions() );\r
 468             getMainPanel().getControlPanel().search0();\r
 469             getMainPanel().getControlPanel().search1();\r
 470         }\r
 471         else if ( o == _show_scale_cbmi ) {\r
 472             updateOptions( getOptions() );\r
 473         }\r
 474         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 475             updateOptions( getOptions() );\r
 476         }\r
 477         else if ( o == _show_confidence_stddev_cbmi ) {\r
 478             updateOptions( getOptions() );\r
 479         }\r
 480         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 481             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 482                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 483             }\r
 484             updateOptions( getOptions() );\r
 485         }\r
 486         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 487             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 488                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 489             }\r
 490             updateOptions( getOptions() );\r
 491         }\r
 492         else if ( o == _label_direction_cbmi ) {\r
 493             updateOptions( getOptions() );\r
 494         }\r
 495         else if ( o == _show_overview_cbmi ) {\r
 496             updateOptions( getOptions() );\r
 497             if ( getCurrentTreePanel() != null ) {\r
 498                 getCurrentTreePanel().updateOvSizes();\r
 499             }\r
 500         }\r
 501         else if ( o == _line_up_renderable_data_cbmi ) {\r
 502             if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
 503                 _right_line_up_domains_cbmi.setSelected( false );\r
 504             }\r
 505             updateOptions( getOptions() );\r
 506         }\r
 507         else if ( o == _right_line_up_domains_cbmi ) {\r
 508             if ( _right_line_up_domains_cbmi.isSelected() ) {\r
 509                 _line_up_renderable_data_cbmi.setSelected( true );\r
 510             }\r
 511             updateOptions( getOptions() );\r
 512         }\r
 513         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 514                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 515                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 516             typeChanged( o );\r
 517         }\r
 518         else if ( o == _about_item ) {\r
 519             about();\r
 520         }\r
 521         else if ( o == _help_item ) {\r
 522             try {\r
 523                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
 524             }\r
 525             catch ( final IOException e1 ) {\r
 526                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 527             }\r
 528         }\r
 529         else if ( o == _website_item ) {\r
 530             try {\r
 531                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 532             }\r
 533             catch ( final IOException e1 ) {\r
 534                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 535             }\r
 536         }\r
 537         else if ( o == _phyloxml_website_item ) {\r
 538             try {\r
 539                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 540             }\r
 541             catch ( final IOException e1 ) {\r
 542                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 543             }\r
 544         }\r
 545         else if ( o == _aptx_ref_item ) {\r
 546             try {\r
 547                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 548             }\r
 549             catch ( final IOException e1 ) {\r
 550                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 551             }\r
 552         }\r
 553         else if ( o == _phyloxml_ref_item ) {\r
 554             try {\r
 555                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 556             }\r
 557             catch ( final IOException e1 ) {\r
 558                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 559             }\r
 560         }\r
 561         else {\r
 562             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 563                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 564                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 565                         readPhylogeniesFromWebservice( i );\r
 566                     }\r
 567                 }\r
 568             }\r
 569         }\r
 570         _contentpane.repaint();\r
 571     }\r
 572 \r
 573     private void deleteSelectedNodes( final boolean delete ) {\r
 574         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
 575         if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
 576             return;\r
 577         }\r
 578         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
 579         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
 580             final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
 581             for( final PhylogenyNode n : all_selected_nodes ) {\r
 582                 if ( n.isExternal() ) {\r
 583                     nodes.add( n );\r
 584                 }\r
 585             }\r
 586         }\r
 587         String function = "Retain";\r
 588         if ( delete ) {\r
 589             function = "Delete";\r
 590         }\r
 591         if ( ( nodes == null ) || nodes.isEmpty() ) {\r
 592             JOptionPane\r
 593                     .showMessageDialog( this,\r
 594                                         "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
 595                                         "No external nodes selected to " + function.toLowerCase(),\r
 596                                         JOptionPane.ERROR_MESSAGE );\r
 597             return;\r
 598         }\r
 599         final int todo = nodes.size();\r
 600         final int ext = phy.getNumberOfExternalNodes();\r
 601         int res = todo;\r
 602         if ( delete ) {\r
 603             res = ext - todo;\r
 604         }\r
 605         if ( res < 1 ) {\r
 606             JOptionPane.showMessageDialog( this,\r
 607                                            "Cannot delete all nodes",\r
 608                                            "Attempt to delete all nodes ",\r
 609                                            JOptionPane.ERROR_MESSAGE );\r
 610             return;\r
 611         }\r
 612         final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
 613                 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
 614                 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
 615         if ( result == JOptionPane.OK_OPTION ) {\r
 616             if ( !delete ) {\r
 617                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
 618                 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
 619                     final PhylogenyNode n = it.next();\r
 620                     if ( !nodes.contains( n ) ) {\r
 621                         to_delete.add( n );\r
 622                     }\r
 623                 }\r
 624                 for( final PhylogenyNode n : to_delete ) {\r
 625                     phy.deleteSubtree( n, true );\r
 626                 }\r
 627             }\r
 628             else {\r
 629                 for( final PhylogenyNode n : nodes ) {\r
 630                     phy.deleteSubtree( n, true );\r
 631                 }\r
 632             }\r
 633             resetSearch();\r
 634             getCurrentTreePanel().setNodeInPreorderToNull();\r
 635             phy.externalNodesHaveChanged();\r
 636             phy.clearHashIdToNodeMap();\r
 637             phy.recalculateNumberOfExternalDescendants( true );\r
 638             getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
 639             getCurrentTreePanel().setEdited( true );\r
 640             repaint();\r
 641         }\r
 642     }\r
 643 \r
 644     void resetSearch() {\r
 645         getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
 646         getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
 647         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
 648         getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
 649         getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
 650         getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
 651         getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
 652         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
 653         getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
 654         getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
 655         getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
 656         getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
 657     }\r
 658 \r
 659     public Configuration getConfiguration() {\r
 660         return _configuration;\r
 661     }\r
 662 \r
 663     /**\r
 664      * This method returns the current external node data which\r
 665      * has been selected by the user by clicking the "Return ..."\r
 666      * menu item. This method is expected to be called from Javascript or\r
 667      * something like it.\r
 668      * \r
 669      * @return current external node data as String\r
 670      */\r
 671     public String getCurrentExternalNodesDataBuffer() {\r
 672         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 673     }\r
 674 \r
 675     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 676         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 677     }\r
 678 \r
 679     public int getCurrentExternalNodesDataBufferLength() {\r
 680         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 681     }\r
 682 \r
 683     public InferenceManager getInferenceManager() {\r
 684         return _inference_manager;\r
 685     }\r
 686 \r
 687     public MainPanel getMainPanel() {\r
 688         return _mainpanel;\r
 689     }\r
 690 \r
 691     public Options getOptions() {\r
 692         return _options;\r
 693     }\r
 694 \r
 695     public ProcessPool getProcessPool() {\r
 696         return _process_pool;\r
 697     }\r
 698 \r
 699     public void showTextFrame( final String s, final String title ) {\r
 700         checkTextFrames();\r
 701         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 702     }\r
 703 \r
 704     public void showWhole() {\r
 705         _mainpanel.getControlPanel().showWhole();\r
 706     }\r
 707 \r
 708     public void updateProcessMenu() {\r
 709         // In general Swing is not thread safe.\r
 710         // See "Swing's Threading Policy".\r
 711         SwingUtilities.invokeLater( new Runnable() {\r
 712 \r
 713             @Override\r
 714             public void run() {\r
 715                 doUpdateProcessMenu();\r
 716             }\r
 717         } );\r
 718     }\r
 719 \r
 720     void activateSaveAllIfNeeded() {\r
 721         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 722             _save_all_item.setEnabled( true );\r
 723         }\r
 724         else {\r
 725             _save_all_item.setEnabled( false );\r
 726         }\r
 727     }\r
 728 \r
 729     void buildFileMenu() {\r
 730         _file_jmenu = createMenu( "File", getConfiguration() );\r
 731         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 732         customizeJMenuItem( _exit_item );\r
 733         _jmenubar.add( _file_jmenu );\r
 734     }\r
 735 \r
 736     void buildFontSizeMenu() {\r
 737         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 738         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 739         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 740         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 741         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 742         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 743         customizeJMenuItem( _super_tiny_fonts_item );\r
 744         customizeJMenuItem( _tiny_fonts_item );\r
 745         customizeJMenuItem( _small_fonts_item );\r
 746         customizeJMenuItem( _medium_fonts_item );\r
 747         customizeJMenuItem( _large_fonts_item );\r
 748         _jmenubar.add( _font_size_menu );\r
 749     }\r
 750 \r
 751     void buildHelpMenu() {\r
 752         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 753         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
 754         _help_jmenu.addSeparator();\r
 755         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 756         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
 757         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 758         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 759         _help_jmenu.addSeparator();\r
 760         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 761         customizeJMenuItem( _help_item );\r
 762         customizeJMenuItem( _website_item );\r
 763         customizeJMenuItem( _phyloxml_website_item );\r
 764         customizeJMenuItem( _aptx_ref_item );\r
 765         customizeJMenuItem( _phyloxml_ref_item );\r
 766         customizeJMenuItem( _about_item );\r
 767         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 768         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 769         _jmenubar.add( _help_jmenu );\r
 770     }\r
 771 \r
 772     void buildTypeMenu() {\r
 773         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 774         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 775         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 776         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 777         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 778         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 779         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 780         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 781         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 782         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 783         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 784         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 785         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 786         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 787         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 788         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 789         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 790         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 791         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 792         initializeTypeMenu( getOptions() );\r
 793         _jmenubar.add( _type_menu );\r
 794     }\r
 795 \r
 796     void buildViewMenu() {\r
 797         _view_jmenu = createMenu( "View", getConfiguration() );\r
 798         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 799         _view_jmenu.addSeparator();\r
 800         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 801         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 802         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 803         customizeJMenuItem( _display_basic_information_item );\r
 804         customizeJMenuItem( _view_as_NH_item );\r
 805         customizeJMenuItem( _view_as_XML_item );\r
 806         customizeJMenuItem( _view_as_nexus_item );\r
 807         _jmenubar.add( _view_jmenu );\r
 808     }\r
 809 \r
 810     void checkTextFrames() {\r
 811         if ( _textframes.size() > 5 ) {\r
 812             try {\r
 813                 if ( _textframes.getFirst() != null ) {\r
 814                     _textframes.getFirst().removeMe();\r
 815                 }\r
 816                 else {\r
 817                     _textframes.removeFirst();\r
 818                 }\r
 819             }\r
 820             catch ( final NoSuchElementException e ) {\r
 821                 // Ignore.\r
 822             }\r
 823         }\r
 824     }\r
 825 \r
 826     void close() {\r
 827         removeAllTextFrames();\r
 828         if ( _mainpanel != null ) {\r
 829             _mainpanel.terminate();\r
 830         }\r
 831         if ( _contentpane != null ) {\r
 832             _contentpane.removeAll();\r
 833         }\r
 834         setVisible( false );\r
 835         dispose();\r
 836     }\r
 837 \r
 838     void colorRank() {\r
 839         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 840             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
 841             final String rank = ( String ) JOptionPane\r
 842                     .showInputDialog( this,\r
 843                                       "What rank should the colorization be based on",\r
 844                                       "Rank Selection",\r
 845                                       JOptionPane.QUESTION_MESSAGE,\r
 846                                       null,\r
 847                                       ranks,\r
 848                                       null );\r
 849             if ( !ForesterUtil.isEmpty( rank ) ) {\r
 850                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
 851             }\r
 852         }\r
 853     }\r
 854 \r
 855     void confColor() {\r
 856         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 857             _mainpanel.getCurrentTreePanel().confColor();\r
 858         }\r
 859     }\r
 860 \r
 861     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
 862         if ( item != null ) {\r
 863             item.setFont( MainFrame.menu_font );\r
 864             if ( !getConfiguration().isUseNativeUI() ) {\r
 865                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 866                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 867             }\r
 868             item.setSelected( is_selected );\r
 869             item.addActionListener( this );\r
 870         }\r
 871     }\r
 872 \r
 873     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
 874         if ( jmi != null ) {\r
 875             jmi.setFont( MainFrame.menu_font );\r
 876             if ( !getConfiguration().isUseNativeUI() ) {\r
 877                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 878                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 879             }\r
 880             jmi.addActionListener( this );\r
 881         }\r
 882         return jmi;\r
 883     }\r
 884 \r
 885     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
 886         if ( item != null ) {\r
 887             item.setFont( MainFrame.menu_font );\r
 888             if ( !getConfiguration().isUseNativeUI() ) {\r
 889                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 890                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 891             }\r
 892             item.setSelected( is_selected );\r
 893             item.addActionListener( this );\r
 894         }\r
 895     }\r
 896 \r
 897     void displayBasicInformation( final File treefile ) {\r
 898         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
 899             String title = "Basic Information";\r
 900             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
 901                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
 902             }\r
 903             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
 904         }\r
 905     }\r
 906 \r
 907     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
 908         try {\r
 909             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 910         }\r
 911         catch ( final Exception ex ) {\r
 912             // Do nothing.\r
 913         }\r
 914         JOptionPane.showMessageDialog( this,\r
 915                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
 916                                        "Error during File|Open",\r
 917                                        JOptionPane.ERROR_MESSAGE );\r
 918     }\r
 919 \r
 920     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
 921         try {\r
 922             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 923         }\r
 924         catch ( final Exception ex ) {\r
 925             // Do nothing.\r
 926         }\r
 927         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
 928     }\r
 929 \r
 930     void executeGSDI() {\r
 931         if ( !isOKforSDI( false, true ) ) {\r
 932             return;\r
 933         }\r
 934         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
 935             JOptionPane.showMessageDialog( this,\r
 936                                            "Gene tree is not rooted.",\r
 937                                            "Cannot execute GSDI",\r
 938                                            JOptionPane.ERROR_MESSAGE );\r
 939             return;\r
 940         }\r
 941         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 942         gene_tree.setAllNodesToNotCollapse();\r
 943         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 944         GSDI gsdi = null;\r
 945         final Phylogeny species_tree = getSpeciesTree().copy();\r
 946         try {\r
 947             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
 948         }\r
 949         catch ( final SDIException e ) {\r
 950             JOptionPane.showMessageDialog( this,\r
 951                                            e.getLocalizedMessage(),\r
 952                                            "Error during GSDI",\r
 953                                            JOptionPane.ERROR_MESSAGE );\r
 954             return;\r
 955         }\r
 956         catch ( final Exception e ) {\r
 957             AptxUtil.unexpectedException( e );\r
 958             return;\r
 959         }\r
 960         gene_tree.setRerootable( false );\r
 961         gene_tree.clearHashIdToNodeMap();\r
 962         gene_tree.recalculateNumberOfExternalDescendants( true );\r
 963         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
 964         getMainPanel().getControlPanel().setShowEvents( true );\r
 965         showWhole();\r
 966         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 967         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 968         showWhole();\r
 969         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 970         showWhole();\r
 971         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 972         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 973         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 974             JOptionPane.showMessageDialog( this,\r
 975                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 976                                                    + "Potential duplications: "\r
 977                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 978                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 979                                                    + "Stripped gene tree nodes: "\r
 980                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 981                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 982                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 983                                            "GSDI successfully completed",\r
 984                                            JOptionPane.WARNING_MESSAGE );\r
 985         }\r
 986         else {\r
 987             JOptionPane.showMessageDialog( this,\r
 988                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 989                                                    + "Potential duplications: "\r
 990                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 991                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 992                                                    + "Stripped gene tree nodes: "\r
 993                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 994                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 995                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 996                                            "GSDI successfully completed",\r
 997                                            JOptionPane.INFORMATION_MESSAGE );\r
 998         }\r
 999     }\r
1000 \r
1001     void executeGSDIR() {\r
1002         if ( !isOKforSDI( false, false ) ) {\r
1003             return;\r
1004         }\r
1005         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
1006         if ( ( p > 0 )\r
1007                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
1008             JOptionPane.showMessageDialog( this,\r
1009                                            "Gene tree is not completely binary",\r
1010                                            "Cannot execute GSDI",\r
1011                                            JOptionPane.ERROR_MESSAGE );\r
1012             return;\r
1013         }\r
1014         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
1015         gene_tree.setAllNodesToNotCollapse();\r
1016         gene_tree.recalculateNumberOfExternalDescendants( false );\r
1017         GSDIR gsdir = null;\r
1018         final Phylogeny species_tree = getSpeciesTree().copy();\r
1019         try {\r
1020             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
1021         }\r
1022         catch ( final SDIException e ) {\r
1023             JOptionPane.showMessageDialog( this,\r
1024                                            e.getLocalizedMessage(),\r
1025                                            "Error during GSDIR",\r
1026                                            JOptionPane.ERROR_MESSAGE );\r
1027             return;\r
1028         }\r
1029         catch ( final Exception e ) {\r
1030             AptxUtil.unexpectedException( e );\r
1031             return;\r
1032         }\r
1033         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
1034         result_gene_tree.setRerootable( false );\r
1035         result_gene_tree.clearHashIdToNodeMap();\r
1036         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
1037         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
1038         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
1039         getMainPanel().getControlPanel().setShowEvents( true );\r
1040         showWhole();\r
1041         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1042         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1043         showWhole();\r
1044         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1045         showWhole();\r
1046         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1047         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1048         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1049             JOptionPane.showMessageDialog( this,\r
1050                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1051                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1052                                                    + "Stripped gene tree nodes: "\r
1053                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1054                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1055                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1056                                            "GSDIR successfully completed",\r
1057                                            JOptionPane.WARNING_MESSAGE );\r
1058         }\r
1059         else {\r
1060             JOptionPane.showMessageDialog( this,\r
1061                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1062                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1063                                                    + "Stripped gene tree nodes: "\r
1064                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1065                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1066                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1067                                            "GSDIR successfully completed",\r
1068                                            JOptionPane.INFORMATION_MESSAGE );\r
1069         }\r
1070     }\r
1071 \r
1072     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
1073         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
1074             JOptionPane.showMessageDialog( this,\r
1075                                            "Gene tree and species tree have no species in common.",\r
1076                                            "Error during SDI",\r
1077                                            JOptionPane.ERROR_MESSAGE );\r
1078             return false;\r
1079         }\r
1080         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
1081             JOptionPane.showMessageDialog( this,\r
1082                                            "Gene tree and species tree have only one species in common.",\r
1083                                            "Error during SDI",\r
1084                                            JOptionPane.ERROR_MESSAGE );\r
1085             return false;\r
1086         }\r
1087         else {\r
1088             return true;\r
1089         }\r
1090     }\r
1091 \r
1092     TreePanel getCurrentTreePanel() {\r
1093         return getMainPanel().getCurrentTreePanel();\r
1094     }\r
1095 \r
1096     JMenu getHelpMenu() {\r
1097         return _help_jmenu;\r
1098     }\r
1099 \r
1100     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
1101         return _label_direction_cbmi;\r
1102     }\r
1103 \r
1104     JMenuBar getMenuBarOfMainFrame() {\r
1105         return _jmenubar;\r
1106     }\r
1107 \r
1108     final Phylogeny getSpeciesTree() {\r
1109         return _species_tree;\r
1110     }\r
1111 \r
1112     void initializeTypeMenu( final Options options ) {\r
1113         setTypeMenuToAllUnselected();\r
1114         switch ( options.getPhylogenyGraphicsType() ) {\r
1115             case CONVEX:\r
1116                 _convex_type_cbmi.setSelected( true );\r
1117                 break;\r
1118             case CURVED:\r
1119                 _curved_type_cbmi.setSelected( true );\r
1120                 break;\r
1121             case EURO_STYLE:\r
1122                 _euro_type_cbmi.setSelected( true );\r
1123                 break;\r
1124             case ROUNDED:\r
1125                 _rounded_type_cbmi.setSelected( true );\r
1126                 break;\r
1127             case TRIANGULAR:\r
1128                 _triangular_type_cbmi.setSelected( true );\r
1129                 break;\r
1130             case UNROOTED:\r
1131                 _unrooted_type_cbmi.setSelected( true );\r
1132                 break;\r
1133             case CIRCULAR:\r
1134                 _circular_type_cbmi.setSelected( true );\r
1135                 break;\r
1136             default:\r
1137                 _rectangular_type_cbmi.setSelected( true );\r
1138                 break;\r
1139         }\r
1140     }\r
1141 \r
1142     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1143         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1144             return false;\r
1145         }\r
1146         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1147             JOptionPane.showMessageDialog( this,\r
1148                                            "No species tree loaded",\r
1149                                            "Cannot execute GSDI",\r
1150                                            JOptionPane.ERROR_MESSAGE );\r
1151             return false;\r
1152         }\r
1153         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1154             JOptionPane.showMessageDialog( this,\r
1155                                            "Species tree is not completely binary",\r
1156                                            "Cannot execute GSDI",\r
1157                                            JOptionPane.ERROR_MESSAGE );\r
1158             return false;\r
1159         }\r
1160         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1161             JOptionPane.showMessageDialog( this,\r
1162                                            "Gene tree is not completely binary",\r
1163                                            "Cannot execute GSDI",\r
1164                                            JOptionPane.ERROR_MESSAGE );\r
1165             return false;\r
1166         }\r
1167         else {\r
1168             return true;\r
1169         }\r
1170     }\r
1171 \r
1172     boolean isSubtreeDisplayed() {\r
1173         if ( getCurrentTreePanel() != null ) {\r
1174             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1175                 JOptionPane\r
1176                         .showMessageDialog( this,\r
1177                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1178                                             "Operation can not be exectuted on a sub-tree",\r
1179                                             JOptionPane.WARNING_MESSAGE );\r
1180                 return true;\r
1181             }\r
1182         }\r
1183         return false;\r
1184     }\r
1185 \r
1186     void midpointRoot() {\r
1187         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1188             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1189         }\r
1190     }\r
1191 \r
1192     void readPhylogeniesFromWebservice( final int i ) {\r
1193         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1194         new Thread( reader ).start();\r
1195     }\r
1196 \r
1197     void removeAllTextFrames() {\r
1198         for( final TextFrame tf : _textframes ) {\r
1199             if ( tf != null ) {\r
1200                 tf.close();\r
1201             }\r
1202         }\r
1203         _textframes.clear();\r
1204     }\r
1205 \r
1206     void setConfiguration( final Configuration configuration ) {\r
1207         _configuration = configuration;\r
1208     }\r
1209 \r
1210     void setInferenceManager( final InferenceManager i ) {\r
1211         _inference_manager = i;\r
1212     }\r
1213 \r
1214     void setOptions( final Options options ) {\r
1215         _options = options;\r
1216     }\r
1217 \r
1218     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1219         setTypeMenuToAllUnselected();\r
1220         switch ( type ) {\r
1221             case CIRCULAR:\r
1222                 _circular_type_cbmi.setSelected( true );\r
1223                 break;\r
1224             case CONVEX:\r
1225                 _convex_type_cbmi.setSelected( true );\r
1226                 break;\r
1227             case CURVED:\r
1228                 _curved_type_cbmi.setSelected( true );\r
1229                 break;\r
1230             case EURO_STYLE:\r
1231                 _euro_type_cbmi.setSelected( true );\r
1232                 break;\r
1233             case ROUNDED:\r
1234                 _rounded_type_cbmi.setSelected( true );\r
1235                 break;\r
1236             case RECTANGULAR:\r
1237                 _rectangular_type_cbmi.setSelected( true );\r
1238                 break;\r
1239             case TRIANGULAR:\r
1240                 _triangular_type_cbmi.setSelected( true );\r
1241                 break;\r
1242             case UNROOTED:\r
1243                 _unrooted_type_cbmi.setSelected( true );\r
1244                 break;\r
1245             default:\r
1246                 throw new IllegalArgumentException( "unknown type: " + type );\r
1247         }\r
1248     }\r
1249 \r
1250     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1251         _species_tree = species_tree;\r
1252     }\r
1253 \r
1254     void setTypeMenuToAllUnselected() {\r
1255         _convex_type_cbmi.setSelected( false );\r
1256         _curved_type_cbmi.setSelected( false );\r
1257         _euro_type_cbmi.setSelected( false );\r
1258         _rounded_type_cbmi.setSelected( false );\r
1259         _triangular_type_cbmi.setSelected( false );\r
1260         _rectangular_type_cbmi.setSelected( false );\r
1261         _unrooted_type_cbmi.setSelected( false );\r
1262         _circular_type_cbmi.setSelected( false );\r
1263     }\r
1264 \r
1265     void switchColors() {\r
1266         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1267         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1268         csc.setVisible( true );\r
1269     }\r
1270 \r
1271     void taxColor() {\r
1272         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1273             _mainpanel.getCurrentTreePanel().taxColor();\r
1274         }\r
1275     }\r
1276 \r
1277     void typeChanged( final Object o ) {\r
1278         updateTypeCheckboxes( getOptions(), o );\r
1279         updateOptions( getOptions() );\r
1280         if ( getCurrentTreePanel() != null ) {\r
1281             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1282             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1283             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1284                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1285                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1286                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1287                 getCurrentTreePanel().getControlPanel().showWhole();\r
1288             }\r
1289             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1290                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1291             }\r
1292             else {\r
1293                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1294             }\r
1295             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1296             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1297             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1298                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1299                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1300                 }\r
1301                 else {\r
1302                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1303                 }\r
1304             }\r
1305         }\r
1306     }\r
1307 \r
1308     void updateOptions( final Options options ) {\r
1309         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1310         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1311                 && _background_gradient_cbmi.isSelected() );\r
1312         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1313         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1314                 && _show_annotation_ref_source.isSelected() );\r
1315         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1316                 && _abbreviate_scientific_names.isSelected() );\r
1317         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1318                 && _color_labels_same_as_parent_branch.isSelected() );\r
1319         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1320                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1321         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1322                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
1323         options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
1324                 && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
1325         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1326             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1327         }\r
1328         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1329             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1330         }\r
1331         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1332             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1333         }\r
1334         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1335                 && _search_case_senstive_cbmi.isSelected() );\r
1336         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1337             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1338         }\r
1339         if ( _label_direction_cbmi != null ) {\r
1340             if ( _label_direction_cbmi.isSelected() ) {\r
1341                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1342             }\r
1343             else {\r
1344                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1345             }\r
1346         }\r
1347         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1348         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1349                 && _show_confidence_stddev_cbmi.isSelected() );\r
1350         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1351             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1352         }\r
1353         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1354                 && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1355         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1356                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1357         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1358         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1359                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1360             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1361         }\r
1362         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1363                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1364             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1365         }\r
1366         else {\r
1367             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1368         }\r
1369         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1370                 && _print_black_and_white_cbmi.isSelected() );\r
1371         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1372                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1373         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1374             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1375         }\r
1376         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1377             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1378         }\r
1379         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1380             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1381         }\r
1382         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1383             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1384         }\r
1385         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1386                 && _replace_underscores_cbmi.isSelected() );\r
1387         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1388                 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1389         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1390                 && _search_whole_words_only_cbmi.isSelected() );\r
1391         options.setSearchWithRegex( ( _search_with_regex_cbmi != null )\r
1392                                     && _search_with_regex_cbmi.isSelected() );\r
1393         \r
1394         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1395                 && _inverse_search_result_cbmi.isSelected() );\r
1396         if ( _graphics_export_visible_only_cbmi != null ) {\r
1397             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1398             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1399                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1400                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1401             }\r
1402             else {\r
1403                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1404             }\r
1405         }\r
1406         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1407             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1408         }\r
1409         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1410             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1411         }\r
1412         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1413             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1414         }\r
1415         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1416             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1417         }\r
1418         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1419             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1420         }\r
1421         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1422             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1423         }\r
1424         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1425             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1426         }\r
1427         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1428             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1429         }\r
1430         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
1431             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
1432         }\r
1433         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
1434             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
1435         }\r
1436     }\r
1437 \r
1438     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1439         setTypeMenuToAllUnselected();\r
1440         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1441     }\r
1442 \r
1443     void viewAsNexus() {\r
1444         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1445             String title = "Nexus";\r
1446             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1447                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1448             }\r
1449             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1450                            title );\r
1451         }\r
1452     }\r
1453 \r
1454     void viewAsNH() {\r
1455         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1456             String title = "New Hampshire";\r
1457             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1458                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1459             }\r
1460             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1461                                    .getNhConversionSupportValueStyle() ),\r
1462                            title );\r
1463         }\r
1464     }\r
1465 \r
1466     void viewAsXML() {\r
1467         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1468             String title = "phyloXML";\r
1469             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1470                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1471             }\r
1472             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1473         }\r
1474     }\r
1475 \r
1476     private void annotateSequences() {\r
1477         if ( getCurrentTreePanel() != null ) {\r
1478             List<PhylogenyNode> nodes = null;\r
1479             if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
1480                     || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
1481                 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
1482             }\r
1483             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1484                 JOptionPane\r
1485                         .showMessageDialog( this,\r
1486                                             "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1487                                             "No nodes selected for annotation",\r
1488                                             JOptionPane.ERROR_MESSAGE );\r
1489                 return;\r
1490             }\r
1491             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1492             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1493                 final JTextField ref_field = new JTextField( 10 );\r
1494                 final JTextField desc_filed = new JTextField( 20 );\r
1495                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1496                         : getPreviousNodeAnnotationReference() );\r
1497                 final JPanel my_panel = new JPanel();\r
1498                 my_panel.add( new JLabel( "Reference " ) );\r
1499                 my_panel.add( ref_field );\r
1500                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1501                 my_panel.add( new JLabel( "Description " ) );\r
1502                 my_panel.add( desc_filed );\r
1503                 final int result = JOptionPane.showConfirmDialog( null,\r
1504                                                                   my_panel,\r
1505                                                                   "Enter the sequence annotation(s) for the "\r
1506                                                                           + nodes.size() + " selected nodes",\r
1507                                                                   JOptionPane.OK_CANCEL_OPTION );\r
1508                 if ( result == JOptionPane.OK_OPTION ) {\r
1509                     String ref = ref_field.getText();\r
1510                     String desc = desc_filed.getText();\r
1511                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1512                         ref = ref.trim();\r
1513                         ref = ref.replaceAll( "\\s+", " " );\r
1514                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1515                                 || ( ref.length() < 3 ) ) {\r
1516                             JOptionPane.showMessageDialog( this,\r
1517                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1518                                                            "Illegal Format for Annotation Reference",\r
1519                                                            JOptionPane.ERROR_MESSAGE );\r
1520                             return;\r
1521                         }\r
1522                     }\r
1523                     if ( ref != null ) {\r
1524                         setPreviousNodeAnnotationReference( ref );\r
1525                     }\r
1526                     if ( desc != null ) {\r
1527                         desc = desc.trim();\r
1528                         desc = desc.replaceAll( "\\s+", " " );\r
1529                     }\r
1530                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1531                         for( final PhylogenyNode n : nodes ) {\r
1532                             ForesterUtil.ensurePresenceOfSequence( n );\r
1533                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1534                                     : new Annotation( ref );\r
1535                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1536                                 ann.setDesc( desc );\r
1537                             }\r
1538                             n.getNodeData().getSequence().addAnnotation( ann );\r
1539                         }\r
1540                     }\r
1541                     getMainPanel().getControlPanel().showAnnotations();\r
1542                 }\r
1543             }\r
1544         }\r
1545     }\r
1546 \r
1547     private void chooseFont() {\r
1548         final FontChooser fc = new FontChooser();\r
1549         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1550         fc.showDialog( this, "Select the Base Font" );\r
1551         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1552     }\r
1553 \r
1554     private void chooseMinimalConfidence() {\r
1555         final String s = ( String ) JOptionPane\r
1556                 .showInputDialog( this,\r
1557                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1558                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1559                                   "Minimal Confidence Value",\r
1560                                   JOptionPane.QUESTION_MESSAGE,\r
1561                                   null,\r
1562                                   null,\r
1563                                   getOptions().getMinConfidenceValue() );\r
1564         if ( !ForesterUtil.isEmpty( s ) ) {\r
1565             boolean success = true;\r
1566             double m = 0.0;\r
1567             final String m_str = s.trim();\r
1568             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1569                 try {\r
1570                     m = Double.parseDouble( m_str );\r
1571                 }\r
1572                 catch ( final Exception ex ) {\r
1573                     success = false;\r
1574                 }\r
1575             }\r
1576             else {\r
1577                 success = false;\r
1578             }\r
1579             if ( success && ( m >= 0.0 ) ) {\r
1580                 getOptions().setMinConfidenceValue( m );\r
1581             }\r
1582         }\r
1583     }\r
1584 \r
1585     private void doUpdateProcessMenu() {\r
1586         if ( _process_pool.size() > 0 ) {\r
1587             if ( _process_menu == null ) {\r
1588                 _process_menu = createMenu( "", getConfiguration() );\r
1589                 _process_menu.setForeground( Color.RED );\r
1590             }\r
1591             _process_menu.removeAll();\r
1592             final String text = "processes running: " + _process_pool.size();\r
1593             _process_menu.setText( text );\r
1594             _jmenubar.add( _process_menu );\r
1595             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1596                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1597                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1598             }\r
1599         }\r
1600         else {\r
1601             if ( _process_menu != null ) {\r
1602                 _process_menu.removeAll();\r
1603                 _jmenubar.remove( _process_menu );\r
1604             }\r
1605         }\r
1606         _jmenubar.validate();\r
1607         _jmenubar.repaint();\r
1608         repaint();\r
1609     }\r
1610 \r
1611     private String getPreviousNodeAnnotationReference() {\r
1612         return _previous_node_annotation_ref;\r
1613     }\r
1614 \r
1615     private void removeBranchColors() {\r
1616         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1617             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1618         }\r
1619     }\r
1620 \r
1621     private void removeVisualStyles() {\r
1622         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1623             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1624         }\r
1625     }\r
1626 \r
1627     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1628         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1629     }\r
1630 \r
1631     /**\r
1632      * Display the about box.\r
1633      */\r
1634     static void about() {\r
1635         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1636         about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
1637         about.append( "All Rights Reserved\n" );\r
1638         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1639         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1640         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1641         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1642         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1643         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1644             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1645         }\r
1646         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1647                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1648             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1649                     + ForesterUtil.OS_VERSION + "]\n" );\r
1650         }\r
1651         final Runtime rt = java.lang.Runtime.getRuntime();\r
1652         final long free_memory = rt.freeMemory() / 1000000;\r
1653         final long total_memory = rt.totalMemory() / 1000000;\r
1654         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1655         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1656         about.append( "References:\n" );\r
1657         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1658         about.append( "For more information & download:\n" );\r
1659         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1660         about.append( "Documentation:\n" );\r
1661         about.append( Constants.APTX_DOC_SITE + "\n" );\r
1662         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1663         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1664     }\r
1665 \r
1666     static void chooseNodeSize( final Options options, final Component parent ) {\r
1667         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1668                                                                  "Please enter the default size for node shapes.\n"\r
1669                                                                          + "[current value: "\r
1670                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1671                                                                  "Node Shape Size",\r
1672                                                                  JOptionPane.QUESTION_MESSAGE,\r
1673                                                                  null,\r
1674                                                                  null,\r
1675                                                                  options.getDefaultNodeShapeSize() );\r
1676         if ( !ForesterUtil.isEmpty( s ) ) {\r
1677             boolean success = true;\r
1678             double m = 0.0;\r
1679             final String m_str = s.trim();\r
1680             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1681                 try {\r
1682                     m = Double.parseDouble( m_str );\r
1683                 }\r
1684                 catch ( final Exception ex ) {\r
1685                     success = false;\r
1686                 }\r
1687             }\r
1688             else {\r
1689                 success = false;\r
1690             }\r
1691             if ( success && ( m >= 0.0 ) ) {\r
1692                 final short size = ForesterUtil.roundToShort( m );\r
1693                 if ( size >= 0.0 ) {\r
1694                     options.setDefaultNodeShapeSize( size );\r
1695                 }\r
1696             }\r
1697         }\r
1698     }\r
1699 \r
1700     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1701         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1702     }\r
1703 \r
1704     static JMenu createMenu( final String title, final Configuration conf ) {\r
1705         final JMenu jmenu = new JMenu( title );\r
1706         if ( !conf.isUseNativeUI() ) {\r
1707             jmenu.setFont( MainFrame.menu_font );\r
1708             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1709             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1710         }\r
1711         return jmenu;\r
1712     }\r
1713 \r
1714     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1715         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1716         if ( !configuration.isUseNativeUI() ) {\r
1717             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1718             label.setForeground( configuration.getGuiMenuTextColor() );\r
1719             label.setOpaque( true );\r
1720         }\r
1721         label.setSelected( false );\r
1722         label.setEnabled( false );\r
1723         return label;\r
1724     }\r
1725 \r
1726     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
1727         switch ( op.getDefaultNodeFill() ) {\r
1728             case GRADIENT:\r
1729                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1730                 break;\r
1731             case NONE:\r
1732                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1733                 break;\r
1734             case SOLID:\r
1735                 op.setDefaultNodeFill( NodeFill.NONE );\r
1736                 break;\r
1737             default:\r
1738                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1739         }\r
1740     }\r
1741 \r
1742     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
1743         switch ( op.getDefaultNodeShape() ) {\r
1744             case CIRCLE:\r
1745                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1746                 break;\r
1747             case RECTANGLE:\r
1748                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1749                 break;\r
1750             default:\r
1751                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1752         }\r
1753     }\r
1754 \r
1755     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1756         switch ( op.getOvPlacement() ) {\r
1757             case LOWER_LEFT:\r
1758                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1759                 break;\r
1760             case LOWER_RIGHT:\r
1761                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1762                 break;\r
1763             case UPPER_LEFT:\r
1764                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1765                 break;\r
1766             case UPPER_RIGHT:\r
1767                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1768                 break;\r
1769             default:\r
1770                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1771         }\r
1772         if ( tree_panel != null ) {\r
1773             tree_panel.updateOvSettings();\r
1774         }\r
1775     }\r
1776 \r
1777     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
1778         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
1779             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1780                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
1781         }\r
1782         else {\r
1783             mi.setText( "Cycle Node Shape Fill Type..." );\r
1784         }\r
1785     }\r
1786 \r
1787     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
1788         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
1789             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1790                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
1791         }\r
1792         else {\r
1793             mi.setText( "Cycle Node Shape Fill Type..." );\r
1794         }\r
1795     }\r
1796 \r
1797     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
1798         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
1799             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
1800         }\r
1801         else {\r
1802             mi.setText( "Cycle Overview Placement..." );\r
1803         }\r
1804     }\r
1805 \r
1806     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
1807         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
1808             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
1809                     + ")" );\r
1810         }\r
1811         else {\r
1812             mi.setText( "Select Color Scheme..." );\r
1813         }\r
1814     }\r
1815 \r
1816     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
1817         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
1818     }\r
1819 \r
1820     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
1821         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
1822             mi.setEnabled( true );\r
1823         }\r
1824         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
1825             mi.setEnabled( true );\r
1826         }\r
1827         else {\r
1828             mi.setEnabled( false );\r
1829         }\r
1830         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
1831     }\r
1832 \r
1833     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
1834         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
1835     }\r
1836 \r
1837     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
1838         for( final TreePanel tree_panel : treepanels ) {\r
1839             tree_panel.setTextAntialias();\r
1840         }\r
1841     }\r
1842 }\r