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         SEARCH_WITH_REGEX_TIP                   = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";\r
 109     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 110     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 111     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 112     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Shapes for External Nodes";\r
 113     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Shapes for Internal Nodes";\r
 114     static final String         DISPLAY_NODE_BOXES_LABEL_MARKED         = "Shapes for Nodes with Visual Data";\r
 115     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 116     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 117     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 118     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 119     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 120     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
 121     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 122     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 123     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 124     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 125     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 126     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 127     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 128     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 129     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 130     static final String         RIGHT_LINE_UP_DOMAINS                   = "Right-align Domain Architectures";\r
 131     static final String         LINE_UP_RENDERABLE_DATA                 = "Line Up Diagrams (such as Domain Architectures)";\r
 132     JMenuBar                    _jmenubar;\r
 133     JMenu                       _file_jmenu;\r
 134     JMenu                       _tools_menu;\r
 135     JMenu                       _view_jmenu;\r
 136     JMenu                       _options_jmenu;\r
 137     JMenu                       _font_size_menu;\r
 138     JMenu                       _help_jmenu;\r
 139     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 140     // Analysis menu\r
 141     JMenu                       _analysis_menu;\r
 142     JMenuItem                   _load_species_tree_item;\r
 143     JMenuItem                   _gsdi_item;\r
 144     JMenuItem                   _gsdir_item;\r
 145     JMenuItem                   _lineage_inference;\r
 146     // file menu:\r
 147     JMenuItem                   _open_item;\r
 148     JMenuItem                   _open_url_item;\r
 149     JMenuItem                   _save_item;\r
 150     JMenuItem                   _save_all_item;\r
 151     JMenuItem                   _close_item;\r
 152     JMenuItem                   _exit_item;\r
 153     JMenuItem                   _new_item;\r
 154     // tools menu:\r
 155     JMenuItem                   _midpoint_root_item;\r
 156     JMenuItem                   _taxcolor_item;\r
 157     JMenuItem                   _confcolor_item;\r
 158     JMenuItem                   _color_rank_jmi;\r
 159     JMenuItem                   _collapse_species_specific_subtrees;\r
 160     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 161     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 162     JMenuItem                   _obtain_seq_information_jmi;\r
 163     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 164     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 165     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 166     JMenuItem                   _annotate_item;\r
 167     JMenuItem                   _remove_branch_color_item;\r
 168     JMenuItem                   _remove_visual_styles_item;\r
 169     JMenuItem                   _delete_selected_nodes_item;\r
 170     JMenuItem                   _delete_not_selected_nodes_item;\r
 171     // font size menu:\r
 172     JMenuItem                   _super_tiny_fonts_item;\r
 173     JMenuItem                   _tiny_fonts_item;\r
 174     JMenuItem                   _small_fonts_item;\r
 175     JMenuItem                   _medium_fonts_item;\r
 176     JMenuItem                   _large_fonts_item;\r
 177     // options menu:\r
 178     // _  screen and print\r
 179     JMenuItem                   _choose_font_mi;\r
 180     JMenuItem                   _switch_colors_mi;\r
 181     JCheckBoxMenuItem           _label_direction_cbmi;\r
 182     // _  screen display\r
 183     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 184     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 185     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 186     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 187     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 188     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 189     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                                      //TODO fix me\r
 190     JCheckBoxMenuItem           _show_overview_cbmi;\r
 191     JCheckBoxMenuItem           _show_domain_labels;\r
 192     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 193     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 194     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 195     JMenuItem                   _overview_placment_mi;\r
 196     JMenuItem                   _choose_minimal_confidence_mi;\r
 197     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 198     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 199     JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;\r
 200     JMenuItem                   _cycle_node_shape_mi;\r
 201     JMenuItem                   _cycle_node_fill_mi;\r
 202     JMenuItem                   _choose_node_size_mi;\r
 203     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 204     JCheckBoxMenuItem           _right_line_up_domains_cbmi;\r
 205     JCheckBoxMenuItem           _line_up_renderable_data_cbmi;\r
 206     // _  print\r
 207     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 208     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 209     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 210     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 211     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 212     JMenuItem                   _print_size_mi;\r
 213     JMenuItem                   _choose_pdf_width_mi;\r
 214     // _  parsing\r
 215     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 216     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 217     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 218     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 219     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 220     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 221     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 222     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 223     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 224     // _  search\r
 225     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 226     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 227     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 228     JCheckBoxMenuItem           _search_with_regex_cbmi;\r
 229     // type menu:\r
 230     JMenu                       _type_menu;\r
 231     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 232     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 233     JCheckBoxMenuItem           _curved_type_cbmi;\r
 234     JCheckBoxMenuItem           _convex_type_cbmi;\r
 235     JCheckBoxMenuItem           _euro_type_cbmi;\r
 236     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 237     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 238     JCheckBoxMenuItem           _circular_type_cbmi;\r
 239     // view as text menu:\r
 240     JMenuItem                   _view_as_NH_item;\r
 241     JMenuItem                   _view_as_XML_item;\r
 242     JMenuItem                   _view_as_nexus_item;\r
 243     JMenuItem                   _display_basic_information_item;\r
 244     // help menu:\r
 245     JMenuItem                   _about_item;\r
 246     JMenuItem                   _help_item;\r
 247     JMenuItem                   _website_item;\r
 248     JMenuItem                   _phyloxml_website_item;\r
 249     JMenuItem                   _phyloxml_ref_item;\r
 250     JMenuItem                   _aptx_ref_item;\r
 251     // process menu:\r
 252     JMenu                       _process_menu;\r
 253     // Handy pointers to child components:\r
 254     MainPanel                   _mainpanel;\r
 255     Container                   _contentpane;\r
 256     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                                  ;\r
 257     Configuration               _configuration;\r
 258     Options                     _options;\r
 259     private Phylogeny           _species_tree;\r
 260     InferenceManager            _inference_manager;\r
 261     final ProcessPool           _process_pool;\r
 262     private String              _previous_node_annotation_ref;\r
 263 \r
 264     MainFrame() {\r
 265         _process_pool = ProcessPool.createInstance();\r
 266     }\r
 267 \r
 268     /**\r
 269      * Action performed.\r
 270      */\r
 271     @Override\r
 272     public void actionPerformed( final ActionEvent e ) {\r
 273         final Object o = e.getSource();\r
 274         boolean is_applet = false;\r
 275         JApplet applet = null;\r
 276         if ( getCurrentTreePanel() != null ) {\r
 277             is_applet = getCurrentTreePanel().isApplet();\r
 278             if ( is_applet ) {\r
 279                 applet = getCurrentTreePanel().obtainApplet();\r
 280             }\r
 281         }\r
 282         if ( o == _exit_item ) {\r
 283             close();\r
 284         }\r
 285         else if ( o == _gsdi_item ) {\r
 286             if ( isSubtreeDisplayed() ) {\r
 287                 return;\r
 288             }\r
 289             executeGSDI();\r
 290         }\r
 291         else if ( o == _gsdir_item ) {\r
 292             if ( isSubtreeDisplayed() ) {\r
 293                 return;\r
 294             }\r
 295             executeGSDIR();\r
 296         }\r
 297         else if ( o == _taxcolor_item ) {\r
 298             taxColor();\r
 299         }\r
 300         else if ( o == _confcolor_item ) {\r
 301             confColor();\r
 302         }\r
 303         else if ( o == _color_rank_jmi ) {\r
 304             colorRank();\r
 305         }\r
 306         else if ( o == _collapse_species_specific_subtrees ) {\r
 307             if ( isSubtreeDisplayed() ) {\r
 308                 return;\r
 309             }\r
 310             if ( getCurrentTreePanel() != null ) {\r
 311                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 312             }\r
 313         }\r
 314         else if ( o == _remove_branch_color_item ) {\r
 315             if ( isSubtreeDisplayed() ) {\r
 316                 return;\r
 317             }\r
 318             removeBranchColors();\r
 319         }\r
 320         else if ( o == _remove_visual_styles_item ) {\r
 321             if ( isSubtreeDisplayed() ) {\r
 322                 return;\r
 323             }\r
 324             removeVisualStyles();\r
 325         }\r
 326         else if ( o == _midpoint_root_item ) {\r
 327             if ( isSubtreeDisplayed() ) {\r
 328                 return;\r
 329             }\r
 330             midpointRoot();\r
 331         }\r
 332         else if ( o == _delete_selected_nodes_item ) {\r
 333             if ( isSubtreeDisplayed() ) {\r
 334                 return;\r
 335             }\r
 336             deleteSelectedNodes( true );\r
 337         }\r
 338         else if ( o == _delete_not_selected_nodes_item ) {\r
 339             if ( isSubtreeDisplayed() ) {\r
 340                 return;\r
 341             }\r
 342             deleteSelectedNodes( false );\r
 343         }\r
 344         else if ( o == _annotate_item ) {\r
 345             annotateSequences();\r
 346         }\r
 347         else if ( o == _switch_colors_mi ) {\r
 348             switchColors();\r
 349         }\r
 350         else if ( o == _display_basic_information_item ) {\r
 351             if ( getCurrentTreePanel() != null ) {\r
 352                 displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 353             }\r
 354         }\r
 355         else if ( o == _view_as_NH_item ) {\r
 356             viewAsNH();\r
 357         }\r
 358         else if ( o == _view_as_XML_item ) {\r
 359             viewAsXML();\r
 360         }\r
 361         else if ( o == _view_as_nexus_item ) {\r
 362             viewAsNexus();\r
 363         }\r
 364         else if ( o == _super_tiny_fonts_item ) {\r
 365             if ( getCurrentTreePanel() != null ) {\r
 366                 getCurrentTreePanel().setSuperTinyFonts();\r
 367                 getCurrentTreePanel().repaint();\r
 368             }\r
 369         }\r
 370         else if ( o == _tiny_fonts_item ) {\r
 371             if ( getCurrentTreePanel() != null ) {\r
 372                 getCurrentTreePanel().setTinyFonts();\r
 373                 getCurrentTreePanel().repaint();\r
 374             }\r
 375         }\r
 376         else if ( o == _small_fonts_item ) {\r
 377             if ( getCurrentTreePanel() != null ) {\r
 378                 getCurrentTreePanel().setSmallFonts();\r
 379                 getCurrentTreePanel().repaint();\r
 380             }\r
 381         }\r
 382         else if ( o == _medium_fonts_item ) {\r
 383             if ( getCurrentTreePanel() != null ) {\r
 384                 getCurrentTreePanel().setMediumFonts();\r
 385                 getCurrentTreePanel().repaint();\r
 386             }\r
 387         }\r
 388         else if ( o == _large_fonts_item ) {\r
 389             if ( getCurrentTreePanel() != null ) {\r
 390                 getCurrentTreePanel().setLargeFonts();\r
 391                 getCurrentTreePanel().repaint();\r
 392             }\r
 393         }\r
 394         else if ( o == _choose_font_mi ) {\r
 395             chooseFont();\r
 396         }\r
 397         else if ( o == _choose_minimal_confidence_mi ) {\r
 398             chooseMinimalConfidence();\r
 399         }\r
 400         else if ( o == _choose_node_size_mi ) {\r
 401             chooseNodeSize( getOptions(), this );\r
 402         }\r
 403         else if ( o == _overview_placment_mi ) {\r
 404             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 405         }\r
 406         else if ( o == _cycle_node_fill_mi ) {\r
 407             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
 408         }\r
 409         else if ( o == _cycle_node_shape_mi ) {\r
 410             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
 411         }\r
 412         else if ( o == _screen_antialias_cbmi ) {\r
 413             updateOptions( getOptions() );\r
 414             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 415         }\r
 416         else if ( o == _background_gradient_cbmi ) {\r
 417             updateOptions( getOptions() );\r
 418         }\r
 419         else if ( o == _show_domain_labels ) {\r
 420             updateOptions( getOptions() );\r
 421         }\r
 422         else if ( o == _show_annotation_ref_source ) {\r
 423             updateOptions( getOptions() );\r
 424         }\r
 425         else if ( o == _abbreviate_scientific_names ) {\r
 426             updateOptions( getOptions() );\r
 427         }\r
 428         else if ( o == _color_labels_same_as_parent_branch ) {\r
 429             updateOptions( getOptions() );\r
 430         }\r
 431         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 432             updateOptions( getOptions() );\r
 433         }\r
 434         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 435             updateOptions( getOptions() );\r
 436         }\r
 437         else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
 438             updateOptions( getOptions() );\r
 439         }\r
 440         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 441             updateOptions( getOptions() );\r
 442             showWhole();\r
 443         }\r
 444         else if ( o == _uniform_cladograms_rbmi ) {\r
 445             updateOptions( getOptions() );\r
 446             showWhole();\r
 447         }\r
 448         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 449             updateOptions( getOptions() );\r
 450             showWhole();\r
 451         }\r
 452         else if ( o == _search_case_senstive_cbmi ) {\r
 453             updateOptions( getOptions() );\r
 454             getMainPanel().getControlPanel().search0();\r
 455             getMainPanel().getControlPanel().search1();\r
 456         }\r
 457         else if ( o == _search_whole_words_only_cbmi ) {\r
 458             if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
 459                 _search_with_regex_cbmi.setSelected( false );\r
 460             }\r
 461             updateOptions( getOptions() );\r
 462             getMainPanel().getControlPanel().search0();\r
 463             getMainPanel().getControlPanel().search1();\r
 464         }\r
 465         else if ( o == _inverse_search_result_cbmi ) {\r
 466             updateOptions( getOptions() );\r
 467             getMainPanel().getControlPanel().search0();\r
 468             getMainPanel().getControlPanel().search1();\r
 469         }\r
 470         else if ( o == _search_with_regex_cbmi ) {\r
 471             if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
 472                 _search_whole_words_only_cbmi.setSelected( false );\r
 473             }\r
 474             if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
 475                 _search_case_senstive_cbmi.setSelected( true );\r
 476             }\r
 477             updateOptions( getOptions() );\r
 478             getMainPanel().getControlPanel().search0();\r
 479             getMainPanel().getControlPanel().search1();\r
 480         }\r
 481         else if ( o == _show_scale_cbmi ) {\r
 482             updateOptions( getOptions() );\r
 483         }\r
 484         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 485             updateOptions( getOptions() );\r
 486         }\r
 487         else if ( o == _show_confidence_stddev_cbmi ) {\r
 488             updateOptions( getOptions() );\r
 489         }\r
 490         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 491             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 492                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 493             }\r
 494             updateOptions( getOptions() );\r
 495         }\r
 496         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 497             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 498                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 499             }\r
 500             updateOptions( getOptions() );\r
 501         }\r
 502         else if ( o == _label_direction_cbmi ) {\r
 503             updateOptions( getOptions() );\r
 504         }\r
 505         else if ( o == _show_overview_cbmi ) {\r
 506             updateOptions( getOptions() );\r
 507             if ( getCurrentTreePanel() != null ) {\r
 508                 getCurrentTreePanel().updateOvSizes();\r
 509             }\r
 510         }\r
 511         else if ( o == _line_up_renderable_data_cbmi ) {\r
 512             if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
 513                 _right_line_up_domains_cbmi.setSelected( false );\r
 514             }\r
 515             updateOptions( getOptions() );\r
 516         }\r
 517         else if ( o == _right_line_up_domains_cbmi ) {\r
 518             if ( _right_line_up_domains_cbmi.isSelected() ) {\r
 519                 _line_up_renderable_data_cbmi.setSelected( true );\r
 520             }\r
 521             updateOptions( getOptions() );\r
 522         }\r
 523         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 524                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 525                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 526             typeChanged( o );\r
 527         }\r
 528         else if ( o == _about_item ) {\r
 529             about();\r
 530         }\r
 531         else if ( o == _help_item ) {\r
 532             try {\r
 533                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
 534             }\r
 535             catch ( final IOException e1 ) {\r
 536                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 537             }\r
 538         }\r
 539         else if ( o == _website_item ) {\r
 540             try {\r
 541                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 542             }\r
 543             catch ( final IOException e1 ) {\r
 544                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 545             }\r
 546         }\r
 547         else if ( o == _phyloxml_website_item ) {\r
 548             try {\r
 549                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 550             }\r
 551             catch ( final IOException e1 ) {\r
 552                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 553             }\r
 554         }\r
 555         else if ( o == _aptx_ref_item ) {\r
 556             try {\r
 557                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 558             }\r
 559             catch ( final IOException e1 ) {\r
 560                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 561             }\r
 562         }\r
 563         else if ( o == _phyloxml_ref_item ) {\r
 564             try {\r
 565                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 566             }\r
 567             catch ( final IOException e1 ) {\r
 568                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 569             }\r
 570         }\r
 571         else {\r
 572             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 573                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 574                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 575                         readPhylogeniesFromWebservice( i );\r
 576                     }\r
 577                 }\r
 578             }\r
 579         }\r
 580         _contentpane.repaint();\r
 581     }\r
 582 \r
 583     private void deleteSelectedNodes( final boolean delete ) {\r
 584         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
 585         if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
 586             return;\r
 587         }\r
 588         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
 589         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
 590             final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
 591             for( final PhylogenyNode n : all_selected_nodes ) {\r
 592                 if ( n.isExternal() ) {\r
 593                     nodes.add( n );\r
 594                 }\r
 595             }\r
 596         }\r
 597         String function = "Retain";\r
 598         if ( delete ) {\r
 599             function = "Delete";\r
 600         }\r
 601         if ( ( nodes == null ) || nodes.isEmpty() ) {\r
 602             JOptionPane\r
 603                     .showMessageDialog( this,\r
 604                                         "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
 605                                         "No external nodes selected to " + function.toLowerCase(),\r
 606                                         JOptionPane.ERROR_MESSAGE );\r
 607             return;\r
 608         }\r
 609         final int todo = nodes.size();\r
 610         final int ext = phy.getNumberOfExternalNodes();\r
 611         int res = todo;\r
 612         if ( delete ) {\r
 613             res = ext - todo;\r
 614         }\r
 615         if ( res < 1 ) {\r
 616             JOptionPane.showMessageDialog( this,\r
 617                                            "Cannot delete all nodes",\r
 618                                            "Attempt to delete all nodes ",\r
 619                                            JOptionPane.ERROR_MESSAGE );\r
 620             return;\r
 621         }\r
 622         final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
 623                 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
 624                 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
 625         if ( result == JOptionPane.OK_OPTION ) {\r
 626             if ( !delete ) {\r
 627                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
 628                 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
 629                     final PhylogenyNode n = it.next();\r
 630                     if ( !nodes.contains( n ) ) {\r
 631                         to_delete.add( n );\r
 632                     }\r
 633                 }\r
 634                 for( final PhylogenyNode n : to_delete ) {\r
 635                     phy.deleteSubtree( n, true );\r
 636                 }\r
 637             }\r
 638             else {\r
 639                 for( final PhylogenyNode n : nodes ) {\r
 640                     phy.deleteSubtree( n, true );\r
 641                 }\r
 642             }\r
 643             resetSearch();\r
 644             getCurrentTreePanel().setNodeInPreorderToNull();\r
 645             phy.externalNodesHaveChanged();\r
 646             phy.clearHashIdToNodeMap();\r
 647             phy.recalculateNumberOfExternalDescendants( true );\r
 648             getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
 649             getCurrentTreePanel().setEdited( true );\r
 650             repaint();\r
 651         }\r
 652     }\r
 653 \r
 654     void resetSearch() {\r
 655         getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
 656         getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
 657         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
 658         getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
 659         getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
 660         getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
 661         getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
 662         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
 663         getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
 664         getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
 665         getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
 666         getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
 667     }\r
 668 \r
 669     public Configuration getConfiguration() {\r
 670         return _configuration;\r
 671     }\r
 672 \r
 673     /**\r
 674      * This method returns the current external node data which\r
 675      * has been selected by the user by clicking the "Return ..."\r
 676      * menu item. This method is expected to be called from Javascript or\r
 677      * something like it.\r
 678      *\r
 679      * @return current external node data as String\r
 680      */\r
 681     public String getCurrentExternalNodesDataBuffer() {\r
 682         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 683     }\r
 684 \r
 685     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 686         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 687     }\r
 688 \r
 689     public int getCurrentExternalNodesDataBufferLength() {\r
 690         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 691     }\r
 692 \r
 693     public InferenceManager getInferenceManager() {\r
 694         return _inference_manager;\r
 695     }\r
 696 \r
 697     public MainPanel getMainPanel() {\r
 698         return _mainpanel;\r
 699     }\r
 700 \r
 701     public Options getOptions() {\r
 702         return _options;\r
 703     }\r
 704 \r
 705     public ProcessPool getProcessPool() {\r
 706         return _process_pool;\r
 707     }\r
 708 \r
 709     public void showTextFrame( final String s, final String title ) {\r
 710         checkTextFrames();\r
 711         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 712     }\r
 713 \r
 714     public void showWhole() {\r
 715         _mainpanel.getControlPanel().showWhole();\r
 716     }\r
 717 \r
 718     public void updateProcessMenu() {\r
 719         // In general Swing is not thread safe.\r
 720         // See "Swing's Threading Policy".\r
 721         SwingUtilities.invokeLater( new Runnable() {\r
 722 \r
 723             @Override\r
 724             public void run() {\r
 725                 doUpdateProcessMenu();\r
 726             }\r
 727         } );\r
 728     }\r
 729 \r
 730     void activateSaveAllIfNeeded() {\r
 731         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 732             _save_all_item.setEnabled( true );\r
 733         }\r
 734         else {\r
 735             _save_all_item.setEnabled( false );\r
 736         }\r
 737     }\r
 738 \r
 739     void buildFileMenu() {\r
 740         _file_jmenu = createMenu( "File", getConfiguration() );\r
 741         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 742         customizeJMenuItem( _exit_item );\r
 743         _jmenubar.add( _file_jmenu );\r
 744     }\r
 745 \r
 746     void buildFontSizeMenu() {\r
 747         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 748         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 749         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 750         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 751         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 752         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 753         customizeJMenuItem( _super_tiny_fonts_item );\r
 754         customizeJMenuItem( _tiny_fonts_item );\r
 755         customizeJMenuItem( _small_fonts_item );\r
 756         customizeJMenuItem( _medium_fonts_item );\r
 757         customizeJMenuItem( _large_fonts_item );\r
 758         _jmenubar.add( _font_size_menu );\r
 759     }\r
 760 \r
 761     void buildHelpMenu() {\r
 762         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 763         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
 764         _help_jmenu.addSeparator();\r
 765         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 766         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
 767         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 768         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 769         _help_jmenu.addSeparator();\r
 770         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 771         customizeJMenuItem( _help_item );\r
 772         customizeJMenuItem( _website_item );\r
 773         customizeJMenuItem( _phyloxml_website_item );\r
 774         customizeJMenuItem( _aptx_ref_item );\r
 775         customizeJMenuItem( _phyloxml_ref_item );\r
 776         customizeJMenuItem( _about_item );\r
 777         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 778         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 779         _jmenubar.add( _help_jmenu );\r
 780     }\r
 781 \r
 782     void buildTypeMenu() {\r
 783         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 784         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 785         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 786         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 787         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 788         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 789         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 790         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 791         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 792         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 793         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 794         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 795         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 796         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 797         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 798         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 799         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 800         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 801         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 802         initializeTypeMenu( getOptions() );\r
 803         _jmenubar.add( _type_menu );\r
 804     }\r
 805 \r
 806     void buildViewMenu() {\r
 807         _view_jmenu = createMenu( "View", getConfiguration() );\r
 808         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 809         _view_jmenu.addSeparator();\r
 810         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 811         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 812         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 813         customizeJMenuItem( _display_basic_information_item );\r
 814         customizeJMenuItem( _view_as_NH_item );\r
 815         customizeJMenuItem( _view_as_XML_item );\r
 816         customizeJMenuItem( _view_as_nexus_item );\r
 817         _jmenubar.add( _view_jmenu );\r
 818     }\r
 819 \r
 820     void checkTextFrames() {\r
 821         if ( _textframes.size() > 5 ) {\r
 822             try {\r
 823                 if ( _textframes.getFirst() != null ) {\r
 824                     _textframes.getFirst().removeMe();\r
 825                 }\r
 826                 else {\r
 827                     _textframes.removeFirst();\r
 828                 }\r
 829             }\r
 830             catch ( final NoSuchElementException e ) {\r
 831                 // Ignore.\r
 832             }\r
 833         }\r
 834     }\r
 835 \r
 836     void close() {\r
 837         removeAllTextFrames();\r
 838         if ( _mainpanel != null ) {\r
 839             _mainpanel.terminate();\r
 840         }\r
 841         if ( _contentpane != null ) {\r
 842             _contentpane.removeAll();\r
 843         }\r
 844         setVisible( false );\r
 845         dispose();\r
 846     }\r
 847 \r
 848     void colorRank() {\r
 849         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 850             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
 851             final String rank = ( String ) JOptionPane\r
 852                     .showInputDialog( this,\r
 853                                       "What rank should the colorization be based on",\r
 854                                       "Rank Selection",\r
 855                                       JOptionPane.QUESTION_MESSAGE,\r
 856                                       null,\r
 857                                       ranks,\r
 858                                       null );\r
 859             if ( !ForesterUtil.isEmpty( rank ) ) {\r
 860                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
 861             }\r
 862         }\r
 863     }\r
 864 \r
 865     void confColor() {\r
 866         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 867             _mainpanel.getCurrentTreePanel().confColor();\r
 868         }\r
 869     }\r
 870 \r
 871     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
 872         if ( item != null ) {\r
 873             item.setFont( MainFrame.menu_font );\r
 874             if ( !getConfiguration().isUseNativeUI() ) {\r
 875                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 876                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 877             }\r
 878             item.setSelected( is_selected );\r
 879             item.addActionListener( this );\r
 880         }\r
 881     }\r
 882 \r
 883     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
 884         if ( jmi != null ) {\r
 885             jmi.setFont( MainFrame.menu_font );\r
 886             if ( !getConfiguration().isUseNativeUI() ) {\r
 887                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 888                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 889             }\r
 890             jmi.addActionListener( this );\r
 891         }\r
 892         return jmi;\r
 893     }\r
 894 \r
 895     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
 896         if ( item != null ) {\r
 897             item.setFont( MainFrame.menu_font );\r
 898             if ( !getConfiguration().isUseNativeUI() ) {\r
 899                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 900                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 901             }\r
 902             item.setSelected( is_selected );\r
 903             item.addActionListener( this );\r
 904         }\r
 905     }\r
 906 \r
 907     void displayBasicInformation( final File treefile ) {\r
 908         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
 909             String title = "Basic Information";\r
 910             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
 911                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
 912             }\r
 913             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
 914         }\r
 915     }\r
 916 \r
 917     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
 918         try {\r
 919             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 920         }\r
 921         catch ( final Exception ex ) {\r
 922             // Do nothing.\r
 923         }\r
 924         JOptionPane.showMessageDialog( this,\r
 925                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
 926                                        "Error during File|Open",\r
 927                                        JOptionPane.ERROR_MESSAGE );\r
 928     }\r
 929 \r
 930     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
 931         try {\r
 932             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 933         }\r
 934         catch ( final Exception ex ) {\r
 935             // Do nothing.\r
 936         }\r
 937         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
 938     }\r
 939 \r
 940     void executeGSDI() {\r
 941         if ( !isOKforSDI( false, true ) ) {\r
 942             return;\r
 943         }\r
 944         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
 945             JOptionPane.showMessageDialog( this,\r
 946                                            "Gene tree is not rooted.",\r
 947                                            "Cannot execute GSDI",\r
 948                                            JOptionPane.ERROR_MESSAGE );\r
 949             return;\r
 950         }\r
 951         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 952         gene_tree.setAllNodesToNotCollapse();\r
 953         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 954         GSDI gsdi = null;\r
 955         final Phylogeny species_tree = getSpeciesTree().copy();\r
 956         try {\r
 957             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
 958         }\r
 959         catch ( final SDIException e ) {\r
 960             JOptionPane.showMessageDialog( this,\r
 961                                            e.getLocalizedMessage(),\r
 962                                            "Error during GSDI",\r
 963                                            JOptionPane.ERROR_MESSAGE );\r
 964             return;\r
 965         }\r
 966         catch ( final Exception e ) {\r
 967             AptxUtil.unexpectedException( e );\r
 968             return;\r
 969         }\r
 970         gene_tree.setRerootable( false );\r
 971         gene_tree.clearHashIdToNodeMap();\r
 972         gene_tree.recalculateNumberOfExternalDescendants( true );\r
 973         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
 974         getMainPanel().getControlPanel().setShowEvents( true );\r
 975         showWhole();\r
 976         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 977         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 978         showWhole();\r
 979         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 980         showWhole();\r
 981         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 982         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 983         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 984             JOptionPane.showMessageDialog( this,\r
 985                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 986                                                    + "Potential duplications: "\r
 987                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 988                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 989                                                    + "Stripped gene tree nodes: "\r
 990                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 991                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 992                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 993                                            "GSDI successfully completed",\r
 994                                            JOptionPane.WARNING_MESSAGE );\r
 995         }\r
 996         else {\r
 997             JOptionPane.showMessageDialog( this,\r
 998                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 999                                                    + "Potential duplications: "\r
1000                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
1001                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
1002                                                    + "Stripped gene tree nodes: "\r
1003                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1004                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
1005                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1006                                            "GSDI successfully completed",\r
1007                                            JOptionPane.INFORMATION_MESSAGE );\r
1008         }\r
1009     }\r
1010 \r
1011     void executeGSDIR() {\r
1012         if ( !isOKforSDI( false, false ) ) {\r
1013             return;\r
1014         }\r
1015         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
1016         if ( ( p > 0 )\r
1017                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
1018             JOptionPane.showMessageDialog( this,\r
1019                                            "Gene tree is not completely binary",\r
1020                                            "Cannot execute GSDI",\r
1021                                            JOptionPane.ERROR_MESSAGE );\r
1022             return;\r
1023         }\r
1024         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
1025         gene_tree.setAllNodesToNotCollapse();\r
1026         gene_tree.recalculateNumberOfExternalDescendants( false );\r
1027         GSDIR gsdir = null;\r
1028         final Phylogeny species_tree = getSpeciesTree().copy();\r
1029         try {\r
1030             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
1031         }\r
1032         catch ( final SDIException e ) {\r
1033             JOptionPane.showMessageDialog( this,\r
1034                                            e.getLocalizedMessage(),\r
1035                                            "Error during GSDIR",\r
1036                                            JOptionPane.ERROR_MESSAGE );\r
1037             return;\r
1038         }\r
1039         catch ( final Exception e ) {\r
1040             AptxUtil.unexpectedException( e );\r
1041             return;\r
1042         }\r
1043         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
1044         result_gene_tree.setRerootable( false );\r
1045         result_gene_tree.clearHashIdToNodeMap();\r
1046         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
1047         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
1048         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
1049         getMainPanel().getControlPanel().setShowEvents( true );\r
1050         showWhole();\r
1051         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1052         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1053         showWhole();\r
1054         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1055         showWhole();\r
1056         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1057         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1058         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1059             JOptionPane.showMessageDialog( this,\r
1060                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1061                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1062                                                    + "Stripped gene tree nodes: "\r
1063                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1064                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1065                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1066                                            "GSDIR successfully completed",\r
1067                                            JOptionPane.WARNING_MESSAGE );\r
1068         }\r
1069         else {\r
1070             JOptionPane.showMessageDialog( this,\r
1071                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1072                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1073                                                    + "Stripped gene tree nodes: "\r
1074                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1075                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1076                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1077                                            "GSDIR successfully completed",\r
1078                                            JOptionPane.INFORMATION_MESSAGE );\r
1079         }\r
1080     }\r
1081 \r
1082     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
1083         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
1084             JOptionPane.showMessageDialog( this,\r
1085                                            "Gene tree and species tree have no species in common.",\r
1086                                            "Error during SDI",\r
1087                                            JOptionPane.ERROR_MESSAGE );\r
1088             return false;\r
1089         }\r
1090         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
1091             JOptionPane.showMessageDialog( this,\r
1092                                            "Gene tree and species tree have only one species in common.",\r
1093                                            "Error during SDI",\r
1094                                            JOptionPane.ERROR_MESSAGE );\r
1095             return false;\r
1096         }\r
1097         else {\r
1098             return true;\r
1099         }\r
1100     }\r
1101 \r
1102     TreePanel getCurrentTreePanel() {\r
1103         return getMainPanel().getCurrentTreePanel();\r
1104     }\r
1105 \r
1106     JMenu getHelpMenu() {\r
1107         return _help_jmenu;\r
1108     }\r
1109 \r
1110     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
1111         return _label_direction_cbmi;\r
1112     }\r
1113 \r
1114     JMenuBar getMenuBarOfMainFrame() {\r
1115         return _jmenubar;\r
1116     }\r
1117 \r
1118     final Phylogeny getSpeciesTree() {\r
1119         return _species_tree;\r
1120     }\r
1121 \r
1122     void initializeTypeMenu( final Options options ) {\r
1123         setTypeMenuToAllUnselected();\r
1124         switch ( options.getPhylogenyGraphicsType() ) {\r
1125             case CONVEX:\r
1126                 _convex_type_cbmi.setSelected( true );\r
1127                 break;\r
1128             case CURVED:\r
1129                 _curved_type_cbmi.setSelected( true );\r
1130                 break;\r
1131             case EURO_STYLE:\r
1132                 _euro_type_cbmi.setSelected( true );\r
1133                 break;\r
1134             case ROUNDED:\r
1135                 _rounded_type_cbmi.setSelected( true );\r
1136                 break;\r
1137             case TRIANGULAR:\r
1138                 _triangular_type_cbmi.setSelected( true );\r
1139                 break;\r
1140             case UNROOTED:\r
1141                 _unrooted_type_cbmi.setSelected( true );\r
1142                 break;\r
1143             case CIRCULAR:\r
1144                 _circular_type_cbmi.setSelected( true );\r
1145                 break;\r
1146             default:\r
1147                 _rectangular_type_cbmi.setSelected( true );\r
1148                 break;\r
1149         }\r
1150     }\r
1151 \r
1152     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1153         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1154             return false;\r
1155         }\r
1156         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1157             JOptionPane.showMessageDialog( this,\r
1158                                            "No species tree loaded",\r
1159                                            "Cannot execute GSDI",\r
1160                                            JOptionPane.ERROR_MESSAGE );\r
1161             return false;\r
1162         }\r
1163         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1164             JOptionPane.showMessageDialog( this,\r
1165                                            "Species tree is not completely binary",\r
1166                                            "Cannot execute GSDI",\r
1167                                            JOptionPane.ERROR_MESSAGE );\r
1168             return false;\r
1169         }\r
1170         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1171             JOptionPane.showMessageDialog( this,\r
1172                                            "Gene tree is not completely binary",\r
1173                                            "Cannot execute GSDI",\r
1174                                            JOptionPane.ERROR_MESSAGE );\r
1175             return false;\r
1176         }\r
1177         else {\r
1178             return true;\r
1179         }\r
1180     }\r
1181 \r
1182     boolean isSubtreeDisplayed() {\r
1183         if ( getCurrentTreePanel() != null ) {\r
1184             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1185                 JOptionPane\r
1186                         .showMessageDialog( this,\r
1187                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1188                                             "Operation can not be exectuted on a sub-tree",\r
1189                                             JOptionPane.WARNING_MESSAGE );\r
1190                 return true;\r
1191             }\r
1192         }\r
1193         return false;\r
1194     }\r
1195 \r
1196     void midpointRoot() {\r
1197         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1198             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1199         }\r
1200     }\r
1201 \r
1202     void readPhylogeniesFromWebservice( final int i ) {\r
1203         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1204         new Thread( reader ).start();\r
1205     }\r
1206 \r
1207     void removeAllTextFrames() {\r
1208         for( final TextFrame tf : _textframes ) {\r
1209             if ( tf != null ) {\r
1210                 tf.close();\r
1211             }\r
1212         }\r
1213         _textframes.clear();\r
1214     }\r
1215 \r
1216     void setConfiguration( final Configuration configuration ) {\r
1217         _configuration = configuration;\r
1218     }\r
1219 \r
1220     void setInferenceManager( final InferenceManager i ) {\r
1221         _inference_manager = i;\r
1222     }\r
1223 \r
1224     void setOptions( final Options options ) {\r
1225         _options = options;\r
1226     }\r
1227 \r
1228     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1229         setTypeMenuToAllUnselected();\r
1230         switch ( type ) {\r
1231             case CIRCULAR:\r
1232                 _circular_type_cbmi.setSelected( true );\r
1233                 break;\r
1234             case CONVEX:\r
1235                 _convex_type_cbmi.setSelected( true );\r
1236                 break;\r
1237             case CURVED:\r
1238                 _curved_type_cbmi.setSelected( true );\r
1239                 break;\r
1240             case EURO_STYLE:\r
1241                 _euro_type_cbmi.setSelected( true );\r
1242                 break;\r
1243             case ROUNDED:\r
1244                 _rounded_type_cbmi.setSelected( true );\r
1245                 break;\r
1246             case RECTANGULAR:\r
1247                 _rectangular_type_cbmi.setSelected( true );\r
1248                 break;\r
1249             case TRIANGULAR:\r
1250                 _triangular_type_cbmi.setSelected( true );\r
1251                 break;\r
1252             case UNROOTED:\r
1253                 _unrooted_type_cbmi.setSelected( true );\r
1254                 break;\r
1255             default:\r
1256                 throw new IllegalArgumentException( "unknown type: " + type );\r
1257         }\r
1258     }\r
1259 \r
1260     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1261         _species_tree = species_tree;\r
1262     }\r
1263 \r
1264     void setTypeMenuToAllUnselected() {\r
1265         _convex_type_cbmi.setSelected( false );\r
1266         _curved_type_cbmi.setSelected( false );\r
1267         _euro_type_cbmi.setSelected( false );\r
1268         _rounded_type_cbmi.setSelected( false );\r
1269         _triangular_type_cbmi.setSelected( false );\r
1270         _rectangular_type_cbmi.setSelected( false );\r
1271         _unrooted_type_cbmi.setSelected( false );\r
1272         _circular_type_cbmi.setSelected( false );\r
1273     }\r
1274 \r
1275     void switchColors() {\r
1276         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1277         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1278         csc.setVisible( true );\r
1279     }\r
1280 \r
1281     void taxColor() {\r
1282         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1283             _mainpanel.getCurrentTreePanel().taxColor();\r
1284         }\r
1285     }\r
1286 \r
1287     void typeChanged( final Object o ) {\r
1288         updateTypeCheckboxes( getOptions(), o );\r
1289         updateOptions( getOptions() );\r
1290         if ( getCurrentTreePanel() != null ) {\r
1291             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1292             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1293             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1294                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1295                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1296                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1297                 getCurrentTreePanel().getControlPanel().showWhole();\r
1298             }\r
1299             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1300                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1301             }\r
1302             else {\r
1303                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1304             }\r
1305             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1306             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1307             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1308                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1309                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1310                 }\r
1311                 else {\r
1312                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1313                 }\r
1314             }\r
1315         }\r
1316     }\r
1317 \r
1318     void updateOptions( final Options options ) {\r
1319         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1320         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1321                 && _background_gradient_cbmi.isSelected() );\r
1322         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1323         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1324                 && _show_annotation_ref_source.isSelected() );\r
1325         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1326                 && _abbreviate_scientific_names.isSelected() );\r
1327         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1328                 && _color_labels_same_as_parent_branch.isSelected() );\r
1329         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1330                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1331         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1332                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
1333         options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
1334                 && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
1335         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1336             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1337         }\r
1338         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1339             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1340         }\r
1341         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1342             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1343         }\r
1344         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1345                 && _search_case_senstive_cbmi.isSelected() );\r
1346         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1347             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1348         }\r
1349         if ( _label_direction_cbmi != null ) {\r
1350             if ( _label_direction_cbmi.isSelected() ) {\r
1351                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1352             }\r
1353             else {\r
1354                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1355             }\r
1356         }\r
1357         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1358         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1359                 && _show_confidence_stddev_cbmi.isSelected() );\r
1360         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1361             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1362         }\r
1363         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1364                 && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1365         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1366                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1367         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1368         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1369                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1370             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1371         }\r
1372         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1373                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1374             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1375         }\r
1376         else {\r
1377             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1378         }\r
1379         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1380                 && _print_black_and_white_cbmi.isSelected() );\r
1381         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1382                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1383         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1384             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1385         }\r
1386         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1387             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1388         }\r
1389         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1390             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1391         }\r
1392         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1393             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1394         }\r
1395         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1396                 && _replace_underscores_cbmi.isSelected() );\r
1397         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1398                 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1399         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1400                 && _search_whole_words_only_cbmi.isSelected() );\r
1401         options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
1402         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1403                 && _inverse_search_result_cbmi.isSelected() );\r
1404         if ( _graphics_export_visible_only_cbmi != null ) {\r
1405             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1406             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1407                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1408                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1409             }\r
1410             else {\r
1411                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1412             }\r
1413         }\r
1414         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1415             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1416         }\r
1417         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1418             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1419         }\r
1420         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1421             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1422         }\r
1423         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1424             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1425         }\r
1426         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1427             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1428         }\r
1429         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1430             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1431         }\r
1432         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1433             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1434         }\r
1435         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1436             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1437         }\r
1438         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
1439             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
1440         }\r
1441         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
1442             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
1443         }\r
1444     }\r
1445 \r
1446     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1447         setTypeMenuToAllUnselected();\r
1448         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1449     }\r
1450 \r
1451     void viewAsNexus() {\r
1452         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1453             String title = "Nexus";\r
1454             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1455                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1456             }\r
1457             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1458                            title );\r
1459         }\r
1460     }\r
1461 \r
1462     void viewAsNH() {\r
1463         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1464             String title = "New Hampshire";\r
1465             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1466                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1467             }\r
1468             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1469                                    .getNhConversionSupportValueStyle() ),\r
1470                            title );\r
1471         }\r
1472     }\r
1473 \r
1474     void viewAsXML() {\r
1475         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1476             String title = "phyloXML";\r
1477             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1478                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1479             }\r
1480             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1481         }\r
1482     }\r
1483 \r
1484     private void annotateSequences() {\r
1485         if ( getCurrentTreePanel() != null ) {\r
1486             List<PhylogenyNode> nodes = null;\r
1487             if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
1488                     || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
1489                 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
1490             }\r
1491             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1492                 JOptionPane\r
1493                         .showMessageDialog( this,\r
1494                                             "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1495                                             "No nodes selected for annotation",\r
1496                                             JOptionPane.ERROR_MESSAGE );\r
1497                 return;\r
1498             }\r
1499             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1500             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1501                 final JTextField ref_field = new JTextField( 10 );\r
1502                 final JTextField desc_filed = new JTextField( 20 );\r
1503                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1504                         : getPreviousNodeAnnotationReference() );\r
1505                 final JPanel my_panel = new JPanel();\r
1506                 my_panel.add( new JLabel( "Reference " ) );\r
1507                 my_panel.add( ref_field );\r
1508                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1509                 my_panel.add( new JLabel( "Description " ) );\r
1510                 my_panel.add( desc_filed );\r
1511                 final int result = JOptionPane.showConfirmDialog( null,\r
1512                                                                   my_panel,\r
1513                                                                   "Enter the sequence annotation(s) for the "\r
1514                                                                           + nodes.size() + " selected nodes",\r
1515                                                                   JOptionPane.OK_CANCEL_OPTION );\r
1516                 if ( result == JOptionPane.OK_OPTION ) {\r
1517                     String ref = ref_field.getText();\r
1518                     String desc = desc_filed.getText();\r
1519                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1520                         ref = ref.trim();\r
1521                         ref = ref.replaceAll( "\\s+", " " );\r
1522                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1523                                 || ( ref.length() < 3 ) ) {\r
1524                             JOptionPane.showMessageDialog( this,\r
1525                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1526                                                            "Illegal Format for Annotation Reference",\r
1527                                                            JOptionPane.ERROR_MESSAGE );\r
1528                             return;\r
1529                         }\r
1530                     }\r
1531                     if ( ref != null ) {\r
1532                         setPreviousNodeAnnotationReference( ref );\r
1533                     }\r
1534                     if ( desc != null ) {\r
1535                         desc = desc.trim();\r
1536                         desc = desc.replaceAll( "\\s+", " " );\r
1537                     }\r
1538                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1539                         for( final PhylogenyNode n : nodes ) {\r
1540                             ForesterUtil.ensurePresenceOfSequence( n );\r
1541                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1542                                     : new Annotation( ref );\r
1543                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1544                                 ann.setDesc( desc );\r
1545                             }\r
1546                             n.getNodeData().getSequence().addAnnotation( ann );\r
1547                         }\r
1548                     }\r
1549                     getMainPanel().getControlPanel().showAnnotations();\r
1550                 }\r
1551             }\r
1552         }\r
1553     }\r
1554 \r
1555     private void chooseFont() {\r
1556         final FontChooser fc = new FontChooser();\r
1557         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1558         fc.showDialog( this, "Select the Base Font" );\r
1559         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1560     }\r
1561 \r
1562     private void chooseMinimalConfidence() {\r
1563         final String s = ( String ) JOptionPane\r
1564                 .showInputDialog( this,\r
1565                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1566                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1567                                   "Minimal Confidence Value",\r
1568                                   JOptionPane.QUESTION_MESSAGE,\r
1569                                   null,\r
1570                                   null,\r
1571                                   getOptions().getMinConfidenceValue() );\r
1572         if ( !ForesterUtil.isEmpty( s ) ) {\r
1573             boolean success = true;\r
1574             double m = 0.0;\r
1575             final String m_str = s.trim();\r
1576             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1577                 try {\r
1578                     m = Double.parseDouble( m_str );\r
1579                 }\r
1580                 catch ( final Exception ex ) {\r
1581                     success = false;\r
1582                 }\r
1583             }\r
1584             else {\r
1585                 success = false;\r
1586             }\r
1587             if ( success && ( m >= 0.0 ) ) {\r
1588                 getOptions().setMinConfidenceValue( m );\r
1589             }\r
1590         }\r
1591     }\r
1592 \r
1593     private void doUpdateProcessMenu() {\r
1594         if ( _process_pool.size() > 0 ) {\r
1595             if ( _process_menu == null ) {\r
1596                 _process_menu = createMenu( "", getConfiguration() );\r
1597                 _process_menu.setForeground( Color.RED );\r
1598             }\r
1599             _process_menu.removeAll();\r
1600             final String text = "processes running: " + _process_pool.size();\r
1601             _process_menu.setText( text );\r
1602             _jmenubar.add( _process_menu );\r
1603             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1604                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1605                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1606             }\r
1607         }\r
1608         else {\r
1609             if ( _process_menu != null ) {\r
1610                 _process_menu.removeAll();\r
1611                 _jmenubar.remove( _process_menu );\r
1612             }\r
1613         }\r
1614         _jmenubar.validate();\r
1615         _jmenubar.repaint();\r
1616         repaint();\r
1617     }\r
1618 \r
1619     private String getPreviousNodeAnnotationReference() {\r
1620         return _previous_node_annotation_ref;\r
1621     }\r
1622 \r
1623     private void removeBranchColors() {\r
1624         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1625             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1626         }\r
1627     }\r
1628 \r
1629     private void removeVisualStyles() {\r
1630         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1631             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1632         }\r
1633     }\r
1634 \r
1635     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1636         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1637     }\r
1638 \r
1639     /**\r
1640      * Display the about box.\r
1641      */\r
1642     static void about() {\r
1643         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1644         about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
1645         about.append( "All Rights Reserved\n" );\r
1646         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1647         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1648         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1649         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1650         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1651         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1652             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1653         }\r
1654         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1655                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1656             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1657                     + ForesterUtil.OS_VERSION + "]\n" );\r
1658         }\r
1659         final Runtime rt = java.lang.Runtime.getRuntime();\r
1660         final long free_memory = rt.freeMemory() / 1000000;\r
1661         final long total_memory = rt.totalMemory() / 1000000;\r
1662         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1663         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1664         about.append( "References:\n" );\r
1665         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1666         about.append( "For more information & download:\n" );\r
1667         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1668         about.append( "Documentation:\n" );\r
1669         about.append( Constants.APTX_DOC_SITE + "\n" );\r
1670         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1671         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1672     }\r
1673 \r
1674     static void chooseNodeSize( final Options options, final Component parent ) {\r
1675         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1676                                                                  "Please enter the default size for node shapes.\n"\r
1677                                                                          + "[current value: "\r
1678                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1679                                                                  "Node Shape Size",\r
1680                                                                  JOptionPane.QUESTION_MESSAGE,\r
1681                                                                  null,\r
1682                                                                  null,\r
1683                                                                  options.getDefaultNodeShapeSize() );\r
1684         if ( !ForesterUtil.isEmpty( s ) ) {\r
1685             boolean success = true;\r
1686             double m = 0.0;\r
1687             final String m_str = s.trim();\r
1688             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1689                 try {\r
1690                     m = Double.parseDouble( m_str );\r
1691                 }\r
1692                 catch ( final Exception ex ) {\r
1693                     success = false;\r
1694                 }\r
1695             }\r
1696             else {\r
1697                 success = false;\r
1698             }\r
1699             if ( success && ( m >= 0.0 ) ) {\r
1700                 final short size = ForesterUtil.roundToShort( m );\r
1701                 if ( size >= 0.0 ) {\r
1702                     options.setDefaultNodeShapeSize( size );\r
1703                 }\r
1704             }\r
1705         }\r
1706     }\r
1707 \r
1708     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1709         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1710     }\r
1711 \r
1712     static JMenu createMenu( final String title, final Configuration conf ) {\r
1713         final JMenu jmenu = new JMenu( title );\r
1714         if ( !conf.isUseNativeUI() ) {\r
1715             jmenu.setFont( MainFrame.menu_font );\r
1716             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1717             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1718         }\r
1719         return jmenu;\r
1720     }\r
1721 \r
1722     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1723         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1724         if ( !configuration.isUseNativeUI() ) {\r
1725             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1726             label.setForeground( configuration.getGuiMenuTextColor() );\r
1727             label.setOpaque( true );\r
1728         }\r
1729         label.setSelected( false );\r
1730         label.setEnabled( false );\r
1731         return label;\r
1732     }\r
1733 \r
1734     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
1735         switch ( op.getDefaultNodeFill() ) {\r
1736             case GRADIENT:\r
1737                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1738                 break;\r
1739             case NONE:\r
1740                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1741                 break;\r
1742             case SOLID:\r
1743                 op.setDefaultNodeFill( NodeFill.NONE );\r
1744                 break;\r
1745             default:\r
1746                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1747         }\r
1748     }\r
1749 \r
1750     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
1751         switch ( op.getDefaultNodeShape() ) {\r
1752             case CIRCLE:\r
1753                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1754                 break;\r
1755             case RECTANGLE:\r
1756                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1757                 break;\r
1758             default:\r
1759                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1760         }\r
1761     }\r
1762 \r
1763     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1764         switch ( op.getOvPlacement() ) {\r
1765             case LOWER_LEFT:\r
1766                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1767                 break;\r
1768             case LOWER_RIGHT:\r
1769                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1770                 break;\r
1771             case UPPER_LEFT:\r
1772                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1773                 break;\r
1774             case UPPER_RIGHT:\r
1775                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1776                 break;\r
1777             default:\r
1778                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1779         }\r
1780         if ( tree_panel != null ) {\r
1781             tree_panel.updateOvSettings();\r
1782         }\r
1783     }\r
1784 \r
1785     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
1786         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
1787             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1788                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
1789         }\r
1790         else {\r
1791             mi.setText( "Cycle Node Shape Fill Type..." );\r
1792         }\r
1793     }\r
1794 \r
1795     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
1796         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
1797             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1798                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
1799         }\r
1800         else {\r
1801             mi.setText( "Cycle Node Shape Fill Type..." );\r
1802         }\r
1803     }\r
1804 \r
1805     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
1806         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
1807             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
1808         }\r
1809         else {\r
1810             mi.setText( "Cycle Overview Placement..." );\r
1811         }\r
1812     }\r
1813 \r
1814     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
1815         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
1816             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
1817                     + ")" );\r
1818         }\r
1819         else {\r
1820             mi.setText( "Select Color Scheme..." );\r
1821         }\r
1822     }\r
1823 \r
1824     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
1825         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
1826     }\r
1827 \r
1828     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
1829         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
1830             mi.setEnabled( true );\r
1831         }\r
1832         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
1833             mi.setEnabled( true );\r
1834         }\r
1835         else {\r
1836             mi.setEnabled( false );\r
1837         }\r
1838         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
1839     }\r
1840 \r
1841     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
1842         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
1843     }\r
1844 \r
1845     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
1846         for( final TreePanel tree_panel : treepanels ) {\r
1847             tree_panel.setTextAntialias();\r
1848         }\r
1849     }\r
1850 }\r