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