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