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

   1 // $Id:\r
   2 // FORESTER -- software libraries and applications\r
   3 // for evolutionary biology research and applications.\r
   4 //\r
   5 // Copyright (C) 2008-2010 Christian M. Zmasek\r
   6 // All rights reserved\r
   7 //\r
   8 // This library is free software; you can redistribute it and/or\r
   9 // modify it under the terms of the GNU Lesser General Public\r
  10 // License as published by the Free Software Foundation; either\r
  11 // version 2.1 of the License, or (at your option) any later version.\r
  12 //\r
  13 // This library is distributed in the hope that it will be useful,\r
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
  16 // Lesser General Public License for more details.\r
  17 //\r
  18 // You should have received a copy of the GNU Lesser General Public\r
  19 // License along with this library; if not, write to the Free Software\r
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
  21 //\r
  22 // Contact: phylosoft @ gmail . com\r
  23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
  24 \r
  25 package org.forester.archaeopteryx;\r
  26 \r
  27 import java.awt.Color;\r
  28 import java.awt.Component;\r
  29 import java.awt.Container;\r
  30 import java.awt.Font;\r
  31 import java.awt.event.ActionEvent;\r
  32 import java.awt.event.ActionListener;\r
  33 import java.io.File;\r
  34 import java.io.IOException;\r
  35 import java.util.ArrayList;\r
  36 import java.util.LinkedList;\r
  37 import java.util.List;\r
  38 import java.util.Locale;\r
  39 import java.util.NoSuchElementException;\r
  40 \r
  41 import javax.swing.Box;\r
  42 import javax.swing.JApplet;\r
  43 import javax.swing.JCheckBoxMenuItem;\r
  44 import javax.swing.JFrame;\r
  45 import javax.swing.JLabel;\r
  46 import javax.swing.JMenu;\r
  47 import javax.swing.JMenuBar;\r
  48 import javax.swing.JMenuItem;\r
  49 import javax.swing.JOptionPane;\r
  50 import javax.swing.JPanel;\r
  51 import javax.swing.JRadioButtonMenuItem;\r
  52 import javax.swing.JTextField;\r
  53 import javax.swing.SwingUtilities;\r
  54 \r
  55 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
  56 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
  57 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
  58 import org.forester.archaeopteryx.tools.InferenceManager;\r
  59 import org.forester.archaeopteryx.tools.ProcessPool;\r
  60 import org.forester.archaeopteryx.tools.ProcessRunning;\r
  61 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
  62 import org.forester.phylogeny.Phylogeny;\r
  63 import org.forester.phylogeny.PhylogenyMethods;\r
  64 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
  65 import org.forester.phylogeny.PhylogenyNode;\r
  66 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
  67 import org.forester.phylogeny.data.Annotation;\r
  68 import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
  69 import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
  70 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
  71 import org.forester.sdi.GSDI;\r
  72 import org.forester.sdi.GSDIR;\r
  73 import org.forester.sdi.SDIException;\r
  74 import org.forester.util.ForesterConstants;\r
  75 import org.forester.util.ForesterUtil;\r
  76 \r
  77 public abstract class MainFrame extends JFrame implements ActionListener {\r
  78 \r
  79     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
  80     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME\r
  81     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
  82     private static final long   serialVersionUID                        = 3655000897845508358L;\r
  83     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
  84                                                                                     Font.PLAIN,\r
  85                                                                                     10 );\r
  86     static final String         TYPE_MENU_HEADER                        = "Type";\r
  87     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
  88     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
  89     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
  90     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
  91     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
  92     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
  93     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO\r
  94     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO\r
  95     static final String         OPTIONS_HEADER                          = "Options";\r
  96     static final String         SEARCH_SUBHEADER                        = "Search:";\r
  97     static final String         DISPLAY_SUBHEADER                       = "Display:";\r
  98     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
  99     static final String         SEARCH_REGEX_LABEL                      = "Search with Regular Expressions";\r
 100     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
 101     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
 102     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
 103     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
 104     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
 105     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
 106     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
 107     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
 108     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 109     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 110     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 111     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Shapes for External Nodes";\r
 112     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Shapes for Internal Nodes";\r
 113     static final String         DISPLAY_NODE_BOXES_LABEL_MARKED         = "Shapes for Nodes with Visual Data";\r
 114     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 115     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 116     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 117     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 118     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 119     static final String         COLOR_LABELS_TIP                        = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";\r
 120     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 121     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 122     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 123     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 124     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 125     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 126     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 127     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 128     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 129     static final String         RIGHT_LINE_UP_DOMAINS                   = "Right-align Domain Architectures";\r
 130     static final String         LINE_UP_RENDERABLE_DATA                 = "Line Up Diagrams (such as Domain Architectures)";\r
 131     JMenuBar                    _jmenubar;\r
 132     JMenu                       _file_jmenu;\r
 133     JMenu                       _tools_menu;\r
 134     JMenu                       _view_jmenu;\r
 135     JMenu                       _options_jmenu;\r
 136     JMenu                       _font_size_menu;\r
 137     JMenu                       _help_jmenu;\r
 138     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 139     // Analysis menu\r
 140     JMenu                       _analysis_menu;\r
 141     JMenuItem                   _load_species_tree_item;\r
 142     JMenuItem                   _gsdi_item;\r
 143     JMenuItem                   _gsdir_item;\r
 144     JMenuItem                   _lineage_inference;\r
 145     // file menu:\r
 146     JMenuItem                   _open_item;\r
 147     JMenuItem                   _open_url_item;\r
 148     JMenuItem                   _save_item;\r
 149     JMenuItem                   _save_all_item;\r
 150     JMenuItem                   _close_item;\r
 151     JMenuItem                   _exit_item;\r
 152     JMenuItem                   _new_item;\r
 153     // tools menu:\r
 154     JMenuItem                   _midpoint_root_item;\r
 155     JMenuItem                   _taxcolor_item;\r
 156     JMenuItem                   _confcolor_item;\r
 157     JMenuItem                   _color_rank_jmi;\r
 158     JMenuItem                   _collapse_species_specific_subtrees;\r
 159     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 160     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 161     JMenuItem                   _obtain_seq_information_jmi;\r
 162     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 163     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 164     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 165     JMenuItem                   _annotate_item;\r
 166     JMenuItem                   _remove_branch_color_item;\r
 167     JMenuItem                   _remove_visual_styles_item;\r
 168     JMenuItem                   _delete_selected_nodes_item;\r
 169     JMenuItem                   _delete_not_selected_nodes_item;\r
 170     // font size menu:\r
 171     JMenuItem                   _super_tiny_fonts_item;\r
 172     JMenuItem                   _tiny_fonts_item;\r
 173     JMenuItem                   _small_fonts_item;\r
 174     JMenuItem                   _medium_fonts_item;\r
 175     JMenuItem                   _large_fonts_item;\r
 176     // options menu:\r
 177     // _  screen and print\r
 178     JMenuItem                   _choose_font_mi;\r
 179     JMenuItem                   _switch_colors_mi;\r
 180     JCheckBoxMenuItem           _label_direction_cbmi;\r
 181     // _  screen display\r
 182     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 183     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 184     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 185     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 186     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 187     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 188     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me\r
 189     JCheckBoxMenuItem           _show_overview_cbmi;\r
 190     JCheckBoxMenuItem           _show_domain_labels;\r
 191     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 192     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 193     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 194     JMenuItem                   _overview_placment_mi;\r
 195     JMenuItem                   _choose_minimal_confidence_mi;\r
 196     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 197     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 198     JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;\r
 199     JMenuItem                   _cycle_node_shape_mi;\r
 200     JMenuItem                   _cycle_node_fill_mi;\r
 201     JMenuItem                   _choose_node_size_mi;\r
 202     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 203     JCheckBoxMenuItem           _right_line_up_domains_cbmi;\r
 204     JCheckBoxMenuItem           _line_up_renderable_data_cbmi;\r
 205     // _  print\r
 206     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 207     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 208     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 209     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 210     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 211     JMenuItem                   _print_size_mi;\r
 212     JMenuItem                   _choose_pdf_width_mi;\r
 213     // _  parsing\r
 214     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 215     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 216     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 217     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 218     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 219     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 220     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 221     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 222     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 223     // _  search\r
 224     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 225     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 226     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 227     JCheckBoxMenuItem           _search_with_regex_cbmi;\r
 228     // type menu:\r
 229     JMenu                       _type_menu;\r
 230     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 231     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 232     JCheckBoxMenuItem           _curved_type_cbmi;\r
 233     JCheckBoxMenuItem           _convex_type_cbmi;\r
 234     JCheckBoxMenuItem           _euro_type_cbmi;\r
 235     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 236     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 237     JCheckBoxMenuItem           _circular_type_cbmi;\r
 238     // view as text menu:\r
 239     JMenuItem                   _view_as_NH_item;\r
 240     JMenuItem                   _view_as_XML_item;\r
 241     JMenuItem                   _view_as_nexus_item;\r
 242     JMenuItem                   _display_basic_information_item;\r
 243     // help menu:\r
 244     JMenuItem                   _about_item;\r
 245     JMenuItem                   _help_item;\r
 246     JMenuItem                   _website_item;\r
 247     JMenuItem                   _phyloxml_website_item;\r
 248     JMenuItem                   _phyloxml_ref_item;\r
 249     JMenuItem                   _aptx_ref_item;\r
 250     // process menu:\r
 251     JMenu                       _process_menu;\r
 252     // Handy pointers to child components:\r
 253     MainPanel                   _mainpanel;\r
 254     Container                   _contentpane;\r
 255     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;\r
 256     Configuration               _configuration;\r
 257     Options                     _options;\r
 258     private Phylogeny           _species_tree;\r
 259     InferenceManager            _inference_manager;\r
 260     final ProcessPool           _process_pool;\r
 261     private String              _previous_node_annotation_ref;\r
 262 \r
 263     MainFrame() {\r
 264         _process_pool = ProcessPool.createInstance();\r
 265     }\r
 266 \r
 267     /**\r
 268      * Action performed.\r
 269      */\r
 270     @Override\r
 271     public void actionPerformed( final ActionEvent e ) {\r
 272         final Object o = e.getSource();\r
 273         boolean is_applet = false;\r
 274         JApplet applet = null;\r
 275         if ( getCurrentTreePanel() != null ) {\r
 276             is_applet = getCurrentTreePanel().isApplet();\r
 277             if ( is_applet ) {\r
 278                 applet = getCurrentTreePanel().obtainApplet();\r
 279             }\r
 280         }\r
 281         if ( o == _exit_item ) {\r
 282             close();\r
 283         }\r
 284         else if ( o == _gsdi_item ) {\r
 285             if ( isSubtreeDisplayed() ) {\r
 286                 return;\r
 287             }\r
 288             executeGSDI();\r
 289         }\r
 290         else if ( o == _gsdir_item ) {\r
 291             if ( isSubtreeDisplayed() ) {\r
 292                 return;\r
 293             }\r
 294             executeGSDIR();\r
 295         }\r
 296         else if ( o == _taxcolor_item ) {\r
 297             taxColor();\r
 298         }\r
 299         else if ( o == _confcolor_item ) {\r
 300             confColor();\r
 301         }\r
 302         else if ( o == _color_rank_jmi ) {\r
 303             colorRank();\r
 304         }\r
 305         else if ( o == _collapse_species_specific_subtrees ) {\r
 306             if ( isSubtreeDisplayed() ) {\r
 307                 return;\r
 308             }\r
 309             if ( getCurrentTreePanel() != null ) {\r
 310                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 311             }\r
 312         }\r
 313         else if ( o == _remove_branch_color_item ) {\r
 314             if ( isSubtreeDisplayed() ) {\r
 315                 return;\r
 316             }\r
 317             removeBranchColors();\r
 318         }\r
 319         else if ( o == _remove_visual_styles_item ) {\r
 320             if ( isSubtreeDisplayed() ) {\r
 321                 return;\r
 322             }\r
 323             removeVisualStyles();\r
 324         }\r
 325         else if ( o == _midpoint_root_item ) {\r
 326             if ( isSubtreeDisplayed() ) {\r
 327                 return;\r
 328             }\r
 329             midpointRoot();\r
 330         }\r
 331         else if ( o == _delete_selected_nodes_item ) {\r
 332             if ( isSubtreeDisplayed() ) {\r
 333                 return;\r
 334             }\r
 335             deleteSelectedNodes( true );\r
 336         }\r
 337         else if ( o == _delete_not_selected_nodes_item ) {\r
 338             if ( isSubtreeDisplayed() ) {\r
 339                 return;\r
 340             }\r
 341             deleteSelectedNodes( false );\r
 342         }\r
 343         else if ( o == _annotate_item ) {\r
 344             annotateSequences();\r
 345         }\r
 346         else if ( o == _switch_colors_mi ) {\r
 347             switchColors();\r
 348         }\r
 349         else if ( o == _display_basic_information_item ) {\r
 350             if ( getCurrentTreePanel() != null ) {\r
 351                 displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 352             }\r
 353         }\r
 354         else if ( o == _view_as_NH_item ) {\r
 355             viewAsNH();\r
 356         }\r
 357         else if ( o == _view_as_XML_item ) {\r
 358             viewAsXML();\r
 359         }\r
 360         else if ( o == _view_as_nexus_item ) {\r
 361             viewAsNexus();\r
 362         }\r
 363         else if ( o == _super_tiny_fonts_item ) {\r
 364             if ( getCurrentTreePanel() != null ) {\r
 365                 getCurrentTreePanel().setSuperTinyFonts();\r
 366                 getCurrentTreePanel().repaint();\r
 367             }\r
 368         }\r
 369         else if ( o == _tiny_fonts_item ) {\r
 370             if ( getCurrentTreePanel() != null ) {\r
 371                 getCurrentTreePanel().setTinyFonts();\r
 372                 getCurrentTreePanel().repaint();\r
 373             }\r
 374         }\r
 375         else if ( o == _small_fonts_item ) {\r
 376             if ( getCurrentTreePanel() != null ) {\r
 377                 getCurrentTreePanel().setSmallFonts();\r
 378                 getCurrentTreePanel().repaint();\r
 379             }\r
 380         }\r
 381         else if ( o == _medium_fonts_item ) {\r
 382             if ( getCurrentTreePanel() != null ) {\r
 383                 getCurrentTreePanel().setMediumFonts();\r
 384                 getCurrentTreePanel().repaint();\r
 385             }\r
 386         }\r
 387         else if ( o == _large_fonts_item ) {\r
 388             if ( getCurrentTreePanel() != null ) {\r
 389                 getCurrentTreePanel().setLargeFonts();\r
 390                 getCurrentTreePanel().repaint();\r
 391             }\r
 392         }\r
 393         else if ( o == _choose_font_mi ) {\r
 394             chooseFont();\r
 395         }\r
 396         else if ( o == _choose_minimal_confidence_mi ) {\r
 397             chooseMinimalConfidence();\r
 398         }\r
 399         else if ( o == _choose_node_size_mi ) {\r
 400             chooseNodeSize( getOptions(), this );\r
 401         }\r
 402         else if ( o == _overview_placment_mi ) {\r
 403             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 404         }\r
 405         else if ( o == _cycle_node_fill_mi ) {\r
 406             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
 407         }\r
 408         else if ( o == _cycle_node_shape_mi ) {\r
 409             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
 410         }\r
 411         else if ( o == _screen_antialias_cbmi ) {\r
 412             updateOptions( getOptions() );\r
 413             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 414         }\r
 415         else if ( o == _background_gradient_cbmi ) {\r
 416             updateOptions( getOptions() );\r
 417         }\r
 418         else if ( o == _show_domain_labels ) {\r
 419             updateOptions( getOptions() );\r
 420         }\r
 421         else if ( o == _show_annotation_ref_source ) {\r
 422             updateOptions( getOptions() );\r
 423         }\r
 424         else if ( o == _abbreviate_scientific_names ) {\r
 425             updateOptions( getOptions() );\r
 426         }\r
 427         else if ( o == _color_labels_same_as_parent_branch ) {\r
 428             updateOptions( getOptions() );\r
 429         }\r
 430         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 431             updateOptions( getOptions() );\r
 432         }\r
 433         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 434             updateOptions( getOptions() );\r
 435         }\r
 436         else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
 437             updateOptions( getOptions() );\r
 438         }\r
 439         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 440             updateOptions( getOptions() );\r
 441             showWhole();\r
 442         }\r
 443         else if ( o == _uniform_cladograms_rbmi ) {\r
 444             updateOptions( getOptions() );\r
 445             showWhole();\r
 446         }\r
 447         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 448             updateOptions( getOptions() );\r
 449             showWhole();\r
 450         }\r
 451         else if ( o == _search_case_senstive_cbmi ) {\r
 452             updateOptions( getOptions() );\r
 453             getMainPanel().getControlPanel().search0();\r
 454             getMainPanel().getControlPanel().search1();\r
 455         }\r
 456         else if ( o == _search_whole_words_only_cbmi ) {\r
 457             if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
 458                 _search_with_regex_cbmi.setSelected( false );\r
 459             }\r
 460             updateOptions( getOptions() );\r
 461             getMainPanel().getControlPanel().search0();\r
 462             getMainPanel().getControlPanel().search1();\r
 463         }\r
 464         else if ( o == _inverse_search_result_cbmi ) {\r
 465             updateOptions( getOptions() );\r
 466             getMainPanel().getControlPanel().search0();\r
 467             getMainPanel().getControlPanel().search1();\r
 468         }\r
 469         else if ( o == _search_with_regex_cbmi ) {\r
 470             if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
 471                 _search_whole_words_only_cbmi.setSelected( false );\r
 472             }\r
 473             if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
 474                 _search_case_senstive_cbmi.setSelected( true );\r
 475             }\r
 476             updateOptions( getOptions() );\r
 477             getMainPanel().getControlPanel().search0();\r
 478             getMainPanel().getControlPanel().search1();\r
 479         }\r
 480         else if ( o == _show_scale_cbmi ) {\r
 481             updateOptions( getOptions() );\r
 482         }\r
 483         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 484             updateOptions( getOptions() );\r
 485         }\r
 486         else if ( o == _show_confidence_stddev_cbmi ) {\r
 487             updateOptions( getOptions() );\r
 488         }\r
 489         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 490             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 491                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 492             }\r
 493             updateOptions( getOptions() );\r
 494         }\r
 495         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 496             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 497                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 498             }\r
 499             updateOptions( getOptions() );\r
 500         }\r
 501         else if ( o == _label_direction_cbmi ) {\r
 502             updateOptions( getOptions() );\r
 503         }\r
 504         else if ( o == _show_overview_cbmi ) {\r
 505             updateOptions( getOptions() );\r
 506             if ( getCurrentTreePanel() != null ) {\r
 507                 getCurrentTreePanel().updateOvSizes();\r
 508             }\r
 509         }\r
 510         else if ( o == _line_up_renderable_data_cbmi ) {\r
 511             if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
 512                 _right_line_up_domains_cbmi.setSelected( false );\r
 513             }\r
 514             updateOptions( getOptions() );\r
 515         }\r
 516         else if ( o == _right_line_up_domains_cbmi ) {\r
 517             if ( _right_line_up_domains_cbmi.isSelected() ) {\r
 518                 _line_up_renderable_data_cbmi.setSelected( true );\r
 519             }\r
 520             updateOptions( getOptions() );\r
 521         }\r
 522         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 523                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 524                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 525             typeChanged( o );\r
 526         }\r
 527         else if ( o == _about_item ) {\r
 528             about();\r
 529         }\r
 530         else if ( o == _help_item ) {\r
 531             try {\r
 532                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
 533             }\r
 534             catch ( final IOException e1 ) {\r
 535                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 536             }\r
 537         }\r
 538         else if ( o == _website_item ) {\r
 539             try {\r
 540                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 541             }\r
 542             catch ( final IOException e1 ) {\r
 543                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 544             }\r
 545         }\r
 546         else if ( o == _phyloxml_website_item ) {\r
 547             try {\r
 548                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 549             }\r
 550             catch ( final IOException e1 ) {\r
 551                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 552             }\r
 553         }\r
 554         else if ( o == _aptx_ref_item ) {\r
 555             try {\r
 556                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 557             }\r
 558             catch ( final IOException e1 ) {\r
 559                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 560             }\r
 561         }\r
 562         else if ( o == _phyloxml_ref_item ) {\r
 563             try {\r
 564                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 565             }\r
 566             catch ( final IOException e1 ) {\r
 567                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 568             }\r
 569         }\r
 570         else {\r
 571             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 572                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 573                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 574                         readPhylogeniesFromWebservice( i );\r
 575                     }\r
 576                 }\r
 577             }\r
 578         }\r
 579         _contentpane.repaint();\r
 580     }\r
 581 \r
 582     private void deleteSelectedNodes( final boolean delete ) {\r
 583         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
 584         if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
 585             return;\r
 586         }\r
 587         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
 588         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
 589             final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
 590             for( final PhylogenyNode n : all_selected_nodes ) {\r
 591                 if ( n.isExternal() ) {\r
 592                     nodes.add( n );\r
 593                 }\r
 594             }\r
 595         }\r
 596         String function = "Retain";\r
 597         if ( delete ) {\r
 598             function = "Delete";\r
 599         }\r
 600         if ( ( nodes == null ) || nodes.isEmpty() ) {\r
 601             JOptionPane\r
 602                     .showMessageDialog( this,\r
 603                                         "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
 604                                         "No external nodes selected to " + function.toLowerCase(),\r
 605                                         JOptionPane.ERROR_MESSAGE );\r
 606             return;\r
 607         }\r
 608         final int todo = nodes.size();\r
 609         final int ext = phy.getNumberOfExternalNodes();\r
 610         int res = todo;\r
 611         if ( delete ) {\r
 612             res = ext - todo;\r
 613         }\r
 614         if ( res < 1 ) {\r
 615             JOptionPane.showMessageDialog( this,\r
 616                                            "Cannot delete all nodes",\r
 617                                            "Attempt to delete all nodes ",\r
 618                                            JOptionPane.ERROR_MESSAGE );\r
 619             return;\r
 620         }\r
 621         final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
 622                 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
 623                 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
 624         if ( result == JOptionPane.OK_OPTION ) {\r
 625             if ( !delete ) {\r
 626                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
 627                 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
 628                     final PhylogenyNode n = it.next();\r
 629                     if ( !nodes.contains( n ) ) {\r
 630                         to_delete.add( n );\r
 631                     }\r
 632                 }\r
 633                 for( final PhylogenyNode n : to_delete ) {\r
 634                     phy.deleteSubtree( n, true );\r
 635                 }\r
 636             }\r
 637             else {\r
 638                 for( final PhylogenyNode n : nodes ) {\r
 639                     phy.deleteSubtree( n, true );\r
 640                 }\r
 641             }\r
 642             resetSearch();\r
 643             getCurrentTreePanel().setNodeInPreorderToNull();\r
 644             phy.externalNodesHaveChanged();\r
 645             phy.clearHashIdToNodeMap();\r
 646             phy.recalculateNumberOfExternalDescendants( true );\r
 647             getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
 648             getCurrentTreePanel().setEdited( true );\r
 649             repaint();\r
 650         }\r
 651     }\r
 652 \r
 653     void resetSearch() {\r
 654         getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
 655         getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
 656         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
 657         getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
 658         getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
 659         getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
 660         getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
 661         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
 662         getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
 663         getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
 664         getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
 665         getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
 666     }\r
 667 \r
 668     public Configuration getConfiguration() {\r
 669         return _configuration;\r
 670     }\r
 671 \r
 672     /**\r
 673      * This method returns the current external node data which\r
 674      * has been selected by the user by clicking the "Return ..."\r
 675      * menu item. This method is expected to be called from Javascript or\r
 676      * something like it.\r
 677      * \r
 678      * @return current external node data as String\r
 679      */\r
 680     public String getCurrentExternalNodesDataBuffer() {\r
 681         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 682     }\r
 683 \r
 684     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 685         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 686     }\r
 687 \r
 688     public int getCurrentExternalNodesDataBufferLength() {\r
 689         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 690     }\r
 691 \r
 692     public InferenceManager getInferenceManager() {\r
 693         return _inference_manager;\r
 694     }\r
 695 \r
 696     public MainPanel getMainPanel() {\r
 697         return _mainpanel;\r
 698     }\r
 699 \r
 700     public Options getOptions() {\r
 701         return _options;\r
 702     }\r
 703 \r
 704     public ProcessPool getProcessPool() {\r
 705         return _process_pool;\r
 706     }\r
 707 \r
 708     public void showTextFrame( final String s, final String title ) {\r
 709         checkTextFrames();\r
 710         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 711     }\r
 712 \r
 713     public void showWhole() {\r
 714         _mainpanel.getControlPanel().showWhole();\r
 715     }\r
 716 \r
 717     public void updateProcessMenu() {\r
 718         // In general Swing is not thread safe.\r
 719         // See "Swing's Threading Policy".\r
 720         SwingUtilities.invokeLater( new Runnable() {\r
 721 \r
 722             @Override\r
 723             public void run() {\r
 724                 doUpdateProcessMenu();\r
 725             }\r
 726         } );\r
 727     }\r
 728 \r
 729     void activateSaveAllIfNeeded() {\r
 730         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 731             _save_all_item.setEnabled( true );\r
 732         }\r
 733         else {\r
 734             _save_all_item.setEnabled( false );\r
 735         }\r
 736     }\r
 737 \r
 738     void buildFileMenu() {\r
 739         _file_jmenu = createMenu( "File", getConfiguration() );\r
 740         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 741         customizeJMenuItem( _exit_item );\r
 742         _jmenubar.add( _file_jmenu );\r
 743     }\r
 744 \r
 745     void buildFontSizeMenu() {\r
 746         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 747         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 748         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 749         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 750         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 751         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 752         customizeJMenuItem( _super_tiny_fonts_item );\r
 753         customizeJMenuItem( _tiny_fonts_item );\r
 754         customizeJMenuItem( _small_fonts_item );\r
 755         customizeJMenuItem( _medium_fonts_item );\r
 756         customizeJMenuItem( _large_fonts_item );\r
 757         _jmenubar.add( _font_size_menu );\r
 758     }\r
 759 \r
 760     void buildHelpMenu() {\r
 761         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 762         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
 763         _help_jmenu.addSeparator();\r
 764         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 765         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
 766         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 767         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 768         _help_jmenu.addSeparator();\r
 769         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 770         customizeJMenuItem( _help_item );\r
 771         customizeJMenuItem( _website_item );\r
 772         customizeJMenuItem( _phyloxml_website_item );\r
 773         customizeJMenuItem( _aptx_ref_item );\r
 774         customizeJMenuItem( _phyloxml_ref_item );\r
 775         customizeJMenuItem( _about_item );\r
 776         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 777         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 778         _jmenubar.add( _help_jmenu );\r
 779     }\r
 780 \r
 781     void buildTypeMenu() {\r
 782         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 783         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 784         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 785         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 786         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 787         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 788         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 789         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 790         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 791         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 792         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 793         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 794         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 795         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 796         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 797         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 798         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 799         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 800         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 801         initializeTypeMenu( getOptions() );\r
 802         _jmenubar.add( _type_menu );\r
 803     }\r
 804 \r
 805     void buildViewMenu() {\r
 806         _view_jmenu = createMenu( "View", getConfiguration() );\r
 807         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 808         _view_jmenu.addSeparator();\r
 809         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 810         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 811         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 812         customizeJMenuItem( _display_basic_information_item );\r
 813         customizeJMenuItem( _view_as_NH_item );\r
 814         customizeJMenuItem( _view_as_XML_item );\r
 815         customizeJMenuItem( _view_as_nexus_item );\r
 816         _jmenubar.add( _view_jmenu );\r
 817     }\r
 818 \r
 819     void checkTextFrames() {\r
 820         if ( _textframes.size() > 5 ) {\r
 821             try {\r
 822                 if ( _textframes.getFirst() != null ) {\r
 823                     _textframes.getFirst().removeMe();\r
 824                 }\r
 825                 else {\r
 826                     _textframes.removeFirst();\r
 827                 }\r
 828             }\r
 829             catch ( final NoSuchElementException e ) {\r
 830                 // Ignore.\r
 831             }\r
 832         }\r
 833     }\r
 834 \r
 835     void close() {\r
 836         removeAllTextFrames();\r
 837         if ( _mainpanel != null ) {\r
 838             _mainpanel.terminate();\r
 839         }\r
 840         if ( _contentpane != null ) {\r
 841             _contentpane.removeAll();\r
 842         }\r
 843         setVisible( false );\r
 844         dispose();\r
 845     }\r
 846 \r
 847     void colorRank() {\r
 848         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 849             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
 850             final String rank = ( String ) JOptionPane\r
 851                     .showInputDialog( this,\r
 852                                       "What rank should the colorization be based on",\r
 853                                       "Rank Selection",\r
 854                                       JOptionPane.QUESTION_MESSAGE,\r
 855                                       null,\r
 856                                       ranks,\r
 857                                       null );\r
 858             if ( !ForesterUtil.isEmpty( rank ) ) {\r
 859                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
 860             }\r
 861         }\r
 862     }\r
 863 \r
 864     void confColor() {\r
 865         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 866             _mainpanel.getCurrentTreePanel().confColor();\r
 867         }\r
 868     }\r
 869 \r
 870     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
 871         if ( item != null ) {\r
 872             item.setFont( MainFrame.menu_font );\r
 873             if ( !getConfiguration().isUseNativeUI() ) {\r
 874                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 875                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 876             }\r
 877             item.setSelected( is_selected );\r
 878             item.addActionListener( this );\r
 879         }\r
 880     }\r
 881 \r
 882     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
 883         if ( jmi != null ) {\r
 884             jmi.setFont( MainFrame.menu_font );\r
 885             if ( !getConfiguration().isUseNativeUI() ) {\r
 886                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 887                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 888             }\r
 889             jmi.addActionListener( this );\r
 890         }\r
 891         return jmi;\r
 892     }\r
 893 \r
 894     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
 895         if ( item != null ) {\r
 896             item.setFont( MainFrame.menu_font );\r
 897             if ( !getConfiguration().isUseNativeUI() ) {\r
 898                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 899                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 900             }\r
 901             item.setSelected( is_selected );\r
 902             item.addActionListener( this );\r
 903         }\r
 904     }\r
 905 \r
 906     void displayBasicInformation( final File treefile ) {\r
 907         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
 908             String title = "Basic Information";\r
 909             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
 910                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
 911             }\r
 912             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
 913         }\r
 914     }\r
 915 \r
 916     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
 917         try {\r
 918             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 919         }\r
 920         catch ( final Exception ex ) {\r
 921             // Do nothing.\r
 922         }\r
 923         JOptionPane.showMessageDialog( this,\r
 924                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
 925                                        "Error during File|Open",\r
 926                                        JOptionPane.ERROR_MESSAGE );\r
 927     }\r
 928 \r
 929     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
 930         try {\r
 931             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 932         }\r
 933         catch ( final Exception ex ) {\r
 934             // Do nothing.\r
 935         }\r
 936         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
 937     }\r
 938 \r
 939     void executeGSDI() {\r
 940         if ( !isOKforSDI( false, true ) ) {\r
 941             return;\r
 942         }\r
 943         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
 944             JOptionPane.showMessageDialog( this,\r
 945                                            "Gene tree is not rooted.",\r
 946                                            "Cannot execute GSDI",\r
 947                                            JOptionPane.ERROR_MESSAGE );\r
 948             return;\r
 949         }\r
 950         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 951         gene_tree.setAllNodesToNotCollapse();\r
 952         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 953         GSDI gsdi = null;\r
 954         final Phylogeny species_tree = getSpeciesTree().copy();\r
 955         try {\r
 956             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
 957         }\r
 958         catch ( final SDIException e ) {\r
 959             JOptionPane.showMessageDialog( this,\r
 960                                            e.getLocalizedMessage(),\r
 961                                            "Error during GSDI",\r
 962                                            JOptionPane.ERROR_MESSAGE );\r
 963             return;\r
 964         }\r
 965         catch ( final Exception e ) {\r
 966             AptxUtil.unexpectedException( e );\r
 967             return;\r
 968         }\r
 969         gene_tree.setRerootable( false );\r
 970         gene_tree.clearHashIdToNodeMap();\r
 971         gene_tree.recalculateNumberOfExternalDescendants( true );\r
 972         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
 973         getMainPanel().getControlPanel().setShowEvents( true );\r
 974         showWhole();\r
 975         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 976         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 977         showWhole();\r
 978         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 979         showWhole();\r
 980         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 981         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 982         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 983             JOptionPane.showMessageDialog( this,\r
 984                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 985                                                    + "Potential duplications: "\r
 986                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 987                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 988                                                    + "Stripped gene tree nodes: "\r
 989                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 990                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 991                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 992                                            "GSDI successfully completed",\r
 993                                            JOptionPane.WARNING_MESSAGE );\r
 994         }\r
 995         else {\r
 996             JOptionPane.showMessageDialog( this,\r
 997                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 998                                                    + "Potential duplications: "\r
 999                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
1000                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
1001                                                    + "Stripped gene tree nodes: "\r
1002                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1003                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
1004                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1005                                            "GSDI successfully completed",\r
1006                                            JOptionPane.INFORMATION_MESSAGE );\r
1007         }\r
1008     }\r
1009 \r
1010     void executeGSDIR() {\r
1011         if ( !isOKforSDI( false, false ) ) {\r
1012             return;\r
1013         }\r
1014         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
1015         if ( ( p > 0 )\r
1016                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
1017             JOptionPane.showMessageDialog( this,\r
1018                                            "Gene tree is not completely binary",\r
1019                                            "Cannot execute GSDI",\r
1020                                            JOptionPane.ERROR_MESSAGE );\r
1021             return;\r
1022         }\r
1023         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
1024         gene_tree.setAllNodesToNotCollapse();\r
1025         gene_tree.recalculateNumberOfExternalDescendants( false );\r
1026         GSDIR gsdir = null;\r
1027         final Phylogeny species_tree = getSpeciesTree().copy();\r
1028         try {\r
1029             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
1030         }\r
1031         catch ( final SDIException e ) {\r
1032             JOptionPane.showMessageDialog( this,\r
1033                                            e.getLocalizedMessage(),\r
1034                                            "Error during GSDIR",\r
1035                                            JOptionPane.ERROR_MESSAGE );\r
1036             return;\r
1037         }\r
1038         catch ( final Exception e ) {\r
1039             AptxUtil.unexpectedException( e );\r
1040             return;\r
1041         }\r
1042         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
1043         result_gene_tree.setRerootable( false );\r
1044         result_gene_tree.clearHashIdToNodeMap();\r
1045         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
1046         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
1047         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
1048         getMainPanel().getControlPanel().setShowEvents( true );\r
1049         showWhole();\r
1050         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1051         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1052         showWhole();\r
1053         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1054         showWhole();\r
1055         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1056         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1057         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1058             JOptionPane.showMessageDialog( this,\r
1059                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1060                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1061                                                    + "Stripped gene tree nodes: "\r
1062                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1063                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1064                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1065                                            "GSDIR successfully completed",\r
1066                                            JOptionPane.WARNING_MESSAGE );\r
1067         }\r
1068         else {\r
1069             JOptionPane.showMessageDialog( this,\r
1070                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1071                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1072                                                    + "Stripped gene tree nodes: "\r
1073                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1074                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1075                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1076                                            "GSDIR successfully completed",\r
1077                                            JOptionPane.INFORMATION_MESSAGE );\r
1078         }\r
1079     }\r
1080 \r
1081     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
1082         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
1083             JOptionPane.showMessageDialog( this,\r
1084                                            "Gene tree and species tree have no species in common.",\r
1085                                            "Error during SDI",\r
1086                                            JOptionPane.ERROR_MESSAGE );\r
1087             return false;\r
1088         }\r
1089         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
1090             JOptionPane.showMessageDialog( this,\r
1091                                            "Gene tree and species tree have only one species in common.",\r
1092                                            "Error during SDI",\r
1093                                            JOptionPane.ERROR_MESSAGE );\r
1094             return false;\r
1095         }\r
1096         else {\r
1097             return true;\r
1098         }\r
1099     }\r
1100 \r
1101     TreePanel getCurrentTreePanel() {\r
1102         return getMainPanel().getCurrentTreePanel();\r
1103     }\r
1104 \r
1105     JMenu getHelpMenu() {\r
1106         return _help_jmenu;\r
1107     }\r
1108 \r
1109     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
1110         return _label_direction_cbmi;\r
1111     }\r
1112 \r
1113     JMenuBar getMenuBarOfMainFrame() {\r
1114         return _jmenubar;\r
1115     }\r
1116 \r
1117     final Phylogeny getSpeciesTree() {\r
1118         return _species_tree;\r
1119     }\r
1120 \r
1121     void initializeTypeMenu( final Options options ) {\r
1122         setTypeMenuToAllUnselected();\r
1123         switch ( options.getPhylogenyGraphicsType() ) {\r
1124             case CONVEX:\r
1125                 _convex_type_cbmi.setSelected( true );\r
1126                 break;\r
1127             case CURVED:\r
1128                 _curved_type_cbmi.setSelected( true );\r
1129                 break;\r
1130             case EURO_STYLE:\r
1131                 _euro_type_cbmi.setSelected( true );\r
1132                 break;\r
1133             case ROUNDED:\r
1134                 _rounded_type_cbmi.setSelected( true );\r
1135                 break;\r
1136             case TRIANGULAR:\r
1137                 _triangular_type_cbmi.setSelected( true );\r
1138                 break;\r
1139             case UNROOTED:\r
1140                 _unrooted_type_cbmi.setSelected( true );\r
1141                 break;\r
1142             case CIRCULAR:\r
1143                 _circular_type_cbmi.setSelected( true );\r
1144                 break;\r
1145             default:\r
1146                 _rectangular_type_cbmi.setSelected( true );\r
1147                 break;\r
1148         }\r
1149     }\r
1150 \r
1151     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1152         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1153             return false;\r
1154         }\r
1155         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1156             JOptionPane.showMessageDialog( this,\r
1157                                            "No species tree loaded",\r
1158                                            "Cannot execute GSDI",\r
1159                                            JOptionPane.ERROR_MESSAGE );\r
1160             return false;\r
1161         }\r
1162         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1163             JOptionPane.showMessageDialog( this,\r
1164                                            "Species tree is not completely binary",\r
1165                                            "Cannot execute GSDI",\r
1166                                            JOptionPane.ERROR_MESSAGE );\r
1167             return false;\r
1168         }\r
1169         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1170             JOptionPane.showMessageDialog( this,\r
1171                                            "Gene tree is not completely binary",\r
1172                                            "Cannot execute GSDI",\r
1173                                            JOptionPane.ERROR_MESSAGE );\r
1174             return false;\r
1175         }\r
1176         else {\r
1177             return true;\r
1178         }\r
1179     }\r
1180 \r
1181     boolean isSubtreeDisplayed() {\r
1182         if ( getCurrentTreePanel() != null ) {\r
1183             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1184                 JOptionPane\r
1185                         .showMessageDialog( this,\r
1186                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1187                                             "Operation can not be exectuted on a sub-tree",\r
1188                                             JOptionPane.WARNING_MESSAGE );\r
1189                 return true;\r
1190             }\r
1191         }\r
1192         return false;\r
1193     }\r
1194 \r
1195     void midpointRoot() {\r
1196         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1197             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1198         }\r
1199     }\r
1200 \r
1201     void readPhylogeniesFromWebservice( final int i ) {\r
1202         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1203         new Thread( reader ).start();\r
1204     }\r
1205 \r
1206     void removeAllTextFrames() {\r
1207         for( final TextFrame tf : _textframes ) {\r
1208             if ( tf != null ) {\r
1209                 tf.close();\r
1210             }\r
1211         }\r
1212         _textframes.clear();\r
1213     }\r
1214 \r
1215     void setConfiguration( final Configuration configuration ) {\r
1216         _configuration = configuration;\r
1217     }\r
1218 \r
1219     void setInferenceManager( final InferenceManager i ) {\r
1220         _inference_manager = i;\r
1221     }\r
1222 \r
1223     void setOptions( final Options options ) {\r
1224         _options = options;\r
1225     }\r
1226 \r
1227     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1228         setTypeMenuToAllUnselected();\r
1229         switch ( type ) {\r
1230             case CIRCULAR:\r
1231                 _circular_type_cbmi.setSelected( true );\r
1232                 break;\r
1233             case CONVEX:\r
1234                 _convex_type_cbmi.setSelected( true );\r
1235                 break;\r
1236             case CURVED:\r
1237                 _curved_type_cbmi.setSelected( true );\r
1238                 break;\r
1239             case EURO_STYLE:\r
1240                 _euro_type_cbmi.setSelected( true );\r
1241                 break;\r
1242             case ROUNDED:\r
1243                 _rounded_type_cbmi.setSelected( true );\r
1244                 break;\r
1245             case RECTANGULAR:\r
1246                 _rectangular_type_cbmi.setSelected( true );\r
1247                 break;\r
1248             case TRIANGULAR:\r
1249                 _triangular_type_cbmi.setSelected( true );\r
1250                 break;\r
1251             case UNROOTED:\r
1252                 _unrooted_type_cbmi.setSelected( true );\r
1253                 break;\r
1254             default:\r
1255                 throw new IllegalArgumentException( "unknown type: " + type );\r
1256         }\r
1257     }\r
1258 \r
1259     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1260         _species_tree = species_tree;\r
1261     }\r
1262 \r
1263     void setTypeMenuToAllUnselected() {\r
1264         _convex_type_cbmi.setSelected( false );\r
1265         _curved_type_cbmi.setSelected( false );\r
1266         _euro_type_cbmi.setSelected( false );\r
1267         _rounded_type_cbmi.setSelected( false );\r
1268         _triangular_type_cbmi.setSelected( false );\r
1269         _rectangular_type_cbmi.setSelected( false );\r
1270         _unrooted_type_cbmi.setSelected( false );\r
1271         _circular_type_cbmi.setSelected( false );\r
1272     }\r
1273 \r
1274     void switchColors() {\r
1275         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1276         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1277         csc.setVisible( true );\r
1278     }\r
1279 \r
1280     void taxColor() {\r
1281         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1282             _mainpanel.getCurrentTreePanel().taxColor();\r
1283         }\r
1284     }\r
1285 \r
1286     void typeChanged( final Object o ) {\r
1287         updateTypeCheckboxes( getOptions(), o );\r
1288         updateOptions( getOptions() );\r
1289         if ( getCurrentTreePanel() != null ) {\r
1290             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1291             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1292             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1293                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1294                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1295                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1296                 getCurrentTreePanel().getControlPanel().showWhole();\r
1297             }\r
1298             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1299                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1300             }\r
1301             else {\r
1302                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1303             }\r
1304             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1305             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1306             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1307                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1308                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1309                 }\r
1310                 else {\r
1311                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1312                 }\r
1313             }\r
1314         }\r
1315     }\r
1316 \r
1317     void updateOptions( final Options options ) {\r
1318         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1319         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1320                 && _background_gradient_cbmi.isSelected() );\r
1321         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1322         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1323                 && _show_annotation_ref_source.isSelected() );\r
1324         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1325                 && _abbreviate_scientific_names.isSelected() );\r
1326         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1327                 && _color_labels_same_as_parent_branch.isSelected() );\r
1328         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1329                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1330         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1331                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
1332         options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
1333                 && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
1334         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1335             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1336         }\r
1337         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1338             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1339         }\r
1340         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1341             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1342         }\r
1343         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1344                 && _search_case_senstive_cbmi.isSelected() );\r
1345         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1346             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1347         }\r
1348         if ( _label_direction_cbmi != null ) {\r
1349             if ( _label_direction_cbmi.isSelected() ) {\r
1350                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1351             }\r
1352             else {\r
1353                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1354             }\r
1355         }\r
1356         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1357         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1358                 && _show_confidence_stddev_cbmi.isSelected() );\r
1359         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1360             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1361         }\r
1362         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1363                 && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1364         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1365                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1366         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1367         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1368                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1369             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1370         }\r
1371         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1372                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1373             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1374         }\r
1375         else {\r
1376             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1377         }\r
1378         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1379                 && _print_black_and_white_cbmi.isSelected() );\r
1380         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1381                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1382         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1383             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1384         }\r
1385         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1386             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1387         }\r
1388         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1389             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1390         }\r
1391         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1392             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1393         }\r
1394         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1395                 && _replace_underscores_cbmi.isSelected() );\r
1396         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1397                 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1398         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1399                 && _search_whole_words_only_cbmi.isSelected() );\r
1400         options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
1401         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1402                 && _inverse_search_result_cbmi.isSelected() );\r
1403         if ( _graphics_export_visible_only_cbmi != null ) {\r
1404             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1405             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1406                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1407                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1408             }\r
1409             else {\r
1410                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1411             }\r
1412         }\r
1413         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1414             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1415         }\r
1416         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1417             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1418         }\r
1419         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1420             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1421         }\r
1422         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1423             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1424         }\r
1425         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1426             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1427         }\r
1428         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1429             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1430         }\r
1431         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1432             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1433         }\r
1434         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1435             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1436         }\r
1437         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
1438             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
1439         }\r
1440         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
1441             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
1442         }\r
1443     }\r
1444 \r
1445     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1446         setTypeMenuToAllUnselected();\r
1447         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1448     }\r
1449 \r
1450     void viewAsNexus() {\r
1451         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1452             String title = "Nexus";\r
1453             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1454                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1455             }\r
1456             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1457                            title );\r
1458         }\r
1459     }\r
1460 \r
1461     void viewAsNH() {\r
1462         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1463             String title = "New Hampshire";\r
1464             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1465                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1466             }\r
1467             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1468                                    .getNhConversionSupportValueStyle() ),\r
1469                            title );\r
1470         }\r
1471     }\r
1472 \r
1473     void viewAsXML() {\r
1474         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1475             String title = "phyloXML";\r
1476             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1477                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1478             }\r
1479             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1480         }\r
1481     }\r
1482 \r
1483     private void annotateSequences() {\r
1484         if ( getCurrentTreePanel() != null ) {\r
1485             List<PhylogenyNode> nodes = null;\r
1486             if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
1487                     || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
1488                 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
1489             }\r
1490             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1491                 JOptionPane\r
1492                         .showMessageDialog( this,\r
1493                                             "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1494                                             "No nodes selected for annotation",\r
1495                                             JOptionPane.ERROR_MESSAGE );\r
1496                 return;\r
1497             }\r
1498             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1499             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1500                 final JTextField ref_field = new JTextField( 10 );\r
1501                 final JTextField desc_filed = new JTextField( 20 );\r
1502                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1503                         : getPreviousNodeAnnotationReference() );\r
1504                 final JPanel my_panel = new JPanel();\r
1505                 my_panel.add( new JLabel( "Reference " ) );\r
1506                 my_panel.add( ref_field );\r
1507                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1508                 my_panel.add( new JLabel( "Description " ) );\r
1509                 my_panel.add( desc_filed );\r
1510                 final int result = JOptionPane.showConfirmDialog( null,\r
1511                                                                   my_panel,\r
1512                                                                   "Enter the sequence annotation(s) for the "\r
1513                                                                           + nodes.size() + " selected nodes",\r
1514                                                                   JOptionPane.OK_CANCEL_OPTION );\r
1515                 if ( result == JOptionPane.OK_OPTION ) {\r
1516                     String ref = ref_field.getText();\r
1517                     String desc = desc_filed.getText();\r
1518                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1519                         ref = ref.trim();\r
1520                         ref = ref.replaceAll( "\\s+", " " );\r
1521                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1522                                 || ( ref.length() < 3 ) ) {\r
1523                             JOptionPane.showMessageDialog( this,\r
1524                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1525                                                            "Illegal Format for Annotation Reference",\r
1526                                                            JOptionPane.ERROR_MESSAGE );\r
1527                             return;\r
1528                         }\r
1529                     }\r
1530                     if ( ref != null ) {\r
1531                         setPreviousNodeAnnotationReference( ref );\r
1532                     }\r
1533                     if ( desc != null ) {\r
1534                         desc = desc.trim();\r
1535                         desc = desc.replaceAll( "\\s+", " " );\r
1536                     }\r
1537                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1538                         for( final PhylogenyNode n : nodes ) {\r
1539                             ForesterUtil.ensurePresenceOfSequence( n );\r
1540                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1541                                     : new Annotation( ref );\r
1542                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1543                                 ann.setDesc( desc );\r
1544                             }\r
1545                             n.getNodeData().getSequence().addAnnotation( ann );\r
1546                         }\r
1547                     }\r
1548                     getMainPanel().getControlPanel().showAnnotations();\r
1549                 }\r
1550             }\r
1551         }\r
1552     }\r
1553 \r
1554     private void chooseFont() {\r
1555         final FontChooser fc = new FontChooser();\r
1556         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1557         fc.showDialog( this, "Select the Base Font" );\r
1558         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1559     }\r
1560 \r
1561     private void chooseMinimalConfidence() {\r
1562         final String s = ( String ) JOptionPane\r
1563                 .showInputDialog( this,\r
1564                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1565                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1566                                   "Minimal Confidence Value",\r
1567                                   JOptionPane.QUESTION_MESSAGE,\r
1568                                   null,\r
1569                                   null,\r
1570                                   getOptions().getMinConfidenceValue() );\r
1571         if ( !ForesterUtil.isEmpty( s ) ) {\r
1572             boolean success = true;\r
1573             double m = 0.0;\r
1574             final String m_str = s.trim();\r
1575             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1576                 try {\r
1577                     m = Double.parseDouble( m_str );\r
1578                 }\r
1579                 catch ( final Exception ex ) {\r
1580                     success = false;\r
1581                 }\r
1582             }\r
1583             else {\r
1584                 success = false;\r
1585             }\r
1586             if ( success && ( m >= 0.0 ) ) {\r
1587                 getOptions().setMinConfidenceValue( m );\r
1588             }\r
1589         }\r
1590     }\r
1591 \r
1592     private void doUpdateProcessMenu() {\r
1593         if ( _process_pool.size() > 0 ) {\r
1594             if ( _process_menu == null ) {\r
1595                 _process_menu = createMenu( "", getConfiguration() );\r
1596                 _process_menu.setForeground( Color.RED );\r
1597             }\r
1598             _process_menu.removeAll();\r
1599             final String text = "processes running: " + _process_pool.size();\r
1600             _process_menu.setText( text );\r
1601             _jmenubar.add( _process_menu );\r
1602             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1603                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1604                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1605             }\r
1606         }\r
1607         else {\r
1608             if ( _process_menu != null ) {\r
1609                 _process_menu.removeAll();\r
1610                 _jmenubar.remove( _process_menu );\r
1611             }\r
1612         }\r
1613         _jmenubar.validate();\r
1614         _jmenubar.repaint();\r
1615         repaint();\r
1616     }\r
1617 \r
1618     private String getPreviousNodeAnnotationReference() {\r
1619         return _previous_node_annotation_ref;\r
1620     }\r
1621 \r
1622     private void removeBranchColors() {\r
1623         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1624             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1625         }\r
1626     }\r
1627 \r
1628     private void removeVisualStyles() {\r
1629         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1630             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1631         }\r
1632     }\r
1633 \r
1634     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1635         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1636     }\r
1637 \r
1638     /**\r
1639      * Display the about box.\r
1640      */\r
1641     static void about() {\r
1642         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1643         about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
1644         about.append( "All Rights Reserved\n" );\r
1645         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1646         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1647         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1648         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1649         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1650         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1651             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1652         }\r
1653         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1654                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1655             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1656                     + ForesterUtil.OS_VERSION + "]\n" );\r
1657         }\r
1658         final Runtime rt = java.lang.Runtime.getRuntime();\r
1659         final long free_memory = rt.freeMemory() / 1000000;\r
1660         final long total_memory = rt.totalMemory() / 1000000;\r
1661         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1662         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1663         about.append( "References:\n" );\r
1664         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1665         about.append( "For more information & download:\n" );\r
1666         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1667         about.append( "Documentation:\n" );\r
1668         about.append( Constants.APTX_DOC_SITE + "\n" );\r
1669         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1670         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1671     }\r
1672 \r
1673     static void chooseNodeSize( final Options options, final Component parent ) {\r
1674         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1675                                                                  "Please enter the default size for node shapes.\n"\r
1676                                                                          + "[current value: "\r
1677                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1678                                                                  "Node Shape Size",\r
1679                                                                  JOptionPane.QUESTION_MESSAGE,\r
1680                                                                  null,\r
1681                                                                  null,\r
1682                                                                  options.getDefaultNodeShapeSize() );\r
1683         if ( !ForesterUtil.isEmpty( s ) ) {\r
1684             boolean success = true;\r
1685             double m = 0.0;\r
1686             final String m_str = s.trim();\r
1687             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1688                 try {\r
1689                     m = Double.parseDouble( m_str );\r
1690                 }\r
1691                 catch ( final Exception ex ) {\r
1692                     success = false;\r
1693                 }\r
1694             }\r
1695             else {\r
1696                 success = false;\r
1697             }\r
1698             if ( success && ( m >= 0.0 ) ) {\r
1699                 final short size = ForesterUtil.roundToShort( m );\r
1700                 if ( size >= 0.0 ) {\r
1701                     options.setDefaultNodeShapeSize( size );\r
1702                 }\r
1703             }\r
1704         }\r
1705     }\r
1706 \r
1707     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1708         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1709     }\r
1710 \r
1711     static JMenu createMenu( final String title, final Configuration conf ) {\r
1712         final JMenu jmenu = new JMenu( title );\r
1713         if ( !conf.isUseNativeUI() ) {\r
1714             jmenu.setFont( MainFrame.menu_font );\r
1715             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1716             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1717         }\r
1718         return jmenu;\r
1719     }\r
1720 \r
1721     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1722         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1723         if ( !configuration.isUseNativeUI() ) {\r
1724             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1725             label.setForeground( configuration.getGuiMenuTextColor() );\r
1726             label.setOpaque( true );\r
1727         }\r
1728         label.setSelected( false );\r
1729         label.setEnabled( false );\r
1730         return label;\r
1731     }\r
1732 \r
1733     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
1734         switch ( op.getDefaultNodeFill() ) {\r
1735             case GRADIENT:\r
1736                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1737                 break;\r
1738             case NONE:\r
1739                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1740                 break;\r
1741             case SOLID:\r
1742                 op.setDefaultNodeFill( NodeFill.NONE );\r
1743                 break;\r
1744             default:\r
1745                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1746         }\r
1747     }\r
1748 \r
1749     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
1750         switch ( op.getDefaultNodeShape() ) {\r
1751             case CIRCLE:\r
1752                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1753                 break;\r
1754             case RECTANGLE:\r
1755                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1756                 break;\r
1757             default:\r
1758                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1759         }\r
1760     }\r
1761 \r
1762     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1763         switch ( op.getOvPlacement() ) {\r
1764             case LOWER_LEFT:\r
1765                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1766                 break;\r
1767             case LOWER_RIGHT:\r
1768                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1769                 break;\r
1770             case UPPER_LEFT:\r
1771                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1772                 break;\r
1773             case UPPER_RIGHT:\r
1774                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1775                 break;\r
1776             default:\r
1777                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1778         }\r
1779         if ( tree_panel != null ) {\r
1780             tree_panel.updateOvSettings();\r
1781         }\r
1782     }\r
1783 \r
1784     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
1785         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
1786             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1787                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
1788         }\r
1789         else {\r
1790             mi.setText( "Cycle Node Shape Fill Type..." );\r
1791         }\r
1792     }\r
1793 \r
1794     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
1795         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
1796             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1797                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
1798         }\r
1799         else {\r
1800             mi.setText( "Cycle Node Shape Fill Type..." );\r
1801         }\r
1802     }\r
1803 \r
1804     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
1805         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
1806             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
1807         }\r
1808         else {\r
1809             mi.setText( "Cycle Overview Placement..." );\r
1810         }\r
1811     }\r
1812 \r
1813     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
1814         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
1815             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
1816                     + ")" );\r
1817         }\r
1818         else {\r
1819             mi.setText( "Select Color Scheme..." );\r
1820         }\r
1821     }\r
1822 \r
1823     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
1824         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
1825     }\r
1826 \r
1827     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
1828         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
1829             mi.setEnabled( true );\r
1830         }\r
1831         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
1832             mi.setEnabled( true );\r
1833         }\r
1834         else {\r
1835             mi.setEnabled( false );\r
1836         }\r
1837         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
1838     }\r
1839 \r
1840     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
1841         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
1842     }\r
1843 \r
1844     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
1845         for( final TreePanel tree_panel : treepanels ) {\r
1846             tree_panel.setTextAntialias();\r
1847         }\r
1848     }\r
1849 }\r