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.NodeDataField;\r
  69 import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
  70 import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
  71 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
  72 import org.forester.sdi.GSDI;\r
  73 import org.forester.sdi.GSDIR;\r
  74 import org.forester.sdi.SDIException;\r
  75 import org.forester.util.ForesterConstants;\r
  76 import org.forester.util.ForesterUtil;\r
  77 \r
  78 public abstract class MainFrame extends JFrame implements ActionListener {\r
  79 \r
  80     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
  81     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                                //TODO //FIXME\r
  82     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
  83     private static final long   serialVersionUID                        = 3655000897845508358L;\r
  84     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
  85                                                                                     Font.PLAIN,\r
  86                                                                                     10 );\r
  87     static final String         TYPE_MENU_HEADER                        = "Type";\r
  88     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
  89     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
  90     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
  91     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
  92     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
  93     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
  94     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                          //TODO\r
  95     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                          //TODO\r
  96     static final String         OPTIONS_HEADER                          = "Options";\r
  97     static final String         SEARCH_SUBHEADER                        = "Search:";\r
  98     static final String         DISPLAY_SUBHEADER                       = "Display:";\r
  99     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
 100     static final String         SEARCH_REGEX_LABEL                      = "Search with Regular Expressions";\r
 101     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
 102     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
 103     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
 104     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
 105     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
 106     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
 107     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
 108     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
 109     static final String         SEARCH_WITH_REGEX_TIP                   = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";\r
 110     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 111     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 112     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 113     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Shapes for External Nodes";\r
 114     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Shapes for Internal Nodes";\r
 115     static final String         DISPLAY_NODE_BOXES_LABEL_MARKED         = "Shapes for Nodes with Visual Data";\r
 116     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 117     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 118     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 119     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 120     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 121     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
 122     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 123     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 124     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 125     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 126     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 127     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 128     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 129     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 130     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 131     static final String         RIGHT_LINE_UP_DOMAINS                   = "Right-align Domain Architectures";\r
 132     static final String         LINE_UP_RENDERABLE_DATA                 = "Line Up Diagrams (such as Domain Architectures)";\r
 133     JMenuBar                    _jmenubar;\r
 134     JMenu                       _file_jmenu;\r
 135     JMenu                       _tools_menu;\r
 136     JMenu                       _view_jmenu;\r
 137     JMenu                       _options_jmenu;\r
 138     JMenu                       _font_size_menu;\r
 139     JMenu                       _help_jmenu;\r
 140     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 141     // Analysis menu\r
 142     JMenu                       _analysis_menu;\r
 143     JMenuItem                   _load_species_tree_item;\r
 144     JMenuItem                   _gsdi_item;\r
 145     JMenuItem                   _gsdir_item;\r
 146     JMenuItem                   _lineage_inference;\r
 147     // file menu:\r
 148     JMenuItem                   _open_item;\r
 149     JMenuItem                   _open_url_item;\r
 150     JMenuItem                   _save_item;\r
 151     JMenuItem                   _save_all_item;\r
 152     JMenuItem                   _close_item;\r
 153     JMenuItem                   _exit_item;\r
 154     JMenuItem                   _new_item;\r
 155     // tools menu:\r
 156     JMenuItem                   _midpoint_root_item;\r
 157     JMenuItem                   _taxcolor_item;\r
 158     JMenuItem                   _confcolor_item;\r
 159     JMenuItem                   _color_rank_jmi;\r
 160     JMenuItem                   _collapse_species_specific_subtrees;\r
 161     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 162     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 163     JMenuItem                   _obtain_seq_information_jmi;\r
 164     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 165     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 166     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 167     JMenuItem                   _annotate_item;\r
 168     JMenuItem                   _remove_branch_color_item;\r
 169     JMenuItem                   _remove_visual_styles_item;\r
 170     JMenuItem                   _delete_selected_nodes_item;\r
 171     JMenuItem                   _delete_not_selected_nodes_item;\r
 172     // font size menu:\r
 173     JMenuItem                   _super_tiny_fonts_item;\r
 174     JMenuItem                   _tiny_fonts_item;\r
 175     JMenuItem                   _small_fonts_item;\r
 176     JMenuItem                   _medium_fonts_item;\r
 177     JMenuItem                   _large_fonts_item;\r
 178     // options menu:\r
 179     // _  screen and print\r
 180     JMenuItem                   _choose_font_mi;\r
 181     JMenuItem                   _switch_colors_mi;\r
 182     JCheckBoxMenuItem           _label_direction_cbmi;\r
 183     // _  screen display\r
 184     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 185     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 186     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 187     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 188     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 189     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 190     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                                      //TODO fix me\r
 191     JCheckBoxMenuItem           _show_overview_cbmi;\r
 192     JCheckBoxMenuItem           _show_domain_labels;\r
 193     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 194     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 195     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 196     JMenuItem                   _overview_placment_mi;\r
 197     JMenuItem                   _choose_minimal_confidence_mi;\r
 198     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 199     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 200     JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;\r
 201     JMenuItem                   _cycle_node_shape_mi;\r
 202     JMenuItem                   _cycle_node_fill_mi;\r
 203     JMenuItem                   _choose_node_size_mi;\r
 204     JMenuItem                   _cycle_data_return;\r
 205     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 206     JCheckBoxMenuItem           _right_line_up_domains_cbmi;\r
 207     JCheckBoxMenuItem           _line_up_renderable_data_cbmi;\r
 208     // _  print\r
 209     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 210     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 211     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 212     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 213     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 214     JMenuItem                   _print_size_mi;\r
 215     JMenuItem                   _choose_pdf_width_mi;\r
 216     // _  parsing\r
 217     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 218     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 219     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 220     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 221     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 222     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 223     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 224     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 225     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 226     // _  search\r
 227     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 228     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 229     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 230     JCheckBoxMenuItem           _search_with_regex_cbmi;\r
 231     // type menu:\r
 232     JMenu                       _type_menu;\r
 233     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 234     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 235     JCheckBoxMenuItem           _curved_type_cbmi;\r
 236     JCheckBoxMenuItem           _convex_type_cbmi;\r
 237     JCheckBoxMenuItem           _euro_type_cbmi;\r
 238     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 239     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 240     JCheckBoxMenuItem           _circular_type_cbmi;\r
 241     // view as text menu:\r
 242     JMenuItem                   _view_as_NH_item;\r
 243     JMenuItem                   _view_as_XML_item;\r
 244     JMenuItem                   _view_as_nexus_item;\r
 245     JMenuItem                   _display_basic_information_item;\r
 246     // help menu:\r
 247     JMenuItem                   _about_item;\r
 248     JMenuItem                   _help_item;\r
 249     JMenuItem                   _website_item;\r
 250     JMenuItem                   _phyloxml_website_item;\r
 251     JMenuItem                   _phyloxml_ref_item;\r
 252     JMenuItem                   _aptx_ref_item;\r
 253     // process menu:\r
 254     JMenu                       _process_menu;\r
 255     // Handy pointers to child components:\r
 256     MainPanel                   _mainpanel;\r
 257     Container                   _contentpane;\r
 258     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                                  ;\r
 259     Configuration               _configuration;\r
 260     Options                     _options;\r
 261     private Phylogeny           _species_tree;\r
 262     InferenceManager            _inference_manager;\r
 263     final ProcessPool           _process_pool;\r
 264     private String              _previous_node_annotation_ref;\r
 265 \r
 266     MainFrame() {\r
 267         _process_pool = ProcessPool.createInstance();\r
 268     }\r
 269 \r
 270     /**\r
 271      * Action performed.\r
 272      */\r
 273     @Override\r
 274     public void actionPerformed( final ActionEvent e ) {\r
 275         final Object o = e.getSource();\r
 276         boolean is_applet = false;\r
 277         JApplet applet = null;\r
 278         if ( getCurrentTreePanel() != null ) {\r
 279             is_applet = getCurrentTreePanel().isApplet();\r
 280             if ( is_applet ) {\r
 281                 applet = getCurrentTreePanel().obtainApplet();\r
 282             }\r
 283         }\r
 284         if ( o == _exit_item ) {\r
 285             close();\r
 286         }\r
 287         else if ( o == _gsdi_item ) {\r
 288             if ( isSubtreeDisplayed() ) {\r
 289                 return;\r
 290             }\r
 291             executeGSDI();\r
 292         }\r
 293         else if ( o == _gsdir_item ) {\r
 294             if ( isSubtreeDisplayed() ) {\r
 295                 return;\r
 296             }\r
 297             executeGSDIR();\r
 298         }\r
 299         else if ( o == _taxcolor_item ) {\r
 300             taxColor();\r
 301         }\r
 302         else if ( o == _confcolor_item ) {\r
 303             confColor();\r
 304         }\r
 305         else if ( o == _color_rank_jmi ) {\r
 306             colorRank();\r
 307         }\r
 308         else if ( o == _collapse_species_specific_subtrees ) {\r
 309             if ( isSubtreeDisplayed() ) {\r
 310                 return;\r
 311             }\r
 312             if ( getCurrentTreePanel() != null ) {\r
 313                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 314             }\r
 315         }\r
 316         else if ( o == _remove_branch_color_item ) {\r
 317             if ( isSubtreeDisplayed() ) {\r
 318                 return;\r
 319             }\r
 320             removeBranchColors();\r
 321         }\r
 322         else if ( o == _remove_visual_styles_item ) {\r
 323             if ( isSubtreeDisplayed() ) {\r
 324                 return;\r
 325             }\r
 326             removeVisualStyles();\r
 327         }\r
 328         else if ( o == _midpoint_root_item ) {\r
 329             if ( isSubtreeDisplayed() ) {\r
 330                 return;\r
 331             }\r
 332             midpointRoot();\r
 333         }\r
 334         else if ( o == _delete_selected_nodes_item ) {\r
 335             if ( isSubtreeDisplayed() ) {\r
 336                 return;\r
 337             }\r
 338             deleteSelectedNodes( true );\r
 339         }\r
 340         else if ( o == _delete_not_selected_nodes_item ) {\r
 341             if ( isSubtreeDisplayed() ) {\r
 342                 return;\r
 343             }\r
 344             deleteSelectedNodes( false );\r
 345         }\r
 346         else if ( o == _annotate_item ) {\r
 347             annotateSequences();\r
 348         }\r
 349         else if ( o == _switch_colors_mi ) {\r
 350             switchColors();\r
 351         }\r
 352         else if ( o == _display_basic_information_item ) {\r
 353             if ( getCurrentTreePanel() != null ) {\r
 354                 displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 355             }\r
 356         }\r
 357         else if ( o == _view_as_NH_item ) {\r
 358             viewAsNH();\r
 359         }\r
 360         else if ( o == _view_as_XML_item ) {\r
 361             viewAsXML();\r
 362         }\r
 363         else if ( o == _view_as_nexus_item ) {\r
 364             viewAsNexus();\r
 365         }\r
 366         else if ( o == _super_tiny_fonts_item ) {\r
 367             if ( getCurrentTreePanel() != null ) {\r
 368                 getCurrentTreePanel().setSuperTinyFonts();\r
 369                 getCurrentTreePanel().repaint();\r
 370             }\r
 371         }\r
 372         else if ( o == _tiny_fonts_item ) {\r
 373             if ( getCurrentTreePanel() != null ) {\r
 374                 getCurrentTreePanel().setTinyFonts();\r
 375                 getCurrentTreePanel().repaint();\r
 376             }\r
 377         }\r
 378         else if ( o == _small_fonts_item ) {\r
 379             if ( getCurrentTreePanel() != null ) {\r
 380                 getCurrentTreePanel().setSmallFonts();\r
 381                 getCurrentTreePanel().repaint();\r
 382             }\r
 383         }\r
 384         else if ( o == _medium_fonts_item ) {\r
 385             if ( getCurrentTreePanel() != null ) {\r
 386                 getCurrentTreePanel().setMediumFonts();\r
 387                 getCurrentTreePanel().repaint();\r
 388             }\r
 389         }\r
 390         else if ( o == _large_fonts_item ) {\r
 391             if ( getCurrentTreePanel() != null ) {\r
 392                 getCurrentTreePanel().setLargeFonts();\r
 393                 getCurrentTreePanel().repaint();\r
 394             }\r
 395         }\r
 396         else if ( o == _choose_font_mi ) {\r
 397             chooseFont();\r
 398         }\r
 399         else if ( o == _choose_minimal_confidence_mi ) {\r
 400             chooseMinimalConfidence();\r
 401         }\r
 402         else if ( o == _choose_node_size_mi ) {\r
 403             chooseNodeSize( getOptions(), this );\r
 404         }\r
 405         else if ( o == _overview_placment_mi ) {\r
 406             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 407         }\r
 408         else if ( o == _cycle_node_fill_mi ) {\r
 409             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
 410         }\r
 411         else if ( o == _cycle_node_shape_mi ) {\r
 412             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
 413         }\r
 414         else if ( o == _cycle_data_return ) {\r
 415             MainFrame.cycleNodeDataReturn( getOptions(), getCurrentTreePanel() );\r
 416         }\r
 417         else if ( o == _screen_antialias_cbmi ) {\r
 418             updateOptions( getOptions() );\r
 419             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 420         }\r
 421         else if ( o == _background_gradient_cbmi ) {\r
 422             updateOptions( getOptions() );\r
 423         }\r
 424         else if ( o == _show_domain_labels ) {\r
 425             updateOptions( getOptions() );\r
 426         }\r
 427         else if ( o == _show_annotation_ref_source ) {\r
 428             updateOptions( getOptions() );\r
 429         }\r
 430         else if ( o == _abbreviate_scientific_names ) {\r
 431             updateOptions( getOptions() );\r
 432         }\r
 433         else if ( o == _color_labels_same_as_parent_branch ) {\r
 434             updateOptions( getOptions() );\r
 435         }\r
 436         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 437             updateOptions( getOptions() );\r
 438         }\r
 439         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 440             updateOptions( getOptions() );\r
 441         }\r
 442         else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
 443             updateOptions( getOptions() );\r
 444         }\r
 445         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 446             updateOptions( getOptions() );\r
 447             showWhole();\r
 448         }\r
 449         else if ( o == _uniform_cladograms_rbmi ) {\r
 450             updateOptions( getOptions() );\r
 451             showWhole();\r
 452         }\r
 453         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 454             updateOptions( getOptions() );\r
 455             showWhole();\r
 456         }\r
 457         else if ( o == _search_case_senstive_cbmi ) {\r
 458             updateOptions( getOptions() );\r
 459             getMainPanel().getControlPanel().search0();\r
 460             getMainPanel().getControlPanel().search1();\r
 461         }\r
 462         else if ( o == _search_whole_words_only_cbmi ) {\r
 463             if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
 464                 _search_with_regex_cbmi.setSelected( false );\r
 465             }\r
 466             updateOptions( getOptions() );\r
 467             getMainPanel().getControlPanel().search0();\r
 468             getMainPanel().getControlPanel().search1();\r
 469         }\r
 470         else if ( o == _inverse_search_result_cbmi ) {\r
 471             updateOptions( getOptions() );\r
 472             getMainPanel().getControlPanel().search0();\r
 473             getMainPanel().getControlPanel().search1();\r
 474         }\r
 475         else if ( o == _search_with_regex_cbmi ) {\r
 476             if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
 477                 _search_whole_words_only_cbmi.setSelected( false );\r
 478             }\r
 479             if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
 480                 _search_case_senstive_cbmi.setSelected( true );\r
 481             }\r
 482             updateOptions( getOptions() );\r
 483             getMainPanel().getControlPanel().search0();\r
 484             getMainPanel().getControlPanel().search1();\r
 485         }\r
 486         else if ( o == _show_scale_cbmi ) {\r
 487             updateOptions( getOptions() );\r
 488         }\r
 489         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 490             updateOptions( getOptions() );\r
 491         }\r
 492         else if ( o == _show_confidence_stddev_cbmi ) {\r
 493             updateOptions( getOptions() );\r
 494         }\r
 495         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 496             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 497                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 498             }\r
 499             updateOptions( getOptions() );\r
 500         }\r
 501         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 502             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 503                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 504             }\r
 505             updateOptions( getOptions() );\r
 506         }\r
 507         else if ( o == _label_direction_cbmi ) {\r
 508             updateOptions( getOptions() );\r
 509         }\r
 510         else if ( o == _show_overview_cbmi ) {\r
 511             updateOptions( getOptions() );\r
 512             if ( getCurrentTreePanel() != null ) {\r
 513                 getCurrentTreePanel().updateOvSizes();\r
 514             }\r
 515         }\r
 516         else if ( o == _line_up_renderable_data_cbmi ) {\r
 517             if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
 518                 _right_line_up_domains_cbmi.setSelected( false );\r
 519             }\r
 520             updateOptions( getOptions() );\r
 521         }\r
 522         else if ( o == _right_line_up_domains_cbmi ) {\r
 523             if ( _right_line_up_domains_cbmi.isSelected() ) {\r
 524                 _line_up_renderable_data_cbmi.setSelected( true );\r
 525             }\r
 526             updateOptions( getOptions() );\r
 527         }\r
 528         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 529                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 530                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 531             typeChanged( o );\r
 532         }\r
 533         else if ( o == _about_item ) {\r
 534             about();\r
 535         }\r
 536         else if ( o == _help_item ) {\r
 537             try {\r
 538                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
 539             }\r
 540             catch ( final IOException e1 ) {\r
 541                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 542             }\r
 543         }\r
 544         else if ( o == _website_item ) {\r
 545             try {\r
 546                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 547             }\r
 548             catch ( final IOException e1 ) {\r
 549                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 550             }\r
 551         }\r
 552         else if ( o == _phyloxml_website_item ) {\r
 553             try {\r
 554                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 555             }\r
 556             catch ( final IOException e1 ) {\r
 557                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 558             }\r
 559         }\r
 560         else if ( o == _aptx_ref_item ) {\r
 561             try {\r
 562                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 563             }\r
 564             catch ( final IOException e1 ) {\r
 565                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 566             }\r
 567         }\r
 568         else if ( o == _phyloxml_ref_item ) {\r
 569             try {\r
 570                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 571             }\r
 572             catch ( final IOException e1 ) {\r
 573                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 574             }\r
 575         }\r
 576         else {\r
 577             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 578                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 579                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 580                         readPhylogeniesFromWebservice( i );\r
 581                     }\r
 582                 }\r
 583             }\r
 584         }\r
 585         _contentpane.repaint();\r
 586     }\r
 587 \r
 588     private void deleteSelectedNodes( final boolean delete ) {\r
 589         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
 590         if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
 591             return;\r
 592         }\r
 593         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
 594         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
 595             final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
 596             for( final PhylogenyNode n : all_selected_nodes ) {\r
 597                 if ( n.isExternal() ) {\r
 598                     nodes.add( n );\r
 599                 }\r
 600             }\r
 601         }\r
 602         String function = "Retain";\r
 603         if ( delete ) {\r
 604             function = "Delete";\r
 605         }\r
 606         if ( ( nodes == null ) || nodes.isEmpty() ) {\r
 607             JOptionPane\r
 608             .showMessageDialog( this,\r
 609                                 "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
 610                                 "No external nodes selected to " + function.toLowerCase(),\r
 611                                 JOptionPane.ERROR_MESSAGE );\r
 612             return;\r
 613         }\r
 614         final int todo = nodes.size();\r
 615         final int ext = phy.getNumberOfExternalNodes();\r
 616         int res = todo;\r
 617         if ( delete ) {\r
 618             res = ext - todo;\r
 619         }\r
 620         if ( res < 1 ) {\r
 621             JOptionPane.showMessageDialog( this,\r
 622                                            "Cannot delete all nodes",\r
 623                                            "Attempt to delete all nodes ",\r
 624                                            JOptionPane.ERROR_MESSAGE );\r
 625             return;\r
 626         }\r
 627         final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
 628                                                           + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
 629                                                           + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
 630         if ( result == JOptionPane.OK_OPTION ) {\r
 631             if ( !delete ) {\r
 632                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
 633                 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
 634                     final PhylogenyNode n = it.next();\r
 635                     if ( !nodes.contains( n ) ) {\r
 636                         to_delete.add( n );\r
 637                     }\r
 638                 }\r
 639                 for( final PhylogenyNode n : to_delete ) {\r
 640                     phy.deleteSubtree( n, true );\r
 641                 }\r
 642             }\r
 643             else {\r
 644                 for( final PhylogenyNode n : nodes ) {\r
 645                     phy.deleteSubtree( n, true );\r
 646                 }\r
 647             }\r
 648             resetSearch();\r
 649             getCurrentTreePanel().setNodeInPreorderToNull();\r
 650             phy.externalNodesHaveChanged();\r
 651             phy.clearHashIdToNodeMap();\r
 652             phy.recalculateNumberOfExternalDescendants( true );\r
 653             getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
 654             getCurrentTreePanel().setEdited( true );\r
 655             repaint();\r
 656         }\r
 657     }\r
 658 \r
 659     void resetSearch() {\r
 660         getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
 661         getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
 662         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
 663         getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
 664         getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
 665         getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
 666         getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
 667         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
 668         getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
 669         getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
 670         getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
 671         getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
 672     }\r
 673 \r
 674     public Configuration getConfiguration() {\r
 675         return _configuration;\r
 676     }\r
 677 \r
 678     /**\r
 679      * This method returns the current external node data which\r
 680      * has been selected by the user by clicking the "Return ..."\r
 681      * menu item. This method is expected to be called from Javascript or\r
 682      * something like it.\r
 683      *\r
 684      * @return current external node data as String\r
 685      */\r
 686     public String getCurrentExternalNodesDataBuffer() {\r
 687         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 688     }\r
 689 \r
 690     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 691         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 692     }\r
 693 \r
 694     public int getCurrentExternalNodesDataBufferLength() {\r
 695         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 696     }\r
 697 \r
 698     public InferenceManager getInferenceManager() {\r
 699         return _inference_manager;\r
 700     }\r
 701 \r
 702     public MainPanel getMainPanel() {\r
 703         return _mainpanel;\r
 704     }\r
 705 \r
 706     public Options getOptions() {\r
 707         return _options;\r
 708     }\r
 709 \r
 710     public ProcessPool getProcessPool() {\r
 711         return _process_pool;\r
 712     }\r
 713 \r
 714     public void showTextFrame( final String s, final String title ) {\r
 715         checkTextFrames();\r
 716         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 717     }\r
 718 \r
 719     public void showWhole() {\r
 720         _mainpanel.getControlPanel().showWhole();\r
 721     }\r
 722 \r
 723     public void updateProcessMenu() {\r
 724         // In general Swing is not thread safe.\r
 725         // See "Swing's Threading Policy".\r
 726         SwingUtilities.invokeLater( new Runnable() {\r
 727 \r
 728             @Override\r
 729             public void run() {\r
 730                 doUpdateProcessMenu();\r
 731             }\r
 732         } );\r
 733     }\r
 734 \r
 735     void activateSaveAllIfNeeded() {\r
 736         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 737             _save_all_item.setEnabled( true );\r
 738         }\r
 739         else {\r
 740             _save_all_item.setEnabled( false );\r
 741         }\r
 742     }\r
 743 \r
 744     void buildFileMenu() {\r
 745         _file_jmenu = createMenu( "File", getConfiguration() );\r
 746         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 747         customizeJMenuItem( _exit_item );\r
 748         _jmenubar.add( _file_jmenu );\r
 749     }\r
 750 \r
 751     void buildFontSizeMenu() {\r
 752         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 753         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 754         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 755         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 756         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 757         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 758         customizeJMenuItem( _super_tiny_fonts_item );\r
 759         customizeJMenuItem( _tiny_fonts_item );\r
 760         customizeJMenuItem( _small_fonts_item );\r
 761         customizeJMenuItem( _medium_fonts_item );\r
 762         customizeJMenuItem( _large_fonts_item );\r
 763         _jmenubar.add( _font_size_menu );\r
 764     }\r
 765 \r
 766     void buildHelpMenu() {\r
 767         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 768         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
 769         _help_jmenu.addSeparator();\r
 770         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 771         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
 772         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 773         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 774         _help_jmenu.addSeparator();\r
 775         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 776         customizeJMenuItem( _help_item );\r
 777         customizeJMenuItem( _website_item );\r
 778         customizeJMenuItem( _phyloxml_website_item );\r
 779         customizeJMenuItem( _aptx_ref_item );\r
 780         customizeJMenuItem( _phyloxml_ref_item );\r
 781         customizeJMenuItem( _about_item );\r
 782         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 783         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 784         _jmenubar.add( _help_jmenu );\r
 785     }\r
 786 \r
 787     void buildTypeMenu() {\r
 788         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 789         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 790         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 791         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 792         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 793         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 794         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 795         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 796         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 797         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 798         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 799         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 800         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 801         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 802         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 803         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 804         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 805         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 806         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 807         initializeTypeMenu( getOptions() );\r
 808         _jmenubar.add( _type_menu );\r
 809     }\r
 810 \r
 811     void buildViewMenu() {\r
 812         _view_jmenu = createMenu( "View", getConfiguration() );\r
 813         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 814         _view_jmenu.addSeparator();\r
 815         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 816         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 817         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 818         customizeJMenuItem( _display_basic_information_item );\r
 819         customizeJMenuItem( _view_as_NH_item );\r
 820         customizeJMenuItem( _view_as_XML_item );\r
 821         customizeJMenuItem( _view_as_nexus_item );\r
 822         _jmenubar.add( _view_jmenu );\r
 823     }\r
 824 \r
 825     void checkTextFrames() {\r
 826         if ( _textframes.size() > 5 ) {\r
 827             try {\r
 828                 if ( _textframes.getFirst() != null ) {\r
 829                     _textframes.getFirst().removeMe();\r
 830                 }\r
 831                 else {\r
 832                     _textframes.removeFirst();\r
 833                 }\r
 834             }\r
 835             catch ( final NoSuchElementException e ) {\r
 836                 // Ignore.\r
 837             }\r
 838         }\r
 839     }\r
 840 \r
 841     void close() {\r
 842         removeAllTextFrames();\r
 843         if ( _mainpanel != null ) {\r
 844             _mainpanel.terminate();\r
 845         }\r
 846         if ( _contentpane != null ) {\r
 847             _contentpane.removeAll();\r
 848         }\r
 849         setVisible( false );\r
 850         dispose();\r
 851     }\r
 852 \r
 853     void colorRank() {\r
 854         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 855             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
 856             final String rank = ( String ) JOptionPane\r
 857                     .showInputDialog( this,\r
 858                                       "What rank should the colorization be based on",\r
 859                                       "Rank Selection",\r
 860                                       JOptionPane.QUESTION_MESSAGE,\r
 861                                       null,\r
 862                                       ranks,\r
 863                                       null );\r
 864             if ( !ForesterUtil.isEmpty( rank ) ) {\r
 865                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
 866             }\r
 867         }\r
 868     }\r
 869 \r
 870     void confColor() {\r
 871         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 872             _mainpanel.getCurrentTreePanel().confColor();\r
 873         }\r
 874     }\r
 875 \r
 876     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
 877         if ( item != null ) {\r
 878             item.setFont( MainFrame.menu_font );\r
 879             if ( !getConfiguration().isUseNativeUI() ) {\r
 880                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 881                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 882             }\r
 883             item.setSelected( is_selected );\r
 884             item.addActionListener( this );\r
 885         }\r
 886     }\r
 887 \r
 888     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
 889         if ( jmi != null ) {\r
 890             jmi.setFont( MainFrame.menu_font );\r
 891             if ( !getConfiguration().isUseNativeUI() ) {\r
 892                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 893                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 894             }\r
 895             jmi.addActionListener( this );\r
 896         }\r
 897         return jmi;\r
 898     }\r
 899 \r
 900     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
 901         if ( item != null ) {\r
 902             item.setFont( MainFrame.menu_font );\r
 903             if ( !getConfiguration().isUseNativeUI() ) {\r
 904                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 905                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 906             }\r
 907             item.setSelected( is_selected );\r
 908             item.addActionListener( this );\r
 909         }\r
 910     }\r
 911 \r
 912     void displayBasicInformation( final File treefile ) {\r
 913         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
 914             String title = "Basic Information";\r
 915             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
 916                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
 917             }\r
 918             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
 919         }\r
 920     }\r
 921 \r
 922     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
 923         try {\r
 924             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 925         }\r
 926         catch ( final Exception ex ) {\r
 927             // Do nothing.\r
 928         }\r
 929         JOptionPane.showMessageDialog( this,\r
 930                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
 931                                        "Error during File|Open",\r
 932                                        JOptionPane.ERROR_MESSAGE );\r
 933     }\r
 934 \r
 935     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
 936         try {\r
 937             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 938         }\r
 939         catch ( final Exception ex ) {\r
 940             // Do nothing.\r
 941         }\r
 942         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
 943     }\r
 944 \r
 945     void executeGSDI() {\r
 946         if ( !isOKforSDI( false, true ) ) {\r
 947             return;\r
 948         }\r
 949         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
 950             JOptionPane.showMessageDialog( this,\r
 951                                            "Gene tree is not rooted.",\r
 952                                            "Cannot execute GSDI",\r
 953                                            JOptionPane.ERROR_MESSAGE );\r
 954             return;\r
 955         }\r
 956         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 957         gene_tree.setAllNodesToNotCollapse();\r
 958         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 959         GSDI gsdi = null;\r
 960         final Phylogeny species_tree = getSpeciesTree().copy();\r
 961         try {\r
 962             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
 963         }\r
 964         catch ( final SDIException e ) {\r
 965             JOptionPane.showMessageDialog( this,\r
 966                                            e.getLocalizedMessage(),\r
 967                                            "Error during GSDI",\r
 968                                            JOptionPane.ERROR_MESSAGE );\r
 969             return;\r
 970         }\r
 971         catch ( final Exception e ) {\r
 972             AptxUtil.unexpectedException( e );\r
 973             return;\r
 974         }\r
 975         gene_tree.setRerootable( false );\r
 976         gene_tree.clearHashIdToNodeMap();\r
 977         gene_tree.recalculateNumberOfExternalDescendants( true );\r
 978         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
 979         getMainPanel().getControlPanel().setShowEvents( true );\r
 980         showWhole();\r
 981         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 982         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 983         showWhole();\r
 984         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 985         showWhole();\r
 986         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 987         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 988         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 989             JOptionPane.showMessageDialog( this,\r
 990                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 991                                                    + "Potential duplications: "\r
 992                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 993                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 994                                                    + "Stripped gene tree nodes: "\r
 995                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 996                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 997                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 998                                                    "GSDI successfully completed",\r
 999                                                    JOptionPane.WARNING_MESSAGE );\r
1000         }\r
1001         else {\r
1002             JOptionPane.showMessageDialog( this,\r
1003                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
1004                                                    + "Potential duplications: "\r
1005                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
1006                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
1007                                                    + "Stripped gene tree nodes: "\r
1008                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1009                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
1010                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1011                                                    "GSDI successfully completed",\r
1012                                                    JOptionPane.INFORMATION_MESSAGE );\r
1013         }\r
1014     }\r
1015 \r
1016     void executeGSDIR() {\r
1017         if ( !isOKforSDI( false, false ) ) {\r
1018             return;\r
1019         }\r
1020         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
1021         if ( ( p > 0 )\r
1022                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
1023             JOptionPane.showMessageDialog( this,\r
1024                                            "Gene tree is not completely binary",\r
1025                                            "Cannot execute GSDI",\r
1026                                            JOptionPane.ERROR_MESSAGE );\r
1027             return;\r
1028         }\r
1029         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
1030         gene_tree.setAllNodesToNotCollapse();\r
1031         gene_tree.recalculateNumberOfExternalDescendants( false );\r
1032         GSDIR gsdir = null;\r
1033         final Phylogeny species_tree = getSpeciesTree().copy();\r
1034         try {\r
1035             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
1036         }\r
1037         catch ( final SDIException e ) {\r
1038             JOptionPane.showMessageDialog( this,\r
1039                                            e.getLocalizedMessage(),\r
1040                                            "Error during GSDIR",\r
1041                                            JOptionPane.ERROR_MESSAGE );\r
1042             return;\r
1043         }\r
1044         catch ( final Exception e ) {\r
1045             AptxUtil.unexpectedException( e );\r
1046             return;\r
1047         }\r
1048         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
1049         result_gene_tree.setRerootable( false );\r
1050         result_gene_tree.clearHashIdToNodeMap();\r
1051         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
1052         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
1053         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
1054         getMainPanel().getControlPanel().setShowEvents( true );\r
1055         showWhole();\r
1056         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1057         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1058         showWhole();\r
1059         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1060         showWhole();\r
1061         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1062         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1063         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1064             JOptionPane.showMessageDialog( this,\r
1065                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1066                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1067                                                    + "Stripped gene tree nodes: "\r
1068                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1069                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1070                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1071                                                    "GSDIR successfully completed",\r
1072                                                    JOptionPane.WARNING_MESSAGE );\r
1073         }\r
1074         else {\r
1075             JOptionPane.showMessageDialog( this,\r
1076                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1077                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1078                                                    + "Stripped gene tree nodes: "\r
1079                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1080                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1081                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1082                                                    "GSDIR successfully completed",\r
1083                                                    JOptionPane.INFORMATION_MESSAGE );\r
1084         }\r
1085     }\r
1086 \r
1087     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
1088         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
1089             JOptionPane.showMessageDialog( this,\r
1090                                            "Gene tree and species tree have no species in common.",\r
1091                                            "Error during SDI",\r
1092                                            JOptionPane.ERROR_MESSAGE );\r
1093             return false;\r
1094         }\r
1095         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
1096             JOptionPane.showMessageDialog( this,\r
1097                                            "Gene tree and species tree have only one species in common.",\r
1098                                            "Error during SDI",\r
1099                                            JOptionPane.ERROR_MESSAGE );\r
1100             return false;\r
1101         }\r
1102         else {\r
1103             return true;\r
1104         }\r
1105     }\r
1106 \r
1107     TreePanel getCurrentTreePanel() {\r
1108         return getMainPanel().getCurrentTreePanel();\r
1109     }\r
1110 \r
1111     JMenu getHelpMenu() {\r
1112         return _help_jmenu;\r
1113     }\r
1114 \r
1115     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
1116         return _label_direction_cbmi;\r
1117     }\r
1118 \r
1119     JMenuBar getMenuBarOfMainFrame() {\r
1120         return _jmenubar;\r
1121     }\r
1122 \r
1123     final Phylogeny getSpeciesTree() {\r
1124         return _species_tree;\r
1125     }\r
1126 \r
1127     void initializeTypeMenu( final Options options ) {\r
1128         setTypeMenuToAllUnselected();\r
1129         switch ( options.getPhylogenyGraphicsType() ) {\r
1130             case CONVEX:\r
1131                 _convex_type_cbmi.setSelected( true );\r
1132                 break;\r
1133             case CURVED:\r
1134                 _curved_type_cbmi.setSelected( true );\r
1135                 break;\r
1136             case EURO_STYLE:\r
1137                 _euro_type_cbmi.setSelected( true );\r
1138                 break;\r
1139             case ROUNDED:\r
1140                 _rounded_type_cbmi.setSelected( true );\r
1141                 break;\r
1142             case TRIANGULAR:\r
1143                 _triangular_type_cbmi.setSelected( true );\r
1144                 break;\r
1145             case UNROOTED:\r
1146                 _unrooted_type_cbmi.setSelected( true );\r
1147                 break;\r
1148             case CIRCULAR:\r
1149                 _circular_type_cbmi.setSelected( true );\r
1150                 break;\r
1151             default:\r
1152                 _rectangular_type_cbmi.setSelected( true );\r
1153                 break;\r
1154         }\r
1155     }\r
1156 \r
1157     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1158         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1159             return false;\r
1160         }\r
1161         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1162             JOptionPane.showMessageDialog( this,\r
1163                                            "No species tree loaded",\r
1164                                            "Cannot execute GSDI",\r
1165                                            JOptionPane.ERROR_MESSAGE );\r
1166             return false;\r
1167         }\r
1168         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1169             JOptionPane.showMessageDialog( this,\r
1170                                            "Species tree is not completely binary",\r
1171                                            "Cannot execute GSDI",\r
1172                                            JOptionPane.ERROR_MESSAGE );\r
1173             return false;\r
1174         }\r
1175         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1176             JOptionPane.showMessageDialog( this,\r
1177                                            "Gene tree is not completely binary",\r
1178                                            "Cannot execute GSDI",\r
1179                                            JOptionPane.ERROR_MESSAGE );\r
1180             return false;\r
1181         }\r
1182         else {\r
1183             return true;\r
1184         }\r
1185     }\r
1186 \r
1187     boolean isSubtreeDisplayed() {\r
1188         if ( getCurrentTreePanel() != null ) {\r
1189             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1190                 JOptionPane\r
1191                 .showMessageDialog( this,\r
1192                                     "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1193                                     "Operation can not be exectuted on a sub-tree",\r
1194                                     JOptionPane.WARNING_MESSAGE );\r
1195                 return true;\r
1196             }\r
1197         }\r
1198         return false;\r
1199     }\r
1200 \r
1201     void midpointRoot() {\r
1202         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1203             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1204         }\r
1205     }\r
1206 \r
1207     void readPhylogeniesFromWebservice( final int i ) {\r
1208         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1209         new Thread( reader ).start();\r
1210     }\r
1211 \r
1212     void removeAllTextFrames() {\r
1213         for( final TextFrame tf : _textframes ) {\r
1214             if ( tf != null ) {\r
1215                 tf.close();\r
1216             }\r
1217         }\r
1218         _textframes.clear();\r
1219     }\r
1220 \r
1221     void setConfiguration( final Configuration configuration ) {\r
1222         _configuration = configuration;\r
1223     }\r
1224 \r
1225     void setInferenceManager( final InferenceManager i ) {\r
1226         _inference_manager = i;\r
1227     }\r
1228 \r
1229     void setOptions( final Options options ) {\r
1230         _options = options;\r
1231     }\r
1232 \r
1233     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1234         setTypeMenuToAllUnselected();\r
1235         switch ( type ) {\r
1236             case CIRCULAR:\r
1237                 _circular_type_cbmi.setSelected( true );\r
1238                 break;\r
1239             case CONVEX:\r
1240                 _convex_type_cbmi.setSelected( true );\r
1241                 break;\r
1242             case CURVED:\r
1243                 _curved_type_cbmi.setSelected( true );\r
1244                 break;\r
1245             case EURO_STYLE:\r
1246                 _euro_type_cbmi.setSelected( true );\r
1247                 break;\r
1248             case ROUNDED:\r
1249                 _rounded_type_cbmi.setSelected( true );\r
1250                 break;\r
1251             case RECTANGULAR:\r
1252                 _rectangular_type_cbmi.setSelected( true );\r
1253                 break;\r
1254             case TRIANGULAR:\r
1255                 _triangular_type_cbmi.setSelected( true );\r
1256                 break;\r
1257             case UNROOTED:\r
1258                 _unrooted_type_cbmi.setSelected( true );\r
1259                 break;\r
1260             default:\r
1261                 throw new IllegalArgumentException( "unknown type: " + type );\r
1262         }\r
1263     }\r
1264 \r
1265     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1266         _species_tree = species_tree;\r
1267     }\r
1268 \r
1269     void setTypeMenuToAllUnselected() {\r
1270         _convex_type_cbmi.setSelected( false );\r
1271         _curved_type_cbmi.setSelected( false );\r
1272         _euro_type_cbmi.setSelected( false );\r
1273         _rounded_type_cbmi.setSelected( false );\r
1274         _triangular_type_cbmi.setSelected( false );\r
1275         _rectangular_type_cbmi.setSelected( false );\r
1276         _unrooted_type_cbmi.setSelected( false );\r
1277         _circular_type_cbmi.setSelected( false );\r
1278     }\r
1279 \r
1280     void switchColors() {\r
1281         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1282         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1283         csc.setVisible( true );\r
1284     }\r
1285 \r
1286     void taxColor() {\r
1287         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1288             _mainpanel.getCurrentTreePanel().taxColor();\r
1289         }\r
1290     }\r
1291 \r
1292     void typeChanged( final Object o ) {\r
1293         updateTypeCheckboxes( getOptions(), o );\r
1294         updateOptions( getOptions() );\r
1295         if ( getCurrentTreePanel() != null ) {\r
1296             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1297             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1298             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1299                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1300                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1301                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1302                 getCurrentTreePanel().getControlPanel().showWhole();\r
1303             }\r
1304             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1305                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1306             }\r
1307             else {\r
1308                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1309             }\r
1310             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1311             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1312             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1313                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1314                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1315                 }\r
1316                 else {\r
1317                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1318                 }\r
1319             }\r
1320         }\r
1321     }\r
1322 \r
1323     void updateOptions( final Options options ) {\r
1324         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1325         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1326                                             && _background_gradient_cbmi.isSelected() );\r
1327         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1328         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1329                                             && _show_annotation_ref_source.isSelected() );\r
1330         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1331                                                    && _abbreviate_scientific_names.isSelected() );\r
1332         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1333                                                   && _color_labels_same_as_parent_branch.isSelected() );\r
1334         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1335                                                   && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1336         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1337                                                   && _show_default_node_shapes_external_cbmi.isSelected() );\r
1338         options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
1339                                                         && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
1340         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1341             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1342         }\r
1343         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1344             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1345         }\r
1346         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1347             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1348         }\r
1349         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1350                                         && _search_case_senstive_cbmi.isSelected() );\r
1351         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1352             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1353         }\r
1354         if ( _label_direction_cbmi != null ) {\r
1355             if ( _label_direction_cbmi.isSelected() ) {\r
1356                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1357             }\r
1358             else {\r
1359                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1360             }\r
1361         }\r
1362         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1363         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1364                                          && _show_confidence_stddev_cbmi.isSelected() );\r
1365         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1366             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1367         }\r
1368         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1369                                          && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1370         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1371                                                   && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1372         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1373         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1374                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1375             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1376         }\r
1377         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1378                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1379             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1380         }\r
1381         else {\r
1382             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1383         }\r
1384         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1385                                        && _print_black_and_white_cbmi.isSelected() );\r
1386         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1387                                                             && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1388         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1389             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1390         }\r
1391         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1392             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1393         }\r
1394         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1395             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1396         }\r
1397         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1398             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1399         }\r
1400         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1401                                                   && _replace_underscores_cbmi.isSelected() );\r
1402         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1403                                                   && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1404         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1405                                         && _search_whole_words_only_cbmi.isSelected() );\r
1406         options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
1407         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1408                                         && _inverse_search_result_cbmi.isSelected() );\r
1409         if ( _graphics_export_visible_only_cbmi != null ) {\r
1410             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1411             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1412                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1413                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1414             }\r
1415             else {\r
1416                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1417             }\r
1418         }\r
1419         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1420             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1421         }\r
1422         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1423             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1424         }\r
1425         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1426             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1427         }\r
1428         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1429             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1430         }\r
1431         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1432             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1433         }\r
1434         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1435             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1436         }\r
1437         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1438             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1439         }\r
1440         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1441             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1442         }\r
1443         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
1444             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
1445         }\r
1446         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
1447             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
1448         }\r
1449     }\r
1450 \r
1451     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1452         setTypeMenuToAllUnselected();\r
1453         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1454     }\r
1455 \r
1456     void viewAsNexus() {\r
1457         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1458             String title = "Nexus";\r
1459             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1460                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1461             }\r
1462             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1463                            title );\r
1464         }\r
1465     }\r
1466 \r
1467     void viewAsNH() {\r
1468         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1469             String title = "New Hampshire";\r
1470             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1471                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1472             }\r
1473             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1474                                                                             .getNhConversionSupportValueStyle() ),\r
1475                                                                             title );\r
1476         }\r
1477     }\r
1478 \r
1479     void viewAsXML() {\r
1480         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1481             String title = "phyloXML";\r
1482             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1483                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1484             }\r
1485             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1486         }\r
1487     }\r
1488 \r
1489     private void annotateSequences() {\r
1490         if ( getCurrentTreePanel() != null ) {\r
1491             List<PhylogenyNode> nodes = null;\r
1492             if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
1493                     || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
1494                 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
1495             }\r
1496             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1497                 JOptionPane\r
1498                 .showMessageDialog( this,\r
1499                                     "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1500                                     "No nodes selected for annotation",\r
1501                                     JOptionPane.ERROR_MESSAGE );\r
1502                 return;\r
1503             }\r
1504             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1505             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1506                 final JTextField ref_field = new JTextField( 10 );\r
1507                 final JTextField desc_filed = new JTextField( 20 );\r
1508                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1509                         : getPreviousNodeAnnotationReference() );\r
1510                 final JPanel my_panel = new JPanel();\r
1511                 my_panel.add( new JLabel( "Reference " ) );\r
1512                 my_panel.add( ref_field );\r
1513                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1514                 my_panel.add( new JLabel( "Description " ) );\r
1515                 my_panel.add( desc_filed );\r
1516                 final int result = JOptionPane.showConfirmDialog( null,\r
1517                                                                   my_panel,\r
1518                                                                   "Enter the sequence annotation(s) for the "\r
1519                                                                           + nodes.size() + " selected nodes",\r
1520                                                                           JOptionPane.OK_CANCEL_OPTION );\r
1521                 if ( result == JOptionPane.OK_OPTION ) {\r
1522                     String ref = ref_field.getText();\r
1523                     String desc = desc_filed.getText();\r
1524                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1525                         ref = ref.trim();\r
1526                         ref = ref.replaceAll( "\\s+", " " );\r
1527                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1528                                 || ( ref.length() < 3 ) ) {\r
1529                             JOptionPane.showMessageDialog( this,\r
1530                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1531                                                            "Illegal Format for Annotation Reference",\r
1532                                                            JOptionPane.ERROR_MESSAGE );\r
1533                             return;\r
1534                         }\r
1535                     }\r
1536                     if ( ref != null ) {\r
1537                         setPreviousNodeAnnotationReference( ref );\r
1538                     }\r
1539                     if ( desc != null ) {\r
1540                         desc = desc.trim();\r
1541                         desc = desc.replaceAll( "\\s+", " " );\r
1542                     }\r
1543                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1544                         for( final PhylogenyNode n : nodes ) {\r
1545                             ForesterUtil.ensurePresenceOfSequence( n );\r
1546                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1547                             : new Annotation( ref );\r
1548                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1549                                 ann.setDesc( desc );\r
1550                             }\r
1551                             n.getNodeData().getSequence().addAnnotation( ann );\r
1552                         }\r
1553                     }\r
1554                     getMainPanel().getControlPanel().showAnnotations();\r
1555                 }\r
1556             }\r
1557         }\r
1558     }\r
1559 \r
1560     private void chooseFont() {\r
1561         final FontChooser fc = new FontChooser();\r
1562         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1563         fc.showDialog( this, "Select the Base Font" );\r
1564         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1565     }\r
1566 \r
1567     private void chooseMinimalConfidence() {\r
1568         final String s = ( String ) JOptionPane\r
1569                 .showInputDialog( this,\r
1570                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1571                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1572                                           "Minimal Confidence Value",\r
1573                                           JOptionPane.QUESTION_MESSAGE,\r
1574                                           null,\r
1575                                           null,\r
1576                                           getOptions().getMinConfidenceValue() );\r
1577         if ( !ForesterUtil.isEmpty( s ) ) {\r
1578             boolean success = true;\r
1579             double m = 0.0;\r
1580             final String m_str = s.trim();\r
1581             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1582                 try {\r
1583                     m = Double.parseDouble( m_str );\r
1584                 }\r
1585                 catch ( final Exception ex ) {\r
1586                     success = false;\r
1587                 }\r
1588             }\r
1589             else {\r
1590                 success = false;\r
1591             }\r
1592             if ( success && ( m >= 0.0 ) ) {\r
1593                 getOptions().setMinConfidenceValue( m );\r
1594             }\r
1595         }\r
1596     }\r
1597 \r
1598     private void doUpdateProcessMenu() {\r
1599         if ( _process_pool.size() > 0 ) {\r
1600             if ( _process_menu == null ) {\r
1601                 _process_menu = createMenu( "", getConfiguration() );\r
1602                 _process_menu.setForeground( Color.RED );\r
1603             }\r
1604             _process_menu.removeAll();\r
1605             final String text = "processes running: " + _process_pool.size();\r
1606             _process_menu.setText( text );\r
1607             _jmenubar.add( _process_menu );\r
1608             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1609                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1610                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1611             }\r
1612         }\r
1613         else {\r
1614             if ( _process_menu != null ) {\r
1615                 _process_menu.removeAll();\r
1616                 _jmenubar.remove( _process_menu );\r
1617             }\r
1618         }\r
1619         _jmenubar.validate();\r
1620         _jmenubar.repaint();\r
1621         repaint();\r
1622     }\r
1623 \r
1624     private String getPreviousNodeAnnotationReference() {\r
1625         return _previous_node_annotation_ref;\r
1626     }\r
1627 \r
1628     private void removeBranchColors() {\r
1629         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1630             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1631         }\r
1632     }\r
1633 \r
1634     private void removeVisualStyles() {\r
1635         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1636             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1637         }\r
1638     }\r
1639 \r
1640     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1641         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1642     }\r
1643 \r
1644     /**\r
1645      * Display the about box.\r
1646      */\r
1647     static void about() {\r
1648         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1649         about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
1650         about.append( "All Rights Reserved\n" );\r
1651         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1652         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1653         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1654         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1655         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1656         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1657             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1658         }\r
1659         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1660                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1661             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1662                     + ForesterUtil.OS_VERSION + "]\n" );\r
1663         }\r
1664         final Runtime rt = java.lang.Runtime.getRuntime();\r
1665         final long free_memory = rt.freeMemory() / 1000000;\r
1666         final long total_memory = rt.totalMemory() / 1000000;\r
1667         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1668         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1669         about.append( "References:\n" );\r
1670         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1671         about.append( "For more information & download:\n" );\r
1672         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1673         about.append( "Documentation:\n" );\r
1674         about.append( Constants.APTX_DOC_SITE + "\n" );\r
1675         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1676         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1677     }\r
1678 \r
1679     static void chooseNodeSize( final Options options, final Component parent ) {\r
1680         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1681                                                                  "Please enter the default size for node shapes.\n"\r
1682                                                                          + "[current value: "\r
1683                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1684                                                                          "Node Shape Size",\r
1685                                                                          JOptionPane.QUESTION_MESSAGE,\r
1686                                                                          null,\r
1687                                                                          null,\r
1688                                                                          options.getDefaultNodeShapeSize() );\r
1689         if ( !ForesterUtil.isEmpty( s ) ) {\r
1690             boolean success = true;\r
1691             double m = 0.0;\r
1692             final String m_str = s.trim();\r
1693             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1694                 try {\r
1695                     m = Double.parseDouble( m_str );\r
1696                 }\r
1697                 catch ( final Exception ex ) {\r
1698                     success = false;\r
1699                 }\r
1700             }\r
1701             else {\r
1702                 success = false;\r
1703             }\r
1704             if ( success && ( m >= 0.0 ) ) {\r
1705                 final short size = ForesterUtil.roundToShort( m );\r
1706                 if ( size >= 0.0 ) {\r
1707                     options.setDefaultNodeShapeSize( size );\r
1708                 }\r
1709             }\r
1710         }\r
1711     }\r
1712 \r
1713     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1714         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1715     }\r
1716 \r
1717     static JMenu createMenu( final String title, final Configuration conf ) {\r
1718         final JMenu jmenu = new JMenu( title );\r
1719         if ( !conf.isUseNativeUI() ) {\r
1720             jmenu.setFont( MainFrame.menu_font );\r
1721             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1722             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1723         }\r
1724         return jmenu;\r
1725     }\r
1726 \r
1727     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1728         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1729         if ( !configuration.isUseNativeUI() ) {\r
1730             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1731             label.setForeground( configuration.getGuiMenuTextColor() );\r
1732             label.setOpaque( true );\r
1733         }\r
1734         label.setSelected( false );\r
1735         label.setEnabled( false );\r
1736         return label;\r
1737     }\r
1738 \r
1739     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
1740         switch ( op.getDefaultNodeFill() ) {\r
1741             case GRADIENT:\r
1742                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1743                 break;\r
1744             case NONE:\r
1745                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1746                 break;\r
1747             case SOLID:\r
1748                 op.setDefaultNodeFill( NodeFill.NONE );\r
1749                 break;\r
1750             default:\r
1751                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1752         }\r
1753     }\r
1754 \r
1755     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
1756         switch ( op.getDefaultNodeShape() ) {\r
1757             case CIRCLE:\r
1758                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1759                 break;\r
1760             case RECTANGLE:\r
1761                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1762                 break;\r
1763             default:\r
1764                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1765         }\r
1766     }\r
1767 \r
1768     static void cycleNodeDataReturn( final Options op, final TreePanel tree_panel ) {\r
1769         switch ( op.getExtDescNodeDataToReturn() ) {\r
1770             case UNKNOWN:\r
1771                 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
1772                 break;\r
1773             case DOMAINS_ALL:\r
1774                 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
1775                 break;\r
1776             case DOMAINS_COLLAPSED_PER_PROTEIN:\r
1777                 op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
1778                 break;\r
1779             case GO_TERM_IDS:\r
1780                 op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
1781                 break;\r
1782             default:\r
1783                 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
1784         }\r
1785     }\r
1786 \r
1787     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1788         switch ( op.getOvPlacement() ) {\r
1789             case LOWER_LEFT:\r
1790                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1791                 break;\r
1792             case LOWER_RIGHT:\r
1793                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1794                 break;\r
1795             case UPPER_LEFT:\r
1796                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1797                 break;\r
1798             case UPPER_RIGHT:\r
1799                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1800                 break;\r
1801             default:\r
1802                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1803         }\r
1804         if ( tree_panel != null ) {\r
1805             tree_panel.updateOvSettings();\r
1806         }\r
1807     }\r
1808 \r
1809     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
1810         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
1811             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1812                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
1813         }\r
1814         else {\r
1815             mi.setText( "Cycle Node Shape Fill Type..." );\r
1816         }\r
1817     }\r
1818 \r
1819     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
1820         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
1821             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1822                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
1823         }\r
1824         else {\r
1825             mi.setText( "Cycle Node Shape Fill Type..." );\r
1826         }\r
1827     }\r
1828 \r
1829     static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
1830         if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
1831             mi.setText( "Cycle Node Return Data... (current: "\r
1832                     + options.getExtDescNodeDataToReturn().toString() + ")" );\r
1833         }\r
1834         else {\r
1835             mi.setText( "Cycle Node Return Data..." );\r
1836         }\r
1837     }\r
1838 \r
1839     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
1840         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
1841             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
1842         }\r
1843         else {\r
1844             mi.setText( "Cycle Overview Placement..." );\r
1845         }\r
1846     }\r
1847 \r
1848     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
1849         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
1850             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
1851                         + ")" );\r
1852         }\r
1853         else {\r
1854             mi.setText( "Select Color Scheme..." );\r
1855         }\r
1856     }\r
1857 \r
1858     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
1859         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
1860     }\r
1861 \r
1862     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
1863         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
1864             mi.setEnabled( true );\r
1865         }\r
1866         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
1867             mi.setEnabled( true );\r
1868         }\r
1869         else {\r
1870             mi.setEnabled( false );\r
1871         }\r
1872         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
1873     }\r
1874 \r
1875     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
1876         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
1877     }\r
1878 \r
1879     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
1880         for( final TreePanel tree_panel : treepanels ) {\r
1881             tree_panel.setTextAntialias();\r
1882         }\r
1883     }\r
1884 }\r