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

   1 // $Id:\r
   2 // FORESTER -- software libraries and applications\r
   3 // for evolutionary biology research and applications.\r
   4 //\r
   5 // Copyright (C) 2008-2010 Christian M. Zmasek\r
   6 // All rights reserved\r
   7 //\r
   8 // This library is free software; you can redistribute it and/or\r
   9 // modify it under the terms of the GNU Lesser General Public\r
  10 // License as published by the Free Software Foundation; either\r
  11 // version 2.1 of the License, or (at your option) any later version.\r
  12 //\r
  13 // This library is distributed in the hope that it will be useful,\r
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
  16 // Lesser General Public License for more details.\r
  17 //\r
  18 // You should have received a copy of the GNU Lesser General Public\r
  19 // License along with this library; if not, write to the Free Software\r
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
  21 //\r
  22 // Contact: phylosoft @ gmail . com\r
  23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
  24 \r
  25 package org.forester.archaeopteryx;\r
  26 \r
  27 import java.awt.Color;\r
  28 import java.awt.Component;\r
  29 import java.awt.Container;\r
  30 import java.awt.Font;\r
  31 import java.awt.event.ActionEvent;\r
  32 import java.awt.event.ActionListener;\r
  33 import java.io.File;\r
  34 import java.io.IOException;\r
  35 import java.util.ArrayList;\r
  36 import java.util.LinkedList;\r
  37 import java.util.List;\r
  38 import java.util.Locale;\r
  39 import java.util.NoSuchElementException;\r
  40 \r
  41 import javax.swing.Box;\r
  42 import javax.swing.JApplet;\r
  43 import javax.swing.JCheckBoxMenuItem;\r
  44 import javax.swing.JFrame;\r
  45 import javax.swing.JLabel;\r
  46 import javax.swing.JMenu;\r
  47 import javax.swing.JMenuBar;\r
  48 import javax.swing.JMenuItem;\r
  49 import javax.swing.JOptionPane;\r
  50 import javax.swing.JPanel;\r
  51 import javax.swing.JRadioButtonMenuItem;\r
  52 import javax.swing.JTextField;\r
  53 import javax.swing.SwingUtilities;\r
  54 \r
  55 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
  56 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
  57 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
  58 import org.forester.archaeopteryx.tools.InferenceManager;\r
  59 import org.forester.archaeopteryx.tools.ProcessPool;\r
  60 import org.forester.archaeopteryx.tools.ProcessRunning;\r
  61 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
  62 import org.forester.phylogeny.Phylogeny;\r
  63 import org.forester.phylogeny.PhylogenyMethods;\r
  64 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
  65 import org.forester.phylogeny.PhylogenyNode;\r
  66 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
  67 import org.forester.phylogeny.data.Annotation;\r
  68 import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
  69 import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
  70 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
  71 import org.forester.sdi.GSDI;\r
  72 import org.forester.sdi.GSDIR;\r
  73 import org.forester.sdi.SDIException;\r
  74 import org.forester.util.ForesterConstants;\r
  75 import org.forester.util.ForesterUtil;\r
  76 \r
  77 public abstract class MainFrame extends JFrame implements ActionListener {\r
  78 \r
  79     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
  80     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME\r
  81     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
  82     private static final long   serialVersionUID                        = 3655000897845508358L;\r
  83     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
  84                                                                                     Font.PLAIN,\r
  85                                                                                     10 );\r
  86     static final String         TYPE_MENU_HEADER                        = "Type";\r
  87     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
  88     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
  89     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
  90     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
  91     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
  92     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
  93     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO\r
  94     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO\r
  95     static final String         OPTIONS_HEADER                          = "Options";\r
  96     static final String         SEARCH_SUBHEADER                        = "Search:";\r
  97     static final String         DISPLAY_SUBHEADER                       = "Display:";\r
  98     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
  99     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
 100     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
 101     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Branch Length Values";\r
 102     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
 103     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
 104     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
 105     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
 106     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
 107     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
 108     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 109     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 110     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 111     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "External Node Shapes";\r
 112     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Internal Node Shapes";\r
 113     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 114     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 115     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 116     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 117     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 118     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
 119     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 120     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 121     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 122     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 123     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 124     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 125     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 126     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 127     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 128     static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";\r
 129     static final String LINE_UP_RENDERABLE_DATA = "Line Up Node Diagrams";\r
 130     JMenuBar                    _jmenubar;\r
 131     JMenu                       _file_jmenu;\r
 132     JMenu                       _tools_menu;\r
 133     JMenu                       _view_jmenu;\r
 134     JMenu                       _options_jmenu;\r
 135     JMenu                       _font_size_menu;\r
 136     JMenu                       _help_jmenu;\r
 137     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 138     // Analysis menu\r
 139     JMenu                       _analysis_menu;\r
 140     JMenuItem                   _load_species_tree_item;\r
 141     JMenuItem                   _gsdi_item;\r
 142     JMenuItem                   _gsdir_item;\r
 143     JMenuItem                   _lineage_inference;\r
 144     // file menu:\r
 145     JMenuItem                   _open_item;\r
 146     JMenuItem                   _open_url_item;\r
 147     JMenuItem                   _save_item;\r
 148     JMenuItem                   _save_all_item;\r
 149     JMenuItem                   _close_item;\r
 150     JMenuItem                   _exit_item;\r
 151     JMenuItem                   _new_item;\r
 152     // tools menu:\r
 153     JMenuItem                   _midpoint_root_item;\r
 154     JMenuItem                   _taxcolor_item;\r
 155     JMenuItem                   _confcolor_item;\r
 156     JMenuItem                   _color_rank_jmi;\r
 157     JMenuItem                   _collapse_species_specific_subtrees;\r
 158     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me\r
 159     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 160     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 161     JMenuItem                   _obtain_seq_information_jmi;\r
 162     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 163     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 164     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 165     JMenuItem                   _annotate_item;\r
 166     JMenuItem                   _remove_branch_color_item;\r
 167     JMenuItem                   _remove_visual_styles_item;\r
 168     JMenuItem                   _delete_selected_nodes_item;\r
 169     JMenuItem                   _delete_not_selected_nodes_item;\r
 170     // font size menu:\r
 171     JMenuItem                   _super_tiny_fonts_item;\r
 172     JMenuItem                   _tiny_fonts_item;\r
 173     JMenuItem                   _small_fonts_item;\r
 174     JMenuItem                   _medium_fonts_item;\r
 175     JMenuItem                   _large_fonts_item;\r
 176     // options menu:\r
 177     // _  screen and print\r
 178     JMenuItem                   _choose_font_mi;\r
 179     JMenuItem                   _switch_colors_mi;\r
 180     JCheckBoxMenuItem           _label_direction_cbmi;\r
 181     // _  screen display\r
 182     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 183     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 184     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 185     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 186     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 187     JCheckBoxMenuItem           _show_branch_length_values_cbmi;\r
 188     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 189     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me\r
 190     JCheckBoxMenuItem           _show_overview_cbmi;\r
 191     JCheckBoxMenuItem           _show_domain_labels;\r
 192     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 193     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 194     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 195     JMenuItem                   _overview_placment_mi;\r
 196     JMenuItem                   _choose_minimal_confidence_mi;\r
 197     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 198     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 199     JMenuItem                   _cycle_node_shape_mi;\r
 200     JMenuItem                   _cycle_node_fill_mi;\r
 201     JMenuItem                   _choose_node_size_mi;\r
 202     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 203    JCheckBoxMenuItem _right_line_up_domains_cbmi;\r
 204     JCheckBoxMenuItem _line_up_renderable_data_cbmi;\r
 205     // _  print\r
 206     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 207     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 208     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 209     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 210     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 211     JMenuItem                   _print_size_mi;\r
 212     JMenuItem                   _choose_pdf_width_mi;\r
 213     // _  parsing\r
 214     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 215     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 216     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 217     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 218     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 219     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 220     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 221     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 222     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 223     // _  search\r
 224     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 225     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 226     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 227     // type menu:\r
 228     JMenu                       _type_menu;\r
 229     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 230     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 231     JCheckBoxMenuItem           _curved_type_cbmi;\r
 232     JCheckBoxMenuItem           _convex_type_cbmi;\r
 233     JCheckBoxMenuItem           _euro_type_cbmi;\r
 234     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 235     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 236     JCheckBoxMenuItem           _circular_type_cbmi;\r
 237     // view as text menu:\r
 238     JMenuItem                   _view_as_NH_item;\r
 239     JMenuItem                   _view_as_XML_item;\r
 240     JMenuItem                   _view_as_nexus_item;\r
 241     JMenuItem                   _display_basic_information_item;\r
 242     // help menu:\r
 243     JMenuItem                   _about_item;\r
 244     JMenuItem                   _help_item;\r
 245     JMenuItem                   _website_item;\r
 246     JMenuItem                   _phyloxml_website_item;\r
 247     JMenuItem                   _phyloxml_ref_item;\r
 248     JMenuItem                   _aptx_ref_item;\r
 249     // process menu:\r
 250     JMenu                       _process_menu;\r
 251     // Handy pointers to child components:\r
 252     MainPanel                   _mainpanel;\r
 253     Container                   _contentpane;\r
 254     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;\r
 255     Configuration               _configuration;\r
 256     Options                     _options;\r
 257     private Phylogeny           _species_tree;\r
 258     InferenceManager            _inference_manager;\r
 259     final ProcessPool           _process_pool;\r
 260     private String              _previous_node_annotation_ref;\r
 261 \r
 262     MainFrame() {\r
 263         _process_pool = ProcessPool.createInstance();\r
 264     }\r
 265 \r
 266     /**\r
 267      * Action performed.\r
 268      */\r
 269     @Override\r
 270     public void actionPerformed( final ActionEvent e ) {\r
 271         final Object o = e.getSource();\r
 272         boolean is_applet = false;\r
 273         JApplet applet = null;\r
 274         if ( getCurrentTreePanel() != null ) {\r
 275             is_applet = getCurrentTreePanel().isApplet();\r
 276             if ( is_applet ) {\r
 277                 applet = getCurrentTreePanel().obtainApplet();\r
 278             }\r
 279         }\r
 280         if ( o == _exit_item ) {\r
 281             close();\r
 282         }\r
 283         else if ( o == _gsdi_item ) {\r
 284             if ( isSubtreeDisplayed() ) {\r
 285                 return;\r
 286             }\r
 287             executeGSDI();\r
 288         }\r
 289         else if ( o == _gsdir_item ) {\r
 290             if ( isSubtreeDisplayed() ) {\r
 291                 return;\r
 292             }\r
 293             executeGSDIR();\r
 294         }\r
 295         else if ( o == _taxcolor_item ) {\r
 296             taxColor();\r
 297         }\r
 298         else if ( o == _confcolor_item ) {\r
 299             confColor();\r
 300         }\r
 301         else if ( o == _color_rank_jmi ) {\r
 302             colorRank();\r
 303         }\r
 304         else if ( o == _collapse_species_specific_subtrees ) {\r
 305             if ( isSubtreeDisplayed() ) {\r
 306                 return;\r
 307             }\r
 308             if ( getCurrentTreePanel() != null ) {\r
 309                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 310             }\r
 311         }\r
 312         else if ( o == _remove_branch_color_item ) {\r
 313             if ( isSubtreeDisplayed() ) {\r
 314                 return;\r
 315             }\r
 316             removeBranchColors();\r
 317         }\r
 318         else if ( o == _remove_visual_styles_item ) {\r
 319             if ( isSubtreeDisplayed() ) {\r
 320                 return;\r
 321             }\r
 322             removeVisualStyles();\r
 323         }\r
 324         else if ( o == _midpoint_root_item ) {\r
 325             if ( isSubtreeDisplayed() ) {\r
 326                 return;\r
 327             }\r
 328             midpointRoot();\r
 329         }\r
 330         else if ( o == _delete_selected_nodes_item ) {\r
 331             if ( isSubtreeDisplayed() ) {\r
 332                 return;\r
 333             }\r
 334             deleteSelectedNodes( true );\r
 335         }\r
 336         else if ( o == _delete_not_selected_nodes_item ) {\r
 337             if ( isSubtreeDisplayed() ) {\r
 338                 return;\r
 339             }\r
 340             deleteSelectedNodes( false );\r
 341         }\r
 342         else if ( o == _annotate_item ) {\r
 343             annotateSequences();\r
 344         }\r
 345         else if ( o == _switch_colors_mi ) {\r
 346             switchColors();\r
 347         }\r
 348         else if ( o == _display_basic_information_item ) {\r
 349             displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 350         }\r
 351         else if ( o == _view_as_NH_item ) {\r
 352             viewAsNH();\r
 353         }\r
 354         else if ( o == _view_as_XML_item ) {\r
 355             viewAsXML();\r
 356         }\r
 357         else if ( o == _view_as_nexus_item ) {\r
 358             viewAsNexus();\r
 359         }\r
 360         else if ( o == _super_tiny_fonts_item ) {\r
 361             if ( getCurrentTreePanel() != null ) {\r
 362                 getCurrentTreePanel().setSuperTinyFonts();\r
 363                 getCurrentTreePanel().repaint();\r
 364             }\r
 365         }\r
 366         else if ( o == _tiny_fonts_item ) {\r
 367             if ( getCurrentTreePanel() != null ) {\r
 368                 getCurrentTreePanel().setTinyFonts();\r
 369                 getCurrentTreePanel().repaint();\r
 370             }\r
 371         }\r
 372         else if ( o == _small_fonts_item ) {\r
 373             if ( getCurrentTreePanel() != null ) {\r
 374                 getCurrentTreePanel().setSmallFonts();\r
 375                 getCurrentTreePanel().repaint();\r
 376             }\r
 377         }\r
 378         else if ( o == _medium_fonts_item ) {\r
 379             if ( getCurrentTreePanel() != null ) {\r
 380                 getCurrentTreePanel().setMediumFonts();\r
 381                 getCurrentTreePanel().repaint();\r
 382             }\r
 383         }\r
 384         else if ( o == _large_fonts_item ) {\r
 385             if ( getCurrentTreePanel() != null ) {\r
 386                 getCurrentTreePanel().setLargeFonts();\r
 387                 getCurrentTreePanel().repaint();\r
 388             }\r
 389         }\r
 390         else if ( o == _choose_font_mi ) {\r
 391             chooseFont();\r
 392         }\r
 393         else if ( o == _choose_minimal_confidence_mi ) {\r
 394             chooseMinimalConfidence();\r
 395         }\r
 396         else if ( o == _choose_node_size_mi ) {\r
 397             chooseNodeSize( getOptions(), this );\r
 398         }\r
 399         else if ( o == _overview_placment_mi ) {\r
 400             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 401         }\r
 402         else if ( o == _cycle_node_fill_mi ) {\r
 403             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
 404         }\r
 405         else if ( o == _cycle_node_shape_mi ) {\r
 406             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
 407         }\r
 408         else if ( o == _screen_antialias_cbmi ) {\r
 409             updateOptions( getOptions() );\r
 410             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 411         }\r
 412         else if ( o == _background_gradient_cbmi ) {\r
 413             updateOptions( getOptions() );\r
 414         }\r
 415         else if ( o == _show_domain_labels ) {\r
 416             updateOptions( getOptions() );\r
 417         }\r
 418         else if ( o == _show_annotation_ref_source ) {\r
 419             updateOptions( getOptions() );\r
 420         }\r
 421         else if ( o == _abbreviate_scientific_names ) {\r
 422             updateOptions( getOptions() );\r
 423         }\r
 424         else if ( o == _color_labels_same_as_parent_branch ) {\r
 425             updateOptions( getOptions() );\r
 426         }\r
 427         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 428             updateOptions( getOptions() );\r
 429         }\r
 430         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 431             updateOptions( getOptions() );\r
 432         }\r
 433         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 434             updateOptions( getOptions() );\r
 435             showWhole();\r
 436         }\r
 437         else if ( o == _uniform_cladograms_rbmi ) {\r
 438             updateOptions( getOptions() );\r
 439             showWhole();\r
 440         }\r
 441         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 442             updateOptions( getOptions() );\r
 443             showWhole();\r
 444         }\r
 445         else if ( o == _search_case_senstive_cbmi ) {\r
 446             updateOptions( getOptions() );\r
 447             getMainPanel().getControlPanel().search0();\r
 448             getMainPanel().getControlPanel().search1();\r
 449         }\r
 450         else if ( o == _search_whole_words_only_cbmi ) {\r
 451             updateOptions( getOptions() );\r
 452             getMainPanel().getControlPanel().search0();\r
 453             getMainPanel().getControlPanel().search1();\r
 454         }\r
 455         else if ( o == _inverse_search_result_cbmi ) {\r
 456             updateOptions( getOptions() );\r
 457             getMainPanel().getControlPanel().search0();\r
 458             getMainPanel().getControlPanel().search1();\r
 459         }\r
 460         else if ( o == _show_scale_cbmi ) {\r
 461             updateOptions( getOptions() );\r
 462         }\r
 463         else if ( o == _show_branch_length_values_cbmi ) {\r
 464             updateOptions( getOptions() );\r
 465         }\r
 466         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 467             updateOptions( getOptions() );\r
 468         }\r
 469         else if ( o == _show_confidence_stddev_cbmi ) {\r
 470             updateOptions( getOptions() );\r
 471         }\r
 472         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 473             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 474                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 475             }\r
 476             updateOptions( getOptions() );\r
 477         }\r
 478         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 479             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 480                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 481             }\r
 482             updateOptions( getOptions() );\r
 483         }\r
 484         else if ( o == _label_direction_cbmi ) {\r
 485             updateOptions( getOptions() );\r
 486         }\r
 487         else if ( o == _show_overview_cbmi ) {\r
 488             updateOptions( getOptions() );\r
 489             if ( getCurrentTreePanel() != null ) {\r
 490                 getCurrentTreePanel().updateOvSizes();\r
 491             }\r
 492         }\r
 493         else if ( o == _line_up_renderable_data_cbmi ) {\r
 494             if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
 495                 _right_line_up_domains_cbmi.setSelected( false );\r
 496             }\r
 497             updateOptions( getOptions() );\r
 498         }\r
 499         else if ( o == _right_line_up_domains_cbmi ) {\r
 500             if ( _right_line_up_domains_cbmi.isSelected() ) {\r
 501                 _line_up_renderable_data_cbmi.setSelected( true );\r
 502             }\r
 503             updateOptions( getOptions() );\r
 504         }\r
 505         \r
 506         \r
 507         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 508                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 509                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 510             typeChanged( o );\r
 511         }\r
 512         \r
 513         else if ( o == _about_item ) {\r
 514             about();\r
 515         }\r
 516         else if ( o == _help_item ) {\r
 517             try {\r
 518                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
 519             }\r
 520             catch ( final IOException e1 ) {\r
 521                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 522             }\r
 523         }\r
 524         else if ( o == _website_item ) {\r
 525             try {\r
 526                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 527             }\r
 528             catch ( final IOException e1 ) {\r
 529                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 530             }\r
 531         }\r
 532         else if ( o == _phyloxml_website_item ) {\r
 533             try {\r
 534                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 535             }\r
 536             catch ( final IOException e1 ) {\r
 537                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 538             }\r
 539         }\r
 540         else if ( o == _aptx_ref_item ) {\r
 541             try {\r
 542                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 543             }\r
 544             catch ( final IOException e1 ) {\r
 545                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 546             }\r
 547         }\r
 548         else if ( o == _phyloxml_ref_item ) {\r
 549             try {\r
 550                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 551             }\r
 552             catch ( final IOException e1 ) {\r
 553                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 554             }\r
 555         }\r
 556        \r
 557         else {\r
 558             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 559                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 560                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 561                         readPhylogeniesFromWebservice( i );\r
 562                     }\r
 563                 }\r
 564             }\r
 565         }\r
 566         _contentpane.repaint();\r
 567     }\r
 568 \r
 569     private void deleteSelectedNodes( boolean delete ) {\r
 570         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
 571         if ( phy == null || phy.getNumberOfExternalNodes() < 2 ) {\r
 572             return;\r
 573         }\r
 574         List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
 575         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
 576             final List<PhylogenyNode>  all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
 577             for( final PhylogenyNode n : all_selected_nodes ) {\r
 578                 if ( n.isExternal() ) {\r
 579                     nodes.add( n );\r
 580                 }\r
 581             }\r
 582         }\r
 583         \r
 584         String function = "Retain";\r
 585         if ( delete ) {\r
 586             function = "Delete";\r
 587         }\r
 588         if ( ( nodes == null ) || nodes.isEmpty() ) {\r
 589             JOptionPane\r
 590                     .showMessageDialog( this,\r
 591                                         "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
 592                                         "No external nodes selected to " + function.toLowerCase(),\r
 593                                         JOptionPane.ERROR_MESSAGE );\r
 594             return;\r
 595         }\r
 596         final int todo = nodes.size();\r
 597         final int ext = phy.getNumberOfExternalNodes();\r
 598         int res = todo;\r
 599         if ( delete ) {\r
 600             res = ext - todo;\r
 601         }\r
 602         if ( res < 1 ) {\r
 603             JOptionPane.showMessageDialog( this,\r
 604                                            "Cannot delete all nodes",\r
 605                                            "Attempt to delete all nodes ",\r
 606                                            JOptionPane.ERROR_MESSAGE );\r
 607             return;\r
 608         }\r
 609         final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
 610                 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
 611                 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
 612         if ( result == JOptionPane.OK_OPTION ) {\r
 613             if ( !delete ) {\r
 614                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
 615                 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
 616                     final PhylogenyNode n = it.next();\r
 617                     if ( !nodes.contains( n ) ) {\r
 618                         to_delete.add( n );\r
 619                     }\r
 620                 }\r
 621                 for( final PhylogenyNode n : to_delete ) {\r
 622                     phy.deleteSubtree( n, true );\r
 623                 }\r
 624             }\r
 625             else {\r
 626                 for( final PhylogenyNode n : nodes ) {\r
 627                     phy.deleteSubtree( n, true );\r
 628                 }\r
 629             }\r
 630             resetSearch();\r
 631             getCurrentTreePanel().setNodeInPreorderToNull();\r
 632             phy.externalNodesHaveChanged();\r
 633             phy.clearHashIdToNodeMap();\r
 634             phy.recalculateNumberOfExternalDescendants( true );\r
 635             getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
 636             getCurrentTreePanel().setEdited( true );\r
 637             repaint();\r
 638         }\r
 639     }\r
 640 \r
 641     void resetSearch() {\r
 642         getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
 643         getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
 644         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
 645         getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
 646         getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
 647         getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
 648         getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
 649         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
 650         getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
 651         getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
 652         getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
 653         getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
 654     }\r
 655 \r
 656     public Configuration getConfiguration() {\r
 657         return _configuration;\r
 658     }\r
 659 \r
 660     /**\r
 661      * This method returns the current external node data which\r
 662      * has been selected by the user by clicking the "Return ..."\r
 663      * menu item. This method is expected to be called from Javascript or\r
 664      * something like it.\r
 665      * \r
 666      * @return current external node data as String\r
 667      */\r
 668     public String getCurrentExternalNodesDataBuffer() {\r
 669         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 670     }\r
 671 \r
 672     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 673         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 674     }\r
 675 \r
 676     public int getCurrentExternalNodesDataBufferLength() {\r
 677         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 678     }\r
 679 \r
 680     public InferenceManager getInferenceManager() {\r
 681         return _inference_manager;\r
 682     }\r
 683 \r
 684     public MainPanel getMainPanel() {\r
 685         return _mainpanel;\r
 686     }\r
 687 \r
 688     public Options getOptions() {\r
 689         return _options;\r
 690     }\r
 691 \r
 692     public ProcessPool getProcessPool() {\r
 693         return _process_pool;\r
 694     }\r
 695 \r
 696     public void showTextFrame( final String s, final String title ) {\r
 697         checkTextFrames();\r
 698         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 699     }\r
 700 \r
 701     public void showWhole() {\r
 702         _mainpanel.getControlPanel().showWhole();\r
 703     }\r
 704 \r
 705     public void updateProcessMenu() {\r
 706         // In general Swing is not thread safe.\r
 707         // See "Swing's Threading Policy".\r
 708         SwingUtilities.invokeLater( new Runnable() {\r
 709 \r
 710             @Override\r
 711             public void run() {\r
 712                 doUpdateProcessMenu();\r
 713             }\r
 714         } );\r
 715     }\r
 716 \r
 717     void activateSaveAllIfNeeded() {\r
 718         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 719             _save_all_item.setEnabled( true );\r
 720         }\r
 721         else {\r
 722             _save_all_item.setEnabled( false );\r
 723         }\r
 724     }\r
 725 \r
 726     void buildFileMenu() {\r
 727         _file_jmenu = createMenu( "File", getConfiguration() );\r
 728         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 729         customizeJMenuItem( _exit_item );\r
 730         _jmenubar.add( _file_jmenu );\r
 731     }\r
 732 \r
 733     void buildFontSizeMenu() {\r
 734         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 735         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 736         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 737         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 738         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 739         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 740         customizeJMenuItem( _super_tiny_fonts_item );\r
 741         customizeJMenuItem( _tiny_fonts_item );\r
 742         customizeJMenuItem( _small_fonts_item );\r
 743         customizeJMenuItem( _medium_fonts_item );\r
 744         customizeJMenuItem( _large_fonts_item );\r
 745         _jmenubar.add( _font_size_menu );\r
 746     }\r
 747 \r
 748     void buildHelpMenu() {\r
 749         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 750         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
 751         _help_jmenu.addSeparator();\r
 752         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 753         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
 754         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 755         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 756         _help_jmenu.addSeparator();\r
 757         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 758         customizeJMenuItem( _help_item );\r
 759         customizeJMenuItem( _website_item );\r
 760         customizeJMenuItem( _phyloxml_website_item );\r
 761         customizeJMenuItem( _aptx_ref_item );\r
 762         customizeJMenuItem( _phyloxml_ref_item );\r
 763         customizeJMenuItem( _about_item );\r
 764         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 765         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 766         _jmenubar.add( _help_jmenu );\r
 767     }\r
 768 \r
 769     void buildTypeMenu() {\r
 770         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 771         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 772         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 773         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 774         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 775         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 776         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 777         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 778         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 779         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 780         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 781         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 782         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 783         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 784         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 785         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 786         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 787         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 788         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 789         initializeTypeMenu( getOptions() );\r
 790         _jmenubar.add( _type_menu );\r
 791     }\r
 792 \r
 793     void buildViewMenu() {\r
 794         _view_jmenu = createMenu( "View", getConfiguration() );\r
 795         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 796         _view_jmenu.addSeparator();\r
 797         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 798         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 799         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 800         customizeJMenuItem( _display_basic_information_item );\r
 801         customizeJMenuItem( _view_as_NH_item );\r
 802         customizeJMenuItem( _view_as_XML_item );\r
 803         customizeJMenuItem( _view_as_nexus_item );\r
 804         _jmenubar.add( _view_jmenu );\r
 805     }\r
 806 \r
 807     void checkTextFrames() {\r
 808         if ( _textframes.size() > 5 ) {\r
 809             try {\r
 810                 if ( _textframes.getFirst() != null ) {\r
 811                     _textframes.getFirst().removeMe();\r
 812                 }\r
 813                 else {\r
 814                     _textframes.removeFirst();\r
 815                 }\r
 816             }\r
 817             catch ( final NoSuchElementException e ) {\r
 818                 // Ignore.\r
 819             }\r
 820         }\r
 821     }\r
 822 \r
 823     void close() {\r
 824         removeAllTextFrames();\r
 825         if ( _mainpanel != null ) {\r
 826             _mainpanel.terminate();\r
 827         }\r
 828         if ( _contentpane != null ) {\r
 829             _contentpane.removeAll();\r
 830         }\r
 831         setVisible( false );\r
 832         dispose();\r
 833     }\r
 834 \r
 835     void colorRank() {\r
 836         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 837             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
 838             final String rank = ( String ) JOptionPane\r
 839                     .showInputDialog( this,\r
 840                                       "What rank should the colorization be based on",\r
 841                                       "Rank Selection",\r
 842                                       JOptionPane.QUESTION_MESSAGE,\r
 843                                       null,\r
 844                                       ranks,\r
 845                                       null );\r
 846             if ( !ForesterUtil.isEmpty( rank ) ) {\r
 847                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
 848             }\r
 849         }\r
 850     }\r
 851 \r
 852     void confColor() {\r
 853         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 854             _mainpanel.getCurrentTreePanel().confColor();\r
 855         }\r
 856     }\r
 857 \r
 858     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
 859         if ( item != null ) {\r
 860             item.setFont( MainFrame.menu_font );\r
 861             if ( !getConfiguration().isUseNativeUI() ) {\r
 862                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 863                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 864             }\r
 865             item.setSelected( is_selected );\r
 866             item.addActionListener( this );\r
 867         }\r
 868     }\r
 869 \r
 870     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
 871         if ( jmi != null ) {\r
 872             jmi.setFont( MainFrame.menu_font );\r
 873             if ( !getConfiguration().isUseNativeUI() ) {\r
 874                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 875                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 876             }\r
 877             jmi.addActionListener( this );\r
 878         }\r
 879         return jmi;\r
 880     }\r
 881 \r
 882     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
 883         if ( item != null ) {\r
 884             item.setFont( MainFrame.menu_font );\r
 885             if ( !getConfiguration().isUseNativeUI() ) {\r
 886                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 887                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 888             }\r
 889             item.setSelected( is_selected );\r
 890             item.addActionListener( this );\r
 891         }\r
 892     }\r
 893 \r
 894     void displayBasicInformation( final File treefile ) {\r
 895         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
 896             String title = "Basic Information";\r
 897             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
 898                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
 899             }\r
 900             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
 901         }\r
 902     }\r
 903 \r
 904     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
 905         try {\r
 906             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 907         }\r
 908         catch ( final Exception ex ) {\r
 909             // Do nothing.\r
 910         }\r
 911         JOptionPane.showMessageDialog( this,\r
 912                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
 913                                        "Error during File|Open",\r
 914                                        JOptionPane.ERROR_MESSAGE );\r
 915     }\r
 916 \r
 917     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
 918         try {\r
 919             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 920         }\r
 921         catch ( final Exception ex ) {\r
 922             // Do nothing.\r
 923         }\r
 924         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
 925     }\r
 926 \r
 927     void executeGSDI() {\r
 928         if ( !isOKforSDI( false, true ) ) {\r
 929             return;\r
 930         }\r
 931         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
 932             JOptionPane.showMessageDialog( this,\r
 933                                            "Gene tree is not rooted.",\r
 934                                            "Cannot execute GSDI",\r
 935                                            JOptionPane.ERROR_MESSAGE );\r
 936             return;\r
 937         }\r
 938         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 939         gene_tree.setAllNodesToNotCollapse();\r
 940         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 941         GSDI gsdi = null;\r
 942         final Phylogeny species_tree = getSpeciesTree().copy();\r
 943         try {\r
 944             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
 945         }\r
 946         catch ( final SDIException e ) {\r
 947             JOptionPane.showMessageDialog( this,\r
 948                                            e.getLocalizedMessage(),\r
 949                                            "Error during GSDI",\r
 950                                            JOptionPane.ERROR_MESSAGE );\r
 951             return;\r
 952         }\r
 953         catch ( final Exception e ) {\r
 954             AptxUtil.unexpectedException( e );\r
 955             return;\r
 956         }\r
 957         gene_tree.setRerootable( false );\r
 958         gene_tree.clearHashIdToNodeMap();\r
 959         gene_tree.recalculateNumberOfExternalDescendants( true );\r
 960         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
 961         getMainPanel().getControlPanel().setShowEvents( true );\r
 962         showWhole();\r
 963         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 964         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 965         showWhole();\r
 966         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 967         showWhole();\r
 968         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 969         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 970         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 971             JOptionPane.showMessageDialog( this,\r
 972                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 973                                                    + "Potential duplications: "\r
 974                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 975                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 976                                                    + "Stripped gene tree nodes: "\r
 977                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 978                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 979                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 980                                            "GSDI successfully completed",\r
 981                                            JOptionPane.WARNING_MESSAGE );\r
 982         }\r
 983         else {\r
 984             JOptionPane.showMessageDialog( this,\r
 985                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 986                                                    + "Potential duplications: "\r
 987                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 988                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 989                                                    + "Stripped gene tree nodes: "\r
 990                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 991                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 992                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 993                                            "GSDI successfully completed",\r
 994                                            JOptionPane.INFORMATION_MESSAGE );\r
 995         }\r
 996     }\r
 997 \r
 998     void executeGSDIR() {\r
 999         if ( !isOKforSDI( false, false ) ) {\r
1000             return;\r
1001         }\r
1002         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
1003         if ( ( p > 0 )\r
1004                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
1005             JOptionPane.showMessageDialog( this,\r
1006                                            "Gene tree is not completely binary",\r
1007                                            "Cannot execute GSDI",\r
1008                                            JOptionPane.ERROR_MESSAGE );\r
1009             return;\r
1010         }\r
1011         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
1012         gene_tree.setAllNodesToNotCollapse();\r
1013         gene_tree.recalculateNumberOfExternalDescendants( false );\r
1014         GSDIR gsdir = null;\r
1015         final Phylogeny species_tree = getSpeciesTree().copy();\r
1016         try {\r
1017             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
1018         }\r
1019         catch ( final SDIException e ) {\r
1020             JOptionPane.showMessageDialog( this,\r
1021                                            e.getLocalizedMessage(),\r
1022                                            "Error during GSDIR",\r
1023                                            JOptionPane.ERROR_MESSAGE );\r
1024             return;\r
1025         }\r
1026         catch ( final Exception e ) {\r
1027             AptxUtil.unexpectedException( e );\r
1028             return;\r
1029         }\r
1030         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
1031         result_gene_tree.setRerootable( false );\r
1032         result_gene_tree.clearHashIdToNodeMap();\r
1033         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
1034         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
1035         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
1036         getMainPanel().getControlPanel().setShowEvents( true );\r
1037         showWhole();\r
1038         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1039         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1040         showWhole();\r
1041         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1042         showWhole();\r
1043         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1044         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1045         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1046             JOptionPane.showMessageDialog( this,\r
1047                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1048                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1049                                                    + "Stripped gene tree nodes: "\r
1050                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1051                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1052                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1053                                            "GSDIR successfully completed",\r
1054                                            JOptionPane.WARNING_MESSAGE );\r
1055         }\r
1056         else {\r
1057             JOptionPane.showMessageDialog( this,\r
1058                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1059                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1060                                                    + "Stripped gene tree nodes: "\r
1061                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1062                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1063                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1064                                            "GSDIR successfully completed",\r
1065                                            JOptionPane.INFORMATION_MESSAGE );\r
1066         }\r
1067     }\r
1068 \r
1069     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
1070         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
1071             JOptionPane.showMessageDialog( this,\r
1072                                            "Gene tree and species tree have no species in common.",\r
1073                                            "Error during SDI",\r
1074                                            JOptionPane.ERROR_MESSAGE );\r
1075             return false;\r
1076         }\r
1077         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
1078             JOptionPane.showMessageDialog( this,\r
1079                                            "Gene tree and species tree have only one species in common.",\r
1080                                            "Error during SDI",\r
1081                                            JOptionPane.ERROR_MESSAGE );\r
1082             return false;\r
1083         }\r
1084         else {\r
1085             return true;\r
1086         }\r
1087     }\r
1088 \r
1089     TreePanel getCurrentTreePanel() {\r
1090         return getMainPanel().getCurrentTreePanel();\r
1091     }\r
1092 \r
1093     JMenu getHelpMenu() {\r
1094         return _help_jmenu;\r
1095     }\r
1096 \r
1097     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
1098         return _label_direction_cbmi;\r
1099     }\r
1100 \r
1101     JMenuBar getMenuBarOfMainFrame() {\r
1102         return _jmenubar;\r
1103     }\r
1104 \r
1105     final Phylogeny getSpeciesTree() {\r
1106         return _species_tree;\r
1107     }\r
1108 \r
1109     \r
1110 \r
1111     void initializeTypeMenu( final Options options ) {\r
1112         setTypeMenuToAllUnselected();\r
1113         switch ( options.getPhylogenyGraphicsType() ) {\r
1114             case CONVEX:\r
1115                 _convex_type_cbmi.setSelected( true );\r
1116                 break;\r
1117             case CURVED:\r
1118                 _curved_type_cbmi.setSelected( true );\r
1119                 break;\r
1120             case EURO_STYLE:\r
1121                 _euro_type_cbmi.setSelected( true );\r
1122                 break;\r
1123             case ROUNDED:\r
1124                 _rounded_type_cbmi.setSelected( true );\r
1125                 break;\r
1126             case TRIANGULAR:\r
1127                 _triangular_type_cbmi.setSelected( true );\r
1128                 break;\r
1129             case UNROOTED:\r
1130                 _unrooted_type_cbmi.setSelected( true );\r
1131                 break;\r
1132             case CIRCULAR:\r
1133                 _circular_type_cbmi.setSelected( true );\r
1134                 break;\r
1135             default:\r
1136                 _rectangular_type_cbmi.setSelected( true );\r
1137                 break;\r
1138         }\r
1139     }\r
1140 \r
1141     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1142         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1143             return false;\r
1144         }\r
1145         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1146             JOptionPane.showMessageDialog( this,\r
1147                                            "No species tree loaded",\r
1148                                            "Cannot execute GSDI",\r
1149                                            JOptionPane.ERROR_MESSAGE );\r
1150             return false;\r
1151         }\r
1152         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1153             JOptionPane.showMessageDialog( this,\r
1154                                            "Species tree is not completely binary",\r
1155                                            "Cannot execute GSDI",\r
1156                                            JOptionPane.ERROR_MESSAGE );\r
1157             return false;\r
1158         }\r
1159         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1160             JOptionPane.showMessageDialog( this,\r
1161                                            "Gene tree is not completely binary",\r
1162                                            "Cannot execute GSDI",\r
1163                                            JOptionPane.ERROR_MESSAGE );\r
1164             return false;\r
1165         }\r
1166         else {\r
1167             return true;\r
1168         }\r
1169     }\r
1170 \r
1171     boolean isSubtreeDisplayed() {\r
1172         if ( getCurrentTreePanel() != null ) {\r
1173             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1174                 JOptionPane\r
1175                         .showMessageDialog( this,\r
1176                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1177                                             "Operation can not be exectuted on a sub-tree",\r
1178                                             JOptionPane.WARNING_MESSAGE );\r
1179                 return true;\r
1180             }\r
1181         }\r
1182         return false;\r
1183     }\r
1184 \r
1185     void midpointRoot() {\r
1186         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1187             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1188         }\r
1189     }\r
1190 \r
1191     void readPhylogeniesFromWebservice( final int i ) {\r
1192         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1193         new Thread( reader ).start();\r
1194     }\r
1195 \r
1196     void removeAllTextFrames() {\r
1197         for( final TextFrame tf : _textframes ) {\r
1198             if ( tf != null ) {\r
1199                 tf.close();\r
1200             }\r
1201         }\r
1202         _textframes.clear();\r
1203     }\r
1204 \r
1205     void setConfiguration( final Configuration configuration ) {\r
1206         _configuration = configuration;\r
1207     }\r
1208 \r
1209     void setInferenceManager( final InferenceManager i ) {\r
1210         _inference_manager = i;\r
1211     }\r
1212 \r
1213     void setOptions( final Options options ) {\r
1214         _options = options;\r
1215     }\r
1216 \r
1217     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1218         setTypeMenuToAllUnselected();\r
1219         switch ( type ) {\r
1220             case CIRCULAR:\r
1221                 _circular_type_cbmi.setSelected( true );\r
1222                 break;\r
1223             case CONVEX:\r
1224                 _convex_type_cbmi.setSelected( true );\r
1225                 break;\r
1226             case CURVED:\r
1227                 _curved_type_cbmi.setSelected( true );\r
1228                 break;\r
1229             case EURO_STYLE:\r
1230                 _euro_type_cbmi.setSelected( true );\r
1231                 break;\r
1232             case ROUNDED:\r
1233                 _rounded_type_cbmi.setSelected( true );\r
1234                 break;\r
1235             case RECTANGULAR:\r
1236                 _rectangular_type_cbmi.setSelected( true );\r
1237                 break;\r
1238             case TRIANGULAR:\r
1239                 _triangular_type_cbmi.setSelected( true );\r
1240                 break;\r
1241             case UNROOTED:\r
1242                 _unrooted_type_cbmi.setSelected( true );\r
1243                 break;\r
1244             default:\r
1245                 throw new IllegalArgumentException( "unknown type: " + type );\r
1246         }\r
1247     }\r
1248 \r
1249     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1250         _species_tree = species_tree;\r
1251     }\r
1252 \r
1253     void setTypeMenuToAllUnselected() {\r
1254         _convex_type_cbmi.setSelected( false );\r
1255         _curved_type_cbmi.setSelected( false );\r
1256         _euro_type_cbmi.setSelected( false );\r
1257         _rounded_type_cbmi.setSelected( false );\r
1258         _triangular_type_cbmi.setSelected( false );\r
1259         _rectangular_type_cbmi.setSelected( false );\r
1260         _unrooted_type_cbmi.setSelected( false );\r
1261         _circular_type_cbmi.setSelected( false );\r
1262     }\r
1263 \r
1264     void switchColors() {\r
1265         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1266         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1267         csc.setVisible( true );\r
1268     }\r
1269 \r
1270     void taxColor() {\r
1271         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1272             _mainpanel.getCurrentTreePanel().taxColor();\r
1273         }\r
1274     }\r
1275 \r
1276     void typeChanged( final Object o ) {\r
1277         updateTypeCheckboxes( getOptions(), o );\r
1278         updateOptions( getOptions() );\r
1279         if ( getCurrentTreePanel() != null ) {\r
1280             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1281             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1282             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1283                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1284                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1285                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1286                 getCurrentTreePanel().getControlPanel().showWhole();\r
1287             }\r
1288             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1289                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1290             }\r
1291             else {\r
1292                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1293             }\r
1294             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1295             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1296             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1297                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1298                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1299                 }\r
1300                 else {\r
1301                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1302                 }\r
1303             }\r
1304         }\r
1305     }\r
1306 \r
1307     void updateOptions( final Options options ) {\r
1308         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1309         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1310                 && _background_gradient_cbmi.isSelected() );\r
1311         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1312         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1313                 && _show_annotation_ref_source.isSelected() );\r
1314         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1315                 && _abbreviate_scientific_names.isSelected() );\r
1316         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1317                 && _color_labels_same_as_parent_branch.isSelected() );\r
1318         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1319                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1320         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1321                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
1322         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1323             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1324         }\r
1325         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1326             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1327         }\r
1328         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1329             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1330         }\r
1331         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1332                 && _search_case_senstive_cbmi.isSelected() );\r
1333         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1334             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1335         }\r
1336         if ( _label_direction_cbmi != null ) {\r
1337             if ( _label_direction_cbmi.isSelected() ) {\r
1338                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1339             }\r
1340             else {\r
1341                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1342             }\r
1343         }\r
1344         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1345         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1346                 && _show_confidence_stddev_cbmi.isSelected() );\r
1347         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {\r
1348             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );\r
1349         }\r
1350         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1351             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1352         }\r
1353         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1354                 && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1355         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1356                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1357         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1358         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1359                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1360             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1361         }\r
1362         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1363                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1364             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1365         }\r
1366         else {\r
1367             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1368         }\r
1369         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1370                 && _print_black_and_white_cbmi.isSelected() );\r
1371         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1372                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1373         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1374             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1375         }\r
1376         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1377             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1378         }\r
1379         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1380             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1381         }\r
1382         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1383             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1384         }\r
1385         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1386                 && _replace_underscores_cbmi.isSelected() );\r
1387         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1388                 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1389         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1390                 && _search_whole_words_only_cbmi.isSelected() );\r
1391         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1392                 && _inverse_search_result_cbmi.isSelected() );\r
1393         if ( _graphics_export_visible_only_cbmi != null ) {\r
1394             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1395             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1396                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1397                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1398             }\r
1399             else {\r
1400                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1401             }\r
1402         }\r
1403         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1404             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1405         }\r
1406         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1407             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1408         }\r
1409         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1410             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1411         }\r
1412         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1413             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1414         }\r
1415         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1416             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1417         }\r
1418         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1419             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1420         }\r
1421         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1422             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1423         }\r
1424         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1425             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1426         }\r
1427         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
1428             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
1429            \r
1430         }\r
1431         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
1432             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
1433         }\r
1434     }\r
1435 \r
1436     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1437         setTypeMenuToAllUnselected();\r
1438         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1439     }\r
1440 \r
1441     void viewAsNexus() {\r
1442         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1443             String title = "Nexus";\r
1444             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1445                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1446             }\r
1447             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1448                            title );\r
1449         }\r
1450     }\r
1451 \r
1452     void viewAsNH() {\r
1453         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1454             String title = "New Hampshire";\r
1455             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1456                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1457             }\r
1458             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1459                                    .getNhConversionSupportValueStyle() ),\r
1460                            title );\r
1461         }\r
1462     }\r
1463 \r
1464     void viewAsXML() {\r
1465         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1466             String title = "phyloXML";\r
1467             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1468                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1469             }\r
1470             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1471         }\r
1472     }\r
1473 \r
1474     private void annotateSequences() {\r
1475         if ( getCurrentTreePanel() != null ) {\r
1476             List<PhylogenyNode> nodes = null;\r
1477             if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
1478                     || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
1479                 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
1480             }\r
1481             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1482                 JOptionPane\r
1483                         .showMessageDialog( this,\r
1484                                             "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1485                                             "No nodes selected for annotation",\r
1486                                             JOptionPane.ERROR_MESSAGE );\r
1487                 return;\r
1488             }\r
1489             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1490             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1491                 final JTextField ref_field = new JTextField( 10 );\r
1492                 final JTextField desc_filed = new JTextField( 20 );\r
1493                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1494                         : getPreviousNodeAnnotationReference() );\r
1495                 final JPanel my_panel = new JPanel();\r
1496                 my_panel.add( new JLabel( "Reference " ) );\r
1497                 my_panel.add( ref_field );\r
1498                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1499                 my_panel.add( new JLabel( "Description " ) );\r
1500                 my_panel.add( desc_filed );\r
1501                 final int result = JOptionPane.showConfirmDialog( null,\r
1502                                                                   my_panel,\r
1503                                                                   "Enter the sequence annotation(s) for the "\r
1504                                                                           + nodes.size() + " selected nodes",\r
1505                                                                   JOptionPane.OK_CANCEL_OPTION );\r
1506                 if ( result == JOptionPane.OK_OPTION ) {\r
1507                     String ref = ref_field.getText();\r
1508                     String desc = desc_filed.getText();\r
1509                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1510                         ref = ref.trim();\r
1511                         ref = ref.replaceAll( "\\s+", " " );\r
1512                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1513                                 || ( ref.length() < 3 ) ) {\r
1514                             JOptionPane.showMessageDialog( this,\r
1515                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1516                                                            "Illegal Format for Annotation Reference",\r
1517                                                            JOptionPane.ERROR_MESSAGE );\r
1518                             return;\r
1519                         }\r
1520                     }\r
1521                     if ( ref != null ) {\r
1522                         setPreviousNodeAnnotationReference( ref );\r
1523                     }\r
1524                     if ( desc != null ) {\r
1525                         desc = desc.trim();\r
1526                         desc = desc.replaceAll( "\\s+", " " );\r
1527                     }\r
1528                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1529                         for( final PhylogenyNode n : nodes ) {\r
1530                             ForesterUtil.ensurePresenceOfSequence( n );\r
1531                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1532                                     : new Annotation( ref );\r
1533                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1534                                 ann.setDesc( desc );\r
1535                             }\r
1536                             n.getNodeData().getSequence().addAnnotation( ann );\r
1537                         }\r
1538                     }\r
1539                     getMainPanel().getControlPanel().showAnnotations();\r
1540                 }\r
1541             }\r
1542         }\r
1543     }\r
1544 \r
1545     private void chooseFont() {\r
1546         final FontChooser fc = new FontChooser();\r
1547         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1548         fc.showDialog( this, "Select the Base Font" );\r
1549         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1550     }\r
1551 \r
1552     private void chooseMinimalConfidence() {\r
1553         final String s = ( String ) JOptionPane\r
1554                 .showInputDialog( this,\r
1555                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1556                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1557                                   "Minimal Confidence Value",\r
1558                                   JOptionPane.QUESTION_MESSAGE,\r
1559                                   null,\r
1560                                   null,\r
1561                                   getOptions().getMinConfidenceValue() );\r
1562         if ( !ForesterUtil.isEmpty( s ) ) {\r
1563             boolean success = true;\r
1564             double m = 0.0;\r
1565             final String m_str = s.trim();\r
1566             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1567                 try {\r
1568                     m = Double.parseDouble( m_str );\r
1569                 }\r
1570                 catch ( final Exception ex ) {\r
1571                     success = false;\r
1572                 }\r
1573             }\r
1574             else {\r
1575                 success = false;\r
1576             }\r
1577             if ( success && ( m >= 0.0 ) ) {\r
1578                 getOptions().setMinConfidenceValue( m );\r
1579             }\r
1580         }\r
1581     }\r
1582 \r
1583     private void doUpdateProcessMenu() {\r
1584         if ( _process_pool.size() > 0 ) {\r
1585             if ( _process_menu == null ) {\r
1586                 _process_menu = createMenu( "", getConfiguration() );\r
1587                 _process_menu.setForeground( Color.RED );\r
1588             }\r
1589             _process_menu.removeAll();\r
1590             final String text = "processes running: " + _process_pool.size();\r
1591             _process_menu.setText( text );\r
1592             _jmenubar.add( _process_menu );\r
1593             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1594                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1595                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1596             }\r
1597         }\r
1598         else {\r
1599             if ( _process_menu != null ) {\r
1600                 _process_menu.removeAll();\r
1601                 _jmenubar.remove( _process_menu );\r
1602             }\r
1603         }\r
1604         _jmenubar.validate();\r
1605         _jmenubar.repaint();\r
1606         repaint();\r
1607     }\r
1608 \r
1609     private String getPreviousNodeAnnotationReference() {\r
1610         return _previous_node_annotation_ref;\r
1611     }\r
1612 \r
1613     private void removeBranchColors() {\r
1614         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1615             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1616         }\r
1617     }\r
1618 \r
1619     private void removeVisualStyles() {\r
1620         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1621             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1622         }\r
1623     }\r
1624 \r
1625     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1626         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1627     }\r
1628 \r
1629     /**\r
1630      * Display the about box.\r
1631      */\r
1632     static void about() {\r
1633         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1634         about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
1635         about.append( "All Rights Reserved\n" );\r
1636         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1637         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1638         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1639         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1640         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1641         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1642             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1643         }\r
1644         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1645                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1646             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1647                     + ForesterUtil.OS_VERSION + "]\n" );\r
1648         }\r
1649         final Runtime rt = java.lang.Runtime.getRuntime();\r
1650         final long free_memory = rt.freeMemory() / 1000000;\r
1651         final long total_memory = rt.totalMemory() / 1000000;\r
1652         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1653         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1654         about.append( "References:\n" );\r
1655         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1656         about.append( "For more information & download:\n" );\r
1657         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1658         about.append( "Documentation:\n" );\r
1659         about.append( Constants.APTX_DOC_SITE + "\n" );\r
1660         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1661         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1662     }\r
1663 \r
1664     static void chooseNodeSize( final Options options, final Component parent ) {\r
1665         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1666                                                                  "Please enter the default size for node shapes.\n"\r
1667                                                                          + "[current value: "\r
1668                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1669                                                                  "Node Shape Size",\r
1670                                                                  JOptionPane.QUESTION_MESSAGE,\r
1671                                                                  null,\r
1672                                                                  null,\r
1673                                                                  options.getDefaultNodeShapeSize() );\r
1674         if ( !ForesterUtil.isEmpty( s ) ) {\r
1675             boolean success = true;\r
1676             double m = 0.0;\r
1677             final String m_str = s.trim();\r
1678             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1679                 try {\r
1680                     m = Double.parseDouble( m_str );\r
1681                 }\r
1682                 catch ( final Exception ex ) {\r
1683                     success = false;\r
1684                 }\r
1685             }\r
1686             else {\r
1687                 success = false;\r
1688             }\r
1689             if ( success && ( m >= 0.0 ) ) {\r
1690                 final short size = ForesterUtil.roundToShort( m );\r
1691                 if ( size >= 0.0 ) {\r
1692                     options.setDefaultNodeShapeSize( size );\r
1693                 }\r
1694             }\r
1695         }\r
1696     }\r
1697 \r
1698     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1699         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1700     }\r
1701 \r
1702     static JMenu createMenu( final String title, final Configuration conf ) {\r
1703         final JMenu jmenu = new JMenu( title );\r
1704         if ( !conf.isUseNativeUI() ) {\r
1705             jmenu.setFont( MainFrame.menu_font );\r
1706             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1707             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1708         }\r
1709         return jmenu;\r
1710     }\r
1711 \r
1712     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1713         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1714         if ( !configuration.isUseNativeUI() ) {\r
1715             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1716             label.setForeground( configuration.getGuiMenuTextColor() );\r
1717             label.setOpaque( true );\r
1718         }\r
1719         label.setSelected( false );\r
1720         label.setEnabled( false );\r
1721         return label;\r
1722     }\r
1723 \r
1724     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
1725         switch ( op.getDefaultNodeFill() ) {\r
1726             case GRADIENT:\r
1727                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1728                 break;\r
1729             case NONE:\r
1730                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1731                 break;\r
1732             case SOLID:\r
1733                 op.setDefaultNodeFill( NodeFill.NONE );\r
1734                 break;\r
1735             default:\r
1736                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1737         }\r
1738     }\r
1739 \r
1740     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
1741         switch ( op.getDefaultNodeShape() ) {\r
1742             case CIRCLE:\r
1743                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1744                 break;\r
1745             case RECTANGLE:\r
1746                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1747                 break;\r
1748             default:\r
1749                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1750         }\r
1751     }\r
1752 \r
1753     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1754         switch ( op.getOvPlacement() ) {\r
1755             case LOWER_LEFT:\r
1756                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1757                 break;\r
1758             case LOWER_RIGHT:\r
1759                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1760                 break;\r
1761             case UPPER_LEFT:\r
1762                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1763                 break;\r
1764             case UPPER_RIGHT:\r
1765                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1766                 break;\r
1767             default:\r
1768                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1769         }\r
1770         if ( tree_panel != null ) {\r
1771             tree_panel.updateOvSettings();\r
1772         }\r
1773     }\r
1774 \r
1775     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
1776         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
1777             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1778                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
1779         }\r
1780         else {\r
1781             mi.setText( "Cycle Node Shape Fill Type..." );\r
1782         }\r
1783     }\r
1784 \r
1785     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
1786         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
1787             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1788                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
1789         }\r
1790         else {\r
1791             mi.setText( "Cycle Node Shape Fill Type..." );\r
1792         }\r
1793     }\r
1794 \r
1795     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
1796         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
1797             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
1798         }\r
1799         else {\r
1800             mi.setText( "Cycle Overview Placement..." );\r
1801         }\r
1802     }\r
1803 \r
1804     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
1805         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
1806             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
1807                     + ")" );\r
1808         }\r
1809         else {\r
1810             mi.setText( "Select Color Scheme..." );\r
1811         }\r
1812     }\r
1813 \r
1814     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
1815         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
1816     }\r
1817 \r
1818     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
1819         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
1820             mi.setEnabled( true );\r
1821         }\r
1822         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
1823             mi.setEnabled( true );\r
1824         }\r
1825         else {\r
1826             mi.setEnabled( false );\r
1827         }\r
1828         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
1829     }\r
1830 \r
1831     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
1832         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
1833     }\r
1834 \r
1835     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,\r
1836                                                            final JCheckBoxMenuItem scale,\r
1837                                                            final JCheckBoxMenuItem branch_lengths,\r
1838                                                            final JRadioButtonMenuItem non_lined_up,\r
1839                                                            final JRadioButtonMenuItem uniform_clado,\r
1840                                                            final JRadioButtonMenuItem nonuniform_clado,\r
1841                                                            final JCheckBoxMenuItem label_direction_cbmi ) {\r
1842         final TreePanel tree_panel = main_panel.getCurrentTreePanel();\r
1843         final ControlPanel control = main_panel.getControlPanel();\r
1844         final Options options = main_panel.getOptions();\r
1845         scale.setSelected( options.isShowScale() );\r
1846         branch_lengths.setSelected( options.isShowBranchLengthValues() );\r
1847         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1848         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {\r
1849             scale.setSelected( false );\r
1850             scale.setEnabled( false );\r
1851             branch_lengths.setSelected( false );\r
1852             branch_lengths.setEnabled( false );\r
1853         }\r
1854         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {\r
1855             scale.setSelected( false );\r
1856             scale.setEnabled( false );\r
1857             branch_lengths.setEnabled( true );\r
1858         }\r
1859         else {\r
1860             scale.setEnabled( true );\r
1861             branch_lengths.setEnabled( true );\r
1862         }\r
1863         if ( ( tree_panel != null )\r
1864                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )\r
1865                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1866                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1867             branch_lengths.setSelected( false );\r
1868             branch_lengths.setEnabled( false );\r
1869         }\r
1870         if ( tree_panel != null ) {\r
1871             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )\r
1872                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {\r
1873                 non_lined_up.setEnabled( false );\r
1874                 uniform_clado.setEnabled( false );\r
1875                 nonuniform_clado.setEnabled( false );\r
1876             }\r
1877             else {\r
1878                 non_lined_up.setEnabled( true );\r
1879                 uniform_clado.setEnabled( true );\r
1880                 nonuniform_clado.setEnabled( true );\r
1881             }\r
1882         }\r
1883         else {\r
1884             if ( ( tree_panel != null )\r
1885                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1886                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1887                 branch_lengths.setSelected( false );\r
1888                 branch_lengths.setEnabled( false );\r
1889             }\r
1890             if ( ( tree_panel != null )\r
1891                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel\r
1892                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {\r
1893                 non_lined_up.setEnabled( false );\r
1894             }\r
1895             else {\r
1896                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1897                 non_lined_up.setEnabled( true );\r
1898             }\r
1899         }\r
1900         label_direction_cbmi.setEnabled( true );\r
1901         if ( tree_panel != null ) {\r
1902             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )\r
1903                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1904                 label_direction_cbmi.setEnabled( false );\r
1905             }\r
1906             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {\r
1907                 scale.setSelected( false );\r
1908                 scale.setEnabled( false );\r
1909             }\r
1910         }\r
1911     }\r
1912 \r
1913     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
1914         for( final TreePanel tree_panel : treepanels ) {\r
1915             tree_panel.setTextAntialias();\r
1916         }\r
1917     }\r
1918 }\r