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.LinkedList;\r
  36 import java.util.List;\r
  37 import java.util.Locale;\r
  38 import java.util.NoSuchElementException;\r
  39 import java.util.Set;\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.sdi.GSDI;\r
  71 import org.forester.sdi.GSDIR;\r
  72 import org.forester.sdi.SDIException;\r
  73 import org.forester.util.ForesterConstants;\r
  74 import org.forester.util.ForesterUtil;\r
  75 \r
  76 public abstract class MainFrame extends JFrame implements ActionListener {\r
  77 \r
  78     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
  79     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME\r
  80     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
  81     private static final long   serialVersionUID                        = 3655000897845508358L;\r
  82     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
  83                                                                                     Font.PLAIN,\r
  84                                                                                     10 );\r
  85     static final String         TYPE_MENU_HEADER                        = "Type";\r
  86     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
  87     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
  88     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
  89     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
  90     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
  91     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
  92     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO\r
  93     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO\r
  94     static final String         OPTIONS_HEADER                          = "Options";\r
  95     static final String         SEARCH_SUBHEADER                        = "Search:";\r
  96     static final String         DISPLAY_SUBHEADER                       = "Display:";\r
  97     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
  98     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
  99     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
 100     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Branch Length Values";\r
 101     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
 102     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
 103     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
 104     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
 105     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
 106     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
 107     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 108     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 109     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 110     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "External Node Shapes";\r
 111     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Internal Node Shapes";\r
 112     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 113     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 114     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 115     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 116     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 117     static final String         COLOR_LABELS_TIP                        = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";\r
 118     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 119     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 120     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 121     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 122     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 123     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 124     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 125     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 126     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 127     JMenuBar                    _jmenubar;\r
 128     JMenu                       _file_jmenu;\r
 129     JMenu                       _tools_menu;\r
 130     JMenu                       _view_jmenu;\r
 131     JMenu                       _options_jmenu;\r
 132     JMenu                       _font_size_menu;\r
 133     JMenu                       _help_jmenu;\r
 134     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 135     // Analysis menu\r
 136     JMenu                       _analysis_menu;\r
 137     JMenuItem                   _load_species_tree_item;\r
 138     JMenuItem                   _gsdi_item;\r
 139     JMenuItem                   _gsdir_item;\r
 140     JMenuItem                   _lineage_inference;\r
 141     // file menu:\r
 142     JMenuItem                   _open_item;\r
 143     JMenuItem                   _open_url_item;\r
 144     JMenuItem                   _save_item;\r
 145     JMenuItem                   _save_all_item;\r
 146     JMenuItem                   _close_item;\r
 147     JMenuItem                   _exit_item;\r
 148     JMenuItem                   _new_item;\r
 149     // tools menu:\r
 150     JMenuItem                   _midpoint_root_item;\r
 151     JMenuItem                   _taxcolor_item;\r
 152     JMenuItem                   _confcolor_item;\r
 153     JMenuItem                   _color_rank_jmi;\r
 154     JMenuItem                   _collapse_species_specific_subtrees;\r
 155     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me\r
 156     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 157     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 158     JMenuItem                   _obtain_seq_information_jmi;\r
 159     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 160     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 161     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 162     JMenuItem                   _annotate_item;\r
 163     JMenuItem                   _remove_branch_color_item;\r
 164     JMenuItem                   _remove_visual_styles_item;\r
 165     // font size menu:\r
 166     JMenuItem                   _super_tiny_fonts_item;\r
 167     JMenuItem                   _tiny_fonts_item;\r
 168     JMenuItem                   _small_fonts_item;\r
 169     JMenuItem                   _medium_fonts_item;\r
 170     JMenuItem                   _large_fonts_item;\r
 171     // options menu:\r
 172     // _  screen and print\r
 173     JMenuItem                   _choose_font_mi;\r
 174     JMenuItem                   _switch_colors_mi;\r
 175     JCheckBoxMenuItem           _label_direction_cbmi;\r
 176     // _  screen display\r
 177     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 178     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 179     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 180     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 181     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 182     JCheckBoxMenuItem           _show_branch_length_values_cbmi;\r
 183     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 184     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me\r
 185     JCheckBoxMenuItem           _show_overview_cbmi;\r
 186     JCheckBoxMenuItem           _show_domain_labels;\r
 187     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 188     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 189     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 190     JMenuItem                   _overview_placment_mi;\r
 191     JMenuItem                   _choose_minimal_confidence_mi;\r
 192     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 193     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 194     JMenuItem                   _cycle_node_shape_mi;\r
 195     JMenuItem                   _cycle_node_fill_mi;\r
 196     JMenuItem                   _choose_node_size_mi;\r
 197     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 198     // _  print\r
 199     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 200     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 201     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 202     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 203     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 204     JMenuItem                   _print_size_mi;\r
 205     JMenuItem                   _choose_pdf_width_mi;\r
 206     // _  parsing\r
 207     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 208     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 209     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 210     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 211     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 212     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 213     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 214     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 215     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 216     // _  search\r
 217     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 218     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 219     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 220     // type menu:\r
 221     JMenu                       _type_menu;\r
 222     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 223     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 224     JCheckBoxMenuItem           _curved_type_cbmi;\r
 225     JCheckBoxMenuItem           _convex_type_cbmi;\r
 226     JCheckBoxMenuItem           _euro_type_cbmi;\r
 227     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 228     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 229     JCheckBoxMenuItem           _circular_type_cbmi;\r
 230     // view as text menu:\r
 231     JMenuItem                   _view_as_NH_item;\r
 232     JMenuItem                   _view_as_XML_item;\r
 233     JMenuItem                   _view_as_nexus_item;\r
 234     JMenuItem                   _display_basic_information_item;\r
 235     // help menu:\r
 236     JMenuItem                   _about_item;\r
 237     JMenuItem                   _help_item;\r
 238     JMenuItem                   _website_item;\r
 239     JMenuItem                   _phyloxml_website_item;\r
 240     JMenuItem                   _phyloxml_ref_item;\r
 241     JMenuItem                   _aptx_ref_item;\r
 242     // process menu:\r
 243     JMenu                       _process_menu;\r
 244     // Handy pointers to child components:\r
 245     MainPanel                   _mainpanel;\r
 246     Container                   _contentpane;\r
 247     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;\r
 248     Configuration               _configuration;\r
 249     Options                     _options;\r
 250     private Phylogeny           _species_tree;\r
 251     InferenceManager            _inference_manager;\r
 252     final ProcessPool           _process_pool;\r
 253     private String              _previous_node_annotation_ref;\r
 254 \r
 255     MainFrame() {\r
 256         _process_pool = ProcessPool.createInstance();\r
 257     }\r
 258 \r
 259     /**\r
 260      * Action performed.\r
 261      */\r
 262     @Override\r
 263     public void actionPerformed( final ActionEvent e ) {\r
 264         final Object o = e.getSource();\r
 265         boolean is_applet = false;\r
 266         JApplet applet = null;\r
 267         if ( getCurrentTreePanel() != null ) {\r
 268             is_applet = getCurrentTreePanel().isApplet();\r
 269             if ( is_applet ) {\r
 270                 applet = getCurrentTreePanel().obtainApplet();\r
 271             }\r
 272         }\r
 273         if ( o == _exit_item ) {\r
 274             close();\r
 275         }\r
 276         else if ( o == _gsdi_item ) {\r
 277             if ( isSubtreeDisplayed() ) {\r
 278                 return;\r
 279             }\r
 280             executeGSDI();\r
 281         }\r
 282         else if ( o == _gsdir_item ) {\r
 283             if ( isSubtreeDisplayed() ) {\r
 284                 return;\r
 285             }\r
 286             executeGSDIR();\r
 287         }\r
 288         else if ( o == _taxcolor_item ) {\r
 289             taxColor();\r
 290         }\r
 291         else if ( o == _confcolor_item ) {\r
 292             confColor();\r
 293         }\r
 294         else if ( o == _color_rank_jmi ) {\r
 295             colorRank();\r
 296         }\r
 297         else if ( o == _collapse_species_specific_subtrees ) {\r
 298             if ( isSubtreeDisplayed() ) {\r
 299                 return;\r
 300             }\r
 301             if ( getCurrentTreePanel() != null ) {\r
 302                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 303             }\r
 304         }\r
 305         else if ( o == _remove_branch_color_item ) {\r
 306             if ( isSubtreeDisplayed() ) {\r
 307                 return;\r
 308             }\r
 309             removeBranchColors();\r
 310         }\r
 311         else if ( o == _remove_visual_styles_item ) {\r
 312             if ( isSubtreeDisplayed() ) {\r
 313                 return;\r
 314             }\r
 315             removeVisualStyles();\r
 316         }\r
 317         else if ( o == _midpoint_root_item ) {\r
 318             if ( isSubtreeDisplayed() ) {\r
 319                 return;\r
 320             }\r
 321             midpointRoot();\r
 322         }\r
 323         else if ( o == _annotate_item ) {\r
 324             annotateSequences();\r
 325         }\r
 326         else if ( o == _switch_colors_mi ) {\r
 327             switchColors();\r
 328         }\r
 329         else if ( o == _display_basic_information_item ) {\r
 330             displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 331         }\r
 332         else if ( o == _view_as_NH_item ) {\r
 333             viewAsNH();\r
 334         }\r
 335         else if ( o == _view_as_XML_item ) {\r
 336             viewAsXML();\r
 337         }\r
 338         else if ( o == _view_as_nexus_item ) {\r
 339             viewAsNexus();\r
 340         }\r
 341         else if ( o == _super_tiny_fonts_item ) {\r
 342             if ( getCurrentTreePanel() != null ) {\r
 343                 getCurrentTreePanel().setSuperTinyFonts();\r
 344                 getCurrentTreePanel().repaint();\r
 345             }\r
 346         }\r
 347         else if ( o == _tiny_fonts_item ) {\r
 348             if ( getCurrentTreePanel() != null ) {\r
 349                 getCurrentTreePanel().setTinyFonts();\r
 350                 getCurrentTreePanel().repaint();\r
 351             }\r
 352         }\r
 353         else if ( o == _small_fonts_item ) {\r
 354             if ( getCurrentTreePanel() != null ) {\r
 355                 getCurrentTreePanel().setSmallFonts();\r
 356                 getCurrentTreePanel().repaint();\r
 357             }\r
 358         }\r
 359         else if ( o == _medium_fonts_item ) {\r
 360             if ( getCurrentTreePanel() != null ) {\r
 361                 getCurrentTreePanel().setMediumFonts();\r
 362                 getCurrentTreePanel().repaint();\r
 363             }\r
 364         }\r
 365         else if ( o == _large_fonts_item ) {\r
 366             if ( getCurrentTreePanel() != null ) {\r
 367                 getCurrentTreePanel().setLargeFonts();\r
 368                 getCurrentTreePanel().repaint();\r
 369             }\r
 370         }\r
 371         else if ( o == _choose_font_mi ) {\r
 372             chooseFont();\r
 373         }\r
 374         else if ( o == _choose_minimal_confidence_mi ) {\r
 375             chooseMinimalConfidence();\r
 376         }\r
 377         else if ( o == _choose_node_size_mi ) {\r
 378             chooseNodeSize( getOptions(), this );\r
 379         }\r
 380         else if ( o == _overview_placment_mi ) {\r
 381             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 382         }\r
 383         else if ( o == _cycle_node_fill_mi ) {\r
 384             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
 385         }\r
 386         else if ( o == _cycle_node_shape_mi ) {\r
 387             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
 388         }\r
 389         else if ( o == _screen_antialias_cbmi ) {\r
 390             updateOptions( getOptions() );\r
 391             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 392         }\r
 393         else if ( o == _background_gradient_cbmi ) {\r
 394             updateOptions( getOptions() );\r
 395         }\r
 396         else if ( o == _show_domain_labels ) {\r
 397             updateOptions( getOptions() );\r
 398         }\r
 399         else if ( o == _show_annotation_ref_source ) {\r
 400             updateOptions( getOptions() );\r
 401         }\r
 402         else if ( o == _abbreviate_scientific_names ) {\r
 403             updateOptions( getOptions() );\r
 404         }\r
 405         else if ( o == _color_labels_same_as_parent_branch ) {\r
 406             updateOptions( getOptions() );\r
 407         }\r
 408         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 409             updateOptions( getOptions() );\r
 410         }\r
 411         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 412             updateOptions( getOptions() );\r
 413         }\r
 414         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 415             updateOptions( getOptions() );\r
 416             showWhole();\r
 417         }\r
 418         else if ( o == _uniform_cladograms_rbmi ) {\r
 419             updateOptions( getOptions() );\r
 420             showWhole();\r
 421         }\r
 422         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 423             updateOptions( getOptions() );\r
 424             showWhole();\r
 425         }\r
 426         else if ( o == _search_case_senstive_cbmi ) {\r
 427             updateOptions( getOptions() );\r
 428             getMainPanel().getControlPanel().search0();\r
 429             getMainPanel().getControlPanel().search1();\r
 430         }\r
 431         else if ( o == _search_whole_words_only_cbmi ) {\r
 432             updateOptions( getOptions() );\r
 433             getMainPanel().getControlPanel().search0();\r
 434             getMainPanel().getControlPanel().search1();\r
 435         }\r
 436         else if ( o == _inverse_search_result_cbmi ) {\r
 437             updateOptions( getOptions() );\r
 438             getMainPanel().getControlPanel().search0();\r
 439             getMainPanel().getControlPanel().search1();\r
 440         }\r
 441         else if ( o == _show_scale_cbmi ) {\r
 442             updateOptions( getOptions() );\r
 443         }\r
 444         else if ( o == _show_branch_length_values_cbmi ) {\r
 445             updateOptions( getOptions() );\r
 446         }\r
 447         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 448             updateOptions( getOptions() );\r
 449         }\r
 450         else if ( o == _show_confidence_stddev_cbmi ) {\r
 451             updateOptions( getOptions() );\r
 452         }\r
 453         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 454             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 455                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 456             }\r
 457             updateOptions( getOptions() );\r
 458         }\r
 459         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 460             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 461                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 462             }\r
 463             updateOptions( getOptions() );\r
 464         }\r
 465         else if ( o == _label_direction_cbmi ) {\r
 466             updateOptions( getOptions() );\r
 467         }\r
 468         else if ( o == _show_overview_cbmi ) {\r
 469             updateOptions( getOptions() );\r
 470             if ( getCurrentTreePanel() != null ) {\r
 471                 getCurrentTreePanel().updateOvSizes();\r
 472             }\r
 473         }\r
 474         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 475                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 476                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 477             typeChanged( o );\r
 478         }\r
 479         else if ( o == _about_item ) {\r
 480             about();\r
 481         }\r
 482         else if ( o == _help_item ) {\r
 483             help();\r
 484         }\r
 485         else if ( o == _website_item ) {\r
 486             try {\r
 487                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 488             }\r
 489             catch ( final IOException e1 ) {\r
 490                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 491             }\r
 492         }\r
 493         else if ( o == _phyloxml_website_item ) {\r
 494             try {\r
 495                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 496             }\r
 497             catch ( final IOException e1 ) {\r
 498                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 499             }\r
 500         }\r
 501         else if ( o == _aptx_ref_item ) {\r
 502             try {\r
 503                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 504             }\r
 505             catch ( final IOException e1 ) {\r
 506                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 507             }\r
 508         }\r
 509         else if ( o == _phyloxml_ref_item ) {\r
 510             try {\r
 511                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 512             }\r
 513             catch ( final IOException e1 ) {\r
 514                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 515             }\r
 516         }\r
 517         else {\r
 518             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 519                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 520                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 521                         readPhylogeniesFromWebservice( i );\r
 522                     }\r
 523                 }\r
 524             }\r
 525         }\r
 526         _contentpane.repaint();\r
 527     }\r
 528 \r
 529     public Configuration getConfiguration() {\r
 530         return _configuration;\r
 531     }\r
 532 \r
 533     /**\r
 534      * This method returns the current external node data which\r
 535      * has been selected by the user by clicking the "Return ..."\r
 536      * menu item. This method is expected to be called from Javascript or\r
 537      * something like it.\r
 538      * \r
 539      * @return current external node data as String\r
 540      */\r
 541     public String getCurrentExternalNodesDataBuffer() {\r
 542         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 543     }\r
 544 \r
 545     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 546         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 547     }\r
 548 \r
 549     public int getCurrentExternalNodesDataBufferLength() {\r
 550         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 551     }\r
 552 \r
 553     public InferenceManager getInferenceManager() {\r
 554         return _inference_manager;\r
 555     }\r
 556 \r
 557     public MainPanel getMainPanel() {\r
 558         return _mainpanel;\r
 559     }\r
 560 \r
 561     public Options getOptions() {\r
 562         return _options;\r
 563     }\r
 564 \r
 565     public ProcessPool getProcessPool() {\r
 566         return _process_pool;\r
 567     }\r
 568 \r
 569     public void showTextFrame( final String s, final String title ) {\r
 570         checkTextFrames();\r
 571         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 572     }\r
 573 \r
 574     public void showWhole() {\r
 575         _mainpanel.getControlPanel().showWhole();\r
 576     }\r
 577 \r
 578     public void updateProcessMenu() {\r
 579         // In general Swing is not thread safe.\r
 580         // See "Swing's Threading Policy".\r
 581         SwingUtilities.invokeLater( new Runnable() {\r
 582 \r
 583             @Override\r
 584             public void run() {\r
 585                 doUpdateProcessMenu();\r
 586             }\r
 587         } );\r
 588     }\r
 589 \r
 590     void activateSaveAllIfNeeded() {\r
 591         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 592             _save_all_item.setEnabled( true );\r
 593         }\r
 594         else {\r
 595             _save_all_item.setEnabled( false );\r
 596         }\r
 597     }\r
 598 \r
 599     void buildFileMenu() {\r
 600         _file_jmenu = createMenu( "File", getConfiguration() );\r
 601         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 602         customizeJMenuItem( _exit_item );\r
 603         _jmenubar.add( _file_jmenu );\r
 604     }\r
 605 \r
 606     void buildFontSizeMenu() {\r
 607         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 608         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 609         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 610         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 611         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 612         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 613         customizeJMenuItem( _super_tiny_fonts_item );\r
 614         customizeJMenuItem( _tiny_fonts_item );\r
 615         customizeJMenuItem( _small_fonts_item );\r
 616         customizeJMenuItem( _medium_fonts_item );\r
 617         customizeJMenuItem( _large_fonts_item );\r
 618         _jmenubar.add( _font_size_menu );\r
 619     }\r
 620 \r
 621     void buildHelpMenu() {\r
 622         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 623         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );\r
 624         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 625         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );\r
 626         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 627         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 628         _help_jmenu.addSeparator();\r
 629         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 630         customizeJMenuItem( _help_item );\r
 631         customizeJMenuItem( _website_item );\r
 632         customizeJMenuItem( _phyloxml_website_item );\r
 633         customizeJMenuItem( _aptx_ref_item );\r
 634         customizeJMenuItem( _phyloxml_ref_item );\r
 635         customizeJMenuItem( _about_item );\r
 636         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 637         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 638         _jmenubar.add( _help_jmenu );\r
 639     }\r
 640 \r
 641     void buildTypeMenu() {\r
 642         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 643         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 644         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 645         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 646         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 647         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 648         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 649         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 650         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 651         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 652         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 653         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 654         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 655         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 656         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 657         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 658         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 659         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 660         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 661         initializeTypeMenu( getOptions() );\r
 662         _jmenubar.add( _type_menu );\r
 663     }\r
 664 \r
 665     void buildViewMenu() {\r
 666         _view_jmenu = createMenu( "View", getConfiguration() );\r
 667         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 668         _view_jmenu.addSeparator();\r
 669         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 670         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 671         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 672         customizeJMenuItem( _display_basic_information_item );\r
 673         customizeJMenuItem( _view_as_NH_item );\r
 674         customizeJMenuItem( _view_as_XML_item );\r
 675         customizeJMenuItem( _view_as_nexus_item );\r
 676         _jmenubar.add( _view_jmenu );\r
 677     }\r
 678 \r
 679     void checkTextFrames() {\r
 680         if ( _textframes.size() > 5 ) {\r
 681             try {\r
 682                 if ( _textframes.getFirst() != null ) {\r
 683                     _textframes.getFirst().removeMe();\r
 684                 }\r
 685                 else {\r
 686                     _textframes.removeFirst();\r
 687                 }\r
 688             }\r
 689             catch ( final NoSuchElementException e ) {\r
 690                 // Ignore.\r
 691             }\r
 692         }\r
 693     }\r
 694 \r
 695     void close() {\r
 696         removeAllTextFrames();\r
 697         if ( _mainpanel != null ) {\r
 698             _mainpanel.terminate();\r
 699         }\r
 700         if ( _contentpane != null ) {\r
 701             _contentpane.removeAll();\r
 702         }\r
 703         setVisible( false );\r
 704         dispose();\r
 705     }\r
 706 \r
 707     void colorRank() {\r
 708         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 709             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
 710             final String rank = ( String ) JOptionPane\r
 711                     .showInputDialog( this,\r
 712                                       "What rank should the colorization be based on",\r
 713                                       "Rank Selection",\r
 714                                       JOptionPane.QUESTION_MESSAGE,\r
 715                                       null,\r
 716                                       ranks,\r
 717                                       null );\r
 718             if ( !ForesterUtil.isEmpty( rank ) ) {\r
 719                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
 720             }\r
 721         }\r
 722     }\r
 723 \r
 724     void confColor() {\r
 725         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 726             _mainpanel.getCurrentTreePanel().confColor();\r
 727         }\r
 728     }\r
 729 \r
 730     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
 731         if ( item != null ) {\r
 732             item.setFont( MainFrame.menu_font );\r
 733             if ( !getConfiguration().isUseNativeUI() ) {\r
 734                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 735                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 736             }\r
 737             item.setSelected( is_selected );\r
 738             item.addActionListener( this );\r
 739         }\r
 740     }\r
 741 \r
 742     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
 743         if ( jmi != null ) {\r
 744             jmi.setFont( MainFrame.menu_font );\r
 745             if ( !getConfiguration().isUseNativeUI() ) {\r
 746                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 747                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 748             }\r
 749             jmi.addActionListener( this );\r
 750         }\r
 751         return jmi;\r
 752     }\r
 753 \r
 754     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
 755         if ( item != null ) {\r
 756             item.setFont( MainFrame.menu_font );\r
 757             if ( !getConfiguration().isUseNativeUI() ) {\r
 758                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 759                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 760             }\r
 761             item.setSelected( is_selected );\r
 762             item.addActionListener( this );\r
 763         }\r
 764     }\r
 765 \r
 766     void displayBasicInformation( final File treefile ) {\r
 767         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
 768             String title = "Basic Information";\r
 769             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
 770                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
 771             }\r
 772             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
 773         }\r
 774     }\r
 775 \r
 776     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
 777         try {\r
 778             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 779         }\r
 780         catch ( final Exception ex ) {\r
 781             // Do nothing.\r
 782         }\r
 783         JOptionPane.showMessageDialog( this,\r
 784                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
 785                                        "Error during File|Open",\r
 786                                        JOptionPane.ERROR_MESSAGE );\r
 787     }\r
 788 \r
 789     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
 790         try {\r
 791             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 792         }\r
 793         catch ( final Exception ex ) {\r
 794             // Do nothing.\r
 795         }\r
 796         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
 797     }\r
 798 \r
 799     void executeGSDI() {\r
 800         if ( !isOKforSDI( false, true ) ) {\r
 801             return;\r
 802         }\r
 803         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
 804             JOptionPane.showMessageDialog( this,\r
 805                                            "Gene tree is not rooted.",\r
 806                                            "Cannot execute GSDI",\r
 807                                            JOptionPane.ERROR_MESSAGE );\r
 808             return;\r
 809         }\r
 810         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 811         gene_tree.setAllNodesToNotCollapse();\r
 812         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 813         GSDI gsdi = null;\r
 814         final Phylogeny species_tree = getSpeciesTree().copy();\r
 815         try {\r
 816             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
 817         }\r
 818         catch ( final SDIException e ) {\r
 819             JOptionPane.showMessageDialog( this,\r
 820                                            e.getLocalizedMessage(),\r
 821                                            "Error during GSDI",\r
 822                                            JOptionPane.ERROR_MESSAGE );\r
 823             return;\r
 824         }\r
 825         catch ( final Exception e ) {\r
 826             AptxUtil.unexpectedException( e );\r
 827             return;\r
 828         }\r
 829         gene_tree.setRerootable( false );\r
 830         gene_tree.clearHashIdToNodeMap();\r
 831         gene_tree.recalculateNumberOfExternalDescendants( true );\r
 832         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
 833         getMainPanel().getControlPanel().setShowEvents( true );\r
 834         showWhole();\r
 835         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 836         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 837         showWhole();\r
 838         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 839         showWhole();\r
 840         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 841         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 842         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 843             JOptionPane.showMessageDialog( this,\r
 844                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 845                                                    + "Potential duplications: "\r
 846                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 847                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 848                                                    + "Stripped gene tree nodes: "\r
 849                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 850                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 851                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 852                                            "GSDI successfully completed",\r
 853                                            JOptionPane.WARNING_MESSAGE );\r
 854         }\r
 855         else {\r
 856             JOptionPane.showMessageDialog( this,\r
 857                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 858                                                    + "Potential duplications: "\r
 859                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 860                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 861                                                    + "Stripped gene tree nodes: "\r
 862                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 863                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 864                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 865                                            "GSDI successfully completed",\r
 866                                            JOptionPane.INFORMATION_MESSAGE );\r
 867         }\r
 868     }\r
 869 \r
 870     void executeGSDIR() {\r
 871         if ( !isOKforSDI( false, false ) ) {\r
 872             return;\r
 873         }\r
 874         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
 875         if ( ( p > 0 )\r
 876                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
 877             JOptionPane.showMessageDialog( this,\r
 878                                            "Gene tree is not completely binary",\r
 879                                            "Cannot execute GSDI",\r
 880                                            JOptionPane.ERROR_MESSAGE );\r
 881             return;\r
 882         }\r
 883         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 884         gene_tree.setAllNodesToNotCollapse();\r
 885         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 886         GSDIR gsdir = null;\r
 887         final Phylogeny species_tree = getSpeciesTree().copy();\r
 888         try {\r
 889             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
 890         }\r
 891         catch ( final SDIException e ) {\r
 892             JOptionPane.showMessageDialog( this,\r
 893                                            e.getLocalizedMessage(),\r
 894                                            "Error during GSDIR",\r
 895                                            JOptionPane.ERROR_MESSAGE );\r
 896             return;\r
 897         }\r
 898         catch ( final Exception e ) {\r
 899             AptxUtil.unexpectedException( e );\r
 900             return;\r
 901         }\r
 902         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
 903         result_gene_tree.setRerootable( false );\r
 904         result_gene_tree.clearHashIdToNodeMap();\r
 905         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
 906         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
 907         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
 908         getMainPanel().getControlPanel().setShowEvents( true );\r
 909         showWhole();\r
 910         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 911         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 912         showWhole();\r
 913         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 914         showWhole();\r
 915         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 916         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 917         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 918             JOptionPane.showMessageDialog( this,\r
 919                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
 920                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
 921                                                    + "Stripped gene tree nodes: "\r
 922                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 923                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
 924                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 925                                            "GSDIR successfully completed",\r
 926                                            JOptionPane.WARNING_MESSAGE );\r
 927         }\r
 928         else {\r
 929             JOptionPane.showMessageDialog( this,\r
 930                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
 931                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
 932                                                    + "Stripped gene tree nodes: "\r
 933                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 934                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
 935                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 936                                            "GSDIR successfully completed",\r
 937                                            JOptionPane.INFORMATION_MESSAGE );\r
 938         }\r
 939     }\r
 940 \r
 941     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
 942         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
 943             JOptionPane.showMessageDialog( this,\r
 944                                            "Gene tree and species tree have no species in common.",\r
 945                                            "Error during SDI",\r
 946                                            JOptionPane.ERROR_MESSAGE );\r
 947             return false;\r
 948         }\r
 949         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
 950             JOptionPane.showMessageDialog( this,\r
 951                                            "Gene tree and species tree have only one species in common.",\r
 952                                            "Error during SDI",\r
 953                                            JOptionPane.ERROR_MESSAGE );\r
 954             return false;\r
 955         }\r
 956         else {\r
 957             return true;\r
 958         }\r
 959     }\r
 960 \r
 961     TreePanel getCurrentTreePanel() {\r
 962         return getMainPanel().getCurrentTreePanel();\r
 963     }\r
 964 \r
 965     JMenu getHelpMenu() {\r
 966         return _help_jmenu;\r
 967     }\r
 968 \r
 969     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
 970         return _label_direction_cbmi;\r
 971     }\r
 972 \r
 973     JMenuBar getMenuBarOfMainFrame() {\r
 974         return _jmenubar;\r
 975     }\r
 976 \r
 977     final Phylogeny getSpeciesTree() {\r
 978         return _species_tree;\r
 979     }\r
 980 \r
 981     void help() {\r
 982         final StringBuilder sb = new StringBuilder();\r
 983         sb.append( "Display options\n" );\r
 984         sb.append( "-------------------\n" );\r
 985         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );\r
 986         sb.append( "Clickable tree nodes\n" );\r
 987         sb.append( "--------------------\n" );\r
 988         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );\r
 989         sb.append( "or by right clicking:\n" );\r
 990         sb.append( "o  Display Node Data -- display information for a node\n" );\r
 991         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );\r
 992         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );\r
 993         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );\r
 994         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );\r
 995         sb.append( "o  Colorize Subtree -- color a subtree\n" );\r
 996         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );\r
 997         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );\r
 998         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );\r
 999         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );\r
1000         sb.append( "Zooming\n" );\r
1001         sb.append( "---------\n" );\r
1002         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );\r
1003         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );\r
1004         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );\r
1005         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );\r
1006         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );\r
1007         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );\r
1008         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );\r
1009         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );\r
1010         sb.append( "Quick tree manipulation:\n" );\r
1011         sb.append( "------------------------\n" );\r
1012         sb.append( "Order Subtrees -- order the tree by branch length\n" );\r
1013         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );\r
1014         sb.append( "Memory problems (Java heap space error)\n" );\r
1015         sb.append( "---------------------------------------\n" );\r
1016         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );\r
1017         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );\r
1018         sb.append( "the '-Xmx' Java command line option. For example:\n" );\r
1019         sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );\r
1020         // + "General remarks\n"\r
1021         // + "---------------\n"\r
1022         // +\r
1023         // "o  The application version permits copying to the clipboard \n"\r
1024         // +\r
1025         // "    in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"\r
1026         // +\r
1027         // "o  Changes made to a subtree affect this subtree and its subtrees,\n"\r
1028         // + "    but not any of its parent tree(s).\n"\r
1029         // +\r
1030         // "o  Archaeopteryx tries to detect whether the numerical values in a NH tree\n"\r
1031         // +\r
1032         // "    are likely to be bootstrap values instead of branch length values.\n\n"\r
1033         // +\r
1034         // " Remarks regarding SDI (Speciation Duplication Inference):\n"\r
1035         // +\r
1036         // "o  Each external node of the gene tree (in display) needs to be associated with\n"\r
1037         // +\r
1038         // "    a species: either directly through the \"Species\" field, or the species\n"\r
1039         // +\r
1040         // "    is part of the sequence name in the form \"XXXX_SPECIES\"\n"\r
1041         // +\r
1042         // "    (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"\r
1043         // +\r
1044         // "o  A species tree for each species of the gene tree needs to be loaded with\n"\r
1045         // +\r
1046         // "   \"SDI\"|\"Load species tree\" prior the SDI execution.\n"\r
1047         // +\r
1048         // "o  !External nodes of the gene tree associated with species not present in\n"\r
1049         // +\r
1050         // "    the species tree are REMOVED prior to SDI execution!\n"\r
1051         // +\r
1052         // "o  Both the gene tree and the species tree must be completely binary.\n"\r
1053         // +\r
1054         // "o  Duplications and speciations are a function of the position of the root.\n"\r
1055         // +\r
1056         // "    Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"\r
1057         // + "    incorrect and need to be inferred again\n"\r
1058         // +\r
1059         // "    with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"\r
1060         sb.append( "phyloXML\n" );\r
1061         sb.append( "-------------------\n" );\r
1062         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );\r
1063         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );\r
1064         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1065         sb.append( "\n" );\r
1066         sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );\r
1067         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );\r
1068         TextFrame.instantiate( sb.toString(), "Help", _textframes );\r
1069     }\r
1070 \r
1071     void initializeTypeMenu( final Options options ) {\r
1072         setTypeMenuToAllUnselected();\r
1073         switch ( options.getPhylogenyGraphicsType() ) {\r
1074             case CONVEX:\r
1075                 _convex_type_cbmi.setSelected( true );\r
1076                 break;\r
1077             case CURVED:\r
1078                 _curved_type_cbmi.setSelected( true );\r
1079                 break;\r
1080             case EURO_STYLE:\r
1081                 _euro_type_cbmi.setSelected( true );\r
1082                 break;\r
1083             case ROUNDED:\r
1084                 _rounded_type_cbmi.setSelected( true );\r
1085                 break;\r
1086             case TRIANGULAR:\r
1087                 _triangular_type_cbmi.setSelected( true );\r
1088                 break;\r
1089             case UNROOTED:\r
1090                 _unrooted_type_cbmi.setSelected( true );\r
1091                 break;\r
1092             case CIRCULAR:\r
1093                 _circular_type_cbmi.setSelected( true );\r
1094                 break;\r
1095             default:\r
1096                 _rectangular_type_cbmi.setSelected( true );\r
1097                 break;\r
1098         }\r
1099     }\r
1100 \r
1101     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1102         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1103             return false;\r
1104         }\r
1105         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1106             JOptionPane.showMessageDialog( this,\r
1107                                            "No species tree loaded",\r
1108                                            "Cannot execute GSDI",\r
1109                                            JOptionPane.ERROR_MESSAGE );\r
1110             return false;\r
1111         }\r
1112         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1113             JOptionPane.showMessageDialog( this,\r
1114                                            "Species tree is not completely binary",\r
1115                                            "Cannot execute GSDI",\r
1116                                            JOptionPane.ERROR_MESSAGE );\r
1117             return false;\r
1118         }\r
1119         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1120             JOptionPane.showMessageDialog( this,\r
1121                                            "Gene tree is not completely binary",\r
1122                                            "Cannot execute GSDI",\r
1123                                            JOptionPane.ERROR_MESSAGE );\r
1124             return false;\r
1125         }\r
1126         else {\r
1127             return true;\r
1128         }\r
1129     }\r
1130 \r
1131     boolean isSubtreeDisplayed() {\r
1132         if ( getCurrentTreePanel() != null ) {\r
1133             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1134                 JOptionPane\r
1135                         .showMessageDialog( this,\r
1136                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1137                                             "Operation can not be exectuted on a sub-tree",\r
1138                                             JOptionPane.WARNING_MESSAGE );\r
1139                 return true;\r
1140             }\r
1141         }\r
1142         return false;\r
1143     }\r
1144 \r
1145     void midpointRoot() {\r
1146         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1147             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1148         }\r
1149     }\r
1150 \r
1151     void readPhylogeniesFromWebservice( final int i ) {\r
1152         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1153         new Thread( reader ).start();\r
1154     }\r
1155 \r
1156     void removeAllTextFrames() {\r
1157         for( final TextFrame tf : _textframes ) {\r
1158             if ( tf != null ) {\r
1159                 tf.close();\r
1160             }\r
1161         }\r
1162         _textframes.clear();\r
1163     }\r
1164 \r
1165     void setConfiguration( final Configuration configuration ) {\r
1166         _configuration = configuration;\r
1167     }\r
1168 \r
1169     void setInferenceManager( final InferenceManager i ) {\r
1170         _inference_manager = i;\r
1171     }\r
1172 \r
1173     void setOptions( final Options options ) {\r
1174         _options = options;\r
1175     }\r
1176 \r
1177     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1178         setTypeMenuToAllUnselected();\r
1179         switch ( type ) {\r
1180             case CIRCULAR:\r
1181                 _circular_type_cbmi.setSelected( true );\r
1182                 break;\r
1183             case CONVEX:\r
1184                 _convex_type_cbmi.setSelected( true );\r
1185                 break;\r
1186             case CURVED:\r
1187                 _curved_type_cbmi.setSelected( true );\r
1188                 break;\r
1189             case EURO_STYLE:\r
1190                 _euro_type_cbmi.setSelected( true );\r
1191                 break;\r
1192             case ROUNDED:\r
1193                 _rounded_type_cbmi.setSelected( true );\r
1194                 break;\r
1195             case RECTANGULAR:\r
1196                 _rectangular_type_cbmi.setSelected( true );\r
1197                 break;\r
1198             case TRIANGULAR:\r
1199                 _triangular_type_cbmi.setSelected( true );\r
1200                 break;\r
1201             case UNROOTED:\r
1202                 _unrooted_type_cbmi.setSelected( true );\r
1203                 break;\r
1204             default:\r
1205                 throw new IllegalArgumentException( "unknown type: " + type );\r
1206         }\r
1207     }\r
1208 \r
1209     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1210         _species_tree = species_tree;\r
1211     }\r
1212 \r
1213     void setTypeMenuToAllUnselected() {\r
1214         _convex_type_cbmi.setSelected( false );\r
1215         _curved_type_cbmi.setSelected( false );\r
1216         _euro_type_cbmi.setSelected( false );\r
1217         _rounded_type_cbmi.setSelected( false );\r
1218         _triangular_type_cbmi.setSelected( false );\r
1219         _rectangular_type_cbmi.setSelected( false );\r
1220         _unrooted_type_cbmi.setSelected( false );\r
1221         _circular_type_cbmi.setSelected( false );\r
1222     }\r
1223 \r
1224     void switchColors() {\r
1225         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1226         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1227         csc.setVisible( true );\r
1228     }\r
1229 \r
1230     void taxColor() {\r
1231         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1232             _mainpanel.getCurrentTreePanel().taxColor();\r
1233         }\r
1234     }\r
1235 \r
1236     void typeChanged( final Object o ) {\r
1237         updateTypeCheckboxes( getOptions(), o );\r
1238         updateOptions( getOptions() );\r
1239         if ( getCurrentTreePanel() != null ) {\r
1240             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1241             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1242             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1243                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1244                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1245                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1246                 getCurrentTreePanel().getControlPanel().showWhole();\r
1247             }\r
1248             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1249                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1250             }\r
1251             else {\r
1252                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1253             }\r
1254             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1255             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1256             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1257                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1258                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1259                 }\r
1260                 else {\r
1261                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1262                 }\r
1263             }\r
1264         }\r
1265     }\r
1266 \r
1267     void updateOptions( final Options options ) {\r
1268         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1269         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1270                 && _background_gradient_cbmi.isSelected() );\r
1271         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1272         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1273                 && _show_annotation_ref_source.isSelected() );\r
1274         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1275                 && _abbreviate_scientific_names.isSelected() );\r
1276         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1277                 && _color_labels_same_as_parent_branch.isSelected() );\r
1278         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1279                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1280         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1281                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
1282         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1283             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1284         }\r
1285         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1286             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1287         }\r
1288         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1289             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1290         }\r
1291         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1292                 && _search_case_senstive_cbmi.isSelected() );\r
1293         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1294             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1295         }\r
1296         if ( _label_direction_cbmi != null ) {\r
1297             if ( _label_direction_cbmi.isSelected() ) {\r
1298                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1299             }\r
1300             else {\r
1301                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1302             }\r
1303         }\r
1304         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1305         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1306                 && _show_confidence_stddev_cbmi.isSelected() );\r
1307         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {\r
1308             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );\r
1309         }\r
1310         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1311             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1312         }\r
1313         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1314                 && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1315         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1316                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1317         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1318         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1319                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1320             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1321         }\r
1322         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1323                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1324             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1325         }\r
1326         else {\r
1327             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1328         }\r
1329         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1330                 && _print_black_and_white_cbmi.isSelected() );\r
1331         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1332                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1333         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1334             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1335         }\r
1336         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1337             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1338         }\r
1339         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1340             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1341         }\r
1342         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1343             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1344         }\r
1345         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1346                 && _replace_underscores_cbmi.isSelected() );\r
1347         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1348                 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1349         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1350                 && _search_whole_words_only_cbmi.isSelected() );\r
1351         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1352                 && _inverse_search_result_cbmi.isSelected() );\r
1353         if ( _graphics_export_visible_only_cbmi != null ) {\r
1354             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1355             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1356                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1357                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1358             }\r
1359             else {\r
1360                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1361             }\r
1362         }\r
1363         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1364             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1365         }\r
1366         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1367             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1368         }\r
1369         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1370             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1371         }\r
1372         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1373             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1374         }\r
1375         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1376             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1377         }\r
1378         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1379             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1380         }\r
1381         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1382             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1383         }\r
1384         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1385             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1386         }\r
1387     }\r
1388 \r
1389     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1390         setTypeMenuToAllUnselected();\r
1391         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1392     }\r
1393 \r
1394     void viewAsNexus() {\r
1395         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1396             String title = "Nexus";\r
1397             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1398                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1399             }\r
1400             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1401                            title );\r
1402         }\r
1403     }\r
1404 \r
1405     void viewAsNH() {\r
1406         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1407             String title = "New Hampshire";\r
1408             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1409                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1410             }\r
1411             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1412                                    .getNhConversionSupportValueStyle() ),\r
1413                            title );\r
1414         }\r
1415     }\r
1416 \r
1417     void viewAsXML() {\r
1418         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1419             String title = "phyloXML";\r
1420             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1421                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1422             }\r
1423             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1424         }\r
1425     }\r
1426 \r
1427     private void annotateSequences() {\r
1428         if ( getCurrentTreePanel() != null ) {\r
1429             final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();\r
1430             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1431                 JOptionPane\r
1432                         .showMessageDialog( this,\r
1433                                             "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1434                                             "No nodes selected for annotation",\r
1435                                             JOptionPane.ERROR_MESSAGE );\r
1436                 return;\r
1437             }\r
1438             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1439             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1440                 final JTextField ref_field = new JTextField( 10 );\r
1441                 final JTextField desc_filed = new JTextField( 20 );\r
1442                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1443                         : getPreviousNodeAnnotationReference() );\r
1444                 final JPanel my_panel = new JPanel();\r
1445                 my_panel.add( new JLabel( "Reference " ) );\r
1446                 my_panel.add( ref_field );\r
1447                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1448                 my_panel.add( new JLabel( "Description " ) );\r
1449                 my_panel.add( desc_filed );\r
1450                 final int result = JOptionPane.showConfirmDialog( null,\r
1451                                                                   my_panel,\r
1452                                                                   "Enter the sequence annotation(s) for the "\r
1453                                                                           + nodes.size() + " selected nodes",\r
1454                                                                   JOptionPane.OK_CANCEL_OPTION );\r
1455                 if ( result == JOptionPane.OK_OPTION ) {\r
1456                     String ref = ref_field.getText();\r
1457                     String desc = desc_filed.getText();\r
1458                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1459                         ref = ref.trim();\r
1460                         ref = ref.replaceAll( "\\s+", " " );\r
1461                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1462                                 || ( ref.length() < 3 ) ) {\r
1463                             JOptionPane.showMessageDialog( this,\r
1464                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1465                                                            "Illegal Format for Annotation Reference",\r
1466                                                            JOptionPane.ERROR_MESSAGE );\r
1467                             return;\r
1468                         }\r
1469                     }\r
1470                     if ( ref != null ) {\r
1471                         setPreviousNodeAnnotationReference( ref );\r
1472                     }\r
1473                     if ( desc != null ) {\r
1474                         desc = desc.trim();\r
1475                         desc = desc.replaceAll( "\\s+", " " );\r
1476                     }\r
1477                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1478                         for( final Long id : nodes ) {\r
1479                             final PhylogenyNode n = phy.getNode( id );\r
1480                             ForesterUtil.ensurePresenceOfSequence( n );\r
1481                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1482                                     : new Annotation( ref );\r
1483                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1484                                 ann.setDesc( desc );\r
1485                             }\r
1486                             n.getNodeData().getSequence().addAnnotation( ann );\r
1487                         }\r
1488                     }\r
1489                     getMainPanel().getControlPanel().showAnnotations();\r
1490                 }\r
1491             }\r
1492         }\r
1493     }\r
1494 \r
1495     private void chooseFont() {\r
1496         final FontChooser fc = new FontChooser();\r
1497         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1498         fc.showDialog( this, "Select the Base Font" );\r
1499         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1500     }\r
1501 \r
1502     private void chooseMinimalConfidence() {\r
1503         final String s = ( String ) JOptionPane\r
1504                 .showInputDialog( this,\r
1505                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1506                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1507                                   "Minimal Confidence Value",\r
1508                                   JOptionPane.QUESTION_MESSAGE,\r
1509                                   null,\r
1510                                   null,\r
1511                                   getOptions().getMinConfidenceValue() );\r
1512         if ( !ForesterUtil.isEmpty( s ) ) {\r
1513             boolean success = true;\r
1514             double m = 0.0;\r
1515             final String m_str = s.trim();\r
1516             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1517                 try {\r
1518                     m = Double.parseDouble( m_str );\r
1519                 }\r
1520                 catch ( final Exception ex ) {\r
1521                     success = false;\r
1522                 }\r
1523             }\r
1524             else {\r
1525                 success = false;\r
1526             }\r
1527             if ( success && ( m >= 0.0 ) ) {\r
1528                 getOptions().setMinConfidenceValue( m );\r
1529             }\r
1530         }\r
1531     }\r
1532 \r
1533     private void doUpdateProcessMenu() {\r
1534         if ( _process_pool.size() > 0 ) {\r
1535             if ( _process_menu == null ) {\r
1536                 _process_menu = createMenu( "", getConfiguration() );\r
1537                 _process_menu.setForeground( Color.RED );\r
1538             }\r
1539             _process_menu.removeAll();\r
1540             final String text = "processes running: " + _process_pool.size();\r
1541             _process_menu.setText( text );\r
1542             _jmenubar.add( _process_menu );\r
1543             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1544                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1545                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1546             }\r
1547         }\r
1548         else {\r
1549             if ( _process_menu != null ) {\r
1550                 _process_menu.removeAll();\r
1551                 _jmenubar.remove( _process_menu );\r
1552             }\r
1553         }\r
1554         _jmenubar.validate();\r
1555         _jmenubar.repaint();\r
1556         repaint();\r
1557     }\r
1558 \r
1559     private String getPreviousNodeAnnotationReference() {\r
1560         return _previous_node_annotation_ref;\r
1561     }\r
1562 \r
1563     private void removeBranchColors() {\r
1564         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1565             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1566         }\r
1567     }\r
1568 \r
1569     private void removeVisualStyles() {\r
1570         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1571             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1572         }\r
1573     }\r
1574 \r
1575     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1576         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1577     }\r
1578 \r
1579     /**\r
1580      * Display the about box.\r
1581      */\r
1582     static void about() {\r
1583         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1584         about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );\r
1585         about.append( "All Rights Reserved\n" );\r
1586         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1587         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1588         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1589         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1590         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1591         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1592             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1593         }\r
1594         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1595                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1596             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1597                     + ForesterUtil.OS_VERSION + "]\n" );\r
1598         }\r
1599         final Runtime rt = java.lang.Runtime.getRuntime();\r
1600         final long free_memory = rt.freeMemory() / 1000000;\r
1601         final long total_memory = rt.totalMemory() / 1000000;\r
1602         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1603         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1604         about.append( "References:\n" );\r
1605         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1606         about.append( "For more information & download:\n" );\r
1607         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1608         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1609         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1610     }\r
1611 \r
1612     static void chooseNodeSize( final Options options, final Component parent ) {\r
1613         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1614                                                                  "Please enter the default size for node shapes.\n"\r
1615                                                                          + "[current value: "\r
1616                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1617                                                                  "Node Shape Size",\r
1618                                                                  JOptionPane.QUESTION_MESSAGE,\r
1619                                                                  null,\r
1620                                                                  null,\r
1621                                                                  options.getDefaultNodeShapeSize() );\r
1622         if ( !ForesterUtil.isEmpty( s ) ) {\r
1623             boolean success = true;\r
1624             double m = 0.0;\r
1625             final String m_str = s.trim();\r
1626             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1627                 try {\r
1628                     m = Double.parseDouble( m_str );\r
1629                 }\r
1630                 catch ( final Exception ex ) {\r
1631                     success = false;\r
1632                 }\r
1633             }\r
1634             else {\r
1635                 success = false;\r
1636             }\r
1637             if ( success && ( m >= 0.0 ) ) {\r
1638                 final short size = ForesterUtil.roundToShort( m );\r
1639                 if ( size >= 0.0 ) {\r
1640                     options.setDefaultNodeShapeSize( size );\r
1641                 }\r
1642             }\r
1643         }\r
1644     }\r
1645 \r
1646     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1647         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1648     }\r
1649 \r
1650     static JMenu createMenu( final String title, final Configuration conf ) {\r
1651         final JMenu jmenu = new JMenu( title );\r
1652         if ( !conf.isUseNativeUI() ) {\r
1653             jmenu.setFont( MainFrame.menu_font );\r
1654             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1655             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1656         }\r
1657         return jmenu;\r
1658     }\r
1659 \r
1660     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1661         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1662         if ( !configuration.isUseNativeUI() ) {\r
1663             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1664             label.setForeground( configuration.getGuiMenuTextColor() );\r
1665             label.setOpaque( true );\r
1666         }\r
1667         label.setSelected( false );\r
1668         label.setEnabled( false );\r
1669         return label;\r
1670     }\r
1671 \r
1672     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
1673         switch ( op.getDefaultNodeFill() ) {\r
1674             case GRADIENT:\r
1675                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1676                 break;\r
1677             case NONE:\r
1678                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1679                 break;\r
1680             case SOLID:\r
1681                 op.setDefaultNodeFill( NodeFill.NONE );\r
1682                 break;\r
1683             default:\r
1684                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1685         }\r
1686     }\r
1687 \r
1688     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
1689         switch ( op.getDefaultNodeShape() ) {\r
1690             case CIRCLE:\r
1691                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1692                 break;\r
1693             case RECTANGLE:\r
1694                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1695                 break;\r
1696             default:\r
1697                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1698         }\r
1699     }\r
1700 \r
1701     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1702         switch ( op.getOvPlacement() ) {\r
1703             case LOWER_LEFT:\r
1704                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1705                 break;\r
1706             case LOWER_RIGHT:\r
1707                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1708                 break;\r
1709             case UPPER_LEFT:\r
1710                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1711                 break;\r
1712             case UPPER_RIGHT:\r
1713                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1714                 break;\r
1715             default:\r
1716                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1717         }\r
1718         if ( tree_panel != null ) {\r
1719             tree_panel.updateOvSettings();\r
1720         }\r
1721     }\r
1722 \r
1723     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
1724         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
1725             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1726                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
1727         }\r
1728         else {\r
1729             mi.setText( "Cycle Node Shape Fill Type..." );\r
1730         }\r
1731     }\r
1732 \r
1733     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
1734         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
1735             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1736                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
1737         }\r
1738         else {\r
1739             mi.setText( "Cycle Node Shape Fill Type..." );\r
1740         }\r
1741     }\r
1742 \r
1743     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
1744         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
1745             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
1746         }\r
1747         else {\r
1748             mi.setText( "Cycle Overview Placement..." );\r
1749         }\r
1750     }\r
1751 \r
1752     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
1753         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
1754             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
1755                     + ")" );\r
1756         }\r
1757         else {\r
1758             mi.setText( "Select Color Scheme..." );\r
1759         }\r
1760     }\r
1761 \r
1762     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
1763         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
1764     }\r
1765 \r
1766     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
1767         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
1768             mi.setEnabled( true );\r
1769         }\r
1770         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
1771             mi.setEnabled( true );\r
1772         }\r
1773         else {\r
1774             mi.setEnabled( false );\r
1775         }\r
1776         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
1777     }\r
1778 \r
1779     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
1780         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
1781     }\r
1782 \r
1783     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,\r
1784                                                            final JCheckBoxMenuItem scale,\r
1785                                                            final JCheckBoxMenuItem branch_lengths,\r
1786                                                            final JRadioButtonMenuItem non_lined_up,\r
1787                                                            final JRadioButtonMenuItem uniform_clado,\r
1788                                                            final JRadioButtonMenuItem nonuniform_clado,\r
1789                                                            final JCheckBoxMenuItem label_direction_cbmi ) {\r
1790         final TreePanel tree_panel = main_panel.getCurrentTreePanel();\r
1791         final ControlPanel control = main_panel.getControlPanel();\r
1792         final Options options = main_panel.getOptions();\r
1793         scale.setSelected( options.isShowScale() );\r
1794         branch_lengths.setSelected( options.isShowBranchLengthValues() );\r
1795         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1796         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {\r
1797             scale.setSelected( false );\r
1798             scale.setEnabled( false );\r
1799             branch_lengths.setSelected( false );\r
1800             branch_lengths.setEnabled( false );\r
1801         }\r
1802         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {\r
1803             scale.setSelected( false );\r
1804             scale.setEnabled( false );\r
1805             branch_lengths.setEnabled( true );\r
1806         }\r
1807         else {\r
1808             scale.setEnabled( true );\r
1809             branch_lengths.setEnabled( true );\r
1810         }\r
1811         if ( ( tree_panel != null )\r
1812                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )\r
1813                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1814                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1815             branch_lengths.setSelected( false );\r
1816             branch_lengths.setEnabled( false );\r
1817         }\r
1818         if ( tree_panel != null ) {\r
1819             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )\r
1820                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {\r
1821                 non_lined_up.setEnabled( false );\r
1822                 uniform_clado.setEnabled( false );\r
1823                 nonuniform_clado.setEnabled( false );\r
1824             }\r
1825             else {\r
1826                 non_lined_up.setEnabled( true );\r
1827                 uniform_clado.setEnabled( true );\r
1828                 nonuniform_clado.setEnabled( true );\r
1829             }\r
1830         }\r
1831         else {\r
1832             if ( ( tree_panel != null )\r
1833                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1834                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1835                 branch_lengths.setSelected( false );\r
1836                 branch_lengths.setEnabled( false );\r
1837             }\r
1838             if ( ( tree_panel != null )\r
1839                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel\r
1840                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {\r
1841                 non_lined_up.setEnabled( false );\r
1842             }\r
1843             else {\r
1844                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1845                 non_lined_up.setEnabled( true );\r
1846             }\r
1847         }\r
1848         label_direction_cbmi.setEnabled( true );\r
1849         if ( tree_panel != null ) {\r
1850             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )\r
1851                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1852                 label_direction_cbmi.setEnabled( false );\r
1853             }\r
1854             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {\r
1855                 scale.setSelected( false );\r
1856                 scale.setEnabled( false );\r
1857             }\r
1858         }\r
1859     }\r
1860 \r
1861     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
1862         for( final TreePanel tree_panel : treepanels ) {\r
1863             tree_panel.setTextAntialias();\r
1864         }\r
1865     }\r
1866 }\r