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

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