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.HashSet;\r
  37 import java.util.LinkedList;\r
  38 import java.util.List;\r
  39 import java.util.Locale;\r
  40 import java.util.NoSuchElementException;\r
  41 import java.util.Set;\r
  42 \r
  43 import javax.swing.Box;\r
  44 import javax.swing.JApplet;\r
  45 import javax.swing.JCheckBoxMenuItem;\r
  46 import javax.swing.JFrame;\r
  47 import javax.swing.JLabel;\r
  48 import javax.swing.JMenu;\r
  49 import javax.swing.JMenuBar;\r
  50 import javax.swing.JMenuItem;\r
  51 import javax.swing.JOptionPane;\r
  52 import javax.swing.JPanel;\r
  53 import javax.swing.JRadioButtonMenuItem;\r
  54 import javax.swing.JTextField;\r
  55 import javax.swing.SwingUtilities;\r
  56 \r
  57 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
  58 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
  59 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
  60 import org.forester.archaeopteryx.tools.InferenceManager;\r
  61 import org.forester.archaeopteryx.tools.ProcessPool;\r
  62 import org.forester.archaeopteryx.tools.ProcessRunning;\r
  63 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
  64 import org.forester.phylogeny.Phylogeny;\r
  65 import org.forester.phylogeny.PhylogenyMethods;\r
  66 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
  67 import org.forester.phylogeny.PhylogenyNode;\r
  68 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
  69 import org.forester.phylogeny.data.Annotation;\r
  70 import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
  71 import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
  72 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
  73 import org.forester.sdi.GSDI;\r
  74 import org.forester.sdi.GSDIR;\r
  75 import org.forester.sdi.SDIException;\r
  76 import org.forester.util.ForesterConstants;\r
  77 import org.forester.util.ForesterUtil;\r
  78 \r
  79 public abstract class MainFrame extends JFrame implements ActionListener {\r
  80 \r
  81     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
  82     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME\r
  83     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
  84     private static final long   serialVersionUID                        = 3655000897845508358L;\r
  85     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
  86                                                                                     Font.PLAIN,\r
  87                                                                                     10 );\r
  88     static final String         TYPE_MENU_HEADER                        = "Type";\r
  89     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
  90     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
  91     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
  92     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
  93     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
  94     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
  95     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO\r
  96     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO\r
  97     static final String         OPTIONS_HEADER                          = "Options";\r
  98     static final String         SEARCH_SUBHEADER                        = "Search:";\r
  99     static final String         DISPLAY_SUBHEADER                       = "Display:";\r
 100     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
 101     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
 102     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
 103     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Branch Length Values";\r
 104     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
 105     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
 106     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
 107     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
 108     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
 109     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
 110     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 111     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 112     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 113     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "External Node Shapes";\r
 114     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Internal Node Shapes";\r
 115     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 116     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 117     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 118     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 119     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 120     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
 121     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 122     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 123     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 124     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 125     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 126     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 127     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 128     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 129     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 130     JMenuBar                    _jmenubar;\r
 131     JMenu                       _file_jmenu;\r
 132     JMenu                       _tools_menu;\r
 133     JMenu                       _view_jmenu;\r
 134     JMenu                       _options_jmenu;\r
 135     JMenu                       _font_size_menu;\r
 136     JMenu                       _help_jmenu;\r
 137     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 138     // Analysis menu\r
 139     JMenu                       _analysis_menu;\r
 140     JMenuItem                   _load_species_tree_item;\r
 141     JMenuItem                   _gsdi_item;\r
 142     JMenuItem                   _gsdir_item;\r
 143     JMenuItem                   _lineage_inference;\r
 144     // file menu:\r
 145     JMenuItem                   _open_item;\r
 146     JMenuItem                   _open_url_item;\r
 147     JMenuItem                   _save_item;\r
 148     JMenuItem                   _save_all_item;\r
 149     JMenuItem                   _close_item;\r
 150     JMenuItem                   _exit_item;\r
 151     JMenuItem                   _new_item;\r
 152     // tools menu:\r
 153     JMenuItem                   _midpoint_root_item;\r
 154     JMenuItem                   _taxcolor_item;\r
 155     JMenuItem                   _confcolor_item;\r
 156     JMenuItem                   _color_rank_jmi;\r
 157     JMenuItem                   _collapse_species_specific_subtrees;\r
 158     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me\r
 159     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 160     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 161     JMenuItem                   _obtain_seq_information_jmi;\r
 162     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 163     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 164     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 165     JMenuItem                   _annotate_item;\r
 166     JMenuItem                   _remove_branch_color_item;\r
 167     JMenuItem                   _remove_visual_styles_item;\r
 168     JMenuItem                   _deleted_selected_nodes_item;\r
 169     JMenuItem                   _deleted_not_selected_nodes_item;\r
 170     // font size menu:\r
 171     JMenuItem                   _super_tiny_fonts_item;\r
 172     JMenuItem                   _tiny_fonts_item;\r
 173     JMenuItem                   _small_fonts_item;\r
 174     JMenuItem                   _medium_fonts_item;\r
 175     JMenuItem                   _large_fonts_item;\r
 176     // options menu:\r
 177     // _  screen and print\r
 178     JMenuItem                   _choose_font_mi;\r
 179     JMenuItem                   _switch_colors_mi;\r
 180     JCheckBoxMenuItem           _label_direction_cbmi;\r
 181     // _  screen display\r
 182     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 183     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 184     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 185     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 186     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 187     JCheckBoxMenuItem           _show_branch_length_values_cbmi;\r
 188     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 189     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me\r
 190     JCheckBoxMenuItem           _show_overview_cbmi;\r
 191     JCheckBoxMenuItem           _show_domain_labels;\r
 192     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 193     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 194     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 195     JMenuItem                   _overview_placment_mi;\r
 196     JMenuItem                   _choose_minimal_confidence_mi;\r
 197     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 198     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 199     JMenuItem                   _cycle_node_shape_mi;\r
 200     JMenuItem                   _cycle_node_fill_mi;\r
 201     JMenuItem                   _choose_node_size_mi;\r
 202     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 203     // _  print\r
 204     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 205     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 206     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 207     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 208     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 209     JMenuItem                   _print_size_mi;\r
 210     JMenuItem                   _choose_pdf_width_mi;\r
 211     // _  parsing\r
 212     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 213     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 214     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 215     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 216     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 217     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 218     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 219     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 220     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 221     // _  search\r
 222     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 223     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 224     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 225     // type menu:\r
 226     JMenu                       _type_menu;\r
 227     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 228     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 229     JCheckBoxMenuItem           _curved_type_cbmi;\r
 230     JCheckBoxMenuItem           _convex_type_cbmi;\r
 231     JCheckBoxMenuItem           _euro_type_cbmi;\r
 232     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 233     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 234     JCheckBoxMenuItem           _circular_type_cbmi;\r
 235     // view as text menu:\r
 236     JMenuItem                   _view_as_NH_item;\r
 237     JMenuItem                   _view_as_XML_item;\r
 238     JMenuItem                   _view_as_nexus_item;\r
 239     JMenuItem                   _display_basic_information_item;\r
 240     // help menu:\r
 241     JMenuItem                   _about_item;\r
 242     JMenuItem                   _help_item;\r
 243     JMenuItem                   _website_item;\r
 244     JMenuItem                   _phyloxml_website_item;\r
 245     JMenuItem                   _phyloxml_ref_item;\r
 246     JMenuItem                   _aptx_ref_item;\r
 247     // process menu:\r
 248     JMenu                       _process_menu;\r
 249     // Handy pointers to child components:\r
 250     MainPanel                   _mainpanel;\r
 251     Container                   _contentpane;\r
 252     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;\r
 253     Configuration               _configuration;\r
 254     Options                     _options;\r
 255     private Phylogeny           _species_tree;\r
 256     InferenceManager            _inference_manager;\r
 257     final ProcessPool           _process_pool;\r
 258     private String              _previous_node_annotation_ref;\r
 259 \r
 260     MainFrame() {\r
 261         _process_pool = ProcessPool.createInstance();\r
 262     }\r
 263 \r
 264     /**\r
 265      * Action performed.\r
 266      */\r
 267     @Override\r
 268     public void actionPerformed( final ActionEvent e ) {\r
 269         final Object o = e.getSource();\r
 270         boolean is_applet = false;\r
 271         JApplet applet = null;\r
 272         if ( getCurrentTreePanel() != null ) {\r
 273             is_applet = getCurrentTreePanel().isApplet();\r
 274             if ( is_applet ) {\r
 275                 applet = getCurrentTreePanel().obtainApplet();\r
 276             }\r
 277         }\r
 278         if ( o == _exit_item ) {\r
 279             close();\r
 280         }\r
 281         else if ( o == _gsdi_item ) {\r
 282             if ( isSubtreeDisplayed() ) {\r
 283                 return;\r
 284             }\r
 285             executeGSDI();\r
 286         }\r
 287         else if ( o == _gsdir_item ) {\r
 288             if ( isSubtreeDisplayed() ) {\r
 289                 return;\r
 290             }\r
 291             executeGSDIR();\r
 292         }\r
 293         else if ( o == _taxcolor_item ) {\r
 294             taxColor();\r
 295         }\r
 296         else if ( o == _confcolor_item ) {\r
 297             confColor();\r
 298         }\r
 299         else if ( o == _color_rank_jmi ) {\r
 300             colorRank();\r
 301         }\r
 302         else if ( o == _collapse_species_specific_subtrees ) {\r
 303             if ( isSubtreeDisplayed() ) {\r
 304                 return;\r
 305             }\r
 306             if ( getCurrentTreePanel() != null ) {\r
 307                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 308             }\r
 309         }\r
 310         else if ( o == _remove_branch_color_item ) {\r
 311             if ( isSubtreeDisplayed() ) {\r
 312                 return;\r
 313             }\r
 314             removeBranchColors();\r
 315         }\r
 316         else if ( o == _remove_visual_styles_item ) {\r
 317             if ( isSubtreeDisplayed() ) {\r
 318                 return;\r
 319             }\r
 320             removeVisualStyles();\r
 321         }\r
 322         else if ( o == _midpoint_root_item ) {\r
 323             if ( isSubtreeDisplayed() ) {\r
 324                 return;\r
 325             }\r
 326             midpointRoot();\r
 327         }\r
 328         else if ( o == _deleted_selected_nodes_item ) {\r
 329             if ( isSubtreeDisplayed() ) {\r
 330                 return;\r
 331             }\r
 332             deleteSelectedNodes( true );\r
 333         }\r
 334         else if ( o == _deleted_not_selected_nodes_item ) {\r
 335             if ( isSubtreeDisplayed() ) {\r
 336                 return;\r
 337             }\r
 338             deleteSelectedNodes( false );\r
 339         }\r
 340         else if ( o == _annotate_item ) {\r
 341             annotateSequences();\r
 342         }\r
 343         else if ( o == _switch_colors_mi ) {\r
 344             switchColors();\r
 345         }\r
 346         else if ( o == _display_basic_information_item ) {\r
 347             displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 348         }\r
 349         else if ( o == _view_as_NH_item ) {\r
 350             viewAsNH();\r
 351         }\r
 352         else if ( o == _view_as_XML_item ) {\r
 353             viewAsXML();\r
 354         }\r
 355         else if ( o == _view_as_nexus_item ) {\r
 356             viewAsNexus();\r
 357         }\r
 358         else if ( o == _super_tiny_fonts_item ) {\r
 359             if ( getCurrentTreePanel() != null ) {\r
 360                 getCurrentTreePanel().setSuperTinyFonts();\r
 361                 getCurrentTreePanel().repaint();\r
 362             }\r
 363         }\r
 364         else if ( o == _tiny_fonts_item ) {\r
 365             if ( getCurrentTreePanel() != null ) {\r
 366                 getCurrentTreePanel().setTinyFonts();\r
 367                 getCurrentTreePanel().repaint();\r
 368             }\r
 369         }\r
 370         else if ( o == _small_fonts_item ) {\r
 371             if ( getCurrentTreePanel() != null ) {\r
 372                 getCurrentTreePanel().setSmallFonts();\r
 373                 getCurrentTreePanel().repaint();\r
 374             }\r
 375         }\r
 376         else if ( o == _medium_fonts_item ) {\r
 377             if ( getCurrentTreePanel() != null ) {\r
 378                 getCurrentTreePanel().setMediumFonts();\r
 379                 getCurrentTreePanel().repaint();\r
 380             }\r
 381         }\r
 382         else if ( o == _large_fonts_item ) {\r
 383             if ( getCurrentTreePanel() != null ) {\r
 384                 getCurrentTreePanel().setLargeFonts();\r
 385                 getCurrentTreePanel().repaint();\r
 386             }\r
 387         }\r
 388         else if ( o == _choose_font_mi ) {\r
 389             chooseFont();\r
 390         }\r
 391         else if ( o == _choose_minimal_confidence_mi ) {\r
 392             chooseMinimalConfidence();\r
 393         }\r
 394         else if ( o == _choose_node_size_mi ) {\r
 395             chooseNodeSize( getOptions(), this );\r
 396         }\r
 397         else if ( o == _overview_placment_mi ) {\r
 398             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 399         }\r
 400         else if ( o == _cycle_node_fill_mi ) {\r
 401             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
 402         }\r
 403         else if ( o == _cycle_node_shape_mi ) {\r
 404             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
 405         }\r
 406         else if ( o == _screen_antialias_cbmi ) {\r
 407             updateOptions( getOptions() );\r
 408             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 409         }\r
 410         else if ( o == _background_gradient_cbmi ) {\r
 411             updateOptions( getOptions() );\r
 412         }\r
 413         else if ( o == _show_domain_labels ) {\r
 414             updateOptions( getOptions() );\r
 415         }\r
 416         else if ( o == _show_annotation_ref_source ) {\r
 417             updateOptions( getOptions() );\r
 418         }\r
 419         else if ( o == _abbreviate_scientific_names ) {\r
 420             updateOptions( getOptions() );\r
 421         }\r
 422         else if ( o == _color_labels_same_as_parent_branch ) {\r
 423             updateOptions( getOptions() );\r
 424         }\r
 425         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 426             updateOptions( getOptions() );\r
 427         }\r
 428         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 429             updateOptions( getOptions() );\r
 430         }\r
 431         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 432             updateOptions( getOptions() );\r
 433             showWhole();\r
 434         }\r
 435         else if ( o == _uniform_cladograms_rbmi ) {\r
 436             updateOptions( getOptions() );\r
 437             showWhole();\r
 438         }\r
 439         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 440             updateOptions( getOptions() );\r
 441             showWhole();\r
 442         }\r
 443         else if ( o == _search_case_senstive_cbmi ) {\r
 444             updateOptions( getOptions() );\r
 445             getMainPanel().getControlPanel().search0();\r
 446             getMainPanel().getControlPanel().search1();\r
 447         }\r
 448         else if ( o == _search_whole_words_only_cbmi ) {\r
 449             updateOptions( getOptions() );\r
 450             getMainPanel().getControlPanel().search0();\r
 451             getMainPanel().getControlPanel().search1();\r
 452         }\r
 453         else if ( o == _inverse_search_result_cbmi ) {\r
 454             updateOptions( getOptions() );\r
 455             getMainPanel().getControlPanel().search0();\r
 456             getMainPanel().getControlPanel().search1();\r
 457         }\r
 458         else if ( o == _show_scale_cbmi ) {\r
 459             updateOptions( getOptions() );\r
 460         }\r
 461         else if ( o == _show_branch_length_values_cbmi ) {\r
 462             updateOptions( getOptions() );\r
 463         }\r
 464         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 465             updateOptions( getOptions() );\r
 466         }\r
 467         else if ( o == _show_confidence_stddev_cbmi ) {\r
 468             updateOptions( getOptions() );\r
 469         }\r
 470         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 471             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 472                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 473             }\r
 474             updateOptions( getOptions() );\r
 475         }\r
 476         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 477             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 478                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 479             }\r
 480             updateOptions( getOptions() );\r
 481         }\r
 482         else if ( o == _label_direction_cbmi ) {\r
 483             updateOptions( getOptions() );\r
 484         }\r
 485         else if ( o == _show_overview_cbmi ) {\r
 486             updateOptions( getOptions() );\r
 487             if ( getCurrentTreePanel() != null ) {\r
 488                 getCurrentTreePanel().updateOvSizes();\r
 489             }\r
 490         }\r
 491         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 492                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 493                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 494             typeChanged( o );\r
 495         }\r
 496         else if ( o == _about_item ) {\r
 497             about();\r
 498         }\r
 499         else if ( o == _help_item ) {\r
 500             help();\r
 501         }\r
 502         else if ( o == _website_item ) {\r
 503             try {\r
 504                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 505             }\r
 506             catch ( final IOException e1 ) {\r
 507                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 508             }\r
 509         }\r
 510         else if ( o == _phyloxml_website_item ) {\r
 511             try {\r
 512                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 513             }\r
 514             catch ( final IOException e1 ) {\r
 515                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 516             }\r
 517         }\r
 518         else if ( o == _aptx_ref_item ) {\r
 519             try {\r
 520                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 521             }\r
 522             catch ( final IOException e1 ) {\r
 523                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 524             }\r
 525         }\r
 526         else if ( o == _phyloxml_ref_item ) {\r
 527             try {\r
 528                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 529             }\r
 530             catch ( final IOException e1 ) {\r
 531                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 532             }\r
 533         }\r
 534         else {\r
 535             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 536                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 537                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 538                         readPhylogeniesFromWebservice( i );\r
 539                     }\r
 540                 }\r
 541             }\r
 542         }\r
 543         _contentpane.repaint();\r
 544     }\r
 545 \r
 546     private void deleteSelectedNodes( boolean delete ) {\r
 547         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
 548         if ( phy == null || phy.getNumberOfExternalNodes() < 2 ) {\r
 549             return;\r
 550         }\r
 551         List<PhylogenyNode> nodes = null;\r
 552         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
 553             nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
 554         }\r
 555         String function = "Retain";\r
 556         if ( delete ) {\r
 557             function = "Delete";\r
 558         }\r
 559         if ( ( nodes == null ) || nodes.isEmpty() ) {\r
 560             JOptionPane\r
 561                     .showMessageDialog( this,\r
 562                                         "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
 563                                         "No external nodes selected to " + function.toLowerCase(),\r
 564                                         JOptionPane.ERROR_MESSAGE );\r
 565             return;\r
 566         }\r
 567         final int todo = nodes.size();\r
 568         final int ext = phy.getNumberOfExternalNodes();\r
 569         int res = todo;\r
 570         if ( delete ) {\r
 571             res = ext - todo;\r
 572         }\r
 573         \r
 574         if ( res < 1 ) {\r
 575             JOptionPane.showMessageDialog( this,\r
 576                                            "Cannot delete all nodes",\r
 577                                            "Attempt to delete all nodes ",\r
 578                                            JOptionPane.ERROR_MESSAGE );\r
 579             return;\r
 580         }\r
 581         final int result = JOptionPane.showConfirmDialog( null, "OK to " + function.toLowerCase() + " " + todo\r
 582                 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
 583                 + " nodes", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
 584         if ( result == JOptionPane.OK_OPTION ) {\r
 585             if ( !delete ) {\r
 586                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
 587                 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
 588                     final PhylogenyNode n = it.next();\r
 589                     if ( !nodes.contains( n ) ) {\r
 590                         to_delete.add( n );\r
 591                     }\r
 592                 }\r
 593                 for( final PhylogenyNode n : to_delete ) {\r
 594                     phy.deleteSubtree( n, true );\r
 595                 }\r
 596             }\r
 597             else {\r
 598                 for( final PhylogenyNode n : nodes ) {\r
 599                     phy.deleteSubtree( n, true );\r
 600                 }\r
 601             }\r
 602             resetSearch();\r
 603             getCurrentTreePanel().setNodeInPreorderToNull();\r
 604             phy.externalNodesHaveChanged();\r
 605             phy.clearHashIdToNodeMap();\r
 606             phy.recalculateNumberOfExternalDescendants( true );\r
 607             getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
 608             getCurrentTreePanel().setEdited( true );\r
 609             repaint();\r
 610         }\r
 611     }\r
 612 \r
 613     void resetSearch() {\r
 614         getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
 615         getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
 616         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
 617         getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
 618         getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
 619         getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
 620         getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
 621         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
 622         getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
 623         getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
 624         getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
 625         getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
 626     }\r
 627 \r
 628     public Configuration getConfiguration() {\r
 629         return _configuration;\r
 630     }\r
 631 \r
 632     /**\r
 633      * This method returns the current external node data which\r
 634      * has been selected by the user by clicking the "Return ..."\r
 635      * menu item. This method is expected to be called from Javascript or\r
 636      * something like it.\r
 637      * \r
 638      * @return current external node data as String\r
 639      */\r
 640     public String getCurrentExternalNodesDataBuffer() {\r
 641         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 642     }\r
 643 \r
 644     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 645         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 646     }\r
 647 \r
 648     public int getCurrentExternalNodesDataBufferLength() {\r
 649         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 650     }\r
 651 \r
 652     public InferenceManager getInferenceManager() {\r
 653         return _inference_manager;\r
 654     }\r
 655 \r
 656     public MainPanel getMainPanel() {\r
 657         return _mainpanel;\r
 658     }\r
 659 \r
 660     public Options getOptions() {\r
 661         return _options;\r
 662     }\r
 663 \r
 664     public ProcessPool getProcessPool() {\r
 665         return _process_pool;\r
 666     }\r
 667 \r
 668     public void showTextFrame( final String s, final String title ) {\r
 669         checkTextFrames();\r
 670         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 671     }\r
 672 \r
 673     public void showWhole() {\r
 674         _mainpanel.getControlPanel().showWhole();\r
 675     }\r
 676 \r
 677     public void updateProcessMenu() {\r
 678         // In general Swing is not thread safe.\r
 679         // See "Swing's Threading Policy".\r
 680         SwingUtilities.invokeLater( new Runnable() {\r
 681 \r
 682             @Override\r
 683             public void run() {\r
 684                 doUpdateProcessMenu();\r
 685             }\r
 686         } );\r
 687     }\r
 688 \r
 689     void activateSaveAllIfNeeded() {\r
 690         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 691             _save_all_item.setEnabled( true );\r
 692         }\r
 693         else {\r
 694             _save_all_item.setEnabled( false );\r
 695         }\r
 696     }\r
 697 \r
 698     void buildFileMenu() {\r
 699         _file_jmenu = createMenu( "File", getConfiguration() );\r
 700         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 701         customizeJMenuItem( _exit_item );\r
 702         _jmenubar.add( _file_jmenu );\r
 703     }\r
 704 \r
 705     void buildFontSizeMenu() {\r
 706         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 707         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 708         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 709         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 710         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 711         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 712         customizeJMenuItem( _super_tiny_fonts_item );\r
 713         customizeJMenuItem( _tiny_fonts_item );\r
 714         customizeJMenuItem( _small_fonts_item );\r
 715         customizeJMenuItem( _medium_fonts_item );\r
 716         customizeJMenuItem( _large_fonts_item );\r
 717         _jmenubar.add( _font_size_menu );\r
 718     }\r
 719 \r
 720     void buildHelpMenu() {\r
 721         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 722         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );\r
 723         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 724         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );\r
 725         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 726         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 727         _help_jmenu.addSeparator();\r
 728         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 729         customizeJMenuItem( _help_item );\r
 730         customizeJMenuItem( _website_item );\r
 731         customizeJMenuItem( _phyloxml_website_item );\r
 732         customizeJMenuItem( _aptx_ref_item );\r
 733         customizeJMenuItem( _phyloxml_ref_item );\r
 734         customizeJMenuItem( _about_item );\r
 735         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 736         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 737         _jmenubar.add( _help_jmenu );\r
 738     }\r
 739 \r
 740     void buildTypeMenu() {\r
 741         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 742         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 743         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 744         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 745         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 746         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 747         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 748         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 749         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 750         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 751         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 752         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 753         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 754         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 755         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 756         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 757         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 758         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 759         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 760         initializeTypeMenu( getOptions() );\r
 761         _jmenubar.add( _type_menu );\r
 762     }\r
 763 \r
 764     void buildViewMenu() {\r
 765         _view_jmenu = createMenu( "View", getConfiguration() );\r
 766         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 767         _view_jmenu.addSeparator();\r
 768         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 769         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 770         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 771         customizeJMenuItem( _display_basic_information_item );\r
 772         customizeJMenuItem( _view_as_NH_item );\r
 773         customizeJMenuItem( _view_as_XML_item );\r
 774         customizeJMenuItem( _view_as_nexus_item );\r
 775         _jmenubar.add( _view_jmenu );\r
 776     }\r
 777 \r
 778     void checkTextFrames() {\r
 779         if ( _textframes.size() > 5 ) {\r
 780             try {\r
 781                 if ( _textframes.getFirst() != null ) {\r
 782                     _textframes.getFirst().removeMe();\r
 783                 }\r
 784                 else {\r
 785                     _textframes.removeFirst();\r
 786                 }\r
 787             }\r
 788             catch ( final NoSuchElementException e ) {\r
 789                 // Ignore.\r
 790             }\r
 791         }\r
 792     }\r
 793 \r
 794     void close() {\r
 795         removeAllTextFrames();\r
 796         if ( _mainpanel != null ) {\r
 797             _mainpanel.terminate();\r
 798         }\r
 799         if ( _contentpane != null ) {\r
 800             _contentpane.removeAll();\r
 801         }\r
 802         setVisible( false );\r
 803         dispose();\r
 804     }\r
 805 \r
 806     void colorRank() {\r
 807         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 808             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
 809             final String rank = ( String ) JOptionPane\r
 810                     .showInputDialog( this,\r
 811                                       "What rank should the colorization be based on",\r
 812                                       "Rank Selection",\r
 813                                       JOptionPane.QUESTION_MESSAGE,\r
 814                                       null,\r
 815                                       ranks,\r
 816                                       null );\r
 817             if ( !ForesterUtil.isEmpty( rank ) ) {\r
 818                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
 819             }\r
 820         }\r
 821     }\r
 822 \r
 823     void confColor() {\r
 824         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 825             _mainpanel.getCurrentTreePanel().confColor();\r
 826         }\r
 827     }\r
 828 \r
 829     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
 830         if ( item != null ) {\r
 831             item.setFont( MainFrame.menu_font );\r
 832             if ( !getConfiguration().isUseNativeUI() ) {\r
 833                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 834                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 835             }\r
 836             item.setSelected( is_selected );\r
 837             item.addActionListener( this );\r
 838         }\r
 839     }\r
 840 \r
 841     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
 842         if ( jmi != null ) {\r
 843             jmi.setFont( MainFrame.menu_font );\r
 844             if ( !getConfiguration().isUseNativeUI() ) {\r
 845                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 846                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 847             }\r
 848             jmi.addActionListener( this );\r
 849         }\r
 850         return jmi;\r
 851     }\r
 852 \r
 853     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
 854         if ( item != null ) {\r
 855             item.setFont( MainFrame.menu_font );\r
 856             if ( !getConfiguration().isUseNativeUI() ) {\r
 857                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 858                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 859             }\r
 860             item.setSelected( is_selected );\r
 861             item.addActionListener( this );\r
 862         }\r
 863     }\r
 864 \r
 865     void displayBasicInformation( final File treefile ) {\r
 866         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
 867             String title = "Basic Information";\r
 868             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
 869                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
 870             }\r
 871             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
 872         }\r
 873     }\r
 874 \r
 875     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
 876         try {\r
 877             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 878         }\r
 879         catch ( final Exception ex ) {\r
 880             // Do nothing.\r
 881         }\r
 882         JOptionPane.showMessageDialog( this,\r
 883                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
 884                                        "Error during File|Open",\r
 885                                        JOptionPane.ERROR_MESSAGE );\r
 886     }\r
 887 \r
 888     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
 889         try {\r
 890             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 891         }\r
 892         catch ( final Exception ex ) {\r
 893             // Do nothing.\r
 894         }\r
 895         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
 896     }\r
 897 \r
 898     void executeGSDI() {\r
 899         if ( !isOKforSDI( false, true ) ) {\r
 900             return;\r
 901         }\r
 902         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
 903             JOptionPane.showMessageDialog( this,\r
 904                                            "Gene tree is not rooted.",\r
 905                                            "Cannot execute GSDI",\r
 906                                            JOptionPane.ERROR_MESSAGE );\r
 907             return;\r
 908         }\r
 909         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 910         gene_tree.setAllNodesToNotCollapse();\r
 911         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 912         GSDI gsdi = null;\r
 913         final Phylogeny species_tree = getSpeciesTree().copy();\r
 914         try {\r
 915             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
 916         }\r
 917         catch ( final SDIException e ) {\r
 918             JOptionPane.showMessageDialog( this,\r
 919                                            e.getLocalizedMessage(),\r
 920                                            "Error during GSDI",\r
 921                                            JOptionPane.ERROR_MESSAGE );\r
 922             return;\r
 923         }\r
 924         catch ( final Exception e ) {\r
 925             AptxUtil.unexpectedException( e );\r
 926             return;\r
 927         }\r
 928         gene_tree.setRerootable( false );\r
 929         gene_tree.clearHashIdToNodeMap();\r
 930         gene_tree.recalculateNumberOfExternalDescendants( true );\r
 931         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
 932         getMainPanel().getControlPanel().setShowEvents( true );\r
 933         showWhole();\r
 934         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 935         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 936         showWhole();\r
 937         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 938         showWhole();\r
 939         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 940         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 941         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 942             JOptionPane.showMessageDialog( this,\r
 943                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 944                                                    + "Potential duplications: "\r
 945                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 946                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 947                                                    + "Stripped gene tree nodes: "\r
 948                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 949                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 950                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 951                                            "GSDI successfully completed",\r
 952                                            JOptionPane.WARNING_MESSAGE );\r
 953         }\r
 954         else {\r
 955             JOptionPane.showMessageDialog( this,\r
 956                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 957                                                    + "Potential duplications: "\r
 958                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 959                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 960                                                    + "Stripped gene tree nodes: "\r
 961                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 962                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 963                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 964                                            "GSDI successfully completed",\r
 965                                            JOptionPane.INFORMATION_MESSAGE );\r
 966         }\r
 967     }\r
 968 \r
 969     void executeGSDIR() {\r
 970         if ( !isOKforSDI( false, false ) ) {\r
 971             return;\r
 972         }\r
 973         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
 974         if ( ( p > 0 )\r
 975                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
 976             JOptionPane.showMessageDialog( this,\r
 977                                            "Gene tree is not completely binary",\r
 978                                            "Cannot execute GSDI",\r
 979                                            JOptionPane.ERROR_MESSAGE );\r
 980             return;\r
 981         }\r
 982         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 983         gene_tree.setAllNodesToNotCollapse();\r
 984         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 985         GSDIR gsdir = null;\r
 986         final Phylogeny species_tree = getSpeciesTree().copy();\r
 987         try {\r
 988             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
 989         }\r
 990         catch ( final SDIException e ) {\r
 991             JOptionPane.showMessageDialog( this,\r
 992                                            e.getLocalizedMessage(),\r
 993                                            "Error during GSDIR",\r
 994                                            JOptionPane.ERROR_MESSAGE );\r
 995             return;\r
 996         }\r
 997         catch ( final Exception e ) {\r
 998             AptxUtil.unexpectedException( e );\r
 999             return;\r
1000         }\r
1001         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
1002         result_gene_tree.setRerootable( false );\r
1003         result_gene_tree.clearHashIdToNodeMap();\r
1004         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
1005         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
1006         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
1007         getMainPanel().getControlPanel().setShowEvents( true );\r
1008         showWhole();\r
1009         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1010         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1011         showWhole();\r
1012         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1013         showWhole();\r
1014         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1015         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1016         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1017             JOptionPane.showMessageDialog( this,\r
1018                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1019                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1020                                                    + "Stripped gene tree nodes: "\r
1021                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1022                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1023                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1024                                            "GSDIR successfully completed",\r
1025                                            JOptionPane.WARNING_MESSAGE );\r
1026         }\r
1027         else {\r
1028             JOptionPane.showMessageDialog( this,\r
1029                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1030                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1031                                                    + "Stripped gene tree nodes: "\r
1032                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1033                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1034                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1035                                            "GSDIR successfully completed",\r
1036                                            JOptionPane.INFORMATION_MESSAGE );\r
1037         }\r
1038     }\r
1039 \r
1040     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
1041         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
1042             JOptionPane.showMessageDialog( this,\r
1043                                            "Gene tree and species tree have no species in common.",\r
1044                                            "Error during SDI",\r
1045                                            JOptionPane.ERROR_MESSAGE );\r
1046             return false;\r
1047         }\r
1048         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
1049             JOptionPane.showMessageDialog( this,\r
1050                                            "Gene tree and species tree have only one species in common.",\r
1051                                            "Error during SDI",\r
1052                                            JOptionPane.ERROR_MESSAGE );\r
1053             return false;\r
1054         }\r
1055         else {\r
1056             return true;\r
1057         }\r
1058     }\r
1059 \r
1060     TreePanel getCurrentTreePanel() {\r
1061         return getMainPanel().getCurrentTreePanel();\r
1062     }\r
1063 \r
1064     JMenu getHelpMenu() {\r
1065         return _help_jmenu;\r
1066     }\r
1067 \r
1068     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
1069         return _label_direction_cbmi;\r
1070     }\r
1071 \r
1072     JMenuBar getMenuBarOfMainFrame() {\r
1073         return _jmenubar;\r
1074     }\r
1075 \r
1076     final Phylogeny getSpeciesTree() {\r
1077         return _species_tree;\r
1078     }\r
1079 \r
1080     void help() {\r
1081         final StringBuilder sb = new StringBuilder();\r
1082         sb.append( "Display options\n" );\r
1083         sb.append( "-------------------\n" );\r
1084         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );\r
1085         sb.append( "Clickable tree nodes\n" );\r
1086         sb.append( "--------------------\n" );\r
1087         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );\r
1088         sb.append( "or by right clicking:\n" );\r
1089         sb.append( "o  Display Node Data -- display information for a node\n" );\r
1090         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );\r
1091         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );\r
1092         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );\r
1093         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );\r
1094         sb.append( "o  Colorize Subtree -- color a subtree\n" );\r
1095         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );\r
1096         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );\r
1097         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );\r
1098         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );\r
1099         sb.append( "Zooming\n" );\r
1100         sb.append( "---------\n" );\r
1101         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );\r
1102         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );\r
1103         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );\r
1104         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );\r
1105         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );\r
1106         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );\r
1107         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );\r
1108         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );\r
1109         sb.append( "Quick tree manipulation:\n" );\r
1110         sb.append( "------------------------\n" );\r
1111         sb.append( "Order Subtrees -- order the tree by branch length\n" );\r
1112         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );\r
1113         sb.append( "Memory problems (Java heap space error)\n" );\r
1114         sb.append( "---------------------------------------\n" );\r
1115         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );\r
1116         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );\r
1117         sb.append( "the '-Xmx' Java command line option. For example:\n" );\r
1118         sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );\r
1119         // + "General remarks\n"\r
1120         // + "---------------\n"\r
1121         // +\r
1122         // "o  The application version permits copying to the clipboard \n"\r
1123         // +\r
1124         // "    in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"\r
1125         // +\r
1126         // "o  Changes made to a subtree affect this subtree and its subtrees,\n"\r
1127         // + "    but not any of its parent tree(s).\n"\r
1128         // +\r
1129         // "o  Archaeopteryx tries to detect whether the numerical values in a NH tree\n"\r
1130         // +\r
1131         // "    are likely to be bootstrap values instead of branch length values.\n\n"\r
1132         // +\r
1133         // " Remarks regarding SDI (Speciation Duplication Inference):\n"\r
1134         // +\r
1135         // "o  Each external node of the gene tree (in display) needs to be associated with\n"\r
1136         // +\r
1137         // "    a species: either directly through the \"Species\" field, or the species\n"\r
1138         // +\r
1139         // "    is part of the sequence name in the form \"XXXX_SPECIES\"\n"\r
1140         // +\r
1141         // "    (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"\r
1142         // +\r
1143         // "o  A species tree for each species of the gene tree needs to be loaded with\n"\r
1144         // +\r
1145         // "   \"SDI\"|\"Load species tree\" prior the SDI execution.\n"\r
1146         // +\r
1147         // "o  !External nodes of the gene tree associated with species not present in\n"\r
1148         // +\r
1149         // "    the species tree are REMOVED prior to SDI execution!\n"\r
1150         // +\r
1151         // "o  Both the gene tree and the species tree must be completely binary.\n"\r
1152         // +\r
1153         // "o  Duplications and speciations are a function of the position of the root.\n"\r
1154         // +\r
1155         // "    Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"\r
1156         // + "    incorrect and need to be inferred again\n"\r
1157         // +\r
1158         // "    with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"\r
1159         sb.append( "phyloXML\n" );\r
1160         sb.append( "-------------------\n" );\r
1161         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );\r
1162         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );\r
1163         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1164         sb.append( "\n" );\r
1165         sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );\r
1166         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );\r
1167         TextFrame.instantiate( sb.toString(), "Help", _textframes );\r
1168     }\r
1169 \r
1170     void initializeTypeMenu( final Options options ) {\r
1171         setTypeMenuToAllUnselected();\r
1172         switch ( options.getPhylogenyGraphicsType() ) {\r
1173             case CONVEX:\r
1174                 _convex_type_cbmi.setSelected( true );\r
1175                 break;\r
1176             case CURVED:\r
1177                 _curved_type_cbmi.setSelected( true );\r
1178                 break;\r
1179             case EURO_STYLE:\r
1180                 _euro_type_cbmi.setSelected( true );\r
1181                 break;\r
1182             case ROUNDED:\r
1183                 _rounded_type_cbmi.setSelected( true );\r
1184                 break;\r
1185             case TRIANGULAR:\r
1186                 _triangular_type_cbmi.setSelected( true );\r
1187                 break;\r
1188             case UNROOTED:\r
1189                 _unrooted_type_cbmi.setSelected( true );\r
1190                 break;\r
1191             case CIRCULAR:\r
1192                 _circular_type_cbmi.setSelected( true );\r
1193                 break;\r
1194             default:\r
1195                 _rectangular_type_cbmi.setSelected( true );\r
1196                 break;\r
1197         }\r
1198     }\r
1199 \r
1200     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1201         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1202             return false;\r
1203         }\r
1204         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1205             JOptionPane.showMessageDialog( this,\r
1206                                            "No species tree loaded",\r
1207                                            "Cannot execute GSDI",\r
1208                                            JOptionPane.ERROR_MESSAGE );\r
1209             return false;\r
1210         }\r
1211         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1212             JOptionPane.showMessageDialog( this,\r
1213                                            "Species tree is not completely binary",\r
1214                                            "Cannot execute GSDI",\r
1215                                            JOptionPane.ERROR_MESSAGE );\r
1216             return false;\r
1217         }\r
1218         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1219             JOptionPane.showMessageDialog( this,\r
1220                                            "Gene tree is not completely binary",\r
1221                                            "Cannot execute GSDI",\r
1222                                            JOptionPane.ERROR_MESSAGE );\r
1223             return false;\r
1224         }\r
1225         else {\r
1226             return true;\r
1227         }\r
1228     }\r
1229 \r
1230     boolean isSubtreeDisplayed() {\r
1231         if ( getCurrentTreePanel() != null ) {\r
1232             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1233                 JOptionPane\r
1234                         .showMessageDialog( this,\r
1235                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1236                                             "Operation can not be exectuted on a sub-tree",\r
1237                                             JOptionPane.WARNING_MESSAGE );\r
1238                 return true;\r
1239             }\r
1240         }\r
1241         return false;\r
1242     }\r
1243 \r
1244     void midpointRoot() {\r
1245         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1246             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1247         }\r
1248     }\r
1249 \r
1250     void readPhylogeniesFromWebservice( final int i ) {\r
1251         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1252         new Thread( reader ).start();\r
1253     }\r
1254 \r
1255     void removeAllTextFrames() {\r
1256         for( final TextFrame tf : _textframes ) {\r
1257             if ( tf != null ) {\r
1258                 tf.close();\r
1259             }\r
1260         }\r
1261         _textframes.clear();\r
1262     }\r
1263 \r
1264     void setConfiguration( final Configuration configuration ) {\r
1265         _configuration = configuration;\r
1266     }\r
1267 \r
1268     void setInferenceManager( final InferenceManager i ) {\r
1269         _inference_manager = i;\r
1270     }\r
1271 \r
1272     void setOptions( final Options options ) {\r
1273         _options = options;\r
1274     }\r
1275 \r
1276     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1277         setTypeMenuToAllUnselected();\r
1278         switch ( type ) {\r
1279             case CIRCULAR:\r
1280                 _circular_type_cbmi.setSelected( true );\r
1281                 break;\r
1282             case CONVEX:\r
1283                 _convex_type_cbmi.setSelected( true );\r
1284                 break;\r
1285             case CURVED:\r
1286                 _curved_type_cbmi.setSelected( true );\r
1287                 break;\r
1288             case EURO_STYLE:\r
1289                 _euro_type_cbmi.setSelected( true );\r
1290                 break;\r
1291             case ROUNDED:\r
1292                 _rounded_type_cbmi.setSelected( true );\r
1293                 break;\r
1294             case RECTANGULAR:\r
1295                 _rectangular_type_cbmi.setSelected( true );\r
1296                 break;\r
1297             case TRIANGULAR:\r
1298                 _triangular_type_cbmi.setSelected( true );\r
1299                 break;\r
1300             case UNROOTED:\r
1301                 _unrooted_type_cbmi.setSelected( true );\r
1302                 break;\r
1303             default:\r
1304                 throw new IllegalArgumentException( "unknown type: " + type );\r
1305         }\r
1306     }\r
1307 \r
1308     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1309         _species_tree = species_tree;\r
1310     }\r
1311 \r
1312     void setTypeMenuToAllUnselected() {\r
1313         _convex_type_cbmi.setSelected( false );\r
1314         _curved_type_cbmi.setSelected( false );\r
1315         _euro_type_cbmi.setSelected( false );\r
1316         _rounded_type_cbmi.setSelected( false );\r
1317         _triangular_type_cbmi.setSelected( false );\r
1318         _rectangular_type_cbmi.setSelected( false );\r
1319         _unrooted_type_cbmi.setSelected( false );\r
1320         _circular_type_cbmi.setSelected( false );\r
1321     }\r
1322 \r
1323     void switchColors() {\r
1324         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1325         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1326         csc.setVisible( true );\r
1327     }\r
1328 \r
1329     void taxColor() {\r
1330         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1331             _mainpanel.getCurrentTreePanel().taxColor();\r
1332         }\r
1333     }\r
1334 \r
1335     void typeChanged( final Object o ) {\r
1336         updateTypeCheckboxes( getOptions(), o );\r
1337         updateOptions( getOptions() );\r
1338         if ( getCurrentTreePanel() != null ) {\r
1339             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1340             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1341             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1342                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1343                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1344                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1345                 getCurrentTreePanel().getControlPanel().showWhole();\r
1346             }\r
1347             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1348                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1349             }\r
1350             else {\r
1351                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1352             }\r
1353             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1354             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1355             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1356                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1357                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1358                 }\r
1359                 else {\r
1360                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1361                 }\r
1362             }\r
1363         }\r
1364     }\r
1365 \r
1366     void updateOptions( final Options options ) {\r
1367         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1368         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1369                 && _background_gradient_cbmi.isSelected() );\r
1370         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1371         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1372                 && _show_annotation_ref_source.isSelected() );\r
1373         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1374                 && _abbreviate_scientific_names.isSelected() );\r
1375         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1376                 && _color_labels_same_as_parent_branch.isSelected() );\r
1377         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1378                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1379         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1380                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
1381         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1382             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1383         }\r
1384         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1385             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1386         }\r
1387         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1388             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1389         }\r
1390         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1391                 && _search_case_senstive_cbmi.isSelected() );\r
1392         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1393             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1394         }\r
1395         if ( _label_direction_cbmi != null ) {\r
1396             if ( _label_direction_cbmi.isSelected() ) {\r
1397                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1398             }\r
1399             else {\r
1400                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1401             }\r
1402         }\r
1403         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1404         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1405                 && _show_confidence_stddev_cbmi.isSelected() );\r
1406         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {\r
1407             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );\r
1408         }\r
1409         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1410             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1411         }\r
1412         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1413                 && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1414         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1415                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1416         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1417         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1418                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1419             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1420         }\r
1421         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1422                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1423             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1424         }\r
1425         else {\r
1426             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1427         }\r
1428         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1429                 && _print_black_and_white_cbmi.isSelected() );\r
1430         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1431                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1432         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1433             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1434         }\r
1435         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1436             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1437         }\r
1438         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1439             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1440         }\r
1441         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1442             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1443         }\r
1444         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1445                 && _replace_underscores_cbmi.isSelected() );\r
1446         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1447                 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1448         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1449                 && _search_whole_words_only_cbmi.isSelected() );\r
1450         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1451                 && _inverse_search_result_cbmi.isSelected() );\r
1452         if ( _graphics_export_visible_only_cbmi != null ) {\r
1453             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1454             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1455                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1456                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1457             }\r
1458             else {\r
1459                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1460             }\r
1461         }\r
1462         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1463             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1464         }\r
1465         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1466             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1467         }\r
1468         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1469             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1470         }\r
1471         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1472             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1473         }\r
1474         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1475             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1476         }\r
1477         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1478             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1479         }\r
1480         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1481             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1482         }\r
1483         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1484             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1485         }\r
1486     }\r
1487 \r
1488     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1489         setTypeMenuToAllUnselected();\r
1490         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1491     }\r
1492 \r
1493     void viewAsNexus() {\r
1494         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1495             String title = "Nexus";\r
1496             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1497                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1498             }\r
1499             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1500                            title );\r
1501         }\r
1502     }\r
1503 \r
1504     void viewAsNH() {\r
1505         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1506             String title = "New Hampshire";\r
1507             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1508                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1509             }\r
1510             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1511                                    .getNhConversionSupportValueStyle() ),\r
1512                            title );\r
1513         }\r
1514     }\r
1515 \r
1516     void viewAsXML() {\r
1517         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1518             String title = "phyloXML";\r
1519             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1520                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1521             }\r
1522             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1523         }\r
1524     }\r
1525 \r
1526     private void annotateSequences() {\r
1527         if ( getCurrentTreePanel() != null ) {\r
1528             List<PhylogenyNode> nodes = null;\r
1529             if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
1530                     || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
1531                 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
1532             }\r
1533             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1534                 JOptionPane\r
1535                         .showMessageDialog( this,\r
1536                                             "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1537                                             "No nodes selected for annotation",\r
1538                                             JOptionPane.ERROR_MESSAGE );\r
1539                 return;\r
1540             }\r
1541             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1542             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1543                 final JTextField ref_field = new JTextField( 10 );\r
1544                 final JTextField desc_filed = new JTextField( 20 );\r
1545                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1546                         : getPreviousNodeAnnotationReference() );\r
1547                 final JPanel my_panel = new JPanel();\r
1548                 my_panel.add( new JLabel( "Reference " ) );\r
1549                 my_panel.add( ref_field );\r
1550                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1551                 my_panel.add( new JLabel( "Description " ) );\r
1552                 my_panel.add( desc_filed );\r
1553                 final int result = JOptionPane.showConfirmDialog( null,\r
1554                                                                   my_panel,\r
1555                                                                   "Enter the sequence annotation(s) for the "\r
1556                                                                           + nodes.size() + " selected nodes",\r
1557                                                                   JOptionPane.OK_CANCEL_OPTION );\r
1558                 if ( result == JOptionPane.OK_OPTION ) {\r
1559                     String ref = ref_field.getText();\r
1560                     String desc = desc_filed.getText();\r
1561                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1562                         ref = ref.trim();\r
1563                         ref = ref.replaceAll( "\\s+", " " );\r
1564                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1565                                 || ( ref.length() < 3 ) ) {\r
1566                             JOptionPane.showMessageDialog( this,\r
1567                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1568                                                            "Illegal Format for Annotation Reference",\r
1569                                                            JOptionPane.ERROR_MESSAGE );\r
1570                             return;\r
1571                         }\r
1572                     }\r
1573                     if ( ref != null ) {\r
1574                         setPreviousNodeAnnotationReference( ref );\r
1575                     }\r
1576                     if ( desc != null ) {\r
1577                         desc = desc.trim();\r
1578                         desc = desc.replaceAll( "\\s+", " " );\r
1579                     }\r
1580                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1581                         for( final PhylogenyNode n : nodes ) {\r
1582                             ForesterUtil.ensurePresenceOfSequence( n );\r
1583                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1584                                     : new Annotation( ref );\r
1585                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1586                                 ann.setDesc( desc );\r
1587                             }\r
1588                             n.getNodeData().getSequence().addAnnotation( ann );\r
1589                         }\r
1590                     }\r
1591                     getMainPanel().getControlPanel().showAnnotations();\r
1592                 }\r
1593             }\r
1594         }\r
1595     }\r
1596 \r
1597     private void chooseFont() {\r
1598         final FontChooser fc = new FontChooser();\r
1599         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1600         fc.showDialog( this, "Select the Base Font" );\r
1601         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1602     }\r
1603 \r
1604     private void chooseMinimalConfidence() {\r
1605         final String s = ( String ) JOptionPane\r
1606                 .showInputDialog( this,\r
1607                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1608                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1609                                   "Minimal Confidence Value",\r
1610                                   JOptionPane.QUESTION_MESSAGE,\r
1611                                   null,\r
1612                                   null,\r
1613                                   getOptions().getMinConfidenceValue() );\r
1614         if ( !ForesterUtil.isEmpty( s ) ) {\r
1615             boolean success = true;\r
1616             double m = 0.0;\r
1617             final String m_str = s.trim();\r
1618             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1619                 try {\r
1620                     m = Double.parseDouble( m_str );\r
1621                 }\r
1622                 catch ( final Exception ex ) {\r
1623                     success = false;\r
1624                 }\r
1625             }\r
1626             else {\r
1627                 success = false;\r
1628             }\r
1629             if ( success && ( m >= 0.0 ) ) {\r
1630                 getOptions().setMinConfidenceValue( m );\r
1631             }\r
1632         }\r
1633     }\r
1634 \r
1635     private void doUpdateProcessMenu() {\r
1636         if ( _process_pool.size() > 0 ) {\r
1637             if ( _process_menu == null ) {\r
1638                 _process_menu = createMenu( "", getConfiguration() );\r
1639                 _process_menu.setForeground( Color.RED );\r
1640             }\r
1641             _process_menu.removeAll();\r
1642             final String text = "processes running: " + _process_pool.size();\r
1643             _process_menu.setText( text );\r
1644             _jmenubar.add( _process_menu );\r
1645             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1646                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1647                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1648             }\r
1649         }\r
1650         else {\r
1651             if ( _process_menu != null ) {\r
1652                 _process_menu.removeAll();\r
1653                 _jmenubar.remove( _process_menu );\r
1654             }\r
1655         }\r
1656         _jmenubar.validate();\r
1657         _jmenubar.repaint();\r
1658         repaint();\r
1659     }\r
1660 \r
1661     private String getPreviousNodeAnnotationReference() {\r
1662         return _previous_node_annotation_ref;\r
1663     }\r
1664 \r
1665     private void removeBranchColors() {\r
1666         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1667             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1668         }\r
1669     }\r
1670 \r
1671     private void removeVisualStyles() {\r
1672         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1673             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1674         }\r
1675     }\r
1676 \r
1677     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1678         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1679     }\r
1680 \r
1681     /**\r
1682      * Display the about box.\r
1683      */\r
1684     static void about() {\r
1685         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1686         about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );\r
1687         about.append( "All Rights Reserved\n" );\r
1688         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1689         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1690         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1691         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1692         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1693         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1694             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1695         }\r
1696         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1697                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1698             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1699                     + ForesterUtil.OS_VERSION + "]\n" );\r
1700         }\r
1701         final Runtime rt = java.lang.Runtime.getRuntime();\r
1702         final long free_memory = rt.freeMemory() / 1000000;\r
1703         final long total_memory = rt.totalMemory() / 1000000;\r
1704         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1705         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1706         about.append( "References:\n" );\r
1707         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1708         about.append( "For more information & download:\n" );\r
1709         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1710         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1711         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1712     }\r
1713 \r
1714     static void chooseNodeSize( final Options options, final Component parent ) {\r
1715         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1716                                                                  "Please enter the default size for node shapes.\n"\r
1717                                                                          + "[current value: "\r
1718                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1719                                                                  "Node Shape Size",\r
1720                                                                  JOptionPane.QUESTION_MESSAGE,\r
1721                                                                  null,\r
1722                                                                  null,\r
1723                                                                  options.getDefaultNodeShapeSize() );\r
1724         if ( !ForesterUtil.isEmpty( s ) ) {\r
1725             boolean success = true;\r
1726             double m = 0.0;\r
1727             final String m_str = s.trim();\r
1728             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1729                 try {\r
1730                     m = Double.parseDouble( m_str );\r
1731                 }\r
1732                 catch ( final Exception ex ) {\r
1733                     success = false;\r
1734                 }\r
1735             }\r
1736             else {\r
1737                 success = false;\r
1738             }\r
1739             if ( success && ( m >= 0.0 ) ) {\r
1740                 final short size = ForesterUtil.roundToShort( m );\r
1741                 if ( size >= 0.0 ) {\r
1742                     options.setDefaultNodeShapeSize( size );\r
1743                 }\r
1744             }\r
1745         }\r
1746     }\r
1747 \r
1748     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1749         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1750     }\r
1751 \r
1752     static JMenu createMenu( final String title, final Configuration conf ) {\r
1753         final JMenu jmenu = new JMenu( title );\r
1754         if ( !conf.isUseNativeUI() ) {\r
1755             jmenu.setFont( MainFrame.menu_font );\r
1756             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1757             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1758         }\r
1759         return jmenu;\r
1760     }\r
1761 \r
1762     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1763         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1764         if ( !configuration.isUseNativeUI() ) {\r
1765             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1766             label.setForeground( configuration.getGuiMenuTextColor() );\r
1767             label.setOpaque( true );\r
1768         }\r
1769         label.setSelected( false );\r
1770         label.setEnabled( false );\r
1771         return label;\r
1772     }\r
1773 \r
1774     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
1775         switch ( op.getDefaultNodeFill() ) {\r
1776             case GRADIENT:\r
1777                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1778                 break;\r
1779             case NONE:\r
1780                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1781                 break;\r
1782             case SOLID:\r
1783                 op.setDefaultNodeFill( NodeFill.NONE );\r
1784                 break;\r
1785             default:\r
1786                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1787         }\r
1788     }\r
1789 \r
1790     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
1791         switch ( op.getDefaultNodeShape() ) {\r
1792             case CIRCLE:\r
1793                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1794                 break;\r
1795             case RECTANGLE:\r
1796                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1797                 break;\r
1798             default:\r
1799                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1800         }\r
1801     }\r
1802 \r
1803     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1804         switch ( op.getOvPlacement() ) {\r
1805             case LOWER_LEFT:\r
1806                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1807                 break;\r
1808             case LOWER_RIGHT:\r
1809                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1810                 break;\r
1811             case UPPER_LEFT:\r
1812                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1813                 break;\r
1814             case UPPER_RIGHT:\r
1815                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1816                 break;\r
1817             default:\r
1818                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1819         }\r
1820         if ( tree_panel != null ) {\r
1821             tree_panel.updateOvSettings();\r
1822         }\r
1823     }\r
1824 \r
1825     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
1826         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
1827             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1828                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
1829         }\r
1830         else {\r
1831             mi.setText( "Cycle Node Shape Fill Type..." );\r
1832         }\r
1833     }\r
1834 \r
1835     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
1836         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
1837             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1838                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
1839         }\r
1840         else {\r
1841             mi.setText( "Cycle Node Shape Fill Type..." );\r
1842         }\r
1843     }\r
1844 \r
1845     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
1846         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
1847             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
1848         }\r
1849         else {\r
1850             mi.setText( "Cycle Overview Placement..." );\r
1851         }\r
1852     }\r
1853 \r
1854     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
1855         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
1856             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
1857                     + ")" );\r
1858         }\r
1859         else {\r
1860             mi.setText( "Select Color Scheme..." );\r
1861         }\r
1862     }\r
1863 \r
1864     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
1865         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
1866     }\r
1867 \r
1868     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
1869         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
1870             mi.setEnabled( true );\r
1871         }\r
1872         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
1873             mi.setEnabled( true );\r
1874         }\r
1875         else {\r
1876             mi.setEnabled( false );\r
1877         }\r
1878         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
1879     }\r
1880 \r
1881     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
1882         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
1883     }\r
1884 \r
1885     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,\r
1886                                                            final JCheckBoxMenuItem scale,\r
1887                                                            final JCheckBoxMenuItem branch_lengths,\r
1888                                                            final JRadioButtonMenuItem non_lined_up,\r
1889                                                            final JRadioButtonMenuItem uniform_clado,\r
1890                                                            final JRadioButtonMenuItem nonuniform_clado,\r
1891                                                            final JCheckBoxMenuItem label_direction_cbmi ) {\r
1892         final TreePanel tree_panel = main_panel.getCurrentTreePanel();\r
1893         final ControlPanel control = main_panel.getControlPanel();\r
1894         final Options options = main_panel.getOptions();\r
1895         scale.setSelected( options.isShowScale() );\r
1896         branch_lengths.setSelected( options.isShowBranchLengthValues() );\r
1897         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1898         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {\r
1899             scale.setSelected( false );\r
1900             scale.setEnabled( false );\r
1901             branch_lengths.setSelected( false );\r
1902             branch_lengths.setEnabled( false );\r
1903         }\r
1904         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {\r
1905             scale.setSelected( false );\r
1906             scale.setEnabled( false );\r
1907             branch_lengths.setEnabled( true );\r
1908         }\r
1909         else {\r
1910             scale.setEnabled( true );\r
1911             branch_lengths.setEnabled( true );\r
1912         }\r
1913         if ( ( tree_panel != null )\r
1914                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )\r
1915                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1916                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1917             branch_lengths.setSelected( false );\r
1918             branch_lengths.setEnabled( false );\r
1919         }\r
1920         if ( tree_panel != null ) {\r
1921             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )\r
1922                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {\r
1923                 non_lined_up.setEnabled( false );\r
1924                 uniform_clado.setEnabled( false );\r
1925                 nonuniform_clado.setEnabled( false );\r
1926             }\r
1927             else {\r
1928                 non_lined_up.setEnabled( true );\r
1929                 uniform_clado.setEnabled( true );\r
1930                 nonuniform_clado.setEnabled( true );\r
1931             }\r
1932         }\r
1933         else {\r
1934             if ( ( tree_panel != null )\r
1935                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1936                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1937                 branch_lengths.setSelected( false );\r
1938                 branch_lengths.setEnabled( false );\r
1939             }\r
1940             if ( ( tree_panel != null )\r
1941                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel\r
1942                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {\r
1943                 non_lined_up.setEnabled( false );\r
1944             }\r
1945             else {\r
1946                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1947                 non_lined_up.setEnabled( true );\r
1948             }\r
1949         }\r
1950         label_direction_cbmi.setEnabled( true );\r
1951         if ( tree_panel != null ) {\r
1952             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )\r
1953                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1954                 label_direction_cbmi.setEnabled( false );\r
1955             }\r
1956             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {\r
1957                 scale.setSelected( false );\r
1958                 scale.setEnabled( false );\r
1959             }\r
1960         }\r
1961     }\r
1962 \r
1963     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
1964         for( final TreePanel tree_panel : treepanels ) {\r
1965             tree_panel.setTextAntialias();\r
1966         }\r
1967     }\r
1968 }\r