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

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