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