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.JFileChooser;\r
  45 import javax.swing.JFrame;\r
  46 import javax.swing.JLabel;\r
  47 import javax.swing.JMenu;\r
  48 import javax.swing.JMenuBar;\r
  49 import javax.swing.JMenuItem;\r
  50 import javax.swing.JOptionPane;\r
  51 import javax.swing.JPanel;\r
  52 import javax.swing.JRadioButtonMenuItem;\r
  53 import javax.swing.JTextField;\r
  54 import javax.swing.SwingUtilities;\r
  55 \r
  56 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
  57 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
  58 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
  59 import org.forester.archaeopteryx.tools.InferenceManager;\r
  60 import org.forester.archaeopteryx.tools.ProcessPool;\r
  61 import org.forester.archaeopteryx.tools.ProcessRunning;\r
  62 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;\r
  63 import org.forester.archaeopteryx.webservices.WebservicesManager;\r
  64 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
  65 import org.forester.phylogeny.Phylogeny;\r
  66 import org.forester.phylogeny.PhylogenyMethods;\r
  67 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
  68 import org.forester.phylogeny.PhylogenyNode;\r
  69 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
  70 import org.forester.phylogeny.data.Annotation;\r
  71 import org.forester.phylogeny.data.NodeDataField;\r
  72 import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
  73 import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
  74 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
  75 import org.forester.sdi.GSDI;\r
  76 import org.forester.sdi.GSDIR;\r
  77 import org.forester.sdi.SDIException;\r
  78 import org.forester.util.ForesterConstants;\r
  79 import org.forester.util.ForesterUtil;\r
  80 import org.forester.util.WindowsUtils;\r
  81 \r
  82 public abstract class MainFrame extends JFrame implements ActionListener {\r
  83 \r
  84     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
  85     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                                //TODO //FIXME\r
  86     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
  87     private static final long   serialVersionUID                        = 3655000897845508358L;\r
  88     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
  89                                                                                     Font.PLAIN,\r
  90                                                                                     10 );\r
  91     static final String         TYPE_MENU_HEADER                        = "Type";\r
  92     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
  93     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
  94     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
  95     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
  96     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
  97     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
  98     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                          //TODO\r
  99     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                          //TODO\r
 100     static final String         OPTIONS_HEADER                          = "Options";\r
 101     static final String         SEARCH_SUBHEADER                        = "Search:";\r
 102     static final String         DISPLAY_SUBHEADER                       = "Display:";\r
 103     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
 104     static final String         SEARCH_REGEX_LABEL                      = "Search with Regular Expressions";\r
 105     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
 106     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
 107     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
 108     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
 109     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
 110     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
 111     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
 112     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
 113     static final String         SEARCH_WITH_REGEX_TIP                   = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits.";\r
 114     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 115     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 116     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 117     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "Shapes for External Nodes";\r
 118     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Shapes for Internal Nodes";\r
 119     static final String         DISPLAY_NODE_BOXES_LABEL_MARKED         = "Shapes for Nodes with Visual Data";\r
 120     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 121     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 122     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 123     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 124     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 125     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
 126     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 127     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 128     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 129     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 130     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 131     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 132     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 133     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 134     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 135     static final String         RIGHT_LINE_UP_DOMAINS                   = "Right-align Domain Architectures";\r
 136     static final String         LINE_UP_RENDERABLE_DATA                 = "Line Up Diagrams (such as Domain Architectures)";\r
 137     JMenuBar                    _jmenubar;\r
 138     JMenu                       _file_jmenu;\r
 139     JMenu                       _tools_menu;\r
 140     JMenu                       _view_jmenu;\r
 141     JMenu                       _options_jmenu;\r
 142     JMenu                       _font_size_menu;\r
 143     JMenu                       _help_jmenu;\r
 144     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 145     // Analysis menu\r
 146     JMenu                       _analysis_menu;\r
 147     JMenuItem                   _load_species_tree_item;\r
 148     JMenuItem                   _gsdi_item;\r
 149     JMenuItem                   _gsdir_item;\r
 150     JMenuItem                   _lineage_inference;\r
 151     // file menu:\r
 152     JMenuItem                   _open_item;\r
 153     JMenuItem                   _open_url_item;\r
 154     JMenuItem                   _save_item;\r
 155     JMenuItem                   _save_all_item;\r
 156     JMenuItem                   _close_item;\r
 157     JMenuItem                   _exit_item;\r
 158     JMenuItem                   _new_item;\r
 159    JMenuItem                        _print_item;\r
 160     JMenuItem                        _write_to_pdf_item;\r
 161     JMenuItem                        _write_to_jpg_item;\r
 162     JMenuItem                        _write_to_gif_item;\r
 163     JMenuItem                        _write_to_tif_item;\r
 164    JMenuItem                        _write_to_png_item;\r
 165     JMenuItem                        _write_to_bmp_item;\r
 166     // tools menu:\r
 167     JMenuItem                   _midpoint_root_item;\r
 168     JMenuItem                   _taxcolor_item;\r
 169     JMenuItem                   _confcolor_item;\r
 170     JMenuItem                   _color_rank_jmi;\r
 171     JMenuItem                   _collapse_species_specific_subtrees;\r
 172     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 173     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 174     JMenuItem                   _obtain_seq_information_jmi;\r
 175     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 176     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 177     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 178     JMenuItem                   _annotate_item;\r
 179     JMenuItem                   _remove_branch_color_item;\r
 180     JMenuItem                   _remove_visual_styles_item;\r
 181     JMenuItem                   _delete_selected_nodes_item;\r
 182     JMenuItem                   _delete_not_selected_nodes_item;\r
 183     // font size menu:\r
 184     JMenuItem                   _super_tiny_fonts_item;\r
 185     JMenuItem                   _tiny_fonts_item;\r
 186     JMenuItem                   _small_fonts_item;\r
 187     JMenuItem                   _medium_fonts_item;\r
 188     JMenuItem                   _large_fonts_item;\r
 189     // options menu:\r
 190     // _  screen and print\r
 191     JMenuItem                   _choose_font_mi;\r
 192     JMenuItem                   _switch_colors_mi;\r
 193     JCheckBoxMenuItem           _label_direction_cbmi;\r
 194     // _  screen display\r
 195     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 196     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 197     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 198     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 199     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 200     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 201     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                                      //TODO fix me\r
 202     JCheckBoxMenuItem           _show_overview_cbmi;\r
 203     JCheckBoxMenuItem           _show_domain_labels;\r
 204     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 205     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 206     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 207     JMenuItem                   _overview_placment_mi;\r
 208     JMenuItem                   _choose_minimal_confidence_mi;\r
 209     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 210     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 211     JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;\r
 212     JMenuItem                   _cycle_node_shape_mi;\r
 213     JMenuItem                   _cycle_node_fill_mi;\r
 214     JMenuItem                   _choose_node_size_mi;\r
 215     JMenuItem                   _cycle_data_return;\r
 216     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 217     JCheckBoxMenuItem           _right_line_up_domains_cbmi;\r
 218     JCheckBoxMenuItem           _line_up_renderable_data_cbmi;\r
 219     // _  print\r
 220     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 221     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 222     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 223     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 224     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 225     JMenuItem                   _print_size_mi;\r
 226     JMenuItem                   _choose_pdf_width_mi;\r
 227     // _  parsing\r
 228     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 229     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 230     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 231     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 232     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 233     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 234     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 235     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 236     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 237     // _  search\r
 238     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 239     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 240     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 241     JCheckBoxMenuItem           _search_with_regex_cbmi;\r
 242     // type menu:\r
 243     JMenu                       _type_menu;\r
 244     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 245     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 246     JCheckBoxMenuItem           _curved_type_cbmi;\r
 247     JCheckBoxMenuItem           _convex_type_cbmi;\r
 248     JCheckBoxMenuItem           _euro_type_cbmi;\r
 249     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 250     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 251     JCheckBoxMenuItem           _circular_type_cbmi;\r
 252     // view as text menu:\r
 253     JMenuItem                   _view_as_NH_item;\r
 254     JMenuItem                   _view_as_XML_item;\r
 255     JMenuItem                   _view_as_nexus_item;\r
 256     JMenuItem                   _display_basic_information_item;\r
 257     // help menu:\r
 258     JMenuItem                   _about_item;\r
 259     JMenuItem                   _help_item;\r
 260     JMenuItem                   _website_item;\r
 261     JMenuItem                   _phyloxml_website_item;\r
 262     JMenuItem                   _phyloxml_ref_item;\r
 263     JMenuItem                   _aptx_ref_item;\r
 264     //\r
 265     JFileChooser               _writetopdf_filechooser;\r
 266     File                             _current_dir;\r
 267     \r
 268     // process menu:\r
 269     JMenu                       _process_menu;\r
 270     // Handy pointers to child components:\r
 271     MainPanel                   _mainpanel;\r
 272     Container                   _contentpane;\r
 273     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                                  ;\r
 274     Configuration               _configuration;\r
 275     Options                     _options;\r
 276     private Phylogeny           _species_tree;\r
 277     InferenceManager            _inference_manager;\r
 278     final ProcessPool           _process_pool;\r
 279     private String              _previous_node_annotation_ref;\r
 280 \r
 281     MainFrame() {\r
 282         _process_pool = ProcessPool.createInstance();\r
 283         _writetopdf_filechooser = new JFileChooser();\r
 284     }\r
 285 \r
 286     /**\r
 287      * Action performed.\r
 288      */\r
 289     @Override\r
 290     public void actionPerformed( final ActionEvent e ) {\r
 291         final Object o = e.getSource();\r
 292         boolean is_applet = false;\r
 293         JApplet applet = null;\r
 294         if ( getCurrentTreePanel() != null ) {\r
 295             is_applet = getCurrentTreePanel().isApplet();\r
 296             if ( is_applet ) {\r
 297                 applet = getCurrentTreePanel().obtainApplet();\r
 298             }\r
 299         }\r
 300         if ( o == _exit_item ) {\r
 301             close();\r
 302         }\r
 303         else if ( o == _gsdi_item ) {\r
 304             if ( isSubtreeDisplayed() ) {\r
 305                 return;\r
 306             }\r
 307             executeGSDI();\r
 308         }\r
 309         else if ( o == _gsdir_item ) {\r
 310             if ( isSubtreeDisplayed() ) {\r
 311                 return;\r
 312             }\r
 313             executeGSDIR();\r
 314         }\r
 315         else if ( o == _taxcolor_item ) {\r
 316             taxColor();\r
 317         }\r
 318         else if ( o == _confcolor_item ) {\r
 319             confColor();\r
 320         }\r
 321         else if ( o == _color_rank_jmi ) {\r
 322             colorRank();\r
 323         }\r
 324         else if ( o == _collapse_species_specific_subtrees ) {\r
 325             if ( isSubtreeDisplayed() ) {\r
 326                 return;\r
 327             }\r
 328             if ( getCurrentTreePanel() != null ) {\r
 329                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 330             }\r
 331         }\r
 332         else if ( o == _remove_branch_color_item ) {\r
 333             if ( isSubtreeDisplayed() ) {\r
 334                 return;\r
 335             }\r
 336             removeBranchColors();\r
 337         }\r
 338         else if ( o == _remove_visual_styles_item ) {\r
 339             if ( isSubtreeDisplayed() ) {\r
 340                 return;\r
 341             }\r
 342             removeVisualStyles();\r
 343         }\r
 344         else if ( o == _midpoint_root_item ) {\r
 345             if ( isSubtreeDisplayed() ) {\r
 346                 return;\r
 347             }\r
 348             midpointRoot();\r
 349         }\r
 350         else if ( o == _delete_selected_nodes_item ) {\r
 351             if ( isSubtreeDisplayed() ) {\r
 352                 return;\r
 353             }\r
 354             deleteSelectedNodes( true );\r
 355         }\r
 356         else if ( o == _delete_not_selected_nodes_item ) {\r
 357             if ( isSubtreeDisplayed() ) {\r
 358                 return;\r
 359             }\r
 360             deleteSelectedNodes( false );\r
 361         }\r
 362         else if ( o == _annotate_item ) {\r
 363             annotateSequences();\r
 364         }\r
 365         else if ( o == _switch_colors_mi ) {\r
 366             switchColors();\r
 367         }\r
 368         else if ( o == _display_basic_information_item ) {\r
 369             if ( getCurrentTreePanel() != null ) {\r
 370                 displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 371             }\r
 372         }\r
 373         else if ( o == _view_as_NH_item ) {\r
 374             viewAsNH();\r
 375         }\r
 376         else if ( o == _view_as_XML_item ) {\r
 377             viewAsXML();\r
 378         }\r
 379         else if ( o == _view_as_nexus_item ) {\r
 380             viewAsNexus();\r
 381         }\r
 382         else if ( o == _super_tiny_fonts_item ) {\r
 383             if ( getCurrentTreePanel() != null ) {\r
 384                 getCurrentTreePanel().setSuperTinyFonts();\r
 385                 getCurrentTreePanel().repaint();\r
 386             }\r
 387         }\r
 388         else if ( o == _tiny_fonts_item ) {\r
 389             if ( getCurrentTreePanel() != null ) {\r
 390                 getCurrentTreePanel().setTinyFonts();\r
 391                 getCurrentTreePanel().repaint();\r
 392             }\r
 393         }\r
 394         else if ( o == _small_fonts_item ) {\r
 395             if ( getCurrentTreePanel() != null ) {\r
 396                 getCurrentTreePanel().setSmallFonts();\r
 397                 getCurrentTreePanel().repaint();\r
 398             }\r
 399         }\r
 400         else if ( o == _medium_fonts_item ) {\r
 401             if ( getCurrentTreePanel() != null ) {\r
 402                 getCurrentTreePanel().setMediumFonts();\r
 403                 getCurrentTreePanel().repaint();\r
 404             }\r
 405         }\r
 406         else if ( o == _large_fonts_item ) {\r
 407             if ( getCurrentTreePanel() != null ) {\r
 408                 getCurrentTreePanel().setLargeFonts();\r
 409                 getCurrentTreePanel().repaint();\r
 410             }\r
 411         }\r
 412         else if ( o == _choose_font_mi ) {\r
 413             chooseFont();\r
 414         }\r
 415         else if ( o == _choose_minimal_confidence_mi ) {\r
 416             chooseMinimalConfidence();\r
 417         }\r
 418         else if ( o == _choose_node_size_mi ) {\r
 419             chooseNodeSize( getOptions(), this );\r
 420         }\r
 421         else if ( o == _overview_placment_mi ) {\r
 422             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 423         }\r
 424         else if ( o == _cycle_node_fill_mi ) {\r
 425             MainFrame.cycleNodeFill( getOptions() );\r
 426         }\r
 427         else if ( o == _cycle_node_shape_mi ) {\r
 428             MainFrame.cycleNodeShape( getOptions() );\r
 429         }\r
 430         else if ( o == _cycle_data_return ) {\r
 431             MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );\r
 432         }\r
 433         else if ( o == _screen_antialias_cbmi ) {\r
 434             updateOptions( getOptions() );\r
 435             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 436         }\r
 437         else if ( o == _background_gradient_cbmi ) {\r
 438             updateOptions( getOptions() );\r
 439         }\r
 440         else if ( o == _show_domain_labels ) {\r
 441             updateOptions( getOptions() );\r
 442         }\r
 443         else if ( o == _show_annotation_ref_source ) {\r
 444             updateOptions( getOptions() );\r
 445         }\r
 446         else if ( o == _abbreviate_scientific_names ) {\r
 447             updateOptions( getOptions() );\r
 448         }\r
 449         else if ( o == _color_labels_same_as_parent_branch ) {\r
 450             updateOptions( getOptions() );\r
 451         }\r
 452         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 453             updateOptions( getOptions() );\r
 454         }\r
 455         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 456             updateOptions( getOptions() );\r
 457         }\r
 458         else if ( o == _show_default_node_shapes_for_marked_cbmi ) {\r
 459             updateOptions( getOptions() );\r
 460         }\r
 461         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 462             updateOptions( getOptions() );\r
 463             showWhole();\r
 464         }\r
 465         else if ( o == _uniform_cladograms_rbmi ) {\r
 466             updateOptions( getOptions() );\r
 467             showWhole();\r
 468         }\r
 469         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 470             updateOptions( getOptions() );\r
 471             showWhole();\r
 472         }\r
 473         else if ( o == _search_case_senstive_cbmi ) {\r
 474             updateOptions( getOptions() );\r
 475             getMainPanel().getControlPanel().search0();\r
 476             getMainPanel().getControlPanel().search1();\r
 477         }\r
 478         else if ( o == _search_whole_words_only_cbmi ) {\r
 479             if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {\r
 480                 _search_with_regex_cbmi.setSelected( false );\r
 481             }\r
 482             updateOptions( getOptions() );\r
 483             getMainPanel().getControlPanel().search0();\r
 484             getMainPanel().getControlPanel().search1();\r
 485         }\r
 486         else if ( o == _inverse_search_result_cbmi ) {\r
 487             updateOptions( getOptions() );\r
 488             getMainPanel().getControlPanel().search0();\r
 489             getMainPanel().getControlPanel().search1();\r
 490         }\r
 491         else if ( o == _search_with_regex_cbmi ) {\r
 492             if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
 493                 _search_whole_words_only_cbmi.setSelected( false );\r
 494             }\r
 495             if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {\r
 496                 _search_case_senstive_cbmi.setSelected( true );\r
 497             }\r
 498             updateOptions( getOptions() );\r
 499             getMainPanel().getControlPanel().search0();\r
 500             getMainPanel().getControlPanel().search1();\r
 501         }\r
 502         else if ( o == _show_scale_cbmi ) {\r
 503             updateOptions( getOptions() );\r
 504         }\r
 505         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 506             updateOptions( getOptions() );\r
 507         }\r
 508         else if ( o == _show_confidence_stddev_cbmi ) {\r
 509             updateOptions( getOptions() );\r
 510         }\r
 511         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 512             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 513                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 514             }\r
 515             updateOptions( getOptions() );\r
 516         }\r
 517         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 518             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 519                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 520             }\r
 521             updateOptions( getOptions() );\r
 522         }\r
 523         else if ( o == _label_direction_cbmi ) {\r
 524             updateOptions( getOptions() );\r
 525         }\r
 526         else if ( o == _show_overview_cbmi ) {\r
 527             updateOptions( getOptions() );\r
 528             if ( getCurrentTreePanel() != null ) {\r
 529                 getCurrentTreePanel().updateOvSizes();\r
 530             }\r
 531         }\r
 532         else if ( o == _line_up_renderable_data_cbmi ) {\r
 533             if ( !_line_up_renderable_data_cbmi.isSelected() ) {\r
 534                 _right_line_up_domains_cbmi.setSelected( false );\r
 535             }\r
 536             updateOptions( getOptions() );\r
 537         }\r
 538         else if ( o == _right_line_up_domains_cbmi ) {\r
 539             if ( _right_line_up_domains_cbmi.isSelected() ) {\r
 540                 _line_up_renderable_data_cbmi.setSelected( true );\r
 541             }\r
 542             updateOptions( getOptions() );\r
 543         }\r
 544         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 545                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 546                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 547             typeChanged( o );\r
 548         }\r
 549         else if ( o == _about_item ) {\r
 550             about();\r
 551         }\r
 552         else if ( o == _help_item ) {\r
 553             try {\r
 554                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
 555             }\r
 556             catch ( final IOException e1 ) {\r
 557                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 558             }\r
 559         }\r
 560         else if ( o == _website_item ) {\r
 561             try {\r
 562                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 563             }\r
 564             catch ( final IOException e1 ) {\r
 565                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 566             }\r
 567         }\r
 568         else if ( o == _phyloxml_website_item ) {\r
 569             try {\r
 570                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 571             }\r
 572             catch ( final IOException e1 ) {\r
 573                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 574             }\r
 575         }\r
 576         else if ( o == _aptx_ref_item ) {\r
 577             try {\r
 578                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 579             }\r
 580             catch ( final IOException e1 ) {\r
 581                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 582             }\r
 583         }\r
 584         else if ( o == _phyloxml_ref_item ) {\r
 585             try {\r
 586                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 587             }\r
 588             catch ( final IOException e1 ) {\r
 589                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 590             }\r
 591         }\r
 592         else if ( o == _write_to_pdf_item ) {\r
 593             writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
 594         }\r
 595         else {\r
 596             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 597                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 598                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 599                         readPhylogeniesFromWebservice( i );\r
 600                     }\r
 601                 }\r
 602             }\r
 603         }\r
 604         _contentpane.repaint();\r
 605     }\r
 606 \r
 607     \r
 608     void setCurrentDir( final File current_dir ) {\r
 609         _current_dir = current_dir;\r
 610     } \r
 611     \r
 612    void writeToPdf( final Phylogeny t ) {\r
 613         if ( ( t == null ) || t.isEmpty() ) {\r
 614             return;\r
 615         }\r
 616         String initial_filename = "";\r
 617         if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
 618             initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
 619         }\r
 620         if ( initial_filename.indexOf( '.' ) > 0 ) {\r
 621             initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
 622         }\r
 623         initial_filename = initial_filename + ".pdf";\r
 624         _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
 625         final File my_dir = getCurrentDir();\r
 626         if ( my_dir != null ) {\r
 627             _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
 628         }\r
 629         final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
 630         File file = _writetopdf_filechooser.getSelectedFile();\r
 631         setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
 632         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
 633             if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
 634                 file = new File( file.toString() + ".pdf" );\r
 635             }\r
 636             if ( file.exists() ) {\r
 637                 final int i = JOptionPane.showConfirmDialog( this,\r
 638                                                              file + " already exists. Overwrite?",\r
 639                                                              "WARNING",\r
 640                                                              JOptionPane.OK_CANCEL_OPTION,\r
 641                                                              JOptionPane.WARNING_MESSAGE );\r
 642                 if ( i != JOptionPane.OK_OPTION ) {\r
 643                     return;\r
 644                 }\r
 645             }\r
 646             printPhylogenyToPdf( file.toString() );\r
 647         }\r
 648     }\r
 649 \r
 650    \r
 651     void printPhylogenyToPdf( final String file_name ) {\r
 652        if ( !getOptions().isPrintUsingActualSize() ) {\r
 653            getCurrentTreePanel()\r
 654            .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );\r
 655            getCurrentTreePanel().resetPreferredSize();\r
 656            getCurrentTreePanel().repaint();\r
 657        }\r
 658        String pdf_written_to = "";\r
 659        boolean error = false;\r
 660        try {\r
 661            if ( getOptions().isPrintUsingActualSize() ) {\r
 662                pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
 663                                                                  getCurrentTreePanel(),\r
 664                                                                  getCurrentTreePanel().getWidth(),\r
 665                                                                  getCurrentTreePanel().getHeight() );\r
 666            }\r
 667            else {\r
 668                pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
 669                        .getPrintSizeX(), getOptions().getPrintSizeY() );\r
 670            }\r
 671        }\r
 672        catch ( final IOException e ) {\r
 673            error = true;\r
 674            JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
 675        }\r
 676        if ( !error ) {\r
 677            if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
 678                JOptionPane.showMessageDialog( this,\r
 679                                               "Wrote PDF to: " + pdf_written_to,\r
 680                                               "Information",\r
 681                                               JOptionPane.INFORMATION_MESSAGE );\r
 682            }\r
 683            else {\r
 684                JOptionPane.showMessageDialog( this,\r
 685                                               "There was an unknown problem when attempting to write to PDF file: \""\r
 686                                                       + file_name + "\"",\r
 687                                               "Error",\r
 688                                               JOptionPane.ERROR_MESSAGE );\r
 689            }\r
 690        }\r
 691        if ( !getOptions().isPrintUsingActualSize() ) {\r
 692            getControlPanel().showWhole();\r
 693        }\r
 694    }\r
 695    \r
 696     ControlPanel getControlPanel() {\r
 697         return getMainPanel().getControlPanel();\r
 698     }\r
 699 \r
 700     \r
 701     File getCurrentDir() {\r
 702        if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
 703            if ( ForesterUtil.isWindows() ) {\r
 704                try {\r
 705                    _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
 706                }\r
 707                catch ( final Exception e ) {\r
 708                    _current_dir = null;\r
 709                }\r
 710            }\r
 711        }\r
 712        if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
 713            if ( System.getProperty( "user.home" ) != null ) {\r
 714                _current_dir = new File( System.getProperty( "user.home" ) );\r
 715            }\r
 716            else if ( System.getProperty( "user.dir" ) != null ) {\r
 717                _current_dir = new File( System.getProperty( "user.dir" ) );\r
 718            }\r
 719        }\r
 720        return _current_dir;\r
 721    }\r
 722     \r
 723     private void deleteSelectedNodes( final boolean delete ) {\r
 724         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
 725         if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
 726             return;\r
 727         }\r
 728         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
 729         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
 730             final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
 731             for( final PhylogenyNode n : all_selected_nodes ) {\r
 732                 if ( n.isExternal() ) {\r
 733                     nodes.add( n );\r
 734                 }\r
 735             }\r
 736         }\r
 737         String function = "Retain";\r
 738         if ( delete ) {\r
 739             function = "Delete";\r
 740         }\r
 741         if ( ( nodes == null ) || nodes.isEmpty() ) {\r
 742             JOptionPane\r
 743             .showMessageDialog( this,\r
 744                                 "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
 745                                 "No external nodes selected to " + function.toLowerCase(),\r
 746                                 JOptionPane.ERROR_MESSAGE );\r
 747             return;\r
 748         }\r
 749         final int todo = nodes.size();\r
 750         final int ext = phy.getNumberOfExternalNodes();\r
 751         int res = todo;\r
 752         if ( delete ) {\r
 753             res = ext - todo;\r
 754         }\r
 755         if ( res < 1 ) {\r
 756             JOptionPane.showMessageDialog( this,\r
 757                                            "Cannot delete all nodes",\r
 758                                            "Attempt to delete all nodes ",\r
 759                                            JOptionPane.ERROR_MESSAGE );\r
 760             return;\r
 761         }\r
 762         final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
 763                                                           + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
 764                                                           + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
 765         if ( result == JOptionPane.OK_OPTION ) {\r
 766             if ( !delete ) {\r
 767                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
 768                 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
 769                     final PhylogenyNode n = it.next();\r
 770                     if ( !nodes.contains( n ) ) {\r
 771                         to_delete.add( n );\r
 772                     }\r
 773                 }\r
 774                 for( final PhylogenyNode n : to_delete ) {\r
 775                     phy.deleteSubtree( n, true );\r
 776                 }\r
 777             }\r
 778             else {\r
 779                 for( final PhylogenyNode n : nodes ) {\r
 780                     phy.deleteSubtree( n, true );\r
 781                 }\r
 782             }\r
 783             resetSearch();\r
 784             getCurrentTreePanel().setNodeInPreorderToNull();\r
 785             phy.externalNodesHaveChanged();\r
 786             phy.clearHashIdToNodeMap();\r
 787             phy.recalculateNumberOfExternalDescendants( true );\r
 788             getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
 789             getCurrentTreePanel().setEdited( true );\r
 790             repaint();\r
 791         }\r
 792     }\r
 793 \r
 794     void resetSearch() {\r
 795         getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
 796         getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
 797         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
 798         getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
 799         getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
 800         getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
 801         getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
 802         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
 803         getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
 804         getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
 805         getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
 806         getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
 807     }\r
 808 \r
 809     public Configuration getConfiguration() {\r
 810         return _configuration;\r
 811     }\r
 812 \r
 813     /**\r
 814      * This method returns the current external node data which\r
 815      * has been selected by the user by clicking the "Return ..."\r
 816      * menu item. This method is expected to be called from Javascript or\r
 817      * something like it.\r
 818      *\r
 819      * @return current external node data as String\r
 820      */\r
 821     public String getCurrentExternalNodesDataBuffer() {\r
 822         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 823     }\r
 824 \r
 825     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 826         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 827     }\r
 828 \r
 829     public int getCurrentExternalNodesDataBufferLength() {\r
 830         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 831     }\r
 832 \r
 833     public InferenceManager getInferenceManager() {\r
 834         return _inference_manager;\r
 835     }\r
 836 \r
 837     public MainPanel getMainPanel() {\r
 838         return _mainpanel;\r
 839     }\r
 840 \r
 841     public Options getOptions() {\r
 842         return _options;\r
 843     }\r
 844 \r
 845     public ProcessPool getProcessPool() {\r
 846         return _process_pool;\r
 847     }\r
 848 \r
 849     public void showTextFrame( final String s, final String title ) {\r
 850         checkTextFrames();\r
 851         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 852     }\r
 853 \r
 854     public void showWhole() {\r
 855         _mainpanel.getControlPanel().showWhole();\r
 856     }\r
 857 \r
 858     public void updateProcessMenu() {\r
 859         // In general Swing is not thread safe.\r
 860         // See "Swing's Threading Policy".\r
 861         SwingUtilities.invokeLater( new Runnable() {\r
 862 \r
 863             @Override\r
 864             public void run() {\r
 865                 doUpdateProcessMenu();\r
 866             }\r
 867         } );\r
 868     }\r
 869 \r
 870     void activateSaveAllIfNeeded() {\r
 871         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 872             _save_all_item.setEnabled( true );\r
 873         }\r
 874         else {\r
 875             _save_all_item.setEnabled( false );\r
 876         }\r
 877     }\r
 878 \r
 879 //    void buildFileMenu() {\r
 880 //        _file_jmenu = createMenu( "File", getConfiguration() );\r
 881 //        _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 882 //        customizeJMenuItem( _exit_item );\r
 883 //        _jmenubar.add( _file_jmenu );\r
 884 //    }\r
 885     \r
 886     void buildFileMenu() {\r
 887         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
 888         \r
 889        // _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
 890        // _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
 891        // _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
 892        // _save_all_item.setEnabled( false );\r
 893        // _file_jmenu.addSeparator();\r
 894         _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
 895 //        if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
 896 //            _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
 897 //        }\r
 898 //        _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
 899 //        _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
 900 //        if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
 901 //            _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
 902 //        }\r
 903 //        if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
 904 //            _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
 905 //        }\r
 906      //   _file_jmenu.addSeparator();\r
 907       //  _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
 908         _file_jmenu.addSeparator();\r
 909 \r
 910         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 911        \r
 912        customizeJMenuItem( _save_item );\r
 913 \r
 914 // customizeJMenuItem( _close_item );\r
 915  //customizeJMenuItem( _save_all_item );\r
 916         customizeJMenuItem( _write_to_pdf_item );\r
 917 //        customizeJMenuItem( _write_to_png_item );\r
 918 //        customizeJMenuItem( _write_to_jpg_item );\r
 919 //        customizeJMenuItem( _write_to_gif_item );\r
 920 //        customizeJMenuItem( _write_to_tif_item );\r
 921 //        customizeJMenuItem( _write_to_bmp_item );\r
 922 //        customizeJMenuItem( _print_item );\r
 923         customizeJMenuItem( _exit_item );\r
 924         _jmenubar.add( _file_jmenu );\r
 925     }\r
 926 \r
 927     void buildFontSizeMenu() {\r
 928         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 929         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 930         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 931         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 932         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 933         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 934         customizeJMenuItem( _super_tiny_fonts_item );\r
 935         customizeJMenuItem( _tiny_fonts_item );\r
 936         customizeJMenuItem( _small_fonts_item );\r
 937         customizeJMenuItem( _medium_fonts_item );\r
 938         customizeJMenuItem( _large_fonts_item );\r
 939         _jmenubar.add( _font_size_menu );\r
 940     }\r
 941 \r
 942     void buildHelpMenu() {\r
 943         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 944         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
 945         _help_jmenu.addSeparator();\r
 946         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 947         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
 948         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 949         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 950         _help_jmenu.addSeparator();\r
 951         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 952         customizeJMenuItem( _help_item );\r
 953         customizeJMenuItem( _website_item );\r
 954         customizeJMenuItem( _phyloxml_website_item );\r
 955         customizeJMenuItem( _aptx_ref_item );\r
 956         customizeJMenuItem( _phyloxml_ref_item );\r
 957         customizeJMenuItem( _about_item );\r
 958         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 959         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 960         _jmenubar.add( _help_jmenu );\r
 961     }\r
 962 \r
 963     void buildTypeMenu() {\r
 964         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 965         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 966         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 967         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 968         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 969         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 970         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 971         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 972         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 973         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 974         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 975         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 976         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 977         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 978         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 979         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 980         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 981         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 982         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 983         initializeTypeMenu( getOptions() );\r
 984         _jmenubar.add( _type_menu );\r
 985     }\r
 986 \r
 987     void buildViewMenu() {\r
 988         _view_jmenu = createMenu( "View", getConfiguration() );\r
 989         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 990         _view_jmenu.addSeparator();\r
 991         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 992         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 993         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 994         customizeJMenuItem( _display_basic_information_item );\r
 995         customizeJMenuItem( _view_as_NH_item );\r
 996         customizeJMenuItem( _view_as_XML_item );\r
 997         customizeJMenuItem( _view_as_nexus_item );\r
 998         _jmenubar.add( _view_jmenu );\r
 999     }\r
1000 \r
1001     void checkTextFrames() {\r
1002         if ( _textframes.size() > 5 ) {\r
1003             try {\r
1004                 if ( _textframes.getFirst() != null ) {\r
1005                     _textframes.getFirst().removeMe();\r
1006                 }\r
1007                 else {\r
1008                     _textframes.removeFirst();\r
1009                 }\r
1010             }\r
1011             catch ( final NoSuchElementException e ) {\r
1012                 // Ignore.\r
1013             }\r
1014         }\r
1015     }\r
1016 \r
1017     void close() {\r
1018         removeAllTextFrames();\r
1019         if ( _mainpanel != null ) {\r
1020             _mainpanel.terminate();\r
1021         }\r
1022         if ( _contentpane != null ) {\r
1023             _contentpane.removeAll();\r
1024         }\r
1025         setVisible( false );\r
1026         dispose();\r
1027     }\r
1028 \r
1029     void colorRank() {\r
1030         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1031             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
1032             final String rank = ( String ) JOptionPane\r
1033                     .showInputDialog( this,\r
1034                                       "What rank should the colorization be based on",\r
1035                                       "Rank Selection",\r
1036                                       JOptionPane.QUESTION_MESSAGE,\r
1037                                       null,\r
1038                                       ranks,\r
1039                                       null );\r
1040             if ( !ForesterUtil.isEmpty( rank ) ) {\r
1041                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
1042             }\r
1043         }\r
1044     }\r
1045 \r
1046     void confColor() {\r
1047         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1048             _mainpanel.getCurrentTreePanel().confColor();\r
1049         }\r
1050     }\r
1051 \r
1052     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
1053         if ( item != null ) {\r
1054             item.setFont( MainFrame.menu_font );\r
1055             if ( !getConfiguration().isUseNativeUI() ) {\r
1056                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
1057                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
1058             }\r
1059             item.setSelected( is_selected );\r
1060             item.addActionListener( this );\r
1061         }\r
1062     }\r
1063 \r
1064     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
1065         if ( jmi != null ) {\r
1066             jmi.setFont( MainFrame.menu_font );\r
1067             if ( !getConfiguration().isUseNativeUI() ) {\r
1068                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
1069                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
1070             }\r
1071             jmi.addActionListener( this );\r
1072         }\r
1073         return jmi;\r
1074     }\r
1075 \r
1076     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
1077         if ( item != null ) {\r
1078             item.setFont( MainFrame.menu_font );\r
1079             if ( !getConfiguration().isUseNativeUI() ) {\r
1080                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
1081                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
1082             }\r
1083             item.setSelected( is_selected );\r
1084             item.addActionListener( this );\r
1085         }\r
1086     }\r
1087 \r
1088     void displayBasicInformation( final File treefile ) {\r
1089         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1090             String title = "Basic Information";\r
1091             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1092                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
1093             }\r
1094             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
1095         }\r
1096     }\r
1097 \r
1098     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
1099         try {\r
1100             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
1101         }\r
1102         catch ( final Exception ex ) {\r
1103             // Do nothing.\r
1104         }\r
1105         JOptionPane.showMessageDialog( this,\r
1106                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
1107                                        "Error during File|Open",\r
1108                                        JOptionPane.ERROR_MESSAGE );\r
1109     }\r
1110 \r
1111     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
1112         try {\r
1113             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
1114         }\r
1115         catch ( final Exception ex ) {\r
1116             // Do nothing.\r
1117         }\r
1118         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
1119     }\r
1120 \r
1121     void executeGSDI() {\r
1122         if ( !isOKforSDI( false, true ) ) {\r
1123             return;\r
1124         }\r
1125         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
1126             JOptionPane.showMessageDialog( this,\r
1127                                            "Gene tree is not rooted.",\r
1128                                            "Cannot execute GSDI",\r
1129                                            JOptionPane.ERROR_MESSAGE );\r
1130             return;\r
1131         }\r
1132         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
1133         gene_tree.setAllNodesToNotCollapse();\r
1134         gene_tree.recalculateNumberOfExternalDescendants( false );\r
1135         GSDI gsdi = null;\r
1136         final Phylogeny species_tree = getSpeciesTree().copy();\r
1137         try {\r
1138             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
1139         }\r
1140         catch ( final SDIException e ) {\r
1141             JOptionPane.showMessageDialog( this,\r
1142                                            e.getLocalizedMessage(),\r
1143                                            "Error during GSDI",\r
1144                                            JOptionPane.ERROR_MESSAGE );\r
1145             return;\r
1146         }\r
1147         catch ( final Exception e ) {\r
1148             AptxUtil.unexpectedException( e );\r
1149             return;\r
1150         }\r
1151         gene_tree.setRerootable( false );\r
1152         gene_tree.clearHashIdToNodeMap();\r
1153         gene_tree.recalculateNumberOfExternalDescendants( true );\r
1154         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
1155         getMainPanel().getControlPanel().setShowEvents( true );\r
1156         showWhole();\r
1157         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1158         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1159         showWhole();\r
1160         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1161         showWhole();\r
1162         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1163         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1164         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1165             JOptionPane.showMessageDialog( this,\r
1166                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
1167                                                    + "Potential duplications: "\r
1168                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
1169                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
1170                                                    + "Stripped gene tree nodes: "\r
1171                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1172                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
1173                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1174                                                    "GSDI successfully completed",\r
1175                                                    JOptionPane.WARNING_MESSAGE );\r
1176         }\r
1177         else {\r
1178             JOptionPane.showMessageDialog( this,\r
1179                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
1180                                                    + "Potential duplications: "\r
1181                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
1182                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
1183                                                    + "Stripped gene tree nodes: "\r
1184                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1185                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
1186                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1187                                                    "GSDI successfully completed",\r
1188                                                    JOptionPane.INFORMATION_MESSAGE );\r
1189         }\r
1190     }\r
1191 \r
1192     void executeGSDIR() {\r
1193         if ( !isOKforSDI( false, false ) ) {\r
1194             return;\r
1195         }\r
1196         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
1197         if ( ( p > 0 )\r
1198                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
1199             JOptionPane.showMessageDialog( this,\r
1200                                            "Gene tree is not completely binary",\r
1201                                            "Cannot execute GSDI",\r
1202                                            JOptionPane.ERROR_MESSAGE );\r
1203             return;\r
1204         }\r
1205         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
1206         gene_tree.setAllNodesToNotCollapse();\r
1207         gene_tree.recalculateNumberOfExternalDescendants( false );\r
1208         GSDIR gsdir = null;\r
1209         final Phylogeny species_tree = getSpeciesTree().copy();\r
1210         try {\r
1211             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
1212         }\r
1213         catch ( final SDIException e ) {\r
1214             JOptionPane.showMessageDialog( this,\r
1215                                            e.getLocalizedMessage(),\r
1216                                            "Error during GSDIR",\r
1217                                            JOptionPane.ERROR_MESSAGE );\r
1218             return;\r
1219         }\r
1220         catch ( final Exception e ) {\r
1221             AptxUtil.unexpectedException( e );\r
1222             return;\r
1223         }\r
1224         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
1225         result_gene_tree.setRerootable( false );\r
1226         result_gene_tree.clearHashIdToNodeMap();\r
1227         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
1228         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
1229         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
1230         getMainPanel().getControlPanel().setShowEvents( true );\r
1231         showWhole();\r
1232         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1233         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1234         showWhole();\r
1235         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1236         showWhole();\r
1237         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1238         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1239         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1240             JOptionPane.showMessageDialog( this,\r
1241                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1242                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1243                                                    + "Stripped gene tree nodes: "\r
1244                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1245                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1246                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1247                                                    "GSDIR successfully completed",\r
1248                                                    JOptionPane.WARNING_MESSAGE );\r
1249         }\r
1250         else {\r
1251             JOptionPane.showMessageDialog( this,\r
1252                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1253                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1254                                                    + "Stripped gene tree nodes: "\r
1255                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1256                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1257                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1258                                                    "GSDIR successfully completed",\r
1259                                                    JOptionPane.INFORMATION_MESSAGE );\r
1260         }\r
1261     }\r
1262 \r
1263     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
1264         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
1265             JOptionPane.showMessageDialog( this,\r
1266                                            "Gene tree and species tree have no species in common.",\r
1267                                            "Error during SDI",\r
1268                                            JOptionPane.ERROR_MESSAGE );\r
1269             return false;\r
1270         }\r
1271         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
1272             JOptionPane.showMessageDialog( this,\r
1273                                            "Gene tree and species tree have only one species in common.",\r
1274                                            "Error during SDI",\r
1275                                            JOptionPane.ERROR_MESSAGE );\r
1276             return false;\r
1277         }\r
1278         else {\r
1279             return true;\r
1280         }\r
1281     }\r
1282 \r
1283     TreePanel getCurrentTreePanel() {\r
1284         return getMainPanel().getCurrentTreePanel();\r
1285     }\r
1286 \r
1287     JMenu getHelpMenu() {\r
1288         return _help_jmenu;\r
1289     }\r
1290 \r
1291     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
1292         return _label_direction_cbmi;\r
1293     }\r
1294 \r
1295     JMenuBar getMenuBarOfMainFrame() {\r
1296         return _jmenubar;\r
1297     }\r
1298 \r
1299     final Phylogeny getSpeciesTree() {\r
1300         return _species_tree;\r
1301     }\r
1302 \r
1303     void initializeTypeMenu( final Options options ) {\r
1304         setTypeMenuToAllUnselected();\r
1305         switch ( options.getPhylogenyGraphicsType() ) {\r
1306             case CONVEX:\r
1307                 _convex_type_cbmi.setSelected( true );\r
1308                 break;\r
1309             case CURVED:\r
1310                 _curved_type_cbmi.setSelected( true );\r
1311                 break;\r
1312             case EURO_STYLE:\r
1313                 _euro_type_cbmi.setSelected( true );\r
1314                 break;\r
1315             case ROUNDED:\r
1316                 _rounded_type_cbmi.setSelected( true );\r
1317                 break;\r
1318             case TRIANGULAR:\r
1319                 _triangular_type_cbmi.setSelected( true );\r
1320                 break;\r
1321             case UNROOTED:\r
1322                 _unrooted_type_cbmi.setSelected( true );\r
1323                 break;\r
1324             case CIRCULAR:\r
1325                 _circular_type_cbmi.setSelected( true );\r
1326                 break;\r
1327             default:\r
1328                 _rectangular_type_cbmi.setSelected( true );\r
1329                 break;\r
1330         }\r
1331     }\r
1332 \r
1333     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1334         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1335             return false;\r
1336         }\r
1337         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1338             JOptionPane.showMessageDialog( this,\r
1339                                            "No species tree loaded",\r
1340                                            "Cannot execute GSDI",\r
1341                                            JOptionPane.ERROR_MESSAGE );\r
1342             return false;\r
1343         }\r
1344         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1345             JOptionPane.showMessageDialog( this,\r
1346                                            "Species tree is not completely binary",\r
1347                                            "Cannot execute GSDI",\r
1348                                            JOptionPane.ERROR_MESSAGE );\r
1349             return false;\r
1350         }\r
1351         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1352             JOptionPane.showMessageDialog( this,\r
1353                                            "Gene tree is not completely binary",\r
1354                                            "Cannot execute GSDI",\r
1355                                            JOptionPane.ERROR_MESSAGE );\r
1356             return false;\r
1357         }\r
1358         else {\r
1359             return true;\r
1360         }\r
1361     }\r
1362 \r
1363     boolean isSubtreeDisplayed() {\r
1364         if ( getCurrentTreePanel() != null ) {\r
1365             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1366                 JOptionPane\r
1367                 .showMessageDialog( this,\r
1368                                     "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1369                                     "Operation can not be exectuted on a sub-tree",\r
1370                                     JOptionPane.WARNING_MESSAGE );\r
1371                 return true;\r
1372             }\r
1373         }\r
1374         return false;\r
1375     }\r
1376 \r
1377     void midpointRoot() {\r
1378         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1379             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1380         }\r
1381     }\r
1382 \r
1383     void readPhylogeniesFromWebservice( final int i ) {\r
1384         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1385         new Thread( reader ).start();\r
1386     }\r
1387 \r
1388     void removeAllTextFrames() {\r
1389         for( final TextFrame tf : _textframes ) {\r
1390             if ( tf != null ) {\r
1391                 tf.close();\r
1392             }\r
1393         }\r
1394         _textframes.clear();\r
1395     }\r
1396 \r
1397     void setConfiguration( final Configuration configuration ) {\r
1398         _configuration = configuration;\r
1399     }\r
1400 \r
1401     void setInferenceManager( final InferenceManager i ) {\r
1402         _inference_manager = i;\r
1403     }\r
1404 \r
1405     void setOptions( final Options options ) {\r
1406         _options = options;\r
1407     }\r
1408 \r
1409     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1410         setTypeMenuToAllUnselected();\r
1411         switch ( type ) {\r
1412             case CIRCULAR:\r
1413                 _circular_type_cbmi.setSelected( true );\r
1414                 break;\r
1415             case CONVEX:\r
1416                 _convex_type_cbmi.setSelected( true );\r
1417                 break;\r
1418             case CURVED:\r
1419                 _curved_type_cbmi.setSelected( true );\r
1420                 break;\r
1421             case EURO_STYLE:\r
1422                 _euro_type_cbmi.setSelected( true );\r
1423                 break;\r
1424             case ROUNDED:\r
1425                 _rounded_type_cbmi.setSelected( true );\r
1426                 break;\r
1427             case RECTANGULAR:\r
1428                 _rectangular_type_cbmi.setSelected( true );\r
1429                 break;\r
1430             case TRIANGULAR:\r
1431                 _triangular_type_cbmi.setSelected( true );\r
1432                 break;\r
1433             case UNROOTED:\r
1434                 _unrooted_type_cbmi.setSelected( true );\r
1435                 break;\r
1436             default:\r
1437                 throw new IllegalArgumentException( "unknown type: " + type );\r
1438         }\r
1439     }\r
1440 \r
1441     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1442         _species_tree = species_tree;\r
1443     }\r
1444 \r
1445     void setTypeMenuToAllUnselected() {\r
1446         _convex_type_cbmi.setSelected( false );\r
1447         _curved_type_cbmi.setSelected( false );\r
1448         _euro_type_cbmi.setSelected( false );\r
1449         _rounded_type_cbmi.setSelected( false );\r
1450         _triangular_type_cbmi.setSelected( false );\r
1451         _rectangular_type_cbmi.setSelected( false );\r
1452         _unrooted_type_cbmi.setSelected( false );\r
1453         _circular_type_cbmi.setSelected( false );\r
1454     }\r
1455 \r
1456     void switchColors() {\r
1457         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1458         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1459         csc.setVisible( true );\r
1460     }\r
1461 \r
1462     void taxColor() {\r
1463         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1464             _mainpanel.getCurrentTreePanel().taxColor();\r
1465         }\r
1466     }\r
1467 \r
1468     void typeChanged( final Object o ) {\r
1469         updateTypeCheckboxes( getOptions(), o );\r
1470         updateOptions( getOptions() );\r
1471         if ( getCurrentTreePanel() != null ) {\r
1472             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1473             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1474             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1475                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1476                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1477                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1478                 getCurrentTreePanel().getControlPanel().showWhole();\r
1479             }\r
1480             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1481                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1482             }\r
1483             else {\r
1484                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1485             }\r
1486             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1487             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1488             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1489                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1490                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1491                 }\r
1492                 else {\r
1493                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1494                 }\r
1495             }\r
1496         }\r
1497     }\r
1498 \r
1499     void updateOptions( final Options options ) {\r
1500         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1501         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1502                                             && _background_gradient_cbmi.isSelected() );\r
1503         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1504         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1505                                             && _show_annotation_ref_source.isSelected() );\r
1506         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1507                                                    && _abbreviate_scientific_names.isSelected() );\r
1508         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1509                                                   && _color_labels_same_as_parent_branch.isSelected() );\r
1510         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1511                                                   && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1512         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1513                                                   && _show_default_node_shapes_external_cbmi.isSelected() );\r
1514         options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
1515                                                         && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
1516         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1517             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1518         }\r
1519         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1520             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1521         }\r
1522         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1523             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1524         }\r
1525         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1526                                         && _search_case_senstive_cbmi.isSelected() );\r
1527         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1528             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1529         }\r
1530         if ( _label_direction_cbmi != null ) {\r
1531             if ( _label_direction_cbmi.isSelected() ) {\r
1532                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1533             }\r
1534             else {\r
1535                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1536             }\r
1537         }\r
1538         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1539         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1540                                          && _show_confidence_stddev_cbmi.isSelected() );\r
1541         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1542             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1543         }\r
1544         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1545                                          && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1546         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1547                                                   && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1548         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1549         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1550                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1551             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1552         }\r
1553         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1554                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1555             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1556         }\r
1557         else {\r
1558             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1559         }\r
1560         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1561                                        && _print_black_and_white_cbmi.isSelected() );\r
1562         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1563                                                             && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1564         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1565             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1566         }\r
1567         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1568             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1569         }\r
1570         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1571             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1572         }\r
1573         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1574             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1575         }\r
1576         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1577                                                   && _replace_underscores_cbmi.isSelected() );\r
1578         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1579                                                   && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1580         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1581                                         && _search_whole_words_only_cbmi.isSelected() );\r
1582         options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
1583         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1584                                         && _inverse_search_result_cbmi.isSelected() );\r
1585         if ( _graphics_export_visible_only_cbmi != null ) {\r
1586             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1587             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1588                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1589                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1590             }\r
1591             else {\r
1592                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1593             }\r
1594         }\r
1595         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1596             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1597         }\r
1598         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1599             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1600         }\r
1601         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1602             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1603         }\r
1604         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1605             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1606         }\r
1607         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1608             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1609         }\r
1610         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1611             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1612         }\r
1613         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1614             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1615         }\r
1616         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1617             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1618         }\r
1619         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
1620             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
1621         }\r
1622         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
1623             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
1624         }\r
1625     }\r
1626 \r
1627     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1628         setTypeMenuToAllUnselected();\r
1629         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1630     }\r
1631 \r
1632     void viewAsNexus() {\r
1633         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1634             String title = "Nexus";\r
1635             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1636                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1637             }\r
1638             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1639                            title );\r
1640         }\r
1641     }\r
1642 \r
1643     void viewAsNH() {\r
1644         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1645             String title = "New Hampshire";\r
1646             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1647                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1648             }\r
1649             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1650                                                                             .getNhConversionSupportValueStyle() ),\r
1651                                                                             title );\r
1652         }\r
1653     }\r
1654 \r
1655     void viewAsXML() {\r
1656         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1657             String title = "phyloXML";\r
1658             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1659                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1660             }\r
1661             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1662         }\r
1663     }\r
1664 \r
1665     private void annotateSequences() {\r
1666         if ( getCurrentTreePanel() != null ) {\r
1667             List<PhylogenyNode> nodes = null;\r
1668             if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
1669                     || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
1670                 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
1671             }\r
1672             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1673                 JOptionPane\r
1674                 .showMessageDialog( this,\r
1675                                     "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1676                                     "No nodes selected for annotation",\r
1677                                     JOptionPane.ERROR_MESSAGE );\r
1678                 return;\r
1679             }\r
1680             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1681             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1682                 final JTextField ref_field = new JTextField( 10 );\r
1683                 final JTextField desc_filed = new JTextField( 20 );\r
1684                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1685                         : getPreviousNodeAnnotationReference() );\r
1686                 final JPanel my_panel = new JPanel();\r
1687                 my_panel.add( new JLabel( "Reference " ) );\r
1688                 my_panel.add( ref_field );\r
1689                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1690                 my_panel.add( new JLabel( "Description " ) );\r
1691                 my_panel.add( desc_filed );\r
1692                 final int result = JOptionPane.showConfirmDialog( null,\r
1693                                                                   my_panel,\r
1694                                                                   "Enter the sequence annotation(s) for the "\r
1695                                                                           + nodes.size() + " selected nodes",\r
1696                                                                           JOptionPane.OK_CANCEL_OPTION );\r
1697                 if ( result == JOptionPane.OK_OPTION ) {\r
1698                     String ref = ref_field.getText();\r
1699                     String desc = desc_filed.getText();\r
1700                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1701                         ref = ref.trim();\r
1702                         ref = ref.replaceAll( "\\s+", " " );\r
1703                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1704                                 || ( ref.length() < 3 ) ) {\r
1705                             JOptionPane.showMessageDialog( this,\r
1706                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1707                                                            "Illegal Format for Annotation Reference",\r
1708                                                            JOptionPane.ERROR_MESSAGE );\r
1709                             return;\r
1710                         }\r
1711                     }\r
1712                     if ( ref != null ) {\r
1713                         setPreviousNodeAnnotationReference( ref );\r
1714                     }\r
1715                     if ( desc != null ) {\r
1716                         desc = desc.trim();\r
1717                         desc = desc.replaceAll( "\\s+", " " );\r
1718                     }\r
1719                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1720                         for( final PhylogenyNode n : nodes ) {\r
1721                             ForesterUtil.ensurePresenceOfSequence( n );\r
1722                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1723                             : new Annotation( ref );\r
1724                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1725                                 ann.setDesc( desc );\r
1726                             }\r
1727                             n.getNodeData().getSequence().addAnnotation( ann );\r
1728                         }\r
1729                     }\r
1730                     getMainPanel().getControlPanel().showAnnotations();\r
1731                 }\r
1732             }\r
1733         }\r
1734     }\r
1735 \r
1736     private void chooseFont() {\r
1737         final FontChooser fc = new FontChooser();\r
1738         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1739         fc.showDialog( this, "Select the Base Font" );\r
1740         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1741     }\r
1742 \r
1743     private void chooseMinimalConfidence() {\r
1744         final String s = ( String ) JOptionPane\r
1745                 .showInputDialog( this,\r
1746                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1747                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1748                                           "Minimal Confidence Value",\r
1749                                           JOptionPane.QUESTION_MESSAGE,\r
1750                                           null,\r
1751                                           null,\r
1752                                           getOptions().getMinConfidenceValue() );\r
1753         if ( !ForesterUtil.isEmpty( s ) ) {\r
1754             boolean success = true;\r
1755             double m = 0.0;\r
1756             final String m_str = s.trim();\r
1757             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1758                 try {\r
1759                     m = Double.parseDouble( m_str );\r
1760                 }\r
1761                 catch ( final Exception ex ) {\r
1762                     success = false;\r
1763                 }\r
1764             }\r
1765             else {\r
1766                 success = false;\r
1767             }\r
1768             if ( success && ( m >= 0.0 ) ) {\r
1769                 getOptions().setMinConfidenceValue( m );\r
1770             }\r
1771         }\r
1772     }\r
1773 \r
1774     private void doUpdateProcessMenu() {\r
1775         if ( _process_pool.size() > 0 ) {\r
1776             if ( _process_menu == null ) {\r
1777                 _process_menu = createMenu( "", getConfiguration() );\r
1778                 _process_menu.setForeground( Color.RED );\r
1779             }\r
1780             _process_menu.removeAll();\r
1781             final String text = "processes running: " + _process_pool.size();\r
1782             _process_menu.setText( text );\r
1783             _jmenubar.add( _process_menu );\r
1784             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1785                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1786                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1787             }\r
1788         }\r
1789         else {\r
1790             if ( _process_menu != null ) {\r
1791                 _process_menu.removeAll();\r
1792                 _jmenubar.remove( _process_menu );\r
1793             }\r
1794         }\r
1795         _jmenubar.validate();\r
1796         _jmenubar.repaint();\r
1797         repaint();\r
1798     }\r
1799 \r
1800     private String getPreviousNodeAnnotationReference() {\r
1801         return _previous_node_annotation_ref;\r
1802     }\r
1803 \r
1804     private void removeBranchColors() {\r
1805         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1806             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1807         }\r
1808     }\r
1809 \r
1810     private void removeVisualStyles() {\r
1811         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1812             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1813         }\r
1814     }\r
1815 \r
1816     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1817         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1818     }\r
1819 \r
1820     /**\r
1821      * Display the about box.\r
1822      */\r
1823     static void about() {\r
1824         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1825         about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
1826         about.append( "All Rights Reserved\n" );\r
1827         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1828         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1829         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1830         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1831         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1832         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1833             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1834         }\r
1835         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1836                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1837             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1838                     + ForesterUtil.OS_VERSION + "]\n" );\r
1839         }\r
1840         final Runtime rt = java.lang.Runtime.getRuntime();\r
1841         final long free_memory = rt.freeMemory() / 1000000;\r
1842         final long total_memory = rt.totalMemory() / 1000000;\r
1843         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1844         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1845         about.append( "References:\n" );\r
1846         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1847         about.append( "For more information & download:\n" );\r
1848         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1849         about.append( "Documentation:\n" );\r
1850         about.append( Constants.APTX_DOC_SITE + "\n" );\r
1851         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1852         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1853     }\r
1854 \r
1855     static void chooseNodeSize( final Options options, final Component parent ) {\r
1856         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1857                                                                  "Please enter the default size for node shapes.\n"\r
1858                                                                          + "[current value: "\r
1859                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1860                                                                          "Node Shape Size",\r
1861                                                                          JOptionPane.QUESTION_MESSAGE,\r
1862                                                                          null,\r
1863                                                                          null,\r
1864                                                                          options.getDefaultNodeShapeSize() );\r
1865         if ( !ForesterUtil.isEmpty( s ) ) {\r
1866             boolean success = true;\r
1867             double m = 0.0;\r
1868             final String m_str = s.trim();\r
1869             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1870                 try {\r
1871                     m = Double.parseDouble( m_str );\r
1872                 }\r
1873                 catch ( final Exception ex ) {\r
1874                     success = false;\r
1875                 }\r
1876             }\r
1877             else {\r
1878                 success = false;\r
1879             }\r
1880             if ( success && ( m >= 0.0 ) ) {\r
1881                 final short size = ForesterUtil.roundToShort( m );\r
1882                 if ( size >= 0.0 ) {\r
1883                     options.setDefaultNodeShapeSize( size );\r
1884                 }\r
1885             }\r
1886         }\r
1887     }\r
1888 \r
1889     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1890         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1891     }\r
1892 \r
1893     static JMenu createMenu( final String title, final Configuration conf ) {\r
1894         final JMenu jmenu = new JMenu( title );\r
1895         if ( !conf.isUseNativeUI() ) {\r
1896             jmenu.setFont( MainFrame.menu_font );\r
1897             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1898             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1899         }\r
1900         return jmenu;\r
1901     }\r
1902 \r
1903     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1904         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1905         if ( !configuration.isUseNativeUI() ) {\r
1906             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1907             label.setForeground( configuration.getGuiMenuTextColor() );\r
1908             label.setOpaque( true );\r
1909         }\r
1910         label.setSelected( false );\r
1911         label.setEnabled( false );\r
1912         return label;\r
1913     }\r
1914 \r
1915     static void cycleNodeFill( final Options op ) {\r
1916         switch ( op.getDefaultNodeFill() ) {\r
1917             case GRADIENT:\r
1918                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1919                 break;\r
1920             case NONE:\r
1921                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1922                 break;\r
1923             case SOLID:\r
1924                 op.setDefaultNodeFill( NodeFill.NONE );\r
1925                 break;\r
1926             default:\r
1927                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1928         }\r
1929     }\r
1930 \r
1931     static void cycleNodeShape( final Options op ) {\r
1932         switch ( op.getDefaultNodeShape() ) {\r
1933             case CIRCLE:\r
1934                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1935                 break;\r
1936             case RECTANGLE:\r
1937                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1938                 break;\r
1939             default:\r
1940                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1941         }\r
1942     }\r
1943 \r
1944     private static void cycleNodeDataReturn( final Options op, Configuration conf ) {\r
1945         switch ( op.getExtDescNodeDataToReturn() ) {\r
1946             case UNKNOWN:\r
1947                 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
1948                 break;\r
1949             case DOMAINS_ALL:\r
1950                 op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
1951                 break;\r
1952             case DOMAINS_COLLAPSED_PER_PROTEIN:\r
1953                 op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
1954                 break;\r
1955             case SEQ_ANNOTATIONS:\r
1956                 op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
1957                 break;\r
1958             case GO_TERM_IDS:\r
1959                 op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
1960                 break;\r
1961             case SEQUENCE_MOL_SEQ_FASTA:\r
1962                 if ( conf != null && conf.getExtDescNodeDataToReturn() != null\r
1963                    &&      conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL\r
1964                    &&      conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN\r
1965                    &&       conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS\r
1966                    &&      conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS\r
1967                    &&       conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA\r
1968                         ) {\r
1969                     op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
1970                 }\r
1971                 else {\r
1972                     op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
1973                 }\r
1974                 break;  \r
1975             default:\r
1976                 op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
1977         }\r
1978     }\r
1979 \r
1980     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1981         switch ( op.getOvPlacement() ) {\r
1982             case LOWER_LEFT:\r
1983                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1984                 break;\r
1985             case LOWER_RIGHT:\r
1986                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1987                 break;\r
1988             case UPPER_LEFT:\r
1989                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1990                 break;\r
1991             case UPPER_RIGHT:\r
1992                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1993                 break;\r
1994             default:\r
1995                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1996         }\r
1997         if ( tree_panel != null ) {\r
1998             tree_panel.updateOvSettings();\r
1999         }\r
2000     }\r
2001 \r
2002     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
2003         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
2004             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
2005                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
2006         }\r
2007         else {\r
2008             mi.setText( "Cycle Node Shape Fill Type..." );\r
2009         }\r
2010     }\r
2011 \r
2012     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
2013         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
2014             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
2015                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
2016         }\r
2017         else {\r
2018             mi.setText( "Cycle Node Shape Fill Type..." );\r
2019         }\r
2020     }\r
2021 \r
2022     static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
2023         if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
2024             mi.setText( "Cycle Node Return Data... (current: "\r
2025                     + options.getExtDescNodeDataToReturn().toString() + ")" );\r
2026         }\r
2027         else {\r
2028             mi.setText( "Cycle Node Return Data..." );\r
2029         }\r
2030     }\r
2031 \r
2032     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
2033         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
2034             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
2035         }\r
2036         else {\r
2037             mi.setText( "Cycle Overview Placement..." );\r
2038         }\r
2039     }\r
2040 \r
2041     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
2042         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
2043             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
2044                         + ")" );\r
2045         }\r
2046         else {\r
2047             mi.setText( "Select Color Scheme..." );\r
2048         }\r
2049     }\r
2050 \r
2051     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
2052         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
2053     }\r
2054 \r
2055     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
2056         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
2057             mi.setEnabled( true );\r
2058         }\r
2059         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
2060             mi.setEnabled( true );\r
2061         }\r
2062         else {\r
2063             mi.setEnabled( false );\r
2064         }\r
2065         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
2066     }\r
2067 \r
2068     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
2069         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
2070     }\r
2071 \r
2072     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
2073         for( final TreePanel tree_panel : treepanels ) {\r
2074             tree_panel.setTextAntialias();\r
2075         }\r
2076     }\r
2077 }\r