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

   1 // $Id:\r
   2 // FORESTER -- software libraries and applications\r
   3 // for evolutionary biology research and applications.\r
   4 //\r
   5 // Copyright (C) 2008-2010 Christian M. Zmasek\r
   6 // All rights reserved\r
   7 //\r
   8 // This library is free software; you can redistribute it and/or\r
   9 // modify it under the terms of the GNU Lesser General Public\r
  10 // License as published by the Free Software Foundation; either\r
  11 // version 2.1 of the License, or (at your option) any later version.\r
  12 //\r
  13 // This library is distributed in the hope that it will be useful,\r
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
  16 // Lesser General Public License for more details.\r
  17 //\r
  18 // You should have received a copy of the GNU Lesser General Public\r
  19 // License along with this library; if not, write to the Free Software\r
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
  21 //\r
  22 // Contact: phylosoft @ gmail . com\r
  23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
  24 \r
  25 package org.forester.archaeopteryx;\r
  26 \r
  27 import java.awt.Color;\r
  28 import java.awt.Component;\r
  29 import java.awt.Container;\r
  30 import java.awt.Font;\r
  31 import java.awt.event.ActionEvent;\r
  32 import java.awt.event.ActionListener;\r
  33 import java.io.File;\r
  34 import java.io.IOException;\r
  35 import java.util.ArrayList;\r
  36 import java.util.HashSet;\r
  37 import java.util.LinkedList;\r
  38 import java.util.List;\r
  39 import java.util.Locale;\r
  40 import java.util.NoSuchElementException;\r
  41 import java.util.Set;\r
  42 \r
  43 import javax.swing.Box;\r
  44 import javax.swing.JApplet;\r
  45 import javax.swing.JCheckBoxMenuItem;\r
  46 import javax.swing.JFrame;\r
  47 import javax.swing.JLabel;\r
  48 import javax.swing.JMenu;\r
  49 import javax.swing.JMenuBar;\r
  50 import javax.swing.JMenuItem;\r
  51 import javax.swing.JOptionPane;\r
  52 import javax.swing.JPanel;\r
  53 import javax.swing.JRadioButtonMenuItem;\r
  54 import javax.swing.JTextField;\r
  55 import javax.swing.SwingUtilities;\r
  56 \r
  57 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
  58 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
  59 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
  60 import org.forester.archaeopteryx.tools.InferenceManager;\r
  61 import org.forester.archaeopteryx.tools.ProcessPool;\r
  62 import org.forester.archaeopteryx.tools.ProcessRunning;\r
  63 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
  64 import org.forester.phylogeny.Phylogeny;\r
  65 import org.forester.phylogeny.PhylogenyMethods;\r
  66 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
  67 import org.forester.phylogeny.PhylogenyNode;\r
  68 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
  69 import org.forester.phylogeny.data.Annotation;\r
  70 import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
  71 import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
  72 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
  73 import org.forester.sdi.GSDI;\r
  74 import org.forester.sdi.GSDIR;\r
  75 import org.forester.sdi.SDIException;\r
  76 import org.forester.util.ForesterConstants;\r
  77 import org.forester.util.ForesterUtil;\r
  78 \r
  79 public abstract class MainFrame extends JFrame implements ActionListener {\r
  80 \r
  81     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
  82     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME\r
  83     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
  84     private static final long   serialVersionUID                        = 3655000897845508358L;\r
  85     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
  86                                                                                     Font.PLAIN,\r
  87                                                                                     10 );\r
  88     static final String         TYPE_MENU_HEADER                        = "Type";\r
  89     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
  90     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
  91     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
  92     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
  93     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
  94     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
  95     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO\r
  96     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO\r
  97     static final String         OPTIONS_HEADER                          = "Options";\r
  98     static final String         SEARCH_SUBHEADER                        = "Search:";\r
  99     static final String         DISPLAY_SUBHEADER                       = "Display:";\r
 100     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
 101     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
 102     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
 103     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Branch Length Values";\r
 104     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
 105     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
 106     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
 107     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
 108     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
 109     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
 110     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 111     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 112     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 113     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "External Node Shapes";\r
 114     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Internal Node Shapes";\r
 115     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 116     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 117     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 118     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 119     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 120     static final String         COLOR_LABELS_TIP                        = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";\r
 121     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 122     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 123     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 124     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 125     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 126     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 127     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 128     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 129     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 130     JMenuBar                    _jmenubar;\r
 131     JMenu                       _file_jmenu;\r
 132     JMenu                       _tools_menu;\r
 133     JMenu                       _view_jmenu;\r
 134     JMenu                       _options_jmenu;\r
 135     JMenu                       _font_size_menu;\r
 136     JMenu                       _help_jmenu;\r
 137     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 138     // Analysis menu\r
 139     JMenu                       _analysis_menu;\r
 140     JMenuItem                   _load_species_tree_item;\r
 141     JMenuItem                   _gsdi_item;\r
 142     JMenuItem                   _gsdir_item;\r
 143     JMenuItem                   _lineage_inference;\r
 144     // file menu:\r
 145     JMenuItem                   _open_item;\r
 146     JMenuItem                   _open_url_item;\r
 147     JMenuItem                   _save_item;\r
 148     JMenuItem                   _save_all_item;\r
 149     JMenuItem                   _close_item;\r
 150     JMenuItem                   _exit_item;\r
 151     JMenuItem                   _new_item;\r
 152     // tools menu:\r
 153     JMenuItem                   _midpoint_root_item;\r
 154     JMenuItem                   _taxcolor_item;\r
 155     JMenuItem                   _confcolor_item;\r
 156     JMenuItem                   _color_rank_jmi;\r
 157     JMenuItem                   _collapse_species_specific_subtrees;\r
 158     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me\r
 159     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 160     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 161     JMenuItem                   _obtain_seq_information_jmi;\r
 162     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 163     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 164     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 165     JMenuItem                   _annotate_item;\r
 166     JMenuItem                   _remove_branch_color_item;\r
 167     JMenuItem                   _remove_visual_styles_item;\r
 168     JMenuItem                   _delete_selected_nodes_item;\r
 169     JMenuItem                   _delete_not_selected_nodes_item;\r
 170     // font size menu:\r
 171     JMenuItem                   _super_tiny_fonts_item;\r
 172     JMenuItem                   _tiny_fonts_item;\r
 173     JMenuItem                   _small_fonts_item;\r
 174     JMenuItem                   _medium_fonts_item;\r
 175     JMenuItem                   _large_fonts_item;\r
 176     // options menu:\r
 177     // _  screen and print\r
 178     JMenuItem                   _choose_font_mi;\r
 179     JMenuItem                   _switch_colors_mi;\r
 180     JCheckBoxMenuItem           _label_direction_cbmi;\r
 181     // _  screen display\r
 182     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 183     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 184     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 185     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 186     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 187     JCheckBoxMenuItem           _show_branch_length_values_cbmi;\r
 188     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 189     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me\r
 190     JCheckBoxMenuItem           _show_overview_cbmi;\r
 191     JCheckBoxMenuItem           _show_domain_labels;\r
 192     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 193     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 194     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 195     JMenuItem                   _overview_placment_mi;\r
 196     JMenuItem                   _choose_minimal_confidence_mi;\r
 197     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 198     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 199     JMenuItem                   _cycle_node_shape_mi;\r
 200     JMenuItem                   _cycle_node_fill_mi;\r
 201     JMenuItem                   _choose_node_size_mi;\r
 202     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 203     // _  print\r
 204     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 205     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 206     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 207     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 208     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 209     JMenuItem                   _print_size_mi;\r
 210     JMenuItem                   _choose_pdf_width_mi;\r
 211     // _  parsing\r
 212     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 213     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 214     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 215     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 216     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 217     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 218     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 219     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 220     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 221     // _  search\r
 222     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 223     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 224     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 225     // type menu:\r
 226     JMenu                       _type_menu;\r
 227     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 228     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 229     JCheckBoxMenuItem           _curved_type_cbmi;\r
 230     JCheckBoxMenuItem           _convex_type_cbmi;\r
 231     JCheckBoxMenuItem           _euro_type_cbmi;\r
 232     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 233     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 234     JCheckBoxMenuItem           _circular_type_cbmi;\r
 235     // view as text menu:\r
 236     JMenuItem                   _view_as_NH_item;\r
 237     JMenuItem                   _view_as_XML_item;\r
 238     JMenuItem                   _view_as_nexus_item;\r
 239     JMenuItem                   _display_basic_information_item;\r
 240     // help menu:\r
 241     JMenuItem                   _about_item;\r
 242     JMenuItem                   _help_item;\r
 243     JMenuItem                   _website_item;\r
 244     JMenuItem                   _phyloxml_website_item;\r
 245     JMenuItem                   _phyloxml_ref_item;\r
 246     JMenuItem                   _aptx_ref_item;\r
 247     // process menu:\r
 248     JMenu                       _process_menu;\r
 249     // Handy pointers to child components:\r
 250     MainPanel                   _mainpanel;\r
 251     Container                   _contentpane;\r
 252     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;\r
 253     Configuration               _configuration;\r
 254     Options                     _options;\r
 255     private Phylogeny           _species_tree;\r
 256     InferenceManager            _inference_manager;\r
 257     final ProcessPool           _process_pool;\r
 258     private String              _previous_node_annotation_ref;\r
 259 \r
 260     MainFrame() {\r
 261         _process_pool = ProcessPool.createInstance();\r
 262     }\r
 263 \r
 264     /**\r
 265      * Action performed.\r
 266      */\r
 267     @Override\r
 268     public void actionPerformed( final ActionEvent e ) {\r
 269         final Object o = e.getSource();\r
 270         boolean is_applet = false;\r
 271         JApplet applet = null;\r
 272         if ( getCurrentTreePanel() != null ) {\r
 273             is_applet = getCurrentTreePanel().isApplet();\r
 274             if ( is_applet ) {\r
 275                 applet = getCurrentTreePanel().obtainApplet();\r
 276             }\r
 277         }\r
 278         if ( o == _exit_item ) {\r
 279             close();\r
 280         }\r
 281         else if ( o == _gsdi_item ) {\r
 282             if ( isSubtreeDisplayed() ) {\r
 283                 return;\r
 284             }\r
 285             executeGSDI();\r
 286         }\r
 287         else if ( o == _gsdir_item ) {\r
 288             if ( isSubtreeDisplayed() ) {\r
 289                 return;\r
 290             }\r
 291             executeGSDIR();\r
 292         }\r
 293         else if ( o == _taxcolor_item ) {\r
 294             taxColor();\r
 295         }\r
 296         else if ( o == _confcolor_item ) {\r
 297             confColor();\r
 298         }\r
 299         else if ( o == _color_rank_jmi ) {\r
 300             colorRank();\r
 301         }\r
 302         else if ( o == _collapse_species_specific_subtrees ) {\r
 303             if ( isSubtreeDisplayed() ) {\r
 304                 return;\r
 305             }\r
 306             if ( getCurrentTreePanel() != null ) {\r
 307                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 308             }\r
 309         }\r
 310         else if ( o == _remove_branch_color_item ) {\r
 311             if ( isSubtreeDisplayed() ) {\r
 312                 return;\r
 313             }\r
 314             removeBranchColors();\r
 315         }\r
 316         else if ( o == _remove_visual_styles_item ) {\r
 317             if ( isSubtreeDisplayed() ) {\r
 318                 return;\r
 319             }\r
 320             removeVisualStyles();\r
 321         }\r
 322         else if ( o == _midpoint_root_item ) {\r
 323             if ( isSubtreeDisplayed() ) {\r
 324                 return;\r
 325             }\r
 326             midpointRoot();\r
 327         }\r
 328         else if ( o == _delete_selected_nodes_item ) {\r
 329             if ( isSubtreeDisplayed() ) {\r
 330                 return;\r
 331             }\r
 332             deleteSelectedNodes( true );\r
 333         }\r
 334         else if ( o == _delete_not_selected_nodes_item ) {\r
 335             if ( isSubtreeDisplayed() ) {\r
 336                 return;\r
 337             }\r
 338             deleteSelectedNodes( false );\r
 339         }\r
 340         else if ( o == _annotate_item ) {\r
 341             annotateSequences();\r
 342         }\r
 343         else if ( o == _switch_colors_mi ) {\r
 344             switchColors();\r
 345         }\r
 346         else if ( o == _display_basic_information_item ) {\r
 347             displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 348         }\r
 349         else if ( o == _view_as_NH_item ) {\r
 350             viewAsNH();\r
 351         }\r
 352         else if ( o == _view_as_XML_item ) {\r
 353             viewAsXML();\r
 354         }\r
 355         else if ( o == _view_as_nexus_item ) {\r
 356             viewAsNexus();\r
 357         }\r
 358         else if ( o == _super_tiny_fonts_item ) {\r
 359             if ( getCurrentTreePanel() != null ) {\r
 360                 getCurrentTreePanel().setSuperTinyFonts();\r
 361                 getCurrentTreePanel().repaint();\r
 362             }\r
 363         }\r
 364         else if ( o == _tiny_fonts_item ) {\r
 365             if ( getCurrentTreePanel() != null ) {\r
 366                 getCurrentTreePanel().setTinyFonts();\r
 367                 getCurrentTreePanel().repaint();\r
 368             }\r
 369         }\r
 370         else if ( o == _small_fonts_item ) {\r
 371             if ( getCurrentTreePanel() != null ) {\r
 372                 getCurrentTreePanel().setSmallFonts();\r
 373                 getCurrentTreePanel().repaint();\r
 374             }\r
 375         }\r
 376         else if ( o == _medium_fonts_item ) {\r
 377             if ( getCurrentTreePanel() != null ) {\r
 378                 getCurrentTreePanel().setMediumFonts();\r
 379                 getCurrentTreePanel().repaint();\r
 380             }\r
 381         }\r
 382         else if ( o == _large_fonts_item ) {\r
 383             if ( getCurrentTreePanel() != null ) {\r
 384                 getCurrentTreePanel().setLargeFonts();\r
 385                 getCurrentTreePanel().repaint();\r
 386             }\r
 387         }\r
 388         else if ( o == _choose_font_mi ) {\r
 389             chooseFont();\r
 390         }\r
 391         else if ( o == _choose_minimal_confidence_mi ) {\r
 392             chooseMinimalConfidence();\r
 393         }\r
 394         else if ( o == _choose_node_size_mi ) {\r
 395             chooseNodeSize( getOptions(), this );\r
 396         }\r
 397         else if ( o == _overview_placment_mi ) {\r
 398             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 399         }\r
 400         else if ( o == _cycle_node_fill_mi ) {\r
 401             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
 402         }\r
 403         else if ( o == _cycle_node_shape_mi ) {\r
 404             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
 405         }\r
 406         else if ( o == _screen_antialias_cbmi ) {\r
 407             updateOptions( getOptions() );\r
 408             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 409         }\r
 410         else if ( o == _background_gradient_cbmi ) {\r
 411             updateOptions( getOptions() );\r
 412         }\r
 413         else if ( o == _show_domain_labels ) {\r
 414             updateOptions( getOptions() );\r
 415         }\r
 416         else if ( o == _show_annotation_ref_source ) {\r
 417             updateOptions( getOptions() );\r
 418         }\r
 419         else if ( o == _abbreviate_scientific_names ) {\r
 420             updateOptions( getOptions() );\r
 421         }\r
 422         else if ( o == _color_labels_same_as_parent_branch ) {\r
 423             updateOptions( getOptions() );\r
 424         }\r
 425         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 426             updateOptions( getOptions() );\r
 427         }\r
 428         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 429             updateOptions( getOptions() );\r
 430         }\r
 431         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 432             updateOptions( getOptions() );\r
 433             showWhole();\r
 434         }\r
 435         else if ( o == _uniform_cladograms_rbmi ) {\r
 436             updateOptions( getOptions() );\r
 437             showWhole();\r
 438         }\r
 439         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 440             updateOptions( getOptions() );\r
 441             showWhole();\r
 442         }\r
 443         else if ( o == _search_case_senstive_cbmi ) {\r
 444             updateOptions( getOptions() );\r
 445             getMainPanel().getControlPanel().search0();\r
 446             getMainPanel().getControlPanel().search1();\r
 447         }\r
 448         else if ( o == _search_whole_words_only_cbmi ) {\r
 449             updateOptions( getOptions() );\r
 450             getMainPanel().getControlPanel().search0();\r
 451             getMainPanel().getControlPanel().search1();\r
 452         }\r
 453         else if ( o == _inverse_search_result_cbmi ) {\r
 454             updateOptions( getOptions() );\r
 455             getMainPanel().getControlPanel().search0();\r
 456             getMainPanel().getControlPanel().search1();\r
 457         }\r
 458         else if ( o == _show_scale_cbmi ) {\r
 459             updateOptions( getOptions() );\r
 460         }\r
 461         else if ( o == _show_branch_length_values_cbmi ) {\r
 462             updateOptions( getOptions() );\r
 463         }\r
 464         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 465             updateOptions( getOptions() );\r
 466         }\r
 467         else if ( o == _show_confidence_stddev_cbmi ) {\r
 468             updateOptions( getOptions() );\r
 469         }\r
 470         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 471             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 472                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 473             }\r
 474             updateOptions( getOptions() );\r
 475         }\r
 476         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 477             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 478                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 479             }\r
 480             updateOptions( getOptions() );\r
 481         }\r
 482         else if ( o == _label_direction_cbmi ) {\r
 483             updateOptions( getOptions() );\r
 484         }\r
 485         else if ( o == _show_overview_cbmi ) {\r
 486             updateOptions( getOptions() );\r
 487             if ( getCurrentTreePanel() != null ) {\r
 488                 getCurrentTreePanel().updateOvSizes();\r
 489             }\r
 490         }\r
 491         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 492                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 493                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 494             typeChanged( o );\r
 495         }\r
 496         else if ( o == _about_item ) {\r
 497             about();\r
 498         }\r
 499         else if ( o == _help_item ) {\r
 500             help();\r
 501         }\r
 502         else if ( o == _website_item ) {\r
 503             try {\r
 504                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 505             }\r
 506             catch ( final IOException e1 ) {\r
 507                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 508             }\r
 509         }\r
 510         else if ( o == _phyloxml_website_item ) {\r
 511             try {\r
 512                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 513             }\r
 514             catch ( final IOException e1 ) {\r
 515                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 516             }\r
 517         }\r
 518         else if ( o == _aptx_ref_item ) {\r
 519             try {\r
 520                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 521             }\r
 522             catch ( final IOException e1 ) {\r
 523                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 524             }\r
 525         }\r
 526         else if ( o == _phyloxml_ref_item ) {\r
 527             try {\r
 528                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 529             }\r
 530             catch ( final IOException e1 ) {\r
 531                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 532             }\r
 533         }\r
 534         else {\r
 535             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 536                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 537                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 538                         readPhylogeniesFromWebservice( i );\r
 539                     }\r
 540                 }\r
 541             }\r
 542         }\r
 543         _contentpane.repaint();\r
 544     }\r
 545 \r
 546     private void deleteSelectedNodes( boolean delete ) {\r
 547         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
 548         if ( phy == null || phy.getNumberOfExternalNodes() < 2 ) {\r
 549             return;\r
 550         }\r
 551         List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
 552         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
 553             final List<PhylogenyNode>  all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
 554             for( final PhylogenyNode n : all_selected_nodes ) {\r
 555                 if ( n.isExternal() ) {\r
 556                     nodes.add( n );\r
 557                 }\r
 558             }\r
 559         }\r
 560         \r
 561         String function = "Retain";\r
 562         if ( delete ) {\r
 563             function = "Delete";\r
 564         }\r
 565         if ( ( nodes == null ) || nodes.isEmpty() ) {\r
 566             JOptionPane\r
 567                     .showMessageDialog( this,\r
 568                                         "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
 569                                         "No external nodes selected to " + function.toLowerCase(),\r
 570                                         JOptionPane.ERROR_MESSAGE );\r
 571             return;\r
 572         }\r
 573         final int todo = nodes.size();\r
 574         final int ext = phy.getNumberOfExternalNodes();\r
 575         int res = todo;\r
 576         if ( delete ) {\r
 577             res = ext - todo;\r
 578         }\r
 579         if ( res < 1 ) {\r
 580             JOptionPane.showMessageDialog( this,\r
 581                                            "Cannot delete all nodes",\r
 582                                            "Attempt to delete all nodes ",\r
 583                                            JOptionPane.ERROR_MESSAGE );\r
 584             return;\r
 585         }\r
 586         final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
 587                 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
 588                 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
 589         if ( result == JOptionPane.OK_OPTION ) {\r
 590             if ( !delete ) {\r
 591                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
 592                 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
 593                     final PhylogenyNode n = it.next();\r
 594                     if ( !nodes.contains( n ) ) {\r
 595                         to_delete.add( n );\r
 596                     }\r
 597                 }\r
 598                 for( final PhylogenyNode n : to_delete ) {\r
 599                     phy.deleteSubtree( n, true );\r
 600                 }\r
 601             }\r
 602             else {\r
 603                 for( final PhylogenyNode n : nodes ) {\r
 604                     phy.deleteSubtree( n, true );\r
 605                 }\r
 606             }\r
 607             resetSearch();\r
 608             getCurrentTreePanel().setNodeInPreorderToNull();\r
 609             phy.externalNodesHaveChanged();\r
 610             phy.clearHashIdToNodeMap();\r
 611             phy.recalculateNumberOfExternalDescendants( true );\r
 612             getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
 613             getCurrentTreePanel().setEdited( true );\r
 614             repaint();\r
 615         }\r
 616     }\r
 617 \r
 618     void resetSearch() {\r
 619         getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
 620         getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
 621         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
 622         getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
 623         getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
 624         getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
 625         getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
 626         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
 627         getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
 628         getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
 629         getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
 630         getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
 631     }\r
 632 \r
 633     public Configuration getConfiguration() {\r
 634         return _configuration;\r
 635     }\r
 636 \r
 637     /**\r
 638      * This method returns the current external node data which\r
 639      * has been selected by the user by clicking the "Return ..."\r
 640      * menu item. This method is expected to be called from Javascript or\r
 641      * something like it.\r
 642      * \r
 643      * @return current external node data as String\r
 644      */\r
 645     public String getCurrentExternalNodesDataBuffer() {\r
 646         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 647     }\r
 648 \r
 649     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 650         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 651     }\r
 652 \r
 653     public int getCurrentExternalNodesDataBufferLength() {\r
 654         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 655     }\r
 656 \r
 657     public InferenceManager getInferenceManager() {\r
 658         return _inference_manager;\r
 659     }\r
 660 \r
 661     public MainPanel getMainPanel() {\r
 662         return _mainpanel;\r
 663     }\r
 664 \r
 665     public Options getOptions() {\r
 666         return _options;\r
 667     }\r
 668 \r
 669     public ProcessPool getProcessPool() {\r
 670         return _process_pool;\r
 671     }\r
 672 \r
 673     public void showTextFrame( final String s, final String title ) {\r
 674         checkTextFrames();\r
 675         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 676     }\r
 677 \r
 678     public void showWhole() {\r
 679         _mainpanel.getControlPanel().showWhole();\r
 680     }\r
 681 \r
 682     public void updateProcessMenu() {\r
 683         // In general Swing is not thread safe.\r
 684         // See "Swing's Threading Policy".\r
 685         SwingUtilities.invokeLater( new Runnable() {\r
 686 \r
 687             @Override\r
 688             public void run() {\r
 689                 doUpdateProcessMenu();\r
 690             }\r
 691         } );\r
 692     }\r
 693 \r
 694     void activateSaveAllIfNeeded() {\r
 695         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 696             _save_all_item.setEnabled( true );\r
 697         }\r
 698         else {\r
 699             _save_all_item.setEnabled( false );\r
 700         }\r
 701     }\r
 702 \r
 703     void buildFileMenu() {\r
 704         _file_jmenu = createMenu( "File", getConfiguration() );\r
 705         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 706         customizeJMenuItem( _exit_item );\r
 707         _jmenubar.add( _file_jmenu );\r
 708     }\r
 709 \r
 710     void buildFontSizeMenu() {\r
 711         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 712         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 713         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 714         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 715         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 716         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 717         customizeJMenuItem( _super_tiny_fonts_item );\r
 718         customizeJMenuItem( _tiny_fonts_item );\r
 719         customizeJMenuItem( _small_fonts_item );\r
 720         customizeJMenuItem( _medium_fonts_item );\r
 721         customizeJMenuItem( _large_fonts_item );\r
 722         _jmenubar.add( _font_size_menu );\r
 723     }\r
 724 \r
 725     void buildHelpMenu() {\r
 726         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 727         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );\r
 728         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 729         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );\r
 730         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 731         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 732         _help_jmenu.addSeparator();\r
 733         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 734         customizeJMenuItem( _help_item );\r
 735         customizeJMenuItem( _website_item );\r
 736         customizeJMenuItem( _phyloxml_website_item );\r
 737         customizeJMenuItem( _aptx_ref_item );\r
 738         customizeJMenuItem( _phyloxml_ref_item );\r
 739         customizeJMenuItem( _about_item );\r
 740         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 741         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 742         _jmenubar.add( _help_jmenu );\r
 743     }\r
 744 \r
 745     void buildTypeMenu() {\r
 746         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 747         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 748         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 749         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 750         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 751         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 752         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 753         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 754         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 755         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 756         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 757         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 758         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 759         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 760         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 761         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 762         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 763         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 764         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 765         initializeTypeMenu( getOptions() );\r
 766         _jmenubar.add( _type_menu );\r
 767     }\r
 768 \r
 769     void buildViewMenu() {\r
 770         _view_jmenu = createMenu( "View", getConfiguration() );\r
 771         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 772         _view_jmenu.addSeparator();\r
 773         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 774         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 775         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 776         customizeJMenuItem( _display_basic_information_item );\r
 777         customizeJMenuItem( _view_as_NH_item );\r
 778         customizeJMenuItem( _view_as_XML_item );\r
 779         customizeJMenuItem( _view_as_nexus_item );\r
 780         _jmenubar.add( _view_jmenu );\r
 781     }\r
 782 \r
 783     void checkTextFrames() {\r
 784         if ( _textframes.size() > 5 ) {\r
 785             try {\r
 786                 if ( _textframes.getFirst() != null ) {\r
 787                     _textframes.getFirst().removeMe();\r
 788                 }\r
 789                 else {\r
 790                     _textframes.removeFirst();\r
 791                 }\r
 792             }\r
 793             catch ( final NoSuchElementException e ) {\r
 794                 // Ignore.\r
 795             }\r
 796         }\r
 797     }\r
 798 \r
 799     void close() {\r
 800         removeAllTextFrames();\r
 801         if ( _mainpanel != null ) {\r
 802             _mainpanel.terminate();\r
 803         }\r
 804         if ( _contentpane != null ) {\r
 805             _contentpane.removeAll();\r
 806         }\r
 807         setVisible( false );\r
 808         dispose();\r
 809     }\r
 810 \r
 811     void colorRank() {\r
 812         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 813             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
 814             final String rank = ( String ) JOptionPane\r
 815                     .showInputDialog( this,\r
 816                                       "What rank should the colorization be based on",\r
 817                                       "Rank Selection",\r
 818                                       JOptionPane.QUESTION_MESSAGE,\r
 819                                       null,\r
 820                                       ranks,\r
 821                                       null );\r
 822             if ( !ForesterUtil.isEmpty( rank ) ) {\r
 823                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
 824             }\r
 825         }\r
 826     }\r
 827 \r
 828     void confColor() {\r
 829         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 830             _mainpanel.getCurrentTreePanel().confColor();\r
 831         }\r
 832     }\r
 833 \r
 834     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
 835         if ( item != null ) {\r
 836             item.setFont( MainFrame.menu_font );\r
 837             if ( !getConfiguration().isUseNativeUI() ) {\r
 838                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 839                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 840             }\r
 841             item.setSelected( is_selected );\r
 842             item.addActionListener( this );\r
 843         }\r
 844     }\r
 845 \r
 846     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
 847         if ( jmi != null ) {\r
 848             jmi.setFont( MainFrame.menu_font );\r
 849             if ( !getConfiguration().isUseNativeUI() ) {\r
 850                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 851                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 852             }\r
 853             jmi.addActionListener( this );\r
 854         }\r
 855         return jmi;\r
 856     }\r
 857 \r
 858     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
 859         if ( item != null ) {\r
 860             item.setFont( MainFrame.menu_font );\r
 861             if ( !getConfiguration().isUseNativeUI() ) {\r
 862                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 863                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 864             }\r
 865             item.setSelected( is_selected );\r
 866             item.addActionListener( this );\r
 867         }\r
 868     }\r
 869 \r
 870     void displayBasicInformation( final File treefile ) {\r
 871         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
 872             String title = "Basic Information";\r
 873             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
 874                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
 875             }\r
 876             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
 877         }\r
 878     }\r
 879 \r
 880     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
 881         try {\r
 882             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 883         }\r
 884         catch ( final Exception ex ) {\r
 885             // Do nothing.\r
 886         }\r
 887         JOptionPane.showMessageDialog( this,\r
 888                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
 889                                        "Error during File|Open",\r
 890                                        JOptionPane.ERROR_MESSAGE );\r
 891     }\r
 892 \r
 893     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
 894         try {\r
 895             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 896         }\r
 897         catch ( final Exception ex ) {\r
 898             // Do nothing.\r
 899         }\r
 900         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
 901     }\r
 902 \r
 903     void executeGSDI() {\r
 904         if ( !isOKforSDI( false, true ) ) {\r
 905             return;\r
 906         }\r
 907         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
 908             JOptionPane.showMessageDialog( this,\r
 909                                            "Gene tree is not rooted.",\r
 910                                            "Cannot execute GSDI",\r
 911                                            JOptionPane.ERROR_MESSAGE );\r
 912             return;\r
 913         }\r
 914         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 915         gene_tree.setAllNodesToNotCollapse();\r
 916         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 917         GSDI gsdi = null;\r
 918         final Phylogeny species_tree = getSpeciesTree().copy();\r
 919         try {\r
 920             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
 921         }\r
 922         catch ( final SDIException e ) {\r
 923             JOptionPane.showMessageDialog( this,\r
 924                                            e.getLocalizedMessage(),\r
 925                                            "Error during GSDI",\r
 926                                            JOptionPane.ERROR_MESSAGE );\r
 927             return;\r
 928         }\r
 929         catch ( final Exception e ) {\r
 930             AptxUtil.unexpectedException( e );\r
 931             return;\r
 932         }\r
 933         gene_tree.setRerootable( false );\r
 934         gene_tree.clearHashIdToNodeMap();\r
 935         gene_tree.recalculateNumberOfExternalDescendants( true );\r
 936         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
 937         getMainPanel().getControlPanel().setShowEvents( true );\r
 938         showWhole();\r
 939         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 940         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 941         showWhole();\r
 942         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 943         showWhole();\r
 944         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 945         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 946         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 947             JOptionPane.showMessageDialog( this,\r
 948                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 949                                                    + "Potential duplications: "\r
 950                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 951                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 952                                                    + "Stripped gene tree nodes: "\r
 953                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 954                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 955                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 956                                            "GSDI successfully completed",\r
 957                                            JOptionPane.WARNING_MESSAGE );\r
 958         }\r
 959         else {\r
 960             JOptionPane.showMessageDialog( this,\r
 961                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 962                                                    + "Potential duplications: "\r
 963                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 964                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 965                                                    + "Stripped gene tree nodes: "\r
 966                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 967                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 968                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 969                                            "GSDI successfully completed",\r
 970                                            JOptionPane.INFORMATION_MESSAGE );\r
 971         }\r
 972     }\r
 973 \r
 974     void executeGSDIR() {\r
 975         if ( !isOKforSDI( false, false ) ) {\r
 976             return;\r
 977         }\r
 978         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
 979         if ( ( p > 0 )\r
 980                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
 981             JOptionPane.showMessageDialog( this,\r
 982                                            "Gene tree is not completely binary",\r
 983                                            "Cannot execute GSDI",\r
 984                                            JOptionPane.ERROR_MESSAGE );\r
 985             return;\r
 986         }\r
 987         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 988         gene_tree.setAllNodesToNotCollapse();\r
 989         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 990         GSDIR gsdir = null;\r
 991         final Phylogeny species_tree = getSpeciesTree().copy();\r
 992         try {\r
 993             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
 994         }\r
 995         catch ( final SDIException e ) {\r
 996             JOptionPane.showMessageDialog( this,\r
 997                                            e.getLocalizedMessage(),\r
 998                                            "Error during GSDIR",\r
 999                                            JOptionPane.ERROR_MESSAGE );\r
1000             return;\r
1001         }\r
1002         catch ( final Exception e ) {\r
1003             AptxUtil.unexpectedException( e );\r
1004             return;\r
1005         }\r
1006         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
1007         result_gene_tree.setRerootable( false );\r
1008         result_gene_tree.clearHashIdToNodeMap();\r
1009         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
1010         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
1011         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
1012         getMainPanel().getControlPanel().setShowEvents( true );\r
1013         showWhole();\r
1014         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1015         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1016         showWhole();\r
1017         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1018         showWhole();\r
1019         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1020         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1021         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1022             JOptionPane.showMessageDialog( this,\r
1023                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1024                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1025                                                    + "Stripped gene tree nodes: "\r
1026                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1027                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1028                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1029                                            "GSDIR successfully completed",\r
1030                                            JOptionPane.WARNING_MESSAGE );\r
1031         }\r
1032         else {\r
1033             JOptionPane.showMessageDialog( this,\r
1034                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1035                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1036                                                    + "Stripped gene tree nodes: "\r
1037                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1038                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1039                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1040                                            "GSDIR successfully completed",\r
1041                                            JOptionPane.INFORMATION_MESSAGE );\r
1042         }\r
1043     }\r
1044 \r
1045     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
1046         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
1047             JOptionPane.showMessageDialog( this,\r
1048                                            "Gene tree and species tree have no species in common.",\r
1049                                            "Error during SDI",\r
1050                                            JOptionPane.ERROR_MESSAGE );\r
1051             return false;\r
1052         }\r
1053         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
1054             JOptionPane.showMessageDialog( this,\r
1055                                            "Gene tree and species tree have only one species in common.",\r
1056                                            "Error during SDI",\r
1057                                            JOptionPane.ERROR_MESSAGE );\r
1058             return false;\r
1059         }\r
1060         else {\r
1061             return true;\r
1062         }\r
1063     }\r
1064 \r
1065     TreePanel getCurrentTreePanel() {\r
1066         return getMainPanel().getCurrentTreePanel();\r
1067     }\r
1068 \r
1069     JMenu getHelpMenu() {\r
1070         return _help_jmenu;\r
1071     }\r
1072 \r
1073     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
1074         return _label_direction_cbmi;\r
1075     }\r
1076 \r
1077     JMenuBar getMenuBarOfMainFrame() {\r
1078         return _jmenubar;\r
1079     }\r
1080 \r
1081     final Phylogeny getSpeciesTree() {\r
1082         return _species_tree;\r
1083     }\r
1084 \r
1085     void help() {\r
1086         final StringBuilder sb = new StringBuilder();\r
1087         sb.append( "Display options\n" );\r
1088         sb.append( "-------------------\n" );\r
1089         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );\r
1090         sb.append( "Clickable tree nodes\n" );\r
1091         sb.append( "--------------------\n" );\r
1092         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );\r
1093         sb.append( "or by right clicking:\n" );\r
1094         sb.append( "o  Display Node Data -- display information for a node\n" );\r
1095         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );\r
1096         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );\r
1097         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );\r
1098         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );\r
1099         sb.append( "o  Colorize Subtree -- color a subtree\n" );\r
1100         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );\r
1101         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );\r
1102         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );\r
1103         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );\r
1104         sb.append( "Zooming\n" );\r
1105         sb.append( "---------\n" );\r
1106         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );\r
1107         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );\r
1108         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );\r
1109         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );\r
1110         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );\r
1111         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );\r
1112         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );\r
1113         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );\r
1114         sb.append( "Quick tree manipulation:\n" );\r
1115         sb.append( "------------------------\n" );\r
1116         sb.append( "Order Subtrees -- order the tree by branch length\n" );\r
1117         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );\r
1118         sb.append( "Memory problems (Java heap space error)\n" );\r
1119         sb.append( "---------------------------------------\n" );\r
1120         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );\r
1121         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );\r
1122         sb.append( "the '-Xmx' Java command line option. For example:\n" );\r
1123         sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );\r
1124         // + "General remarks\n"\r
1125         // + "---------------\n"\r
1126         // +\r
1127         // "o  The application version permits copying to the clipboard \n"\r
1128         // +\r
1129         // "    in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"\r
1130         // +\r
1131         // "o  Changes made to a subtree affect this subtree and its subtrees,\n"\r
1132         // + "    but not any of its parent tree(s).\n"\r
1133         // +\r
1134         // "o  Archaeopteryx tries to detect whether the numerical values in a NH tree\n"\r
1135         // +\r
1136         // "    are likely to be bootstrap values instead of branch length values.\n\n"\r
1137         // +\r
1138         // " Remarks regarding SDI (Speciation Duplication Inference):\n"\r
1139         // +\r
1140         // "o  Each external node of the gene tree (in display) needs to be associated with\n"\r
1141         // +\r
1142         // "    a species: either directly through the \"Species\" field, or the species\n"\r
1143         // +\r
1144         // "    is part of the sequence name in the form \"XXXX_SPECIES\"\n"\r
1145         // +\r
1146         // "    (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"\r
1147         // +\r
1148         // "o  A species tree for each species of the gene tree needs to be loaded with\n"\r
1149         // +\r
1150         // "   \"SDI\"|\"Load species tree\" prior the SDI execution.\n"\r
1151         // +\r
1152         // "o  !External nodes of the gene tree associated with species not present in\n"\r
1153         // +\r
1154         // "    the species tree are REMOVED prior to SDI execution!\n"\r
1155         // +\r
1156         // "o  Both the gene tree and the species tree must be completely binary.\n"\r
1157         // +\r
1158         // "o  Duplications and speciations are a function of the position of the root.\n"\r
1159         // +\r
1160         // "    Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"\r
1161         // + "    incorrect and need to be inferred again\n"\r
1162         // +\r
1163         // "    with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"\r
1164         sb.append( "phyloXML\n" );\r
1165         sb.append( "-------------------\n" );\r
1166         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );\r
1167         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );\r
1168         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1169         sb.append( "\n" );\r
1170         sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );\r
1171         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );\r
1172         TextFrame.instantiate( sb.toString(), "Help", _textframes );\r
1173     }\r
1174 \r
1175     void initializeTypeMenu( final Options options ) {\r
1176         setTypeMenuToAllUnselected();\r
1177         switch ( options.getPhylogenyGraphicsType() ) {\r
1178             case CONVEX:\r
1179                 _convex_type_cbmi.setSelected( true );\r
1180                 break;\r
1181             case CURVED:\r
1182                 _curved_type_cbmi.setSelected( true );\r
1183                 break;\r
1184             case EURO_STYLE:\r
1185                 _euro_type_cbmi.setSelected( true );\r
1186                 break;\r
1187             case ROUNDED:\r
1188                 _rounded_type_cbmi.setSelected( true );\r
1189                 break;\r
1190             case TRIANGULAR:\r
1191                 _triangular_type_cbmi.setSelected( true );\r
1192                 break;\r
1193             case UNROOTED:\r
1194                 _unrooted_type_cbmi.setSelected( true );\r
1195                 break;\r
1196             case CIRCULAR:\r
1197                 _circular_type_cbmi.setSelected( true );\r
1198                 break;\r
1199             default:\r
1200                 _rectangular_type_cbmi.setSelected( true );\r
1201                 break;\r
1202         }\r
1203     }\r
1204 \r
1205     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1206         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1207             return false;\r
1208         }\r
1209         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1210             JOptionPane.showMessageDialog( this,\r
1211                                            "No species tree loaded",\r
1212                                            "Cannot execute GSDI",\r
1213                                            JOptionPane.ERROR_MESSAGE );\r
1214             return false;\r
1215         }\r
1216         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1217             JOptionPane.showMessageDialog( this,\r
1218                                            "Species tree is not completely binary",\r
1219                                            "Cannot execute GSDI",\r
1220                                            JOptionPane.ERROR_MESSAGE );\r
1221             return false;\r
1222         }\r
1223         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1224             JOptionPane.showMessageDialog( this,\r
1225                                            "Gene tree is not completely binary",\r
1226                                            "Cannot execute GSDI",\r
1227                                            JOptionPane.ERROR_MESSAGE );\r
1228             return false;\r
1229         }\r
1230         else {\r
1231             return true;\r
1232         }\r
1233     }\r
1234 \r
1235     boolean isSubtreeDisplayed() {\r
1236         if ( getCurrentTreePanel() != null ) {\r
1237             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1238                 JOptionPane\r
1239                         .showMessageDialog( this,\r
1240                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1241                                             "Operation can not be exectuted on a sub-tree",\r
1242                                             JOptionPane.WARNING_MESSAGE );\r
1243                 return true;\r
1244             }\r
1245         }\r
1246         return false;\r
1247     }\r
1248 \r
1249     void midpointRoot() {\r
1250         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1251             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1252         }\r
1253     }\r
1254 \r
1255     void readPhylogeniesFromWebservice( final int i ) {\r
1256         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1257         new Thread( reader ).start();\r
1258     }\r
1259 \r
1260     void removeAllTextFrames() {\r
1261         for( final TextFrame tf : _textframes ) {\r
1262             if ( tf != null ) {\r
1263                 tf.close();\r
1264             }\r
1265         }\r
1266         _textframes.clear();\r
1267     }\r
1268 \r
1269     void setConfiguration( final Configuration configuration ) {\r
1270         _configuration = configuration;\r
1271     }\r
1272 \r
1273     void setInferenceManager( final InferenceManager i ) {\r
1274         _inference_manager = i;\r
1275     }\r
1276 \r
1277     void setOptions( final Options options ) {\r
1278         _options = options;\r
1279     }\r
1280 \r
1281     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1282         setTypeMenuToAllUnselected();\r
1283         switch ( type ) {\r
1284             case CIRCULAR:\r
1285                 _circular_type_cbmi.setSelected( true );\r
1286                 break;\r
1287             case CONVEX:\r
1288                 _convex_type_cbmi.setSelected( true );\r
1289                 break;\r
1290             case CURVED:\r
1291                 _curved_type_cbmi.setSelected( true );\r
1292                 break;\r
1293             case EURO_STYLE:\r
1294                 _euro_type_cbmi.setSelected( true );\r
1295                 break;\r
1296             case ROUNDED:\r
1297                 _rounded_type_cbmi.setSelected( true );\r
1298                 break;\r
1299             case RECTANGULAR:\r
1300                 _rectangular_type_cbmi.setSelected( true );\r
1301                 break;\r
1302             case TRIANGULAR:\r
1303                 _triangular_type_cbmi.setSelected( true );\r
1304                 break;\r
1305             case UNROOTED:\r
1306                 _unrooted_type_cbmi.setSelected( true );\r
1307                 break;\r
1308             default:\r
1309                 throw new IllegalArgumentException( "unknown type: " + type );\r
1310         }\r
1311     }\r
1312 \r
1313     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1314         _species_tree = species_tree;\r
1315     }\r
1316 \r
1317     void setTypeMenuToAllUnselected() {\r
1318         _convex_type_cbmi.setSelected( false );\r
1319         _curved_type_cbmi.setSelected( false );\r
1320         _euro_type_cbmi.setSelected( false );\r
1321         _rounded_type_cbmi.setSelected( false );\r
1322         _triangular_type_cbmi.setSelected( false );\r
1323         _rectangular_type_cbmi.setSelected( false );\r
1324         _unrooted_type_cbmi.setSelected( false );\r
1325         _circular_type_cbmi.setSelected( false );\r
1326     }\r
1327 \r
1328     void switchColors() {\r
1329         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1330         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1331         csc.setVisible( true );\r
1332     }\r
1333 \r
1334     void taxColor() {\r
1335         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1336             _mainpanel.getCurrentTreePanel().taxColor();\r
1337         }\r
1338     }\r
1339 \r
1340     void typeChanged( final Object o ) {\r
1341         updateTypeCheckboxes( getOptions(), o );\r
1342         updateOptions( getOptions() );\r
1343         if ( getCurrentTreePanel() != null ) {\r
1344             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1345             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1346             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1347                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1348                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1349                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1350                 getCurrentTreePanel().getControlPanel().showWhole();\r
1351             }\r
1352             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1353                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1354             }\r
1355             else {\r
1356                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1357             }\r
1358             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1359             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1360             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1361                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1362                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1363                 }\r
1364                 else {\r
1365                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1366                 }\r
1367             }\r
1368         }\r
1369     }\r
1370 \r
1371     void updateOptions( final Options options ) {\r
1372         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1373         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1374                 && _background_gradient_cbmi.isSelected() );\r
1375         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1376         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1377                 && _show_annotation_ref_source.isSelected() );\r
1378         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1379                 && _abbreviate_scientific_names.isSelected() );\r
1380         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1381                 && _color_labels_same_as_parent_branch.isSelected() );\r
1382         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1383                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1384         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1385                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
1386         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1387             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1388         }\r
1389         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1390             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1391         }\r
1392         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1393             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1394         }\r
1395         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1396                 && _search_case_senstive_cbmi.isSelected() );\r
1397         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1398             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1399         }\r
1400         if ( _label_direction_cbmi != null ) {\r
1401             if ( _label_direction_cbmi.isSelected() ) {\r
1402                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1403             }\r
1404             else {\r
1405                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1406             }\r
1407         }\r
1408         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1409         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1410                 && _show_confidence_stddev_cbmi.isSelected() );\r
1411         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {\r
1412             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );\r
1413         }\r
1414         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1415             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1416         }\r
1417         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1418                 && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1419         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1420                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1421         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1422         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1423                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1424             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1425         }\r
1426         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1427                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1428             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1429         }\r
1430         else {\r
1431             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1432         }\r
1433         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1434                 && _print_black_and_white_cbmi.isSelected() );\r
1435         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1436                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1437         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1438             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1439         }\r
1440         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1441             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1442         }\r
1443         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1444             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1445         }\r
1446         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1447             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1448         }\r
1449         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1450                 && _replace_underscores_cbmi.isSelected() );\r
1451         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1452                 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1453         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1454                 && _search_whole_words_only_cbmi.isSelected() );\r
1455         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1456                 && _inverse_search_result_cbmi.isSelected() );\r
1457         if ( _graphics_export_visible_only_cbmi != null ) {\r
1458             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1459             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1460                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1461                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1462             }\r
1463             else {\r
1464                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1465             }\r
1466         }\r
1467         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1468             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1469         }\r
1470         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1471             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1472         }\r
1473         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1474             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1475         }\r
1476         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1477             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1478         }\r
1479         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1480             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1481         }\r
1482         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1483             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1484         }\r
1485         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1486             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1487         }\r
1488         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1489             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1490         }\r
1491     }\r
1492 \r
1493     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1494         setTypeMenuToAllUnselected();\r
1495         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1496     }\r
1497 \r
1498     void viewAsNexus() {\r
1499         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1500             String title = "Nexus";\r
1501             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1502                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1503             }\r
1504             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1505                            title );\r
1506         }\r
1507     }\r
1508 \r
1509     void viewAsNH() {\r
1510         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1511             String title = "New Hampshire";\r
1512             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1513                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1514             }\r
1515             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1516                                    .getNhConversionSupportValueStyle() ),\r
1517                            title );\r
1518         }\r
1519     }\r
1520 \r
1521     void viewAsXML() {\r
1522         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1523             String title = "phyloXML";\r
1524             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1525                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1526             }\r
1527             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1528         }\r
1529     }\r
1530 \r
1531     private void annotateSequences() {\r
1532         if ( getCurrentTreePanel() != null ) {\r
1533             List<PhylogenyNode> nodes = null;\r
1534             if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
1535                     || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
1536                 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
1537             }\r
1538             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1539                 JOptionPane\r
1540                         .showMessageDialog( this,\r
1541                                             "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1542                                             "No nodes selected for annotation",\r
1543                                             JOptionPane.ERROR_MESSAGE );\r
1544                 return;\r
1545             }\r
1546             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1547             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1548                 final JTextField ref_field = new JTextField( 10 );\r
1549                 final JTextField desc_filed = new JTextField( 20 );\r
1550                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1551                         : getPreviousNodeAnnotationReference() );\r
1552                 final JPanel my_panel = new JPanel();\r
1553                 my_panel.add( new JLabel( "Reference " ) );\r
1554                 my_panel.add( ref_field );\r
1555                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1556                 my_panel.add( new JLabel( "Description " ) );\r
1557                 my_panel.add( desc_filed );\r
1558                 final int result = JOptionPane.showConfirmDialog( null,\r
1559                                                                   my_panel,\r
1560                                                                   "Enter the sequence annotation(s) for the "\r
1561                                                                           + nodes.size() + " selected nodes",\r
1562                                                                   JOptionPane.OK_CANCEL_OPTION );\r
1563                 if ( result == JOptionPane.OK_OPTION ) {\r
1564                     String ref = ref_field.getText();\r
1565                     String desc = desc_filed.getText();\r
1566                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1567                         ref = ref.trim();\r
1568                         ref = ref.replaceAll( "\\s+", " " );\r
1569                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1570                                 || ( ref.length() < 3 ) ) {\r
1571                             JOptionPane.showMessageDialog( this,\r
1572                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1573                                                            "Illegal Format for Annotation Reference",\r
1574                                                            JOptionPane.ERROR_MESSAGE );\r
1575                             return;\r
1576                         }\r
1577                     }\r
1578                     if ( ref != null ) {\r
1579                         setPreviousNodeAnnotationReference( ref );\r
1580                     }\r
1581                     if ( desc != null ) {\r
1582                         desc = desc.trim();\r
1583                         desc = desc.replaceAll( "\\s+", " " );\r
1584                     }\r
1585                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1586                         for( final PhylogenyNode n : nodes ) {\r
1587                             ForesterUtil.ensurePresenceOfSequence( n );\r
1588                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1589                                     : new Annotation( ref );\r
1590                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1591                                 ann.setDesc( desc );\r
1592                             }\r
1593                             n.getNodeData().getSequence().addAnnotation( ann );\r
1594                         }\r
1595                     }\r
1596                     getMainPanel().getControlPanel().showAnnotations();\r
1597                 }\r
1598             }\r
1599         }\r
1600     }\r
1601 \r
1602     private void chooseFont() {\r
1603         final FontChooser fc = new FontChooser();\r
1604         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1605         fc.showDialog( this, "Select the Base Font" );\r
1606         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1607     }\r
1608 \r
1609     private void chooseMinimalConfidence() {\r
1610         final String s = ( String ) JOptionPane\r
1611                 .showInputDialog( this,\r
1612                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1613                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1614                                   "Minimal Confidence Value",\r
1615                                   JOptionPane.QUESTION_MESSAGE,\r
1616                                   null,\r
1617                                   null,\r
1618                                   getOptions().getMinConfidenceValue() );\r
1619         if ( !ForesterUtil.isEmpty( s ) ) {\r
1620             boolean success = true;\r
1621             double m = 0.0;\r
1622             final String m_str = s.trim();\r
1623             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1624                 try {\r
1625                     m = Double.parseDouble( m_str );\r
1626                 }\r
1627                 catch ( final Exception ex ) {\r
1628                     success = false;\r
1629                 }\r
1630             }\r
1631             else {\r
1632                 success = false;\r
1633             }\r
1634             if ( success && ( m >= 0.0 ) ) {\r
1635                 getOptions().setMinConfidenceValue( m );\r
1636             }\r
1637         }\r
1638     }\r
1639 \r
1640     private void doUpdateProcessMenu() {\r
1641         if ( _process_pool.size() > 0 ) {\r
1642             if ( _process_menu == null ) {\r
1643                 _process_menu = createMenu( "", getConfiguration() );\r
1644                 _process_menu.setForeground( Color.RED );\r
1645             }\r
1646             _process_menu.removeAll();\r
1647             final String text = "processes running: " + _process_pool.size();\r
1648             _process_menu.setText( text );\r
1649             _jmenubar.add( _process_menu );\r
1650             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1651                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1652                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1653             }\r
1654         }\r
1655         else {\r
1656             if ( _process_menu != null ) {\r
1657                 _process_menu.removeAll();\r
1658                 _jmenubar.remove( _process_menu );\r
1659             }\r
1660         }\r
1661         _jmenubar.validate();\r
1662         _jmenubar.repaint();\r
1663         repaint();\r
1664     }\r
1665 \r
1666     private String getPreviousNodeAnnotationReference() {\r
1667         return _previous_node_annotation_ref;\r
1668     }\r
1669 \r
1670     private void removeBranchColors() {\r
1671         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1672             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1673         }\r
1674     }\r
1675 \r
1676     private void removeVisualStyles() {\r
1677         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1678             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1679         }\r
1680     }\r
1681 \r
1682     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1683         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1684     }\r
1685 \r
1686     /**\r
1687      * Display the about box.\r
1688      */\r
1689     static void about() {\r
1690         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1691         about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );\r
1692         about.append( "All Rights Reserved\n" );\r
1693         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1694         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1695         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1696         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1697         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1698         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1699             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1700         }\r
1701         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1702                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1703             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1704                     + ForesterUtil.OS_VERSION + "]\n" );\r
1705         }\r
1706         final Runtime rt = java.lang.Runtime.getRuntime();\r
1707         final long free_memory = rt.freeMemory() / 1000000;\r
1708         final long total_memory = rt.totalMemory() / 1000000;\r
1709         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1710         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1711         about.append( "References:\n" );\r
1712         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1713         about.append( "For more information & download:\n" );\r
1714         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1715         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1716         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1717     }\r
1718 \r
1719     static void chooseNodeSize( final Options options, final Component parent ) {\r
1720         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1721                                                                  "Please enter the default size for node shapes.\n"\r
1722                                                                          + "[current value: "\r
1723                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1724                                                                  "Node Shape Size",\r
1725                                                                  JOptionPane.QUESTION_MESSAGE,\r
1726                                                                  null,\r
1727                                                                  null,\r
1728                                                                  options.getDefaultNodeShapeSize() );\r
1729         if ( !ForesterUtil.isEmpty( s ) ) {\r
1730             boolean success = true;\r
1731             double m = 0.0;\r
1732             final String m_str = s.trim();\r
1733             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1734                 try {\r
1735                     m = Double.parseDouble( m_str );\r
1736                 }\r
1737                 catch ( final Exception ex ) {\r
1738                     success = false;\r
1739                 }\r
1740             }\r
1741             else {\r
1742                 success = false;\r
1743             }\r
1744             if ( success && ( m >= 0.0 ) ) {\r
1745                 final short size = ForesterUtil.roundToShort( m );\r
1746                 if ( size >= 0.0 ) {\r
1747                     options.setDefaultNodeShapeSize( size );\r
1748                 }\r
1749             }\r
1750         }\r
1751     }\r
1752 \r
1753     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1754         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1755     }\r
1756 \r
1757     static JMenu createMenu( final String title, final Configuration conf ) {\r
1758         final JMenu jmenu = new JMenu( title );\r
1759         if ( !conf.isUseNativeUI() ) {\r
1760             jmenu.setFont( MainFrame.menu_font );\r
1761             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1762             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1763         }\r
1764         return jmenu;\r
1765     }\r
1766 \r
1767     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1768         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1769         if ( !configuration.isUseNativeUI() ) {\r
1770             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1771             label.setForeground( configuration.getGuiMenuTextColor() );\r
1772             label.setOpaque( true );\r
1773         }\r
1774         label.setSelected( false );\r
1775         label.setEnabled( false );\r
1776         return label;\r
1777     }\r
1778 \r
1779     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
1780         switch ( op.getDefaultNodeFill() ) {\r
1781             case GRADIENT:\r
1782                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1783                 break;\r
1784             case NONE:\r
1785                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1786                 break;\r
1787             case SOLID:\r
1788                 op.setDefaultNodeFill( NodeFill.NONE );\r
1789                 break;\r
1790             default:\r
1791                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1792         }\r
1793     }\r
1794 \r
1795     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
1796         switch ( op.getDefaultNodeShape() ) {\r
1797             case CIRCLE:\r
1798                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1799                 break;\r
1800             case RECTANGLE:\r
1801                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1802                 break;\r
1803             default:\r
1804                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1805         }\r
1806     }\r
1807 \r
1808     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1809         switch ( op.getOvPlacement() ) {\r
1810             case LOWER_LEFT:\r
1811                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1812                 break;\r
1813             case LOWER_RIGHT:\r
1814                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1815                 break;\r
1816             case UPPER_LEFT:\r
1817                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1818                 break;\r
1819             case UPPER_RIGHT:\r
1820                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1821                 break;\r
1822             default:\r
1823                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1824         }\r
1825         if ( tree_panel != null ) {\r
1826             tree_panel.updateOvSettings();\r
1827         }\r
1828     }\r
1829 \r
1830     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
1831         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
1832             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1833                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
1834         }\r
1835         else {\r
1836             mi.setText( "Cycle Node Shape Fill Type..." );\r
1837         }\r
1838     }\r
1839 \r
1840     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
1841         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
1842             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1843                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
1844         }\r
1845         else {\r
1846             mi.setText( "Cycle Node Shape Fill Type..." );\r
1847         }\r
1848     }\r
1849 \r
1850     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
1851         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
1852             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
1853         }\r
1854         else {\r
1855             mi.setText( "Cycle Overview Placement..." );\r
1856         }\r
1857     }\r
1858 \r
1859     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
1860         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
1861             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
1862                     + ")" );\r
1863         }\r
1864         else {\r
1865             mi.setText( "Select Color Scheme..." );\r
1866         }\r
1867     }\r
1868 \r
1869     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
1870         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
1871     }\r
1872 \r
1873     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
1874         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
1875             mi.setEnabled( true );\r
1876         }\r
1877         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
1878             mi.setEnabled( true );\r
1879         }\r
1880         else {\r
1881             mi.setEnabled( false );\r
1882         }\r
1883         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
1884     }\r
1885 \r
1886     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
1887         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
1888     }\r
1889 \r
1890     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,\r
1891                                                            final JCheckBoxMenuItem scale,\r
1892                                                            final JCheckBoxMenuItem branch_lengths,\r
1893                                                            final JRadioButtonMenuItem non_lined_up,\r
1894                                                            final JRadioButtonMenuItem uniform_clado,\r
1895                                                            final JRadioButtonMenuItem nonuniform_clado,\r
1896                                                            final JCheckBoxMenuItem label_direction_cbmi ) {\r
1897         final TreePanel tree_panel = main_panel.getCurrentTreePanel();\r
1898         final ControlPanel control = main_panel.getControlPanel();\r
1899         final Options options = main_panel.getOptions();\r
1900         scale.setSelected( options.isShowScale() );\r
1901         branch_lengths.setSelected( options.isShowBranchLengthValues() );\r
1902         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1903         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {\r
1904             scale.setSelected( false );\r
1905             scale.setEnabled( false );\r
1906             branch_lengths.setSelected( false );\r
1907             branch_lengths.setEnabled( false );\r
1908         }\r
1909         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {\r
1910             scale.setSelected( false );\r
1911             scale.setEnabled( false );\r
1912             branch_lengths.setEnabled( true );\r
1913         }\r
1914         else {\r
1915             scale.setEnabled( true );\r
1916             branch_lengths.setEnabled( true );\r
1917         }\r
1918         if ( ( tree_panel != null )\r
1919                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )\r
1920                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1921                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1922             branch_lengths.setSelected( false );\r
1923             branch_lengths.setEnabled( false );\r
1924         }\r
1925         if ( tree_panel != null ) {\r
1926             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )\r
1927                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {\r
1928                 non_lined_up.setEnabled( false );\r
1929                 uniform_clado.setEnabled( false );\r
1930                 nonuniform_clado.setEnabled( false );\r
1931             }\r
1932             else {\r
1933                 non_lined_up.setEnabled( true );\r
1934                 uniform_clado.setEnabled( true );\r
1935                 nonuniform_clado.setEnabled( true );\r
1936             }\r
1937         }\r
1938         else {\r
1939             if ( ( tree_panel != null )\r
1940                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1941                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1942                 branch_lengths.setSelected( false );\r
1943                 branch_lengths.setEnabled( false );\r
1944             }\r
1945             if ( ( tree_panel != null )\r
1946                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel\r
1947                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {\r
1948                 non_lined_up.setEnabled( false );\r
1949             }\r
1950             else {\r
1951                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1952                 non_lined_up.setEnabled( true );\r
1953             }\r
1954         }\r
1955         label_direction_cbmi.setEnabled( true );\r
1956         if ( tree_panel != null ) {\r
1957             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )\r
1958                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1959                 label_direction_cbmi.setEnabled( false );\r
1960             }\r
1961             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {\r
1962                 scale.setSelected( false );\r
1963                 scale.setEnabled( false );\r
1964             }\r
1965         }\r
1966     }\r
1967 \r
1968     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
1969         for( final TreePanel tree_panel : treepanels ) {\r
1970             tree_panel.setTextAntialias();\r
1971         }\r
1972     }\r
1973 }\r