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

   1 // $Id:\r
   2 // FORESTER -- software libraries and applications\r
   3 // for evolutionary biology research and applications.\r
   4 //\r
   5 // Copyright (C) 2008-2010 Christian M. Zmasek\r
   6 // All rights reserved\r
   7 //\r
   8 // This library is free software; you can redistribute it and/or\r
   9 // modify it under the terms of the GNU Lesser General Public\r
  10 // License as published by the Free Software Foundation; either\r
  11 // version 2.1 of the License, or (at your option) any later version.\r
  12 //\r
  13 // This library is distributed in the hope that it will be useful,\r
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
  16 // Lesser General Public License for more details.\r
  17 //\r
  18 // You should have received a copy of the GNU Lesser General Public\r
  19 // License along with this library; if not, write to the Free Software\r
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
  21 //\r
  22 // Contact: phylosoft @ gmail . com\r
  23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
  24 \r
  25 package org.forester.archaeopteryx;\r
  26 \r
  27 import java.awt.Color;\r
  28 import java.awt.Component;\r
  29 import java.awt.Container;\r
  30 import java.awt.Font;\r
  31 import java.awt.event.ActionEvent;\r
  32 import java.awt.event.ActionListener;\r
  33 import java.io.File;\r
  34 import java.io.IOException;\r
  35 import java.util.ArrayList;\r
  36 import java.util.LinkedList;\r
  37 import java.util.List;\r
  38 import java.util.Locale;\r
  39 import java.util.NoSuchElementException;\r
  40 \r
  41 import javax.swing.Box;\r
  42 import javax.swing.JApplet;\r
  43 import javax.swing.JCheckBoxMenuItem;\r
  44 import javax.swing.JFrame;\r
  45 import javax.swing.JLabel;\r
  46 import javax.swing.JMenu;\r
  47 import javax.swing.JMenuBar;\r
  48 import javax.swing.JMenuItem;\r
  49 import javax.swing.JOptionPane;\r
  50 import javax.swing.JPanel;\r
  51 import javax.swing.JRadioButtonMenuItem;\r
  52 import javax.swing.JTextField;\r
  53 import javax.swing.SwingUtilities;\r
  54 \r
  55 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
  56 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
  57 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
  58 import org.forester.archaeopteryx.tools.InferenceManager;\r
  59 import org.forester.archaeopteryx.tools.ProcessPool;\r
  60 import org.forester.archaeopteryx.tools.ProcessRunning;\r
  61 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
  62 import org.forester.phylogeny.Phylogeny;\r
  63 import org.forester.phylogeny.PhylogenyMethods;\r
  64 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
  65 import org.forester.phylogeny.PhylogenyNode;\r
  66 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
  67 import org.forester.phylogeny.data.Annotation;\r
  68 import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
  69 import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
  70 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
  71 import org.forester.sdi.GSDI;\r
  72 import org.forester.sdi.GSDIR;\r
  73 import org.forester.sdi.SDIException;\r
  74 import org.forester.util.ForesterConstants;\r
  75 import org.forester.util.ForesterUtil;\r
  76 \r
  77 public abstract class MainFrame extends JFrame implements ActionListener {\r
  78 \r
  79     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
  80     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME\r
  81     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
  82     private static final long   serialVersionUID                        = 3655000897845508358L;\r
  83     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
  84                                                                                     Font.PLAIN,\r
  85                                                                                     10 );\r
  86     static final String         TYPE_MENU_HEADER                        = "Type";\r
  87     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
  88     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
  89     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
  90     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
  91     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
  92     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
  93     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO\r
  94     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO\r
  95     static final String         OPTIONS_HEADER                          = "Options";\r
  96     static final String         SEARCH_SUBHEADER                        = "Search:";\r
  97     static final String         DISPLAY_SUBHEADER                       = "Display:";\r
  98     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
  99     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
 100     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
 101     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Branch Length Values";\r
 102     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
 103     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
 104     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
 105     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
 106     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
 107     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
 108     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 109     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 110     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 111     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "External Node Shapes";\r
 112     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Internal Node Shapes";\r
 113     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 114     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 115     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 116     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 117     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 118     static final String         COLOR_LABELS_TIP                        = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";\r
 119     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 120     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 121     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 122     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 123     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 124     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 125     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 126     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 127     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 128     JMenuBar                    _jmenubar;\r
 129     JMenu                       _file_jmenu;\r
 130     JMenu                       _tools_menu;\r
 131     JMenu                       _view_jmenu;\r
 132     JMenu                       _options_jmenu;\r
 133     JMenu                       _font_size_menu;\r
 134     JMenu                       _help_jmenu;\r
 135     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 136     // Analysis menu\r
 137     JMenu                       _analysis_menu;\r
 138     JMenuItem                   _load_species_tree_item;\r
 139     JMenuItem                   _gsdi_item;\r
 140     JMenuItem                   _gsdir_item;\r
 141     JMenuItem                   _lineage_inference;\r
 142     // file menu:\r
 143     JMenuItem                   _open_item;\r
 144     JMenuItem                   _open_url_item;\r
 145     JMenuItem                   _save_item;\r
 146     JMenuItem                   _save_all_item;\r
 147     JMenuItem                   _close_item;\r
 148     JMenuItem                   _exit_item;\r
 149     JMenuItem                   _new_item;\r
 150     // tools menu:\r
 151     JMenuItem                   _midpoint_root_item;\r
 152     JMenuItem                   _taxcolor_item;\r
 153     JMenuItem                   _confcolor_item;\r
 154     JMenuItem                   _color_rank_jmi;\r
 155     JMenuItem                   _collapse_species_specific_subtrees;\r
 156     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me\r
 157     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 158     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 159     JMenuItem                   _obtain_seq_information_jmi;\r
 160     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 161     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 162     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 163     JMenuItem                   _annotate_item;\r
 164     JMenuItem                   _remove_branch_color_item;\r
 165     JMenuItem                   _remove_visual_styles_item;\r
 166     JMenuItem                   _delete_selected_nodes_item;\r
 167     JMenuItem                   _delete_not_selected_nodes_item;\r
 168     // font size menu:\r
 169     JMenuItem                   _super_tiny_fonts_item;\r
 170     JMenuItem                   _tiny_fonts_item;\r
 171     JMenuItem                   _small_fonts_item;\r
 172     JMenuItem                   _medium_fonts_item;\r
 173     JMenuItem                   _large_fonts_item;\r
 174     // options menu:\r
 175     // _  screen and print\r
 176     JMenuItem                   _choose_font_mi;\r
 177     JMenuItem                   _switch_colors_mi;\r
 178     JCheckBoxMenuItem           _label_direction_cbmi;\r
 179     // _  screen display\r
 180     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 181     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 182     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 183     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 184     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 185     JCheckBoxMenuItem           _show_branch_length_values_cbmi;\r
 186     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 187     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me\r
 188     JCheckBoxMenuItem           _show_overview_cbmi;\r
 189     JCheckBoxMenuItem           _show_domain_labels;\r
 190     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 191     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 192     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 193     JMenuItem                   _overview_placment_mi;\r
 194     JMenuItem                   _choose_minimal_confidence_mi;\r
 195     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 196     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 197     JMenuItem                   _cycle_node_shape_mi;\r
 198     JMenuItem                   _cycle_node_fill_mi;\r
 199     JMenuItem                   _choose_node_size_mi;\r
 200     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 201     // _  print\r
 202     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 203     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 204     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 205     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 206     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 207     JMenuItem                   _print_size_mi;\r
 208     JMenuItem                   _choose_pdf_width_mi;\r
 209     // _  parsing\r
 210     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 211     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 212     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 213     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 214     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 215     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 216     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 217     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 218     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 219     // _  search\r
 220     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 221     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 222     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 223     // type menu:\r
 224     JMenu                       _type_menu;\r
 225     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 226     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 227     JCheckBoxMenuItem           _curved_type_cbmi;\r
 228     JCheckBoxMenuItem           _convex_type_cbmi;\r
 229     JCheckBoxMenuItem           _euro_type_cbmi;\r
 230     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 231     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 232     JCheckBoxMenuItem           _circular_type_cbmi;\r
 233     // view as text menu:\r
 234     JMenuItem                   _view_as_NH_item;\r
 235     JMenuItem                   _view_as_XML_item;\r
 236     JMenuItem                   _view_as_nexus_item;\r
 237     JMenuItem                   _display_basic_information_item;\r
 238     // help menu:\r
 239     JMenuItem                   _about_item;\r
 240     JMenuItem                   _help_item;\r
 241     JMenuItem                   _website_item;\r
 242     JMenuItem                   _phyloxml_website_item;\r
 243     JMenuItem                   _phyloxml_ref_item;\r
 244     JMenuItem                   _aptx_ref_item;\r
 245     // process menu:\r
 246     JMenu                       _process_menu;\r
 247     // Handy pointers to child components:\r
 248     MainPanel                   _mainpanel;\r
 249     Container                   _contentpane;\r
 250     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;\r
 251     Configuration               _configuration;\r
 252     Options                     _options;\r
 253     private Phylogeny           _species_tree;\r
 254     InferenceManager            _inference_manager;\r
 255     final ProcessPool           _process_pool;\r
 256     private String              _previous_node_annotation_ref;\r
 257 \r
 258     MainFrame() {\r
 259         _process_pool = ProcessPool.createInstance();\r
 260     }\r
 261 \r
 262     /**\r
 263      * Action performed.\r
 264      */\r
 265     @Override\r
 266     public void actionPerformed( final ActionEvent e ) {\r
 267         final Object o = e.getSource();\r
 268         boolean is_applet = false;\r
 269         JApplet applet = null;\r
 270         if ( getCurrentTreePanel() != null ) {\r
 271             is_applet = getCurrentTreePanel().isApplet();\r
 272             if ( is_applet ) {\r
 273                 applet = getCurrentTreePanel().obtainApplet();\r
 274             }\r
 275         }\r
 276         if ( o == _exit_item ) {\r
 277             close();\r
 278         }\r
 279         else if ( o == _gsdi_item ) {\r
 280             if ( isSubtreeDisplayed() ) {\r
 281                 return;\r
 282             }\r
 283             executeGSDI();\r
 284         }\r
 285         else if ( o == _gsdir_item ) {\r
 286             if ( isSubtreeDisplayed() ) {\r
 287                 return;\r
 288             }\r
 289             executeGSDIR();\r
 290         }\r
 291         else if ( o == _taxcolor_item ) {\r
 292             taxColor();\r
 293         }\r
 294         else if ( o == _confcolor_item ) {\r
 295             confColor();\r
 296         }\r
 297         else if ( o == _color_rank_jmi ) {\r
 298             colorRank();\r
 299         }\r
 300         else if ( o == _collapse_species_specific_subtrees ) {\r
 301             if ( isSubtreeDisplayed() ) {\r
 302                 return;\r
 303             }\r
 304             if ( getCurrentTreePanel() != null ) {\r
 305                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 306             }\r
 307         }\r
 308         else if ( o == _remove_branch_color_item ) {\r
 309             if ( isSubtreeDisplayed() ) {\r
 310                 return;\r
 311             }\r
 312             removeBranchColors();\r
 313         }\r
 314         else if ( o == _remove_visual_styles_item ) {\r
 315             if ( isSubtreeDisplayed() ) {\r
 316                 return;\r
 317             }\r
 318             removeVisualStyles();\r
 319         }\r
 320         else if ( o == _midpoint_root_item ) {\r
 321             if ( isSubtreeDisplayed() ) {\r
 322                 return;\r
 323             }\r
 324             midpointRoot();\r
 325         }\r
 326         else if ( o == _delete_selected_nodes_item ) {\r
 327             if ( isSubtreeDisplayed() ) {\r
 328                 return;\r
 329             }\r
 330             deleteSelectedNodes( true );\r
 331         }\r
 332         else if ( o == _delete_not_selected_nodes_item ) {\r
 333             if ( isSubtreeDisplayed() ) {\r
 334                 return;\r
 335             }\r
 336             deleteSelectedNodes( false );\r
 337         }\r
 338         else if ( o == _annotate_item ) {\r
 339             annotateSequences();\r
 340         }\r
 341         else if ( o == _switch_colors_mi ) {\r
 342             switchColors();\r
 343         }\r
 344         else if ( o == _display_basic_information_item ) {\r
 345             displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 346         }\r
 347         else if ( o == _view_as_NH_item ) {\r
 348             viewAsNH();\r
 349         }\r
 350         else if ( o == _view_as_XML_item ) {\r
 351             viewAsXML();\r
 352         }\r
 353         else if ( o == _view_as_nexus_item ) {\r
 354             viewAsNexus();\r
 355         }\r
 356         else if ( o == _super_tiny_fonts_item ) {\r
 357             if ( getCurrentTreePanel() != null ) {\r
 358                 getCurrentTreePanel().setSuperTinyFonts();\r
 359                 getCurrentTreePanel().repaint();\r
 360             }\r
 361         }\r
 362         else if ( o == _tiny_fonts_item ) {\r
 363             if ( getCurrentTreePanel() != null ) {\r
 364                 getCurrentTreePanel().setTinyFonts();\r
 365                 getCurrentTreePanel().repaint();\r
 366             }\r
 367         }\r
 368         else if ( o == _small_fonts_item ) {\r
 369             if ( getCurrentTreePanel() != null ) {\r
 370                 getCurrentTreePanel().setSmallFonts();\r
 371                 getCurrentTreePanel().repaint();\r
 372             }\r
 373         }\r
 374         else if ( o == _medium_fonts_item ) {\r
 375             if ( getCurrentTreePanel() != null ) {\r
 376                 getCurrentTreePanel().setMediumFonts();\r
 377                 getCurrentTreePanel().repaint();\r
 378             }\r
 379         }\r
 380         else if ( o == _large_fonts_item ) {\r
 381             if ( getCurrentTreePanel() != null ) {\r
 382                 getCurrentTreePanel().setLargeFonts();\r
 383                 getCurrentTreePanel().repaint();\r
 384             }\r
 385         }\r
 386         else if ( o == _choose_font_mi ) {\r
 387             chooseFont();\r
 388         }\r
 389         else if ( o == _choose_minimal_confidence_mi ) {\r
 390             chooseMinimalConfidence();\r
 391         }\r
 392         else if ( o == _choose_node_size_mi ) {\r
 393             chooseNodeSize( getOptions(), this );\r
 394         }\r
 395         else if ( o == _overview_placment_mi ) {\r
 396             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 397         }\r
 398         else if ( o == _cycle_node_fill_mi ) {\r
 399             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
 400         }\r
 401         else if ( o == _cycle_node_shape_mi ) {\r
 402             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
 403         }\r
 404         else if ( o == _screen_antialias_cbmi ) {\r
 405             updateOptions( getOptions() );\r
 406             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 407         }\r
 408         else if ( o == _background_gradient_cbmi ) {\r
 409             updateOptions( getOptions() );\r
 410         }\r
 411         else if ( o == _show_domain_labels ) {\r
 412             updateOptions( getOptions() );\r
 413         }\r
 414         else if ( o == _show_annotation_ref_source ) {\r
 415             updateOptions( getOptions() );\r
 416         }\r
 417         else if ( o == _abbreviate_scientific_names ) {\r
 418             updateOptions( getOptions() );\r
 419         }\r
 420         else if ( o == _color_labels_same_as_parent_branch ) {\r
 421             updateOptions( getOptions() );\r
 422         }\r
 423         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 424             updateOptions( getOptions() );\r
 425         }\r
 426         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 427             updateOptions( getOptions() );\r
 428         }\r
 429         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 430             updateOptions( getOptions() );\r
 431             showWhole();\r
 432         }\r
 433         else if ( o == _uniform_cladograms_rbmi ) {\r
 434             updateOptions( getOptions() );\r
 435             showWhole();\r
 436         }\r
 437         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 438             updateOptions( getOptions() );\r
 439             showWhole();\r
 440         }\r
 441         else if ( o == _search_case_senstive_cbmi ) {\r
 442             updateOptions( getOptions() );\r
 443             getMainPanel().getControlPanel().search0();\r
 444             getMainPanel().getControlPanel().search1();\r
 445         }\r
 446         else if ( o == _search_whole_words_only_cbmi ) {\r
 447             updateOptions( getOptions() );\r
 448             getMainPanel().getControlPanel().search0();\r
 449             getMainPanel().getControlPanel().search1();\r
 450         }\r
 451         else if ( o == _inverse_search_result_cbmi ) {\r
 452             updateOptions( getOptions() );\r
 453             getMainPanel().getControlPanel().search0();\r
 454             getMainPanel().getControlPanel().search1();\r
 455         }\r
 456         else if ( o == _show_scale_cbmi ) {\r
 457             updateOptions( getOptions() );\r
 458         }\r
 459         else if ( o == _show_branch_length_values_cbmi ) {\r
 460             updateOptions( getOptions() );\r
 461         }\r
 462         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 463             updateOptions( getOptions() );\r
 464         }\r
 465         else if ( o == _show_confidence_stddev_cbmi ) {\r
 466             updateOptions( getOptions() );\r
 467         }\r
 468         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 469             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 470                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 471             }\r
 472             updateOptions( getOptions() );\r
 473         }\r
 474         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 475             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 476                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 477             }\r
 478             updateOptions( getOptions() );\r
 479         }\r
 480         else if ( o == _label_direction_cbmi ) {\r
 481             updateOptions( getOptions() );\r
 482         }\r
 483         else if ( o == _show_overview_cbmi ) {\r
 484             updateOptions( getOptions() );\r
 485             if ( getCurrentTreePanel() != null ) {\r
 486                 getCurrentTreePanel().updateOvSizes();\r
 487             }\r
 488         }\r
 489         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 490                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 491                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 492             typeChanged( o );\r
 493         }\r
 494         \r
 495         else if ( o == _about_item ) {\r
 496             about();\r
 497         }\r
 498         else if ( o == _help_item ) {\r
 499             try {\r
 500                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
 501             }\r
 502             catch ( final IOException e1 ) {\r
 503                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 504             }\r
 505         }\r
 506         else if ( o == _website_item ) {\r
 507             try {\r
 508                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 509             }\r
 510             catch ( final IOException e1 ) {\r
 511                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 512             }\r
 513         }\r
 514         else if ( o == _phyloxml_website_item ) {\r
 515             try {\r
 516                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 517             }\r
 518             catch ( final IOException e1 ) {\r
 519                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 520             }\r
 521         }\r
 522         else if ( o == _aptx_ref_item ) {\r
 523             try {\r
 524                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 525             }\r
 526             catch ( final IOException e1 ) {\r
 527                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 528             }\r
 529         }\r
 530         else if ( o == _phyloxml_ref_item ) {\r
 531             try {\r
 532                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 533             }\r
 534             catch ( final IOException e1 ) {\r
 535                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 536             }\r
 537         }\r
 538         else {\r
 539             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 540                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 541                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 542                         readPhylogeniesFromWebservice( i );\r
 543                     }\r
 544                 }\r
 545             }\r
 546         }\r
 547         _contentpane.repaint();\r
 548     }\r
 549 \r
 550     private void deleteSelectedNodes( boolean delete ) {\r
 551         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
 552         if ( phy == null || phy.getNumberOfExternalNodes() < 2 ) {\r
 553             return;\r
 554         }\r
 555         List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
 556         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
 557             final List<PhylogenyNode>  all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
 558             for( final PhylogenyNode n : all_selected_nodes ) {\r
 559                 if ( n.isExternal() ) {\r
 560                     nodes.add( n );\r
 561                 }\r
 562             }\r
 563         }\r
 564         \r
 565         String function = "Retain";\r
 566         if ( delete ) {\r
 567             function = "Delete";\r
 568         }\r
 569         if ( ( nodes == null ) || nodes.isEmpty() ) {\r
 570             JOptionPane\r
 571                     .showMessageDialog( this,\r
 572                                         "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
 573                                         "No external nodes selected to " + function.toLowerCase(),\r
 574                                         JOptionPane.ERROR_MESSAGE );\r
 575             return;\r
 576         }\r
 577         final int todo = nodes.size();\r
 578         final int ext = phy.getNumberOfExternalNodes();\r
 579         int res = todo;\r
 580         if ( delete ) {\r
 581             res = ext - todo;\r
 582         }\r
 583         if ( res < 1 ) {\r
 584             JOptionPane.showMessageDialog( this,\r
 585                                            "Cannot delete all nodes",\r
 586                                            "Attempt to delete all nodes ",\r
 587                                            JOptionPane.ERROR_MESSAGE );\r
 588             return;\r
 589         }\r
 590         final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
 591                 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
 592                 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
 593         if ( result == JOptionPane.OK_OPTION ) {\r
 594             if ( !delete ) {\r
 595                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
 596                 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
 597                     final PhylogenyNode n = it.next();\r
 598                     if ( !nodes.contains( n ) ) {\r
 599                         to_delete.add( n );\r
 600                     }\r
 601                 }\r
 602                 for( final PhylogenyNode n : to_delete ) {\r
 603                     phy.deleteSubtree( n, true );\r
 604                 }\r
 605             }\r
 606             else {\r
 607                 for( final PhylogenyNode n : nodes ) {\r
 608                     phy.deleteSubtree( n, true );\r
 609                 }\r
 610             }\r
 611             resetSearch();\r
 612             getCurrentTreePanel().setNodeInPreorderToNull();\r
 613             phy.externalNodesHaveChanged();\r
 614             phy.clearHashIdToNodeMap();\r
 615             phy.recalculateNumberOfExternalDescendants( true );\r
 616             getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
 617             getCurrentTreePanel().setEdited( true );\r
 618             repaint();\r
 619         }\r
 620     }\r
 621 \r
 622     void resetSearch() {\r
 623         getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
 624         getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
 625         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
 626         getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
 627         getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
 628         getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
 629         getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
 630         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
 631         getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
 632         getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
 633         getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
 634         getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
 635     }\r
 636 \r
 637     public Configuration getConfiguration() {\r
 638         return _configuration;\r
 639     }\r
 640 \r
 641     /**\r
 642      * This method returns the current external node data which\r
 643      * has been selected by the user by clicking the "Return ..."\r
 644      * menu item. This method is expected to be called from Javascript or\r
 645      * something like it.\r
 646      * \r
 647      * @return current external node data as String\r
 648      */\r
 649     public String getCurrentExternalNodesDataBuffer() {\r
 650         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 651     }\r
 652 \r
 653     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 654         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 655     }\r
 656 \r
 657     public int getCurrentExternalNodesDataBufferLength() {\r
 658         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 659     }\r
 660 \r
 661     public InferenceManager getInferenceManager() {\r
 662         return _inference_manager;\r
 663     }\r
 664 \r
 665     public MainPanel getMainPanel() {\r
 666         return _mainpanel;\r
 667     }\r
 668 \r
 669     public Options getOptions() {\r
 670         return _options;\r
 671     }\r
 672 \r
 673     public ProcessPool getProcessPool() {\r
 674         return _process_pool;\r
 675     }\r
 676 \r
 677     public void showTextFrame( final String s, final String title ) {\r
 678         checkTextFrames();\r
 679         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 680     }\r
 681 \r
 682     public void showWhole() {\r
 683         _mainpanel.getControlPanel().showWhole();\r
 684     }\r
 685 \r
 686     public void updateProcessMenu() {\r
 687         // In general Swing is not thread safe.\r
 688         // See "Swing's Threading Policy".\r
 689         SwingUtilities.invokeLater( new Runnable() {\r
 690 \r
 691             @Override\r
 692             public void run() {\r
 693                 doUpdateProcessMenu();\r
 694             }\r
 695         } );\r
 696     }\r
 697 \r
 698     void activateSaveAllIfNeeded() {\r
 699         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 700             _save_all_item.setEnabled( true );\r
 701         }\r
 702         else {\r
 703             _save_all_item.setEnabled( false );\r
 704         }\r
 705     }\r
 706 \r
 707     void buildFileMenu() {\r
 708         _file_jmenu = createMenu( "File", getConfiguration() );\r
 709         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 710         customizeJMenuItem( _exit_item );\r
 711         _jmenubar.add( _file_jmenu );\r
 712     }\r
 713 \r
 714     void buildFontSizeMenu() {\r
 715         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 716         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 717         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 718         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 719         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 720         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 721         customizeJMenuItem( _super_tiny_fonts_item );\r
 722         customizeJMenuItem( _tiny_fonts_item );\r
 723         customizeJMenuItem( _small_fonts_item );\r
 724         customizeJMenuItem( _medium_fonts_item );\r
 725         customizeJMenuItem( _large_fonts_item );\r
 726         _jmenubar.add( _font_size_menu );\r
 727     }\r
 728 \r
 729     void buildHelpMenu() {\r
 730         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 731         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
 732         _help_jmenu.addSeparator();\r
 733         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 734         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
 735         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 736         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 737         _help_jmenu.addSeparator();\r
 738         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 739         customizeJMenuItem( _help_item );\r
 740         customizeJMenuItem( _website_item );\r
 741         customizeJMenuItem( _phyloxml_website_item );\r
 742         customizeJMenuItem( _aptx_ref_item );\r
 743         customizeJMenuItem( _phyloxml_ref_item );\r
 744         customizeJMenuItem( _about_item );\r
 745         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 746         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 747         _jmenubar.add( _help_jmenu );\r
 748     }\r
 749 \r
 750     void buildTypeMenu() {\r
 751         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 752         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 753         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 754         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 755         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 756         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 757         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 758         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 759         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 760         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 761         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 762         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 763         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 764         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 765         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 766         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 767         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 768         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 769         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 770         initializeTypeMenu( getOptions() );\r
 771         _jmenubar.add( _type_menu );\r
 772     }\r
 773 \r
 774     void buildViewMenu() {\r
 775         _view_jmenu = createMenu( "View", getConfiguration() );\r
 776         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 777         _view_jmenu.addSeparator();\r
 778         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 779         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 780         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 781         customizeJMenuItem( _display_basic_information_item );\r
 782         customizeJMenuItem( _view_as_NH_item );\r
 783         customizeJMenuItem( _view_as_XML_item );\r
 784         customizeJMenuItem( _view_as_nexus_item );\r
 785         _jmenubar.add( _view_jmenu );\r
 786     }\r
 787 \r
 788     void checkTextFrames() {\r
 789         if ( _textframes.size() > 5 ) {\r
 790             try {\r
 791                 if ( _textframes.getFirst() != null ) {\r
 792                     _textframes.getFirst().removeMe();\r
 793                 }\r
 794                 else {\r
 795                     _textframes.removeFirst();\r
 796                 }\r
 797             }\r
 798             catch ( final NoSuchElementException e ) {\r
 799                 // Ignore.\r
 800             }\r
 801         }\r
 802     }\r
 803 \r
 804     void close() {\r
 805         removeAllTextFrames();\r
 806         if ( _mainpanel != null ) {\r
 807             _mainpanel.terminate();\r
 808         }\r
 809         if ( _contentpane != null ) {\r
 810             _contentpane.removeAll();\r
 811         }\r
 812         setVisible( false );\r
 813         dispose();\r
 814     }\r
 815 \r
 816     void colorRank() {\r
 817         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 818             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
 819             final String rank = ( String ) JOptionPane\r
 820                     .showInputDialog( this,\r
 821                                       "What rank should the colorization be based on",\r
 822                                       "Rank Selection",\r
 823                                       JOptionPane.QUESTION_MESSAGE,\r
 824                                       null,\r
 825                                       ranks,\r
 826                                       null );\r
 827             if ( !ForesterUtil.isEmpty( rank ) ) {\r
 828                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
 829             }\r
 830         }\r
 831     }\r
 832 \r
 833     void confColor() {\r
 834         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 835             _mainpanel.getCurrentTreePanel().confColor();\r
 836         }\r
 837     }\r
 838 \r
 839     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
 840         if ( item != null ) {\r
 841             item.setFont( MainFrame.menu_font );\r
 842             if ( !getConfiguration().isUseNativeUI() ) {\r
 843                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 844                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 845             }\r
 846             item.setSelected( is_selected );\r
 847             item.addActionListener( this );\r
 848         }\r
 849     }\r
 850 \r
 851     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
 852         if ( jmi != null ) {\r
 853             jmi.setFont( MainFrame.menu_font );\r
 854             if ( !getConfiguration().isUseNativeUI() ) {\r
 855                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 856                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 857             }\r
 858             jmi.addActionListener( this );\r
 859         }\r
 860         return jmi;\r
 861     }\r
 862 \r
 863     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
 864         if ( item != null ) {\r
 865             item.setFont( MainFrame.menu_font );\r
 866             if ( !getConfiguration().isUseNativeUI() ) {\r
 867                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 868                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 869             }\r
 870             item.setSelected( is_selected );\r
 871             item.addActionListener( this );\r
 872         }\r
 873     }\r
 874 \r
 875     void displayBasicInformation( final File treefile ) {\r
 876         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
 877             String title = "Basic Information";\r
 878             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
 879                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
 880             }\r
 881             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
 882         }\r
 883     }\r
 884 \r
 885     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
 886         try {\r
 887             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 888         }\r
 889         catch ( final Exception ex ) {\r
 890             // Do nothing.\r
 891         }\r
 892         JOptionPane.showMessageDialog( this,\r
 893                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
 894                                        "Error during File|Open",\r
 895                                        JOptionPane.ERROR_MESSAGE );\r
 896     }\r
 897 \r
 898     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
 899         try {\r
 900             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 901         }\r
 902         catch ( final Exception ex ) {\r
 903             // Do nothing.\r
 904         }\r
 905         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
 906     }\r
 907 \r
 908     void executeGSDI() {\r
 909         if ( !isOKforSDI( false, true ) ) {\r
 910             return;\r
 911         }\r
 912         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
 913             JOptionPane.showMessageDialog( this,\r
 914                                            "Gene tree is not rooted.",\r
 915                                            "Cannot execute GSDI",\r
 916                                            JOptionPane.ERROR_MESSAGE );\r
 917             return;\r
 918         }\r
 919         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 920         gene_tree.setAllNodesToNotCollapse();\r
 921         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 922         GSDI gsdi = null;\r
 923         final Phylogeny species_tree = getSpeciesTree().copy();\r
 924         try {\r
 925             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
 926         }\r
 927         catch ( final SDIException e ) {\r
 928             JOptionPane.showMessageDialog( this,\r
 929                                            e.getLocalizedMessage(),\r
 930                                            "Error during GSDI",\r
 931                                            JOptionPane.ERROR_MESSAGE );\r
 932             return;\r
 933         }\r
 934         catch ( final Exception e ) {\r
 935             AptxUtil.unexpectedException( e );\r
 936             return;\r
 937         }\r
 938         gene_tree.setRerootable( false );\r
 939         gene_tree.clearHashIdToNodeMap();\r
 940         gene_tree.recalculateNumberOfExternalDescendants( true );\r
 941         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
 942         getMainPanel().getControlPanel().setShowEvents( true );\r
 943         showWhole();\r
 944         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 945         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 946         showWhole();\r
 947         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 948         showWhole();\r
 949         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 950         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 951         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 952             JOptionPane.showMessageDialog( this,\r
 953                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 954                                                    + "Potential duplications: "\r
 955                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 956                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 957                                                    + "Stripped gene tree nodes: "\r
 958                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 959                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 960                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 961                                            "GSDI successfully completed",\r
 962                                            JOptionPane.WARNING_MESSAGE );\r
 963         }\r
 964         else {\r
 965             JOptionPane.showMessageDialog( this,\r
 966                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 967                                                    + "Potential duplications: "\r
 968                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 969                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 970                                                    + "Stripped gene tree nodes: "\r
 971                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 972                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 973                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 974                                            "GSDI successfully completed",\r
 975                                            JOptionPane.INFORMATION_MESSAGE );\r
 976         }\r
 977     }\r
 978 \r
 979     void executeGSDIR() {\r
 980         if ( !isOKforSDI( false, false ) ) {\r
 981             return;\r
 982         }\r
 983         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
 984         if ( ( p > 0 )\r
 985                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
 986             JOptionPane.showMessageDialog( this,\r
 987                                            "Gene tree is not completely binary",\r
 988                                            "Cannot execute GSDI",\r
 989                                            JOptionPane.ERROR_MESSAGE );\r
 990             return;\r
 991         }\r
 992         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 993         gene_tree.setAllNodesToNotCollapse();\r
 994         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 995         GSDIR gsdir = null;\r
 996         final Phylogeny species_tree = getSpeciesTree().copy();\r
 997         try {\r
 998             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
 999         }\r
1000         catch ( final SDIException e ) {\r
1001             JOptionPane.showMessageDialog( this,\r
1002                                            e.getLocalizedMessage(),\r
1003                                            "Error during GSDIR",\r
1004                                            JOptionPane.ERROR_MESSAGE );\r
1005             return;\r
1006         }\r
1007         catch ( final Exception e ) {\r
1008             AptxUtil.unexpectedException( e );\r
1009             return;\r
1010         }\r
1011         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
1012         result_gene_tree.setRerootable( false );\r
1013         result_gene_tree.clearHashIdToNodeMap();\r
1014         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
1015         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
1016         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
1017         getMainPanel().getControlPanel().setShowEvents( true );\r
1018         showWhole();\r
1019         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1020         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1021         showWhole();\r
1022         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1023         showWhole();\r
1024         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1025         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1026         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1027             JOptionPane.showMessageDialog( this,\r
1028                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1029                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1030                                                    + "Stripped gene tree nodes: "\r
1031                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1032                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1033                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1034                                            "GSDIR successfully completed",\r
1035                                            JOptionPane.WARNING_MESSAGE );\r
1036         }\r
1037         else {\r
1038             JOptionPane.showMessageDialog( this,\r
1039                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1040                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1041                                                    + "Stripped gene tree nodes: "\r
1042                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1043                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1044                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1045                                            "GSDIR successfully completed",\r
1046                                            JOptionPane.INFORMATION_MESSAGE );\r
1047         }\r
1048     }\r
1049 \r
1050     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
1051         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
1052             JOptionPane.showMessageDialog( this,\r
1053                                            "Gene tree and species tree have no species in common.",\r
1054                                            "Error during SDI",\r
1055                                            JOptionPane.ERROR_MESSAGE );\r
1056             return false;\r
1057         }\r
1058         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
1059             JOptionPane.showMessageDialog( this,\r
1060                                            "Gene tree and species tree have only one species in common.",\r
1061                                            "Error during SDI",\r
1062                                            JOptionPane.ERROR_MESSAGE );\r
1063             return false;\r
1064         }\r
1065         else {\r
1066             return true;\r
1067         }\r
1068     }\r
1069 \r
1070     TreePanel getCurrentTreePanel() {\r
1071         return getMainPanel().getCurrentTreePanel();\r
1072     }\r
1073 \r
1074     JMenu getHelpMenu() {\r
1075         return _help_jmenu;\r
1076     }\r
1077 \r
1078     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
1079         return _label_direction_cbmi;\r
1080     }\r
1081 \r
1082     JMenuBar getMenuBarOfMainFrame() {\r
1083         return _jmenubar;\r
1084     }\r
1085 \r
1086     final Phylogeny getSpeciesTree() {\r
1087         return _species_tree;\r
1088     }\r
1089 \r
1090     \r
1091 \r
1092     void initializeTypeMenu( final Options options ) {\r
1093         setTypeMenuToAllUnselected();\r
1094         switch ( options.getPhylogenyGraphicsType() ) {\r
1095             case CONVEX:\r
1096                 _convex_type_cbmi.setSelected( true );\r
1097                 break;\r
1098             case CURVED:\r
1099                 _curved_type_cbmi.setSelected( true );\r
1100                 break;\r
1101             case EURO_STYLE:\r
1102                 _euro_type_cbmi.setSelected( true );\r
1103                 break;\r
1104             case ROUNDED:\r
1105                 _rounded_type_cbmi.setSelected( true );\r
1106                 break;\r
1107             case TRIANGULAR:\r
1108                 _triangular_type_cbmi.setSelected( true );\r
1109                 break;\r
1110             case UNROOTED:\r
1111                 _unrooted_type_cbmi.setSelected( true );\r
1112                 break;\r
1113             case CIRCULAR:\r
1114                 _circular_type_cbmi.setSelected( true );\r
1115                 break;\r
1116             default:\r
1117                 _rectangular_type_cbmi.setSelected( true );\r
1118                 break;\r
1119         }\r
1120     }\r
1121 \r
1122     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1123         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1124             return false;\r
1125         }\r
1126         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1127             JOptionPane.showMessageDialog( this,\r
1128                                            "No species tree loaded",\r
1129                                            "Cannot execute GSDI",\r
1130                                            JOptionPane.ERROR_MESSAGE );\r
1131             return false;\r
1132         }\r
1133         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1134             JOptionPane.showMessageDialog( this,\r
1135                                            "Species tree is not completely binary",\r
1136                                            "Cannot execute GSDI",\r
1137                                            JOptionPane.ERROR_MESSAGE );\r
1138             return false;\r
1139         }\r
1140         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1141             JOptionPane.showMessageDialog( this,\r
1142                                            "Gene tree is not completely binary",\r
1143                                            "Cannot execute GSDI",\r
1144                                            JOptionPane.ERROR_MESSAGE );\r
1145             return false;\r
1146         }\r
1147         else {\r
1148             return true;\r
1149         }\r
1150     }\r
1151 \r
1152     boolean isSubtreeDisplayed() {\r
1153         if ( getCurrentTreePanel() != null ) {\r
1154             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1155                 JOptionPane\r
1156                         .showMessageDialog( this,\r
1157                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1158                                             "Operation can not be exectuted on a sub-tree",\r
1159                                             JOptionPane.WARNING_MESSAGE );\r
1160                 return true;\r
1161             }\r
1162         }\r
1163         return false;\r
1164     }\r
1165 \r
1166     void midpointRoot() {\r
1167         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1168             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1169         }\r
1170     }\r
1171 \r
1172     void readPhylogeniesFromWebservice( final int i ) {\r
1173         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1174         new Thread( reader ).start();\r
1175     }\r
1176 \r
1177     void removeAllTextFrames() {\r
1178         for( final TextFrame tf : _textframes ) {\r
1179             if ( tf != null ) {\r
1180                 tf.close();\r
1181             }\r
1182         }\r
1183         _textframes.clear();\r
1184     }\r
1185 \r
1186     void setConfiguration( final Configuration configuration ) {\r
1187         _configuration = configuration;\r
1188     }\r
1189 \r
1190     void setInferenceManager( final InferenceManager i ) {\r
1191         _inference_manager = i;\r
1192     }\r
1193 \r
1194     void setOptions( final Options options ) {\r
1195         _options = options;\r
1196     }\r
1197 \r
1198     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1199         setTypeMenuToAllUnselected();\r
1200         switch ( type ) {\r
1201             case CIRCULAR:\r
1202                 _circular_type_cbmi.setSelected( true );\r
1203                 break;\r
1204             case CONVEX:\r
1205                 _convex_type_cbmi.setSelected( true );\r
1206                 break;\r
1207             case CURVED:\r
1208                 _curved_type_cbmi.setSelected( true );\r
1209                 break;\r
1210             case EURO_STYLE:\r
1211                 _euro_type_cbmi.setSelected( true );\r
1212                 break;\r
1213             case ROUNDED:\r
1214                 _rounded_type_cbmi.setSelected( true );\r
1215                 break;\r
1216             case RECTANGULAR:\r
1217                 _rectangular_type_cbmi.setSelected( true );\r
1218                 break;\r
1219             case TRIANGULAR:\r
1220                 _triangular_type_cbmi.setSelected( true );\r
1221                 break;\r
1222             case UNROOTED:\r
1223                 _unrooted_type_cbmi.setSelected( true );\r
1224                 break;\r
1225             default:\r
1226                 throw new IllegalArgumentException( "unknown type: " + type );\r
1227         }\r
1228     }\r
1229 \r
1230     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1231         _species_tree = species_tree;\r
1232     }\r
1233 \r
1234     void setTypeMenuToAllUnselected() {\r
1235         _convex_type_cbmi.setSelected( false );\r
1236         _curved_type_cbmi.setSelected( false );\r
1237         _euro_type_cbmi.setSelected( false );\r
1238         _rounded_type_cbmi.setSelected( false );\r
1239         _triangular_type_cbmi.setSelected( false );\r
1240         _rectangular_type_cbmi.setSelected( false );\r
1241         _unrooted_type_cbmi.setSelected( false );\r
1242         _circular_type_cbmi.setSelected( false );\r
1243     }\r
1244 \r
1245     void switchColors() {\r
1246         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1247         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1248         csc.setVisible( true );\r
1249     }\r
1250 \r
1251     void taxColor() {\r
1252         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1253             _mainpanel.getCurrentTreePanel().taxColor();\r
1254         }\r
1255     }\r
1256 \r
1257     void typeChanged( final Object o ) {\r
1258         updateTypeCheckboxes( getOptions(), o );\r
1259         updateOptions( getOptions() );\r
1260         if ( getCurrentTreePanel() != null ) {\r
1261             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1262             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1263             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1264                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1265                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1266                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1267                 getCurrentTreePanel().getControlPanel().showWhole();\r
1268             }\r
1269             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1270                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1271             }\r
1272             else {\r
1273                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1274             }\r
1275             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1276             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1277             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1278                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1279                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1280                 }\r
1281                 else {\r
1282                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1283                 }\r
1284             }\r
1285         }\r
1286     }\r
1287 \r
1288     void updateOptions( final Options options ) {\r
1289         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1290         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1291                 && _background_gradient_cbmi.isSelected() );\r
1292         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1293         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1294                 && _show_annotation_ref_source.isSelected() );\r
1295         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1296                 && _abbreviate_scientific_names.isSelected() );\r
1297         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1298                 && _color_labels_same_as_parent_branch.isSelected() );\r
1299         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1300                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1301         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1302                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
1303         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1304             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1305         }\r
1306         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1307             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1308         }\r
1309         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1310             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1311         }\r
1312         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1313                 && _search_case_senstive_cbmi.isSelected() );\r
1314         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1315             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1316         }\r
1317         if ( _label_direction_cbmi != null ) {\r
1318             if ( _label_direction_cbmi.isSelected() ) {\r
1319                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1320             }\r
1321             else {\r
1322                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1323             }\r
1324         }\r
1325         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1326         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1327                 && _show_confidence_stddev_cbmi.isSelected() );\r
1328         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {\r
1329             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );\r
1330         }\r
1331         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1332             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1333         }\r
1334         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1335                 && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1336         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1337                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1338         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1339         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1340                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1341             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1342         }\r
1343         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1344                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1345             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1346         }\r
1347         else {\r
1348             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1349         }\r
1350         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1351                 && _print_black_and_white_cbmi.isSelected() );\r
1352         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1353                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1354         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1355             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1356         }\r
1357         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1358             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1359         }\r
1360         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1361             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1362         }\r
1363         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1364             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1365         }\r
1366         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1367                 && _replace_underscores_cbmi.isSelected() );\r
1368         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1369                 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1370         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1371                 && _search_whole_words_only_cbmi.isSelected() );\r
1372         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1373                 && _inverse_search_result_cbmi.isSelected() );\r
1374         if ( _graphics_export_visible_only_cbmi != null ) {\r
1375             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1376             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1377                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1378                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1379             }\r
1380             else {\r
1381                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1382             }\r
1383         }\r
1384         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1385             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1386         }\r
1387         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1388             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1389         }\r
1390         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1391             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1392         }\r
1393         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1394             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1395         }\r
1396         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1397             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1398         }\r
1399         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1400             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1401         }\r
1402         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1403             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1404         }\r
1405         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1406             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1407         }\r
1408     }\r
1409 \r
1410     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1411         setTypeMenuToAllUnselected();\r
1412         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1413     }\r
1414 \r
1415     void viewAsNexus() {\r
1416         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1417             String title = "Nexus";\r
1418             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1419                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1420             }\r
1421             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1422                            title );\r
1423         }\r
1424     }\r
1425 \r
1426     void viewAsNH() {\r
1427         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1428             String title = "New Hampshire";\r
1429             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1430                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1431             }\r
1432             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1433                                    .getNhConversionSupportValueStyle() ),\r
1434                            title );\r
1435         }\r
1436     }\r
1437 \r
1438     void viewAsXML() {\r
1439         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1440             String title = "phyloXML";\r
1441             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1442                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1443             }\r
1444             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1445         }\r
1446     }\r
1447 \r
1448     private void annotateSequences() {\r
1449         if ( getCurrentTreePanel() != null ) {\r
1450             List<PhylogenyNode> nodes = null;\r
1451             if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
1452                     || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
1453                 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
1454             }\r
1455             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1456                 JOptionPane\r
1457                         .showMessageDialog( this,\r
1458                                             "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1459                                             "No nodes selected for annotation",\r
1460                                             JOptionPane.ERROR_MESSAGE );\r
1461                 return;\r
1462             }\r
1463             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1464             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1465                 final JTextField ref_field = new JTextField( 10 );\r
1466                 final JTextField desc_filed = new JTextField( 20 );\r
1467                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1468                         : getPreviousNodeAnnotationReference() );\r
1469                 final JPanel my_panel = new JPanel();\r
1470                 my_panel.add( new JLabel( "Reference " ) );\r
1471                 my_panel.add( ref_field );\r
1472                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1473                 my_panel.add( new JLabel( "Description " ) );\r
1474                 my_panel.add( desc_filed );\r
1475                 final int result = JOptionPane.showConfirmDialog( null,\r
1476                                                                   my_panel,\r
1477                                                                   "Enter the sequence annotation(s) for the "\r
1478                                                                           + nodes.size() + " selected nodes",\r
1479                                                                   JOptionPane.OK_CANCEL_OPTION );\r
1480                 if ( result == JOptionPane.OK_OPTION ) {\r
1481                     String ref = ref_field.getText();\r
1482                     String desc = desc_filed.getText();\r
1483                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1484                         ref = ref.trim();\r
1485                         ref = ref.replaceAll( "\\s+", " " );\r
1486                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1487                                 || ( ref.length() < 3 ) ) {\r
1488                             JOptionPane.showMessageDialog( this,\r
1489                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1490                                                            "Illegal Format for Annotation Reference",\r
1491                                                            JOptionPane.ERROR_MESSAGE );\r
1492                             return;\r
1493                         }\r
1494                     }\r
1495                     if ( ref != null ) {\r
1496                         setPreviousNodeAnnotationReference( ref );\r
1497                     }\r
1498                     if ( desc != null ) {\r
1499                         desc = desc.trim();\r
1500                         desc = desc.replaceAll( "\\s+", " " );\r
1501                     }\r
1502                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1503                         for( final PhylogenyNode n : nodes ) {\r
1504                             ForesterUtil.ensurePresenceOfSequence( n );\r
1505                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1506                                     : new Annotation( ref );\r
1507                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1508                                 ann.setDesc( desc );\r
1509                             }\r
1510                             n.getNodeData().getSequence().addAnnotation( ann );\r
1511                         }\r
1512                     }\r
1513                     getMainPanel().getControlPanel().showAnnotations();\r
1514                 }\r
1515             }\r
1516         }\r
1517     }\r
1518 \r
1519     private void chooseFont() {\r
1520         final FontChooser fc = new FontChooser();\r
1521         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1522         fc.showDialog( this, "Select the Base Font" );\r
1523         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1524     }\r
1525 \r
1526     private void chooseMinimalConfidence() {\r
1527         final String s = ( String ) JOptionPane\r
1528                 .showInputDialog( this,\r
1529                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1530                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1531                                   "Minimal Confidence Value",\r
1532                                   JOptionPane.QUESTION_MESSAGE,\r
1533                                   null,\r
1534                                   null,\r
1535                                   getOptions().getMinConfidenceValue() );\r
1536         if ( !ForesterUtil.isEmpty( s ) ) {\r
1537             boolean success = true;\r
1538             double m = 0.0;\r
1539             final String m_str = s.trim();\r
1540             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1541                 try {\r
1542                     m = Double.parseDouble( m_str );\r
1543                 }\r
1544                 catch ( final Exception ex ) {\r
1545                     success = false;\r
1546                 }\r
1547             }\r
1548             else {\r
1549                 success = false;\r
1550             }\r
1551             if ( success && ( m >= 0.0 ) ) {\r
1552                 getOptions().setMinConfidenceValue( m );\r
1553             }\r
1554         }\r
1555     }\r
1556 \r
1557     private void doUpdateProcessMenu() {\r
1558         if ( _process_pool.size() > 0 ) {\r
1559             if ( _process_menu == null ) {\r
1560                 _process_menu = createMenu( "", getConfiguration() );\r
1561                 _process_menu.setForeground( Color.RED );\r
1562             }\r
1563             _process_menu.removeAll();\r
1564             final String text = "processes running: " + _process_pool.size();\r
1565             _process_menu.setText( text );\r
1566             _jmenubar.add( _process_menu );\r
1567             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1568                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1569                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1570             }\r
1571         }\r
1572         else {\r
1573             if ( _process_menu != null ) {\r
1574                 _process_menu.removeAll();\r
1575                 _jmenubar.remove( _process_menu );\r
1576             }\r
1577         }\r
1578         _jmenubar.validate();\r
1579         _jmenubar.repaint();\r
1580         repaint();\r
1581     }\r
1582 \r
1583     private String getPreviousNodeAnnotationReference() {\r
1584         return _previous_node_annotation_ref;\r
1585     }\r
1586 \r
1587     private void removeBranchColors() {\r
1588         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1589             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1590         }\r
1591     }\r
1592 \r
1593     private void removeVisualStyles() {\r
1594         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1595             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1596         }\r
1597     }\r
1598 \r
1599     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1600         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1601     }\r
1602 \r
1603     /**\r
1604      * Display the about box.\r
1605      */\r
1606     static void about() {\r
1607         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1608         about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
1609         about.append( "All Rights Reserved\n" );\r
1610         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1611         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1612         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1613         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1614         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1615         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1616             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1617         }\r
1618         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1619                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1620             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1621                     + ForesterUtil.OS_VERSION + "]\n" );\r
1622         }\r
1623         final Runtime rt = java.lang.Runtime.getRuntime();\r
1624         final long free_memory = rt.freeMemory() / 1000000;\r
1625         final long total_memory = rt.totalMemory() / 1000000;\r
1626         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1627         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1628         about.append( "References:\n" );\r
1629         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1630         about.append( "For more information & download:\n" );\r
1631         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1632         about.append( "Documentation:\n" );\r
1633         about.append( Constants.APTX_DOC_SITE + "\n" );\r
1634         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1635         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1636     }\r
1637 \r
1638     static void chooseNodeSize( final Options options, final Component parent ) {\r
1639         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1640                                                                  "Please enter the default size for node shapes.\n"\r
1641                                                                          + "[current value: "\r
1642                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1643                                                                  "Node Shape Size",\r
1644                                                                  JOptionPane.QUESTION_MESSAGE,\r
1645                                                                  null,\r
1646                                                                  null,\r
1647                                                                  options.getDefaultNodeShapeSize() );\r
1648         if ( !ForesterUtil.isEmpty( s ) ) {\r
1649             boolean success = true;\r
1650             double m = 0.0;\r
1651             final String m_str = s.trim();\r
1652             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1653                 try {\r
1654                     m = Double.parseDouble( m_str );\r
1655                 }\r
1656                 catch ( final Exception ex ) {\r
1657                     success = false;\r
1658                 }\r
1659             }\r
1660             else {\r
1661                 success = false;\r
1662             }\r
1663             if ( success && ( m >= 0.0 ) ) {\r
1664                 final short size = ForesterUtil.roundToShort( m );\r
1665                 if ( size >= 0.0 ) {\r
1666                     options.setDefaultNodeShapeSize( size );\r
1667                 }\r
1668             }\r
1669         }\r
1670     }\r
1671 \r
1672     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1673         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1674     }\r
1675 \r
1676     static JMenu createMenu( final String title, final Configuration conf ) {\r
1677         final JMenu jmenu = new JMenu( title );\r
1678         if ( !conf.isUseNativeUI() ) {\r
1679             jmenu.setFont( MainFrame.menu_font );\r
1680             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1681             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1682         }\r
1683         return jmenu;\r
1684     }\r
1685 \r
1686     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1687         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1688         if ( !configuration.isUseNativeUI() ) {\r
1689             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1690             label.setForeground( configuration.getGuiMenuTextColor() );\r
1691             label.setOpaque( true );\r
1692         }\r
1693         label.setSelected( false );\r
1694         label.setEnabled( false );\r
1695         return label;\r
1696     }\r
1697 \r
1698     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
1699         switch ( op.getDefaultNodeFill() ) {\r
1700             case GRADIENT:\r
1701                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1702                 break;\r
1703             case NONE:\r
1704                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1705                 break;\r
1706             case SOLID:\r
1707                 op.setDefaultNodeFill( NodeFill.NONE );\r
1708                 break;\r
1709             default:\r
1710                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1711         }\r
1712     }\r
1713 \r
1714     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
1715         switch ( op.getDefaultNodeShape() ) {\r
1716             case CIRCLE:\r
1717                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1718                 break;\r
1719             case RECTANGLE:\r
1720                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1721                 break;\r
1722             default:\r
1723                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1724         }\r
1725     }\r
1726 \r
1727     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1728         switch ( op.getOvPlacement() ) {\r
1729             case LOWER_LEFT:\r
1730                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1731                 break;\r
1732             case LOWER_RIGHT:\r
1733                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1734                 break;\r
1735             case UPPER_LEFT:\r
1736                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1737                 break;\r
1738             case UPPER_RIGHT:\r
1739                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1740                 break;\r
1741             default:\r
1742                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1743         }\r
1744         if ( tree_panel != null ) {\r
1745             tree_panel.updateOvSettings();\r
1746         }\r
1747     }\r
1748 \r
1749     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
1750         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
1751             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1752                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
1753         }\r
1754         else {\r
1755             mi.setText( "Cycle Node Shape Fill Type..." );\r
1756         }\r
1757     }\r
1758 \r
1759     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
1760         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
1761             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1762                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
1763         }\r
1764         else {\r
1765             mi.setText( "Cycle Node Shape Fill Type..." );\r
1766         }\r
1767     }\r
1768 \r
1769     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
1770         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
1771             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
1772         }\r
1773         else {\r
1774             mi.setText( "Cycle Overview Placement..." );\r
1775         }\r
1776     }\r
1777 \r
1778     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
1779         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
1780             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
1781                     + ")" );\r
1782         }\r
1783         else {\r
1784             mi.setText( "Select Color Scheme..." );\r
1785         }\r
1786     }\r
1787 \r
1788     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
1789         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
1790     }\r
1791 \r
1792     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
1793         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
1794             mi.setEnabled( true );\r
1795         }\r
1796         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
1797             mi.setEnabled( true );\r
1798         }\r
1799         else {\r
1800             mi.setEnabled( false );\r
1801         }\r
1802         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
1803     }\r
1804 \r
1805     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
1806         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
1807     }\r
1808 \r
1809     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,\r
1810                                                            final JCheckBoxMenuItem scale,\r
1811                                                            final JCheckBoxMenuItem branch_lengths,\r
1812                                                            final JRadioButtonMenuItem non_lined_up,\r
1813                                                            final JRadioButtonMenuItem uniform_clado,\r
1814                                                            final JRadioButtonMenuItem nonuniform_clado,\r
1815                                                            final JCheckBoxMenuItem label_direction_cbmi ) {\r
1816         final TreePanel tree_panel = main_panel.getCurrentTreePanel();\r
1817         final ControlPanel control = main_panel.getControlPanel();\r
1818         final Options options = main_panel.getOptions();\r
1819         scale.setSelected( options.isShowScale() );\r
1820         branch_lengths.setSelected( options.isShowBranchLengthValues() );\r
1821         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1822         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {\r
1823             scale.setSelected( false );\r
1824             scale.setEnabled( false );\r
1825             branch_lengths.setSelected( false );\r
1826             branch_lengths.setEnabled( false );\r
1827         }\r
1828         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {\r
1829             scale.setSelected( false );\r
1830             scale.setEnabled( false );\r
1831             branch_lengths.setEnabled( true );\r
1832         }\r
1833         else {\r
1834             scale.setEnabled( true );\r
1835             branch_lengths.setEnabled( true );\r
1836         }\r
1837         if ( ( tree_panel != null )\r
1838                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )\r
1839                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1840                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1841             branch_lengths.setSelected( false );\r
1842             branch_lengths.setEnabled( false );\r
1843         }\r
1844         if ( tree_panel != null ) {\r
1845             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )\r
1846                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {\r
1847                 non_lined_up.setEnabled( false );\r
1848                 uniform_clado.setEnabled( false );\r
1849                 nonuniform_clado.setEnabled( false );\r
1850             }\r
1851             else {\r
1852                 non_lined_up.setEnabled( true );\r
1853                 uniform_clado.setEnabled( true );\r
1854                 nonuniform_clado.setEnabled( true );\r
1855             }\r
1856         }\r
1857         else {\r
1858             if ( ( tree_panel != null )\r
1859                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1860                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1861                 branch_lengths.setSelected( false );\r
1862                 branch_lengths.setEnabled( false );\r
1863             }\r
1864             if ( ( tree_panel != null )\r
1865                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel\r
1866                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {\r
1867                 non_lined_up.setEnabled( false );\r
1868             }\r
1869             else {\r
1870                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1871                 non_lined_up.setEnabled( true );\r
1872             }\r
1873         }\r
1874         label_direction_cbmi.setEnabled( true );\r
1875         if ( tree_panel != null ) {\r
1876             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )\r
1877                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1878                 label_direction_cbmi.setEnabled( false );\r
1879             }\r
1880             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {\r
1881                 scale.setSelected( false );\r
1882                 scale.setEnabled( false );\r
1883             }\r
1884         }\r
1885     }\r
1886 \r
1887     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
1888         for( final TreePanel tree_panel : treepanels ) {\r
1889             tree_panel.setTextAntialias();\r
1890         }\r
1891     }\r
1892 }\r