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

   1 // $Id:\r
   2 // FORESTER -- software libraries and applications\r
   3 // for evolutionary biology research and applications.\r
   4 //\r
   5 // Copyright (C) 2008-2010 Christian M. Zmasek\r
   6 // All rights reserved\r
   7 //\r
   8 // This library is free software; you can redistribute it and/or\r
   9 // modify it under the terms of the GNU Lesser General Public\r
  10 // License as published by the Free Software Foundation; either\r
  11 // version 2.1 of the License, or (at your option) any later version.\r
  12 //\r
  13 // This library is distributed in the hope that it will be useful,\r
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
  16 // Lesser General Public License for more details.\r
  17 //\r
  18 // You should have received a copy of the GNU Lesser General Public\r
  19 // License along with this library; if not, write to the Free Software\r
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
  21 //\r
  22 // Contact: phylosoft @ gmail . com\r
  23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
  24 \r
  25 package org.forester.archaeopteryx;\r
  26 \r
  27 import java.awt.Color;\r
  28 import java.awt.Component;\r
  29 import java.awt.Container;\r
  30 import java.awt.Font;\r
  31 import java.awt.event.ActionEvent;\r
  32 import java.awt.event.ActionListener;\r
  33 import java.io.File;\r
  34 import java.io.IOException;\r
  35 import java.util.ArrayList;\r
  36 import java.util.HashSet;\r
  37 import java.util.LinkedList;\r
  38 import java.util.List;\r
  39 import java.util.Locale;\r
  40 import java.util.NoSuchElementException;\r
  41 import java.util.Set;\r
  42 \r
  43 import javax.swing.Box;\r
  44 import javax.swing.JApplet;\r
  45 import javax.swing.JCheckBoxMenuItem;\r
  46 import javax.swing.JFrame;\r
  47 import javax.swing.JLabel;\r
  48 import javax.swing.JMenu;\r
  49 import javax.swing.JMenuBar;\r
  50 import javax.swing.JMenuItem;\r
  51 import javax.swing.JOptionPane;\r
  52 import javax.swing.JPanel;\r
  53 import javax.swing.JRadioButtonMenuItem;\r
  54 import javax.swing.JTextField;\r
  55 import javax.swing.SwingUtilities;\r
  56 \r
  57 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
  58 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
  59 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
  60 import org.forester.archaeopteryx.tools.InferenceManager;\r
  61 import org.forester.archaeopteryx.tools.ProcessPool;\r
  62 import org.forester.archaeopteryx.tools.ProcessRunning;\r
  63 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
  64 import org.forester.phylogeny.Phylogeny;\r
  65 import org.forester.phylogeny.PhylogenyMethods;\r
  66 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
  67 import org.forester.phylogeny.PhylogenyNode;\r
  68 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
  69 import org.forester.phylogeny.data.Annotation;\r
  70 import org.forester.phylogeny.data.NodeVisualData.NodeFill;\r
  71 import org.forester.phylogeny.data.NodeVisualData.NodeShape;\r
  72 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
  73 import org.forester.sdi.GSDI;\r
  74 import org.forester.sdi.GSDIR;\r
  75 import org.forester.sdi.SDIException;\r
  76 import org.forester.util.ForesterConstants;\r
  77 import org.forester.util.ForesterUtil;\r
  78 \r
  79 public abstract class MainFrame extends JFrame implements ActionListener {\r
  80 \r
  81     static final String         USE_MOUSEWHEEL_SHIFT_TO_ROTATE          = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
  82     static final String         PHYLOXML_REF_TOOL_TIP                   = Constants.PHYLOXML_REFERENCE;                                                                                                                                       //TODO //FIXME\r
  83     static final String         APTX_REF_TOOL_TIP                       = Constants.APTX_REFERENCE;\r
  84     private static final long   serialVersionUID                        = 3655000897845508358L;\r
  85     final static Font           menu_font                               = new Font( Configuration.getDefaultFontFamilyName(),\r
  86                                                                                     Font.PLAIN,\r
  87                                                                                     10 );\r
  88     static final String         TYPE_MENU_HEADER                        = "Type";\r
  89     static final String         RECTANGULAR_TYPE_CBMI_LABEL             = "Rectangular";\r
  90     static final String         EURO_TYPE_CBMI_LABEL                    = "Euro Type";\r
  91     static final String         CURVED_TYPE_CBMI_LABEL                  = "Curved";\r
  92     static final String         TRIANGULAR_TYPE_CBMI_LABEL              = "Triangular";\r
  93     static final String         CONVEX_TYPE_CBMI_LABEL                  = "Convex";\r
  94     static final String         ROUNDED_TYPE_CBMI_LABEL                 = "Rounded";\r
  95     static final String         UNROOTED_TYPE_CBMI_LABEL                = "Unrooted (alpha)";                                                                                                                                                 //TODO\r
  96     static final String         CIRCULAR_TYPE_CBMI_LABEL                = "Circular (alpha)";                                                                                                                                                 //TODO\r
  97     static final String         OPTIONS_HEADER                          = "Options";\r
  98     static final String         SEARCH_SUBHEADER                        = "Search:";\r
  99     static final String         DISPLAY_SUBHEADER                       = "Display:";\r
 100     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
 101     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
 102     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
 103     static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Branch Length Values";\r
 104     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
 105     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
 106     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
 107     static final String         UNIFORM_CLADOGRAMS_LABEL                = "Total Node Sum Dependent Cladograms";\r
 108     static final String         LABEL_DIRECTION_LABEL                   = "Radial Labels";\r
 109     static final String         LABEL_DIRECTION_TIP                     = "To use radial node labels in radial and unrooted display types";\r
 110     static final String         SCREEN_ANTIALIAS_LABEL                  = "Antialias";\r
 111     static final String         COLOR_LABELS_LABEL                      = "Colorize Labels Same as Parent Branch";\r
 112     static final String         BG_GRAD_LABEL                           = "Background Color Gradient";\r
 113     static final String         DISPLAY_NODE_BOXES_LABEL_EXT            = "External Node Shapes";\r
 114     static final String         DISPLAY_NODE_BOXES_LABEL_INT            = "Internal Node Shapes";\r
 115     static final String         SHOW_OVERVIEW_LABEL                     = "Overview";\r
 116     static final String         FONT_SIZE_MENU_LABEL                    = "Font Size";\r
 117     static final String         NONUNIFORM_CLADOGRAMS_LABEL             = "External Node Sum Dependent Cladograms";\r
 118     static final String         SHOW_DOMAIN_LABELS_LABEL                = "Domain Labels";\r
 119     static final String         SHOW_ANN_REF_SOURCE_LABEL               = "Seq Annotation Ref Sources";\r
 120     static final String         COLOR_LABELS_TIP                        = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";\r
 121     static final String         ABBREV_SN_LABEL                         = "Abbreviate Scientific Taxonomic Names";\r
 122     static final String         TAXONOMY_COLORIZE_NODE_SHAPES_LABEL     = "Colorize Node Shapes According to Taxonomy";\r
 123     static final String         CYCLE_NODE_SHAPE_LABEL                  = "Cycle Node Shapes";\r
 124     static final String         CYCLE_NODE_FILL_LABEL                   = "Cycle Node Fill Type";\r
 125     static final String         CHOOSE_NODE_SIZE_LABEL                  = "Choose Node Shape Size";\r
 126     static final String         SHOW_CONF_STDDEV_LABEL                  = "Confidence Standard Deviations";\r
 127     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";\r
 128     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
 129     static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Basic Tree Information";\r
 130     JMenuBar                    _jmenubar;\r
 131     JMenu                       _file_jmenu;\r
 132     JMenu                       _tools_menu;\r
 133     JMenu                       _view_jmenu;\r
 134     JMenu                       _options_jmenu;\r
 135     JMenu                       _font_size_menu;\r
 136     JMenu                       _help_jmenu;\r
 137     JMenuItem[]                 _load_phylogeny_from_webservice_menu_items;\r
 138     // Analysis menu\r
 139     JMenu                       _analysis_menu;\r
 140     JMenuItem                   _load_species_tree_item;\r
 141     JMenuItem                   _gsdi_item;\r
 142     JMenuItem                   _gsdir_item;\r
 143     JMenuItem                   _lineage_inference;\r
 144     // file menu:\r
 145     JMenuItem                   _open_item;\r
 146     JMenuItem                   _open_url_item;\r
 147     JMenuItem                   _save_item;\r
 148     JMenuItem                   _save_all_item;\r
 149     JMenuItem                   _close_item;\r
 150     JMenuItem                   _exit_item;\r
 151     JMenuItem                   _new_item;\r
 152     // tools menu:\r
 153     JMenuItem                   _midpoint_root_item;\r
 154     JMenuItem                   _taxcolor_item;\r
 155     JMenuItem                   _confcolor_item;\r
 156     JMenuItem                   _color_rank_jmi;\r
 157     JMenuItem                   _collapse_species_specific_subtrees;\r
 158     JMenuItem                   _collapse_below_threshold;                                                                                                                                                                                    //TODO implememt me\r
 159     JMenuItem                   _obtain_detailed_taxonomic_information_jmi;\r
 160     JMenuItem                   _obtain_detailed_taxonomic_information_deleting_jmi;\r
 161     JMenuItem                   _obtain_seq_information_jmi;\r
 162     JMenuItem                   _move_node_names_to_tax_sn_jmi;\r
 163     JMenuItem                   _move_node_names_to_seq_names_jmi;\r
 164     JMenuItem                   _extract_tax_code_from_node_names_jmi;\r
 165     JMenuItem                   _annotate_item;\r
 166     JMenuItem                   _remove_branch_color_item;\r
 167     JMenuItem                   _remove_visual_styles_item;\r
 168     JMenuItem                   _delete_selected_nodes_item;\r
 169     JMenuItem                   _delete_not_selected_nodes_item;\r
 170     // font size menu:\r
 171     JMenuItem                   _super_tiny_fonts_item;\r
 172     JMenuItem                   _tiny_fonts_item;\r
 173     JMenuItem                   _small_fonts_item;\r
 174     JMenuItem                   _medium_fonts_item;\r
 175     JMenuItem                   _large_fonts_item;\r
 176     // options menu:\r
 177     // _  screen and print\r
 178     JMenuItem                   _choose_font_mi;\r
 179     JMenuItem                   _switch_colors_mi;\r
 180     JCheckBoxMenuItem           _label_direction_cbmi;\r
 181     // _  screen display\r
 182     JCheckBoxMenuItem           _screen_antialias_cbmi;\r
 183     JCheckBoxMenuItem           _background_gradient_cbmi;\r
 184     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
 185     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
 186     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
 187     JCheckBoxMenuItem           _show_branch_length_values_cbmi;\r
 188     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
 189     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me\r
 190     JCheckBoxMenuItem           _show_overview_cbmi;\r
 191     JCheckBoxMenuItem           _show_domain_labels;\r
 192     JCheckBoxMenuItem           _show_annotation_ref_source;\r
 193     JCheckBoxMenuItem           _abbreviate_scientific_names;\r
 194     JCheckBoxMenuItem           _color_labels_same_as_parent_branch;\r
 195     JMenuItem                   _overview_placment_mi;\r
 196     JMenuItem                   _choose_minimal_confidence_mi;\r
 197     JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;\r
 198     JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;\r
 199     JMenuItem                   _cycle_node_shape_mi;\r
 200     JMenuItem                   _cycle_node_fill_mi;\r
 201     JMenuItem                   _choose_node_size_mi;\r
 202     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;\r
 203     // _  print\r
 204     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;\r
 205     JCheckBoxMenuItem           _antialias_print_cbmi;\r
 206     JCheckBoxMenuItem           _print_black_and_white_cbmi;\r
 207     JCheckBoxMenuItem           _print_using_actual_size_cbmi;\r
 208     JCheckBoxMenuItem           _graphics_export_using_actual_size_cbmi;\r
 209     JMenuItem                   _print_size_mi;\r
 210     JMenuItem                   _choose_pdf_width_mi;\r
 211     // _  parsing\r
 212     JCheckBoxMenuItem           _internal_number_are_confidence_for_nh_parsing_cbmi;\r
 213     JRadioButtonMenuItem        _extract_taxonomy_no_rbmi;\r
 214     JRadioButtonMenuItem        _extract_taxonomy_agressive_rbmi;\r
 215     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;\r
 216     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;\r
 217     JCheckBoxMenuItem           _replace_underscores_cbmi;\r
 218     JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;\r
 219     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;\r
 220     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;\r
 221     // _  search\r
 222     JCheckBoxMenuItem           _search_case_senstive_cbmi;\r
 223     JCheckBoxMenuItem           _search_whole_words_only_cbmi;\r
 224     JCheckBoxMenuItem           _inverse_search_result_cbmi;\r
 225     // type menu:\r
 226     JMenu                       _type_menu;\r
 227     JCheckBoxMenuItem           _rectangular_type_cbmi;\r
 228     JCheckBoxMenuItem           _triangular_type_cbmi;\r
 229     JCheckBoxMenuItem           _curved_type_cbmi;\r
 230     JCheckBoxMenuItem           _convex_type_cbmi;\r
 231     JCheckBoxMenuItem           _euro_type_cbmi;\r
 232     JCheckBoxMenuItem           _rounded_type_cbmi;\r
 233     JCheckBoxMenuItem           _unrooted_type_cbmi;\r
 234     JCheckBoxMenuItem           _circular_type_cbmi;\r
 235     // view as text menu:\r
 236     JMenuItem                   _view_as_NH_item;\r
 237     JMenuItem                   _view_as_XML_item;\r
 238     JMenuItem                   _view_as_nexus_item;\r
 239     JMenuItem                   _display_basic_information_item;\r
 240     // help menu:\r
 241     JMenuItem                   _about_item;\r
 242     JMenuItem                   _help_item;\r
 243     JMenuItem                   _website_item;\r
 244     JMenuItem                   _phyloxml_website_item;\r
 245     JMenuItem                   _phyloxml_ref_item;\r
 246     JMenuItem                   _aptx_ref_item;\r
 247     // process menu:\r
 248     JMenu                       _process_menu;\r
 249     // Handy pointers to child components:\r
 250     MainPanel                   _mainpanel;\r
 251     Container                   _contentpane;\r
 252     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;\r
 253     Configuration               _configuration;\r
 254     Options                     _options;\r
 255     private Phylogeny           _species_tree;\r
 256     InferenceManager            _inference_manager;\r
 257     final ProcessPool           _process_pool;\r
 258     private String              _previous_node_annotation_ref;\r
 259 \r
 260     MainFrame() {\r
 261         _process_pool = ProcessPool.createInstance();\r
 262     }\r
 263 \r
 264     /**\r
 265      * Action performed.\r
 266      */\r
 267     @Override\r
 268     public void actionPerformed( final ActionEvent e ) {\r
 269         final Object o = e.getSource();\r
 270         boolean is_applet = false;\r
 271         JApplet applet = null;\r
 272         if ( getCurrentTreePanel() != null ) {\r
 273             is_applet = getCurrentTreePanel().isApplet();\r
 274             if ( is_applet ) {\r
 275                 applet = getCurrentTreePanel().obtainApplet();\r
 276             }\r
 277         }\r
 278         if ( o == _exit_item ) {\r
 279             close();\r
 280         }\r
 281         else if ( o == _gsdi_item ) {\r
 282             if ( isSubtreeDisplayed() ) {\r
 283                 return;\r
 284             }\r
 285             executeGSDI();\r
 286         }\r
 287         else if ( o == _gsdir_item ) {\r
 288             if ( isSubtreeDisplayed() ) {\r
 289                 return;\r
 290             }\r
 291             executeGSDIR();\r
 292         }\r
 293         else if ( o == _taxcolor_item ) {\r
 294             taxColor();\r
 295         }\r
 296         else if ( o == _confcolor_item ) {\r
 297             confColor();\r
 298         }\r
 299         else if ( o == _color_rank_jmi ) {\r
 300             colorRank();\r
 301         }\r
 302         else if ( o == _collapse_species_specific_subtrees ) {\r
 303             if ( isSubtreeDisplayed() ) {\r
 304                 return;\r
 305             }\r
 306             if ( getCurrentTreePanel() != null ) {\r
 307                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();\r
 308             }\r
 309         }\r
 310         else if ( o == _remove_branch_color_item ) {\r
 311             if ( isSubtreeDisplayed() ) {\r
 312                 return;\r
 313             }\r
 314             removeBranchColors();\r
 315         }\r
 316         else if ( o == _remove_visual_styles_item ) {\r
 317             if ( isSubtreeDisplayed() ) {\r
 318                 return;\r
 319             }\r
 320             removeVisualStyles();\r
 321         }\r
 322         else if ( o == _midpoint_root_item ) {\r
 323             if ( isSubtreeDisplayed() ) {\r
 324                 return;\r
 325             }\r
 326             midpointRoot();\r
 327         }\r
 328         else if ( o == _delete_selected_nodes_item ) {\r
 329             if ( isSubtreeDisplayed() ) {\r
 330                 return;\r
 331             }\r
 332             deleteSelectedNodes( true );\r
 333         }\r
 334         else if ( o == _delete_not_selected_nodes_item ) {\r
 335             if ( isSubtreeDisplayed() ) {\r
 336                 return;\r
 337             }\r
 338             deleteSelectedNodes( false );\r
 339         }\r
 340         else if ( o == _annotate_item ) {\r
 341             annotateSequences();\r
 342         }\r
 343         else if ( o == _switch_colors_mi ) {\r
 344             switchColors();\r
 345         }\r
 346         else if ( o == _display_basic_information_item ) {\r
 347             displayBasicInformation( getCurrentTreePanel().getTreeFile() );\r
 348         }\r
 349         else if ( o == _view_as_NH_item ) {\r
 350             viewAsNH();\r
 351         }\r
 352         else if ( o == _view_as_XML_item ) {\r
 353             viewAsXML();\r
 354         }\r
 355         else if ( o == _view_as_nexus_item ) {\r
 356             viewAsNexus();\r
 357         }\r
 358         else if ( o == _super_tiny_fonts_item ) {\r
 359             if ( getCurrentTreePanel() != null ) {\r
 360                 getCurrentTreePanel().setSuperTinyFonts();\r
 361                 getCurrentTreePanel().repaint();\r
 362             }\r
 363         }\r
 364         else if ( o == _tiny_fonts_item ) {\r
 365             if ( getCurrentTreePanel() != null ) {\r
 366                 getCurrentTreePanel().setTinyFonts();\r
 367                 getCurrentTreePanel().repaint();\r
 368             }\r
 369         }\r
 370         else if ( o == _small_fonts_item ) {\r
 371             if ( getCurrentTreePanel() != null ) {\r
 372                 getCurrentTreePanel().setSmallFonts();\r
 373                 getCurrentTreePanel().repaint();\r
 374             }\r
 375         }\r
 376         else if ( o == _medium_fonts_item ) {\r
 377             if ( getCurrentTreePanel() != null ) {\r
 378                 getCurrentTreePanel().setMediumFonts();\r
 379                 getCurrentTreePanel().repaint();\r
 380             }\r
 381         }\r
 382         else if ( o == _large_fonts_item ) {\r
 383             if ( getCurrentTreePanel() != null ) {\r
 384                 getCurrentTreePanel().setLargeFonts();\r
 385                 getCurrentTreePanel().repaint();\r
 386             }\r
 387         }\r
 388         else if ( o == _choose_font_mi ) {\r
 389             chooseFont();\r
 390         }\r
 391         else if ( o == _choose_minimal_confidence_mi ) {\r
 392             chooseMinimalConfidence();\r
 393         }\r
 394         else if ( o == _choose_node_size_mi ) {\r
 395             chooseNodeSize( getOptions(), this );\r
 396         }\r
 397         else if ( o == _overview_placment_mi ) {\r
 398             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
 399         }\r
 400         else if ( o == _cycle_node_fill_mi ) {\r
 401             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
 402         }\r
 403         else if ( o == _cycle_node_shape_mi ) {\r
 404             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
 405         }\r
 406         else if ( o == _screen_antialias_cbmi ) {\r
 407             updateOptions( getOptions() );\r
 408             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
 409         }\r
 410         else if ( o == _background_gradient_cbmi ) {\r
 411             updateOptions( getOptions() );\r
 412         }\r
 413         else if ( o == _show_domain_labels ) {\r
 414             updateOptions( getOptions() );\r
 415         }\r
 416         else if ( o == _show_annotation_ref_source ) {\r
 417             updateOptions( getOptions() );\r
 418         }\r
 419         else if ( o == _abbreviate_scientific_names ) {\r
 420             updateOptions( getOptions() );\r
 421         }\r
 422         else if ( o == _color_labels_same_as_parent_branch ) {\r
 423             updateOptions( getOptions() );\r
 424         }\r
 425         else if ( o == _show_default_node_shapes_internal_cbmi ) {\r
 426             updateOptions( getOptions() );\r
 427         }\r
 428         else if ( o == _show_default_node_shapes_external_cbmi ) {\r
 429             updateOptions( getOptions() );\r
 430         }\r
 431         else if ( o == _non_lined_up_cladograms_rbmi ) {\r
 432             updateOptions( getOptions() );\r
 433             showWhole();\r
 434         }\r
 435         else if ( o == _uniform_cladograms_rbmi ) {\r
 436             updateOptions( getOptions() );\r
 437             showWhole();\r
 438         }\r
 439         else if ( o == _ext_node_dependent_cladogram_rbmi ) {\r
 440             updateOptions( getOptions() );\r
 441             showWhole();\r
 442         }\r
 443         else if ( o == _search_case_senstive_cbmi ) {\r
 444             updateOptions( getOptions() );\r
 445             getMainPanel().getControlPanel().search0();\r
 446             getMainPanel().getControlPanel().search1();\r
 447         }\r
 448         else if ( o == _search_whole_words_only_cbmi ) {\r
 449             updateOptions( getOptions() );\r
 450             getMainPanel().getControlPanel().search0();\r
 451             getMainPanel().getControlPanel().search1();\r
 452         }\r
 453         else if ( o == _inverse_search_result_cbmi ) {\r
 454             updateOptions( getOptions() );\r
 455             getMainPanel().getControlPanel().search0();\r
 456             getMainPanel().getControlPanel().search1();\r
 457         }\r
 458         else if ( o == _show_scale_cbmi ) {\r
 459             updateOptions( getOptions() );\r
 460         }\r
 461         else if ( o == _show_branch_length_values_cbmi ) {\r
 462             updateOptions( getOptions() );\r
 463         }\r
 464         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
 465             updateOptions( getOptions() );\r
 466         }\r
 467         else if ( o == _show_confidence_stddev_cbmi ) {\r
 468             updateOptions( getOptions() );\r
 469         }\r
 470         else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) {\r
 471             if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 472                 _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false );\r
 473             }\r
 474             updateOptions( getOptions() );\r
 475         }\r
 476         else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) {\r
 477             if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
 478                 _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false );\r
 479             }\r
 480             updateOptions( getOptions() );\r
 481         }\r
 482         else if ( o == _label_direction_cbmi ) {\r
 483             updateOptions( getOptions() );\r
 484         }\r
 485         else if ( o == _show_overview_cbmi ) {\r
 486             updateOptions( getOptions() );\r
 487             if ( getCurrentTreePanel() != null ) {\r
 488                 getCurrentTreePanel().updateOvSizes();\r
 489             }\r
 490         }\r
 491         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
 492                 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
 493                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
 494             typeChanged( o );\r
 495         }\r
 496         \r
 497         else if ( o == _about_item ) {\r
 498             about();\r
 499         }\r
 500         else if ( o == _help_item ) {\r
 501             help();\r
 502         }\r
 503         else if ( o == _website_item ) {\r
 504             try {\r
 505                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );\r
 506             }\r
 507             catch ( final IOException e1 ) {\r
 508                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 509             }\r
 510         }\r
 511         else if ( o == _phyloxml_website_item ) {\r
 512             try {\r
 513                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );\r
 514             }\r
 515             catch ( final IOException e1 ) {\r
 516                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 517             }\r
 518         }\r
 519         else if ( o == _aptx_ref_item ) {\r
 520             try {\r
 521                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );\r
 522             }\r
 523             catch ( final IOException e1 ) {\r
 524                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 525             }\r
 526         }\r
 527         else if ( o == _phyloxml_ref_item ) {\r
 528             try {\r
 529                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
 530             }\r
 531             catch ( final IOException e1 ) {\r
 532                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
 533             }\r
 534         }\r
 535         else {\r
 536             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
 537                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
 538                     if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
 539                         readPhylogeniesFromWebservice( i );\r
 540                     }\r
 541                 }\r
 542             }\r
 543         }\r
 544         _contentpane.repaint();\r
 545     }\r
 546 \r
 547     private void deleteSelectedNodes( boolean delete ) {\r
 548         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
 549         if ( phy == null || phy.getNumberOfExternalNodes() < 2 ) {\r
 550             return;\r
 551         }\r
 552         List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
 553         if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
 554             final List<PhylogenyNode>  all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
 555             for( final PhylogenyNode n : all_selected_nodes ) {\r
 556                 if ( n.isExternal() ) {\r
 557                     nodes.add( n );\r
 558                 }\r
 559             }\r
 560         }\r
 561         \r
 562         String function = "Retain";\r
 563         if ( delete ) {\r
 564             function = "Delete";\r
 565         }\r
 566         if ( ( nodes == null ) || nodes.isEmpty() ) {\r
 567             JOptionPane\r
 568                     .showMessageDialog( this,\r
 569                                         "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
 570                                         "No external nodes selected to " + function.toLowerCase(),\r
 571                                         JOptionPane.ERROR_MESSAGE );\r
 572             return;\r
 573         }\r
 574         final int todo = nodes.size();\r
 575         final int ext = phy.getNumberOfExternalNodes();\r
 576         int res = todo;\r
 577         if ( delete ) {\r
 578             res = ext - todo;\r
 579         }\r
 580         if ( res < 1 ) {\r
 581             JOptionPane.showMessageDialog( this,\r
 582                                            "Cannot delete all nodes",\r
 583                                            "Attempt to delete all nodes ",\r
 584                                            JOptionPane.ERROR_MESSAGE );\r
 585             return;\r
 586         }\r
 587         final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
 588                 + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
 589                 + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
 590         if ( result == JOptionPane.OK_OPTION ) {\r
 591             if ( !delete ) {\r
 592                 final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
 593                 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
 594                     final PhylogenyNode n = it.next();\r
 595                     if ( !nodes.contains( n ) ) {\r
 596                         to_delete.add( n );\r
 597                     }\r
 598                 }\r
 599                 for( final PhylogenyNode n : to_delete ) {\r
 600                     phy.deleteSubtree( n, true );\r
 601                 }\r
 602             }\r
 603             else {\r
 604                 for( final PhylogenyNode n : nodes ) {\r
 605                     phy.deleteSubtree( n, true );\r
 606                 }\r
 607             }\r
 608             resetSearch();\r
 609             getCurrentTreePanel().setNodeInPreorderToNull();\r
 610             phy.externalNodesHaveChanged();\r
 611             phy.clearHashIdToNodeMap();\r
 612             phy.recalculateNumberOfExternalDescendants( true );\r
 613             getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
 614             getCurrentTreePanel().setEdited( true );\r
 615             repaint();\r
 616         }\r
 617     }\r
 618 \r
 619     void resetSearch() {\r
 620         getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
 621         getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
 622         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
 623         getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
 624         getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
 625         getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
 626         getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
 627         getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
 628         getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
 629         getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
 630         getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
 631         getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
 632     }\r
 633 \r
 634     public Configuration getConfiguration() {\r
 635         return _configuration;\r
 636     }\r
 637 \r
 638     /**\r
 639      * This method returns the current external node data which\r
 640      * has been selected by the user by clicking the "Return ..."\r
 641      * menu item. This method is expected to be called from Javascript or\r
 642      * something like it.\r
 643      * \r
 644      * @return current external node data as String\r
 645      */\r
 646     public String getCurrentExternalNodesDataBuffer() {\r
 647         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
 648     }\r
 649 \r
 650     public int getCurrentExternalNodesDataBufferChangeCounter() {\r
 651         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
 652     }\r
 653 \r
 654     public int getCurrentExternalNodesDataBufferLength() {\r
 655         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
 656     }\r
 657 \r
 658     public InferenceManager getInferenceManager() {\r
 659         return _inference_manager;\r
 660     }\r
 661 \r
 662     public MainPanel getMainPanel() {\r
 663         return _mainpanel;\r
 664     }\r
 665 \r
 666     public Options getOptions() {\r
 667         return _options;\r
 668     }\r
 669 \r
 670     public ProcessPool getProcessPool() {\r
 671         return _process_pool;\r
 672     }\r
 673 \r
 674     public void showTextFrame( final String s, final String title ) {\r
 675         checkTextFrames();\r
 676         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
 677     }\r
 678 \r
 679     public void showWhole() {\r
 680         _mainpanel.getControlPanel().showWhole();\r
 681     }\r
 682 \r
 683     public void updateProcessMenu() {\r
 684         // In general Swing is not thread safe.\r
 685         // See "Swing's Threading Policy".\r
 686         SwingUtilities.invokeLater( new Runnable() {\r
 687 \r
 688             @Override\r
 689             public void run() {\r
 690                 doUpdateProcessMenu();\r
 691             }\r
 692         } );\r
 693     }\r
 694 \r
 695     void activateSaveAllIfNeeded() {\r
 696         if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
 697             _save_all_item.setEnabled( true );\r
 698         }\r
 699         else {\r
 700             _save_all_item.setEnabled( false );\r
 701         }\r
 702     }\r
 703 \r
 704     void buildFileMenu() {\r
 705         _file_jmenu = createMenu( "File", getConfiguration() );\r
 706         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
 707         customizeJMenuItem( _exit_item );\r
 708         _jmenubar.add( _file_jmenu );\r
 709     }\r
 710 \r
 711     void buildFontSizeMenu() {\r
 712         _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
 713         _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
 714         _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
 715         _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
 716         _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
 717         _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
 718         customizeJMenuItem( _super_tiny_fonts_item );\r
 719         customizeJMenuItem( _tiny_fonts_item );\r
 720         customizeJMenuItem( _small_fonts_item );\r
 721         customizeJMenuItem( _medium_fonts_item );\r
 722         customizeJMenuItem( _large_fonts_item );\r
 723         _jmenubar.add( _font_size_menu );\r
 724     }\r
 725 \r
 726     void buildHelpMenu() {\r
 727         _help_jmenu = createMenu( "Help", getConfiguration() );\r
 728         _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );\r
 729         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
 730         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );\r
 731         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
 732         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
 733         _help_jmenu.addSeparator();\r
 734         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
 735         customizeJMenuItem( _help_item );\r
 736         customizeJMenuItem( _website_item );\r
 737         customizeJMenuItem( _phyloxml_website_item );\r
 738         customizeJMenuItem( _aptx_ref_item );\r
 739         customizeJMenuItem( _phyloxml_ref_item );\r
 740         customizeJMenuItem( _about_item );\r
 741         _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
 742         _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
 743         _jmenubar.add( _help_jmenu );\r
 744     }\r
 745 \r
 746     void buildTypeMenu() {\r
 747         _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
 748         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
 749         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
 750         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
 751         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
 752         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
 753         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
 754         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
 755         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
 756         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
 757         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
 758         customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
 759         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
 760         customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
 761         customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
 762         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
 763         customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
 764         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 765         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
 766         initializeTypeMenu( getOptions() );\r
 767         _jmenubar.add( _type_menu );\r
 768     }\r
 769 \r
 770     void buildViewMenu() {\r
 771         _view_jmenu = createMenu( "View", getConfiguration() );\r
 772         _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
 773         _view_jmenu.addSeparator();\r
 774         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
 775         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
 776         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
 777         customizeJMenuItem( _display_basic_information_item );\r
 778         customizeJMenuItem( _view_as_NH_item );\r
 779         customizeJMenuItem( _view_as_XML_item );\r
 780         customizeJMenuItem( _view_as_nexus_item );\r
 781         _jmenubar.add( _view_jmenu );\r
 782     }\r
 783 \r
 784     void checkTextFrames() {\r
 785         if ( _textframes.size() > 5 ) {\r
 786             try {\r
 787                 if ( _textframes.getFirst() != null ) {\r
 788                     _textframes.getFirst().removeMe();\r
 789                 }\r
 790                 else {\r
 791                     _textframes.removeFirst();\r
 792                 }\r
 793             }\r
 794             catch ( final NoSuchElementException e ) {\r
 795                 // Ignore.\r
 796             }\r
 797         }\r
 798     }\r
 799 \r
 800     void close() {\r
 801         removeAllTextFrames();\r
 802         if ( _mainpanel != null ) {\r
 803             _mainpanel.terminate();\r
 804         }\r
 805         if ( _contentpane != null ) {\r
 806             _contentpane.removeAll();\r
 807         }\r
 808         setVisible( false );\r
 809         dispose();\r
 810     }\r
 811 \r
 812     void colorRank() {\r
 813         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 814             final String[] ranks = AptxUtil.getAllPossibleRanks();\r
 815             final String rank = ( String ) JOptionPane\r
 816                     .showInputDialog( this,\r
 817                                       "What rank should the colorization be based on",\r
 818                                       "Rank Selection",\r
 819                                       JOptionPane.QUESTION_MESSAGE,\r
 820                                       null,\r
 821                                       ranks,\r
 822                                       null );\r
 823             if ( !ForesterUtil.isEmpty( rank ) ) {\r
 824                 _mainpanel.getCurrentTreePanel().colorRank( rank );\r
 825             }\r
 826         }\r
 827     }\r
 828 \r
 829     void confColor() {\r
 830         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
 831             _mainpanel.getCurrentTreePanel().confColor();\r
 832         }\r
 833     }\r
 834 \r
 835     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
 836         if ( item != null ) {\r
 837             item.setFont( MainFrame.menu_font );\r
 838             if ( !getConfiguration().isUseNativeUI() ) {\r
 839                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 840                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 841             }\r
 842             item.setSelected( is_selected );\r
 843             item.addActionListener( this );\r
 844         }\r
 845     }\r
 846 \r
 847     JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
 848         if ( jmi != null ) {\r
 849             jmi.setFont( MainFrame.menu_font );\r
 850             if ( !getConfiguration().isUseNativeUI() ) {\r
 851                 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 852                 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 853             }\r
 854             jmi.addActionListener( this );\r
 855         }\r
 856         return jmi;\r
 857     }\r
 858 \r
 859     void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
 860         if ( item != null ) {\r
 861             item.setFont( MainFrame.menu_font );\r
 862             if ( !getConfiguration().isUseNativeUI() ) {\r
 863                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
 864                 item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
 865             }\r
 866             item.setSelected( is_selected );\r
 867             item.addActionListener( this );\r
 868         }\r
 869     }\r
 870 \r
 871     void displayBasicInformation( final File treefile ) {\r
 872         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
 873             String title = "Basic Information";\r
 874             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
 875                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
 876             }\r
 877             showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
 878         }\r
 879     }\r
 880 \r
 881     void exceptionOccuredDuringOpenFile( final Exception e ) {\r
 882         try {\r
 883             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 884         }\r
 885         catch ( final Exception ex ) {\r
 886             // Do nothing.\r
 887         }\r
 888         JOptionPane.showMessageDialog( this,\r
 889                                        ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
 890                                        "Error during File|Open",\r
 891                                        JOptionPane.ERROR_MESSAGE );\r
 892     }\r
 893 \r
 894     void exceptionOccuredDuringSaveAs( final Exception e ) {\r
 895         try {\r
 896             _mainpanel.getCurrentTreePanel().setArrowCursor();\r
 897         }\r
 898         catch ( final Exception ex ) {\r
 899             // Do nothing.\r
 900         }\r
 901         JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
 902     }\r
 903 \r
 904     void executeGSDI() {\r
 905         if ( !isOKforSDI( false, true ) ) {\r
 906             return;\r
 907         }\r
 908         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
 909             JOptionPane.showMessageDialog( this,\r
 910                                            "Gene tree is not rooted.",\r
 911                                            "Cannot execute GSDI",\r
 912                                            JOptionPane.ERROR_MESSAGE );\r
 913             return;\r
 914         }\r
 915         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 916         gene_tree.setAllNodesToNotCollapse();\r
 917         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 918         GSDI gsdi = null;\r
 919         final Phylogeny species_tree = getSpeciesTree().copy();\r
 920         try {\r
 921             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
 922         }\r
 923         catch ( final SDIException e ) {\r
 924             JOptionPane.showMessageDialog( this,\r
 925                                            e.getLocalizedMessage(),\r
 926                                            "Error during GSDI",\r
 927                                            JOptionPane.ERROR_MESSAGE );\r
 928             return;\r
 929         }\r
 930         catch ( final Exception e ) {\r
 931             AptxUtil.unexpectedException( e );\r
 932             return;\r
 933         }\r
 934         gene_tree.setRerootable( false );\r
 935         gene_tree.clearHashIdToNodeMap();\r
 936         gene_tree.recalculateNumberOfExternalDescendants( true );\r
 937         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
 938         getMainPanel().getControlPanel().setShowEvents( true );\r
 939         showWhole();\r
 940         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
 941         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
 942         showWhole();\r
 943         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
 944         showWhole();\r
 945         _mainpanel.getCurrentTreePanel().setEdited( true );\r
 946         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
 947         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
 948             JOptionPane.showMessageDialog( this,\r
 949                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 950                                                    + "Potential duplications: "\r
 951                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 952                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 953                                                    + "Stripped gene tree nodes: "\r
 954                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 955                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 956                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 957                                            "GSDI successfully completed",\r
 958                                            JOptionPane.WARNING_MESSAGE );\r
 959         }\r
 960         else {\r
 961             JOptionPane.showMessageDialog( this,\r
 962                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
 963                                                    + "Potential duplications: "\r
 964                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
 965                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
 966                                                    + "Stripped gene tree nodes: "\r
 967                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
 968                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
 969                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
 970                                            "GSDI successfully completed",\r
 971                                            JOptionPane.INFORMATION_MESSAGE );\r
 972         }\r
 973     }\r
 974 \r
 975     void executeGSDIR() {\r
 976         if ( !isOKforSDI( false, false ) ) {\r
 977             return;\r
 978         }\r
 979         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
 980         if ( ( p > 0 )\r
 981                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
 982             JOptionPane.showMessageDialog( this,\r
 983                                            "Gene tree is not completely binary",\r
 984                                            "Cannot execute GSDI",\r
 985                                            JOptionPane.ERROR_MESSAGE );\r
 986             return;\r
 987         }\r
 988         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
 989         gene_tree.setAllNodesToNotCollapse();\r
 990         gene_tree.recalculateNumberOfExternalDescendants( false );\r
 991         GSDIR gsdir = null;\r
 992         final Phylogeny species_tree = getSpeciesTree().copy();\r
 993         try {\r
 994             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
 995         }\r
 996         catch ( final SDIException e ) {\r
 997             JOptionPane.showMessageDialog( this,\r
 998                                            e.getLocalizedMessage(),\r
 999                                            "Error during GSDIR",\r
1000                                            JOptionPane.ERROR_MESSAGE );\r
1001             return;\r
1002         }\r
1003         catch ( final Exception e ) {\r
1004             AptxUtil.unexpectedException( e );\r
1005             return;\r
1006         }\r
1007         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
1008         result_gene_tree.setRerootable( false );\r
1009         result_gene_tree.clearHashIdToNodeMap();\r
1010         result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
1011         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
1012         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
1013         getMainPanel().getControlPanel().setShowEvents( true );\r
1014         showWhole();\r
1015         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
1016         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
1017         showWhole();\r
1018         _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
1019         showWhole();\r
1020         _mainpanel.getCurrentTreePanel().setEdited( true );\r
1021         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
1022         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
1023             JOptionPane.showMessageDialog( this,\r
1024                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1025                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1026                                                    + "Stripped gene tree nodes: "\r
1027                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1028                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1029                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1030                                            "GSDIR successfully completed",\r
1031                                            JOptionPane.WARNING_MESSAGE );\r
1032         }\r
1033         else {\r
1034             JOptionPane.showMessageDialog( this,\r
1035                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
1036                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
1037                                                    + "Stripped gene tree nodes: "\r
1038                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
1039                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
1040                                                    + "Number of polytomies in species tree used: " + poly + "\n",\r
1041                                            "GSDIR successfully completed",\r
1042                                            JOptionPane.INFORMATION_MESSAGE );\r
1043         }\r
1044     }\r
1045 \r
1046     boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
1047         if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
1048             JOptionPane.showMessageDialog( this,\r
1049                                            "Gene tree and species tree have no species in common.",\r
1050                                            "Error during SDI",\r
1051                                            JOptionPane.ERROR_MESSAGE );\r
1052             return false;\r
1053         }\r
1054         else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
1055             JOptionPane.showMessageDialog( this,\r
1056                                            "Gene tree and species tree have only one species in common.",\r
1057                                            "Error during SDI",\r
1058                                            JOptionPane.ERROR_MESSAGE );\r
1059             return false;\r
1060         }\r
1061         else {\r
1062             return true;\r
1063         }\r
1064     }\r
1065 \r
1066     TreePanel getCurrentTreePanel() {\r
1067         return getMainPanel().getCurrentTreePanel();\r
1068     }\r
1069 \r
1070     JMenu getHelpMenu() {\r
1071         return _help_jmenu;\r
1072     }\r
1073 \r
1074     JCheckBoxMenuItem getlabelDirectionCbmi() {\r
1075         return _label_direction_cbmi;\r
1076     }\r
1077 \r
1078     JMenuBar getMenuBarOfMainFrame() {\r
1079         return _jmenubar;\r
1080     }\r
1081 \r
1082     final Phylogeny getSpeciesTree() {\r
1083         return _species_tree;\r
1084     }\r
1085 \r
1086     void help() {\r
1087         final StringBuilder sb = new StringBuilder();\r
1088         sb.append( "Display options\n" );\r
1089         sb.append( "-------------------\n" );\r
1090         sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );\r
1091         sb.append( "Clickable tree nodes\n" );\r
1092         sb.append( "--------------------\n" );\r
1093         sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );\r
1094         sb.append( "or by right clicking:\n" );\r
1095         sb.append( "o  Display Node Data -- display information for a node\n" );\r
1096         sb.append( "o  Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );\r
1097         sb.append( "o  Root/Reroot -- change tree root to clicked node\n" );\r
1098         sb.append( "o  Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );\r
1099         sb.append( "o  Swap Descendants -- switch descendant on either side of clicked node\n" );\r
1100         sb.append( "o  Colorize Subtree -- color a subtree\n" );\r
1101         sb.append( "o  Open Sequence Web -- launch a web browser to display sequence information\n" );\r
1102         sb.append( "o  Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );\r
1103         sb.append( "-  there may be additional choices depending on this particular setup\n\n" );\r
1104         sb.append( "Right clicking on a node always displays the information of a node.\n\n" );\r
1105         sb.append( "Zooming\n" );\r
1106         sb.append( "---------\n" );\r
1107         sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );\r
1108         sb.append( "Mouse wheel+Ctrl changes the text size.\n" );\r
1109         sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );\r
1110         sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );\r
1111         sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );\r
1112         sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );\r
1113         sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );\r
1114         sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );\r
1115         sb.append( "Quick tree manipulation:\n" );\r
1116         sb.append( "------------------------\n" );\r
1117         sb.append( "Order Subtrees -- order the tree by branch length\n" );\r
1118         sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );\r
1119         sb.append( "Memory problems (Java heap space error)\n" );\r
1120         sb.append( "---------------------------------------\n" );\r
1121         sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );\r
1122         sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );\r
1123         sb.append( "the '-Xmx' Java command line option. For example:\n" );\r
1124         sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );\r
1125         // + "General remarks\n"\r
1126         // + "---------------\n"\r
1127         // +\r
1128         // "o  The application version permits copying to the clipboard \n"\r
1129         // +\r
1130         // "    in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"\r
1131         // +\r
1132         // "o  Changes made to a subtree affect this subtree and its subtrees,\n"\r
1133         // + "    but not any of its parent tree(s).\n"\r
1134         // +\r
1135         // "o  Archaeopteryx tries to detect whether the numerical values in a NH tree\n"\r
1136         // +\r
1137         // "    are likely to be bootstrap values instead of branch length values.\n\n"\r
1138         // +\r
1139         // " Remarks regarding SDI (Speciation Duplication Inference):\n"\r
1140         // +\r
1141         // "o  Each external node of the gene tree (in display) needs to be associated with\n"\r
1142         // +\r
1143         // "    a species: either directly through the \"Species\" field, or the species\n"\r
1144         // +\r
1145         // "    is part of the sequence name in the form \"XXXX_SPECIES\"\n"\r
1146         // +\r
1147         // "    (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"\r
1148         // +\r
1149         // "o  A species tree for each species of the gene tree needs to be loaded with\n"\r
1150         // +\r
1151         // "   \"SDI\"|\"Load species tree\" prior the SDI execution.\n"\r
1152         // +\r
1153         // "o  !External nodes of the gene tree associated with species not present in\n"\r
1154         // +\r
1155         // "    the species tree are REMOVED prior to SDI execution!\n"\r
1156         // +\r
1157         // "o  Both the gene tree and the species tree must be completely binary.\n"\r
1158         // +\r
1159         // "o  Duplications and speciations are a function of the position of the root.\n"\r
1160         // +\r
1161         // "    Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"\r
1162         // + "    incorrect and need to be inferred again\n"\r
1163         // +\r
1164         // "    with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"\r
1165         sb.append( "phyloXML\n" );\r
1166         sb.append( "-------------------\n" );\r
1167         sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );\r
1168         sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );\r
1169         sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1170         sb.append( "\n" );\r
1171         sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );\r
1172         sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );\r
1173         TextFrame.instantiate( sb.toString(), "Help", _textframes );\r
1174     }\r
1175 \r
1176     void initializeTypeMenu( final Options options ) {\r
1177         setTypeMenuToAllUnselected();\r
1178         switch ( options.getPhylogenyGraphicsType() ) {\r
1179             case CONVEX:\r
1180                 _convex_type_cbmi.setSelected( true );\r
1181                 break;\r
1182             case CURVED:\r
1183                 _curved_type_cbmi.setSelected( true );\r
1184                 break;\r
1185             case EURO_STYLE:\r
1186                 _euro_type_cbmi.setSelected( true );\r
1187                 break;\r
1188             case ROUNDED:\r
1189                 _rounded_type_cbmi.setSelected( true );\r
1190                 break;\r
1191             case TRIANGULAR:\r
1192                 _triangular_type_cbmi.setSelected( true );\r
1193                 break;\r
1194             case UNROOTED:\r
1195                 _unrooted_type_cbmi.setSelected( true );\r
1196                 break;\r
1197             case CIRCULAR:\r
1198                 _circular_type_cbmi.setSelected( true );\r
1199                 break;\r
1200             default:\r
1201                 _rectangular_type_cbmi.setSelected( true );\r
1202                 break;\r
1203         }\r
1204     }\r
1205 \r
1206     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
1207         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1208             return false;\r
1209         }\r
1210         else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
1211             JOptionPane.showMessageDialog( this,\r
1212                                            "No species tree loaded",\r
1213                                            "Cannot execute GSDI",\r
1214                                            JOptionPane.ERROR_MESSAGE );\r
1215             return false;\r
1216         }\r
1217         else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
1218             JOptionPane.showMessageDialog( this,\r
1219                                            "Species tree is not completely binary",\r
1220                                            "Cannot execute GSDI",\r
1221                                            JOptionPane.ERROR_MESSAGE );\r
1222             return false;\r
1223         }\r
1224         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
1225             JOptionPane.showMessageDialog( this,\r
1226                                            "Gene tree is not completely binary",\r
1227                                            "Cannot execute GSDI",\r
1228                                            JOptionPane.ERROR_MESSAGE );\r
1229             return false;\r
1230         }\r
1231         else {\r
1232             return true;\r
1233         }\r
1234     }\r
1235 \r
1236     boolean isSubtreeDisplayed() {\r
1237         if ( getCurrentTreePanel() != null ) {\r
1238             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
1239                 JOptionPane\r
1240                         .showMessageDialog( this,\r
1241                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
1242                                             "Operation can not be exectuted on a sub-tree",\r
1243                                             JOptionPane.WARNING_MESSAGE );\r
1244                 return true;\r
1245             }\r
1246         }\r
1247         return false;\r
1248     }\r
1249 \r
1250     void midpointRoot() {\r
1251         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1252             _mainpanel.getCurrentTreePanel().midpointRoot();\r
1253         }\r
1254     }\r
1255 \r
1256     void readPhylogeniesFromWebservice( final int i ) {\r
1257         final UrlTreeReader reader = new UrlTreeReader( this, i );\r
1258         new Thread( reader ).start();\r
1259     }\r
1260 \r
1261     void removeAllTextFrames() {\r
1262         for( final TextFrame tf : _textframes ) {\r
1263             if ( tf != null ) {\r
1264                 tf.close();\r
1265             }\r
1266         }\r
1267         _textframes.clear();\r
1268     }\r
1269 \r
1270     void setConfiguration( final Configuration configuration ) {\r
1271         _configuration = configuration;\r
1272     }\r
1273 \r
1274     void setInferenceManager( final InferenceManager i ) {\r
1275         _inference_manager = i;\r
1276     }\r
1277 \r
1278     void setOptions( final Options options ) {\r
1279         _options = options;\r
1280     }\r
1281 \r
1282     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
1283         setTypeMenuToAllUnselected();\r
1284         switch ( type ) {\r
1285             case CIRCULAR:\r
1286                 _circular_type_cbmi.setSelected( true );\r
1287                 break;\r
1288             case CONVEX:\r
1289                 _convex_type_cbmi.setSelected( true );\r
1290                 break;\r
1291             case CURVED:\r
1292                 _curved_type_cbmi.setSelected( true );\r
1293                 break;\r
1294             case EURO_STYLE:\r
1295                 _euro_type_cbmi.setSelected( true );\r
1296                 break;\r
1297             case ROUNDED:\r
1298                 _rounded_type_cbmi.setSelected( true );\r
1299                 break;\r
1300             case RECTANGULAR:\r
1301                 _rectangular_type_cbmi.setSelected( true );\r
1302                 break;\r
1303             case TRIANGULAR:\r
1304                 _triangular_type_cbmi.setSelected( true );\r
1305                 break;\r
1306             case UNROOTED:\r
1307                 _unrooted_type_cbmi.setSelected( true );\r
1308                 break;\r
1309             default:\r
1310                 throw new IllegalArgumentException( "unknown type: " + type );\r
1311         }\r
1312     }\r
1313 \r
1314     final void setSpeciesTree( final Phylogeny species_tree ) {\r
1315         _species_tree = species_tree;\r
1316     }\r
1317 \r
1318     void setTypeMenuToAllUnselected() {\r
1319         _convex_type_cbmi.setSelected( false );\r
1320         _curved_type_cbmi.setSelected( false );\r
1321         _euro_type_cbmi.setSelected( false );\r
1322         _rounded_type_cbmi.setSelected( false );\r
1323         _triangular_type_cbmi.setSelected( false );\r
1324         _rectangular_type_cbmi.setSelected( false );\r
1325         _unrooted_type_cbmi.setSelected( false );\r
1326         _circular_type_cbmi.setSelected( false );\r
1327     }\r
1328 \r
1329     void switchColors() {\r
1330         final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
1331         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
1332         csc.setVisible( true );\r
1333     }\r
1334 \r
1335     void taxColor() {\r
1336         if ( _mainpanel.getCurrentTreePanel() != null ) {\r
1337             _mainpanel.getCurrentTreePanel().taxColor();\r
1338         }\r
1339     }\r
1340 \r
1341     void typeChanged( final Object o ) {\r
1342         updateTypeCheckboxes( getOptions(), o );\r
1343         updateOptions( getOptions() );\r
1344         if ( getCurrentTreePanel() != null ) {\r
1345             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
1346             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
1347             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1348                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
1349                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
1350                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
1351                 getCurrentTreePanel().getControlPanel().showWhole();\r
1352             }\r
1353             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1354                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
1355             }\r
1356             else {\r
1357                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
1358             }\r
1359             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
1360             updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
1361             if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
1362                 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
1363                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
1364                 }\r
1365                 else {\r
1366                     getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
1367                 }\r
1368             }\r
1369         }\r
1370     }\r
1371 \r
1372     void updateOptions( final Options options ) {\r
1373         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
1374         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
1375                 && _background_gradient_cbmi.isSelected() );\r
1376         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
1377         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
1378                 && _show_annotation_ref_source.isSelected() );\r
1379         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
1380                 && _abbreviate_scientific_names.isSelected() );\r
1381         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
1382                 && _color_labels_same_as_parent_branch.isSelected() );\r
1383         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
1384                 && _show_default_node_shapes_internal_cbmi.isSelected() );\r
1385         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
1386                 && _show_default_node_shapes_external_cbmi.isSelected() );\r
1387         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
1388             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
1389         }\r
1390         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
1391             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
1392         }\r
1393         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
1394             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
1395         }\r
1396         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
1397                 && _search_case_senstive_cbmi.isSelected() );\r
1398         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
1399             options.setShowScale( _show_scale_cbmi.isSelected() );\r
1400         }\r
1401         if ( _label_direction_cbmi != null ) {\r
1402             if ( _label_direction_cbmi.isSelected() ) {\r
1403                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
1404             }\r
1405             else {\r
1406                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
1407             }\r
1408         }\r
1409         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
1410         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
1411                 && _show_confidence_stddev_cbmi.isSelected() );\r
1412         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {\r
1413             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );\r
1414         }\r
1415         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
1416             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
1417         }\r
1418         options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
1419                 && ( _print_using_actual_size_cbmi.isSelected() ) );\r
1420         options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
1421                 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
1422         options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
1423         if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
1424                 && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1425             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
1426         }\r
1427         else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
1428                 && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
1429             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
1430         }\r
1431         else {\r
1432             options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
1433         }\r
1434         options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
1435                 && _print_black_and_white_cbmi.isSelected() );\r
1436         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
1437                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
1438         if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
1439             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
1440         }\r
1441         else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
1442             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
1443         }\r
1444         else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
1445             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
1446         }\r
1447         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
1448             options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
1449         }\r
1450         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
1451                 && _replace_underscores_cbmi.isSelected() );\r
1452         options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
1453                 && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
1454         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
1455                 && _search_whole_words_only_cbmi.isSelected() );\r
1456         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
1457                 && _inverse_search_result_cbmi.isSelected() );\r
1458         if ( _graphics_export_visible_only_cbmi != null ) {\r
1459             options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
1460             if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
1461                 _graphics_export_using_actual_size_cbmi.setSelected( true );\r
1462                 _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
1463             }\r
1464             else {\r
1465                 _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
1466             }\r
1467         }\r
1468         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
1469             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
1470         }\r
1471         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
1472             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
1473         }\r
1474         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
1475             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
1476         }\r
1477         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
1478             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
1479         }\r
1480         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
1481             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
1482         }\r
1483         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
1484             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
1485         }\r
1486         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
1487             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
1488         }\r
1489         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
1490             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
1491         }\r
1492     }\r
1493 \r
1494     void updateTypeCheckboxes( final Options options, final Object o ) {\r
1495         setTypeMenuToAllUnselected();\r
1496         ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
1497     }\r
1498 \r
1499     void viewAsNexus() {\r
1500         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1501             String title = "Nexus";\r
1502             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1503                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1504             }\r
1505             showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
1506                            title );\r
1507         }\r
1508     }\r
1509 \r
1510     void viewAsNH() {\r
1511         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1512             String title = "New Hampshire";\r
1513             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1514                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1515             }\r
1516             showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
1517                                    .getNhConversionSupportValueStyle() ),\r
1518                            title );\r
1519         }\r
1520     }\r
1521 \r
1522     void viewAsXML() {\r
1523         if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
1524             String title = "phyloXML";\r
1525             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
1526                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
1527             }\r
1528             showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
1529         }\r
1530     }\r
1531 \r
1532     private void annotateSequences() {\r
1533         if ( getCurrentTreePanel() != null ) {\r
1534             List<PhylogenyNode> nodes = null;\r
1535             if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
1536                     || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
1537                 nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
1538             }\r
1539             if ( ( nodes == null ) || nodes.isEmpty() ) {\r
1540                 JOptionPane\r
1541                         .showMessageDialog( this,\r
1542                                             "Need to select nodes, either via direct selection or via the \"Search\" function",\r
1543                                             "No nodes selected for annotation",\r
1544                                             JOptionPane.ERROR_MESSAGE );\r
1545                 return;\r
1546             }\r
1547             final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
1548             if ( ( phy != null ) && !phy.isEmpty() ) {\r
1549                 final JTextField ref_field = new JTextField( 10 );\r
1550                 final JTextField desc_filed = new JTextField( 20 );\r
1551                 ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
1552                         : getPreviousNodeAnnotationReference() );\r
1553                 final JPanel my_panel = new JPanel();\r
1554                 my_panel.add( new JLabel( "Reference " ) );\r
1555                 my_panel.add( ref_field );\r
1556                 my_panel.add( Box.createHorizontalStrut( 15 ) );\r
1557                 my_panel.add( new JLabel( "Description " ) );\r
1558                 my_panel.add( desc_filed );\r
1559                 final int result = JOptionPane.showConfirmDialog( null,\r
1560                                                                   my_panel,\r
1561                                                                   "Enter the sequence annotation(s) for the "\r
1562                                                                           + nodes.size() + " selected nodes",\r
1563                                                                   JOptionPane.OK_CANCEL_OPTION );\r
1564                 if ( result == JOptionPane.OK_OPTION ) {\r
1565                     String ref = ref_field.getText();\r
1566                     String desc = desc_filed.getText();\r
1567                     if ( !ForesterUtil.isEmpty( ref ) ) {\r
1568                         ref = ref.trim();\r
1569                         ref = ref.replaceAll( "\\s+", " " );\r
1570                         if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
1571                                 || ( ref.length() < 3 ) ) {\r
1572                             JOptionPane.showMessageDialog( this,\r
1573                                                            "Reference needs to be in the form of \"GO:1234567\"",\r
1574                                                            "Illegal Format for Annotation Reference",\r
1575                                                            JOptionPane.ERROR_MESSAGE );\r
1576                             return;\r
1577                         }\r
1578                     }\r
1579                     if ( ref != null ) {\r
1580                         setPreviousNodeAnnotationReference( ref );\r
1581                     }\r
1582                     if ( desc != null ) {\r
1583                         desc = desc.trim();\r
1584                         desc = desc.replaceAll( "\\s+", " " );\r
1585                     }\r
1586                     if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
1587                         for( final PhylogenyNode n : nodes ) {\r
1588                             ForesterUtil.ensurePresenceOfSequence( n );\r
1589                             final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
1590                                     : new Annotation( ref );\r
1591                             if ( !ForesterUtil.isEmpty( desc ) ) {\r
1592                                 ann.setDesc( desc );\r
1593                             }\r
1594                             n.getNodeData().getSequence().addAnnotation( ann );\r
1595                         }\r
1596                     }\r
1597                     getMainPanel().getControlPanel().showAnnotations();\r
1598                 }\r
1599             }\r
1600         }\r
1601     }\r
1602 \r
1603     private void chooseFont() {\r
1604         final FontChooser fc = new FontChooser();\r
1605         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
1606         fc.showDialog( this, "Select the Base Font" );\r
1607         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
1608     }\r
1609 \r
1610     private void chooseMinimalConfidence() {\r
1611         final String s = ( String ) JOptionPane\r
1612                 .showInputDialog( this,\r
1613                                   "Please enter the minimum for confidence values to be displayed.\n"\r
1614                                           + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
1615                                   "Minimal Confidence Value",\r
1616                                   JOptionPane.QUESTION_MESSAGE,\r
1617                                   null,\r
1618                                   null,\r
1619                                   getOptions().getMinConfidenceValue() );\r
1620         if ( !ForesterUtil.isEmpty( s ) ) {\r
1621             boolean success = true;\r
1622             double m = 0.0;\r
1623             final String m_str = s.trim();\r
1624             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1625                 try {\r
1626                     m = Double.parseDouble( m_str );\r
1627                 }\r
1628                 catch ( final Exception ex ) {\r
1629                     success = false;\r
1630                 }\r
1631             }\r
1632             else {\r
1633                 success = false;\r
1634             }\r
1635             if ( success && ( m >= 0.0 ) ) {\r
1636                 getOptions().setMinConfidenceValue( m );\r
1637             }\r
1638         }\r
1639     }\r
1640 \r
1641     private void doUpdateProcessMenu() {\r
1642         if ( _process_pool.size() > 0 ) {\r
1643             if ( _process_menu == null ) {\r
1644                 _process_menu = createMenu( "", getConfiguration() );\r
1645                 _process_menu.setForeground( Color.RED );\r
1646             }\r
1647             _process_menu.removeAll();\r
1648             final String text = "processes running: " + _process_pool.size();\r
1649             _process_menu.setText( text );\r
1650             _jmenubar.add( _process_menu );\r
1651             for( int i = 0; i < _process_pool.size(); ++i ) {\r
1652                 final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
1653                 _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
1654             }\r
1655         }\r
1656         else {\r
1657             if ( _process_menu != null ) {\r
1658                 _process_menu.removeAll();\r
1659                 _jmenubar.remove( _process_menu );\r
1660             }\r
1661         }\r
1662         _jmenubar.validate();\r
1663         _jmenubar.repaint();\r
1664         repaint();\r
1665     }\r
1666 \r
1667     private String getPreviousNodeAnnotationReference() {\r
1668         return _previous_node_annotation_ref;\r
1669     }\r
1670 \r
1671     private void removeBranchColors() {\r
1672         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1673             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
1674         }\r
1675     }\r
1676 \r
1677     private void removeVisualStyles() {\r
1678         if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
1679             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
1680         }\r
1681     }\r
1682 \r
1683     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
1684         _previous_node_annotation_ref = previous_node_annotation_ref;\r
1685     }\r
1686 \r
1687     /**\r
1688      * Display the about box.\r
1689      */\r
1690     static void about() {\r
1691         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
1692         about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );\r
1693         about.append( "All Rights Reserved\n" );\r
1694         about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
1695         about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
1696         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
1697         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
1698         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
1699         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
1700             about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
1701         }\r
1702         if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
1703                 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
1704             about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
1705                     + ForesterUtil.OS_VERSION + "]\n" );\r
1706         }\r
1707         final Runtime rt = java.lang.Runtime.getRuntime();\r
1708         final long free_memory = rt.freeMemory() / 1000000;\r
1709         final long total_memory = rt.totalMemory() / 1000000;\r
1710         about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
1711         about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
1712         about.append( "References:\n" );\r
1713         about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
1714         about.append( "For more information & download:\n" );\r
1715         about.append( Constants.APTX_WEB_SITE + "\n" );\r
1716         about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
1717         JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
1718     }\r
1719 \r
1720     static void chooseNodeSize( final Options options, final Component parent ) {\r
1721         final String s = ( String ) JOptionPane.showInputDialog( parent,\r
1722                                                                  "Please enter the default size for node shapes.\n"\r
1723                                                                          + "[current value: "\r
1724                                                                          + options.getDefaultNodeShapeSize() + "]\n",\r
1725                                                                  "Node Shape Size",\r
1726                                                                  JOptionPane.QUESTION_MESSAGE,\r
1727                                                                  null,\r
1728                                                                  null,\r
1729                                                                  options.getDefaultNodeShapeSize() );\r
1730         if ( !ForesterUtil.isEmpty( s ) ) {\r
1731             boolean success = true;\r
1732             double m = 0.0;\r
1733             final String m_str = s.trim();\r
1734             if ( !ForesterUtil.isEmpty( m_str ) ) {\r
1735                 try {\r
1736                     m = Double.parseDouble( m_str );\r
1737                 }\r
1738                 catch ( final Exception ex ) {\r
1739                     success = false;\r
1740                 }\r
1741             }\r
1742             else {\r
1743                 success = false;\r
1744             }\r
1745             if ( success && ( m >= 0.0 ) ) {\r
1746                 final short size = ForesterUtil.roundToShort( m );\r
1747                 if ( size >= 0.0 ) {\r
1748                     options.setDefaultNodeShapeSize( size );\r
1749                 }\r
1750             }\r
1751         }\r
1752     }\r
1753 \r
1754     static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
1755         return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
1756     }\r
1757 \r
1758     static JMenu createMenu( final String title, final Configuration conf ) {\r
1759         final JMenu jmenu = new JMenu( title );\r
1760         if ( !conf.isUseNativeUI() ) {\r
1761             jmenu.setFont( MainFrame.menu_font );\r
1762             jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
1763             jmenu.setForeground( conf.getGuiMenuTextColor() );\r
1764         }\r
1765         return jmenu;\r
1766     }\r
1767 \r
1768     static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
1769         label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
1770         if ( !configuration.isUseNativeUI() ) {\r
1771             label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
1772             label.setForeground( configuration.getGuiMenuTextColor() );\r
1773             label.setOpaque( true );\r
1774         }\r
1775         label.setSelected( false );\r
1776         label.setEnabled( false );\r
1777         return label;\r
1778     }\r
1779 \r
1780     static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
1781         switch ( op.getDefaultNodeFill() ) {\r
1782             case GRADIENT:\r
1783                 op.setDefaultNodeFill( NodeFill.SOLID );\r
1784                 break;\r
1785             case NONE:\r
1786                 op.setDefaultNodeFill( NodeFill.GRADIENT );\r
1787                 break;\r
1788             case SOLID:\r
1789                 op.setDefaultNodeFill( NodeFill.NONE );\r
1790                 break;\r
1791             default:\r
1792                 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
1793         }\r
1794     }\r
1795 \r
1796     static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
1797         switch ( op.getDefaultNodeShape() ) {\r
1798             case CIRCLE:\r
1799                 op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
1800                 break;\r
1801             case RECTANGLE:\r
1802                 op.setDefaultNodeShape( NodeShape.CIRCLE );\r
1803                 break;\r
1804             default:\r
1805                 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
1806         }\r
1807     }\r
1808 \r
1809     static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
1810         switch ( op.getOvPlacement() ) {\r
1811             case LOWER_LEFT:\r
1812                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
1813                 break;\r
1814             case LOWER_RIGHT:\r
1815                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
1816                 break;\r
1817             case UPPER_LEFT:\r
1818                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
1819                 break;\r
1820             case UPPER_RIGHT:\r
1821                 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
1822                 break;\r
1823             default:\r
1824                 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
1825         }\r
1826         if ( tree_panel != null ) {\r
1827             tree_panel.updateOvSettings();\r
1828         }\r
1829     }\r
1830 \r
1831     static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
1832         if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
1833             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1834                     + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
1835         }\r
1836         else {\r
1837             mi.setText( "Cycle Node Shape Fill Type..." );\r
1838         }\r
1839     }\r
1840 \r
1841     static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
1842         if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
1843             mi.setText( "Cycle Node Shape Fill Type... (current: "\r
1844                     + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
1845         }\r
1846         else {\r
1847             mi.setText( "Cycle Node Shape Fill Type..." );\r
1848         }\r
1849     }\r
1850 \r
1851     static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
1852         if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
1853             mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
1854         }\r
1855         else {\r
1856             mi.setText( "Cycle Overview Placement..." );\r
1857         }\r
1858     }\r
1859 \r
1860     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
1861         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
1862             mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
1863                     + ")" );\r
1864         }\r
1865         else {\r
1866             mi.setText( "Select Color Scheme..." );\r
1867         }\r
1868     }\r
1869 \r
1870     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
1871         mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
1872     }\r
1873 \r
1874     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
1875         if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
1876             mi.setEnabled( true );\r
1877         }\r
1878         else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
1879             mi.setEnabled( true );\r
1880         }\r
1881         else {\r
1882             mi.setEnabled( false );\r
1883         }\r
1884         mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
1885     }\r
1886 \r
1887     static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
1888         mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
1889     }\r
1890 \r
1891     static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,\r
1892                                                            final JCheckBoxMenuItem scale,\r
1893                                                            final JCheckBoxMenuItem branch_lengths,\r
1894                                                            final JRadioButtonMenuItem non_lined_up,\r
1895                                                            final JRadioButtonMenuItem uniform_clado,\r
1896                                                            final JRadioButtonMenuItem nonuniform_clado,\r
1897                                                            final JCheckBoxMenuItem label_direction_cbmi ) {\r
1898         final TreePanel tree_panel = main_panel.getCurrentTreePanel();\r
1899         final ControlPanel control = main_panel.getControlPanel();\r
1900         final Options options = main_panel.getOptions();\r
1901         scale.setSelected( options.isShowScale() );\r
1902         branch_lengths.setSelected( options.isShowBranchLengthValues() );\r
1903         // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1904         if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {\r
1905             scale.setSelected( false );\r
1906             scale.setEnabled( false );\r
1907             branch_lengths.setSelected( false );\r
1908             branch_lengths.setEnabled( false );\r
1909         }\r
1910         else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {\r
1911             scale.setSelected( false );\r
1912             scale.setEnabled( false );\r
1913             branch_lengths.setEnabled( true );\r
1914         }\r
1915         else {\r
1916             scale.setEnabled( true );\r
1917             branch_lengths.setEnabled( true );\r
1918         }\r
1919         if ( ( tree_panel != null )\r
1920                 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )\r
1921                         && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1922                         .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1923             branch_lengths.setSelected( false );\r
1924             branch_lengths.setEnabled( false );\r
1925         }\r
1926         if ( tree_panel != null ) {\r
1927             if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )\r
1928                     || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {\r
1929                 non_lined_up.setEnabled( false );\r
1930                 uniform_clado.setEnabled( false );\r
1931                 nonuniform_clado.setEnabled( false );\r
1932             }\r
1933             else {\r
1934                 non_lined_up.setEnabled( true );\r
1935                 uniform_clado.setEnabled( true );\r
1936                 nonuniform_clado.setEnabled( true );\r
1937             }\r
1938         }\r
1939         else {\r
1940             if ( ( tree_panel != null )\r
1941                     && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel\r
1942                             .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {\r
1943                 branch_lengths.setSelected( false );\r
1944                 branch_lengths.setEnabled( false );\r
1945             }\r
1946             if ( ( tree_panel != null )\r
1947                     && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel\r
1948                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {\r
1949                 non_lined_up.setEnabled( false );\r
1950             }\r
1951             else {\r
1952                 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );\r
1953                 non_lined_up.setEnabled( true );\r
1954             }\r
1955         }\r
1956         label_direction_cbmi.setEnabled( true );\r
1957         if ( tree_panel != null ) {\r
1958             if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )\r
1959                     && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
1960                 label_direction_cbmi.setEnabled( false );\r
1961             }\r
1962             if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {\r
1963                 scale.setSelected( false );\r
1964                 scale.setEnabled( false );\r
1965             }\r
1966         }\r
1967     }\r
1968 \r
1969     static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
1970         for( final TreePanel tree_panel : treepanels ) {\r
1971             tree_panel.setTextAntialias();\r
1972         }\r
1973     }\r
1974 }\r