forester/java/src/org/forester/archaeopteryx/ControlPanel.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 //
   8 // This library is free software; you can redistribute it and/or
   9 // modify it under the terms of the GNU Lesser General Public
  10 // License as published by the Free Software Foundation; either
  11 // version 2.1 of the License, or (at your option) any later version.
  12 //
  13 // This library is distributed in the hope that it will be useful,
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  16 // Lesser General Public License for more details.
  17 //
  18 // You should have received a copy of the GNU Lesser General Public
  19 // License along with this library; if not, write to the Free Software
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  21 //
  22 // Contact: phylosoft @ gmail . com
  23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  24
  25 package org.forester.archaeopteryx;
  26
  27 import java.awt.BorderLayout;
  28 import java.awt.Color;
  29 import java.awt.Component;
  30 import java.awt.Dimension;
  31 import java.awt.Font;
  32 import java.awt.GridBagLayout;
  33 import java.awt.GridLayout;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.ItemEvent;
  37 import java.awt.event.ItemListener;
  38 import java.awt.event.KeyAdapter;
  39 import java.awt.event.KeyEvent;
  40 import java.util.ArrayList;
  41 import java.util.Arrays;
  42 import java.util.Collection;
  43 import java.util.HashMap;
  44 import java.util.HashSet;
  45 import java.util.List;
  46 import java.util.Map;
  47
  48 import javax.swing.BorderFactory;
  49 import javax.swing.DefaultListCellRenderer;
  50 import javax.swing.JButton;
  51 import javax.swing.JCheckBox;
  52 import javax.swing.JComboBox;
  53 import javax.swing.JLabel;
  54 import javax.swing.JList;
  55 import javax.swing.JPanel;
  56 import javax.swing.JScrollBar;
  57 import javax.swing.JTextField;
  58 import javax.swing.ListCellRenderer;
  59
  60 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  61 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  62 import org.forester.phylogeny.Phylogeny;
  63 import org.forester.phylogeny.PhylogenyMethods;
  64 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  65 import org.forester.phylogeny.PhylogenyNode;
  66 import org.forester.phylogeny.data.Sequence;
  67 import org.forester.phylogeny.data.SequenceRelation;
  68 import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE;
  69 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  70 import org.forester.util.ForesterUtil;
  71
  72 final class ControlPanel extends JPanel implements ActionListener {
  73
  74     final static Font                         jcb_bold_font             = new Font( Configuration.getDefaultFontFamilyName(),
  75                                                                                     Font.BOLD,
  76                                                                                     9 );
  77     final static Font                         jcb_font                  = new Font( Configuration.getDefaultFontFamilyName(),
  78                                                                                     Font.PLAIN,
  79                                                                                     9 );
  80     final static Font                         js_font                   = new Font( Configuration.getDefaultFontFamilyName(),
  81                                                                                     Font.PLAIN,
  82                                                                                     9 );
  83     private static final String               RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
  84     private static final String               SEARCH_TIP_TEXT           = "Enter text to search for. Use ',' for logical OR and '+' for logical AND (not used in this manner for regular expression searches).";
  85     private static final long                 serialVersionUID          = -8463483932821545633L;
  86     private NodeClickAction                   _action_when_node_clicked;
  87     private int                               _add_new_node_item;
  88     private Map<Integer, String>              _all_click_to_names;
  89     private Map<String, Color>                _annotation_colors;
  90     private int                               _blast_item;
  91     private JComboBox<String>                 _click_to_combobox;
  92     private JLabel                            _click_to_label;
  93     private List<String>                      _click_to_names;
  94     private int                               _collapse_cb_item;
  95     private JCheckBox                         _color_acc_species;
  96     private JCheckBox                         _color_acc_sequence;
  97     private JCheckBox                         _color_according_to_annotation;
  98     private boolean                           _color_branches;
  99     private JCheckBox                         _use_visual_styles_cb;
 100     private int                               _color_subtree_cb_item;
 101     private int                               _change_node_font_item;
 102     // The settings from the conf file
 103     private final Configuration               _configuration;
 104     private int                               _copy_subtree_item;
 105     private int                               _cut_subtree_item;
 106     private JButton                           _decr_domain_structure_evalue_thr;
 107     private int                               _delete_node_or_subtree_item;
 108     private JCheckBox                         _display_as_phylogram_cb;
 109     // Tree checkboxes
 110     private JCheckBox                         _display_internal_data;
 111     private JLabel                            _domain_display_label;
 112     private JTextField                        _domain_structure_evalue_thr_tf;
 113     private List<Boolean>                     _draw_phylogram;
 114     private JCheckBox                         _dynamically_hide_data;
 115     private int                               _edit_node_data_item;
 116     private int                               _get_ext_desc_data;
 117     private JButton                           _incr_domain_structure_evalue_thr;
 118     private final MainPanel                   _mainpanel;
 119     private JCheckBox                         _node_desc_popup_cb;
 120     private int                               _open_pdb_item;
 121     private int                               _open_seq_web_item;
 122     private int                               _open_tax_web_item;
 123     private int                               _color_node_font_item;
 124     private JButton                           _order;
 125     private boolean                           _order_of_appearance;
 126     private int                               _paste_subtree_item;
 127     private int                               _reroot_cb_item;
 128     private JButton                           _return_to_super_tree;
 129     // Search
 130     private JLabel                            _search_found_label_0;
 131     private JLabel                            _search_found_label_1;
 132     private JButton                           _search_reset_button_0;
 133     private JButton                           _search_reset_button_1;
 134     private JTextField                        _search_tf_0;
 135     private JTextField                        _search_tf_1;
 136     private int                               _select_nodes_item;
 137     private Sequence                          _selected_query_seq;
 138     private JCheckBox                         _seq_relation_confidence_switch;
 139     private JComboBox<SEQUENCE_RELATION_TYPE> _sequence_relation_type_box;
 140     private JCheckBox                         _show_annotation;
 141     private JCheckBox                         _show_binary_character_counts;
 142     private JCheckBox                         _show_binary_characters;
 143     // Indices for the click-to options in the combo box
 144     private int                               _show_data_item;
 145     private JCheckBox                         _show_domain_architectures;
 146     private JCheckBox                         _show_mol_seqs;
 147     private JCheckBox                         _write_branch_length_values;
 148     private JCheckBox                         _show_events;
 149     private JCheckBox                         _show_gene_names;
 150     private JCheckBox                         _show_node_names;
 151     private JCheckBox                         _show_properties_cb;
 152     private JCheckBox                         _show_seq_names;
 153     private JCheckBox                         _show_seq_symbols;
 154     private JCheckBox                         _show_sequence_acc;
 155     private JComboBox<String>                 _show_sequence_relations;
 156     private JCheckBox                         _show_taxo_code;
 157     private JCheckBox                         _show_taxo_common_names;
 158     private JCheckBox                         _show_taxo_images_cb;
 159     private JCheckBox                         _show_taxo_scientific_names;
 160     private JCheckBox                         _show_vector_data_cb;
 161     private JButton                           _show_whole;
 162     private int                               _sort_descendents_item;
 163     private Map<String, Color>                _species_colors;
 164     private Map<String, Color>                _sequence_colors;
 165     private int                               _subtree_cb_item;
 166     private int                               _swap_cb_item;
 167     private JButton                           _uncollapse_all;
 168     private JCheckBox                         _width_branches;
 169     private JCheckBox                         _write_confidence;
 170     private JButton                           _zoom_in_domain_structure;
 171     private JButton                           _zoom_in_x;
 172     private JButton                           _zoom_in_y;
 173     private JLabel                            _zoom_label;
 174     private JButton                           _zoom_out_domain_structure;
 175     private JButton                           _zoom_out_x;
 176     private JButton                           _zoom_out_y;
 177
 178     ControlPanel( final MainPanel ap, final Configuration configuration ) {
 179         init();
 180         _mainpanel = ap;
 181         _configuration = configuration;
 182         if ( !_configuration.isUseNativeUI() ) {
 183             setBackground( getConfiguration().getGuiBackgroundColor() );
 184             setBorder( BorderFactory.createRaisedBevelBorder() );
 185         }
 186         setLayout( new GridLayout( 0, 1, 2, 2 ) );
 187         _order_of_appearance = true;
 188         setupControls();
 189     }
 190
 191     /**
 192      * Handle an action.
 193      */
 194     @Override
 195     public void actionPerformed( final ActionEvent e ) {
 196         try {
 197             if ( e.getSource() == _color_acc_sequence ) {
 198                 if ( _color_acc_species != null ) {
 199                     _color_acc_species.setSelected( false );
 200                 }
 201             }
 202             else if ( e.getSource() == _color_acc_species ) {
 203                 if ( _color_acc_sequence != null ) {
 204                     _color_acc_sequence.setSelected( false );
 205                 }
 206             }
 207             final TreePanel tp = getMainPanel().getCurrentTreePanel();
 208             if ( tp == null ) {
 209                 return;
 210             }
 211             if ( e.getSource() == _click_to_combobox ) {
 212                 setClickToAction( _click_to_combobox.getSelectedIndex() );
 213                 getCurrentTreePanel().repaint();
 214             }
 215             else if ( e.getSource() == _show_binary_characters ) {
 216                 if ( ( _show_binary_character_counts != null ) && _show_binary_characters.isSelected() ) {
 217                     _show_binary_character_counts.setSelected( false );
 218                 }
 219                 displayedPhylogenyMightHaveChanged( true );
 220             }
 221             else if ( e.getSource() == _show_binary_character_counts ) {
 222                 if ( ( _show_binary_characters != null ) && _show_binary_character_counts.isSelected() ) {
 223                     _show_binary_characters.setSelected( false );
 224                 }
 225                 displayedPhylogenyMightHaveChanged( true );
 226             }
 227             else if ( e.getSource() == _show_domain_architectures ) {
 228                 search0();
 229                 search1();
 230                 displayedPhylogenyMightHaveChanged( true );
 231             }
 232             else if ( ( tp != null ) && ( tp.getPhylogeny() != null ) ) {
 233                 if ( e.getSource() == getDisplayAsPhylogramCb() ) {
 234                     setDrawPhylogram( getDisplayAsPhylogramCb().isSelected() );
 235                     showWhole();
 236                 }
 237                 // Zoom buttons
 238                 else if ( e.getSource() == _zoom_in_x ) {
 239                     zoomInX( Constants.BUTTON_ZOOM_IN_FACTOR, Constants.BUTTON_ZOOM_IN_X_CORRECTION_FACTOR );
 240                     displayedPhylogenyMightHaveChanged( false );
 241                 }
 242                 else if ( e.getSource() == _zoom_in_y ) {
 243                     zoomInY( Constants.BUTTON_ZOOM_IN_FACTOR );
 244                     displayedPhylogenyMightHaveChanged( false );
 245                 }
 246                 else if ( e.getSource() == _zoom_out_x ) {
 247                     zoomOutX( Constants.BUTTON_ZOOM_OUT_FACTOR, Constants.BUTTON_ZOOM_OUT_X_CORRECTION_FACTOR );
 248                     displayedPhylogenyMightHaveChanged( false );
 249                 }
 250                 else if ( e.getSource() == _zoom_out_y ) {
 251                     zoomOutY( Constants.BUTTON_ZOOM_OUT_FACTOR );
 252                     displayedPhylogenyMightHaveChanged( false );
 253                 }
 254                 else if ( e.getSource() == _show_whole ) {
 255                     displayedPhylogenyMightHaveChanged( true );
 256                     showWhole();
 257                 }
 258                 else if ( e.getSource() == _return_to_super_tree ) {
 259                     _mainpanel.getCurrentTreePanel().superTree();
 260                     showWhole();
 261                 }
 262                 else if ( e.getSource() == _order ) {
 263                     DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
 264                     if ( isShowTaxonomyScientificNames() || isShowTaxonomyCode() ) {
 265                         pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
 266                     }
 267                     else if ( isShowSeqNames() || isShowSeqSymbols() || isShowGeneNames() ) {
 268                         pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
 269                     }
 270                     PhylogenyMethods.orderAppearance( tp.getPhylogeny().getRoot(), _order_of_appearance, true, pri );
 271                     _order_of_appearance = !_order_of_appearance;
 272                     tp.setNodeInPreorderToNull();
 273                     tp.getPhylogeny().externalNodesHaveChanged();
 274                     tp.getPhylogeny().clearHashIdToNodeMap();
 275                     tp.getPhylogeny().recalculateNumberOfExternalDescendants( true );
 276                     tp.resetNodeIdToDistToLeafMap();
 277                     tp.setEdited( true );
 278                     displayedPhylogenyMightHaveChanged( true );
 279                 }
 280                 else if ( e.getSource() == _uncollapse_all ) {
 281                     uncollapseAll( tp );
 282                     displayedPhylogenyMightHaveChanged( false );
 283                 }
 284                 else if ( e.getSource() == _zoom_in_domain_structure ) {
 285                     _mainpanel.getCurrentTreePanel().zoomInDomainStructure();
 286                     displayedPhylogenyMightHaveChanged( true );
 287                 }
 288                 else if ( e.getSource() == _zoom_out_domain_structure ) {
 289                     _mainpanel.getCurrentTreePanel().zoomOutDomainStructure();
 290                     displayedPhylogenyMightHaveChanged( true );
 291                 }
 292                 else if ( e.getSource() == _decr_domain_structure_evalue_thr ) {
 293                     _mainpanel.getCurrentTreePanel().decreaseDomainStructureEvalueThresholdExp();
 294                     displayedPhylogenyMightHaveChanged( true );
 295                 }
 296                 else if ( e.getSource() == _incr_domain_structure_evalue_thr ) {
 297                     _mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThresholdExp();
 298                     displayedPhylogenyMightHaveChanged( true );
 299                 }
 300                 else if ( e.getSource() == _search_tf_0 ) {
 301                     search0();
 302                     displayedPhylogenyMightHaveChanged( true );
 303                 }
 304                 else if ( e.getSource() == _search_tf_1 ) {
 305                     search1();
 306                     displayedPhylogenyMightHaveChanged( true );
 307                 }
 308                 else if ( ( _dynamically_hide_data != null ) && ( e.getSource() == _dynamically_hide_data )
 309                         && !_dynamically_hide_data.isSelected() ) {
 310                     setDynamicHidingIsOn( false );
 311                     displayedPhylogenyMightHaveChanged( true );
 312                 }
 313                 else {
 314                     displayedPhylogenyMightHaveChanged( true );
 315                 }
 316             }
 317             tp.requestFocus();
 318             tp.requestFocusInWindow();
 319             tp.requestFocus();
 320         }
 321         catch ( final Exception ex ) {
 322             AptxUtil.unexpectedException( ex );
 323         }
 324         catch ( final Error err ) {
 325             AptxUtil.unexpectedError( err );
 326         }
 327     }
 328
 329     public JCheckBox getColorAccSpeciesCb() {
 330         return _color_acc_species;
 331     }
 332
 333     public JCheckBox getColorAccSequenceCb() {
 334         return _color_acc_sequence;
 335     }
 336
 337     public JCheckBox getUseVisualStylesCb() {
 338         return _use_visual_styles_cb;
 339     }
 340
 341     public JCheckBox getDisplayAsPhylogramCb() {
 342         return _display_as_phylogram_cb;
 343     }
 344
 345     public JCheckBox getDynamicallyHideData() {
 346         return _dynamically_hide_data;
 347     }
 348
 349     public JCheckBox getNodeDescPopupCb() {
 350         return _node_desc_popup_cb;
 351     }
 352
 353     public Sequence getSelectedQuerySequence() {
 354         return _selected_query_seq;
 355     }
 356
 357     public JComboBox<String> getSequenceRelationBox() {
 358         if ( _show_sequence_relations == null ) {
 359             _show_sequence_relations = new JComboBox<String>();
 360             _show_sequence_relations.setFocusable( false );
 361             _show_sequence_relations.setMaximumRowCount( 20 );
 362             _show_sequence_relations.setFont( ControlPanel.js_font );
 363             if ( !_configuration.isUseNativeUI() ) {
 364                 _show_sequence_relations.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 365                 _show_sequence_relations.setForeground( getConfiguration().getGuiButtonTextColor() );
 366             }
 367             _show_sequence_relations.addItem( "-----" );
 368             _show_sequence_relations.setToolTipText( "To display orthology information for selected query" );
 369         }
 370         return _show_sequence_relations;
 371     }
 372
 373     /* GUILHEM_BEG */
 374     public JComboBox<SEQUENCE_RELATION_TYPE> getSequenceRelationTypeBox() {
 375         if ( _sequence_relation_type_box == null ) {
 376             _sequence_relation_type_box = new JComboBox<SEQUENCE_RELATION_TYPE>();
 377             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : SequenceRelation.SEQUENCE_RELATION_TYPE.values() ) {
 378                 _sequence_relation_type_box.addItem( type );
 379             }
 380             _sequence_relation_type_box.addActionListener( new ActionListener() {
 381
 382                 @Override
 383                 public void actionPerformed( final ActionEvent e ) {
 384                     if ( _mainpanel.getCurrentPhylogeny() != null ) {
 385                         setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
 386                     }
 387                 }
 388             } );
 389         }
 390         return _sequence_relation_type_box;
 391     }
 392
 393     public JCheckBox getShowEventsCb() {
 394         return _show_events;
 395     }
 396
 397     public JCheckBox getWriteConfidenceCb() {
 398         return _write_confidence;
 399     }
 400
 401     public boolean isShowProperties() {
 402         return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
 403     }
 404
 405     public boolean isShowTaxonomyImages() {
 406         return ( ( _show_taxo_images_cb != null ) && _show_taxo_images_cb.isSelected() );
 407     }
 408
 409     public boolean isShowVectorData() {
 410         return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
 411     }
 412
 413     public void setSequenceRelationQueries( final Collection<Sequence> sequenceRelationQueries ) {
 414         final JComboBox<String> box = getSequenceRelationBox();
 415         while ( box.getItemCount() > 1 ) {
 416             box.removeItemAt( 1 );
 417         }
 418         final HashMap<String, Sequence> sequencesByName = new HashMap<String, Sequence>();
 419         final SequenceRelation.SEQUENCE_RELATION_TYPE relationType = ( SequenceRelation.SEQUENCE_RELATION_TYPE ) _sequence_relation_type_box
 420                 .getSelectedItem();
 421         if ( relationType == null ) {
 422             return;
 423         }
 424         final ArrayList<String> sequenceNamesToAdd = new ArrayList<String>();
 425         for( final Sequence seq : sequenceRelationQueries ) {
 426             if ( seq.hasSequenceRelations() ) {
 427                 boolean fFoundForCurrentType = false;
 428                 for( final SequenceRelation sq : seq.getSequenceRelations() ) {
 429                     if ( sq.getType().equals( relationType ) ) {
 430                         fFoundForCurrentType = true;
 431                         break;
 432                     }
 433                 }
 434                 if ( fFoundForCurrentType ) {
 435                     sequenceNamesToAdd.add( seq.getName() );
 436                     sequencesByName.put( seq.getName(), seq );
 437                 }
 438             }
 439         }
 440         // sort sequences by name before adding them to the combo
 441         final String[] sequenceNameArray = sequenceNamesToAdd.toArray( new String[ sequenceNamesToAdd.size() ] );
 442         Arrays.sort( sequenceNameArray, String.CASE_INSENSITIVE_ORDER );
 443         for( final String seqName : sequenceNameArray ) {
 444             box.addItem( seqName );
 445         }
 446         for( final ItemListener oldItemListener : box.getItemListeners() ) {
 447             box.removeItemListener( oldItemListener );
 448         }
 449         box.addItemListener( new ItemListener() {
 450
 451             @Override
 452             public void itemStateChanged( final ItemEvent e ) {
 453                 _selected_query_seq = sequencesByName.get( e.getItem() );
 454                 _mainpanel.getCurrentTreePanel().repaint();
 455             }
 456         } );
 457     }
 458
 459     void activateButtonToReturnToSuperTree( int index ) {
 460         --index;
 461         if ( index > 0 ) {
 462             _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT + " " + index );
 463         }
 464         else {
 465             _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
 466         }
 467         _return_to_super_tree.setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
 468         _return_to_super_tree.setEnabled( true );
 469     }
 470
 471     /**
 472      * Add zoom and quick edit buttons. (Last modified 8/9/04)
 473      */
 474     void addButtons() {
 475         final JLabel spacer = new JLabel( "" );
 476         spacer.setOpaque( false );
 477         add( spacer );
 478         final JPanel x_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
 479         final JPanel y_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
 480         final JPanel z_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
 481         if ( !getConfiguration().isUseNativeUI() ) {
 482             x_panel.setBackground( getBackground() );
 483             y_panel.setBackground( getBackground() );
 484             z_panel.setBackground( getBackground() );
 485         }
 486         add( _zoom_label = new JLabel( "Zoom:" ) );
 487         customizeLabel( _zoom_label, getConfiguration() );
 488         add( x_panel );
 489         add( y_panel );
 490         add( z_panel );
 491         if ( getConfiguration().isUseNativeUI() ) {
 492             _zoom_in_x = new JButton( "+" );
 493             _zoom_out_x = new JButton( "-" );
 494         }
 495         else {
 496             _zoom_in_x = new JButton( "X+" );
 497             _zoom_out_x = new JButton( "X-" );
 498         }
 499         _zoom_in_y = new JButton( "Y+" );
 500         _zoom_out_y = new JButton( "Y-" );
 501         _show_whole = new JButton( "F" );
 502         _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [F or Home]" );
 503         _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+cursor-right]" );
 504         _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+cursor-up]" );
 505         _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+cursor-left]" );
 506         _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+cursor-down]" );
 507         if ( getConfiguration().isUseNativeUI() && ForesterUtil.isMac() ) {
 508             _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
 509             _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );
 510         }
 511         else {
 512             _zoom_out_x.setPreferredSize( new Dimension( 10, 10 ) );
 513             _zoom_in_x.setPreferredSize( new Dimension( 10, 10 ) );
 514         }
 515         _zoom_out_y.setPreferredSize( new Dimension( 10, 10 ) );
 516         _zoom_in_y.setPreferredSize( new Dimension( 10, 10 ) );
 517         _show_whole.setPreferredSize( new Dimension( 10, 10 ) );
 518         _return_to_super_tree = new JButton( RETURN_TO_SUPER_TREE_TEXT );
 519         _return_to_super_tree.setEnabled( false );
 520         _order = new JButton( "Order Subtrees" );
 521         _uncollapse_all = new JButton( "Uncollapse All" );
 522         addJButton( _zoom_in_y, x_panel );
 523         addJButton( _zoom_out_x, y_panel );
 524         addJButton( _show_whole, y_panel );
 525         addJButton( _zoom_in_x, y_panel );
 526         addJButton( _zoom_out_y, z_panel );
 527         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 528             setUpControlsForDomainStrucures();
 529         }
 530         final JLabel spacer2 = new JLabel( "" );
 531         add( spacer2 );
 532         addJButton( _return_to_super_tree, this );
 533         addJButton( _order, this );
 534         addJButton( _uncollapse_all, this );
 535         final JLabel spacer3 = new JLabel( "" );
 536         add( spacer3 );
 537         setVisibilityOfDomainStrucureControls();
 538     }
 539
 540     void addCheckbox( final int which, final String title ) {
 541         final JPanel ch_panel = new JPanel( new BorderLayout( 0, 0 ) );
 542         switch ( which ) {
 543             case Configuration.display_as_phylogram:
 544                 _display_as_phylogram_cb = new JCheckBox( title );
 545                 getDisplayAsPhylogramCb().setToolTipText( "To switch between phylogram and cladogram display" );
 546                 addJCheckBox( getDisplayAsPhylogramCb(), ch_panel );
 547                 add( ch_panel );
 548                 break;
 549             case Configuration.display_internal_data:
 550                 _display_internal_data = new JCheckBox( title );
 551                 _display_internal_data.setToolTipText( "To allow or disallow display of internal labels" );
 552                 addJCheckBox( _display_internal_data, ch_panel );
 553                 add( ch_panel );
 554                 break;
 555             case Configuration.color_according_to_species:
 556                 _color_acc_species = new JCheckBox( title );
 557                 _color_acc_species.setToolTipText( "To colorize node labels as a function of taxonomy" );
 558                 addJCheckBox( _color_acc_species, ch_panel );
 559                 add( ch_panel );
 560                 break;
 561             case Configuration.color_according_to_sequence:
 562                 _color_acc_sequence = new JCheckBox( title );
 563                 _color_acc_sequence.setToolTipText( "To colorize node labels as a function of sequence name" );
 564                 addJCheckBox( _color_acc_sequence, ch_panel );
 565                 add( ch_panel );
 566                 break;
 567             case Configuration.color_according_to_annotation:
 568                 _color_according_to_annotation = new JCheckBox( title );
 569                 _color_according_to_annotation
 570                         .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" );
 571                 addJCheckBox( _color_according_to_annotation, ch_panel );
 572                 add( ch_panel );
 573                 break;
 574             case Configuration.show_node_names:
 575                 _show_node_names = new JCheckBox( title );
 576                 addJCheckBox( _show_node_names, ch_panel );
 577                 add( ch_panel );
 578                 break;
 579             case Configuration.show_taxonomy_scientific_names:
 580                 _show_taxo_scientific_names = new JCheckBox( title );
 581                 addJCheckBox( _show_taxo_scientific_names, ch_panel );
 582                 add( ch_panel );
 583                 break;
 584             case Configuration.show_taxonomy_common_names:
 585                 _show_taxo_common_names = new JCheckBox( title );
 586                 addJCheckBox( _show_taxo_common_names, ch_panel );
 587                 add( ch_panel );
 588                 break;
 589             case Configuration.show_tax_code:
 590                 _show_taxo_code = new JCheckBox( title );
 591                 addJCheckBox( _show_taxo_code, ch_panel );
 592                 add( ch_panel );
 593                 break;
 594             case Configuration.show_taxonomy_images:
 595                 _show_taxo_images_cb = new JCheckBox( title );
 596                 addJCheckBox( _show_taxo_images_cb, ch_panel );
 597                 add( ch_panel );
 598                 break;
 599             case Configuration.show_binary_characters:
 600                 _show_binary_characters = new JCheckBox( title );
 601                 addJCheckBox( _show_binary_characters, ch_panel );
 602                 add( ch_panel );
 603                 break;
 604             case Configuration.show_annotation:
 605                 _show_annotation = new JCheckBox( title );
 606                 addJCheckBox( _show_annotation, ch_panel );
 607                 add( ch_panel );
 608                 break;
 609             case Configuration.show_binary_character_counts:
 610                 _show_binary_character_counts = new JCheckBox( title );
 611                 addJCheckBox( _show_binary_character_counts, ch_panel );
 612                 add( ch_panel );
 613                 break;
 614             case Configuration.write_confidence_values:
 615                 _write_confidence = new JCheckBox( title );
 616                 addJCheckBox( getWriteConfidenceCb(), ch_panel );
 617                 add( ch_panel );
 618                 break;
 619             case Configuration.write_events:
 620                 _show_events = new JCheckBox( title );
 621                 addJCheckBox( getShowEventsCb(), ch_panel );
 622                 add( ch_panel );
 623                 break;
 624             case Configuration.use_style:
 625                 _use_visual_styles_cb = new JCheckBox( title );
 626                 getUseVisualStylesCb()
 627                         .setToolTipText( "To use visual styles (node colors, fonts) and branch colors, if present" );
 628                 addJCheckBox( getUseVisualStylesCb(), ch_panel );
 629                 add( ch_panel );
 630                 break;
 631             case Configuration.width_branches:
 632                 _width_branches = new JCheckBox( title );
 633                 _width_branches.setToolTipText( "To use branch width values, if present" );
 634                 addJCheckBox( _width_branches, ch_panel );
 635                 add( ch_panel );
 636                 break;
 637             case Configuration.write_branch_length_values:
 638                 _write_branch_length_values = new JCheckBox( title );
 639                 addJCheckBox( _write_branch_length_values, ch_panel );
 640                 add( ch_panel );
 641                 break;
 642             case Configuration.show_domain_architectures:
 643                 _show_domain_architectures = new JCheckBox( title );
 644                 addJCheckBox( _show_domain_architectures, ch_panel );
 645                 add( ch_panel );
 646                 break;
 647             case Configuration.show_mol_seqs:
 648                 _show_mol_seqs = new JCheckBox( title );
 649                 addJCheckBox( _show_mol_seqs, ch_panel );
 650                 add( ch_panel );
 651                 break;
 652             case Configuration.show_seq_names:
 653                 _show_seq_names = new JCheckBox( title );
 654                 addJCheckBox( _show_seq_names, ch_panel );
 655                 add( ch_panel );
 656                 break;
 657             case Configuration.show_gene_names:
 658                 _show_gene_names = new JCheckBox( title );
 659                 addJCheckBox( _show_gene_names, ch_panel );
 660                 add( ch_panel );
 661                 break;
 662             case Configuration.show_seq_symbols:
 663                 _show_seq_symbols = new JCheckBox( title );
 664                 addJCheckBox( _show_seq_symbols, ch_panel );
 665                 add( ch_panel );
 666                 break;
 667             case Configuration.show_sequence_acc:
 668                 _show_sequence_acc = new JCheckBox( title );
 669                 addJCheckBox( _show_sequence_acc, ch_panel );
 670                 add( ch_panel );
 671                 break;
 672             case Configuration.dynamically_hide_data:
 673                 _dynamically_hide_data = new JCheckBox( title );
 674                 getDynamicallyHideData().setToolTipText( "To hide labels depending on expected visibility" );
 675                 addJCheckBox( getDynamicallyHideData(), ch_panel );
 676                 add( ch_panel );
 677                 break;
 678             case Configuration.node_data_popup:
 679                 _node_desc_popup_cb = new JCheckBox( title );
 680                 getNodeDescPopupCb().setToolTipText( "To enable mouse rollover display of basic node data" );
 681                 addJCheckBox( getNodeDescPopupCb(), ch_panel );
 682                 add( ch_panel );
 683                 break;
 684             case Configuration.show_relation_confidence:
 685                 _seq_relation_confidence_switch = new JCheckBox( title );
 686                 addJCheckBox( _seq_relation_confidence_switch, ch_panel );
 687                 add( ch_panel );
 688                 break;
 689             case Configuration.show_vector_data:
 690                 _show_vector_data_cb = new JCheckBox( title );
 691                 addJCheckBox( _show_vector_data_cb, ch_panel );
 692                 add( ch_panel );
 693                 break;
 694             case Configuration.show_properties:
 695                 _show_properties_cb = new JCheckBox( title );
 696                 addJCheckBox( _show_properties_cb, ch_panel );
 697                 add( ch_panel );
 698                 break;
 699             default:
 700                 throw new RuntimeException( "unknown checkbox: " + which );
 701         }
 702     }// addCheckbox
 703
 704     void addJButton( final JButton jb, final JPanel p ) {
 705         jb.setFocusPainted( false );
 706         jb.setFont( ControlPanel.jcb_font );
 707         if ( !_configuration.isUseNativeUI() ) {
 708             jb.setBorder( BorderFactory.createLineBorder( getConfiguration().getGuiButtonBorderColor() ) );
 709             jb.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 710             jb.setForeground( getConfiguration().getGuiButtonTextColor() );
 711         }
 712         p.add( jb );
 713         jb.addActionListener( this );
 714     }
 715
 716     void addJCheckBox( final JCheckBox jcb, final JPanel p ) {
 717         jcb.setFocusPainted( false );
 718         jcb.setFont( ControlPanel.jcb_font );
 719         if ( !_configuration.isUseNativeUI() ) {
 720             jcb.setBackground( getConfiguration().getGuiBackgroundColor() );
 721             jcb.setForeground( getConfiguration().getGuiCheckboxTextColor() );
 722         }
 723         p.add( jcb, "Center" );
 724         jcb.addActionListener( this );
 725     }
 726
 727     void addJTextField( final JTextField tf, final JPanel p ) {
 728         if ( !_configuration.isUseNativeUI() ) {
 729             tf.setForeground( getConfiguration().getGuiBackgroundColor() );
 730             tf.setFont( ControlPanel.jcb_font );
 731         }
 732         p.add( tf );
 733         tf.addActionListener( this );
 734     }
 735
 736     void deactivateButtonToReturnToSuperTree() {
 737         _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
 738         _return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
 739         _return_to_super_tree.setEnabled( false );
 740     }
 741
 742     void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
 743         if ( ( _mainpanel != null )
 744                 && ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
 745             if ( getOptions().isShowOverview() ) {
 746                 _mainpanel.getCurrentTreePanel().updateOvSizes();
 747             }
 748             _mainpanel.getCurrentTreePanel().recalculateMaxDistanceToRoot();
 749             setVisibilityOfDomainStrucureControls();
 750             updateDomainStructureEvaluethresholdDisplay();
 751             _mainpanel.getCurrentTreePanel().calculateScaleDistance();
 752             _mainpanel.getCurrentTreePanel().calcMaxDepth();
 753             _mainpanel.adjustJScrollPane();
 754             if ( recalc_longest_ext_node_info ) {
 755                 _mainpanel.getCurrentTreePanel().initNodeData();
 756                 _mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
 757             }
 758             _mainpanel.getCurrentTreePanel().repaint();
 759             // _mainpanel.getCurrentTreePanel().setUpUrtFactors();
 760         }
 761     }
 762
 763     void endClickToOptions() {
 764         _click_to_combobox.addActionListener( this );
 765     }
 766
 767     /**
 768      * Indicates what action should be execute when a node is clicked
 769      *
 770      * @return the click-on action
 771      */
 772     NodeClickAction getActionWhenNodeClicked() {
 773         return _action_when_node_clicked;
 774     }
 775
 776     Map<Integer, String> getAllClickToItems() {
 777         return _all_click_to_names;
 778     }
 779
 780     Map<String, Color> getAnnotationColors() {
 781         return _annotation_colors;
 782     }
 783
 784     Configuration getConfiguration() {
 785         return _configuration;
 786     }
 787
 788     TreePanel getCurrentTreePanel() {
 789         return getMainPanel().getCurrentTreePanel();
 790     }
 791
 792     MainPanel getMainPanel() {
 793         return _mainpanel;
 794     }
 795
 796     Options getOptions() {
 797         return getMainPanel().getOptions();
 798     }
 799
 800     JLabel getSearchFoundCountsLabel0() {
 801         return _search_found_label_0;
 802     }
 803
 804     JLabel getSearchFoundCountsLabel1() {
 805         return _search_found_label_1;
 806     }
 807
 808     JButton getSearchResetButton0() {
 809         return _search_reset_button_0;
 810     }
 811
 812     JButton getSearchResetButton1() {
 813         return _search_reset_button_1;
 814     }
 815
 816     JTextField getSearchTextField0() {
 817         return _search_tf_0;
 818     }
 819
 820     JTextField getSearchTextField1() {
 821         return _search_tf_1;
 822     }
 823
 824     List<String> getSingleClickToNames() {
 825         return _click_to_names;
 826     }
 827
 828     Map<String, Color> getSpeciesColors() {
 829         return _species_colors;
 830     }
 831
 832     Map<String, Color> getSequenceColors() {
 833         return _sequence_colors;
 834     }
 835
 836     boolean isAntialiasScreenText() {
 837         return true;
 838     }
 839
 840     boolean isColorAccordingToAnnotation() {
 841         return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
 842     }
 843
 844     boolean isColorAccordingToTaxonomy() {
 845         return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
 846     }
 847
 848     boolean isColorAccordingToSequence() {
 849         return ( ( _color_acc_sequence != null ) && _color_acc_sequence.isSelected() );
 850     }
 851
 852     boolean isUseVisualStyles() {
 853         return ( ( ( getUseVisualStylesCb() != null ) && getUseVisualStylesCb().isSelected() ) || ( ( getUseVisualStylesCb() == null ) && _color_branches ) );
 854     }
 855
 856     boolean isDrawPhylogram() {
 857         return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
 858     }
 859
 860     boolean isDynamicallyHideData() {
 861         return ( ( getDynamicallyHideData() != null ) && getDynamicallyHideData().isSelected() );
 862     }
 863
 864     boolean isEvents() {
 865         return ( ( getShowEventsCb() != null ) && getShowEventsCb().isSelected() );
 866     }
 867
 868     boolean isNodeDescPopup() {
 869         return ( ( getNodeDescPopupCb() != null ) && getNodeDescPopupCb().isSelected() );
 870     }
 871
 872     boolean isShowAnnotation() {
 873         return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
 874     }
 875
 876     boolean isShowBinaryCharacterCounts() {
 877         return ( ( _show_binary_character_counts != null ) && _show_binary_character_counts.isSelected() );
 878     }
 879
 880     boolean isShowBinaryCharacters() {
 881         return ( ( _show_binary_characters != null ) && _show_binary_characters.isSelected() );
 882     }
 883
 884     boolean isShowConfidenceValues() {
 885         return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
 886     }
 887
 888     boolean isWriteBranchLengthValues() {
 889         return ( ( _write_branch_length_values != null ) && _write_branch_length_values.isSelected() );
 890     }
 891
 892     boolean isShowDomainArchitectures() {
 893         return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
 894     }
 895
 896     public boolean isShowMolSequences() {
 897         return ( ( _show_mol_seqs != null ) && _show_mol_seqs.isSelected() );
 898     }
 899
 900     boolean isShowGeneNames() {
 901         return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
 902     }
 903
 904     boolean isShowInternalData() {
 905         return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() );
 906     }
 907
 908     boolean isShowNodeNames() {
 909         return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
 910     }
 911
 912     boolean isShowSeqNames() {
 913         return ( ( _show_seq_names != null ) && _show_seq_names.isSelected() );
 914     }
 915
 916     boolean isShowSeqSymbols() {
 917         return ( ( _show_seq_symbols != null ) && _show_seq_symbols.isSelected() );
 918     }
 919
 920     boolean isShowSequenceAcc() {
 921         return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
 922     }
 923
 924     boolean isShowSequenceRelationConfidence() {
 925         return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
 926     }
 927
 928     boolean isShowSequenceRelations() {
 929         return ( ( _show_sequence_relations != null ) && ( _show_sequence_relations.getSelectedIndex() > 0 ) );
 930     }
 931
 932     boolean isShowTaxonomyCode() {
 933         return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
 934     }
 935
 936     boolean isShowTaxonomyCommonNames() {
 937         return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
 938     }
 939
 940     boolean isShowTaxonomyScientificNames() {
 941         return ( ( _show_taxo_scientific_names != null ) && _show_taxo_scientific_names.isSelected() );
 942     }
 943
 944     boolean isWidthBranches() {
 945         return ( ( _width_branches != null ) && _width_branches.isSelected() );
 946     }
 947
 948     void phylogenyAdded( final Configuration configuration ) {
 949         getIsDrawPhylogramList().add( configuration.isDrawAsPhylogram() );
 950     }
 951
 952     void phylogenyRemoved( final int index ) {
 953         getIsDrawPhylogramList().remove( index );
 954     }
 955
 956     void search0() {
 957         final MainPanel main_panel = getMainPanel();
 958         final Phylogeny tree = main_panel.getCurrentPhylogeny();
 959         if ( ( tree == null ) || tree.isEmpty() ) {
 960             return;
 961         }
 962         String query = getSearchTextField0().getText();
 963         if ( query != null ) {
 964             query = query.trim();
 965         }
 966         if ( !ForesterUtil.isEmpty( query ) ) {
 967             search0( main_panel, tree, query );
 968         }
 969         else {
 970             getSearchFoundCountsLabel0().setVisible( false );
 971             getSearchResetButton0().setEnabled( false );
 972             getSearchResetButton0().setVisible( false );
 973             searchReset0();
 974         }
 975     }
 976
 977     void search1() {
 978         final MainPanel main_panel = getMainPanel();
 979         final Phylogeny tree = main_panel.getCurrentPhylogeny();
 980         if ( ( tree == null ) || tree.isEmpty() ) {
 981             return;
 982         }
 983         String query = getSearchTextField1().getText();
 984         if ( query != null ) {
 985             query = query.trim();
 986         }
 987         if ( !ForesterUtil.isEmpty( query ) ) {
 988             search1( main_panel, tree, query );
 989         }
 990         else {
 991             getSearchFoundCountsLabel1().setVisible( false );
 992             getSearchResetButton1().setEnabled( false );
 993             getSearchResetButton1().setVisible( false );
 994             searchReset1();
 995         }
 996     }
 997
 998     void searchReset0() {
 999         if ( getMainPanel().getCurrentTreePanel() != null ) {
1000             getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
1001         }
1002     }
1003
1004     void searchReset1() {
1005         if ( getMainPanel().getCurrentTreePanel() != null ) {
1006             getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
1007         }
1008     }
1009
1010     void setActionWhenNodeClicked( final NodeClickAction action ) {
1011         _action_when_node_clicked = action;
1012     }
1013
1014     void setAnnotationColors( final Map<String, Color> annotation_colors ) {
1015         _annotation_colors = annotation_colors;
1016     }
1017
1018     void setCheckbox( final int which, final boolean state ) {
1019         switch ( which ) {
1020             case Configuration.display_as_phylogram:
1021                 if ( getDisplayAsPhylogramCb() != null ) {
1022                     getDisplayAsPhylogramCb().setSelected( state );
1023                 }
1024                 break;
1025             case Configuration.display_internal_data:
1026                 if ( _display_internal_data != null ) {
1027                     _display_internal_data.setSelected( state );
1028                 }
1029                 break;
1030             case Configuration.color_according_to_species:
1031                 if ( _color_acc_species != null ) {
1032                     _color_acc_species.setSelected( state );
1033                 }
1034                 break;
1035             case Configuration.color_according_to_sequence:
1036                 if ( _color_acc_sequence != null ) {
1037                     _color_acc_sequence.setSelected( state );
1038                 }
1039                 break;
1040             case Configuration.color_according_to_annotation:
1041                 if ( _color_according_to_annotation != null ) {
1042                     _color_according_to_annotation.setSelected( state );
1043                 }
1044                 break;
1045             case Configuration.show_node_names:
1046                 if ( _show_node_names != null ) {
1047                     _show_node_names.setSelected( state );
1048                 }
1049                 break;
1050             case Configuration.show_taxonomy_scientific_names:
1051                 if ( _show_taxo_scientific_names != null ) {
1052                     _show_taxo_scientific_names.setSelected( state );
1053                 }
1054                 break;
1055             case Configuration.show_taxonomy_common_names:
1056                 if ( _show_taxo_common_names != null ) {
1057                     _show_taxo_common_names.setSelected( state );
1058                 }
1059                 break;
1060             case Configuration.show_tax_code:
1061                 if ( _show_taxo_code != null ) {
1062                     _show_taxo_code.setSelected( state );
1063                 }
1064                 break;
1065             case Configuration.show_taxonomy_images:
1066                 if ( _show_taxo_images_cb != null ) {
1067                     _show_taxo_images_cb.setSelected( state );
1068                 }
1069                 break;
1070             case Configuration.show_annotation:
1071                 if ( _show_annotation != null ) {
1072                     _show_annotation.setSelected( state );
1073                 }
1074                 break;
1075             case Configuration.show_binary_characters:
1076                 if ( _show_binary_characters != null ) {
1077                     _show_binary_characters.setSelected( state );
1078                 }
1079                 break;
1080             case Configuration.show_binary_character_counts:
1081                 if ( _show_binary_character_counts != null ) {
1082                     _show_binary_character_counts.setSelected( state );
1083                 }
1084                 break;
1085             case Configuration.write_confidence_values:
1086                 if ( getWriteConfidenceCb() != null ) {
1087                     getWriteConfidenceCb().setSelected( state );
1088                 }
1089                 break;
1090             case Configuration.write_events:
1091                 if ( getShowEventsCb() != null ) {
1092                     getShowEventsCb().setSelected( state );
1093                 }
1094                 break;
1095             case Configuration.use_style:
1096                 if ( getUseVisualStylesCb() != null ) {
1097                     getUseVisualStylesCb().setSelected( state );
1098                 }
1099                 break;
1100             case Configuration.width_branches:
1101                 if ( _width_branches != null ) {
1102                     _width_branches.setSelected( state );
1103                 }
1104                 break;
1105             case Configuration.show_domain_architectures:
1106                 if ( _show_domain_architectures != null ) {
1107                     _show_domain_architectures.setSelected( state );
1108                 }
1109                 break;
1110             case Configuration.write_branch_length_values:
1111                 if ( _write_branch_length_values != null ) {
1112                     _write_branch_length_values.setSelected( state );
1113                 }
1114                 break;
1115             case Configuration.show_mol_seqs:
1116                 if ( _show_mol_seqs != null ) {
1117                     _show_mol_seqs.setSelected( state );
1118                 }
1119                 break;
1120             case Configuration.show_seq_names:
1121                 if ( _show_seq_names != null ) {
1122                     _show_seq_names.setSelected( state );
1123                 }
1124                 break;
1125             case Configuration.show_gene_names:
1126                 if ( _show_gene_names != null ) {
1127                     _show_gene_names.setSelected( state );
1128                 }
1129                 break;
1130             case Configuration.show_seq_symbols:
1131                 if ( _show_seq_symbols != null ) {
1132                     _show_seq_symbols.setSelected( state );
1133                 }
1134                 break;
1135             case Configuration.show_vector_data:
1136                 if ( _show_vector_data_cb != null ) {
1137                     _show_vector_data_cb.setSelected( state );
1138                 }
1139                 break;
1140             case Configuration.show_properties:
1141                 if ( _show_properties_cb != null ) {
1142                     _show_properties_cb.setSelected( state );
1143                 }
1144                 break;
1145             case Configuration.show_sequence_acc:
1146                 if ( _show_sequence_acc != null ) {
1147                     _show_sequence_acc.setSelected( state );
1148                 }
1149                 break;
1150             case Configuration.dynamically_hide_data:
1151                 if ( getDynamicallyHideData() != null ) {
1152                     getDynamicallyHideData().setSelected( state );
1153                 }
1154                 break;
1155             case Configuration.node_data_popup:
1156                 if ( getNodeDescPopupCb() != null ) {
1157                     getNodeDescPopupCb().setSelected( state );
1158                 }
1159                 break;
1160             /* GUILHEM_BEG */
1161             case Configuration.show_relation_confidence:
1162                 if ( _seq_relation_confidence_switch != null ) {
1163                     _seq_relation_confidence_switch.setSelected( state );
1164                 }
1165                 break;
1166             /* GUILHEM_END */
1167             default:
1168                 throw new AssertionError( "unknown checkbox: " + which );
1169         }
1170     }
1171
1172     /**
1173      * Set this checkbox state. Not all checkboxes have been instantiated
1174      * depending on the config.
1175      */
1176     void setCheckbox( final JCheckBox cb, final boolean state ) {
1177         if ( cb != null ) {
1178             cb.setSelected( state );
1179         }
1180     }
1181
1182     void setClickToAction( final int action ) {
1183         // Set click-to action
1184         if ( action == _show_data_item ) {
1185             setActionWhenNodeClicked( NodeClickAction.SHOW_DATA );
1186         }
1187         else if ( action == _collapse_cb_item ) {
1188             setActionWhenNodeClicked( NodeClickAction.COLLAPSE );
1189         }
1190         else if ( action == _reroot_cb_item ) {
1191             setActionWhenNodeClicked( NodeClickAction.REROOT );
1192         }
1193         else if ( action == _subtree_cb_item ) {
1194             setActionWhenNodeClicked( NodeClickAction.SUBTREE );
1195         }
1196         else if ( action == _swap_cb_item ) {
1197             setActionWhenNodeClicked( NodeClickAction.SWAP );
1198         }
1199         else if ( action == _color_subtree_cb_item ) {
1200             setActionWhenNodeClicked( NodeClickAction.COLOR_SUBTREE );
1201         }
1202         else if ( action == _open_seq_web_item ) {
1203             setActionWhenNodeClicked( NodeClickAction.OPEN_SEQ_WEB );
1204         }
1205         else if ( action == _sort_descendents_item ) {
1206             setActionWhenNodeClicked( NodeClickAction.SORT_DESCENDENTS );
1207         }
1208         else if ( action == _blast_item ) {
1209             setActionWhenNodeClicked( NodeClickAction.BLAST );
1210         }
1211         else if ( action == _open_tax_web_item ) {
1212             setActionWhenNodeClicked( NodeClickAction.OPEN_TAX_WEB );
1213         }
1214         else if ( action == _cut_subtree_item ) {
1215             setActionWhenNodeClicked( NodeClickAction.CUT_SUBTREE );
1216         }
1217         else if ( action == _copy_subtree_item ) {
1218             setActionWhenNodeClicked( NodeClickAction.COPY_SUBTREE );
1219         }
1220         else if ( action == _delete_node_or_subtree_item ) {
1221             setActionWhenNodeClicked( NodeClickAction.DELETE_NODE_OR_SUBTREE );
1222         }
1223         else if ( action == _paste_subtree_item ) {
1224             setActionWhenNodeClicked( NodeClickAction.PASTE_SUBTREE );
1225         }
1226         else if ( action == _add_new_node_item ) {
1227             setActionWhenNodeClicked( NodeClickAction.ADD_NEW_NODE );
1228         }
1229         else if ( action == _edit_node_data_item ) {
1230             setActionWhenNodeClicked( NodeClickAction.EDIT_NODE_DATA );
1231         }
1232         else if ( action == _select_nodes_item ) {
1233             setActionWhenNodeClicked( NodeClickAction.SELECT_NODES );
1234         }
1235         else if ( action == _get_ext_desc_data ) {
1236             setActionWhenNodeClicked( NodeClickAction.GET_EXT_DESC_DATA );
1237         }
1238         else if ( action == _open_pdb_item ) {
1239             setActionWhenNodeClicked( NodeClickAction.OPEN_PDB_WEB );
1240         }
1241         else if ( action == _color_node_font_item ) {
1242             setActionWhenNodeClicked( NodeClickAction.COLOR_NODE_FONT );
1243         }
1244         else if ( action == _change_node_font_item ) {
1245             setActionWhenNodeClicked( NodeClickAction.CHANGE_NODE_FONT );
1246         }
1247         else {
1248             throw new RuntimeException( "unknown action: " + action );
1249         }
1250         // make sure drop down is displaying the correct action
1251         // in case this was called from outside the class
1252         _click_to_combobox.setSelectedIndex( action );
1253     }
1254
1255     void setColorBranches( final boolean color_branches ) {
1256         _color_branches = color_branches;
1257     }
1258
1259     void setDrawPhylogram( final boolean b ) {
1260         getDisplayAsPhylogramCb().setSelected( b );
1261         setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
1262     }
1263
1264     void setDrawPhylogramEnabled( final boolean b ) {
1265         getDisplayAsPhylogramCb().setEnabled( b );
1266     }
1267
1268     void setDynamicHidingIsOn( final boolean is_on ) {
1269         if ( is_on ) {
1270             getDynamicallyHideData().setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
1271         }
1272         else {
1273             if ( !_configuration.isUseNativeUI() ) {
1274                 getDynamicallyHideData().setForeground( getConfiguration().getGuiButtonTextColor() );
1275             }
1276             else {
1277                 getDynamicallyHideData().setForeground( Color.BLACK );
1278             }
1279         }
1280     }
1281
1282     void setSearchFoundCountsOnLabel0( final int counts ) {
1283         getSearchFoundCountsLabel0().setText( "Found: " + counts );
1284     }
1285
1286     void setSearchFoundCountsOnLabel1( final int counts ) {
1287         getSearchFoundCountsLabel1().setText( "Found: " + counts );
1288     }
1289
1290     void setShowEvents( final boolean show_events ) {
1291         if ( getShowEventsCb() == null ) {
1292             _show_events = new JCheckBox( "" );
1293         }
1294         getShowEventsCb().setSelected( show_events );
1295     }
1296
1297     void setSpeciesColors( final Map<String, Color> species_colors ) {
1298         _species_colors = species_colors;
1299     }
1300
1301     void setSequenceColors( final Map<String, Color> sequence_colors ) {
1302         _sequence_colors = sequence_colors;
1303     }
1304
1305     /* GUILHEM_END */
1306     /*
1307      * Set up the controls from the config settings. 11/26/05
1308      */
1309     void setupControls() {
1310         // The tree display options:
1311         setupDisplayCheckboxes();
1312         /* GUILHEM_BEG */
1313         // The sequence relation query selection combo-box
1314         if ( _configuration.displaySequenceRelations() ) {
1315             addSequenceRelationBlock();
1316         }
1317         /* GUILHEM_END */
1318         // Click-to options
1319         startClickToOptions();
1320         setupClickToOptions();
1321         endClickToOptions();
1322         // Zoom and quick edit buttons
1323         addButtons();
1324         setupSearchTools0();
1325         setupSearchTools1();
1326     }
1327
1328     void setUpControlsForDomainStrucures() {
1329         _domain_display_label = new JLabel( "Domain Architectures:" );
1330         add( customizeLabel( _domain_display_label, getConfiguration() ) );
1331         add( _domain_display_label );
1332         _zoom_in_domain_structure = new JButton( "d+" );
1333         _zoom_out_domain_structure = new JButton( "d-" );
1334         _decr_domain_structure_evalue_thr = new JButton( "-" );
1335         _incr_domain_structure_evalue_thr = new JButton( "+" );
1336         _zoom_in_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
1337         _zoom_out_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
1338         _decr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
1339         _incr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
1340         _incr_domain_structure_evalue_thr.setToolTipText( "Increase the E-value threshold by a factor of 10" );
1341         _decr_domain_structure_evalue_thr.setToolTipText( "Decrease the E-value threshold by a factor of 10" );
1342         _domain_structure_evalue_thr_tf = new JTextField( 3 );
1343         _domain_structure_evalue_thr_tf.setEditable( false );
1344         if ( !getConfiguration().isUseNativeUI() ) {
1345             _domain_structure_evalue_thr_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1346             _domain_structure_evalue_thr_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1347             _domain_structure_evalue_thr_tf.setBorder( null );
1348         }
1349         final JPanel d1_panel = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1350         final JPanel d2_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
1351         if ( !_configuration.isUseNativeUI() ) {
1352             d1_panel.setBackground( getBackground() );
1353             d2_panel.setBackground( getBackground() );
1354         }
1355         add( d1_panel );
1356         add( d2_panel );
1357         addJButton( _zoom_out_domain_structure, d1_panel );
1358         addJButton( _zoom_in_domain_structure, d1_panel );
1359         addJButton( _decr_domain_structure_evalue_thr, d2_panel );
1360         addJTextField( _domain_structure_evalue_thr_tf, d2_panel );
1361         addJButton( _incr_domain_structure_evalue_thr, d2_panel );
1362     }
1363
1364     void setupSearchTools0() {
1365         final JLabel search_label = new JLabel( "Search (A):" );
1366         search_label.setFont( ControlPanel.jcb_bold_font );
1367         if ( !getConfiguration().isUseNativeUI() ) {
1368             search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1369         }
1370         add( search_label );
1371         search_label.setToolTipText( SEARCH_TIP_TEXT );
1372         _search_found_label_0 = new JLabel();
1373         getSearchFoundCountsLabel0().setVisible( false );
1374         _search_found_label_0.setFont( ControlPanel.jcb_bold_font );
1375         if ( !getConfiguration().isUseNativeUI() ) {
1376             _search_found_label_0.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1377         }
1378         _search_tf_0 = new JTextField( 3 );
1379         _search_tf_0.setToolTipText( SEARCH_TIP_TEXT );
1380         _search_tf_0.setEditable( true );
1381         if ( !getConfiguration().isUseNativeUI() ) {
1382             _search_tf_0.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1383             _search_tf_0.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1384             _search_tf_0.setBorder( null );
1385         }
1386         _search_reset_button_0 = new JButton();
1387         getSearchResetButton0().setText( "Reset" );
1388         getSearchResetButton0().setEnabled( false );
1389         getSearchResetButton0().setVisible( false );
1390         final JPanel s_panel_1 = new JPanel( new BorderLayout() );
1391         final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1392         s_panel_1.setBackground( getBackground() );
1393         add( s_panel_1 );
1394         s_panel_2.setBackground( getBackground() );
1395         add( s_panel_2 );
1396         final KeyAdapter key_adapter = new KeyAdapter() {
1397
1398             @Override
1399             public void keyReleased( final KeyEvent key_event ) {
1400                 search0();
1401                 displayedPhylogenyMightHaveChanged( true );
1402             }
1403         };
1404         final ActionListener action_listener = new ActionListener() {
1405
1406             @Override
1407             public void actionPerformed( final ActionEvent e ) {
1408                 searchReset0();
1409                 setSearchFoundCountsOnLabel0( 0 );
1410                 getSearchFoundCountsLabel0().setVisible( false );
1411                 getSearchTextField0().setText( "" );
1412                 getSearchResetButton0().setEnabled( false );
1413                 getSearchResetButton0().setVisible( false );
1414                 displayedPhylogenyMightHaveChanged( true );
1415             }
1416         };
1417         _search_reset_button_0.addActionListener( action_listener );
1418         _search_tf_0.addKeyListener( key_adapter );
1419         addJTextField( _search_tf_0, s_panel_1 );
1420         s_panel_2.add( _search_found_label_0 );
1421         addJButton( _search_reset_button_0, s_panel_2 );
1422     }
1423
1424     void setupSearchTools1() {
1425         final JLabel search_label = new JLabel( "Search (B):" );
1426         search_label.setFont( ControlPanel.jcb_bold_font );
1427         if ( !getConfiguration().isUseNativeUI() ) {
1428             search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1429         }
1430         add( search_label );
1431         search_label.setToolTipText( SEARCH_TIP_TEXT );
1432         _search_found_label_1 = new JLabel();
1433         getSearchFoundCountsLabel1().setVisible( false );
1434         _search_found_label_1.setFont( ControlPanel.jcb_bold_font );
1435         if ( !getConfiguration().isUseNativeUI() ) {
1436             _search_found_label_1.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1437         }
1438         _search_tf_1 = new JTextField( 3 );
1439         _search_tf_1.setToolTipText( SEARCH_TIP_TEXT );
1440         _search_tf_1.setEditable( true );
1441         if ( !getConfiguration().isUseNativeUI() ) {
1442             _search_tf_1.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1443             _search_tf_1.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1444             _search_tf_1.setBorder( null );
1445         }
1446         _search_reset_button_1 = new JButton();
1447         getSearchResetButton1().setText( "Reset" );
1448         getSearchResetButton1().setEnabled( false );
1449         getSearchResetButton1().setVisible( false );
1450         final JPanel s_panel_1 = new JPanel( new BorderLayout() );
1451         final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1452         s_panel_1.setBackground( getBackground() );
1453         add( s_panel_1 );
1454         s_panel_2.setBackground( getBackground() );
1455         add( s_panel_2 );
1456         final KeyAdapter key_adapter = new KeyAdapter() {
1457
1458             @Override
1459             public void keyReleased( final KeyEvent key_event ) {
1460                 search1();
1461                 displayedPhylogenyMightHaveChanged( true );
1462             }
1463         };
1464         final ActionListener action_listener = new ActionListener() {
1465
1466             @Override
1467             public void actionPerformed( final ActionEvent e ) {
1468                 searchReset1();
1469                 setSearchFoundCountsOnLabel1( 0 );
1470                 getSearchFoundCountsLabel1().setVisible( false );
1471                 getSearchTextField1().setText( "" );
1472                 getSearchResetButton1().setEnabled( false );
1473                 getSearchResetButton1().setVisible( false );
1474                 displayedPhylogenyMightHaveChanged( true );
1475             }
1476         };
1477         _search_reset_button_1.addActionListener( action_listener );
1478         _search_tf_1.addKeyListener( key_adapter );
1479         addJTextField( _search_tf_1, s_panel_1 );
1480         s_panel_2.add( _search_found_label_1 );
1481         addJButton( _search_reset_button_1, s_panel_2 );
1482     }
1483
1484     void showAnnotations() {
1485         if ( _show_annotation != null ) {
1486             _show_annotation.setSelected( true );
1487         }
1488         if ( _color_according_to_annotation != null ) {
1489             _color_according_to_annotation.setSelected( true );
1490         }
1491         if ( _color_acc_species != null ) {
1492             _color_acc_species.setSelected( false );
1493         }
1494         if ( _color_acc_sequence != null ) {
1495             _color_acc_sequence.setSelected( false );
1496         }
1497         _mainpanel.getCurrentTreePanel().repaint();
1498     }
1499
1500     /**
1501      * Fit entire tree into window.
1502      */
1503     void showWhole() {
1504         if ( ( _mainpanel.getCurrentScrollPane() == null ) || _mainpanel.getCurrentTreePanel().getPhylogeny().isEmpty() ) {
1505             return;
1506         }
1507         getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1508         displayedPhylogenyMightHaveChanged( true );
1509         _mainpanel.getCurrentTreePanel().updateOvSettings();
1510         _mainpanel.getCurrentTreePanel().validate();
1511         _mainpanel.validate();
1512         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
1513                                                                     _mainpanel.getSizeOfViewport().height );
1514         _mainpanel.getCurrentTreePanel().resetPreferredSize();
1515         _mainpanel.adjustJScrollPane();
1516         _mainpanel.getCurrentTreePanel().repaint();
1517         _mainpanel.getCurrentTreePanel().validate();
1518         _mainpanel.validate();
1519         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
1520                                                                     _mainpanel.getSizeOfViewport().height );
1521         _mainpanel.getCurrentTreePanel().resetPreferredSize();
1522         _mainpanel.adjustJScrollPane();
1523         _mainpanel.getCurrentTreePanel().repaint();
1524         _mainpanel.getCurrentTreePanel().updateOvSizes();
1525     }
1526
1527     void showWholeAll() {
1528         for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
1529             if ( tree_panel != null ) {
1530                 tree_panel.validate();
1531                 tree_panel.calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
1532                                                       _mainpanel.getSizeOfViewport().height );
1533                 tree_panel.resetPreferredSize();
1534                 tree_panel.repaint();
1535             }
1536         }
1537     }
1538
1539     // Create header for click-to combo box.
1540     void startClickToOptions() {
1541         final JLabel spacer = new JLabel( "" );
1542         spacer.setFont( ControlPanel.jcb_font );
1543         add( spacer );
1544         _click_to_label = new JLabel( "Click on Node to:" );
1545         add( customizeLabel( _click_to_label, getConfiguration() ) );
1546         _click_to_combobox = new JComboBox<String>();
1547         _click_to_combobox.setFocusable( false );
1548         _click_to_combobox.setMaximumRowCount( 14 );
1549         _click_to_combobox.setFont( ControlPanel.js_font );
1550         if ( !_configuration.isUseNativeUI() ) {
1551             _click_to_combobox.setBackground( getConfiguration().getGuiBackgroundColor() );
1552         }
1553         // don't add listener until all items are set (or each one will trigger
1554         // an event)
1555         // click_to_list.addActionListener(this);
1556         add( _click_to_combobox );
1557         // Correlates option names to titles
1558         _all_click_to_names = new HashMap<Integer, String>();
1559         _click_to_names = new ArrayList<String>();
1560     }
1561
1562     void tabChanged() {
1563         if ( getMainPanel().getTabbedPane().getTabCount() > 0 ) {
1564             if ( getCurrentTreePanel().isPhyHasBranchLengths()
1565                     && ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1566                 setDrawPhylogramEnabled( true );
1567                 setDrawPhylogram( isDrawPhylogram() );
1568             }
1569             else {
1570                 setDrawPhylogramEnabled( false );
1571                 setDrawPhylogram( false );
1572             }
1573             if ( getMainPanel().getMainFrame() == null ) {
1574                 // Must be "E" applet version.
1575                 final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1576                 e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() );
1577             }
1578             else {
1579                 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel()
1580                         .getPhylogenyGraphicsType() );
1581             }
1582             getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
1583             getMainPanel().getControlPanel().search0();
1584             getMainPanel().getControlPanel().search1();
1585             getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
1586             getSequenceRelationTypeBox().removeAllItems();
1587             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
1588                     .getRelevantSequenceRelationTypes() ) {
1589                 _sequence_relation_type_box.addItem( type );
1590             }
1591             getMainPanel().getCurrentTreePanel().repaint();
1592             //setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
1593             // according to GUILHEM the line above can be removed.
1594         }
1595     }
1596
1597     /**
1598      * Uncollapse all nodes.
1599      */
1600     void uncollapseAll( final TreePanel tp ) {
1601         final Phylogeny t = tp.getPhylogeny();
1602         if ( ( t != null ) && !t.isEmpty() ) {
1603             for( final PhylogenyNodeIterator iter = t.iteratorPreorder(); iter.hasNext(); ) {
1604                 final PhylogenyNode node = iter.next();
1605                 node.setCollapse( false );
1606             }
1607             tp.resetNodeIdToDistToLeafMap();
1608             tp.updateSetOfCollapsedExternalNodes();
1609             t.recalculateNumberOfExternalDescendants( false );
1610             tp.setNodeInPreorderToNull();
1611             t.clearHashIdToNodeMap();
1612             showWhole();
1613         }
1614     }
1615
1616     void updateDomainStructureEvaluethresholdDisplay() {
1617         if ( _domain_structure_evalue_thr_tf != null ) {
1618             _domain_structure_evalue_thr_tf.setText( "10^"
1619                     + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThresholdExp() );
1620         }
1621     }
1622
1623     void zoomInX( final float factor, final float x_correction_factor ) {
1624         final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
1625         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1626         treepanel.multiplyUrtFactor( 1f );
1627         if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1628                 || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1629                 || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
1630                 || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
1631             final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1632             treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1633             treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1634             getMainPanel().adjustJScrollPane();
1635             treepanel.resetPreferredSize();
1636             getMainPanel().getCurrentScrollPane().getViewport().validate();
1637             sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1638                     - ( sb.getVisibleAmount() / 2.0 ) ) );
1639         }
1640         else {
1641             final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
1642             treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1643             treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1644             getMainPanel().adjustJScrollPane();
1645             treepanel.resetPreferredSize();
1646             getMainPanel().getCurrentScrollPane().getViewport().validate();
1647             sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
1648         }
1649         treepanel.resetPreferredSize();
1650         treepanel.updateOvSizes();
1651     }
1652
1653     void zoomInY( final float factor ) {
1654         final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
1655         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1656         treepanel.multiplyUrtFactor( 1.1f );
1657         final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1658         treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
1659         getMainPanel().adjustJScrollPane();
1660         treepanel.resetPreferredSize();
1661         getMainPanel().getCurrentScrollPane().getViewport().validate();
1662         sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1663                 - ( sb.getVisibleAmount() / 2.0 ) ) );
1664         treepanel.resetPreferredSize();
1665         treepanel.updateOvSizes();
1666     }
1667
1668     void zoomOutX( final float factor, final float x_correction_factor ) {
1669         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1670         treepanel.multiplyUrtFactor( 1f );
1671         if ( ( treepanel.getXdistance() * factor ) > 0.0 ) {
1672             final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
1673             if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1674                     || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1675                     || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
1676                     || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
1677                 getMainPanel().adjustJScrollPane();
1678                 treepanel.resetPreferredSize();
1679                 getMainPanel().getCurrentScrollPane().getViewport().validate();
1680                 final double x = ( sb.getMaximum() - sb.getMinimum() )
1681                         / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1682                 treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1683                 treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1684                 getMainPanel().adjustJScrollPane();
1685                 treepanel.resetPreferredSize();
1686                 getMainPanel().getCurrentScrollPane().getViewport().validate();
1687                 sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1688                         - ( sb.getVisibleAmount() / 2.0 ) ) );
1689             }
1690             else {
1691                 final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
1692                 treepanel.setXdistance( treepanel.getXdistance() * factor );
1693                 treepanel.setXcorrectionFactor( treepanel.getXcorrectionFactor() * x_correction_factor );
1694                 if ( x > 0 ) {
1695                     getMainPanel().adjustJScrollPane();
1696                     treepanel.resetPreferredSize();
1697                     getMainPanel().getCurrentScrollPane().getViewport().validate();
1698                     sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
1699                 }
1700             }
1701             treepanel.resetPreferredSize();
1702             treepanel.updateOvSizes();
1703         }
1704     }
1705
1706     void zoomOutY( final float factor ) {
1707         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1708         treepanel.multiplyUrtFactor( 0.9f );
1709         if ( ( treepanel.getYdistance() * factor ) > 0.0 ) {
1710             final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
1711             final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1712             treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
1713             getMainPanel().adjustJScrollPane();
1714             treepanel.resetPreferredSize();
1715             getMainPanel().getCurrentScrollPane().getViewport().validate();
1716             sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1717                     - ( sb.getVisibleAmount() / 2.0 ) ) );
1718             treepanel.resetPreferredSize();
1719             treepanel.updateOvSizes();
1720         }
1721     }
1722
1723     private void addClickToOption( final int which, final String title ) {
1724         _click_to_combobox.addItem( title );
1725         _click_to_names.add( title );
1726         _all_click_to_names.put( new Integer( which ), title );
1727         if ( !_configuration.isUseNativeUI() ) {
1728             _click_to_combobox.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
1729             _click_to_combobox.setForeground( getConfiguration().getGuiButtonTextColor() );
1730         }
1731     }
1732
1733     /* GUILHEM_BEG */
1734     private void addSequenceRelationBlock() {
1735         final JLabel spacer = new JLabel( "" );
1736         spacer.setSize( 1, 1 );
1737         add( spacer );
1738         final JLabel mainLabel = new JLabel( "Sequence relations to display" );
1739         final JLabel typeLabel = customizeLabel( new JLabel( "(type) " ), getConfiguration() );
1740         typeLabel.setFont( ControlPanel.js_font.deriveFont( 7 ) );
1741         getSequenceRelationTypeBox().setFocusable( false );
1742         _sequence_relation_type_box.setFont( ControlPanel.js_font );
1743         if ( !_configuration.isUseNativeUI() ) {
1744             _sequence_relation_type_box.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
1745             _sequence_relation_type_box.setForeground( getConfiguration().getGuiButtonTextColor() );
1746         }
1747         _sequence_relation_type_box.setRenderer( new ListCellRenderer<Object>() {
1748
1749             @Override
1750             public Component getListCellRendererComponent( final JList<?> list,
1751                                                            final Object value,
1752                                                            final int index,
1753                                                            final boolean isSelected,
1754                                                            final boolean cellHasFocus ) {
1755                 final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
1756                                                                                                         value,
1757                                                                                                         index,
1758                                                                                                         isSelected,
1759                                                                                                         cellHasFocus );
1760                 if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) {
1761                     ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation
1762                             .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) );
1763                 }
1764                 return component;
1765             }
1766         } );
1767         final GridBagLayout gbl = new GridBagLayout();
1768         _sequence_relation_type_box.setMinimumSize( new Dimension( 115, 17 ) );
1769         _sequence_relation_type_box.setPreferredSize( new Dimension( 115, 20 ) );
1770         final JPanel horizGrid = new JPanel( gbl );
1771         horizGrid.setBackground( getBackground() );
1772         horizGrid.add( typeLabel );
1773         horizGrid.add( _sequence_relation_type_box );
1774         add( customizeLabel( mainLabel, getConfiguration() ) );
1775         add( horizGrid );
1776         add( getSequenceRelationBox() );
1777         if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
1778             addCheckbox( Configuration.show_relation_confidence,
1779                          _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
1780             setCheckbox( Configuration.show_relation_confidence,
1781                          _configuration.doCheckOption( Configuration.show_relation_confidence ) );
1782         }
1783     }// addSequenceRelationBlock
1784
1785     /* GUILHEM_END */
1786     private List<Boolean> getIsDrawPhylogramList() {
1787         return _draw_phylogram;
1788     }
1789
1790     private void init() {
1791         _draw_phylogram = new ArrayList<Boolean>();
1792         setSpeciesColors( new HashMap<String, Color>() );
1793         setSequenceColors( new HashMap<String, Color>() );
1794         setAnnotationColors( new HashMap<String, Color>() );
1795     }
1796
1797     private boolean isDrawPhylogram( final int index ) {
1798         return getIsDrawPhylogramList().get( index );
1799     }
1800
1801     private void search0( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
1802         getSearchFoundCountsLabel0().setVisible( true );
1803         getSearchResetButton0().setEnabled( true );
1804         getSearchResetButton0().setVisible( true );
1805         String[] queries = null;
1806         List<PhylogenyNode> nodes = null;
1807         if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
1808             queries = query_str.split( ",+" );
1809         }
1810         else {
1811             queries = new String[ 1 ];
1812             queries[ 0 ] = query_str.trim();
1813         }
1814         if ( ( queries != null ) && ( queries.length > 0 ) ) {
1815             nodes = new ArrayList<PhylogenyNode>();
1816             for( String query : queries ) {
1817                 if ( ForesterUtil.isEmpty( query ) ) {
1818                     continue;
1819                 }
1820                 query = query.trim();
1821                 if ( ( query.indexOf( '+' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
1822                     nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
1823                                                                          tree,
1824                                                                          getOptions().isSearchCaseSensitive(),
1825                                                                          !getOptions().isMatchWholeTermsOnly(),
1826                                                                          isShowDomainArchitectures() ) );
1827                 }
1828                 else {
1829                     nodes.addAll( PhylogenyMethods.searchData( query,
1830                                                                tree,
1831                                                                getOptions().isSearchCaseSensitive(),
1832                                                                !getOptions().isMatchWholeTermsOnly(),
1833                                                                getOptions().isSearchWithRegex(),
1834                                                                isShowDomainArchitectures() ) );
1835                 }
1836             }
1837             if ( getOptions().isInverseSearchResult() ) {
1838                 final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
1839                 all.removeAll( nodes );
1840                 nodes = all;
1841             }
1842         }
1843         if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
1844             main_panel.getCurrentTreePanel().setFoundNodes0( new HashSet<Long>() );
1845             for( final PhylogenyNode node : nodes ) {
1846                 main_panel.getCurrentTreePanel().getFoundNodes0().add( node.getId() );
1847             }
1848             setSearchFoundCountsOnLabel0( nodes.size() );
1849         }
1850         else {
1851             setSearchFoundCountsOnLabel0( 0 );
1852             searchReset0();
1853         }
1854     }
1855
1856     private void search1( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
1857         getSearchFoundCountsLabel1().setVisible( true );
1858         getSearchResetButton1().setEnabled( true );
1859         getSearchResetButton1().setVisible( true );
1860         String[] queries = null;
1861         List<PhylogenyNode> nodes = null;
1862         if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
1863             queries = query_str.split( ",+" );
1864         }
1865         else {
1866             queries = new String[ 1 ];
1867             queries[ 0 ] = query_str.trim();
1868         }
1869         if ( ( queries != null ) && ( queries.length > 0 ) ) {
1870             nodes = new ArrayList<PhylogenyNode>();
1871             for( String query : queries ) {
1872                 if ( ForesterUtil.isEmpty( query ) ) {
1873                     continue;
1874                 }
1875                 query = query.trim();
1876                 if ( ( query.indexOf( '+' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
1877                     nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
1878                                                                          tree,
1879                                                                          getOptions().isSearchCaseSensitive(),
1880                                                                          !getOptions().isMatchWholeTermsOnly(),
1881                                                                          isShowDomainArchitectures() ) );
1882                 }
1883                 else {
1884                     nodes.addAll( PhylogenyMethods.searchData( query,
1885                                                                tree,
1886                                                                getOptions().isSearchCaseSensitive(),
1887                                                                !getOptions().isMatchWholeTermsOnly(),
1888                                                                getOptions().isSearchWithRegex(),
1889                                                                isShowDomainArchitectures() ) );
1890                 }
1891             }
1892             if ( getOptions().isInverseSearchResult() ) {
1893                 final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
1894                 all.removeAll( nodes );
1895                 nodes = all;
1896             }
1897         }
1898         if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
1899             main_panel.getCurrentTreePanel().setFoundNodes1( new HashSet<Long>() );
1900             for( final PhylogenyNode node : nodes ) {
1901                 main_panel.getCurrentTreePanel().getFoundNodes1().add( node.getId() );
1902             }
1903             setSearchFoundCountsOnLabel1( nodes.size() );
1904         }
1905         else {
1906             setSearchFoundCountsOnLabel1( 0 );
1907             searchReset1();
1908         }
1909     }
1910
1911     private void setDrawPhylogram( final int index, final boolean b ) {
1912         getIsDrawPhylogramList().set( index, b );
1913     }
1914
1915     private void setupClickToOptions() {
1916         final int default_option = _configuration.getDefaultDisplayClicktoOption();
1917         int selected_index = 0;
1918         int cb_index = 0;
1919         if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
1920             _show_data_item = cb_index;
1921             addClickToOption( Configuration.display_node_data,
1922                               _configuration.getClickToTitle( Configuration.display_node_data ) );
1923             if ( default_option == Configuration.display_node_data ) {
1924                 selected_index = cb_index;
1925             }
1926             cb_index++;
1927         }
1928         if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
1929             _collapse_cb_item = cb_index;
1930             addClickToOption( Configuration.collapse_uncollapse,
1931                               _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
1932             if ( default_option == Configuration.collapse_uncollapse ) {
1933                 selected_index = cb_index;
1934             }
1935             cb_index++;
1936         }
1937         if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
1938             _reroot_cb_item = cb_index;
1939             addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
1940             if ( default_option == Configuration.reroot ) {
1941                 selected_index = cb_index;
1942             }
1943             cb_index++;
1944         }
1945         if ( _configuration.doDisplayClickToOption( Configuration.subtree ) ) {
1946             _subtree_cb_item = cb_index;
1947             addClickToOption( Configuration.subtree, _configuration.getClickToTitle( Configuration.subtree ) );
1948             if ( default_option == Configuration.subtree ) {
1949                 selected_index = cb_index;
1950             }
1951             cb_index++;
1952         }
1953         if ( _configuration.doDisplayClickToOption( Configuration.swap ) ) {
1954             _swap_cb_item = cb_index;
1955             addClickToOption( Configuration.swap, _configuration.getClickToTitle( Configuration.swap ) );
1956             if ( default_option == Configuration.swap ) {
1957                 selected_index = cb_index;
1958             }
1959             cb_index++;
1960         }
1961         if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
1962             _sort_descendents_item = cb_index;
1963             addClickToOption( Configuration.sort_descendents,
1964                               _configuration.getClickToTitle( Configuration.sort_descendents ) );
1965             if ( default_option == Configuration.sort_descendents ) {
1966                 selected_index = cb_index;
1967             }
1968             cb_index++;
1969         }
1970         if ( _configuration.doDisplayClickToOption( Configuration.color_node_font ) ) {
1971             _color_node_font_item = cb_index;
1972             addClickToOption( Configuration.color_node_font,
1973                               _configuration.getClickToTitle( Configuration.color_node_font ) );
1974             if ( default_option == Configuration.color_node_font ) {
1975                 selected_index = cb_index;
1976             }
1977             cb_index++;
1978         }
1979         if ( _configuration.doDisplayClickToOption( Configuration.change_node_font ) ) {
1980             _change_node_font_item = cb_index;
1981             addClickToOption( Configuration.change_node_font,
1982                               _configuration.getClickToTitle( Configuration.change_node_font ) );
1983             if ( default_option == Configuration.change_node_font ) {
1984                 selected_index = cb_index;
1985             }
1986             cb_index++;
1987         }
1988         if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
1989             _color_subtree_cb_item = cb_index;
1990             addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
1991             if ( default_option == Configuration.color_subtree ) {
1992                 selected_index = cb_index;
1993             }
1994             cb_index++;
1995         }
1996         if ( _configuration.doDisplayClickToOption( Configuration.open_seq_web ) ) {
1997             _open_seq_web_item = cb_index;
1998             addClickToOption( Configuration.open_seq_web, _configuration.getClickToTitle( Configuration.open_seq_web ) );
1999             if ( default_option == Configuration.open_seq_web ) {
2000                 selected_index = cb_index;
2001             }
2002             cb_index++;
2003         }
2004         if ( _configuration.doDisplayClickToOption( Configuration.open_pdb_web ) ) {
2005             _open_pdb_item = cb_index;
2006             addClickToOption( Configuration.open_pdb_web, _configuration.getClickToTitle( Configuration.open_pdb_web ) );
2007             if ( default_option == Configuration.open_pdb_web ) {
2008                 selected_index = cb_index;
2009             }
2010             cb_index++;
2011         }
2012         if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
2013             _open_tax_web_item = cb_index;
2014             addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
2015             if ( default_option == Configuration.open_tax_web ) {
2016                 selected_index = cb_index;
2017             }
2018             cb_index++;
2019         }
2020         if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
2021             _blast_item = cb_index;
2022             addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
2023             if ( default_option == Configuration.blast ) {
2024                 selected_index = cb_index;
2025             }
2026             cb_index++;
2027         }
2028         if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) {
2029             _select_nodes_item = cb_index;
2030             addClickToOption( Configuration.select_nodes, _configuration.getClickToTitle( Configuration.select_nodes ) );
2031             if ( default_option == Configuration.select_nodes ) {
2032                 selected_index = cb_index;
2033             }
2034             cb_index++;
2035         }
2036         if ( _configuration.doDisplayClickToOption( Configuration.get_ext_desc_data ) ) {
2037             _get_ext_desc_data = cb_index;
2038             if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) {
2039                 addClickToOption( Configuration.get_ext_desc_data, getConfiguration()
2040                         .getLabelForGetExtDescendentsData() );
2041             }
2042             else {
2043                 String s = ";";
2044                 switch ( getConfiguration().getExtDescNodeDataToReturn() ) {
2045                     case NODE_NAME:
2046                         s = "Node Names";
2047                         break;
2048                     case SEQUENCE_ACC:
2049                         s = "Sequence Accessors";
2050                         break;
2051                     case SEQUENCE_MOL_SEQ:
2052                         s = "Molecular Sequence";
2053                         break;
2054                     case SEQUENCE_MOL_SEQ_FASTA:
2055                         s = "Molecular Sequence (Fasta)";
2056                         break;
2057                     case SEQUENCE_NAME:
2058                         s = "Sequence Names";
2059                         break;
2060                     case GENE_NAME:
2061                         s = "Gene Names";
2062                         break;
2063                     case SEQUENCE_SYMBOL:
2064                         s = "Sequence Symbols";
2065                         break;
2066                     case TAXONOMY_CODE:
2067                         s = "Taxonomy Codes";
2068                         break;
2069                     case TAXONOMY_COMM0N_NAME:
2070                         s = "Taxonomy Common Names";
2071                         break;
2072                     case TAXONOMY_SCIENTIFIC_NAME:
2073                         s = "Scientific Names";
2074                         break;
2075                     case UNKNOWN:
2076                         s = "User Selected Data";
2077                         break;
2078                     default:
2079                         throw new IllegalStateException( "dont know how to deal with "
2080                                 + getConfiguration().getExtDescNodeDataToReturn() );
2081                 }
2082                 final String label = _configuration.getClickToTitle( Configuration.get_ext_desc_data ) + " " + s;
2083                 addClickToOption( Configuration.get_ext_desc_data, label );
2084             }
2085             if ( default_option == Configuration.get_ext_desc_data ) {
2086                 selected_index = cb_index;
2087             }
2088             cb_index++;
2089         }
2090         if ( getOptions().isEditable() ) {
2091             if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
2092                 _cut_subtree_item = cb_index;
2093                 addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
2094                 if ( default_option == Configuration.cut_subtree ) {
2095                     selected_index = cb_index;
2096                 }
2097                 cb_index++;
2098             }
2099             if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
2100                 _copy_subtree_item = cb_index;
2101                 addClickToOption( Configuration.copy_subtree,
2102                                   _configuration.getClickToTitle( Configuration.copy_subtree ) );
2103                 if ( default_option == Configuration.copy_subtree ) {
2104                     selected_index = cb_index;
2105                 }
2106                 cb_index++;
2107             }
2108             if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
2109                 _paste_subtree_item = cb_index;
2110                 addClickToOption( Configuration.paste_subtree,
2111                                   _configuration.getClickToTitle( Configuration.paste_subtree ) );
2112                 if ( default_option == Configuration.paste_subtree ) {
2113                     selected_index = cb_index;
2114                 }
2115                 cb_index++;
2116             }
2117             if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
2118                 _delete_node_or_subtree_item = cb_index;
2119                 addClickToOption( Configuration.delete_subtree_or_node,
2120                                   _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
2121                 if ( default_option == Configuration.delete_subtree_or_node ) {
2122                     selected_index = cb_index;
2123                 }
2124                 cb_index++;
2125             }
2126             if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
2127                 _add_new_node_item = cb_index;
2128                 addClickToOption( Configuration.add_new_node,
2129                                   _configuration.getClickToTitle( Configuration.add_new_node ) );
2130                 if ( default_option == Configuration.add_new_node ) {
2131                     selected_index = cb_index;
2132                 }
2133                 cb_index++;
2134             }
2135             if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
2136                 _edit_node_data_item = cb_index;
2137                 addClickToOption( Configuration.edit_node_data,
2138                                   _configuration.getClickToTitle( Configuration.edit_node_data ) );
2139                 if ( default_option == Configuration.edit_node_data ) {
2140                     selected_index = cb_index;
2141                 }
2142                 cb_index++;
2143             }
2144         }
2145         // Set default selection and its action
2146         _click_to_combobox.setSelectedIndex( selected_index );
2147         setClickToAction( selected_index );
2148     }
2149
2150     private void setupDisplayCheckboxes() {
2151         if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
2152             addCheckbox( Configuration.display_as_phylogram,
2153                          _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
2154             setCheckbox( Configuration.display_as_phylogram,
2155                          _configuration.doCheckOption( Configuration.display_as_phylogram ) );
2156         }
2157         if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
2158             addCheckbox( Configuration.dynamically_hide_data,
2159                          _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
2160             setCheckbox( Configuration.dynamically_hide_data,
2161                          _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
2162         }
2163         if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
2164             addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
2165             setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
2166         }
2167         if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
2168             addCheckbox( Configuration.display_internal_data,
2169                          _configuration.getDisplayTitle( Configuration.display_internal_data ) );
2170             setCheckbox( Configuration.display_internal_data,
2171                          _configuration.doCheckOption( Configuration.display_internal_data ) );
2172         }
2173         if ( _configuration.doDisplayOption( Configuration.color_according_to_sequence ) ) {
2174             addCheckbox( Configuration.color_according_to_sequence,
2175                          _configuration.getDisplayTitle( Configuration.color_according_to_sequence ) );
2176             setCheckbox( Configuration.color_according_to_sequence,
2177                          _configuration.doCheckOption( Configuration.color_according_to_sequence ) );
2178         }
2179         if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
2180             addCheckbox( Configuration.color_according_to_species,
2181                          _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
2182             setCheckbox( Configuration.color_according_to_species,
2183                          _configuration.doCheckOption( Configuration.color_according_to_species ) );
2184         }
2185         if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
2186             addCheckbox( Configuration.color_according_to_annotation,
2187                          _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
2188             setCheckbox( Configuration.color_according_to_annotation,
2189                          _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
2190         }
2191         if ( _configuration.doDisplayOption( Configuration.use_style ) ) {
2192             addCheckbox( Configuration.use_style, _configuration.getDisplayTitle( Configuration.use_style ) );
2193             setCheckbox( Configuration.use_style, _configuration.doCheckOption( Configuration.use_style ) );
2194         }
2195         if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
2196             addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
2197             setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
2198         }
2199         final JLabel label = new JLabel( "Display Data:" );
2200         label.setFont( ControlPanel.jcb_bold_font );
2201         if ( !getConfiguration().isUseNativeUI() ) {
2202             label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
2203         }
2204         add( label );
2205         if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
2206             addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
2207             setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
2208         }
2209         if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
2210             addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
2211             setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
2212         }
2213         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
2214             addCheckbox( Configuration.show_taxonomy_scientific_names,
2215                          _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
2216             setCheckbox( Configuration.show_taxonomy_scientific_names,
2217                          _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
2218         }
2219         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
2220             addCheckbox( Configuration.show_taxonomy_common_names,
2221                          _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
2222             setCheckbox( Configuration.show_taxonomy_common_names,
2223                          _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
2224         }
2225         if ( _configuration.doDisplayOption( Configuration.show_seq_names ) ) {
2226             addCheckbox( Configuration.show_seq_names, _configuration.getDisplayTitle( Configuration.show_seq_names ) );
2227             setCheckbox( Configuration.show_seq_names, _configuration.doCheckOption( Configuration.show_seq_names ) );
2228         }
2229         if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
2230             addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
2231             setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
2232         }
2233         if ( _configuration.doDisplayOption( Configuration.show_seq_symbols ) ) {
2234             addCheckbox( Configuration.show_seq_symbols,
2235                          _configuration.getDisplayTitle( Configuration.show_seq_symbols ) );
2236             setCheckbox( Configuration.show_seq_symbols, _configuration.doCheckOption( Configuration.show_seq_symbols ) );
2237         }
2238         if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
2239             addCheckbox( Configuration.show_sequence_acc,
2240                          _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
2241             setCheckbox( Configuration.show_sequence_acc,
2242                          _configuration.doCheckOption( Configuration.show_sequence_acc ) );
2243         }
2244         if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
2245             addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
2246             setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
2247         }
2248         if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
2249             addCheckbox( Configuration.write_confidence_values,
2250                          _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
2251             setCheckbox( Configuration.write_confidence_values,
2252                          _configuration.doCheckOption( Configuration.write_confidence_values ) );
2253         }
2254         if ( _configuration.doDisplayOption( Configuration.write_branch_length_values ) ) {
2255             addCheckbox( Configuration.write_branch_length_values,
2256                          _configuration.getDisplayTitle( Configuration.write_branch_length_values ) );
2257             setCheckbox( Configuration.write_branch_length_values,
2258                          _configuration.doCheckOption( Configuration.write_branch_length_values ) );
2259         }
2260         if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
2261             addCheckbox( Configuration.show_binary_characters,
2262                          _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
2263             setCheckbox( Configuration.show_binary_characters,
2264                          _configuration.doCheckOption( Configuration.show_binary_characters ) );
2265         }
2266         if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
2267             addCheckbox( Configuration.show_binary_character_counts,
2268                          _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
2269             setCheckbox( Configuration.show_binary_character_counts,
2270                          _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
2271         }
2272         if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
2273             addCheckbox( Configuration.show_domain_architectures,
2274                          _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
2275             setCheckbox( Configuration.show_domain_architectures,
2276                          _configuration.doCheckOption( Configuration.show_domain_architectures ) );
2277         }
2278         if ( _configuration.doDisplayOption( Configuration.show_mol_seqs ) ) {
2279             addCheckbox( Configuration.show_mol_seqs, _configuration.getDisplayTitle( Configuration.show_mol_seqs ) );
2280             setCheckbox( Configuration.show_mol_seqs, _configuration.doCheckOption( Configuration.show_mol_seqs ) );
2281         }
2282         if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
2283             addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
2284             setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
2285         }
2286         if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
2287             addCheckbox( Configuration.show_vector_data,
2288                          _configuration.getDisplayTitle( Configuration.show_vector_data ) );
2289             setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
2290         }
2291         if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
2292             addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
2293             setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
2294         }
2295         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
2296             addCheckbox( Configuration.show_taxonomy_images,
2297                          _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
2298             setCheckbox( Configuration.show_taxonomy_images,
2299                          _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
2300         }
2301     }
2302
2303     private void setVisibilityOfDomainStrucureControls() {
2304         if ( _zoom_in_domain_structure != null ) {
2305             final MainFrame mf = getMainFrame();
2306             if ( mf != null ) {
2307                 if ( isShowDomainArchitectures() ) {
2308                     _domain_display_label.setVisible( true );
2309                     _zoom_in_domain_structure.setVisible( true );
2310                     _zoom_out_domain_structure.setVisible( true );
2311                     _decr_domain_structure_evalue_thr.setVisible( true );
2312                     _incr_domain_structure_evalue_thr.setVisible( true );
2313                     _domain_structure_evalue_thr_tf.setVisible( true );
2314                     if ( mf._right_line_up_domains_cbmi != null ) {
2315                         mf._right_line_up_domains_cbmi.setVisible( true );
2316                     }
2317                     if ( mf._show_domain_labels != null ) {
2318                         mf._show_domain_labels.setVisible( true );
2319                     }
2320                 }
2321                 else {
2322                     _domain_display_label.setVisible( false );
2323                     _zoom_in_domain_structure.setVisible( false );
2324                     _zoom_out_domain_structure.setVisible( false );
2325                     _decr_domain_structure_evalue_thr.setVisible( false );
2326                     _incr_domain_structure_evalue_thr.setVisible( false );
2327                     _domain_structure_evalue_thr_tf.setVisible( false );
2328                     if ( mf._right_line_up_domains_cbmi != null ) {
2329                         mf._right_line_up_domains_cbmi.setVisible( false );
2330                     }
2331                     if ( mf._show_domain_labels != null ) {
2332                         mf._show_domain_labels.setVisible( false );
2333                     }
2334                 }
2335             }
2336         }
2337     }
2338
2339     // This takes care of ArchaeopteryxE-issue.
2340     // Can, and will, return null prior to  ArchaeopteryxE initialization completion.
2341     final private MainFrame getMainFrame() {
2342         MainFrame mf = getMainPanel().getMainFrame();
2343         if ( mf == null ) {
2344             // Must be "E" applet version.
2345             final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
2346             if ( e.getMainPanel() == null ) {
2347                 return null;
2348             }
2349             mf = e.getMainPanel().getMainFrame();
2350         }
2351         return mf;
2352     }
2353
2354     void setVisibilityOfX() {
2355         final MainFrame mf = getMainFrame();
2356         if ( mf != null ) {
2357             if ( ( getCurrentTreePanel() != null ) && ( getCurrentTreePanel().getPhylogeny() != null ) ) {
2358                 if ( AptxUtil.isHasAtLeastOneBranchWithSupportSD( getCurrentTreePanel().getPhylogeny() ) ) {
2359                     if ( mf._show_confidence_stddev_cbmi != null ) {
2360                         mf._show_confidence_stddev_cbmi.setVisible( true );
2361                     }
2362                 }
2363                 else {
2364                     if ( mf._show_confidence_stddev_cbmi != null ) {
2365                         mf._show_confidence_stddev_cbmi.setVisible( false );
2366                     }
2367                 }
2368                 if ( AptxUtil.isHasAtLeastOneNodeWithScientificName( getCurrentTreePanel().getPhylogeny() ) ) {
2369                     if ( mf._abbreviate_scientific_names != null ) {
2370                         mf._abbreviate_scientific_names.setVisible( true );
2371                     }
2372                 }
2373                 else {
2374                     if ( mf._abbreviate_scientific_names != null ) {
2375                         mf._abbreviate_scientific_names.setVisible( false );
2376                     }
2377                 }
2378                 if ( AptxUtil.isHasAtLeastOneNodeWithSequenceAnnotation( getCurrentTreePanel().getPhylogeny() ) ) {
2379                     if ( mf._show_annotation_ref_source != null ) {
2380                         mf._show_annotation_ref_source.setVisible( true );
2381                     }
2382                 }
2383                 else {
2384                     if ( mf._show_annotation_ref_source != null ) {
2385                         mf._show_annotation_ref_source.setVisible( false );
2386                     }
2387                 }
2388             }
2389             if ( isDrawPhylogram()
2390                     || ( ( getCurrentTreePanel() != null ) && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
2391                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) ) {
2392                 if ( mf._non_lined_up_cladograms_rbmi != null ) {
2393                     mf._non_lined_up_cladograms_rbmi.setVisible( false );
2394                 }
2395                 if ( mf._uniform_cladograms_rbmi != null ) {
2396                     mf._uniform_cladograms_rbmi.setVisible( false );
2397                 }
2398                 if ( mf._ext_node_dependent_cladogram_rbmi != null ) {
2399                     mf._ext_node_dependent_cladogram_rbmi.setVisible( false );
2400                 }
2401             }
2402             else {
2403                 if ( mf._non_lined_up_cladograms_rbmi != null ) {
2404                     mf._non_lined_up_cladograms_rbmi.setVisible( true );
2405                 }
2406                 if ( mf._uniform_cladograms_rbmi != null ) {
2407                     mf._uniform_cladograms_rbmi.setVisible( true );
2408                 }
2409                 if ( mf._ext_node_dependent_cladogram_rbmi != null ) {
2410                     mf._ext_node_dependent_cladogram_rbmi.setVisible( true );
2411                 }
2412             }
2413             if ( isDrawPhylogram() ) {
2414                 if ( mf._show_scale_cbmi != null ) {
2415                     mf._show_scale_cbmi.setVisible( true );
2416                 }
2417             }
2418             else {
2419                 if ( mf._show_scale_cbmi != null ) {
2420                     mf._show_scale_cbmi.setVisible( false );
2421                 }
2422             }
2423             if ( getCurrentTreePanel() != null ) {
2424                 if ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
2425                         || ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
2426                     if ( mf._label_direction_cbmi != null ) {
2427                         mf._label_direction_cbmi.setVisible( true );
2428                     }
2429                 }
2430                 else {
2431                     if ( mf._label_direction_cbmi != null ) {
2432                         mf._label_direction_cbmi.setVisible( false );
2433                     }
2434                 }
2435             }
2436         }
2437     }
2438
2439     void setVisibilityOfDomainStrucureCB() {
2440         try {
2441             if ( ( getCurrentTreePanel() != null )
2442                     && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
2443                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
2444                 if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
2445                     getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false );
2446                 }
2447                 if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
2448                     getMainPanel().getMainFrame()._show_domain_labels.setVisible( false );
2449                 }
2450             }
2451             else if ( isShowDomainArchitectures() ) {
2452                 if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
2453                     getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( true );
2454                 }
2455                 if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
2456                     getMainPanel().getMainFrame()._show_domain_labels.setVisible( true );
2457                 }
2458             }
2459             else {
2460                 if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
2461                     getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false );
2462                 }
2463                 if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
2464                     getMainPanel().getMainFrame()._show_domain_labels.setVisible( false );
2465                 }
2466             }
2467         }
2468         catch ( final Exception ignore ) {
2469             //not important...
2470         }
2471     }
2472
2473     static JLabel customizeLabel( final JLabel label, final Configuration configuration ) {
2474         label.setFont( ControlPanel.jcb_bold_font );
2475         if ( !configuration.isUseNativeUI() ) {
2476             label.setForeground( configuration.getGuiCheckboxTextColor() );
2477             label.setBackground( configuration.getGuiBackgroundColor() );
2478         }
2479         return label;
2480     }
2481
2482     enum NodeClickAction {
2483         ADD_NEW_NODE,
2484         BLAST,
2485         COLLAPSE,
2486         COLOR_SUBTREE,
2487         COPY_SUBTREE,
2488         CUT_SUBTREE,
2489         DELETE_NODE_OR_SUBTREE,
2490         EDIT_NODE_DATA,
2491         GET_EXT_DESC_DATA,
2492         OPEN_PDB_WEB,
2493         OPEN_SEQ_WEB,
2494         OPEN_TAX_WEB,
2495         PASTE_SUBTREE,
2496         REROOT,
2497         SELECT_NODES,
2498         SHOW_DATA,
2499         SORT_DESCENDENTS,
2500         SUBTREE,
2501         SWAP,
2502         CHANGE_NODE_FONT,
2503         COLOR_NODE_FONT;
2504     }
2505 }