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.iterators.PhylogenyNodeIterator;
  69 import org.forester.util.ForesterUtil;
  70
  71 final class ControlPanel extends JPanel implements ActionListener {
  72
  73     final static Font            jcb_bold_font             = new Font( Configuration.getDefaultFontFamilyName(),
  74                                                                        Font.BOLD,
  75                                                                        9 );
  76     final static Font            jcb_font                  = new Font( Configuration.getDefaultFontFamilyName(),
  77                                                                        Font.PLAIN,
  78                                                                        9 );
  79     final static Font            js_font                   = new Font( Configuration.getDefaultFontFamilyName(),
  80                                                                        Font.PLAIN,
  81                                                                        9 );
  82     private static final String  RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
  83     private static final long    serialVersionUID          = -8463483932821545633L;
  84     private NodeClickAction      _action_when_node_clicked;
  85     private int                  _add_new_node_item;
  86     private Map<Integer, String> _all_click_to_names;
  87     private Map<String, Color>   _annotation_colors;
  88     private int                  _blast_item;
  89     private JComboBox            _click_to_combobox;
  90     private JLabel               _click_to_label;
  91     private List<String>         _click_to_names;
  92     private int                  _collapse_cb_item;
  93     private JCheckBox            _color_acc_species;
  94     private JCheckBox            _color_acc_sequence;
  95     private JCheckBox            _color_according_to_annotation;
  96     private boolean              _color_branches;
  97     private JCheckBox            _use_visual_styles_cb;
  98     private int                  _color_subtree_cb_item;
  99     private int                  _change_node_font_item;
 100     // The settings from the conf file
 101     private final Configuration  _configuration;
 102     private int                  _copy_subtree_item;
 103     private int                  _cut_subtree_item;
 104     private JButton              _decr_domain_structure_evalue_thr;
 105     private int                  _delete_node_or_subtree_item;
 106     private JCheckBox            _display_as_phylogram_cb;
 107     // Tree checkboxes
 108     private JCheckBox            _display_internal_data;
 109     private JLabel               _domain_display_label;
 110     private JTextField           _domain_structure_evalue_thr_tf;
 111     private List<Boolean>        _draw_phylogram;
 112     private JCheckBox            _dynamically_hide_data;
 113     private int                  _edit_node_data_item;
 114     private int                  _get_ext_desc_data;
 115     private JButton              _incr_domain_structure_evalue_thr;
 116     private final MainPanel      _mainpanel;
 117     private JCheckBox            _node_desc_popup_cb;
 118     private int                  _open_pdb_item;
 119     private int                  _open_seq_web_item;
 120     private int                  _open_tax_web_item;
 121     private int                  _color_node_font_item;
 122     private JButton              _order;
 123     private boolean              _order_of_appearance;
 124     private int                  _paste_subtree_item;
 125     private int                  _reroot_cb_item;
 126     private JButton              _return_to_super_tree;
 127     // Search
 128     private JLabel               _search_found_label_0;
 129     private JLabel               _search_found_label_1;
 130     private JButton              _search_reset_button_0;
 131     private JButton              _search_reset_button_1;
 132     private JTextField           _search_tf_0;
 133     private JTextField           _search_tf_1;
 134     private int                  _select_nodes_item;
 135     private Sequence             _selected_query_seq;
 136     private JCheckBox            _seq_relation_confidence_switch;
 137     private JComboBox            _sequence_relation_type_box;
 138     private JCheckBox            _show_annotation;
 139     private JCheckBox            _show_binary_character_counts;
 140     private JCheckBox            _show_binary_characters;
 141     // Indices for the click-to options in the combo box
 142     private int                  _show_data_item;
 143     private JCheckBox            _show_domain_architectures;
 144     private JCheckBox            _show_events;
 145     private JCheckBox            _show_gene_names;
 146     private JCheckBox            _show_node_names;
 147     private JCheckBox            _show_properties_cb;
 148     private JCheckBox            _show_seq_names;
 149     private JCheckBox            _show_seq_symbols;
 150     private JCheckBox            _show_sequence_acc;
 151     private JComboBox            _show_sequence_relations;
 152     private JCheckBox            _show_taxo_code;
 153     private JCheckBox            _show_taxo_common_names;
 154     private JCheckBox            _show_taxo_images_cb;
 155     private JCheckBox            _show_taxo_scientific_names;
 156     private JCheckBox            _show_vector_data_cb;
 157     private JButton              _show_whole;
 158     private int                  _sort_descendents_item;
 159     private Map<String, Color>   _species_colors;
 160     private Map<String, Color>   _sequence_colors;
 161     private int                  _subtree_cb_item;
 162     private int                  _swap_cb_item;
 163     private JButton              _uncollapse_all;
 164     private JCheckBox            _width_branches;
 165     private JCheckBox            _write_confidence;
 166     private JButton              _zoom_in_domain_structure;
 167     // zooming and quick tree manipulation buttons:
 168     private JButton              _zoom_in_x;
 169     private JButton              _zoom_in_y;
 170     private JLabel               _zoom_label;
 171     private JButton              _zoom_out_domain_structure;
 172     private JButton              _zoom_out_x;
 173     private JButton              _zoom_out_y;
 174
 175     ControlPanel( final MainPanel ap, final Configuration configuration ) {
 176         init();
 177         _mainpanel = ap;
 178         _configuration = configuration;
 179         if ( !_configuration.isUseNativeUI() ) {
 180             setBackground( getConfiguration().getGuiBackgroundColor() );
 181             setBorder( BorderFactory.createRaisedBevelBorder() );
 182         }
 183         setLayout( new GridLayout( 0, 1, 2, 2 ) );
 184         _order_of_appearance = true;
 185         setupControls();
 186     }
 187
 188     /**
 189      * Handle an action.
 190      */
 191     @Override
 192     public void actionPerformed( final ActionEvent e ) {
 193         try {
 194             if ( e.getSource() == _color_acc_sequence ) {
 195                 if ( _color_acc_species != null  ) {
 196                     _color_acc_species.setSelected( false );
 197                 }
 198              }
 199             else if ( e.getSource() == _color_acc_species ) {
 200                 if ( _color_acc_sequence != null  ) {
 201                     _color_acc_sequence.setSelected( false );
 202                 }
 203
 204             }
 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                     showWhole();
 256                 }
 257                 else if ( e.getSource() == _return_to_super_tree ) {
 258                     _mainpanel.getCurrentTreePanel().superTree();
 259                     showWhole();
 260                 }
 261                 else if ( e.getSource() == _order ) {
 262                     DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
 263                     if ( ( !isShowTaxonomyScientificNames() && !isShowTaxonomyCode() && !isShowTaxonomyCommonNames() ) ) {
 264                         if ( ( isShowSequenceAcc() || isShowSeqNames() || isShowSeqSymbols() ) ) {
 265                             pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
 266                         }
 267                         else if ( isShowNodeNames() ) {
 268                             pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
 269                         }
 270                     }
 271                     PhylogenyMethods.orderAppearance( tp.getPhylogeny().getRoot(), _order_of_appearance, true, pri );
 272                     _order_of_appearance = !_order_of_appearance;
 273                     tp.setNodeInPreorderToNull();
 274                     tp.getPhylogeny().externalNodesHaveChanged();
 275                     tp.getPhylogeny().clearHashIdToNodeMap();
 276                     tp.getPhylogeny().recalculateNumberOfExternalDescendants( true );
 277                     tp.resetNodeIdToDistToLeafMap();
 278                     tp.setEdited( true );
 279                     displayedPhylogenyMightHaveChanged( false );
 280                 }
 281                 else if ( e.getSource() == _uncollapse_all ) {
 282                     uncollapseAll( tp );
 283                     displayedPhylogenyMightHaveChanged( false );
 284                 }
 285                 else if ( e.getSource() == _zoom_in_domain_structure ) {
 286                     _mainpanel.getCurrentTreePanel().zoomInDomainStructure();
 287                     displayedPhylogenyMightHaveChanged( true );
 288                 }
 289                 else if ( e.getSource() == _zoom_out_domain_structure ) {
 290                     _mainpanel.getCurrentTreePanel().zoomOutDomainStructure();
 291                     displayedPhylogenyMightHaveChanged( true );
 292                 }
 293                 else if ( e.getSource() == _decr_domain_structure_evalue_thr ) {
 294                     _mainpanel.getCurrentTreePanel().decreaseDomainStructureEvalueThreshold();
 295                     displayedPhylogenyMightHaveChanged( true );
 296                 }
 297                 else if ( e.getSource() == _incr_domain_structure_evalue_thr ) {
 298                     _mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThreshold();
 299                     displayedPhylogenyMightHaveChanged( true );
 300                 }
 301                 else if ( e.getSource() == _search_tf_0 ) {
 302                     search0();
 303                     displayedPhylogenyMightHaveChanged( true );
 304                 }
 305                 else if ( e.getSource() == _search_tf_1 ) {
 306                     search1();
 307                     displayedPhylogenyMightHaveChanged( true );
 308                 }
 309
 310
 311
 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 getSequenceRelationBox() {
 358         if ( _show_sequence_relations == null ) {
 359             _show_sequence_relations = new JComboBox();
 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 getSequenceRelationTypeBox() {
 375         if ( _sequence_relation_type_box == null ) {
 376             _sequence_relation_type_box = new JComboBox();
 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 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
 558                         .setToolTipText( "To colorize node labels as a function of taxonomy" );
 559                 addJCheckBox( _color_acc_species, ch_panel );
 560                 add( ch_panel );
 561                 break;
 562             case Configuration.color_according_to_sequence:
 563                 _color_acc_sequence = new JCheckBox( title );
 564                 _color_acc_sequence
 565                         .setToolTipText( "To colorize node labels as a function of sequence name" );
 566                 addJCheckBox( _color_acc_sequence, ch_panel );
 567                 add( ch_panel );
 568                 break;
 569             case Configuration.color_according_to_annotation:
 570                 _color_according_to_annotation = new JCheckBox( title );
 571                 _color_according_to_annotation
 572                         .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" );
 573                 addJCheckBox( _color_according_to_annotation, ch_panel );
 574                 add( ch_panel );
 575                 break;
 576             case Configuration.show_node_names:
 577                 _show_node_names = new JCheckBox( title );
 578                 addJCheckBox( _show_node_names, ch_panel );
 579                 add( ch_panel );
 580                 break;
 581             case Configuration.show_taxonomy_scientific_names:
 582                 _show_taxo_scientific_names = new JCheckBox( title );
 583                 addJCheckBox( _show_taxo_scientific_names, ch_panel );
 584                 add( ch_panel );
 585                 break;
 586             case Configuration.show_taxonomy_common_names:
 587                 _show_taxo_common_names = new JCheckBox( title );
 588                 addJCheckBox( _show_taxo_common_names, ch_panel );
 589                 add( ch_panel );
 590                 break;
 591             case Configuration.show_tax_code:
 592                 _show_taxo_code = new JCheckBox( title );
 593                 addJCheckBox( _show_taxo_code, ch_panel );
 594                 add( ch_panel );
 595                 break;
 596             case Configuration.show_taxonomy_images:
 597                 _show_taxo_images_cb = new JCheckBox( title );
 598                 addJCheckBox( _show_taxo_images_cb, ch_panel );
 599                 add( ch_panel );
 600                 break;
 601             case Configuration.show_binary_characters:
 602                 _show_binary_characters = new JCheckBox( title );
 603                 addJCheckBox( _show_binary_characters, ch_panel );
 604                 add( ch_panel );
 605                 break;
 606             case Configuration.show_annotation:
 607                 _show_annotation = new JCheckBox( title );
 608                 addJCheckBox( _show_annotation, ch_panel );
 609                 add( ch_panel );
 610                 break;
 611             case Configuration.show_binary_character_counts:
 612                 _show_binary_character_counts = new JCheckBox( title );
 613                 addJCheckBox( _show_binary_character_counts, ch_panel );
 614                 add( ch_panel );
 615                 break;
 616             case Configuration.write_confidence_values:
 617                 _write_confidence = new JCheckBox( title );
 618                 addJCheckBox( getWriteConfidenceCb(), ch_panel );
 619                 add( ch_panel );
 620                 break;
 621             case Configuration.write_events:
 622                 _show_events = new JCheckBox( title );
 623                 addJCheckBox( getShowEventsCb(), ch_panel );
 624                 add( ch_panel );
 625                 break;
 626             case Configuration.use_style:
 627                 _use_visual_styles_cb = new JCheckBox( title );
 628                 getUseVisualStylesCb()
 629                         .setToolTipText( "To use visual styles (node colors, fonts) and branch colors, if present" );
 630                 addJCheckBox( getUseVisualStylesCb(), ch_panel );
 631                 add( ch_panel );
 632                 break;
 633             case Configuration.width_branches:
 634                 _width_branches = new JCheckBox( title );
 635                 _width_branches.setToolTipText( "To use branch width values, if present" );
 636                 addJCheckBox( _width_branches, ch_panel );
 637                 add( ch_panel );
 638                 break;
 639             case Configuration.show_domain_architectures:
 640                 _show_domain_architectures = new JCheckBox( title );
 641                 addJCheckBox( _show_domain_architectures, ch_panel );
 642                 add( ch_panel );
 643                 break;
 644             case Configuration.show_seq_names:
 645                 _show_seq_names = new JCheckBox( title );
 646                 addJCheckBox( _show_seq_names, ch_panel );
 647                 add( ch_panel );
 648                 break;
 649             case Configuration.show_gene_names:
 650                 _show_gene_names = new JCheckBox( title );
 651                 addJCheckBox( _show_gene_names, ch_panel );
 652                 add( ch_panel );
 653                 break;
 654             case Configuration.show_seq_symbols:
 655                 _show_seq_symbols = new JCheckBox( title );
 656                 addJCheckBox( _show_seq_symbols, ch_panel );
 657                 add( ch_panel );
 658                 break;
 659             case Configuration.show_sequence_acc:
 660                 _show_sequence_acc = new JCheckBox( title );
 661                 addJCheckBox( _show_sequence_acc, ch_panel );
 662                 add( ch_panel );
 663                 break;
 664             case Configuration.dynamically_hide_data:
 665                 _dynamically_hide_data = new JCheckBox( title );
 666                 getDynamicallyHideData().setToolTipText( "To hide labels depending on likely visibility" );
 667                 addJCheckBox( getDynamicallyHideData(), ch_panel );
 668                 add( ch_panel );
 669                 break;
 670             case Configuration.node_data_popup:
 671                 _node_desc_popup_cb = new JCheckBox( title );
 672                 getNodeDescPopupCb().setToolTipText( "To enable mouse rollover display of basic node data" );
 673                 addJCheckBox( getNodeDescPopupCb(), ch_panel );
 674                 add( ch_panel );
 675                 break;
 676             case Configuration.show_relation_confidence:
 677                 _seq_relation_confidence_switch = new JCheckBox( title );
 678                 addJCheckBox( _seq_relation_confidence_switch, ch_panel );
 679                 add( ch_panel );
 680                 break;
 681             case Configuration.show_vector_data:
 682                 _show_vector_data_cb = new JCheckBox( title );
 683                 addJCheckBox( _show_vector_data_cb, ch_panel );
 684                 add( ch_panel );
 685                 break;
 686             case Configuration.show_properties:
 687                 _show_properties_cb = new JCheckBox( title );
 688                 addJCheckBox( _show_properties_cb, ch_panel );
 689                 add( ch_panel );
 690                 break;
 691             default:
 692                 throw new RuntimeException( "unknown checkbox: " + which );
 693         }
 694     }// addCheckbox
 695
 696     void addJButton( final JButton jb, final JPanel p ) {
 697         jb.setFocusPainted( false );
 698         jb.setFont( ControlPanel.jcb_font );
 699         if ( !_configuration.isUseNativeUI() ) {
 700             jb.setBorder( BorderFactory.createLineBorder( getConfiguration().getGuiButtonBorderColor() ) );
 701             jb.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 702             jb.setForeground( getConfiguration().getGuiButtonTextColor() );
 703         }
 704         p.add( jb );
 705         jb.addActionListener( this );
 706     }
 707
 708     void addJCheckBox( final JCheckBox jcb, final JPanel p ) {
 709         jcb.setFocusPainted( false );
 710         jcb.setFont( ControlPanel.jcb_font );
 711         if ( !_configuration.isUseNativeUI() ) {
 712             jcb.setBackground( getConfiguration().getGuiBackgroundColor() );
 713             jcb.setForeground( getConfiguration().getGuiCheckboxTextColor() );
 714         }
 715         p.add( jcb, "Center" );
 716         jcb.addActionListener( this );
 717     }
 718
 719     void addJTextField( final JTextField tf, final JPanel p ) {
 720         if ( !_configuration.isUseNativeUI() ) {
 721             tf.setForeground( getConfiguration().getGuiBackgroundColor() );
 722             tf.setFont( ControlPanel.jcb_font );
 723         }
 724         p.add( tf );
 725         tf.addActionListener( this );
 726     }
 727
 728     void deactivateButtonToReturnToSuperTree() {
 729         _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
 730         _return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
 731         _return_to_super_tree.setEnabled( false );
 732     }
 733
 734     void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
 735         if ( ( _mainpanel != null )
 736                 && ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
 737             if ( getOptions().isShowOverview() ) {
 738                 _mainpanel.getCurrentTreePanel().updateOvSizes();
 739             }
 740             _mainpanel.getCurrentTreePanel().recalculateMaxDistanceToRoot();
 741             setVisibilityOfDomainStrucureControls();
 742             updateDomainStructureEvaluethresholdDisplay();
 743             _mainpanel.getCurrentTreePanel().calculateScaleDistance();
 744             _mainpanel.getCurrentTreePanel().calcMaxDepth();
 745             _mainpanel.adjustJScrollPane();
 746             if ( recalc_longest_ext_node_info ) {
 747                 _mainpanel.getCurrentTreePanel().initNodeData();
 748                 _mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
 749             }
 750             _mainpanel.getCurrentTreePanel().repaint();
 751             // _mainpanel.getCurrentTreePanel().setUpUrtFactors();
 752         }
 753     }
 754
 755     void endClickToOptions() {
 756         _click_to_combobox.addActionListener( this );
 757     }
 758
 759     /**
 760      * Indicates what action should be execute when a node is clicked
 761      *
 762      * @return the click-on action
 763      */
 764     NodeClickAction getActionWhenNodeClicked() {
 765         return _action_when_node_clicked;
 766     }
 767
 768     Map<Integer, String> getAllClickToItems() {
 769         return _all_click_to_names;
 770     }
 771
 772     Map<String, Color> getAnnotationColors() {
 773         return _annotation_colors;
 774     }
 775
 776     Configuration getConfiguration() {
 777         return _configuration;
 778     }
 779
 780     TreePanel getCurrentTreePanel() {
 781         return getMainPanel().getCurrentTreePanel();
 782     }
 783
 784     MainPanel getMainPanel() {
 785         return _mainpanel;
 786     }
 787
 788     Options getOptions() {
 789         return getMainPanel().getOptions();
 790     }
 791
 792     JLabel getSearchFoundCountsLabel0() {
 793         return _search_found_label_0;
 794     }
 795
 796     JLabel getSearchFoundCountsLabel1() {
 797         return _search_found_label_1;
 798     }
 799
 800     JButton getSearchResetButton0() {
 801         return _search_reset_button_0;
 802     }
 803
 804     JButton getSearchResetButton1() {
 805         return _search_reset_button_1;
 806     }
 807
 808     JTextField getSearchTextField0() {
 809         return _search_tf_0;
 810     }
 811
 812     JTextField getSearchTextField1() {
 813         return _search_tf_1;
 814     }
 815
 816     List<String> getSingleClickToNames() {
 817         return _click_to_names;
 818     }
 819
 820     Map<String, Color> getSpeciesColors() {
 821         return _species_colors;
 822     }
 823
 824     Map<String, Color> getSequenceColors() {
 825         return _sequence_colors;
 826     }
 827
 828     boolean isAntialiasScreenText() {
 829         return true;
 830     }
 831
 832     boolean isColorAccordingToAnnotation() {
 833         return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
 834     }
 835
 836     boolean isColorAccordingToTaxonomy() {
 837         return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
 838     }
 839
 840     boolean isColorAccordingToSequence() {
 841         return ( ( _color_acc_sequence != null ) && _color_acc_sequence.isSelected() );
 842     }
 843
 844     boolean isUseVisualStyles() {
 845         return ( ( ( getUseVisualStylesCb() != null ) && getUseVisualStylesCb().isSelected() ) || ( ( getUseVisualStylesCb() == null ) && _color_branches ) );
 846     }
 847
 848     boolean isDrawPhylogram() {
 849         return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
 850     }
 851
 852     boolean isDynamicallyHideData() {
 853         return ( ( getDynamicallyHideData() != null ) && getDynamicallyHideData().isSelected() );
 854     }
 855
 856     boolean isEvents() {
 857         return ( ( getShowEventsCb() != null ) && getShowEventsCb().isSelected() );
 858     }
 859
 860     boolean isNodeDescPopup() {
 861         return ( ( getNodeDescPopupCb() != null ) && getNodeDescPopupCb().isSelected() );
 862     }
 863
 864     boolean isShowAnnotation() {
 865         return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
 866     }
 867
 868     boolean isShowBinaryCharacterCounts() {
 869         return ( ( _show_binary_character_counts != null ) && _show_binary_character_counts.isSelected() );
 870     }
 871
 872     boolean isShowBinaryCharacters() {
 873         return ( ( _show_binary_characters != null ) && _show_binary_characters.isSelected() );
 874     }
 875
 876     boolean isShowConfidenceValues() {
 877         return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
 878     }
 879
 880     boolean isShowDomainArchitectures() {
 881         return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
 882     }
 883
 884     boolean isShowGeneNames() {
 885         return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
 886     }
 887
 888     boolean isShowInternalData() {
 889         return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() );
 890     }
 891
 892     boolean isShowNodeNames() {
 893         return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
 894     }
 895
 896     boolean isShowSeqNames() {
 897         return ( ( _show_seq_names != null ) && _show_seq_names.isSelected() );
 898     }
 899
 900     boolean isShowSeqSymbols() {
 901         return ( ( _show_seq_symbols != null ) && _show_seq_symbols.isSelected() );
 902     }
 903
 904     boolean isShowSequenceAcc() {
 905         return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
 906     }
 907
 908     boolean isShowSequenceRelationConfidence() {
 909         return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
 910     }
 911
 912     boolean isShowSequenceRelations() {
 913         return ( ( _show_sequence_relations != null ) && ( _show_sequence_relations.getSelectedIndex() > 0 ) );
 914     }
 915
 916     boolean isShowTaxonomyCode() {
 917         return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
 918     }
 919
 920     boolean isShowTaxonomyCommonNames() {
 921         return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
 922     }
 923
 924     boolean isShowTaxonomyScientificNames() {
 925         return ( ( _show_taxo_scientific_names != null ) && _show_taxo_scientific_names.isSelected() );
 926     }
 927
 928     boolean isWidthBranches() {
 929         return ( ( _width_branches != null ) && _width_branches.isSelected() );
 930     }
 931
 932     void phylogenyAdded( final Configuration configuration ) {
 933         getIsDrawPhylogramList().add( configuration.isDrawAsPhylogram() );
 934     }
 935
 936     void phylogenyRemoved( final int index ) {
 937         getIsDrawPhylogramList().remove( index );
 938     }
 939
 940     void search0() {
 941         final MainPanel main_panel = getMainPanel();
 942         final Phylogeny tree = main_panel.getCurrentPhylogeny();
 943         if ( ( tree == null ) || tree.isEmpty() ) {
 944             return;
 945         }
 946         String query = getSearchTextField0().getText();
 947         if ( query != null ) {
 948             query = query.trim();
 949         }
 950         if ( !ForesterUtil.isEmpty( query ) ) {
 951             search0( main_panel, tree, query );
 952         }
 953         else {
 954             getSearchFoundCountsLabel0().setVisible( false );
 955             getSearchResetButton0().setEnabled( false );
 956             getSearchResetButton0().setVisible( false );
 957             searchReset0();
 958         }
 959     }
 960
 961     void search1() {
 962         final MainPanel main_panel = getMainPanel();
 963         final Phylogeny tree = main_panel.getCurrentPhylogeny();
 964         if ( ( tree == null ) || tree.isEmpty() ) {
 965             return;
 966         }
 967         String query = getSearchTextField1().getText();
 968         if ( query != null ) {
 969             query = query.trim();
 970         }
 971         if ( !ForesterUtil.isEmpty( query ) ) {
 972             search1( main_panel, tree, query );
 973         }
 974         else {
 975             getSearchFoundCountsLabel1().setVisible( false );
 976             getSearchResetButton1().setEnabled( false );
 977             getSearchResetButton1().setVisible( false );
 978             searchReset1();
 979         }
 980     }
 981
 982     void searchReset0() {
 983         if ( getMainPanel().getCurrentTreePanel() != null ) {
 984             getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
 985         }
 986     }
 987
 988     void searchReset1() {
 989         if ( getMainPanel().getCurrentTreePanel() != null ) {
 990             getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
 991         }
 992     }
 993
 994     void setActionWhenNodeClicked( final NodeClickAction action ) {
 995         _action_when_node_clicked = action;
 996     }
 997
 998     void setAnnotationColors( final Map<String, Color> annotation_colors ) {
 999         _annotation_colors = annotation_colors;
1000     }
1001
1002     void setCheckbox( final int which, final boolean state ) {
1003         switch ( which ) {
1004             case Configuration.display_as_phylogram:
1005                 if ( getDisplayAsPhylogramCb() != null ) {
1006                     getDisplayAsPhylogramCb().setSelected( state );
1007                 }
1008                 break;
1009             case Configuration.display_internal_data:
1010                 if ( _display_internal_data != null ) {
1011                     _display_internal_data.setSelected( state );
1012                 }
1013                 break;
1014             case Configuration.color_according_to_species:
1015                 if ( _color_acc_species != null ) {
1016                     _color_acc_species.setSelected( state );
1017                 }
1018                 break;
1019             case Configuration.color_according_to_sequence:
1020                 if ( _color_acc_sequence != null ) {
1021                     _color_acc_sequence.setSelected( state );
1022                 }
1023                 break;
1024             case Configuration.color_according_to_annotation:
1025                 if ( _color_according_to_annotation != null ) {
1026                     _color_according_to_annotation.setSelected( state );
1027                 }
1028                 break;
1029             case Configuration.show_node_names:
1030                 if ( _show_node_names != null ) {
1031                     _show_node_names.setSelected( state );
1032                 }
1033                 break;
1034             case Configuration.show_taxonomy_scientific_names:
1035                 if ( _show_taxo_scientific_names != null ) {
1036                     _show_taxo_scientific_names.setSelected( state );
1037                 }
1038                 break;
1039             case Configuration.show_taxonomy_common_names:
1040                 if ( _show_taxo_common_names != null ) {
1041                     _show_taxo_common_names.setSelected( state );
1042                 }
1043                 break;
1044             case Configuration.show_tax_code:
1045                 if ( _show_taxo_code != null ) {
1046                     _show_taxo_code.setSelected( state );
1047                 }
1048                 break;
1049             case Configuration.show_taxonomy_images:
1050                 if ( _show_taxo_images_cb != null ) {
1051                     _show_taxo_images_cb.setSelected( state );
1052                 }
1053                 break;
1054             case Configuration.show_annotation:
1055                 if ( _show_annotation != null ) {
1056                     _show_annotation.setSelected( state );
1057                 }
1058                 break;
1059             case Configuration.show_binary_characters:
1060                 if ( _show_binary_characters != null ) {
1061                     _show_binary_characters.setSelected( state );
1062                 }
1063                 break;
1064             case Configuration.show_binary_character_counts:
1065                 if ( _show_binary_character_counts != null ) {
1066                     _show_binary_character_counts.setSelected( state );
1067                 }
1068                 break;
1069             case Configuration.write_confidence_values:
1070                 if ( getWriteConfidenceCb() != null ) {
1071                     getWriteConfidenceCb().setSelected( state );
1072                 }
1073                 break;
1074             case Configuration.write_events:
1075                 if ( getShowEventsCb() != null ) {
1076                     getShowEventsCb().setSelected( state );
1077                 }
1078                 break;
1079             case Configuration.use_style:
1080                 if ( getUseVisualStylesCb() != null ) {
1081                     getUseVisualStylesCb().setSelected( state );
1082                 }
1083                 break;
1084             case Configuration.width_branches:
1085                 if ( _width_branches != null ) {
1086                     _width_branches.setSelected( state );
1087                 }
1088                 break;
1089             case Configuration.show_domain_architectures:
1090                 if ( _show_domain_architectures != null ) {
1091                     _show_domain_architectures.setSelected( state );
1092                 }
1093                 break;
1094             case Configuration.show_seq_names:
1095                 if ( _show_seq_names != null ) {
1096                     _show_seq_names.setSelected( state );
1097                 }
1098                 break;
1099             case Configuration.show_gene_names:
1100                 if ( _show_gene_names != null ) {
1101                     _show_gene_names.setSelected( state );
1102                 }
1103                 break;
1104             case Configuration.show_seq_symbols:
1105                 if ( _show_seq_symbols != null ) {
1106                     _show_seq_symbols.setSelected( state );
1107                 }
1108                 break;
1109             case Configuration.show_vector_data:
1110                 if ( _show_vector_data_cb != null ) {
1111                     _show_vector_data_cb.setSelected( state );
1112                 }
1113                 break;
1114             case Configuration.show_properties:
1115                 if ( _show_properties_cb != null ) {
1116                     _show_properties_cb.setSelected( state );
1117                 }
1118                 break;
1119             case Configuration.show_sequence_acc:
1120                 if ( _show_sequence_acc != null ) {
1121                     _show_sequence_acc.setSelected( state );
1122                 }
1123                 break;
1124             case Configuration.dynamically_hide_data:
1125                 if ( getDynamicallyHideData() != null ) {
1126                     getDynamicallyHideData().setSelected( state );
1127                 }
1128                 break;
1129             case Configuration.node_data_popup:
1130                 if ( getNodeDescPopupCb() != null ) {
1131                     getNodeDescPopupCb().setSelected( state );
1132                 }
1133                 break;
1134             /* GUILHEM_BEG */
1135             case Configuration.show_relation_confidence:
1136                 if ( _seq_relation_confidence_switch != null ) {
1137                     _seq_relation_confidence_switch.setSelected( state );
1138                 }
1139                 break;
1140             /* GUILHEM_END */
1141             default:
1142                 throw new AssertionError( "unknown checkbox: " + which );
1143         }
1144     }
1145
1146     /**
1147      * Set this checkbox state. Not all checkboxes have been instantiated
1148      * depending on the config.
1149      */
1150     void setCheckbox( final JCheckBox cb, final boolean state ) {
1151         if ( cb != null ) {
1152             cb.setSelected( state );
1153         }
1154     }
1155
1156     void setClickToAction( final int action ) {
1157         // Set click-to action
1158         if ( action == _show_data_item ) {
1159             setActionWhenNodeClicked( NodeClickAction.SHOW_DATA );
1160         }
1161         else if ( action == _collapse_cb_item ) {
1162             setActionWhenNodeClicked( NodeClickAction.COLLAPSE );
1163         }
1164         else if ( action == _reroot_cb_item ) {
1165             setActionWhenNodeClicked( NodeClickAction.REROOT );
1166         }
1167         else if ( action == _subtree_cb_item ) {
1168             setActionWhenNodeClicked( NodeClickAction.SUBTREE );
1169         }
1170         else if ( action == _swap_cb_item ) {
1171             setActionWhenNodeClicked( NodeClickAction.SWAP );
1172         }
1173         else if ( action == _color_subtree_cb_item ) {
1174             setActionWhenNodeClicked( NodeClickAction.COLOR_SUBTREE );
1175         }
1176         else if ( action == _open_seq_web_item ) {
1177             setActionWhenNodeClicked( NodeClickAction.OPEN_SEQ_WEB );
1178         }
1179         else if ( action == _sort_descendents_item ) {
1180             setActionWhenNodeClicked( NodeClickAction.SORT_DESCENDENTS );
1181         }
1182         else if ( action == _blast_item ) {
1183             setActionWhenNodeClicked( NodeClickAction.BLAST );
1184         }
1185         else if ( action == _open_tax_web_item ) {
1186             setActionWhenNodeClicked( NodeClickAction.OPEN_TAX_WEB );
1187         }
1188         else if ( action == _cut_subtree_item ) {
1189             setActionWhenNodeClicked( NodeClickAction.CUT_SUBTREE );
1190         }
1191         else if ( action == _copy_subtree_item ) {
1192             setActionWhenNodeClicked( NodeClickAction.COPY_SUBTREE );
1193         }
1194         else if ( action == _delete_node_or_subtree_item ) {
1195             setActionWhenNodeClicked( NodeClickAction.DELETE_NODE_OR_SUBTREE );
1196         }
1197         else if ( action == _paste_subtree_item ) {
1198             setActionWhenNodeClicked( NodeClickAction.PASTE_SUBTREE );
1199         }
1200         else if ( action == _add_new_node_item ) {
1201             setActionWhenNodeClicked( NodeClickAction.ADD_NEW_NODE );
1202         }
1203         else if ( action == _edit_node_data_item ) {
1204             setActionWhenNodeClicked( NodeClickAction.EDIT_NODE_DATA );
1205         }
1206         else if ( action == _select_nodes_item ) {
1207             setActionWhenNodeClicked( NodeClickAction.SELECT_NODES );
1208         }
1209         else if ( action == _get_ext_desc_data ) {
1210             setActionWhenNodeClicked( NodeClickAction.GET_EXT_DESC_DATA );
1211         }
1212         else if ( action == _open_pdb_item ) {
1213             setActionWhenNodeClicked( NodeClickAction.OPEN_PDB_WEB );
1214         }
1215         else if ( action == _color_node_font_item ) {
1216             setActionWhenNodeClicked( NodeClickAction.COLOR_NODE_FONT );
1217         }
1218         else if ( action == _change_node_font_item ) {
1219             setActionWhenNodeClicked( NodeClickAction.CHANGE_NODE_FONT );
1220         }
1221         else {
1222             throw new RuntimeException( "unknown action: " + action );
1223         }
1224         // make sure drop down is displaying the correct action
1225         // in case this was called from outside the class
1226         _click_to_combobox.setSelectedIndex( action );
1227     }
1228
1229     void setColorBranches( final boolean color_branches ) {
1230         _color_branches = color_branches;
1231     }
1232
1233     void setDrawPhylogram( final boolean b ) {
1234         getDisplayAsPhylogramCb().setSelected( b );
1235         setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
1236     }
1237
1238     void setDrawPhylogramEnabled( final boolean b ) {
1239         getDisplayAsPhylogramCb().setEnabled( b );
1240     }
1241
1242     void setDynamicHidingIsOn( final boolean is_on ) {
1243         //  if ( !_configuration.isUseNativeUI() ) {
1244         if ( is_on ) {
1245             getDynamicallyHideData().setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
1246         }
1247         else {
1248             if ( !_configuration.isUseNativeUI() ) {
1249                 getDynamicallyHideData().setForeground( getConfiguration().getGuiButtonTextColor() );
1250             }
1251             else {
1252                 getDynamicallyHideData().setForeground( Color.BLACK );
1253             }
1254         }
1255         // }
1256     }
1257
1258     void setSearchFoundCountsOnLabel0( final int counts ) {
1259         getSearchFoundCountsLabel0().setText( "Found: " + counts );
1260     }
1261
1262     void setSearchFoundCountsOnLabel1( final int counts ) {
1263         getSearchFoundCountsLabel1().setText( "Found: " + counts );
1264     }
1265
1266     void setShowEvents( final boolean show_events ) {
1267         if ( getShowEventsCb() == null ) {
1268             _show_events = new JCheckBox( "" );
1269         }
1270         getShowEventsCb().setSelected( show_events );
1271     }
1272
1273     void setSpeciesColors( final Map<String, Color> species_colors ) {
1274         _species_colors = species_colors;
1275     }
1276
1277     void setSequenceColors( final Map<String, Color> sequence_colors ) {
1278         _sequence_colors = sequence_colors;
1279     }
1280
1281     /* GUILHEM_END */
1282     /*
1283      * Set up the controls from the config settings. 11/26/05
1284      */
1285     void setupControls() {
1286         // The tree display options:
1287         setupDisplayCheckboxes();
1288         /* GUILHEM_BEG */
1289         // The sequence relation query selection combo-box
1290         if ( _configuration.displaySequenceRelations() ) {
1291             addSequenceRelationBlock();
1292         }
1293         /* GUILHEM_END */
1294         // Click-to options
1295         startClickToOptions();
1296         setupClickToOptions();
1297         endClickToOptions();
1298         // Zoom and quick edit buttons
1299         addButtons();
1300         setupSearchTools0();
1301         setupSearchTools1();
1302     }
1303
1304     void setUpControlsForDomainStrucures() {
1305         _domain_display_label = new JLabel( "Domain Display:" );
1306         add( customizeLabel( _domain_display_label, getConfiguration() ) );
1307         add( _domain_display_label );
1308         _zoom_in_domain_structure = new JButton( "d+" );
1309         _zoom_out_domain_structure = new JButton( "d-" );
1310         _decr_domain_structure_evalue_thr = new JButton( "-" );
1311         _incr_domain_structure_evalue_thr = new JButton( "+" );
1312         _zoom_in_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
1313         _zoom_out_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
1314         _decr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
1315         _incr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
1316         _incr_domain_structure_evalue_thr.setToolTipText( "Increase the E-value threshold by a factor of 10" );
1317         _decr_domain_structure_evalue_thr.setToolTipText( "Decrease the E-value threshold by a factor of 10" );
1318         _domain_structure_evalue_thr_tf = new JTextField( 3 );
1319         _domain_structure_evalue_thr_tf.setEditable( false );
1320         if ( !getConfiguration().isUseNativeUI() ) {
1321             _domain_structure_evalue_thr_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1322             _domain_structure_evalue_thr_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1323             _domain_structure_evalue_thr_tf.setBorder( null );
1324         }
1325         final JPanel d1_panel = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1326         final JPanel d2_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
1327         if ( !_configuration.isUseNativeUI() ) {
1328             d1_panel.setBackground( getBackground() );
1329             d2_panel.setBackground( getBackground() );
1330         }
1331         add( d1_panel );
1332         add( d2_panel );
1333         addJButton( _zoom_out_domain_structure, d1_panel );
1334         addJButton( _zoom_in_domain_structure, d1_panel );
1335         addJButton( _decr_domain_structure_evalue_thr, d2_panel );
1336         addJTextField( _domain_structure_evalue_thr_tf, d2_panel );
1337         addJButton( _incr_domain_structure_evalue_thr, d2_panel );
1338     }
1339
1340     void setupSearchTools0() {
1341         final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
1342         final JLabel search_label = new JLabel( "Search (A):" );
1343         search_label.setFont( ControlPanel.jcb_bold_font );
1344         if ( !getConfiguration().isUseNativeUI() ) {
1345             search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1346         }
1347         add( search_label );
1348         search_label.setToolTipText( tip );
1349         _search_found_label_0 = new JLabel();
1350         getSearchFoundCountsLabel0().setVisible( false );
1351         _search_found_label_0.setFont( ControlPanel.jcb_bold_font );
1352         if ( !getConfiguration().isUseNativeUI() ) {
1353             _search_found_label_0.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1354         }
1355         _search_tf_0 = new JTextField( 3 );
1356         _search_tf_0.setToolTipText( tip );
1357         _search_tf_0.setEditable( true );
1358         if ( !getConfiguration().isUseNativeUI() ) {
1359             _search_tf_0.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1360             _search_tf_0.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1361             _search_tf_0.setBorder( null );
1362         }
1363         _search_reset_button_0 = new JButton();
1364         getSearchResetButton0().setText( "Reset" );
1365         getSearchResetButton0().setEnabled( false );
1366         getSearchResetButton0().setVisible( false );
1367         final JPanel s_panel_1 = new JPanel( new BorderLayout() );
1368         final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1369         s_panel_1.setBackground( getBackground() );
1370         add( s_panel_1 );
1371         s_panel_2.setBackground( getBackground() );
1372         add( s_panel_2 );
1373         final KeyAdapter key_adapter = new KeyAdapter() {
1374
1375             @Override
1376             public void keyReleased( final KeyEvent key_event ) {
1377                 search0();
1378                 displayedPhylogenyMightHaveChanged( true );
1379             }
1380         };
1381         final ActionListener action_listener = new ActionListener() {
1382
1383             @Override
1384             public void actionPerformed( final ActionEvent e ) {
1385                 searchReset0();
1386                 setSearchFoundCountsOnLabel0( 0 );
1387                 getSearchFoundCountsLabel0().setVisible( false );
1388                 getSearchTextField0().setText( "" );
1389                 getSearchResetButton0().setEnabled( false );
1390                 getSearchResetButton0().setVisible( false );
1391                 displayedPhylogenyMightHaveChanged( true );
1392             }
1393         };
1394         _search_reset_button_0.addActionListener( action_listener );
1395         _search_tf_0.addKeyListener( key_adapter );
1396         addJTextField( _search_tf_0, s_panel_1 );
1397         s_panel_2.add( _search_found_label_0 );
1398         addJButton( _search_reset_button_0, s_panel_2 );
1399     }
1400
1401     void setupSearchTools1() {
1402         final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
1403         final JLabel search_label = new JLabel( "Search (B):" );
1404         search_label.setFont( ControlPanel.jcb_bold_font );
1405         if ( !getConfiguration().isUseNativeUI() ) {
1406             search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1407         }
1408         add( search_label );
1409         search_label.setToolTipText( tip );
1410         _search_found_label_1 = new JLabel();
1411         getSearchFoundCountsLabel1().setVisible( false );
1412         _search_found_label_1.setFont( ControlPanel.jcb_bold_font );
1413         if ( !getConfiguration().isUseNativeUI() ) {
1414             _search_found_label_1.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1415         }
1416         _search_tf_1 = new JTextField( 3 );
1417         _search_tf_1.setToolTipText( tip );
1418         _search_tf_1.setEditable( true );
1419         if ( !getConfiguration().isUseNativeUI() ) {
1420             _search_tf_1.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1421             _search_tf_1.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1422             _search_tf_1.setBorder( null );
1423         }
1424         _search_reset_button_1 = new JButton();
1425         getSearchResetButton1().setText( "Reset" );
1426         getSearchResetButton1().setEnabled( false );
1427         getSearchResetButton1().setVisible( false );
1428         final JPanel s_panel_1 = new JPanel( new BorderLayout() );
1429         final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1430         s_panel_1.setBackground( getBackground() );
1431         add( s_panel_1 );
1432         s_panel_2.setBackground( getBackground() );
1433         add( s_panel_2 );
1434         final KeyAdapter key_adapter = new KeyAdapter() {
1435
1436             @Override
1437             public void keyReleased( final KeyEvent key_event ) {
1438                 search1();
1439                 displayedPhylogenyMightHaveChanged( true );
1440             }
1441         };
1442         final ActionListener action_listener = new ActionListener() {
1443
1444             @Override
1445             public void actionPerformed( final ActionEvent e ) {
1446                 searchReset1();
1447                 setSearchFoundCountsOnLabel1( 0 );
1448                 getSearchFoundCountsLabel1().setVisible( false );
1449                 getSearchTextField1().setText( "" );
1450                 getSearchResetButton1().setEnabled( false );
1451                 getSearchResetButton1().setVisible( false );
1452                 displayedPhylogenyMightHaveChanged( true );
1453             }
1454         };
1455         _search_reset_button_1.addActionListener( action_listener );
1456         _search_tf_1.addKeyListener( key_adapter );
1457         addJTextField( _search_tf_1, s_panel_1 );
1458         s_panel_2.add( _search_found_label_1 );
1459         addJButton( _search_reset_button_1, s_panel_2 );
1460     }
1461
1462     void showAnnotations() {
1463         if ( _show_annotation != null ) {
1464             _show_annotation.setSelected( true );
1465         }
1466         if ( _color_according_to_annotation != null ) {
1467             _color_according_to_annotation.setSelected( true );
1468         }
1469         if ( _color_acc_species != null ) {
1470             _color_acc_species.setSelected( false );
1471         }
1472         if ( _color_acc_sequence != null ) {
1473             _color_acc_sequence.setSelected( false );
1474         }
1475         _mainpanel.getCurrentTreePanel().repaint();
1476     }
1477
1478     /**
1479      * Fit entire tree into window.
1480      */
1481     void showWhole() {
1482         if ( ( _mainpanel.getCurrentScrollPane() == null ) || _mainpanel.getCurrentTreePanel().getPhylogeny().isEmpty() ) {
1483             return;
1484         }
1485         getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1486         displayedPhylogenyMightHaveChanged( true );
1487         _mainpanel.getCurrentTreePanel().updateOvSettings();
1488         _mainpanel.getCurrentTreePanel().validate();
1489         _mainpanel.validate();
1490         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
1491                                                                     _mainpanel.getSizeOfViewport().height,
1492                                                                     true );
1493         _mainpanel.getCurrentTreePanel().resetPreferredSize();
1494         _mainpanel.adjustJScrollPane();
1495         _mainpanel.getCurrentTreePanel().repaint();
1496         _mainpanel.getCurrentTreePanel().validate();
1497         _mainpanel.validate();
1498         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
1499                                                                     _mainpanel.getSizeOfViewport().height,
1500                                                                     true );
1501         _mainpanel.getCurrentTreePanel().resetPreferredSize();
1502         _mainpanel.adjustJScrollPane();
1503         _mainpanel.getCurrentTreePanel().repaint();
1504         _mainpanel.getCurrentTreePanel().updateOvSizes();
1505     }
1506
1507     void showWholeAll() {
1508         for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
1509             if ( tree_panel != null ) {
1510                 tree_panel.validate();
1511                 tree_panel.calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
1512                                                       _mainpanel.getSizeOfViewport().height,
1513                                                       true );
1514                 tree_panel.resetPreferredSize();
1515                 tree_panel.repaint();
1516             }
1517         }
1518     }
1519
1520     // Create header for click-to combo box.
1521     void startClickToOptions() {
1522         final JLabel spacer = new JLabel( "" );
1523         spacer.setFont( ControlPanel.jcb_font );
1524         add( spacer );
1525         _click_to_label = new JLabel( "Click on Node to:" );
1526         add( customizeLabel( _click_to_label, getConfiguration() ) );
1527         _click_to_combobox = new JComboBox();
1528         _click_to_combobox.setFocusable( false );
1529         _click_to_combobox.setMaximumRowCount( 14 );
1530         _click_to_combobox.setFont( ControlPanel.js_font );
1531         if ( !_configuration.isUseNativeUI() ) {
1532             _click_to_combobox.setBackground( getConfiguration().getGuiBackgroundColor() );
1533         }
1534         // don't add listener until all items are set (or each one will trigger
1535         // an event)
1536         // click_to_list.addActionListener(this);
1537         add( _click_to_combobox );
1538         // Correlates option names to titles
1539         _all_click_to_names = new HashMap<Integer, String>();
1540         _click_to_names = new ArrayList<String>();
1541     }
1542
1543     void tabChanged() {
1544         if ( getMainPanel().getTabbedPane().getTabCount() > 0 ) {
1545             if ( getCurrentTreePanel().isPhyHasBranchLengths()
1546                     && ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1547                 setDrawPhylogramEnabled( true );
1548                 setDrawPhylogram( isDrawPhylogram() );
1549             }
1550             else {
1551                 setDrawPhylogramEnabled( false );
1552                 setDrawPhylogram( false );
1553             }
1554             if ( getMainPanel().getMainFrame() == null ) {
1555                 // Must be "E" applet version.
1556                 final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1557                 e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() );
1558             }
1559             else {
1560                 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel()
1561                         .getPhylogenyGraphicsType() );
1562             }
1563             getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
1564             getMainPanel().getControlPanel().search0();
1565             getMainPanel().getControlPanel().search1();
1566             getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
1567             getSequenceRelationTypeBox().removeAllItems();
1568             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
1569                     .getRelevantSequenceRelationTypes() ) {
1570                 _sequence_relation_type_box.addItem( type );
1571             }
1572             getMainPanel().getCurrentTreePanel().repaint();
1573             //setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
1574             // according to GUILHEM the line above can be removed.
1575         }
1576     }
1577
1578     /**
1579      * Uncollapse all nodes.
1580      */
1581     void uncollapseAll( final TreePanel tp ) {
1582         final Phylogeny t = tp.getPhylogeny();
1583         if ( ( t != null ) && !t.isEmpty() ) {
1584             for( final PhylogenyNodeIterator iter = t.iteratorPreorder(); iter.hasNext(); ) {
1585                 final PhylogenyNode node = iter.next();
1586                 node.setCollapse( false );
1587             }
1588             tp.resetNodeIdToDistToLeafMap();
1589             tp.updateSetOfCollapsedExternalNodes();
1590             t.recalculateNumberOfExternalDescendants( false );
1591             tp.setNodeInPreorderToNull();
1592             t.clearHashIdToNodeMap();
1593             showWhole();
1594         }
1595     }
1596
1597     void updateDomainStructureEvaluethresholdDisplay() {
1598         if ( _domain_structure_evalue_thr_tf != null ) {
1599             _domain_structure_evalue_thr_tf.setText( "10^"
1600                     + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThreshold() );
1601         }
1602     }
1603
1604     void zoomInX( final float factor, final float x_correction_factor ) {
1605         final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
1606         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1607         treepanel.multiplyUrtFactor( 1f );
1608         if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1609                 || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1610                 || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
1611                 || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
1612             final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1613             treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1614             treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1615             getMainPanel().adjustJScrollPane();
1616             treepanel.resetPreferredSize();
1617             getMainPanel().getCurrentScrollPane().getViewport().validate();
1618             sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1619                     - ( sb.getVisibleAmount() / 2.0 ) ) );
1620         }
1621         else {
1622             final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
1623             treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1624             treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1625             getMainPanel().adjustJScrollPane();
1626             treepanel.resetPreferredSize();
1627             getMainPanel().getCurrentScrollPane().getViewport().validate();
1628             sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
1629         }
1630         treepanel.resetPreferredSize();
1631         treepanel.updateOvSizes();
1632     }
1633
1634     void zoomInY( final float factor ) {
1635         final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
1636         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1637         treepanel.multiplyUrtFactor( 1.1f );
1638         final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1639         treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
1640         getMainPanel().adjustJScrollPane();
1641         treepanel.resetPreferredSize();
1642         getMainPanel().getCurrentScrollPane().getViewport().validate();
1643         sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1644                 - ( sb.getVisibleAmount() / 2.0 ) ) );
1645         treepanel.resetPreferredSize();
1646         treepanel.updateOvSizes();
1647     }
1648
1649     void zoomOutX( final float factor, final float x_correction_factor ) {
1650         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1651         treepanel.multiplyUrtFactor( 1f );
1652         if ( ( treepanel.getXdistance() * factor ) > 0.0 ) {
1653             final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
1654             if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1655                     || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1656                     || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
1657                     || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
1658                 getMainPanel().adjustJScrollPane();
1659                 treepanel.resetPreferredSize();
1660                 getMainPanel().getCurrentScrollPane().getViewport().validate();
1661                 final double x = ( sb.getMaximum() - sb.getMinimum() )
1662                         / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1663                 treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1664                 treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1665                 getMainPanel().adjustJScrollPane();
1666                 treepanel.resetPreferredSize();
1667                 getMainPanel().getCurrentScrollPane().getViewport().validate();
1668                 sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1669                         - ( sb.getVisibleAmount() / 2.0 ) ) );
1670             }
1671             else {
1672                 final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
1673                 treepanel.setXdistance( treepanel.getXdistance() * factor );
1674                 treepanel.setXcorrectionFactor( treepanel.getXcorrectionFactor() * x_correction_factor );
1675                 if ( x > 0 ) {
1676                     getMainPanel().adjustJScrollPane();
1677                     treepanel.resetPreferredSize();
1678                     getMainPanel().getCurrentScrollPane().getViewport().validate();
1679                     sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
1680                 }
1681             }
1682             treepanel.resetPreferredSize();
1683             treepanel.updateOvSizes();
1684         }
1685     }
1686
1687     void zoomOutY( final float factor ) {
1688         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1689         treepanel.multiplyUrtFactor( 0.9f );
1690         if ( ( treepanel.getYdistance() * factor ) > 0.0 ) {
1691             final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
1692             final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1693             treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
1694             getMainPanel().adjustJScrollPane();
1695             treepanel.resetPreferredSize();
1696             getMainPanel().getCurrentScrollPane().getViewport().validate();
1697             sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1698                     - ( sb.getVisibleAmount() / 2.0 ) ) );
1699             treepanel.resetPreferredSize();
1700             treepanel.updateOvSizes();
1701         }
1702     }
1703
1704     private void addClickToOption( final int which, final String title ) {
1705         _click_to_combobox.addItem( title );
1706         _click_to_names.add( title );
1707         _all_click_to_names.put( new Integer( which ), title );
1708         if ( !_configuration.isUseNativeUI() ) {
1709             _click_to_combobox.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
1710             _click_to_combobox.setForeground( getConfiguration().getGuiButtonTextColor() );
1711         }
1712     }
1713
1714     /* GUILHEM_BEG */
1715     private void addSequenceRelationBlock() {
1716         final JLabel spacer = new JLabel( "" );
1717         spacer.setSize( 1, 1 );
1718         add( spacer );
1719         final JLabel mainLabel = new JLabel( "Sequence relations to display" );
1720         final JLabel typeLabel = customizeLabel( new JLabel( "(type) " ), getConfiguration() );
1721         typeLabel.setFont( ControlPanel.js_font.deriveFont( 7 ) );
1722         getSequenceRelationTypeBox().setFocusable( false );
1723         _sequence_relation_type_box.setFont( ControlPanel.js_font );
1724         if ( !_configuration.isUseNativeUI() ) {
1725             _sequence_relation_type_box.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
1726             _sequence_relation_type_box.setForeground( getConfiguration().getGuiButtonTextColor() );
1727         }
1728         _sequence_relation_type_box.setRenderer( new ListCellRenderer() {
1729
1730             @Override
1731             public Component getListCellRendererComponent( final JList list,
1732                                                            final Object value,
1733                                                            final int index,
1734                                                            final boolean isSelected,
1735                                                            final boolean cellHasFocus ) {
1736                 final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
1737                                                                                                         value,
1738                                                                                                         index,
1739                                                                                                         isSelected,
1740                                                                                                         cellHasFocus );
1741                 if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) {
1742                     ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation
1743                             .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) );
1744                 }
1745                 return component;
1746             }
1747         } );
1748         final GridBagLayout gbl = new GridBagLayout();
1749         _sequence_relation_type_box.setMinimumSize( new Dimension( 115, 17 ) );
1750         _sequence_relation_type_box.setPreferredSize( new Dimension( 115, 20 ) );
1751         final JPanel horizGrid = new JPanel( gbl );
1752         horizGrid.setBackground( getBackground() );
1753         horizGrid.add( typeLabel );
1754         horizGrid.add( _sequence_relation_type_box );
1755         add( customizeLabel( mainLabel, getConfiguration() ) );
1756         add( horizGrid );
1757         add( getSequenceRelationBox() );
1758         if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
1759             addCheckbox( Configuration.show_relation_confidence,
1760                          _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
1761             setCheckbox( Configuration.show_relation_confidence,
1762                          _configuration.doCheckOption( Configuration.show_relation_confidence ) );
1763         }
1764     }// addSequenceRelationBlock
1765
1766     /* GUILHEM_END */
1767     private List<Boolean> getIsDrawPhylogramList() {
1768         return _draw_phylogram;
1769     }
1770
1771     private void init() {
1772         _draw_phylogram = new ArrayList<Boolean>();
1773         setSpeciesColors( new HashMap<String, Color>() );
1774         setSequenceColors( new HashMap<String, Color>() );
1775         setAnnotationColors( new HashMap<String, Color>() );
1776     }
1777
1778     private boolean isDrawPhylogram( final int index ) {
1779         return getIsDrawPhylogramList().get( index );
1780     }
1781
1782     private void search0( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
1783         getSearchFoundCountsLabel0().setVisible( true );
1784         getSearchResetButton0().setEnabled( true );
1785         getSearchResetButton0().setVisible( true );
1786         String[] queries = null;
1787         List<PhylogenyNode> nodes = null;
1788         if ( query_str.indexOf( ',' ) >= 0 ) {
1789             queries = query_str.split( ",+" );
1790         }
1791         else {
1792             queries = new String[ 1 ];
1793             queries[ 0 ] = query_str.trim();
1794         }
1795         if ( ( queries != null ) && ( queries.length > 0 ) ) {
1796             nodes = new ArrayList<PhylogenyNode>();
1797             for( String query : queries ) {
1798                 if ( ForesterUtil.isEmpty( query ) ) {
1799                     continue;
1800                 }
1801                 query = query.trim();
1802                 if ( query.indexOf( '+' ) >= 0 ) {
1803                     nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
1804                                                                          tree,
1805                                                                          getOptions().isSearchCaseSensitive(),
1806                                                                          !getOptions().isMatchWholeTermsOnly(),
1807                                                                          isShowDomainArchitectures() ) );
1808                 }
1809                 else {
1810                     nodes.addAll( PhylogenyMethods.searchData( query,
1811                                                                tree,
1812                                                                getOptions().isSearchCaseSensitive(),
1813                                                                !getOptions().isMatchWholeTermsOnly(),
1814                                                                isShowDomainArchitectures() ) );
1815                 }
1816             }
1817             if ( getOptions().isInverseSearchResult() ) {
1818                 final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
1819                 all.removeAll( nodes );
1820                 nodes = all;
1821             }
1822         }
1823         if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
1824             main_panel.getCurrentTreePanel().setFoundNodes0( new HashSet<Long>() );
1825             for( final PhylogenyNode node : nodes ) {
1826                 main_panel.getCurrentTreePanel().getFoundNodes0().add( node.getId() );
1827             }
1828             setSearchFoundCountsOnLabel0( nodes.size() );
1829         }
1830         else {
1831             setSearchFoundCountsOnLabel0( 0 );
1832             searchReset0();
1833         }
1834     }
1835
1836     private void search1( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
1837         getSearchFoundCountsLabel1().setVisible( true );
1838         getSearchResetButton1().setEnabled( true );
1839         getSearchResetButton1().setVisible( true );
1840         String[] queries = null;
1841         List<PhylogenyNode> nodes = null;
1842         if ( query_str.indexOf( ',' ) >= 0 ) {
1843             queries = query_str.split( ",+" );
1844         }
1845         else {
1846             queries = new String[ 1 ];
1847             queries[ 0 ] = query_str.trim();
1848         }
1849         if ( ( queries != null ) && ( queries.length > 0 ) ) {
1850             nodes = new ArrayList<PhylogenyNode>();
1851             for( String query : queries ) {
1852                 if ( ForesterUtil.isEmpty( query ) ) {
1853                     continue;
1854                 }
1855                 query = query.trim();
1856                 if ( query.indexOf( '+' ) >= 0 ) {
1857                     nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
1858                                                                          tree,
1859                                                                          getOptions().isSearchCaseSensitive(),
1860                                                                          !getOptions().isMatchWholeTermsOnly(),
1861                                                                          isShowDomainArchitectures() ) );
1862                 }
1863                 else {
1864                     nodes.addAll( PhylogenyMethods.searchData( query,
1865                                                                tree,
1866                                                                getOptions().isSearchCaseSensitive(),
1867                                                                !getOptions().isMatchWholeTermsOnly(),
1868                                                                isShowDomainArchitectures() ) );
1869                 }
1870             }
1871             if ( getOptions().isInverseSearchResult() ) {
1872                 final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
1873                 all.removeAll( nodes );
1874                 nodes = all;
1875             }
1876         }
1877         if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
1878             main_panel.getCurrentTreePanel().setFoundNodes1( new HashSet<Long>() );
1879             for( final PhylogenyNode node : nodes ) {
1880                 main_panel.getCurrentTreePanel().getFoundNodes1().add( node.getId() );
1881             }
1882             setSearchFoundCountsOnLabel1( nodes.size() );
1883         }
1884         else {
1885             setSearchFoundCountsOnLabel1( 0 );
1886             searchReset1();
1887         }
1888     }
1889
1890     private void setDrawPhylogram( final int index, final boolean b ) {
1891         getIsDrawPhylogramList().set( index, b );
1892     }
1893
1894     private void setupClickToOptions() {
1895         final int default_option = _configuration.getDefaultDisplayClicktoOption();
1896         int selected_index = 0;
1897         int cb_index = 0;
1898         if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
1899             _show_data_item = cb_index;
1900             addClickToOption( Configuration.display_node_data,
1901                               _configuration.getClickToTitle( Configuration.display_node_data ) );
1902             if ( default_option == Configuration.display_node_data ) {
1903                 selected_index = cb_index;
1904             }
1905             cb_index++;
1906         }
1907         if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
1908             _collapse_cb_item = cb_index;
1909             addClickToOption( Configuration.collapse_uncollapse,
1910                               _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
1911             if ( default_option == Configuration.collapse_uncollapse ) {
1912                 selected_index = cb_index;
1913             }
1914             cb_index++;
1915         }
1916         if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
1917             _reroot_cb_item = cb_index;
1918             addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
1919             if ( default_option == Configuration.reroot ) {
1920                 selected_index = cb_index;
1921             }
1922             cb_index++;
1923         }
1924         if ( _configuration.doDisplayClickToOption( Configuration.subtree ) ) {
1925             _subtree_cb_item = cb_index;
1926             addClickToOption( Configuration.subtree, _configuration.getClickToTitle( Configuration.subtree ) );
1927             if ( default_option == Configuration.subtree ) {
1928                 selected_index = cb_index;
1929             }
1930             cb_index++;
1931         }
1932         if ( _configuration.doDisplayClickToOption( Configuration.swap ) ) {
1933             _swap_cb_item = cb_index;
1934             addClickToOption( Configuration.swap, _configuration.getClickToTitle( Configuration.swap ) );
1935             if ( default_option == Configuration.swap ) {
1936                 selected_index = cb_index;
1937             }
1938             cb_index++;
1939         }
1940         if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
1941             _sort_descendents_item = cb_index;
1942             addClickToOption( Configuration.sort_descendents,
1943                               _configuration.getClickToTitle( Configuration.sort_descendents ) );
1944             if ( default_option == Configuration.sort_descendents ) {
1945                 selected_index = cb_index;
1946             }
1947             cb_index++;
1948         }
1949         if ( _configuration.doDisplayClickToOption( Configuration.color_node_font ) ) {
1950             _color_node_font_item = cb_index;
1951             addClickToOption( Configuration.color_node_font,
1952                               _configuration.getClickToTitle( Configuration.color_node_font ) );
1953             if ( default_option == Configuration.color_node_font ) {
1954                 selected_index = cb_index;
1955             }
1956             cb_index++;
1957         }
1958         if ( _configuration.doDisplayClickToOption( Configuration.change_node_font ) ) {
1959             _change_node_font_item = cb_index;
1960             addClickToOption( Configuration.change_node_font,
1961                               _configuration.getClickToTitle( Configuration.change_node_font ) );
1962             if ( default_option == Configuration.change_node_font ) {
1963                 selected_index = cb_index;
1964             }
1965             cb_index++;
1966         }
1967         if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
1968             _color_subtree_cb_item = cb_index;
1969             addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
1970             if ( default_option == Configuration.color_subtree ) {
1971                 selected_index = cb_index;
1972             }
1973             cb_index++;
1974         }
1975         if ( _configuration.doDisplayClickToOption( Configuration.open_seq_web ) ) {
1976             _open_seq_web_item = cb_index;
1977             addClickToOption( Configuration.open_seq_web, _configuration.getClickToTitle( Configuration.open_seq_web ) );
1978             if ( default_option == Configuration.open_seq_web ) {
1979                 selected_index = cb_index;
1980             }
1981             cb_index++;
1982         }
1983         if ( _configuration.doDisplayClickToOption( Configuration.open_pdb_web ) ) {
1984             _open_pdb_item = cb_index;
1985             addClickToOption( Configuration.open_pdb_web, _configuration.getClickToTitle( Configuration.open_pdb_web ) );
1986             if ( default_option == Configuration.open_pdb_web ) {
1987                 selected_index = cb_index;
1988             }
1989             cb_index++;
1990         }
1991         if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
1992             _open_tax_web_item = cb_index;
1993             addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
1994             if ( default_option == Configuration.open_tax_web ) {
1995                 selected_index = cb_index;
1996             }
1997             cb_index++;
1998         }
1999         if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
2000             _blast_item = cb_index;
2001             addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
2002             if ( default_option == Configuration.blast ) {
2003                 selected_index = cb_index;
2004             }
2005             cb_index++;
2006         }
2007         if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) {
2008             _select_nodes_item = cb_index;
2009             addClickToOption( Configuration.select_nodes, _configuration.getClickToTitle( Configuration.select_nodes ) );
2010             if ( default_option == Configuration.select_nodes ) {
2011                 selected_index = cb_index;
2012             }
2013             cb_index++;
2014         }
2015         if ( _configuration.doDisplayClickToOption( Configuration.get_ext_desc_data ) ) {
2016             _get_ext_desc_data = cb_index;
2017             if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) {
2018                 addClickToOption( Configuration.get_ext_desc_data, getConfiguration()
2019                         .getLabelForGetExtDescendentsData() );
2020             }
2021             else {
2022                 String s = ";";
2023                 switch ( getConfiguration().getExtDescNodeDataToReturn() ) {
2024                     case NODE_NAME:
2025                         s = "Node Names";
2026                         break;
2027                     case SEQUENCE_ACC:
2028                         s = "Sequence Accessors";
2029                         break;
2030                     case SEQUENCE_MOL_SEQ:
2031                         s = "Molecular Sequence";
2032                         break;
2033                     case SEQUENCE_MOL_SEQ_FASTA:
2034                         s = "Molecular Sequence (Fasta)";
2035                         break;
2036                     case SEQUENCE_NAME:
2037                         s = "Sequence Names";
2038                         break;
2039                     case GENE_NAME:
2040                         s = "Gene Names";
2041                         break;
2042                     case SEQUENCE_SYMBOL:
2043                         s = "Sequence Symbols";
2044                         break;
2045                     case TAXONOMY_CODE:
2046                         s = "Taxonomy Codes";
2047                         break;
2048                     case TAXONOMY_COMM0N_NAME:
2049                         s = "Taxonomy Common Names";
2050                         break;
2051                     case TAXONOMY_SCIENTIFIC_NAME:
2052                         s = "Scientific Names";
2053                         break;
2054                     case UNKNOWN:
2055                         s = "User Selected Data";
2056                         break;
2057                 }
2058                 final String label = _configuration.getClickToTitle( Configuration.get_ext_desc_data ) + " " + s;
2059                 addClickToOption( Configuration.get_ext_desc_data, label );
2060             }
2061             if ( default_option == Configuration.get_ext_desc_data ) {
2062                 selected_index = cb_index;
2063             }
2064             cb_index++;
2065         }
2066         if ( getOptions().isEditable() ) {
2067             if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
2068                 _cut_subtree_item = cb_index;
2069                 addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
2070                 if ( default_option == Configuration.cut_subtree ) {
2071                     selected_index = cb_index;
2072                 }
2073                 cb_index++;
2074             }
2075             if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
2076                 _copy_subtree_item = cb_index;
2077                 addClickToOption( Configuration.copy_subtree,
2078                                   _configuration.getClickToTitle( Configuration.copy_subtree ) );
2079                 if ( default_option == Configuration.copy_subtree ) {
2080                     selected_index = cb_index;
2081                 }
2082                 cb_index++;
2083             }
2084             if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
2085                 _paste_subtree_item = cb_index;
2086                 addClickToOption( Configuration.paste_subtree,
2087                                   _configuration.getClickToTitle( Configuration.paste_subtree ) );
2088                 if ( default_option == Configuration.paste_subtree ) {
2089                     selected_index = cb_index;
2090                 }
2091                 cb_index++;
2092             }
2093             if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
2094                 _delete_node_or_subtree_item = cb_index;
2095                 addClickToOption( Configuration.delete_subtree_or_node,
2096                                   _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
2097                 if ( default_option == Configuration.delete_subtree_or_node ) {
2098                     selected_index = cb_index;
2099                 }
2100                 cb_index++;
2101             }
2102             if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
2103                 _add_new_node_item = cb_index;
2104                 addClickToOption( Configuration.add_new_node,
2105                                   _configuration.getClickToTitle( Configuration.add_new_node ) );
2106                 if ( default_option == Configuration.add_new_node ) {
2107                     selected_index = cb_index;
2108                 }
2109                 cb_index++;
2110             }
2111             if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
2112                 _edit_node_data_item = cb_index;
2113                 addClickToOption( Configuration.edit_node_data,
2114                                   _configuration.getClickToTitle( Configuration.edit_node_data ) );
2115                 if ( default_option == Configuration.edit_node_data ) {
2116                     selected_index = cb_index;
2117                 }
2118                 cb_index++;
2119             }
2120         }
2121         // Set default selection and its action
2122         _click_to_combobox.setSelectedIndex( selected_index );
2123         setClickToAction( selected_index );
2124     }
2125
2126     private void setupDisplayCheckboxes() {
2127         if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
2128             addCheckbox( Configuration.display_as_phylogram,
2129                          _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
2130             setCheckbox( Configuration.display_as_phylogram,
2131                          _configuration.doCheckOption( Configuration.display_as_phylogram ) );
2132         }
2133         if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
2134             addCheckbox( Configuration.dynamically_hide_data,
2135                          _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
2136             setCheckbox( Configuration.dynamically_hide_data,
2137                          _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
2138         }
2139         if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
2140             addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
2141             setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
2142         }
2143         if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
2144             addCheckbox( Configuration.display_internal_data,
2145                          _configuration.getDisplayTitle( Configuration.display_internal_data ) );
2146             setCheckbox( Configuration.display_internal_data,
2147                          _configuration.doCheckOption( Configuration.display_internal_data ) );
2148         }
2149
2150
2151         if ( _configuration.doDisplayOption( Configuration.color_according_to_sequence ) ) {
2152             addCheckbox( Configuration.color_according_to_sequence,
2153                          _configuration.getDisplayTitle( Configuration.color_according_to_sequence ) );
2154             setCheckbox( Configuration.color_according_to_sequence,
2155                          _configuration.doCheckOption( Configuration.color_according_to_sequence ) );
2156         }
2157
2158
2159
2160
2161         if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
2162             addCheckbox( Configuration.color_according_to_species,
2163                          _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
2164             setCheckbox( Configuration.color_according_to_species,
2165                          _configuration.doCheckOption( Configuration.color_according_to_species ) );
2166         }
2167         if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
2168             addCheckbox( Configuration.color_according_to_annotation,
2169                          _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
2170             setCheckbox( Configuration.color_according_to_annotation,
2171                          _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
2172         }
2173         if ( _configuration.doDisplayOption( Configuration.use_style ) ) {
2174             addCheckbox( Configuration.use_style, _configuration.getDisplayTitle( Configuration.use_style ) );
2175             setCheckbox( Configuration.use_style, _configuration.doCheckOption( Configuration.use_style ) );
2176         }
2177         if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
2178             addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
2179             setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
2180         }
2181         final JLabel label = new JLabel( "Display Data:" );
2182         label.setFont( ControlPanel.jcb_bold_font );
2183         if ( !getConfiguration().isUseNativeUI() ) {
2184             label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
2185         }
2186         add( label );
2187         if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
2188             addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
2189             setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
2190         }
2191         if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
2192             addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
2193             setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
2194         }
2195         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
2196             addCheckbox( Configuration.show_taxonomy_scientific_names,
2197                          _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
2198             setCheckbox( Configuration.show_taxonomy_scientific_names,
2199                          _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
2200         }
2201         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
2202             addCheckbox( Configuration.show_taxonomy_common_names,
2203                          _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
2204             setCheckbox( Configuration.show_taxonomy_common_names,
2205                          _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
2206         }
2207         if ( _configuration.doDisplayOption( Configuration.show_seq_names ) ) {
2208             addCheckbox( Configuration.show_seq_names, _configuration.getDisplayTitle( Configuration.show_seq_names ) );
2209             setCheckbox( Configuration.show_seq_names, _configuration.doCheckOption( Configuration.show_seq_names ) );
2210         }
2211         if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
2212             addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
2213             setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
2214         }
2215         if ( _configuration.doDisplayOption( Configuration.show_seq_symbols ) ) {
2216             addCheckbox( Configuration.show_seq_symbols,
2217                          _configuration.getDisplayTitle( Configuration.show_seq_symbols ) );
2218             setCheckbox( Configuration.show_seq_symbols, _configuration.doCheckOption( Configuration.show_seq_symbols ) );
2219         }
2220         if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
2221             addCheckbox( Configuration.show_sequence_acc,
2222                          _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
2223             setCheckbox( Configuration.show_sequence_acc,
2224                          _configuration.doCheckOption( Configuration.show_sequence_acc ) );
2225         }
2226         if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
2227             addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
2228             setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
2229         }
2230         if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
2231             addCheckbox( Configuration.show_binary_characters,
2232                          _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
2233             setCheckbox( Configuration.show_binary_characters,
2234                          _configuration.doCheckOption( Configuration.show_binary_characters ) );
2235         }
2236         if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
2237             addCheckbox( Configuration.show_binary_character_counts,
2238                          _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
2239             setCheckbox( Configuration.show_binary_character_counts,
2240                          _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
2241         }
2242         if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
2243             addCheckbox( Configuration.show_domain_architectures,
2244                          _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
2245             setCheckbox( Configuration.show_domain_architectures,
2246                          _configuration.doCheckOption( Configuration.show_domain_architectures ) );
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_events ) ) {
2255             addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
2256             setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
2257         }
2258         if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
2259             addCheckbox( Configuration.show_vector_data,
2260                          _configuration.getDisplayTitle( Configuration.show_vector_data ) );
2261             setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
2262         }
2263         if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
2264             addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
2265             setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
2266         }
2267         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
2268             addCheckbox( Configuration.show_taxonomy_images,
2269                          _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
2270             setCheckbox( Configuration.show_taxonomy_images,
2271                          _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
2272         }
2273     }
2274
2275     private void setVisibilityOfDomainStrucureControls() {
2276         if ( _zoom_in_domain_structure != null ) {
2277             if ( isShowDomainArchitectures() ) {
2278                 _domain_display_label.setVisible( true );
2279                 _zoom_in_domain_structure.setVisible( true );
2280                 _zoom_out_domain_structure.setVisible( true );
2281                 _decr_domain_structure_evalue_thr.setVisible( true );
2282                 _incr_domain_structure_evalue_thr.setVisible( true );
2283                 _domain_structure_evalue_thr_tf.setVisible( true );
2284             }
2285             else {
2286                 _domain_display_label.setVisible( false );
2287                 _zoom_in_domain_structure.setVisible( false );
2288                 _zoom_out_domain_structure.setVisible( false );
2289                 _decr_domain_structure_evalue_thr.setVisible( false );
2290                 _incr_domain_structure_evalue_thr.setVisible( false );
2291                 _domain_structure_evalue_thr_tf.setVisible( false );
2292             }
2293         }
2294     }
2295
2296     static JLabel customizeLabel( final JLabel label, final Configuration configuration ) {
2297         label.setFont( ControlPanel.jcb_bold_font );
2298         if ( !configuration.isUseNativeUI() ) {
2299             label.setForeground( configuration.getGuiCheckboxTextColor() );
2300             label.setBackground( configuration.getGuiBackgroundColor() );
2301         }
2302         return label;
2303     }
2304
2305     enum NodeClickAction {
2306         ADD_NEW_NODE,
2307         BLAST,
2308         COLLAPSE,
2309         COLOR_SUBTREE,
2310         COPY_SUBTREE,
2311         CUT_SUBTREE,
2312         DELETE_NODE_OR_SUBTREE,
2313         EDIT_NODE_DATA,
2314         GET_EXT_DESC_DATA,
2315         OPEN_PDB_WEB,
2316         OPEN_SEQ_WEB,
2317         OPEN_TAX_WEB,
2318         PASTE_SUBTREE,
2319         REROOT,
2320         SELECT_NODES,
2321         SHOW_DATA,
2322         SORT_DESCENDENTS,
2323         SUBTREE,
2324         SWAP,
2325         CHANGE_NODE_FONT,
2326         COLOR_NODE_FONT;
2327     }
2328 }