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