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: www.phylosoft.org/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.PhylogenyNode;
  65 import org.forester.phylogeny.data.Sequence;
  66 import org.forester.phylogeny.data.SequenceRelation;
  67 import org.forester.util.ForesterUtil;
  68
  69 final class ControlPanel extends JPanel implements ActionListener {
  70
  71     private static final String  RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
  72     final static Font            jcb_font                  = new Font( Configuration.getDefaultFontFamilyName(),
  73                                                                        Font.PLAIN,
  74                                                                        9 );
  75     final static Font            js_font                   = new Font( Configuration.getDefaultFontFamilyName(),
  76                                                                        Font.PLAIN,
  77                                                                        9 );
  78     final static Font            jcb_bold_font             = new Font( Configuration.getDefaultFontFamilyName(),
  79                                                                        Font.BOLD,
  80                                                                        9 );
  81     private static final long    serialVersionUID          = -8463483932821545633L;
  82     private final MainPanel      _mainpanel;
  83     // The settings from the conf file
  84     private final Configuration  _configuration;
  85     // Tree checkboxes
  86     private JCheckBox            _display_internal_data;
  87     private JCheckBox            _show_node_names;
  88     private JCheckBox            _show_taxo_code;
  89     private JCheckBox            _write_confidence;
  90     private JCheckBox            _show_events;
  91     private JCheckBox            _color_acc_species;
  92     private JCheckBox            _color_branches_cb;
  93     private JCheckBox            _width_branches;
  94     private JCheckBox            _show_domain_architectures;
  95     private JCheckBox            _show_annotation;
  96     private JCheckBox            _show_binary_characters;
  97     private JCheckBox            _show_binary_character_counts;
  98     private JCheckBox            _show_gene_names;
  99     private JCheckBox            _show_gene_symbols;
 100     private JCheckBox            _show_sequence_acc;
 101     private JCheckBox            _node_desc_popup_cb;
 102     private JCheckBox            _dynamically_hide_data;
 103     private JCheckBox            _show_taxo_scientific_names;
 104     private JCheckBox            _show_taxo_common_names;
 105     private JCheckBox            _show_taxo_images_cb;
 106     private JCheckBox            _color_according_to_annotation;
 107     private JCheckBox            _display_as_phylogram_cb;
 108     private JCheckBox            _seq_relation_confidence_switch;
 109     private JComboBox            _show_sequence_relations;
 110     private JComboBox            _sequence_relation_type_box;
 111     private JCheckBox            _show_vector_data_cb;
 112     private JCheckBox            _show_properties_cb;
 113     private JLabel               _click_to_label;
 114     private JLabel               _zoom_label;
 115     private JLabel               _domain_display_label;
 116     private JComboBox            _click_to_combobox;
 117     private Map<Integer, String> _all_click_to_names;
 118     private List<String>         _click_to_names;
 119     // Indices for the click-to options in the combo box
 120     private int                  _show_data_item;
 121     private int                  _collapse_cb_item;
 122     private int                  _reroot_cb_item;
 123     private int                  _swap_cb_item;
 124     private int                  _subtree_cb_item;
 125     private int                  _color_subtree_cb_item;
 126     private int                  _open_seq_web_item;
 127     private int                  _open_tax_web_item;
 128     private int                  _cut_subtree_item;
 129     private int                  _copy_subtree_item;
 130     private int                  _delete_node_or_subtree_item;
 131     private int                  _paste_subtree_item;
 132     private int                  _add_new_node_item;
 133     private int                  _edit_node_data_item;
 134     private int                  _blast_item;
 135     // zooming and quick tree manipulation buttons:
 136     private JButton              _zoom_in_x;
 137     private JButton              _zoom_in_y;
 138     private JButton              _zoom_out_x;
 139     private JButton              _zoom_out_y;
 140     private JButton              _show_whole;
 141     private JButton              _order;
 142     private JButton              _uncollapse_all;
 143     private JButton              _zoom_in_domain_structure;
 144     private JButton              _zoom_out_domain_structure;
 145     private JButton              _decr_domain_structure_evalue_thr;
 146     private JButton              _incr_domain_structure_evalue_thr;
 147     private JButton              _return_to_super_tree;
 148     private JTextField           _domain_structure_evalue_thr_tf;
 149     private JTextField           _search_tf;
 150     private boolean              _order_of_appearance;
 151     private boolean              _color_branches;
 152     private NodeClickAction      _action_when_node_clicked;
 153     private List<Boolean>        _draw_phylogram;
 154     private Map<String, Color>   _annotation_colors;
 155     private Map<String, Color>   _species_colors;
 156     private JButton              _search_reset_button;
 157     private JLabel               _search_found_label;
 158     private Sequence             _selected_query_seq;
 159
 160     ControlPanel( final MainPanel ap, final Configuration configuration ) {
 161         init();
 162         _mainpanel = ap;
 163         _configuration = configuration;
 164         if ( !_configuration.isUseNativeUI() ) {
 165             setBackground( getConfiguration().getGuiBackgroundColor() );
 166             setBorder( BorderFactory.createRaisedBevelBorder() );
 167         }
 168         setLayout( new GridLayout( 0, 1, 2, 2 ) );
 169         _order_of_appearance = true;
 170         setupControls();
 171     }
 172
 173     /**
 174      * Handle an action.
 175      */
 176     @Override
 177     public void actionPerformed( final ActionEvent e ) {
 178         try {
 179             final TreePanel tp = getMainPanel().getCurrentTreePanel();
 180             if ( tp == null ) {
 181                 return;
 182             }
 183             if ( e.getSource() == _click_to_combobox ) {
 184                 setClickToAction( _click_to_combobox.getSelectedIndex() );
 185                 getCurrentTreePanel().repaint();
 186             }
 187             else if ( e.getSource() == _show_binary_characters ) {
 188                 if ( ( _show_binary_character_counts != null ) && _show_binary_characters.isSelected() ) {
 189                     _show_binary_character_counts.setSelected( false );
 190                 }
 191                 displayedPhylogenyMightHaveChanged( true );
 192             }
 193             else if ( e.getSource() == _show_binary_character_counts ) {
 194                 if ( ( _show_binary_characters != null ) && _show_binary_character_counts.isSelected() ) {
 195                     _show_binary_characters.setSelected( false );
 196                 }
 197                 displayedPhylogenyMightHaveChanged( true );
 198             }
 199             else if ( e.getSource() == _color_according_to_annotation ) {
 200                 if ( ( _show_annotation != null ) && _color_according_to_annotation.isSelected() ) {
 201                     _show_annotation.setSelected( true );
 202                 }
 203                 displayedPhylogenyMightHaveChanged( false );
 204             }
 205             else if ( e.getSource() == _show_annotation ) {
 206                 if ( ( _color_according_to_annotation != null ) && !_show_annotation.isSelected() ) {
 207                     _color_according_to_annotation.setSelected( false );
 208                 }
 209                 displayedPhylogenyMightHaveChanged( false );
 210             }
 211             else if ( ( tp != null ) && ( tp.getPhylogeny() != null ) ) {
 212                 if ( e.getSource() == getDisplayAsPhylogramCb() ) {
 213                     setDrawPhylogram( getDisplayAsPhylogramCb().isSelected() );
 214                     showWhole();
 215                 }
 216                 // Zoom buttons
 217                 else if ( e.getSource() == _zoom_in_x ) {
 218                     zoomInX( Constants.BUTTON_ZOOM_IN_FACTOR, Constants.BUTTON_ZOOM_IN_X_CORRECTION_FACTOR );
 219                     displayedPhylogenyMightHaveChanged( false );
 220                 }
 221                 else if ( e.getSource() == _zoom_in_y ) {
 222                     zoomInY( Constants.BUTTON_ZOOM_IN_FACTOR );
 223                     displayedPhylogenyMightHaveChanged( false );
 224                 }
 225                 else if ( e.getSource() == _zoom_out_x ) {
 226                     zoomOutX( Constants.BUTTON_ZOOM_OUT_FACTOR, Constants.BUTTON_ZOOM_OUT_X_CORRECTION_FACTOR );
 227                     displayedPhylogenyMightHaveChanged( false );
 228                 }
 229                 else if ( e.getSource() == _zoom_out_y ) {
 230                     zoomOutY( Constants.BUTTON_ZOOM_OUT_FACTOR );
 231                     displayedPhylogenyMightHaveChanged( false );
 232                 }
 233                 else if ( e.getSource() == _show_whole ) {
 234                     showWhole();
 235                 }
 236                 else if ( e.getSource() == _return_to_super_tree ) {
 237                     _mainpanel.getCurrentTreePanel().superTree();
 238                     showWhole();
 239                 }
 240                 else if ( e.getSource() == _order ) {
 241                     tp.getPhylogeny().orderAppearance( _order_of_appearance );
 242                     _order_of_appearance = !_order_of_appearance;
 243                     displayedPhylogenyMightHaveChanged( false );
 244                 }
 245                 else if ( e.getSource() == _uncollapse_all ) {
 246                     uncollapseAll( tp );
 247                     displayedPhylogenyMightHaveChanged( false );
 248                 }
 249                 else if ( e.getSource() == _zoom_in_domain_structure ) {
 250                     _mainpanel.getCurrentTreePanel().zoomInDomainStructure();
 251                     displayedPhylogenyMightHaveChanged( true );
 252                 }
 253                 else if ( e.getSource() == _zoom_out_domain_structure ) {
 254                     _mainpanel.getCurrentTreePanel().zoomOutDomainStructure();
 255                     displayedPhylogenyMightHaveChanged( true );
 256                 }
 257                 else if ( e.getSource() == _decr_domain_structure_evalue_thr ) {
 258                     _mainpanel.getCurrentTreePanel().decreaseDomainStructureEvalueThreshold();
 259                     displayedPhylogenyMightHaveChanged( true );
 260                 }
 261                 else if ( e.getSource() == _incr_domain_structure_evalue_thr ) {
 262                     _mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThreshold();
 263                     displayedPhylogenyMightHaveChanged( true );
 264                 }
 265                 else if ( e.getSource() == _search_tf ) {
 266                     search();
 267                     displayedPhylogenyMightHaveChanged( true );
 268                 }
 269                 else {
 270                     displayedPhylogenyMightHaveChanged( true );
 271                 }
 272             }
 273             tp.requestFocus();
 274             tp.requestFocusInWindow();
 275             tp.requestFocus();
 276         }
 277         catch ( final Exception ex ) {
 278             Util.unexpectedException( ex );
 279         }
 280         catch ( final Error err ) {
 281             Util.unexpectedError( err );
 282         }
 283     }
 284
 285     void activateButtonToReturnToSuperTree( int index ) {
 286         --index;
 287         if ( index > 0 ) {
 288             _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT + " " + index );
 289         }
 290         else {
 291             _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
 292         }
 293         _return_to_super_tree.setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
 294         _return_to_super_tree.setEnabled( true );
 295     }
 296
 297     /**
 298      * Add zoom and quick edit buttons. (Last modified 8/9/04)
 299      */
 300     void addButtons() {
 301         final JLabel spacer = new JLabel( "" );
 302         spacer.setOpaque( false );
 303         add( spacer );
 304         final JPanel x_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
 305         final JPanel y_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
 306         final JPanel z_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
 307         if ( !getConfiguration().isUseNativeUI() ) {
 308             x_panel.setBackground( getBackground() );
 309             y_panel.setBackground( getBackground() );
 310             z_panel.setBackground( getBackground() );
 311         }
 312         add( _zoom_label = new JLabel( "Zoom:" ) );
 313         customizeLabel( _zoom_label, getConfiguration() );
 314         add( x_panel );
 315         add( y_panel );
 316         add( z_panel );
 317         if ( getConfiguration().isUseNativeUI() ) {
 318             _zoom_in_x = new JButton( "+" );
 319             _zoom_out_x = new JButton( "-" );
 320         }
 321         else {
 322             _zoom_in_x = new JButton( "X+" );
 323             _zoom_out_x = new JButton( "X-" );
 324         }
 325         _zoom_in_y = new JButton( "Y+" );
 326         _zoom_out_y = new JButton( "Y-" );
 327         _show_whole = new JButton( "F" );
 328         _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [Backspace]" );
 329         _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+Right]" );
 330         _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+Up]" );
 331         _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+Left]" );
 332         _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+Down]" );
 333         if ( getConfiguration().isUseNativeUI() && Util.isMac() ) {
 334             _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
 335             _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );
 336         }
 337         else {
 338             _zoom_out_x.setPreferredSize( new Dimension( 10, 10 ) );
 339             _zoom_in_x.setPreferredSize( new Dimension( 10, 10 ) );
 340         }
 341         _zoom_out_y.setPreferredSize( new Dimension( 10, 10 ) );
 342         _zoom_in_y.setPreferredSize( new Dimension( 10, 10 ) );
 343         _show_whole.setPreferredSize( new Dimension( 10, 10 ) );
 344         _return_to_super_tree = new JButton( RETURN_TO_SUPER_TREE_TEXT );
 345         _return_to_super_tree.setEnabled( false );
 346         _order = new JButton( "Order Subtrees" );
 347         _uncollapse_all = new JButton( "Uncollapse All" );
 348         addJButton( _zoom_in_y, x_panel );
 349         addJButton( _zoom_out_x, y_panel );
 350         addJButton( _show_whole, y_panel );
 351         addJButton( _zoom_in_x, y_panel );
 352         addJButton( _zoom_out_y, z_panel );
 353         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 354             setUpControlsForDomainStrucures();
 355         }
 356         final JLabel spacer2 = new JLabel( "" );
 357         add( spacer2 );
 358         addJButton( _return_to_super_tree, this );
 359         addJButton( _order, this );
 360         addJButton( _uncollapse_all, this );
 361         final JLabel spacer3 = new JLabel( "" );
 362         add( spacer3 );
 363         setVisibilityOfDomainStrucureControls();
 364     }
 365
 366     void addCheckbox( final int which, final String title ) {
 367         final JPanel ch_panel = new JPanel( new BorderLayout( 0, 0 ) );
 368         switch ( which ) {
 369             case Configuration.display_as_phylogram:
 370                 _display_as_phylogram_cb = new JCheckBox( title );
 371                 getDisplayAsPhylogramCb().setToolTipText( "To switch between phylogram and cladogram display" );
 372                 addJCheckBox( getDisplayAsPhylogramCb(), ch_panel );
 373                 add( ch_panel );
 374                 break;
 375             case Configuration.display_internal_data:
 376                 _display_internal_data = new JCheckBox( title );
 377                 _display_internal_data.setToolTipText( "To allow or disallow display of internal labels" );
 378                 addJCheckBox( _display_internal_data, ch_panel );
 379                 add( ch_panel );
 380                 break;
 381             case Configuration.color_according_to_species:
 382                 _color_acc_species = new JCheckBox( title );
 383                 _color_acc_species
 384                         .setToolTipText( "To colorize taxonomy and sequence labels as a function of taxonomy" );
 385                 addJCheckBox( _color_acc_species, ch_panel );
 386                 add( ch_panel );
 387                 break;
 388             case Configuration.color_according_to_annotation:
 389                 _color_according_to_annotation = new JCheckBox( title );
 390                 _color_according_to_annotation
 391                         .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" );
 392                 addJCheckBox( _color_according_to_annotation, ch_panel );
 393                 add( ch_panel );
 394                 break;
 395             case Configuration.show_node_names:
 396                 _show_node_names = new JCheckBox( title );
 397                 addJCheckBox( _show_node_names, ch_panel );
 398                 add( ch_panel );
 399                 break;
 400             case Configuration.show_taxonomy_scientific_names:
 401                 _show_taxo_scientific_names = new JCheckBox( title );
 402                 addJCheckBox( _show_taxo_scientific_names, ch_panel );
 403                 add( ch_panel );
 404                 break;
 405             case Configuration.show_taxonomy_common_names:
 406                 _show_taxo_common_names = new JCheckBox( title );
 407                 addJCheckBox( _show_taxo_common_names, ch_panel );
 408                 add( ch_panel );
 409                 break;
 410             case Configuration.show_tax_code:
 411                 _show_taxo_code = new JCheckBox( title );
 412                 addJCheckBox( _show_taxo_code, ch_panel );
 413                 add( ch_panel );
 414                 break;
 415             case Configuration.show_taxonomy_images:
 416                 _show_taxo_images_cb = new JCheckBox( title );
 417                 addJCheckBox( _show_taxo_images_cb, ch_panel );
 418                 add( ch_panel );
 419                 break;
 420             case Configuration.show_binary_characters:
 421                 _show_binary_characters = new JCheckBox( title );
 422                 addJCheckBox( _show_binary_characters, ch_panel );
 423                 add( ch_panel );
 424                 break;
 425             case Configuration.show_annotation:
 426                 _show_annotation = new JCheckBox( title );
 427                 addJCheckBox( _show_annotation, ch_panel );
 428                 add( ch_panel );
 429                 break;
 430             case Configuration.show_binary_character_counts:
 431                 _show_binary_character_counts = new JCheckBox( title );
 432                 addJCheckBox( _show_binary_character_counts, ch_panel );
 433                 add( ch_panel );
 434                 break;
 435             case Configuration.write_confidence_values:
 436                 _write_confidence = new JCheckBox( title );
 437                 addJCheckBox( getWriteConfidenceCb(), ch_panel );
 438                 add( ch_panel );
 439                 break;
 440             case Configuration.write_events:
 441                 _show_events = new JCheckBox( title );
 442                 addJCheckBox( getShowEventsCb(), ch_panel );
 443                 add( ch_panel );
 444                 break;
 445             case Configuration.color_branches:
 446                 _color_branches_cb = new JCheckBox( title );
 447                 getColorBranchesCb().setToolTipText( "To use branch color values, if present" );
 448                 addJCheckBox( getColorBranchesCb(), ch_panel );
 449                 add( ch_panel );
 450                 break;
 451             case Configuration.width_branches:
 452                 _width_branches = new JCheckBox( title );
 453                 _width_branches.setToolTipText( "To use branch width values, if present" );
 454                 addJCheckBox( _width_branches, ch_panel );
 455                 add( ch_panel );
 456                 break;
 457             case Configuration.show_domain_architectures:
 458                 _show_domain_architectures = new JCheckBox( title );
 459                 addJCheckBox( _show_domain_architectures, ch_panel );
 460                 add( ch_panel );
 461                 break;
 462             case Configuration.show_gene_names:
 463                 _show_gene_names = new JCheckBox( title );
 464                 addJCheckBox( _show_gene_names, ch_panel );
 465                 add( ch_panel );
 466                 break;
 467             case Configuration.show_gene_symbols:
 468                 _show_gene_symbols = new JCheckBox( title );
 469                 addJCheckBox( _show_gene_symbols, ch_panel );
 470                 add( ch_panel );
 471                 break;
 472             case Configuration.show_sequence_acc:
 473                 _show_sequence_acc = new JCheckBox( title );
 474                 addJCheckBox( _show_sequence_acc, ch_panel );
 475                 add( ch_panel );
 476                 break;
 477             case Configuration.dynamically_hide_data:
 478                 _dynamically_hide_data = new JCheckBox( title );
 479                 getDynamicallyHideData().setToolTipText( "To hide labels depending on likely visibility" );
 480                 addJCheckBox( getDynamicallyHideData(), ch_panel );
 481                 add( ch_panel );
 482                 break;
 483             case Configuration.node_data_popup:
 484                 _node_desc_popup_cb = new JCheckBox( title );
 485                 getNodeDescPopupCb().setToolTipText( "To enable mouse rollover display of basic node data" );
 486                 addJCheckBox( getNodeDescPopupCb(), ch_panel );
 487                 add( ch_panel );
 488                 break;
 489             case Configuration.show_relation_confidence:
 490                 _seq_relation_confidence_switch = new JCheckBox( title );
 491                 addJCheckBox( _seq_relation_confidence_switch, ch_panel );
 492                 add( ch_panel );
 493                 break;
 494             case Configuration.show_vector_data:
 495                 _show_vector_data_cb = new JCheckBox( title );
 496                 addJCheckBox( _show_vector_data_cb, ch_panel );
 497                 add( ch_panel );
 498                 break;
 499             case Configuration.show_properties:
 500                 _show_properties_cb = new JCheckBox( title );
 501                 addJCheckBox( _show_properties_cb, ch_panel );
 502                 add( ch_panel );
 503                 break;
 504             default:
 505                 throw new RuntimeException( "unknown checkbox: " + which );
 506         }
 507     }// addCheckbox
 508
 509     private void addClickToOption( final int which, final String title ) {
 510         _click_to_combobox.addItem( title );
 511         _click_to_names.add( title );
 512         _all_click_to_names.put( new Integer( which ), title );
 513         if ( !_configuration.isUseNativeUI() ) {
 514             _click_to_combobox.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 515             _click_to_combobox.setForeground( getConfiguration().getGuiButtonTextColor() );
 516         }
 517     }
 518
 519     void addJButton( final JButton jb, final JPanel p ) {
 520         jb.setFocusPainted( false );
 521         jb.setFont( ControlPanel.jcb_font );
 522         if ( !_configuration.isUseNativeUI() ) {
 523             jb.setBorder( BorderFactory.createLineBorder( getConfiguration().getGuiButtonBorderColor() ) );
 524             jb.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 525             jb.setForeground( getConfiguration().getGuiButtonTextColor() );
 526         }
 527         p.add( jb );
 528         jb.addActionListener( this );
 529     }
 530
 531     void addJCheckBox( final JCheckBox jcb, final JPanel p ) {
 532         jcb.setFocusPainted( false );
 533         jcb.setFont( ControlPanel.jcb_font );
 534         if ( !_configuration.isUseNativeUI() ) {
 535             jcb.setBackground( getConfiguration().getGuiBackgroundColor() );
 536             jcb.setForeground( getConfiguration().getGuiCheckboxTextColor() );
 537         }
 538         p.add( jcb, "Center" );
 539         jcb.addActionListener( this );
 540     }
 541
 542     void addJTextField( final JTextField tf, final JPanel p ) {
 543         if ( !_configuration.isUseNativeUI() ) {
 544             tf.setForeground( getConfiguration().getGuiBackgroundColor() );
 545             tf.setFont( ControlPanel.jcb_font );
 546         }
 547         p.add( tf );
 548         tf.addActionListener( this );
 549     }
 550
 551     /* GUILHEM_BEG */
 552     private void addSequenceRelationBlock() {
 553         final JLabel spacer = new JLabel( "" );
 554         spacer.setSize( 1, 1 );
 555         add( spacer );
 556         final JLabel mainLabel = new JLabel( "Sequence relations to display" );
 557         final JLabel typeLabel = customizeLabel( new JLabel( "(type) " ), getConfiguration() );
 558         typeLabel.setFont( ControlPanel.js_font.deriveFont( 7 ) );
 559         getSequenceRelationTypeBox().setFocusable( false );
 560         _sequence_relation_type_box.setFont( ControlPanel.js_font );
 561         if ( !_configuration.isUseNativeUI() ) {
 562             _sequence_relation_type_box.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 563             _sequence_relation_type_box.setForeground( getConfiguration().getGuiButtonTextColor() );
 564         }
 565         _sequence_relation_type_box.setRenderer( new ListCellRenderer() {
 566
 567             @Override
 568             public Component getListCellRendererComponent( final JList list,
 569                                                            final Object value,
 570                                                            final int index,
 571                                                            final boolean isSelected,
 572                                                            final boolean cellHasFocus ) {
 573                 final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
 574                                                                                                         value,
 575                                                                                                         index,
 576                                                                                                         isSelected,
 577                                                                                                         cellHasFocus );
 578                 if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) {
 579                     ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation
 580                             .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) );
 581                 }
 582                 return component;
 583             }
 584         } );
 585         final GridBagLayout gbl = new GridBagLayout();
 586         _sequence_relation_type_box.setMinimumSize( new Dimension( 115, 17 ) );
 587         _sequence_relation_type_box.setPreferredSize( new Dimension( 115, 20 ) );
 588         final JPanel horizGrid = new JPanel( gbl );
 589         horizGrid.setBackground( getBackground() );
 590         horizGrid.add( typeLabel );
 591         horizGrid.add( _sequence_relation_type_box );
 592         add( customizeLabel( mainLabel, getConfiguration() ) );
 593         add( horizGrid );
 594         add( getSequenceRelationBox() );
 595         if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
 596             addCheckbox( Configuration.show_relation_confidence,
 597                          _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
 598             setCheckbox( Configuration.show_relation_confidence,
 599                          _configuration.doCheckOption( Configuration.show_relation_confidence ) );
 600         }
 601     }// addSequenceRelationBlock
 602
 603     void deactivateButtonToReturnToSuperTree() {
 604         _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
 605         _return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
 606         _return_to_super_tree.setEnabled( false );
 607     }
 608
 609     void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
 610         if ( ( _mainpanel != null ) && ( _mainpanel.getCurrentPhylogeny() != null ) ) {
 611             if ( getOptions().isShowOverview() ) {
 612                 _mainpanel.getCurrentTreePanel().updateOvSizes();
 613             }
 614             _mainpanel.getCurrentTreePanel().recalculateMaxDistanceToRoot();
 615             setVisibilityOfDomainStrucureControls();
 616             updateDomainStructureEvaluethresholdDisplay();
 617             _mainpanel.getCurrentTreePanel().calculateScaleDistance();
 618             _mainpanel.getCurrentTreePanel().calcMaxDepth();
 619             _mainpanel.adjustJScrollPane();
 620             if ( recalc_longest_ext_node_info ) {
 621                 _mainpanel.getCurrentTreePanel().initNodeData();
 622                 _mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
 623             }
 624             _mainpanel.getCurrentTreePanel().repaint();
 625             // _mainpanel.getCurrentTreePanel().setUpUrtFactors();
 626         }
 627     }
 628
 629     void endClickToOptions() {
 630         _click_to_combobox.addActionListener( this );
 631     }
 632
 633     /**
 634      * Indicates what action should be execute when a node is clicked
 635      *
 636      * @return the click-on action
 637      */
 638     NodeClickAction getActionWhenNodeClicked() {
 639         return _action_when_node_clicked;
 640     }
 641
 642     Map<Integer, String> getAllClickToItems() {
 643         return _all_click_to_names;
 644     }
 645
 646     Map<String, Color> getAnnotationColors() {
 647         return _annotation_colors;
 648     }
 649
 650     public JCheckBox getColorBranchesCb() {
 651         return _color_branches_cb;
 652     }
 653
 654     public JCheckBox getColorAccSpeciesCb() {
 655         return _color_acc_species;
 656     }
 657
 658     Configuration getConfiguration() {
 659         return _configuration;
 660     }
 661
 662     TreePanel getCurrentTreePanel() {
 663         return getMainPanel().getCurrentTreePanel();
 664     }
 665
 666     public JCheckBox getDisplayAsPhylogramCb() {
 667         return _display_as_phylogram_cb;
 668     }
 669
 670     public JCheckBox getDynamicallyHideData() {
 671         return _dynamically_hide_data;
 672     }
 673
 674     /* GUILHEM_END */
 675     private List<Boolean> getIsDrawPhylogramList() {
 676         return _draw_phylogram;
 677     }
 678
 679     MainPanel getMainPanel() {
 680         return _mainpanel;
 681     }
 682
 683     public JCheckBox getNodeDescPopupCb() {
 684         return _node_desc_popup_cb;
 685     }
 686
 687     Options getOptions() {
 688         return getMainPanel().getOptions();
 689     }
 690
 691     private JLabel getSearchFoundCountsLabel() {
 692         return _search_found_label;
 693     }
 694
 695     private JButton getSearchResetButton() {
 696         return _search_reset_button;
 697     }
 698
 699     JTextField getSearchTextField() {
 700         return _search_tf;
 701     }
 702
 703     public Sequence getSelectedQuerySequence() {
 704         return _selected_query_seq;
 705     }
 706
 707     public JComboBox getSequenceRelationBox() {
 708         if ( _show_sequence_relations == null ) {
 709             _show_sequence_relations = new JComboBox();
 710             _show_sequence_relations.setFocusable( false );
 711             _show_sequence_relations.setMaximumRowCount( 20 );
 712             _show_sequence_relations.setFont( ControlPanel.js_font );
 713             if ( !_configuration.isUseNativeUI() ) {
 714                 _show_sequence_relations.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 715                 _show_sequence_relations.setForeground( getConfiguration().getGuiButtonTextColor() );
 716             }
 717             _show_sequence_relations.addItem( "-----" );
 718             _show_sequence_relations.setToolTipText( "To display orthology information for selected query" );
 719         }
 720         return _show_sequence_relations;
 721     }
 722
 723     /* GUILHEM_BEG */
 724     public JComboBox getSequenceRelationTypeBox() {
 725         if ( _sequence_relation_type_box == null ) {
 726             _sequence_relation_type_box = new JComboBox();
 727             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : SequenceRelation.SEQUENCE_RELATION_TYPE.values() ) {
 728                 _sequence_relation_type_box.addItem( type );
 729             }
 730             _sequence_relation_type_box.addActionListener( new ActionListener() {
 731
 732                 @Override
 733                 public void actionPerformed( final ActionEvent e ) {
 734                     if ( _mainpanel.getCurrentPhylogeny() != null ) {
 735                         setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
 736                     }
 737                 }
 738             } );
 739         }
 740         return _sequence_relation_type_box;
 741     }
 742
 743     public JCheckBox getShowEventsCb() {
 744         return _show_events;
 745     }
 746
 747     List<String> getSingleClickToNames() {
 748         return _click_to_names;
 749     }
 750
 751     Map<String, Color> getSpeciesColors() {
 752         return _species_colors;
 753     }
 754
 755     public JCheckBox getWriteConfidenceCb() {
 756         return _write_confidence;
 757     }
 758
 759     private void init() {
 760         _draw_phylogram = new ArrayList<Boolean>();
 761         setSpeciesColors( new HashMap<String, Color>() );
 762         setAnnotationColors( new HashMap<String, Color>() );
 763     }
 764
 765     boolean isAntialiasScreenText() {
 766         return true;
 767     }
 768
 769     boolean isColorAccordingToAnnotation() {
 770         return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
 771     }
 772
 773     boolean isColorAccordingToTaxonomy() {
 774         return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
 775     }
 776
 777     boolean isColorBranches() {
 778         return ( ( ( getColorBranchesCb() != null ) && getColorBranchesCb().isSelected() ) || ( ( getColorBranchesCb() == null ) && _color_branches ) );
 779     }
 780
 781     boolean isDrawPhylogram() {
 782         return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
 783     }
 784
 785     private boolean isDrawPhylogram( final int index ) {
 786         return getIsDrawPhylogramList().get( index );
 787     }
 788
 789     boolean isDynamicallyHideData() {
 790         return ( ( getDynamicallyHideData() != null ) && getDynamicallyHideData().isSelected() );
 791     }
 792
 793     boolean isEvents() {
 794         return ( ( getShowEventsCb() != null ) && getShowEventsCb().isSelected() );
 795     }
 796
 797     boolean isNodeDescPopup() {
 798         return ( ( getNodeDescPopupCb() != null ) && getNodeDescPopupCb().isSelected() );
 799     }
 800
 801     boolean isShowAnnotation() {
 802         return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
 803     }
 804
 805     boolean isShowBinaryCharacterCounts() {
 806         return ( ( _show_binary_character_counts != null ) && _show_binary_character_counts.isSelected() );
 807     }
 808
 809     boolean isShowBinaryCharacters() {
 810         return ( ( _show_binary_characters != null ) && _show_binary_characters.isSelected() );
 811     }
 812
 813     boolean isShowBootstrapValues() {
 814         return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
 815     }
 816
 817     boolean isShowDomainArchitectures() {
 818         return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
 819     }
 820
 821     boolean isShowGeneNames() {
 822         return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
 823     }
 824
 825     public boolean isShowVectorData() {
 826         return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
 827     }
 828
 829     public boolean isShowProperties() {
 830         return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
 831     }
 832
 833     boolean isShowGeneSymbols() {
 834         return ( ( _show_gene_symbols != null ) && _show_gene_symbols.isSelected() );
 835     }
 836
 837     boolean isShowInternalData() {
 838         return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() );
 839     }
 840
 841     boolean isShowNodeNames() {
 842         return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
 843     }
 844
 845     boolean isShowSequenceAcc() {
 846         return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
 847     }
 848
 849     boolean isShowSequenceRelationConfidence() {
 850         return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
 851     }
 852
 853     boolean isShowSequenceRelations() {
 854         return ( ( _show_sequence_relations != null ) && ( _show_sequence_relations.getSelectedIndex() > 0 ) );
 855     }
 856
 857     boolean isShowTaxonomyCode() {
 858         return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
 859     }
 860
 861     public boolean isShowTaxonomyImages() {
 862         return ( ( _show_taxo_images_cb != null ) && _show_taxo_images_cb.isSelected() );
 863     }
 864
 865     boolean isShowTaxonomyCommonNames() {
 866         return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
 867     }
 868
 869     boolean isShowTaxonomyScientificNames() {
 870         return ( ( _show_taxo_scientific_names != null ) && _show_taxo_scientific_names.isSelected() );
 871     }
 872
 873     boolean isWidthBranches() {
 874         return ( ( _width_branches != null ) && _width_branches.isSelected() );
 875     }
 876
 877     void phylogenyAdded( final Configuration configuration ) {
 878         getIsDrawPhylogramList().add( configuration.isDrawAsPhylogram() );
 879     }
 880
 881     void phylogenyRemoved( final int index ) {
 882         getIsDrawPhylogramList().remove( index );
 883     }
 884
 885     void search() {
 886         final MainPanel main_panel = getMainPanel();
 887         final Phylogeny tree = main_panel.getCurrentPhylogeny();
 888         if ( ( tree == null ) || tree.isEmpty() ) {
 889             return;
 890         }
 891         String query = getSearchTextField().getText();
 892         if ( query != null ) {
 893             query = query.trim();
 894         }
 895         else {
 896             getSearchFoundCountsLabel().setVisible( false );
 897             getSearchResetButton().setEnabled( false );
 898             getSearchResetButton().setVisible( false );
 899             searchReset();
 900         }
 901         if ( !ForesterUtil.isEmpty( query ) ) {
 902             search( main_panel, tree, query );
 903         }
 904         else {
 905             getSearchFoundCountsLabel().setVisible( false );
 906             getSearchResetButton().setEnabled( false );
 907             getSearchResetButton().setVisible( false );
 908             searchReset();
 909         }
 910     }
 911
 912     private void search( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
 913         getSearchFoundCountsLabel().setVisible( true );
 914         getSearchResetButton().setEnabled( true );
 915         getSearchResetButton().setVisible( true );
 916         String[] queries = null;
 917         List<PhylogenyNode> nodes = null;
 918         if ( query_str.indexOf( ',' ) >= 0 ) {
 919             queries = query_str.split( ",+" );
 920         }
 921         else {
 922             queries = new String[ 1 ];
 923             queries[ 0 ] = query_str.trim();
 924         }
 925         if ( ( queries != null ) && ( queries.length > 0 ) ) {
 926             nodes = new ArrayList<PhylogenyNode>();
 927             for( String query : queries ) {
 928                 if ( ForesterUtil.isEmpty( query ) ) {
 929                     continue;
 930                 }
 931                 query = query.trim();
 932                 if ( query.indexOf( '+' ) >= 0 ) {
 933                     nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ), tree, getOptions()
 934                             .isSearchCaseSensitive(), !getOptions().isMatchWholeTermsOnly() ) );
 935                 }
 936                 else {
 937                     nodes.addAll( PhylogenyMethods.searchData( query,
 938                                                                tree,
 939                                                                getOptions().isSearchCaseSensitive(),
 940                                                                !getOptions().isMatchWholeTermsOnly() ) );
 941                 }
 942             }
 943             if ( getOptions().isInverseSearchResult() ) {
 944                 final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
 945                 all.removeAll( nodes );
 946                 nodes = all;
 947             }
 948         }
 949         if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
 950             main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Integer>() );
 951             for( final PhylogenyNode node : nodes ) {
 952                 main_panel.getCurrentTreePanel().getFoundNodes().add( node.getId() );
 953             }
 954             setSearchFoundCountsOnLabel( nodes.size() );
 955         }
 956         else {
 957             setSearchFoundCountsOnLabel( 0 );
 958             searchReset();
 959         }
 960     }
 961
 962     private void searchReset() {
 963         if ( getMainPanel().getCurrentTreePanel() != null ) {
 964             getMainPanel().getCurrentTreePanel().setFoundNodes( null );
 965         }
 966     }
 967
 968     void setActionWhenNodeClicked( final NodeClickAction action ) {
 969         _action_when_node_clicked = action;
 970     }
 971
 972     void setAnnotationColors( final Map<String, Color> annotation_colors ) {
 973         _annotation_colors = annotation_colors;
 974     }
 975
 976     void setCheckbox( final int which, final boolean state ) {
 977         switch ( which ) {
 978             case Configuration.display_as_phylogram:
 979                 if ( getDisplayAsPhylogramCb() != null ) {
 980                     getDisplayAsPhylogramCb().setSelected( state );
 981                 }
 982                 break;
 983             case Configuration.display_internal_data:
 984                 if ( _display_internal_data != null ) {
 985                     _display_internal_data.setSelected( state );
 986                 }
 987                 break;
 988             case Configuration.color_according_to_species:
 989                 if ( _color_acc_species != null ) {
 990                     _color_acc_species.setSelected( state );
 991                 }
 992                 break;
 993             case Configuration.color_according_to_annotation:
 994                 if ( _color_according_to_annotation != null ) {
 995                     _color_according_to_annotation.setSelected( state );
 996                 }
 997                 break;
 998             case Configuration.show_node_names:
 999                 if ( _show_node_names != null ) {
1000                     _show_node_names.setSelected( state );
1001                 }
1002                 break;
1003             case Configuration.show_taxonomy_scientific_names:
1004                 if ( _show_taxo_scientific_names != null ) {
1005                     _show_taxo_scientific_names.setSelected( state );
1006                 }
1007                 break;
1008             case Configuration.show_taxonomy_common_names:
1009                 if ( _show_taxo_common_names != null ) {
1010                     _show_taxo_common_names.setSelected( state );
1011                 }
1012                 break;
1013             case Configuration.show_tax_code:
1014                 if ( _show_taxo_code != null ) {
1015                     _show_taxo_code.setSelected( state );
1016                 }
1017                 break;
1018             case Configuration.show_taxonomy_images:
1019                 if ( _show_taxo_images_cb != null ) {
1020                     _show_taxo_images_cb.setSelected( state );
1021                 }
1022                 break;
1023             case Configuration.show_annotation:
1024                 if ( _show_annotation != null ) {
1025                     _show_annotation.setSelected( state );
1026                 }
1027                 break;
1028             case Configuration.show_binary_characters:
1029                 if ( _show_binary_characters != null ) {
1030                     _show_binary_characters.setSelected( state );
1031                 }
1032                 break;
1033             case Configuration.show_binary_character_counts:
1034                 if ( _show_binary_character_counts != null ) {
1035                     _show_binary_character_counts.setSelected( state );
1036                 }
1037                 break;
1038             case Configuration.write_confidence_values:
1039                 if ( getWriteConfidenceCb() != null ) {
1040                     getWriteConfidenceCb().setSelected( state );
1041                 }
1042                 break;
1043             case Configuration.write_events:
1044                 if ( getShowEventsCb() != null ) {
1045                     getShowEventsCb().setSelected( state );
1046                 }
1047                 break;
1048             case Configuration.color_branches:
1049                 if ( getColorBranchesCb() != null ) {
1050                     getColorBranchesCb().setSelected( state );
1051                 }
1052                 break;
1053             case Configuration.width_branches:
1054                 if ( _width_branches != null ) {
1055                     _width_branches.setSelected( state );
1056                 }
1057                 break;
1058             case Configuration.show_domain_architectures:
1059                 if ( _show_domain_architectures != null ) {
1060                     _show_domain_architectures.setSelected( state );
1061                 }
1062                 break;
1063             case Configuration.show_gene_names:
1064                 if ( _show_gene_names != null ) {
1065                     _show_gene_names.setSelected( state );
1066                 }
1067                 break;
1068             case Configuration.show_gene_symbols:
1069                 if ( _show_gene_symbols != null ) {
1070                     _show_gene_symbols.setSelected( state );
1071                 }
1072                 break;
1073             case Configuration.show_vector_data:
1074                 if ( _show_vector_data_cb != null ) {
1075                     _show_vector_data_cb.setSelected( state );
1076                 }
1077                 break;
1078             case Configuration.show_properties:
1079                 if ( _show_properties_cb != null ) {
1080                     _show_properties_cb.setSelected( state );
1081                 }
1082                 break;
1083             case Configuration.show_sequence_acc:
1084                 if ( _show_sequence_acc != null ) {
1085                     _show_sequence_acc.setSelected( state );
1086                 }
1087                 break;
1088             case Configuration.dynamically_hide_data:
1089                 if ( getDynamicallyHideData() != null ) {
1090                     getDynamicallyHideData().setSelected( state );
1091                 }
1092                 break;
1093             case Configuration.node_data_popup:
1094                 if ( getNodeDescPopupCb() != null ) {
1095                     getNodeDescPopupCb().setSelected( state );
1096                 }
1097                 break;
1098             /* GUILHEM_BEG */
1099             case Configuration.show_relation_confidence:
1100                 if ( _seq_relation_confidence_switch != null ) {
1101                     _seq_relation_confidence_switch.setSelected( state );
1102                 }
1103                 break;
1104             /* GUILHEM_END */
1105             default:
1106                 throw new AssertionError( "unknown checkbox: " + which );
1107         }
1108     }
1109
1110     /**
1111      * Set this checkbox state. Not all checkboxes have been instantiated
1112      * depending on the config.
1113      */
1114     void setCheckbox( final JCheckBox cb, final boolean state ) {
1115         if ( cb != null ) {
1116             cb.setSelected( state );
1117         }
1118     }
1119
1120     void setClickToAction( final int action ) {
1121         // Set click-to action
1122         if ( action == _show_data_item ) {
1123             setActionWhenNodeClicked( NodeClickAction.SHOW_DATA );
1124         }
1125         else if ( action == _collapse_cb_item ) {
1126             setActionWhenNodeClicked( NodeClickAction.COLLAPSE );
1127         }
1128         else if ( action == _reroot_cb_item ) {
1129             setActionWhenNodeClicked( NodeClickAction.REROOT );
1130         }
1131         else if ( action == _subtree_cb_item ) {
1132             setActionWhenNodeClicked( NodeClickAction.SUBTREE );
1133         }
1134         else if ( action == _swap_cb_item ) {
1135             setActionWhenNodeClicked( NodeClickAction.SWAP );
1136         }
1137         else if ( action == _color_subtree_cb_item ) {
1138             setActionWhenNodeClicked( NodeClickAction.COLOR_SUBTREE );
1139         }
1140         else if ( action == _open_seq_web_item ) {
1141             setActionWhenNodeClicked( NodeClickAction.OPEN_SEQ_WEB );
1142         }
1143         else if ( action == _blast_item ) {
1144             if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
1145                 setActionWhenNodeClicked( NodeClickAction.BLAST );
1146             }
1147         }
1148         else if ( action == _open_tax_web_item ) {
1149             setActionWhenNodeClicked( NodeClickAction.OPEN_TAX_WEB );
1150         }
1151         else if ( action == _cut_subtree_item ) {
1152             setActionWhenNodeClicked( NodeClickAction.CUT_SUBTREE );
1153         }
1154         else if ( action == _copy_subtree_item ) {
1155             setActionWhenNodeClicked( NodeClickAction.COPY_SUBTREE );
1156         }
1157         else if ( action == _delete_node_or_subtree_item ) {
1158             setActionWhenNodeClicked( NodeClickAction.DELETE_NODE_OR_SUBTREE );
1159         }
1160         else if ( action == _paste_subtree_item ) {
1161             setActionWhenNodeClicked( NodeClickAction.PASTE_SUBTREE );
1162         }
1163         else if ( action == _add_new_node_item ) {
1164             setActionWhenNodeClicked( NodeClickAction.ADD_NEW_NODE );
1165         }
1166         else if ( action == _edit_node_data_item ) {
1167             setActionWhenNodeClicked( NodeClickAction.EDIT_NODE_DATA );
1168         }
1169         else {
1170             throw new RuntimeException( "unknown action: " + action );
1171         }
1172         // make sure drop down is displaying the correct action
1173         // in case this was called from outside the class
1174         _click_to_combobox.setSelectedIndex( action );
1175     }
1176
1177     void setColorBranches( final boolean color_branches ) {
1178         _color_branches = color_branches;
1179     }
1180
1181     void setDrawPhylogram( final boolean b ) {
1182         getDisplayAsPhylogramCb().setSelected( b );
1183         setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
1184     }
1185
1186     private void setDrawPhylogram( final int index, final boolean b ) {
1187         getIsDrawPhylogramList().set( index, b );
1188     }
1189
1190     void setDrawPhylogramEnabled( final boolean b ) {
1191         getDisplayAsPhylogramCb().setEnabled( b );
1192     }
1193
1194     void setDynamicHidingIsOn( final boolean is_on ) {
1195         //  if ( !_configuration.isUseNativeUI() ) {
1196         if ( is_on ) {
1197             getDynamicallyHideData().setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
1198         }
1199         else {
1200             if ( !_configuration.isUseNativeUI() ) {
1201                 getDynamicallyHideData().setForeground( getConfiguration().getGuiButtonTextColor() );
1202             }
1203             else {
1204                 getDynamicallyHideData().setForeground( Color.BLACK );
1205             }
1206         }
1207         // }
1208     }
1209
1210     private void setSearchFoundCountsOnLabel( final int counts ) {
1211         getSearchFoundCountsLabel().setText( "Found: " + counts );
1212     }
1213
1214     public void setSequenceRelationQueries( final Collection<Sequence> sequenceRelationQueries ) {
1215         final JComboBox box = getSequenceRelationBox();
1216         while ( box.getItemCount() > 1 ) {
1217             box.removeItemAt( 1 );
1218         }
1219         final HashMap<String, Sequence> sequencesByName = new HashMap<String, Sequence>();
1220         final SequenceRelation.SEQUENCE_RELATION_TYPE relationType = ( SequenceRelation.SEQUENCE_RELATION_TYPE ) _sequence_relation_type_box
1221                 .getSelectedItem();
1222         if ( relationType == null ) {
1223             return;
1224         }
1225         final ArrayList<String> sequenceNamesToAdd = new ArrayList<String>();
1226         for( final Sequence seq : sequenceRelationQueries ) {
1227             if ( seq.hasSequenceRelations() ) {
1228                 boolean fFoundForCurrentType = false;
1229                 for( final SequenceRelation sq : seq.getSequenceRelations() ) {
1230                     if ( sq.getType().equals( relationType ) ) {
1231                         fFoundForCurrentType = true;
1232                         break;
1233                     }
1234                 }
1235                 if ( fFoundForCurrentType ) {
1236                     sequenceNamesToAdd.add( seq.getName() );
1237                     sequencesByName.put( seq.getName(), seq );
1238                 }
1239             }
1240         }
1241         // sort sequences by name before adding them to the combo
1242         final String[] sequenceNameArray = sequenceNamesToAdd.toArray( new String[ sequenceNamesToAdd.size() ] );
1243         Arrays.sort( sequenceNameArray, String.CASE_INSENSITIVE_ORDER );
1244         for( final String seqName : sequenceNameArray ) {
1245             box.addItem( seqName );
1246         }
1247         for( final ItemListener oldItemListener : box.getItemListeners() ) {
1248             box.removeItemListener( oldItemListener );
1249         }
1250         box.addItemListener( new ItemListener() {
1251
1252             @Override
1253             public void itemStateChanged( final ItemEvent e ) {
1254                 _selected_query_seq = sequencesByName.get( e.getItem() );
1255                 _mainpanel.getCurrentTreePanel().repaint();
1256             }
1257         } );
1258     }
1259
1260     void setShowEvents( final boolean show_events ) {
1261         if ( getShowEventsCb() == null ) {
1262             _show_events = new JCheckBox( "" );
1263         }
1264         getShowEventsCb().setSelected( show_events );
1265     }
1266
1267     void setSpeciesColors( final Map<String, Color> species_colors ) {
1268         _species_colors = species_colors;
1269     }
1270
1271     private void setupClickToOptions() {
1272         final int default_option = _configuration.getDefaultDisplayClicktoOption();
1273         int selected_index = 0;
1274         int cb_index = 0;
1275         if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
1276             _show_data_item = cb_index;
1277             addClickToOption( Configuration.display_node_data,
1278                               _configuration.getClickToTitle( Configuration.display_node_data ) );
1279             if ( default_option == Configuration.display_node_data ) {
1280                 selected_index = cb_index;
1281             }
1282             cb_index++;
1283         }
1284         if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
1285             _collapse_cb_item = cb_index;
1286             addClickToOption( Configuration.collapse_uncollapse,
1287                               _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
1288             if ( default_option == Configuration.collapse_uncollapse ) {
1289                 selected_index = cb_index;
1290             }
1291             cb_index++;
1292         }
1293         if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
1294             _reroot_cb_item = cb_index;
1295             addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
1296             if ( default_option == Configuration.reroot ) {
1297                 selected_index = cb_index;
1298             }
1299             cb_index++;
1300         }
1301         if ( _configuration.doDisplayClickToOption( Configuration.subtree ) ) {
1302             _subtree_cb_item = cb_index;
1303             addClickToOption( Configuration.subtree, _configuration.getClickToTitle( Configuration.subtree ) );
1304             if ( default_option == Configuration.subtree ) {
1305                 selected_index = cb_index;
1306             }
1307             cb_index++;
1308         }
1309         if ( _configuration.doDisplayClickToOption( Configuration.swap ) ) {
1310             _swap_cb_item = cb_index;
1311             addClickToOption( Configuration.swap, _configuration.getClickToTitle( Configuration.swap ) );
1312             if ( default_option == Configuration.swap ) {
1313                 selected_index = cb_index;
1314             }
1315             cb_index++;
1316         }
1317         if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
1318             _color_subtree_cb_item = cb_index;
1319             addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
1320             if ( default_option == Configuration.color_subtree ) {
1321                 selected_index = cb_index;
1322             }
1323             cb_index++;
1324         }
1325         if ( _configuration.doDisplayClickToOption( Configuration.open_seq_web ) ) {
1326             _open_seq_web_item = cb_index;
1327             addClickToOption( Configuration.open_seq_web, _configuration.getClickToTitle( Configuration.open_seq_web ) );
1328             if ( default_option == Configuration.open_seq_web ) {
1329                 selected_index = cb_index;
1330             }
1331             cb_index++;
1332         }
1333         if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
1334             _open_tax_web_item = cb_index;
1335             addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
1336             if ( default_option == Configuration.open_tax_web ) {
1337                 selected_index = cb_index;
1338             }
1339             cb_index++;
1340         }
1341         if ( getOptions().isEditable() ) {
1342             if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
1343                 _cut_subtree_item = cb_index;
1344                 addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
1345                 if ( default_option == Configuration.cut_subtree ) {
1346                     selected_index = cb_index;
1347                 }
1348                 cb_index++;
1349             }
1350             if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
1351                 _copy_subtree_item = cb_index;
1352                 addClickToOption( Configuration.copy_subtree,
1353                                   _configuration.getClickToTitle( Configuration.copy_subtree ) );
1354                 if ( default_option == Configuration.copy_subtree ) {
1355                     selected_index = cb_index;
1356                 }
1357                 cb_index++;
1358             }
1359             if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
1360                 _paste_subtree_item = cb_index;
1361                 addClickToOption( Configuration.paste_subtree,
1362                                   _configuration.getClickToTitle( Configuration.paste_subtree ) );
1363                 if ( default_option == Configuration.paste_subtree ) {
1364                     selected_index = cb_index;
1365                 }
1366                 cb_index++;
1367             }
1368             if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
1369                 _delete_node_or_subtree_item = cb_index;
1370                 addClickToOption( Configuration.delete_subtree_or_node,
1371                                   _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
1372                 if ( default_option == Configuration.delete_subtree_or_node ) {
1373                     selected_index = cb_index;
1374                 }
1375                 cb_index++;
1376             }
1377             if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
1378                 _add_new_node_item = cb_index;
1379                 addClickToOption( Configuration.add_new_node,
1380                                   _configuration.getClickToTitle( Configuration.add_new_node ) );
1381                 if ( default_option == Configuration.add_new_node ) {
1382                     selected_index = cb_index;
1383                 }
1384                 cb_index++;
1385             }
1386             if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
1387                 _edit_node_data_item = cb_index;
1388                 addClickToOption( Configuration.edit_node_data,
1389                                   _configuration.getClickToTitle( Configuration.edit_node_data ) );
1390                 if ( default_option == Configuration.edit_node_data ) {
1391                     selected_index = cb_index;
1392                 }
1393                 cb_index++;
1394             }
1395             if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
1396                 if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
1397                     _blast_item = cb_index;
1398                     addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
1399                     if ( default_option == Configuration.blast ) {
1400                         selected_index = cb_index;
1401                     }
1402                     cb_index++;
1403                 }
1404             }
1405         }
1406         // Set default selection and its action
1407         _click_to_combobox.setSelectedIndex( selected_index );
1408         setClickToAction( selected_index );
1409     }
1410
1411     /* GUILHEM_END */
1412     /*
1413      * Set up the controls from the config settings. 11/26/05
1414      */
1415     void setupControls() {
1416         // The tree display options:
1417         setupDisplayCheckboxes();
1418         /* GUILHEM_BEG */
1419         // The sequence relation query selection combo-box
1420         if ( _configuration.displaySequenceRelations() ) {
1421             addSequenceRelationBlock();
1422         }
1423         /* GUILHEM_END */
1424         // Click-to options
1425         startClickToOptions();
1426         setupClickToOptions();
1427         endClickToOptions();
1428         // Zoom and quick edit buttons
1429         addButtons();
1430         setupSearchTools();
1431     }
1432
1433     void setUpControlsForDomainStrucures() {
1434         _domain_display_label = new JLabel( "Domain Display:" );
1435         add( customizeLabel( _domain_display_label, getConfiguration() ) );
1436         add( _domain_display_label );
1437         _zoom_in_domain_structure = new JButton( "d+" );
1438         _zoom_out_domain_structure = new JButton( "d-" );
1439         _decr_domain_structure_evalue_thr = new JButton( "-" );
1440         _incr_domain_structure_evalue_thr = new JButton( "+" );
1441         _zoom_in_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
1442         _zoom_out_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
1443         _decr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
1444         _incr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
1445         _incr_domain_structure_evalue_thr.setToolTipText( "Increase the E-value threshold by a factor of 10" );
1446         _decr_domain_structure_evalue_thr.setToolTipText( "Decrease the E-value threshold by a factor of 10" );
1447         _domain_structure_evalue_thr_tf = new JTextField( 3 );
1448         _domain_structure_evalue_thr_tf.setEditable( false );
1449         if ( !getConfiguration().isUseNativeUI() ) {
1450             _domain_structure_evalue_thr_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1451             _domain_structure_evalue_thr_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1452             _domain_structure_evalue_thr_tf.setBorder( null );
1453         }
1454         final JPanel d1_panel = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1455         final JPanel d2_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
1456         if ( !_configuration.isUseNativeUI() ) {
1457             d1_panel.setBackground( getBackground() );
1458             d2_panel.setBackground( getBackground() );
1459         }
1460         add( d1_panel );
1461         add( d2_panel );
1462         addJButton( _zoom_out_domain_structure, d1_panel );
1463         addJButton( _zoom_in_domain_structure, d1_panel );
1464         addJButton( _decr_domain_structure_evalue_thr, d2_panel );
1465         addJTextField( _domain_structure_evalue_thr_tf, d2_panel );
1466         addJButton( _incr_domain_structure_evalue_thr, d2_panel );
1467     }
1468
1469     private void setupDisplayCheckboxes() {
1470         if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
1471             addCheckbox( Configuration.display_as_phylogram,
1472                          _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
1473             setCheckbox( Configuration.display_as_phylogram,
1474                          _configuration.doCheckOption( Configuration.display_as_phylogram ) );
1475         }
1476         if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
1477             addCheckbox( Configuration.dynamically_hide_data,
1478                          _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
1479             setCheckbox( Configuration.dynamically_hide_data,
1480                          _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
1481         }
1482         if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
1483             addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
1484             setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
1485         }
1486         if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
1487             addCheckbox( Configuration.display_internal_data,
1488                          _configuration.getDisplayTitle( Configuration.display_internal_data ) );
1489             setCheckbox( Configuration.display_internal_data,
1490                          _configuration.doCheckOption( Configuration.display_internal_data ) );
1491         }
1492         if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
1493             addCheckbox( Configuration.color_according_to_species,
1494                          _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
1495             setCheckbox( Configuration.color_according_to_species,
1496                          _configuration.doCheckOption( Configuration.color_according_to_species ) );
1497         }
1498         if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
1499             addCheckbox( Configuration.color_according_to_annotation,
1500                          _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
1501             setCheckbox( Configuration.color_according_to_annotation,
1502                          _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
1503         }
1504         if ( _configuration.doDisplayOption( Configuration.color_branches ) ) {
1505             addCheckbox( Configuration.color_branches, _configuration.getDisplayTitle( Configuration.color_branches ) );
1506             setCheckbox( Configuration.color_branches, _configuration.doCheckOption( Configuration.color_branches ) );
1507         }
1508         if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
1509             addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
1510             setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
1511         }
1512         final JLabel label = new JLabel( "Display Data:" );
1513         label.setFont( ControlPanel.jcb_bold_font );
1514         if ( !getConfiguration().isUseNativeUI() ) {
1515             label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1516         }
1517         add( label );
1518         if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
1519             addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
1520             setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
1521         }
1522         if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
1523             addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
1524             setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
1525         }
1526         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
1527             addCheckbox( Configuration.show_taxonomy_scientific_names,
1528                          _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
1529             setCheckbox( Configuration.show_taxonomy_scientific_names,
1530                          _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
1531         }
1532         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
1533             addCheckbox( Configuration.show_taxonomy_common_names,
1534                          _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
1535             setCheckbox( Configuration.show_taxonomy_common_names,
1536                          _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
1537         }
1538         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
1539             addCheckbox( Configuration.show_taxonomy_images,
1540                          _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
1541             setCheckbox( Configuration.show_taxonomy_images,
1542                          _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
1543         }
1544         if ( _configuration.doDisplayOption( Configuration.show_gene_symbols ) ) {
1545             addCheckbox( Configuration.show_gene_symbols,
1546                          _configuration.getDisplayTitle( Configuration.show_gene_symbols ) );
1547             setCheckbox( Configuration.show_gene_symbols,
1548                          _configuration.doCheckOption( Configuration.show_gene_symbols ) );
1549         }
1550         if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
1551             addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
1552             setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
1553         }
1554         if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
1555             addCheckbox( Configuration.show_sequence_acc,
1556                          _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
1557             setCheckbox( Configuration.show_sequence_acc,
1558                          _configuration.doCheckOption( Configuration.show_sequence_acc ) );
1559         }
1560         if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
1561             addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
1562             setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
1563         }
1564         if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
1565             addCheckbox( Configuration.show_binary_characters,
1566                          _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
1567             setCheckbox( Configuration.show_binary_characters,
1568                          _configuration.doCheckOption( Configuration.show_binary_characters ) );
1569         }
1570         if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
1571             addCheckbox( Configuration.show_binary_character_counts,
1572                          _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
1573             setCheckbox( Configuration.show_binary_character_counts,
1574                          _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
1575         }
1576         if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
1577             addCheckbox( Configuration.show_domain_architectures,
1578                          _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
1579             setCheckbox( Configuration.show_domain_architectures,
1580                          _configuration.doCheckOption( Configuration.show_domain_architectures ) );
1581         }
1582         if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
1583             addCheckbox( Configuration.write_confidence_values,
1584                          _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
1585             setCheckbox( Configuration.write_confidence_values,
1586                          _configuration.doCheckOption( Configuration.write_confidence_values ) );
1587         }
1588         if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
1589             addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
1590             setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
1591         }
1592         if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
1593             addCheckbox( Configuration.show_vector_data,
1594                          _configuration.getDisplayTitle( Configuration.show_vector_data ) );
1595             setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
1596         }
1597         if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
1598             addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
1599             setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
1600         }
1601     }
1602
1603     void setupSearchTools() {
1604         final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
1605         final JLabel search_label = new JLabel( "Search:" );
1606         search_label.setFont( ControlPanel.jcb_bold_font );
1607         if ( !getConfiguration().isUseNativeUI() ) {
1608             search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1609         }
1610         add( search_label );
1611         search_label.setToolTipText( tip );
1612         _search_found_label = new JLabel();
1613         getSearchFoundCountsLabel().setVisible( false );
1614         _search_found_label.setFont( ControlPanel.jcb_bold_font );
1615         if ( !getConfiguration().isUseNativeUI() ) {
1616             _search_found_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1617         }
1618         _search_tf = new JTextField( 3 );
1619         _search_tf.setToolTipText( tip );
1620         _search_tf.setEditable( true );
1621         if ( !getConfiguration().isUseNativeUI() ) {
1622             _search_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1623             _search_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1624             _search_tf.setBorder( null );
1625         }
1626         _search_reset_button = new JButton();
1627         getSearchResetButton().setText( "Reset" );
1628         getSearchResetButton().setEnabled( false );
1629         getSearchResetButton().setVisible( false );
1630         final JPanel s_panel_1 = new JPanel( new BorderLayout() );
1631         final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1632         s_panel_1.setBackground( getBackground() );
1633         add( s_panel_1 );
1634         s_panel_2.setBackground( getBackground() );
1635         add( s_panel_2 );
1636         final KeyAdapter key_adapter = new KeyAdapter() {
1637
1638             @Override
1639             public void keyReleased( final KeyEvent key_event ) {
1640                 search();
1641                 displayedPhylogenyMightHaveChanged( true );
1642             }
1643         };
1644         final ActionListener action_listener = new ActionListener() {
1645
1646             @Override
1647             public void actionPerformed( final ActionEvent e ) {
1648                 searchReset();
1649                 setSearchFoundCountsOnLabel( 0 );
1650                 getSearchFoundCountsLabel().setVisible( false );
1651                 getSearchTextField().setText( "" );
1652                 getSearchResetButton().setEnabled( false );
1653                 getSearchResetButton().setVisible( false );
1654                 displayedPhylogenyMightHaveChanged( true );
1655             }
1656         };
1657         _search_reset_button.addActionListener( action_listener );
1658         _search_tf.addKeyListener( key_adapter );
1659         addJTextField( _search_tf, s_panel_1 );
1660         s_panel_2.add( _search_found_label );
1661         addJButton( _search_reset_button, s_panel_2 );
1662     }
1663
1664     private void setVisibilityOfDomainStrucureControls() {
1665         if ( _zoom_in_domain_structure != null ) {
1666             if ( isShowDomainArchitectures() ) {
1667                 _domain_display_label.setVisible( true );
1668                 _zoom_in_domain_structure.setVisible( true );
1669                 _zoom_out_domain_structure.setVisible( true );
1670                 _decr_domain_structure_evalue_thr.setVisible( true );
1671                 _incr_domain_structure_evalue_thr.setVisible( true );
1672                 _domain_structure_evalue_thr_tf.setVisible( true );
1673             }
1674             else {
1675                 _domain_display_label.setVisible( false );
1676                 _zoom_in_domain_structure.setVisible( false );
1677                 _zoom_out_domain_structure.setVisible( false );
1678                 _decr_domain_structure_evalue_thr.setVisible( false );
1679                 _incr_domain_structure_evalue_thr.setVisible( false );
1680                 _domain_structure_evalue_thr_tf.setVisible( false );
1681             }
1682         }
1683     }
1684
1685     /**
1686      * Fit entire tree into window.
1687      */
1688     void showWhole() {
1689         if ( _mainpanel.getCurrentScrollPane() == null ) {
1690             return;
1691         }
1692         displayedPhylogenyMightHaveChanged( false );
1693         _mainpanel.getCurrentTreePanel().updateOvSettings();
1694         _mainpanel.getCurrentTreePanel().validate();
1695         _mainpanel.validate();
1696         _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
1697                                                                    _mainpanel.getSizeOfViewport().height,
1698                                                                    true );
1699         _mainpanel.getCurrentTreePanel().resetPreferredSize();
1700         _mainpanel.adjustJScrollPane();
1701         _mainpanel.getCurrentTreePanel().repaint();
1702         _mainpanel.getCurrentTreePanel().validate();
1703         _mainpanel.validate();
1704         _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
1705                                                                    _mainpanel.getSizeOfViewport().height,
1706                                                                    true );
1707         _mainpanel.getCurrentTreePanel().resetPreferredSize();
1708         _mainpanel.adjustJScrollPane();
1709         _mainpanel.getCurrentTreePanel().repaint();
1710         _mainpanel.getCurrentTreePanel().updateOvSizes();
1711     }
1712
1713     void showWholeAll() {
1714         for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
1715             if ( tree_panel != null ) {
1716                 tree_panel.validate();
1717                 tree_panel.setParametersForPainting( _mainpanel.getSizeOfViewport().width,
1718                                                      _mainpanel.getSizeOfViewport().height,
1719                                                      true );
1720                 tree_panel.resetPreferredSize();
1721                 tree_panel.repaint();
1722             }
1723         }
1724     }
1725
1726     // Create header for click-to combo box.
1727     void startClickToOptions() {
1728         final JLabel spacer = new JLabel( "" );
1729         spacer.setFont( ControlPanel.jcb_font );
1730         add( spacer );
1731         _click_to_label = new JLabel( "Click on Node to:" );
1732         add( customizeLabel( _click_to_label, getConfiguration() ) );
1733         _click_to_combobox = new JComboBox();
1734         _click_to_combobox.setFocusable( false );
1735         _click_to_combobox.setMaximumRowCount( 14 );
1736         _click_to_combobox.setFont( ControlPanel.js_font );
1737         if ( !_configuration.isUseNativeUI() ) {
1738             _click_to_combobox.setBackground( getConfiguration().getGuiBackgroundColor() );
1739         }
1740         // don't add listener until all items are set (or each one will trigger
1741         // an event)
1742         // click_to_list.addActionListener(this);
1743         add( _click_to_combobox );
1744         // Correlates option names to titles
1745         _all_click_to_names = new HashMap<Integer, String>();
1746         _click_to_names = new ArrayList<String>();
1747     }
1748
1749     void tabChanged() {
1750         if ( getMainPanel().getTabbedPane().getTabCount() > 0 ) {
1751             if ( getCurrentTreePanel().isPhyHasBranchLengths()
1752                     && ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1753                 setDrawPhylogramEnabled( true );
1754                 setDrawPhylogram( isDrawPhylogram() );
1755             }
1756             else {
1757                 setDrawPhylogramEnabled( false );
1758                 setDrawPhylogram( false );
1759             }
1760             if ( getMainPanel().getMainFrame() == null ) {
1761                 // Must be "E" applet version.
1762                 final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1763                 e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() );
1764             }
1765             else {
1766                 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel()
1767                         .getPhylogenyGraphicsType() );
1768             }
1769             getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
1770             getMainPanel().getControlPanel().search();
1771             getSequenceRelationTypeBox().removeAllItems();
1772             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
1773                     .getRelevantSequenceRelationTypes() ) {
1774                 _sequence_relation_type_box.addItem( type );
1775             }
1776             //setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
1777             // according to GUILHEM the line above can be removed.
1778         }
1779     }
1780
1781     /**
1782      * Uncollapse all nodes.
1783      */
1784     void uncollapseAll( final TreePanel tp ) {
1785         final Phylogeny t = tp.getPhylogeny();
1786         if ( ( t != null ) && !t.isEmpty() ) {
1787             t.setAllNodesToNotCollapse();
1788             t.recalculateNumberOfExternalDescendants( false );
1789             showWhole();
1790         }
1791     }
1792
1793     void updateDomainStructureEvaluethresholdDisplay() {
1794         if ( _domain_structure_evalue_thr_tf != null ) {
1795             _domain_structure_evalue_thr_tf.setText( "10^"
1796                     + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThreshold() );
1797         }
1798     }
1799
1800     void zoomInX( final float factor, final float x_correction_factor ) {
1801         final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
1802         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1803         treepanel.multiplyUrtFactor( 1f );
1804         if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1805                 || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1806                 || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
1807                 || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
1808             final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1809             treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1810             treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1811             getMainPanel().adjustJScrollPane();
1812             treepanel.resetPreferredSize();
1813             getMainPanel().getCurrentScrollPane().getViewport().validate();
1814             sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1815                     - ( sb.getVisibleAmount() / 2.0 ) ) );
1816         }
1817         else {
1818             final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
1819             treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1820             treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1821             getMainPanel().adjustJScrollPane();
1822             treepanel.resetPreferredSize();
1823             getMainPanel().getCurrentScrollPane().getViewport().validate();
1824             sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
1825         }
1826         treepanel.resetPreferredSize();
1827         treepanel.updateOvSizes();
1828     }
1829
1830     void zoomInY( final float factor ) {
1831         final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
1832         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1833         treepanel.multiplyUrtFactor( 1.1f );
1834         final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1835         treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
1836         getMainPanel().adjustJScrollPane();
1837         treepanel.resetPreferredSize();
1838         getMainPanel().getCurrentScrollPane().getViewport().validate();
1839         sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1840                 - ( sb.getVisibleAmount() / 2.0 ) ) );
1841         treepanel.resetPreferredSize();
1842         treepanel.updateOvSizes();
1843     }
1844
1845     void zoomOutX( final float factor, final float x_correction_factor ) {
1846         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1847         treepanel.multiplyUrtFactor( 1f );
1848         if ( ( treepanel.getXdistance() * factor ) > 0.0 ) {
1849             final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
1850             if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1851                     || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1852                     || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
1853                     || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
1854                 getMainPanel().adjustJScrollPane();
1855                 treepanel.resetPreferredSize();
1856                 getMainPanel().getCurrentScrollPane().getViewport().validate();
1857                 final double x = ( sb.getMaximum() - sb.getMinimum() )
1858                         / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1859                 treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1860                 treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1861                 getMainPanel().adjustJScrollPane();
1862                 treepanel.resetPreferredSize();
1863                 getMainPanel().getCurrentScrollPane().getViewport().validate();
1864                 sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1865                         - ( sb.getVisibleAmount() / 2.0 ) ) );
1866             }
1867             else {
1868                 final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
1869                 treepanel.setXdistance( treepanel.getXdistance() * factor );
1870                 treepanel.setXcorrectionFactor( treepanel.getXcorrectionFactor() * x_correction_factor );
1871                 if ( x > 0 ) {
1872                     getMainPanel().adjustJScrollPane();
1873                     treepanel.resetPreferredSize();
1874                     getMainPanel().getCurrentScrollPane().getViewport().validate();
1875                     sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
1876                 }
1877             }
1878             treepanel.resetPreferredSize();
1879             treepanel.updateOvSizes();
1880         }
1881     }
1882
1883     void zoomOutY( final float factor ) {
1884         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1885         treepanel.multiplyUrtFactor( 0.9f );
1886         if ( ( treepanel.getYdistance() * factor ) > 0.0 ) {
1887             final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
1888             final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1889             treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
1890             getMainPanel().adjustJScrollPane();
1891             treepanel.resetPreferredSize();
1892             getMainPanel().getCurrentScrollPane().getViewport().validate();
1893             sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1894                     - ( sb.getVisibleAmount() / 2.0 ) ) );
1895             treepanel.resetPreferredSize();
1896             treepanel.updateOvSizes();
1897         }
1898     }
1899
1900     static JLabel customizeLabel( final JLabel label, final Configuration configuration ) {
1901         label.setFont( ControlPanel.jcb_bold_font );
1902         if ( !configuration.isUseNativeUI() ) {
1903             label.setForeground( configuration.getGuiCheckboxTextColor() );
1904             label.setBackground( configuration.getGuiBackgroundColor() );
1905         }
1906         return label;
1907     }
1908
1909     enum NodeClickAction {
1910         SHOW_DATA,
1911         COLLAPSE,
1912         REROOT,
1913         SUBTREE,
1914         SWAP,
1915         COLOR_SUBTREE,
1916         OPEN_TAX_WEB,
1917         OPEN_SEQ_WEB,
1918         CUT_SUBTREE,
1919         COPY_SUBTREE,
1920         DELETE_NODE_OR_SUBTREE,
1921         PASTE_SUBTREE,
1922         ADD_NEW_NODE,
1923         EDIT_NODE_DATA,
1924         BLAST;
1925     }
1926 }