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.phylogeny.iterators.PhylogenyNodeIterator;
  68 import org.forester.util.ForesterUtil;
  69
  70 final class ControlPanel extends JPanel implements ActionListener {
  71
  72     private static final String  RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
  73     final static Font            jcb_font                  = new Font( Configuration.getDefaultFontFamilyName(),
  74                                                                        Font.PLAIN,
  75                                                                        9 );
  76     final static Font            js_font                   = new Font( Configuration.getDefaultFontFamilyName(),
  77                                                                        Font.PLAIN,
  78                                                                        9 );
  79     final static Font            jcb_bold_font             = new Font( Configuration.getDefaultFontFamilyName(),
  80                                                                        Font.BOLD,
  81                                                                        9 );
  82     private static final long    serialVersionUID          = -8463483932821545633L;
  83     private final MainPanel      _mainpanel;
  84     // The settings from the conf file
  85     private final Configuration  _configuration;
  86     // Tree checkboxes
  87     private JCheckBox            _display_internal_data;
  88     private JCheckBox            _show_node_names;
  89     private JCheckBox            _show_taxo_code;
  90     private JCheckBox            _write_confidence;
  91     private JCheckBox            _show_events;
  92     private JCheckBox            _color_acc_species;
  93     private JCheckBox            _color_branches_cb;
  94     private JCheckBox            _width_branches;
  95     private JCheckBox            _show_domain_architectures;
  96     private JCheckBox            _show_annotation;
  97     private JCheckBox            _show_binary_characters;
  98     private JCheckBox            _show_binary_character_counts;
  99     private JCheckBox            _show_gene_names;
 100     private JCheckBox            _show_gene_symbols;
 101     private JCheckBox            _show_sequence_acc;
 102     private JCheckBox            _node_desc_popup_cb;
 103     private JCheckBox            _dynamically_hide_data;
 104     private JCheckBox            _show_taxo_scientific_names;
 105     private JCheckBox            _show_taxo_common_names;
 106     private JCheckBox            _show_taxo_images_cb;
 107     private JCheckBox            _color_according_to_annotation;
 108     private JCheckBox            _display_as_phylogram_cb;
 109     private JCheckBox            _seq_relation_confidence_switch;
 110     private JComboBox            _show_sequence_relations;
 111     private JComboBox            _sequence_relation_type_box;
 112     private JCheckBox            _show_vector_data_cb;
 113     private JCheckBox            _show_properties_cb;
 114     private JLabel               _click_to_label;
 115     private JLabel               _zoom_label;
 116     private JLabel               _domain_display_label;
 117     private JComboBox            _click_to_combobox;
 118     private Map<Integer, String> _all_click_to_names;
 119     private List<String>         _click_to_names;
 120     // Indices for the click-to options in the combo box
 121     private int                  _show_data_item;
 122     private int                  _collapse_cb_item;
 123     private int                  _reroot_cb_item;
 124     private int                  _swap_cb_item;
 125     private int                  _subtree_cb_item;
 126     private int                  _color_subtree_cb_item;
 127     private int                  _open_seq_web_item;
 128     private int                  _sort_descendents_item;
 129     private int                  _open_tax_web_item;
 130     private int                  _cut_subtree_item;
 131     private int                  _copy_subtree_item;
 132     private int                  _delete_node_or_subtree_item;
 133     private int                  _paste_subtree_item;
 134     private int                  _add_new_node_item;
 135     private int                  _edit_node_data_item;
 136     private int                  _blast_item;
 137     // zooming and quick tree manipulation buttons:
 138     private JButton              _zoom_in_x;
 139     private JButton              _zoom_in_y;
 140     private JButton              _zoom_out_x;
 141     private JButton              _zoom_out_y;
 142     private JButton              _show_whole;
 143     private JButton              _order;
 144     private JButton              _uncollapse_all;
 145     private JButton              _zoom_in_domain_structure;
 146     private JButton              _zoom_out_domain_structure;
 147     private JButton              _decr_domain_structure_evalue_thr;
 148     private JButton              _incr_domain_structure_evalue_thr;
 149     private JButton              _return_to_super_tree;
 150     private JTextField           _domain_structure_evalue_thr_tf;
 151     private JTextField           _search_tf;
 152     private boolean              _order_of_appearance;
 153     private boolean              _color_branches;
 154     private NodeClickAction      _action_when_node_clicked;
 155     private List<Boolean>        _draw_phylogram;
 156     private Map<String, Color>   _annotation_colors;
 157     private Map<String, Color>   _species_colors;
 158     private JButton              _search_reset_button;
 159     private JLabel               _search_found_label;
 160     private Sequence             _selected_query_seq;
 161
 162     ControlPanel( final MainPanel ap, final Configuration configuration ) {
 163         init();
 164         _mainpanel = ap;
 165         _configuration = configuration;
 166         if ( !_configuration.isUseNativeUI() ) {
 167             setBackground( getConfiguration().getGuiBackgroundColor() );
 168             setBorder( BorderFactory.createRaisedBevelBorder() );
 169         }
 170         setLayout( new GridLayout( 0, 1, 2, 2 ) );
 171         _order_of_appearance = true;
 172         setupControls();
 173     }
 174
 175     /**
 176      * Handle an action.
 177      */
 178     @Override
 179     public void actionPerformed( final ActionEvent e ) {
 180         try {
 181             final TreePanel tp = getMainPanel().getCurrentTreePanel();
 182             if ( tp == null ) {
 183                 return;
 184             }
 185             if ( e.getSource() == _click_to_combobox ) {
 186                 setClickToAction( _click_to_combobox.getSelectedIndex() );
 187                 getCurrentTreePanel().repaint();
 188             }
 189             else if ( e.getSource() == _show_binary_characters ) {
 190                 if ( ( _show_binary_character_counts != null ) && _show_binary_characters.isSelected() ) {
 191                     _show_binary_character_counts.setSelected( false );
 192                 }
 193                 displayedPhylogenyMightHaveChanged( true );
 194             }
 195             else if ( e.getSource() == _show_binary_character_counts ) {
 196                 if ( ( _show_binary_characters != null ) && _show_binary_character_counts.isSelected() ) {
 197                     _show_binary_characters.setSelected( false );
 198                 }
 199                 displayedPhylogenyMightHaveChanged( true );
 200             }
 201             else if ( e.getSource() == _color_according_to_annotation ) {
 202                 if ( ( _show_annotation != null ) && _color_according_to_annotation.isSelected() ) {
 203                     _show_annotation.setSelected( true );
 204                 }
 205                 displayedPhylogenyMightHaveChanged( false );
 206             }
 207             else if ( e.getSource() == _show_annotation ) {
 208                 if ( ( _color_according_to_annotation != null ) && !_show_annotation.isSelected() ) {
 209                     _color_according_to_annotation.setSelected( false );
 210                 }
 211                 displayedPhylogenyMightHaveChanged( false );
 212             }
 213             else if ( ( tp != null ) && ( tp.getPhylogeny() != null ) ) {
 214                 if ( e.getSource() == getDisplayAsPhylogramCb() ) {
 215                     setDrawPhylogram( getDisplayAsPhylogramCb().isSelected() );
 216                     showWhole();
 217                 }
 218                 // Zoom buttons
 219                 else if ( e.getSource() == _zoom_in_x ) {
 220                     zoomInX( Constants.BUTTON_ZOOM_IN_FACTOR, Constants.BUTTON_ZOOM_IN_X_CORRECTION_FACTOR );
 221                     displayedPhylogenyMightHaveChanged( false );
 222                 }
 223                 else if ( e.getSource() == _zoom_in_y ) {
 224                     zoomInY( Constants.BUTTON_ZOOM_IN_FACTOR );
 225                     displayedPhylogenyMightHaveChanged( false );
 226                 }
 227                 else if ( e.getSource() == _zoom_out_x ) {
 228                     zoomOutX( Constants.BUTTON_ZOOM_OUT_FACTOR, Constants.BUTTON_ZOOM_OUT_X_CORRECTION_FACTOR );
 229                     displayedPhylogenyMightHaveChanged( false );
 230                 }
 231                 else if ( e.getSource() == _zoom_out_y ) {
 232                     zoomOutY( Constants.BUTTON_ZOOM_OUT_FACTOR );
 233                     displayedPhylogenyMightHaveChanged( false );
 234                 }
 235                 else if ( e.getSource() == _show_whole ) {
 236                     showWhole();
 237                 }
 238                 else if ( e.getSource() == _return_to_super_tree ) {
 239                     _mainpanel.getCurrentTreePanel().superTree();
 240                     showWhole();
 241                 }
 242                 else if ( e.getSource() == _order ) {
 243                     tp.getPhylogeny().orderAppearance( _order_of_appearance );
 244                     _order_of_appearance = !_order_of_appearance;
 245                     displayedPhylogenyMightHaveChanged( false );
 246                 }
 247                 else if ( e.getSource() == _uncollapse_all ) {
 248                     uncollapseAll( tp );
 249                     displayedPhylogenyMightHaveChanged( false );
 250                 }
 251                 else if ( e.getSource() == _zoom_in_domain_structure ) {
 252                     _mainpanel.getCurrentTreePanel().zoomInDomainStructure();
 253                     displayedPhylogenyMightHaveChanged( true );
 254                 }
 255                 else if ( e.getSource() == _zoom_out_domain_structure ) {
 256                     _mainpanel.getCurrentTreePanel().zoomOutDomainStructure();
 257                     displayedPhylogenyMightHaveChanged( true );
 258                 }
 259                 else if ( e.getSource() == _decr_domain_structure_evalue_thr ) {
 260                     _mainpanel.getCurrentTreePanel().decreaseDomainStructureEvalueThreshold();
 261                     displayedPhylogenyMightHaveChanged( true );
 262                 }
 263                 else if ( e.getSource() == _incr_domain_structure_evalue_thr ) {
 264                     _mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThreshold();
 265                     displayedPhylogenyMightHaveChanged( true );
 266                 }
 267                 else if ( e.getSource() == _search_tf ) {
 268                     search();
 269                     displayedPhylogenyMightHaveChanged( true );
 270                 }
 271                 else {
 272                     displayedPhylogenyMightHaveChanged( true );
 273                 }
 274             }
 275             tp.requestFocus();
 276             tp.requestFocusInWindow();
 277             tp.requestFocus();
 278         }
 279         catch ( final Exception ex ) {
 280             AptxUtil.unexpectedException( ex );
 281         }
 282         catch ( final Error err ) {
 283             AptxUtil.unexpectedError( err );
 284         }
 285     }
 286
 287     void activateButtonToReturnToSuperTree( int index ) {
 288         --index;
 289         if ( index > 0 ) {
 290             _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT + " " + index );
 291         }
 292         else {
 293             _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
 294         }
 295         _return_to_super_tree.setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
 296         _return_to_super_tree.setEnabled( true );
 297     }
 298
 299     /**
 300      * Add zoom and quick edit buttons. (Last modified 8/9/04)
 301      */
 302     void addButtons() {
 303         final JLabel spacer = new JLabel( "" );
 304         spacer.setOpaque( false );
 305         add( spacer );
 306         final JPanel x_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
 307         final JPanel y_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
 308         final JPanel z_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
 309         if ( !getConfiguration().isUseNativeUI() ) {
 310             x_panel.setBackground( getBackground() );
 311             y_panel.setBackground( getBackground() );
 312             z_panel.setBackground( getBackground() );
 313         }
 314         add( _zoom_label = new JLabel( "Zoom:" ) );
 315         customizeLabel( _zoom_label, getConfiguration() );
 316         add( x_panel );
 317         add( y_panel );
 318         add( z_panel );
 319         if ( getConfiguration().isUseNativeUI() ) {
 320             _zoom_in_x = new JButton( "+" );
 321             _zoom_out_x = new JButton( "-" );
 322         }
 323         else {
 324             _zoom_in_x = new JButton( "X+" );
 325             _zoom_out_x = new JButton( "X-" );
 326         }
 327         _zoom_in_y = new JButton( "Y+" );
 328         _zoom_out_y = new JButton( "Y-" );
 329         _show_whole = new JButton( "F" );
 330         _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [Backspace]" );
 331         _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+Right]" );
 332         _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+Up]" );
 333         _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+Left]" );
 334         _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+Down]" );
 335         if ( getConfiguration().isUseNativeUI() && AptxUtil.isMac() ) {
 336             _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
 337             _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );
 338         }
 339         else {
 340             _zoom_out_x.setPreferredSize( new Dimension( 10, 10 ) );
 341             _zoom_in_x.setPreferredSize( new Dimension( 10, 10 ) );
 342         }
 343         _zoom_out_y.setPreferredSize( new Dimension( 10, 10 ) );
 344         _zoom_in_y.setPreferredSize( new Dimension( 10, 10 ) );
 345         _show_whole.setPreferredSize( new Dimension( 10, 10 ) );
 346         _return_to_super_tree = new JButton( RETURN_TO_SUPER_TREE_TEXT );
 347         _return_to_super_tree.setEnabled( false );
 348         _order = new JButton( "Order Subtrees" );
 349         _uncollapse_all = new JButton( "Uncollapse All" );
 350         addJButton( _zoom_in_y, x_panel );
 351         addJButton( _zoom_out_x, y_panel );
 352         addJButton( _show_whole, y_panel );
 353         addJButton( _zoom_in_x, y_panel );
 354         addJButton( _zoom_out_y, z_panel );
 355         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 356             setUpControlsForDomainStrucures();
 357         }
 358         final JLabel spacer2 = new JLabel( "" );
 359         add( spacer2 );
 360         addJButton( _return_to_super_tree, this );
 361         addJButton( _order, this );
 362         addJButton( _uncollapse_all, this );
 363         final JLabel spacer3 = new JLabel( "" );
 364         add( spacer3 );
 365         setVisibilityOfDomainStrucureControls();
 366     }
 367
 368     void addCheckbox( final int which, final String title ) {
 369         final JPanel ch_panel = new JPanel( new BorderLayout( 0, 0 ) );
 370         switch ( which ) {
 371             case Configuration.display_as_phylogram:
 372                 _display_as_phylogram_cb = new JCheckBox( title );
 373                 getDisplayAsPhylogramCb().setToolTipText( "To switch between phylogram and cladogram display" );
 374                 addJCheckBox( getDisplayAsPhylogramCb(), ch_panel );
 375                 add( ch_panel );
 376                 break;
 377             case Configuration.display_internal_data:
 378                 _display_internal_data = new JCheckBox( title );
 379                 _display_internal_data.setToolTipText( "To allow or disallow display of internal labels" );
 380                 addJCheckBox( _display_internal_data, ch_panel );
 381                 add( ch_panel );
 382                 break;
 383             case Configuration.color_according_to_species:
 384                 _color_acc_species = new JCheckBox( title );
 385                 _color_acc_species
 386                         .setToolTipText( "To colorize taxonomy and sequence labels as a function of taxonomy" );
 387                 addJCheckBox( _color_acc_species, ch_panel );
 388                 add( ch_panel );
 389                 break;
 390             case Configuration.color_according_to_annotation:
 391                 _color_according_to_annotation = new JCheckBox( title );
 392                 _color_according_to_annotation
 393                         .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" );
 394                 addJCheckBox( _color_according_to_annotation, ch_panel );
 395                 add( ch_panel );
 396                 break;
 397             case Configuration.show_node_names:
 398                 _show_node_names = new JCheckBox( title );
 399                 addJCheckBox( _show_node_names, ch_panel );
 400                 add( ch_panel );
 401                 break;
 402             case Configuration.show_taxonomy_scientific_names:
 403                 _show_taxo_scientific_names = new JCheckBox( title );
 404                 addJCheckBox( _show_taxo_scientific_names, ch_panel );
 405                 add( ch_panel );
 406                 break;
 407             case Configuration.show_taxonomy_common_names:
 408                 _show_taxo_common_names = new JCheckBox( title );
 409                 addJCheckBox( _show_taxo_common_names, ch_panel );
 410                 add( ch_panel );
 411                 break;
 412             case Configuration.show_tax_code:
 413                 _show_taxo_code = new JCheckBox( title );
 414                 addJCheckBox( _show_taxo_code, ch_panel );
 415                 add( ch_panel );
 416                 break;
 417             case Configuration.show_taxonomy_images:
 418                 _show_taxo_images_cb = new JCheckBox( title );
 419                 addJCheckBox( _show_taxo_images_cb, ch_panel );
 420                 add( ch_panel );
 421                 break;
 422             case Configuration.show_binary_characters:
 423                 _show_binary_characters = new JCheckBox( title );
 424                 addJCheckBox( _show_binary_characters, ch_panel );
 425                 add( ch_panel );
 426                 break;
 427             case Configuration.show_annotation:
 428                 _show_annotation = new JCheckBox( title );
 429                 addJCheckBox( _show_annotation, ch_panel );
 430                 add( ch_panel );
 431                 break;
 432             case Configuration.show_binary_character_counts:
 433                 _show_binary_character_counts = new JCheckBox( title );
 434                 addJCheckBox( _show_binary_character_counts, ch_panel );
 435                 add( ch_panel );
 436                 break;
 437             case Configuration.write_confidence_values:
 438                 _write_confidence = new JCheckBox( title );
 439                 addJCheckBox( getWriteConfidenceCb(), ch_panel );
 440                 add( ch_panel );
 441                 break;
 442             case Configuration.write_events:
 443                 _show_events = new JCheckBox( title );
 444                 addJCheckBox( getShowEventsCb(), ch_panel );
 445                 add( ch_panel );
 446                 break;
 447             case Configuration.color_branches:
 448                 _color_branches_cb = new JCheckBox( title );
 449                 getColorBranchesCb().setToolTipText( "To use branch color values, if present" );
 450                 addJCheckBox( getColorBranchesCb(), ch_panel );
 451                 add( ch_panel );
 452                 break;
 453             case Configuration.width_branches:
 454                 _width_branches = new JCheckBox( title );
 455                 _width_branches.setToolTipText( "To use branch width values, if present" );
 456                 addJCheckBox( _width_branches, ch_panel );
 457                 add( ch_panel );
 458                 break;
 459             case Configuration.show_domain_architectures:
 460                 _show_domain_architectures = new JCheckBox( title );
 461                 addJCheckBox( _show_domain_architectures, ch_panel );
 462                 add( ch_panel );
 463                 break;
 464             case Configuration.show_gene_names:
 465                 _show_gene_names = new JCheckBox( title );
 466                 addJCheckBox( _show_gene_names, ch_panel );
 467                 add( ch_panel );
 468                 break;
 469             case Configuration.show_gene_symbols:
 470                 _show_gene_symbols = new JCheckBox( title );
 471                 addJCheckBox( _show_gene_symbols, ch_panel );
 472                 add( ch_panel );
 473                 break;
 474             case Configuration.show_sequence_acc:
 475                 _show_sequence_acc = new JCheckBox( title );
 476                 addJCheckBox( _show_sequence_acc, ch_panel );
 477                 add( ch_panel );
 478                 break;
 479             case Configuration.dynamically_hide_data:
 480                 _dynamically_hide_data = new JCheckBox( title );
 481                 getDynamicallyHideData().setToolTipText( "To hide labels depending on likely visibility" );
 482                 addJCheckBox( getDynamicallyHideData(), ch_panel );
 483                 add( ch_panel );
 484                 break;
 485             case Configuration.node_data_popup:
 486                 _node_desc_popup_cb = new JCheckBox( title );
 487                 getNodeDescPopupCb().setToolTipText( "To enable mouse rollover display of basic node data" );
 488                 addJCheckBox( getNodeDescPopupCb(), ch_panel );
 489                 add( ch_panel );
 490                 break;
 491             case Configuration.show_relation_confidence:
 492                 _seq_relation_confidence_switch = new JCheckBox( title );
 493                 addJCheckBox( _seq_relation_confidence_switch, ch_panel );
 494                 add( ch_panel );
 495                 break;
 496             case Configuration.show_vector_data:
 497                 _show_vector_data_cb = new JCheckBox( title );
 498                 addJCheckBox( _show_vector_data_cb, ch_panel );
 499                 add( ch_panel );
 500                 break;
 501             case Configuration.show_properties:
 502                 _show_properties_cb = new JCheckBox( title );
 503                 addJCheckBox( _show_properties_cb, ch_panel );
 504                 add( ch_panel );
 505                 break;
 506             default:
 507                 throw new RuntimeException( "unknown checkbox: " + which );
 508         }
 509     }// addCheckbox
 510
 511     private void addClickToOption( final int which, final String title ) {
 512         _click_to_combobox.addItem( title );
 513         _click_to_names.add( title );
 514         _all_click_to_names.put( new Integer( which ), title );
 515         if ( !_configuration.isUseNativeUI() ) {
 516             _click_to_combobox.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 517             _click_to_combobox.setForeground( getConfiguration().getGuiButtonTextColor() );
 518         }
 519     }
 520
 521     void addJButton( final JButton jb, final JPanel p ) {
 522         jb.setFocusPainted( false );
 523         jb.setFont( ControlPanel.jcb_font );
 524         if ( !_configuration.isUseNativeUI() ) {
 525             jb.setBorder( BorderFactory.createLineBorder( getConfiguration().getGuiButtonBorderColor() ) );
 526             jb.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 527             jb.setForeground( getConfiguration().getGuiButtonTextColor() );
 528         }
 529         p.add( jb );
 530         jb.addActionListener( this );
 531     }
 532
 533     void addJCheckBox( final JCheckBox jcb, final JPanel p ) {
 534         jcb.setFocusPainted( false );
 535         jcb.setFont( ControlPanel.jcb_font );
 536         if ( !_configuration.isUseNativeUI() ) {
 537             jcb.setBackground( getConfiguration().getGuiBackgroundColor() );
 538             jcb.setForeground( getConfiguration().getGuiCheckboxTextColor() );
 539         }
 540         p.add( jcb, "Center" );
 541         jcb.addActionListener( this );
 542     }
 543
 544     void addJTextField( final JTextField tf, final JPanel p ) {
 545         if ( !_configuration.isUseNativeUI() ) {
 546             tf.setForeground( getConfiguration().getGuiBackgroundColor() );
 547             tf.setFont( ControlPanel.jcb_font );
 548         }
 549         p.add( tf );
 550         tf.addActionListener( this );
 551     }
 552
 553     /* GUILHEM_BEG */
 554     private void addSequenceRelationBlock() {
 555         final JLabel spacer = new JLabel( "" );
 556         spacer.setSize( 1, 1 );
 557         add( spacer );
 558         final JLabel mainLabel = new JLabel( "Sequence relations to display" );
 559         final JLabel typeLabel = customizeLabel( new JLabel( "(type) " ), getConfiguration() );
 560         typeLabel.setFont( ControlPanel.js_font.deriveFont( 7 ) );
 561         getSequenceRelationTypeBox().setFocusable( false );
 562         _sequence_relation_type_box.setFont( ControlPanel.js_font );
 563         if ( !_configuration.isUseNativeUI() ) {
 564             _sequence_relation_type_box.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 565             _sequence_relation_type_box.setForeground( getConfiguration().getGuiButtonTextColor() );
 566         }
 567         _sequence_relation_type_box.setRenderer( new ListCellRenderer() {
 568
 569             @Override
 570             public Component getListCellRendererComponent( final JList list,
 571                                                            final Object value,
 572                                                            final int index,
 573                                                            final boolean isSelected,
 574                                                            final boolean cellHasFocus ) {
 575                 final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
 576                                                                                                         value,
 577                                                                                                         index,
 578                                                                                                         isSelected,
 579                                                                                                         cellHasFocus );
 580                 if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) {
 581                     ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation
 582                             .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) );
 583                 }
 584                 return component;
 585             }
 586         } );
 587         final GridBagLayout gbl = new GridBagLayout();
 588         _sequence_relation_type_box.setMinimumSize( new Dimension( 115, 17 ) );
 589         _sequence_relation_type_box.setPreferredSize( new Dimension( 115, 20 ) );
 590         final JPanel horizGrid = new JPanel( gbl );
 591         horizGrid.setBackground( getBackground() );
 592         horizGrid.add( typeLabel );
 593         horizGrid.add( _sequence_relation_type_box );
 594         add( customizeLabel( mainLabel, getConfiguration() ) );
 595         add( horizGrid );
 596         add( getSequenceRelationBox() );
 597         if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
 598             addCheckbox( Configuration.show_relation_confidence,
 599                          _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
 600             setCheckbox( Configuration.show_relation_confidence,
 601                          _configuration.doCheckOption( Configuration.show_relation_confidence ) );
 602         }
 603     }// addSequenceRelationBlock
 604
 605     void deactivateButtonToReturnToSuperTree() {
 606         _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
 607         _return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
 608         _return_to_super_tree.setEnabled( false );
 609     }
 610
 611     void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
 612         if ( ( _mainpanel != null ) && ( _mainpanel.getCurrentPhylogeny() != null ) ) {
 613             if ( getOptions().isShowOverview() ) {
 614                 _mainpanel.getCurrentTreePanel().updateOvSizes();
 615             }
 616             _mainpanel.getCurrentTreePanel().recalculateMaxDistanceToRoot();
 617             setVisibilityOfDomainStrucureControls();
 618             updateDomainStructureEvaluethresholdDisplay();
 619             _mainpanel.getCurrentTreePanel().calculateScaleDistance();
 620             _mainpanel.getCurrentTreePanel().calcMaxDepth();
 621             _mainpanel.adjustJScrollPane();
 622             if ( recalc_longest_ext_node_info ) {
 623                 _mainpanel.getCurrentTreePanel().initNodeData();
 624                 _mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
 625             }
 626             _mainpanel.getCurrentTreePanel().repaint();
 627             // _mainpanel.getCurrentTreePanel().setUpUrtFactors();
 628         }
 629     }
 630
 631     void endClickToOptions() {
 632         _click_to_combobox.addActionListener( this );
 633     }
 634
 635     /**
 636      * Indicates what action should be execute when a node is clicked
 637      *
 638      * @return the click-on action
 639      */
 640     NodeClickAction getActionWhenNodeClicked() {
 641         return _action_when_node_clicked;
 642     }
 643
 644     Map<Integer, String> getAllClickToItems() {
 645         return _all_click_to_names;
 646     }
 647
 648     Map<String, Color> getAnnotationColors() {
 649         return _annotation_colors;
 650     }
 651
 652     public JCheckBox getColorBranchesCb() {
 653         return _color_branches_cb;
 654     }
 655
 656     public JCheckBox getColorAccSpeciesCb() {
 657         return _color_acc_species;
 658     }
 659
 660     Configuration getConfiguration() {
 661         return _configuration;
 662     }
 663
 664     TreePanel getCurrentTreePanel() {
 665         return getMainPanel().getCurrentTreePanel();
 666     }
 667
 668     public JCheckBox getDisplayAsPhylogramCb() {
 669         return _display_as_phylogram_cb;
 670     }
 671
 672     public JCheckBox getDynamicallyHideData() {
 673         return _dynamically_hide_data;
 674     }
 675
 676     /* GUILHEM_END */
 677     private List<Boolean> getIsDrawPhylogramList() {
 678         return _draw_phylogram;
 679     }
 680
 681     MainPanel getMainPanel() {
 682         return _mainpanel;
 683     }
 684
 685     public JCheckBox getNodeDescPopupCb() {
 686         return _node_desc_popup_cb;
 687     }
 688
 689     Options getOptions() {
 690         return getMainPanel().getOptions();
 691     }
 692
 693     private JLabel getSearchFoundCountsLabel() {
 694         return _search_found_label;
 695     }
 696
 697     private JButton getSearchResetButton() {
 698         return _search_reset_button;
 699     }
 700
 701     JTextField getSearchTextField() {
 702         return _search_tf;
 703     }
 704
 705     public Sequence getSelectedQuerySequence() {
 706         return _selected_query_seq;
 707     }
 708
 709     public JComboBox getSequenceRelationBox() {
 710         if ( _show_sequence_relations == null ) {
 711             _show_sequence_relations = new JComboBox();
 712             _show_sequence_relations.setFocusable( false );
 713             _show_sequence_relations.setMaximumRowCount( 20 );
 714             _show_sequence_relations.setFont( ControlPanel.js_font );
 715             if ( !_configuration.isUseNativeUI() ) {
 716                 _show_sequence_relations.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 717                 _show_sequence_relations.setForeground( getConfiguration().getGuiButtonTextColor() );
 718             }
 719             _show_sequence_relations.addItem( "-----" );
 720             _show_sequence_relations.setToolTipText( "To display orthology information for selected query" );
 721         }
 722         return _show_sequence_relations;
 723     }
 724
 725     /* GUILHEM_BEG */
 726     public JComboBox getSequenceRelationTypeBox() {
 727         if ( _sequence_relation_type_box == null ) {
 728             _sequence_relation_type_box = new JComboBox();
 729             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : SequenceRelation.SEQUENCE_RELATION_TYPE.values() ) {
 730                 _sequence_relation_type_box.addItem( type );
 731             }
 732             _sequence_relation_type_box.addActionListener( new ActionListener() {
 733
 734                 @Override
 735                 public void actionPerformed( final ActionEvent e ) {
 736                     if ( _mainpanel.getCurrentPhylogeny() != null ) {
 737                         setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
 738                     }
 739                 }
 740             } );
 741         }
 742         return _sequence_relation_type_box;
 743     }
 744
 745     public JCheckBox getShowEventsCb() {
 746         return _show_events;
 747     }
 748
 749     List<String> getSingleClickToNames() {
 750         return _click_to_names;
 751     }
 752
 753     Map<String, Color> getSpeciesColors() {
 754         return _species_colors;
 755     }
 756
 757     public JCheckBox getWriteConfidenceCb() {
 758         return _write_confidence;
 759     }
 760
 761     private void init() {
 762         _draw_phylogram = new ArrayList<Boolean>();
 763         setSpeciesColors( new HashMap<String, Color>() );
 764         setAnnotationColors( new HashMap<String, Color>() );
 765     }
 766
 767     boolean isAntialiasScreenText() {
 768         return true;
 769     }
 770
 771     boolean isColorAccordingToAnnotation() {
 772         return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
 773     }
 774
 775     boolean isColorAccordingToTaxonomy() {
 776         return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
 777     }
 778
 779     boolean isColorBranches() {
 780         return ( ( ( getColorBranchesCb() != null ) && getColorBranchesCb().isSelected() ) || ( ( getColorBranchesCb() == null ) && _color_branches ) );
 781     }
 782
 783     boolean isDrawPhylogram() {
 784         return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
 785     }
 786
 787     private boolean isDrawPhylogram( final int index ) {
 788         return getIsDrawPhylogramList().get( index );
 789     }
 790
 791     boolean isDynamicallyHideData() {
 792         return ( ( getDynamicallyHideData() != null ) && getDynamicallyHideData().isSelected() );
 793     }
 794
 795     boolean isEvents() {
 796         return ( ( getShowEventsCb() != null ) && getShowEventsCb().isSelected() );
 797     }
 798
 799     boolean isNodeDescPopup() {
 800         return ( ( getNodeDescPopupCb() != null ) && getNodeDescPopupCb().isSelected() );
 801     }
 802
 803     boolean isShowAnnotation() {
 804         return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
 805     }
 806
 807     boolean isShowBinaryCharacterCounts() {
 808         return ( ( _show_binary_character_counts != null ) && _show_binary_character_counts.isSelected() );
 809     }
 810
 811     boolean isShowBinaryCharacters() {
 812         return ( ( _show_binary_characters != null ) && _show_binary_characters.isSelected() );
 813     }
 814
 815     boolean isShowConfidenceValues() {
 816         return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
 817     }
 818
 819     boolean isShowDomainArchitectures() {
 820         return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
 821     }
 822
 823     boolean isShowGeneNames() {
 824         return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
 825     }
 826
 827     public boolean isShowVectorData() {
 828         return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
 829     }
 830
 831     public boolean isShowProperties() {
 832         return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
 833     }
 834
 835     boolean isShowGeneSymbols() {
 836         return ( ( _show_gene_symbols != null ) && _show_gene_symbols.isSelected() );
 837     }
 838
 839     boolean isShowInternalData() {
 840         return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() );
 841     }
 842
 843     boolean isShowNodeNames() {
 844         return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
 845     }
 846
 847     boolean isShowSequenceAcc() {
 848         return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
 849     }
 850
 851     boolean isShowSequenceRelationConfidence() {
 852         return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
 853     }
 854
 855     boolean isShowSequenceRelations() {
 856         return ( ( _show_sequence_relations != null ) && ( _show_sequence_relations.getSelectedIndex() > 0 ) );
 857     }
 858
 859     boolean isShowTaxonomyCode() {
 860         return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
 861     }
 862
 863     public boolean isShowTaxonomyImages() {
 864         return ( ( _show_taxo_images_cb != null ) && _show_taxo_images_cb.isSelected() );
 865     }
 866
 867     boolean isShowTaxonomyCommonNames() {
 868         return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
 869     }
 870
 871     boolean isShowTaxonomyScientificNames() {
 872         return ( ( _show_taxo_scientific_names != null ) && _show_taxo_scientific_names.isSelected() );
 873     }
 874
 875     boolean isWidthBranches() {
 876         return ( ( _width_branches != null ) && _width_branches.isSelected() );
 877     }
 878
 879     void phylogenyAdded( final Configuration configuration ) {
 880         getIsDrawPhylogramList().add( configuration.isDrawAsPhylogram() );
 881     }
 882
 883     void phylogenyRemoved( final int index ) {
 884         getIsDrawPhylogramList().remove( index );
 885     }
 886
 887     void search() {
 888         final MainPanel main_panel = getMainPanel();
 889         final Phylogeny tree = main_panel.getCurrentPhylogeny();
 890         if ( ( tree == null ) || tree.isEmpty() ) {
 891             return;
 892         }
 893         String query = getSearchTextField().getText();
 894         if ( query != null ) {
 895             query = query.trim();
 896         }
 897         else {
 898             getSearchFoundCountsLabel().setVisible( false );
 899             getSearchResetButton().setEnabled( false );
 900             getSearchResetButton().setVisible( false );
 901             searchReset();
 902         }
 903         if ( !ForesterUtil.isEmpty( query ) ) {
 904             search( main_panel, tree, query );
 905         }
 906         else {
 907             getSearchFoundCountsLabel().setVisible( false );
 908             getSearchResetButton().setEnabled( false );
 909             getSearchResetButton().setVisible( false );
 910             searchReset();
 911         }
 912     }
 913
 914     private void search( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
 915         getSearchFoundCountsLabel().setVisible( true );
 916         getSearchResetButton().setEnabled( true );
 917         getSearchResetButton().setVisible( true );
 918         String[] queries = null;
 919         List<PhylogenyNode> nodes = null;
 920         if ( query_str.indexOf( ',' ) >= 0 ) {
 921             queries = query_str.split( ",+" );
 922         }
 923         else {
 924             queries = new String[ 1 ];
 925             queries[ 0 ] = query_str.trim();
 926         }
 927         if ( ( queries != null ) && ( queries.length > 0 ) ) {
 928             nodes = new ArrayList<PhylogenyNode>();
 929             for( String query : queries ) {
 930                 if ( ForesterUtil.isEmpty( query ) ) {
 931                     continue;
 932                 }
 933                 query = query.trim();
 934                 if ( query.indexOf( '+' ) >= 0 ) {
 935                     nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ), tree, getOptions()
 936                             .isSearchCaseSensitive(), !getOptions().isMatchWholeTermsOnly() ) );
 937                 }
 938                 else {
 939                     nodes.addAll( PhylogenyMethods.searchData( query,
 940                                                                tree,
 941                                                                getOptions().isSearchCaseSensitive(),
 942                                                                !getOptions().isMatchWholeTermsOnly() ) );
 943                 }
 944             }
 945             if ( getOptions().isInverseSearchResult() ) {
 946                 final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
 947                 all.removeAll( nodes );
 948                 nodes = all;
 949             }
 950         }
 951         if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
 952             main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Integer>() );
 953             for( final PhylogenyNode node : nodes ) {
 954                 main_panel.getCurrentTreePanel().getFoundNodes().add( node.getId() );
 955             }
 956             setSearchFoundCountsOnLabel( nodes.size() );
 957         }
 958         else {
 959             setSearchFoundCountsOnLabel( 0 );
 960             searchReset();
 961         }
 962     }
 963
 964     private void searchReset() {
 965         if ( getMainPanel().getCurrentTreePanel() != null ) {
 966             getMainPanel().getCurrentTreePanel().setFoundNodes( null );
 967         }
 968     }
 969
 970     void setActionWhenNodeClicked( final NodeClickAction action ) {
 971         _action_when_node_clicked = action;
 972     }
 973
 974     void setAnnotationColors( final Map<String, Color> annotation_colors ) {
 975         _annotation_colors = annotation_colors;
 976     }
 977
 978     void setCheckbox( final int which, final boolean state ) {
 979         switch ( which ) {
 980             case Configuration.display_as_phylogram:
 981                 if ( getDisplayAsPhylogramCb() != null ) {
 982                     getDisplayAsPhylogramCb().setSelected( state );
 983                 }
 984                 break;
 985             case Configuration.display_internal_data:
 986                 if ( _display_internal_data != null ) {
 987                     _display_internal_data.setSelected( state );
 988                 }
 989                 break;
 990             case Configuration.color_according_to_species:
 991                 if ( _color_acc_species != null ) {
 992                     _color_acc_species.setSelected( state );
 993                 }
 994                 break;
 995             case Configuration.color_according_to_annotation:
 996                 if ( _color_according_to_annotation != null ) {
 997                     _color_according_to_annotation.setSelected( state );
 998                 }
 999                 break;
1000             case Configuration.show_node_names:
1001                 if ( _show_node_names != null ) {
1002                     _show_node_names.setSelected( state );
1003                 }
1004                 break;
1005             case Configuration.show_taxonomy_scientific_names:
1006                 if ( _show_taxo_scientific_names != null ) {
1007                     _show_taxo_scientific_names.setSelected( state );
1008                 }
1009                 break;
1010             case Configuration.show_taxonomy_common_names:
1011                 if ( _show_taxo_common_names != null ) {
1012                     _show_taxo_common_names.setSelected( state );
1013                 }
1014                 break;
1015             case Configuration.show_tax_code:
1016                 if ( _show_taxo_code != null ) {
1017                     _show_taxo_code.setSelected( state );
1018                 }
1019                 break;
1020             case Configuration.show_taxonomy_images:
1021                 if ( _show_taxo_images_cb != null ) {
1022                     _show_taxo_images_cb.setSelected( state );
1023                 }
1024                 break;
1025             case Configuration.show_annotation:
1026                 if ( _show_annotation != null ) {
1027                     _show_annotation.setSelected( state );
1028                 }
1029                 break;
1030             case Configuration.show_binary_characters:
1031                 if ( _show_binary_characters != null ) {
1032                     _show_binary_characters.setSelected( state );
1033                 }
1034                 break;
1035             case Configuration.show_binary_character_counts:
1036                 if ( _show_binary_character_counts != null ) {
1037                     _show_binary_character_counts.setSelected( state );
1038                 }
1039                 break;
1040             case Configuration.write_confidence_values:
1041                 if ( getWriteConfidenceCb() != null ) {
1042                     getWriteConfidenceCb().setSelected( state );
1043                 }
1044                 break;
1045             case Configuration.write_events:
1046                 if ( getShowEventsCb() != null ) {
1047                     getShowEventsCb().setSelected( state );
1048                 }
1049                 break;
1050             case Configuration.color_branches:
1051                 if ( getColorBranchesCb() != null ) {
1052                     getColorBranchesCb().setSelected( state );
1053                 }
1054                 break;
1055             case Configuration.width_branches:
1056                 if ( _width_branches != null ) {
1057                     _width_branches.setSelected( state );
1058                 }
1059                 break;
1060             case Configuration.show_domain_architectures:
1061                 if ( _show_domain_architectures != null ) {
1062                     _show_domain_architectures.setSelected( state );
1063                 }
1064                 break;
1065             case Configuration.show_gene_names:
1066                 if ( _show_gene_names != null ) {
1067                     _show_gene_names.setSelected( state );
1068                 }
1069                 break;
1070             case Configuration.show_gene_symbols:
1071                 if ( _show_gene_symbols != null ) {
1072                     _show_gene_symbols.setSelected( state );
1073                 }
1074                 break;
1075             case Configuration.show_vector_data:
1076                 if ( _show_vector_data_cb != null ) {
1077                     _show_vector_data_cb.setSelected( state );
1078                 }
1079                 break;
1080             case Configuration.show_properties:
1081                 if ( _show_properties_cb != null ) {
1082                     _show_properties_cb.setSelected( state );
1083                 }
1084                 break;
1085             case Configuration.show_sequence_acc:
1086                 if ( _show_sequence_acc != null ) {
1087                     _show_sequence_acc.setSelected( state );
1088                 }
1089                 break;
1090             case Configuration.dynamically_hide_data:
1091                 if ( getDynamicallyHideData() != null ) {
1092                     getDynamicallyHideData().setSelected( state );
1093                 }
1094                 break;
1095             case Configuration.node_data_popup:
1096                 if ( getNodeDescPopupCb() != null ) {
1097                     getNodeDescPopupCb().setSelected( state );
1098                 }
1099                 break;
1100             /* GUILHEM_BEG */
1101             case Configuration.show_relation_confidence:
1102                 if ( _seq_relation_confidence_switch != null ) {
1103                     _seq_relation_confidence_switch.setSelected( state );
1104                 }
1105                 break;
1106             /* GUILHEM_END */
1107             default:
1108                 throw new AssertionError( "unknown checkbox: " + which );
1109         }
1110     }
1111
1112     /**
1113      * Set this checkbox state. Not all checkboxes have been instantiated
1114      * depending on the config.
1115      */
1116     void setCheckbox( final JCheckBox cb, final boolean state ) {
1117         if ( cb != null ) {
1118             cb.setSelected( state );
1119         }
1120     }
1121
1122     void setClickToAction( final int action ) {
1123         // Set click-to action
1124         if ( action == _show_data_item ) {
1125             setActionWhenNodeClicked( NodeClickAction.SHOW_DATA );
1126         }
1127         else if ( action == _collapse_cb_item ) {
1128             setActionWhenNodeClicked( NodeClickAction.COLLAPSE );
1129         }
1130         else if ( action == _reroot_cb_item ) {
1131             setActionWhenNodeClicked( NodeClickAction.REROOT );
1132         }
1133         else if ( action == _subtree_cb_item ) {
1134             setActionWhenNodeClicked( NodeClickAction.SUBTREE );
1135         }
1136         else if ( action == _swap_cb_item ) {
1137             setActionWhenNodeClicked( NodeClickAction.SWAP );
1138         }
1139         else if ( action == _color_subtree_cb_item ) {
1140             setActionWhenNodeClicked( NodeClickAction.COLOR_SUBTREE );
1141         }
1142         else if ( action == _open_seq_web_item ) {
1143             setActionWhenNodeClicked( NodeClickAction.OPEN_SEQ_WEB );
1144         }
1145         else if ( action == _sort_descendents_item ) {
1146             setActionWhenNodeClicked( NodeClickAction.SORT_DESCENDENTS );
1147         }
1148         else if ( action == _blast_item ) {
1149             if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
1150                 setActionWhenNodeClicked( NodeClickAction.BLAST );
1151             }
1152         }
1153         else if ( action == _open_tax_web_item ) {
1154             setActionWhenNodeClicked( NodeClickAction.OPEN_TAX_WEB );
1155         }
1156         else if ( action == _cut_subtree_item ) {
1157             setActionWhenNodeClicked( NodeClickAction.CUT_SUBTREE );
1158         }
1159         else if ( action == _copy_subtree_item ) {
1160             setActionWhenNodeClicked( NodeClickAction.COPY_SUBTREE );
1161         }
1162         else if ( action == _delete_node_or_subtree_item ) {
1163             setActionWhenNodeClicked( NodeClickAction.DELETE_NODE_OR_SUBTREE );
1164         }
1165         else if ( action == _paste_subtree_item ) {
1166             setActionWhenNodeClicked( NodeClickAction.PASTE_SUBTREE );
1167         }
1168         else if ( action == _add_new_node_item ) {
1169             setActionWhenNodeClicked( NodeClickAction.ADD_NEW_NODE );
1170         }
1171         else if ( action == _edit_node_data_item ) {
1172             setActionWhenNodeClicked( NodeClickAction.EDIT_NODE_DATA );
1173         }
1174         else {
1175             throw new RuntimeException( "unknown action: " + action );
1176         }
1177         // make sure drop down is displaying the correct action
1178         // in case this was called from outside the class
1179         _click_to_combobox.setSelectedIndex( action );
1180     }
1181
1182     void setColorBranches( final boolean color_branches ) {
1183         _color_branches = color_branches;
1184     }
1185
1186     void setDrawPhylogram( final boolean b ) {
1187         getDisplayAsPhylogramCb().setSelected( b );
1188         setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
1189     }
1190
1191     private void setDrawPhylogram( final int index, final boolean b ) {
1192         getIsDrawPhylogramList().set( index, b );
1193     }
1194
1195     void setDrawPhylogramEnabled( final boolean b ) {
1196         getDisplayAsPhylogramCb().setEnabled( b );
1197     }
1198
1199     void setDynamicHidingIsOn( final boolean is_on ) {
1200         //  if ( !_configuration.isUseNativeUI() ) {
1201         if ( is_on ) {
1202             getDynamicallyHideData().setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
1203         }
1204         else {
1205             if ( !_configuration.isUseNativeUI() ) {
1206                 getDynamicallyHideData().setForeground( getConfiguration().getGuiButtonTextColor() );
1207             }
1208             else {
1209                 getDynamicallyHideData().setForeground( Color.BLACK );
1210             }
1211         }
1212         // }
1213     }
1214
1215     private void setSearchFoundCountsOnLabel( final int counts ) {
1216         getSearchFoundCountsLabel().setText( "Found: " + counts );
1217     }
1218
1219     public void setSequenceRelationQueries( final Collection<Sequence> sequenceRelationQueries ) {
1220         final JComboBox box = getSequenceRelationBox();
1221         while ( box.getItemCount() > 1 ) {
1222             box.removeItemAt( 1 );
1223         }
1224         final HashMap<String, Sequence> sequencesByName = new HashMap<String, Sequence>();
1225         final SequenceRelation.SEQUENCE_RELATION_TYPE relationType = ( SequenceRelation.SEQUENCE_RELATION_TYPE ) _sequence_relation_type_box
1226                 .getSelectedItem();
1227         if ( relationType == null ) {
1228             return;
1229         }
1230         final ArrayList<String> sequenceNamesToAdd = new ArrayList<String>();
1231         for( final Sequence seq : sequenceRelationQueries ) {
1232             if ( seq.hasSequenceRelations() ) {
1233                 boolean fFoundForCurrentType = false;
1234                 for( final SequenceRelation sq : seq.getSequenceRelations() ) {
1235                     if ( sq.getType().equals( relationType ) ) {
1236                         fFoundForCurrentType = true;
1237                         break;
1238                     }
1239                 }
1240                 if ( fFoundForCurrentType ) {
1241                     sequenceNamesToAdd.add( seq.getName() );
1242                     sequencesByName.put( seq.getName(), seq );
1243                 }
1244             }
1245         }
1246         // sort sequences by name before adding them to the combo
1247         final String[] sequenceNameArray = sequenceNamesToAdd.toArray( new String[ sequenceNamesToAdd.size() ] );
1248         Arrays.sort( sequenceNameArray, String.CASE_INSENSITIVE_ORDER );
1249         for( final String seqName : sequenceNameArray ) {
1250             box.addItem( seqName );
1251         }
1252         for( final ItemListener oldItemListener : box.getItemListeners() ) {
1253             box.removeItemListener( oldItemListener );
1254         }
1255         box.addItemListener( new ItemListener() {
1256
1257             @Override
1258             public void itemStateChanged( final ItemEvent e ) {
1259                 _selected_query_seq = sequencesByName.get( e.getItem() );
1260                 _mainpanel.getCurrentTreePanel().repaint();
1261             }
1262         } );
1263     }
1264
1265     void setShowEvents( final boolean show_events ) {
1266         if ( getShowEventsCb() == null ) {
1267             _show_events = new JCheckBox( "" );
1268         }
1269         getShowEventsCb().setSelected( show_events );
1270     }
1271
1272     void setSpeciesColors( final Map<String, Color> species_colors ) {
1273         _species_colors = species_colors;
1274     }
1275
1276     private void setupClickToOptions() {
1277         final int default_option = _configuration.getDefaultDisplayClicktoOption();
1278         int selected_index = 0;
1279         int cb_index = 0;
1280         if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
1281             _show_data_item = cb_index;
1282             addClickToOption( Configuration.display_node_data,
1283                               _configuration.getClickToTitle( Configuration.display_node_data ) );
1284             if ( default_option == Configuration.display_node_data ) {
1285                 selected_index = cb_index;
1286             }
1287             cb_index++;
1288         }
1289         if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
1290             _collapse_cb_item = cb_index;
1291             addClickToOption( Configuration.collapse_uncollapse,
1292                               _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
1293             if ( default_option == Configuration.collapse_uncollapse ) {
1294                 selected_index = cb_index;
1295             }
1296             cb_index++;
1297         }
1298         if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
1299             _reroot_cb_item = cb_index;
1300             addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
1301             if ( default_option == Configuration.reroot ) {
1302                 selected_index = cb_index;
1303             }
1304             cb_index++;
1305         }
1306         if ( _configuration.doDisplayClickToOption( Configuration.subtree ) ) {
1307             _subtree_cb_item = cb_index;
1308             addClickToOption( Configuration.subtree, _configuration.getClickToTitle( Configuration.subtree ) );
1309             if ( default_option == Configuration.subtree ) {
1310                 selected_index = cb_index;
1311             }
1312             cb_index++;
1313         }
1314         if ( _configuration.doDisplayClickToOption( Configuration.swap ) ) {
1315             _swap_cb_item = cb_index;
1316             addClickToOption( Configuration.swap, _configuration.getClickToTitle( Configuration.swap ) );
1317             if ( default_option == Configuration.swap ) {
1318                 selected_index = cb_index;
1319             }
1320             cb_index++;
1321         }
1322         if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
1323             _sort_descendents_item = cb_index;
1324             addClickToOption( Configuration.sort_descendents,
1325                               _configuration.getClickToTitle( Configuration.sort_descendents ) );
1326             if ( default_option == Configuration.sort_descendents ) {
1327                 selected_index = cb_index;
1328             }
1329             cb_index++;
1330         }
1331         if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
1332             _color_subtree_cb_item = cb_index;
1333             addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
1334             if ( default_option == Configuration.color_subtree ) {
1335                 selected_index = cb_index;
1336             }
1337             cb_index++;
1338         }
1339         if ( _configuration.doDisplayClickToOption( Configuration.open_seq_web ) ) {
1340             _open_seq_web_item = cb_index;
1341             addClickToOption( Configuration.open_seq_web, _configuration.getClickToTitle( Configuration.open_seq_web ) );
1342             if ( default_option == Configuration.open_seq_web ) {
1343                 selected_index = cb_index;
1344             }
1345             cb_index++;
1346         }
1347         if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
1348             _open_tax_web_item = cb_index;
1349             addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
1350             if ( default_option == Configuration.open_tax_web ) {
1351                 selected_index = cb_index;
1352             }
1353             cb_index++;
1354         }
1355         if ( getOptions().isEditable() ) {
1356             if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
1357                 _cut_subtree_item = cb_index;
1358                 addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
1359                 if ( default_option == Configuration.cut_subtree ) {
1360                     selected_index = cb_index;
1361                 }
1362                 cb_index++;
1363             }
1364             if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
1365                 _copy_subtree_item = cb_index;
1366                 addClickToOption( Configuration.copy_subtree,
1367                                   _configuration.getClickToTitle( Configuration.copy_subtree ) );
1368                 if ( default_option == Configuration.copy_subtree ) {
1369                     selected_index = cb_index;
1370                 }
1371                 cb_index++;
1372             }
1373             if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
1374                 _paste_subtree_item = cb_index;
1375                 addClickToOption( Configuration.paste_subtree,
1376                                   _configuration.getClickToTitle( Configuration.paste_subtree ) );
1377                 if ( default_option == Configuration.paste_subtree ) {
1378                     selected_index = cb_index;
1379                 }
1380                 cb_index++;
1381             }
1382             if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
1383                 _delete_node_or_subtree_item = cb_index;
1384                 addClickToOption( Configuration.delete_subtree_or_node,
1385                                   _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
1386                 if ( default_option == Configuration.delete_subtree_or_node ) {
1387                     selected_index = cb_index;
1388                 }
1389                 cb_index++;
1390             }
1391             if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
1392                 _add_new_node_item = cb_index;
1393                 addClickToOption( Configuration.add_new_node,
1394                                   _configuration.getClickToTitle( Configuration.add_new_node ) );
1395                 if ( default_option == Configuration.add_new_node ) {
1396                     selected_index = cb_index;
1397                 }
1398                 cb_index++;
1399             }
1400             if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
1401                 _edit_node_data_item = cb_index;
1402                 addClickToOption( Configuration.edit_node_data,
1403                                   _configuration.getClickToTitle( Configuration.edit_node_data ) );
1404                 if ( default_option == Configuration.edit_node_data ) {
1405                     selected_index = cb_index;
1406                 }
1407                 cb_index++;
1408             }
1409             if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
1410                 if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
1411                     _blast_item = cb_index;
1412                     addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
1413                     if ( default_option == Configuration.blast ) {
1414                         selected_index = cb_index;
1415                     }
1416                     cb_index++;
1417                 }
1418             }
1419         }
1420         // Set default selection and its action
1421         _click_to_combobox.setSelectedIndex( selected_index );
1422         setClickToAction( selected_index );
1423     }
1424
1425     /* GUILHEM_END */
1426     /*
1427      * Set up the controls from the config settings. 11/26/05
1428      */
1429     void setupControls() {
1430         // The tree display options:
1431         setupDisplayCheckboxes();
1432         /* GUILHEM_BEG */
1433         // The sequence relation query selection combo-box
1434         if ( _configuration.displaySequenceRelations() ) {
1435             addSequenceRelationBlock();
1436         }
1437         /* GUILHEM_END */
1438         // Click-to options
1439         startClickToOptions();
1440         setupClickToOptions();
1441         endClickToOptions();
1442         // Zoom and quick edit buttons
1443         addButtons();
1444         setupSearchTools();
1445     }
1446
1447     void setUpControlsForDomainStrucures() {
1448         _domain_display_label = new JLabel( "Domain Display:" );
1449         add( customizeLabel( _domain_display_label, getConfiguration() ) );
1450         add( _domain_display_label );
1451         _zoom_in_domain_structure = new JButton( "d+" );
1452         _zoom_out_domain_structure = new JButton( "d-" );
1453         _decr_domain_structure_evalue_thr = new JButton( "-" );
1454         _incr_domain_structure_evalue_thr = new JButton( "+" );
1455         _zoom_in_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
1456         _zoom_out_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
1457         _decr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
1458         _incr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
1459         _incr_domain_structure_evalue_thr.setToolTipText( "Increase the E-value threshold by a factor of 10" );
1460         _decr_domain_structure_evalue_thr.setToolTipText( "Decrease the E-value threshold by a factor of 10" );
1461         _domain_structure_evalue_thr_tf = new JTextField( 3 );
1462         _domain_structure_evalue_thr_tf.setEditable( false );
1463         if ( !getConfiguration().isUseNativeUI() ) {
1464             _domain_structure_evalue_thr_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1465             _domain_structure_evalue_thr_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1466             _domain_structure_evalue_thr_tf.setBorder( null );
1467         }
1468         final JPanel d1_panel = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1469         final JPanel d2_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
1470         if ( !_configuration.isUseNativeUI() ) {
1471             d1_panel.setBackground( getBackground() );
1472             d2_panel.setBackground( getBackground() );
1473         }
1474         add( d1_panel );
1475         add( d2_panel );
1476         addJButton( _zoom_out_domain_structure, d1_panel );
1477         addJButton( _zoom_in_domain_structure, d1_panel );
1478         addJButton( _decr_domain_structure_evalue_thr, d2_panel );
1479         addJTextField( _domain_structure_evalue_thr_tf, d2_panel );
1480         addJButton( _incr_domain_structure_evalue_thr, d2_panel );
1481     }
1482
1483     private void setupDisplayCheckboxes() {
1484         if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
1485             addCheckbox( Configuration.display_as_phylogram,
1486                          _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
1487             setCheckbox( Configuration.display_as_phylogram,
1488                          _configuration.doCheckOption( Configuration.display_as_phylogram ) );
1489         }
1490         if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
1491             addCheckbox( Configuration.dynamically_hide_data,
1492                          _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
1493             setCheckbox( Configuration.dynamically_hide_data,
1494                          _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
1495         }
1496         if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
1497             addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
1498             setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
1499         }
1500         if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
1501             addCheckbox( Configuration.display_internal_data,
1502                          _configuration.getDisplayTitle( Configuration.display_internal_data ) );
1503             setCheckbox( Configuration.display_internal_data,
1504                          _configuration.doCheckOption( Configuration.display_internal_data ) );
1505         }
1506         if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
1507             addCheckbox( Configuration.color_according_to_species,
1508                          _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
1509             setCheckbox( Configuration.color_according_to_species,
1510                          _configuration.doCheckOption( Configuration.color_according_to_species ) );
1511         }
1512         if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
1513             addCheckbox( Configuration.color_according_to_annotation,
1514                          _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
1515             setCheckbox( Configuration.color_according_to_annotation,
1516                          _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
1517         }
1518         if ( _configuration.doDisplayOption( Configuration.color_branches ) ) {
1519             addCheckbox( Configuration.color_branches, _configuration.getDisplayTitle( Configuration.color_branches ) );
1520             setCheckbox( Configuration.color_branches, _configuration.doCheckOption( Configuration.color_branches ) );
1521         }
1522         if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
1523             addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
1524             setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
1525         }
1526         final JLabel label = new JLabel( "Display Data:" );
1527         label.setFont( ControlPanel.jcb_bold_font );
1528         if ( !getConfiguration().isUseNativeUI() ) {
1529             label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1530         }
1531         add( label );
1532         if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
1533             addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
1534             setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
1535         }
1536         if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
1537             addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
1538             setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
1539         }
1540         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
1541             addCheckbox( Configuration.show_taxonomy_scientific_names,
1542                          _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
1543             setCheckbox( Configuration.show_taxonomy_scientific_names,
1544                          _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
1545         }
1546         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
1547             addCheckbox( Configuration.show_taxonomy_common_names,
1548                          _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
1549             setCheckbox( Configuration.show_taxonomy_common_names,
1550                          _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
1551         }
1552         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
1553             addCheckbox( Configuration.show_taxonomy_images,
1554                          _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
1555             setCheckbox( Configuration.show_taxonomy_images,
1556                          _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
1557         }
1558         if ( _configuration.doDisplayOption( Configuration.show_gene_symbols ) ) {
1559             addCheckbox( Configuration.show_gene_symbols,
1560                          _configuration.getDisplayTitle( Configuration.show_gene_symbols ) );
1561             setCheckbox( Configuration.show_gene_symbols,
1562                          _configuration.doCheckOption( Configuration.show_gene_symbols ) );
1563         }
1564         if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
1565             addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
1566             setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
1567         }
1568         if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
1569             addCheckbox( Configuration.show_sequence_acc,
1570                          _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
1571             setCheckbox( Configuration.show_sequence_acc,
1572                          _configuration.doCheckOption( Configuration.show_sequence_acc ) );
1573         }
1574         if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
1575             addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
1576             setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
1577         }
1578         if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
1579             addCheckbox( Configuration.show_binary_characters,
1580                          _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
1581             setCheckbox( Configuration.show_binary_characters,
1582                          _configuration.doCheckOption( Configuration.show_binary_characters ) );
1583         }
1584         if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
1585             addCheckbox( Configuration.show_binary_character_counts,
1586                          _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
1587             setCheckbox( Configuration.show_binary_character_counts,
1588                          _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
1589         }
1590         if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
1591             addCheckbox( Configuration.show_domain_architectures,
1592                          _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
1593             setCheckbox( Configuration.show_domain_architectures,
1594                          _configuration.doCheckOption( Configuration.show_domain_architectures ) );
1595         }
1596         if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
1597             addCheckbox( Configuration.write_confidence_values,
1598                          _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
1599             setCheckbox( Configuration.write_confidence_values,
1600                          _configuration.doCheckOption( Configuration.write_confidence_values ) );
1601         }
1602         if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
1603             addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
1604             setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
1605         }
1606         if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
1607             addCheckbox( Configuration.show_vector_data,
1608                          _configuration.getDisplayTitle( Configuration.show_vector_data ) );
1609             setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
1610         }
1611         if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
1612             addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
1613             setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
1614         }
1615     }
1616
1617     void setupSearchTools() {
1618         final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
1619         final JLabel search_label = new JLabel( "Search:" );
1620         search_label.setFont( ControlPanel.jcb_bold_font );
1621         if ( !getConfiguration().isUseNativeUI() ) {
1622             search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1623         }
1624         add( search_label );
1625         search_label.setToolTipText( tip );
1626         _search_found_label = new JLabel();
1627         getSearchFoundCountsLabel().setVisible( false );
1628         _search_found_label.setFont( ControlPanel.jcb_bold_font );
1629         if ( !getConfiguration().isUseNativeUI() ) {
1630             _search_found_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1631         }
1632         _search_tf = new JTextField( 3 );
1633         _search_tf.setToolTipText( tip );
1634         _search_tf.setEditable( true );
1635         if ( !getConfiguration().isUseNativeUI() ) {
1636             _search_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1637             _search_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1638             _search_tf.setBorder( null );
1639         }
1640         _search_reset_button = new JButton();
1641         getSearchResetButton().setText( "Reset" );
1642         getSearchResetButton().setEnabled( false );
1643         getSearchResetButton().setVisible( false );
1644         final JPanel s_panel_1 = new JPanel( new BorderLayout() );
1645         final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1646         s_panel_1.setBackground( getBackground() );
1647         add( s_panel_1 );
1648         s_panel_2.setBackground( getBackground() );
1649         add( s_panel_2 );
1650         final KeyAdapter key_adapter = new KeyAdapter() {
1651
1652             @Override
1653             public void keyReleased( final KeyEvent key_event ) {
1654                 search();
1655                 displayedPhylogenyMightHaveChanged( true );
1656             }
1657         };
1658         final ActionListener action_listener = new ActionListener() {
1659
1660             @Override
1661             public void actionPerformed( final ActionEvent e ) {
1662                 searchReset();
1663                 setSearchFoundCountsOnLabel( 0 );
1664                 getSearchFoundCountsLabel().setVisible( false );
1665                 getSearchTextField().setText( "" );
1666                 getSearchResetButton().setEnabled( false );
1667                 getSearchResetButton().setVisible( false );
1668                 displayedPhylogenyMightHaveChanged( true );
1669             }
1670         };
1671         _search_reset_button.addActionListener( action_listener );
1672         _search_tf.addKeyListener( key_adapter );
1673         addJTextField( _search_tf, s_panel_1 );
1674         s_panel_2.add( _search_found_label );
1675         addJButton( _search_reset_button, s_panel_2 );
1676     }
1677
1678     private void setVisibilityOfDomainStrucureControls() {
1679         if ( _zoom_in_domain_structure != null ) {
1680             if ( isShowDomainArchitectures() ) {
1681                 _domain_display_label.setVisible( true );
1682                 _zoom_in_domain_structure.setVisible( true );
1683                 _zoom_out_domain_structure.setVisible( true );
1684                 _decr_domain_structure_evalue_thr.setVisible( true );
1685                 _incr_domain_structure_evalue_thr.setVisible( true );
1686                 _domain_structure_evalue_thr_tf.setVisible( true );
1687             }
1688             else {
1689                 _domain_display_label.setVisible( false );
1690                 _zoom_in_domain_structure.setVisible( false );
1691                 _zoom_out_domain_structure.setVisible( false );
1692                 _decr_domain_structure_evalue_thr.setVisible( false );
1693                 _incr_domain_structure_evalue_thr.setVisible( false );
1694                 _domain_structure_evalue_thr_tf.setVisible( false );
1695             }
1696         }
1697     }
1698
1699     /**
1700      * Fit entire tree into window.
1701      */
1702     void showWhole() {
1703         if ( _mainpanel.getCurrentScrollPane() == null ) {
1704             return;
1705         }
1706         displayedPhylogenyMightHaveChanged( false );
1707         _mainpanel.getCurrentTreePanel().updateOvSettings();
1708         _mainpanel.getCurrentTreePanel().validate();
1709         _mainpanel.validate();
1710         _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
1711                                                                    _mainpanel.getSizeOfViewport().height,
1712                                                                    true );
1713         _mainpanel.getCurrentTreePanel().resetPreferredSize();
1714         _mainpanel.adjustJScrollPane();
1715         _mainpanel.getCurrentTreePanel().repaint();
1716         _mainpanel.getCurrentTreePanel().validate();
1717         _mainpanel.validate();
1718         _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
1719                                                                    _mainpanel.getSizeOfViewport().height,
1720                                                                    true );
1721         _mainpanel.getCurrentTreePanel().resetPreferredSize();
1722         _mainpanel.adjustJScrollPane();
1723         _mainpanel.getCurrentTreePanel().repaint();
1724         _mainpanel.getCurrentTreePanel().updateOvSizes();
1725     }
1726
1727     void showWholeAll() {
1728         for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
1729             if ( tree_panel != null ) {
1730                 tree_panel.validate();
1731                 tree_panel.setParametersForPainting( _mainpanel.getSizeOfViewport().width,
1732                                                      _mainpanel.getSizeOfViewport().height,
1733                                                      true );
1734                 tree_panel.resetPreferredSize();
1735                 tree_panel.repaint();
1736             }
1737         }
1738     }
1739
1740     // Create header for click-to combo box.
1741     void startClickToOptions() {
1742         final JLabel spacer = new JLabel( "" );
1743         spacer.setFont( ControlPanel.jcb_font );
1744         add( spacer );
1745         _click_to_label = new JLabel( "Click on Node to:" );
1746         add( customizeLabel( _click_to_label, getConfiguration() ) );
1747         _click_to_combobox = new JComboBox();
1748         _click_to_combobox.setFocusable( false );
1749         _click_to_combobox.setMaximumRowCount( 14 );
1750         _click_to_combobox.setFont( ControlPanel.js_font );
1751         if ( !_configuration.isUseNativeUI() ) {
1752             _click_to_combobox.setBackground( getConfiguration().getGuiBackgroundColor() );
1753         }
1754         // don't add listener until all items are set (or each one will trigger
1755         // an event)
1756         // click_to_list.addActionListener(this);
1757         add( _click_to_combobox );
1758         // Correlates option names to titles
1759         _all_click_to_names = new HashMap<Integer, String>();
1760         _click_to_names = new ArrayList<String>();
1761     }
1762
1763     void tabChanged() {
1764         if ( getMainPanel().getTabbedPane().getTabCount() > 0 ) {
1765             if ( getCurrentTreePanel().isPhyHasBranchLengths()
1766                     && ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1767                 setDrawPhylogramEnabled( true );
1768                 setDrawPhylogram( isDrawPhylogram() );
1769             }
1770             else {
1771                 setDrawPhylogramEnabled( false );
1772                 setDrawPhylogram( false );
1773             }
1774             if ( getMainPanel().getMainFrame() == null ) {
1775                 // Must be "E" applet version.
1776                 final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1777                 e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() );
1778             }
1779             else {
1780                 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel()
1781                         .getPhylogenyGraphicsType() );
1782             }
1783             getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
1784             getMainPanel().getControlPanel().search();
1785             getSequenceRelationTypeBox().removeAllItems();
1786             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
1787                     .getRelevantSequenceRelationTypes() ) {
1788                 _sequence_relation_type_box.addItem( type );
1789             }
1790             //setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
1791             // according to GUILHEM the line above can be removed.
1792         }
1793     }
1794
1795     /**
1796      * Uncollapse all nodes.
1797      */
1798     void uncollapseAll( final TreePanel tp ) {
1799         final Phylogeny t = tp.getPhylogeny();
1800         if ( ( t != null ) && !t.isEmpty() ) {
1801             for( final PhylogenyNodeIterator iter = t.iteratorPreorder(); iter.hasNext(); ) {
1802                 final PhylogenyNode node = iter.next();
1803                 node.setCollapse( false );
1804             }
1805             tp.resetNodeIdToDistToLeafMap();
1806             tp.updateSetOfCollapsedExternalNodes( t );
1807             t.recalculateNumberOfExternalDescendants( false );
1808             tp.setNodeInPreorderToNull();
1809             t.hashIDs();
1810             showWhole();
1811         }
1812     }
1813
1814     void updateDomainStructureEvaluethresholdDisplay() {
1815         if ( _domain_structure_evalue_thr_tf != null ) {
1816             _domain_structure_evalue_thr_tf.setText( "10^"
1817                     + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThreshold() );
1818         }
1819     }
1820
1821     void zoomInX( final float factor, final float x_correction_factor ) {
1822         final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
1823         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1824         treepanel.multiplyUrtFactor( 1f );
1825         if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1826                 || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1827                 || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
1828                 || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
1829             final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1830             treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1831             treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1832             getMainPanel().adjustJScrollPane();
1833             treepanel.resetPreferredSize();
1834             getMainPanel().getCurrentScrollPane().getViewport().validate();
1835             sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1836                     - ( sb.getVisibleAmount() / 2.0 ) ) );
1837         }
1838         else {
1839             final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
1840             treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1841             treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1842             getMainPanel().adjustJScrollPane();
1843             treepanel.resetPreferredSize();
1844             getMainPanel().getCurrentScrollPane().getViewport().validate();
1845             sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
1846         }
1847         treepanel.resetPreferredSize();
1848         treepanel.updateOvSizes();
1849     }
1850
1851     void zoomInY( final float factor ) {
1852         final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
1853         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1854         treepanel.multiplyUrtFactor( 1.1f );
1855         final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1856         treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
1857         getMainPanel().adjustJScrollPane();
1858         treepanel.resetPreferredSize();
1859         getMainPanel().getCurrentScrollPane().getViewport().validate();
1860         sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1861                 - ( sb.getVisibleAmount() / 2.0 ) ) );
1862         treepanel.resetPreferredSize();
1863         treepanel.updateOvSizes();
1864     }
1865
1866     void zoomOutX( final float factor, final float x_correction_factor ) {
1867         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1868         treepanel.multiplyUrtFactor( 1f );
1869         if ( ( treepanel.getXdistance() * factor ) > 0.0 ) {
1870             final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
1871             if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1872                     || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1873                     || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
1874                     || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
1875                 getMainPanel().adjustJScrollPane();
1876                 treepanel.resetPreferredSize();
1877                 getMainPanel().getCurrentScrollPane().getViewport().validate();
1878                 final double x = ( sb.getMaximum() - sb.getMinimum() )
1879                         / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1880                 treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1881                 treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1882                 getMainPanel().adjustJScrollPane();
1883                 treepanel.resetPreferredSize();
1884                 getMainPanel().getCurrentScrollPane().getViewport().validate();
1885                 sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1886                         - ( sb.getVisibleAmount() / 2.0 ) ) );
1887             }
1888             else {
1889                 final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
1890                 treepanel.setXdistance( treepanel.getXdistance() * factor );
1891                 treepanel.setXcorrectionFactor( treepanel.getXcorrectionFactor() * x_correction_factor );
1892                 if ( x > 0 ) {
1893                     getMainPanel().adjustJScrollPane();
1894                     treepanel.resetPreferredSize();
1895                     getMainPanel().getCurrentScrollPane().getViewport().validate();
1896                     sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
1897                 }
1898             }
1899             treepanel.resetPreferredSize();
1900             treepanel.updateOvSizes();
1901         }
1902     }
1903
1904     void zoomOutY( final float factor ) {
1905         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1906         treepanel.multiplyUrtFactor( 0.9f );
1907         if ( ( treepanel.getYdistance() * factor ) > 0.0 ) {
1908             final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
1909             final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1910             treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
1911             getMainPanel().adjustJScrollPane();
1912             treepanel.resetPreferredSize();
1913             getMainPanel().getCurrentScrollPane().getViewport().validate();
1914             sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1915                     - ( sb.getVisibleAmount() / 2.0 ) ) );
1916             treepanel.resetPreferredSize();
1917             treepanel.updateOvSizes();
1918         }
1919     }
1920
1921     static JLabel customizeLabel( final JLabel label, final Configuration configuration ) {
1922         label.setFont( ControlPanel.jcb_bold_font );
1923         if ( !configuration.isUseNativeUI() ) {
1924             label.setForeground( configuration.getGuiCheckboxTextColor() );
1925             label.setBackground( configuration.getGuiBackgroundColor() );
1926         }
1927         return label;
1928     }
1929
1930     enum NodeClickAction {
1931         SHOW_DATA,
1932         COLLAPSE,
1933         REROOT,
1934         SUBTREE,
1935         SWAP,
1936         COLOR_SUBTREE,
1937         OPEN_TAX_WEB,
1938         OPEN_SEQ_WEB,
1939         CUT_SUBTREE,
1940         COPY_SUBTREE,
1941         DELETE_NODE_OR_SUBTREE,
1942         PASTE_SUBTREE,
1943         ADD_NEW_NODE,
1944         EDIT_NODE_DATA,
1945         SORT_DESCENDENTS,
1946         BLAST;
1947     }
1948 }