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

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 //
   8 // This library is free software; you can redistribute it and/or
   9 // modify it under the terms of the GNU Lesser General Public
  10 // License as published by the Free Software Foundation; either
  11 // version 2.1 of the License, or (at your option) any later version.
  12 //
  13 // This library is distributed in the hope that it will be useful,
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  16 // Lesser General Public License for more details.
  17 //
  18 // You should have received a copy of the GNU Lesser General Public
  19 // License along with this library; if not, write to the Free Software
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  21 //
  22 // Contact: phylosoft @ gmail . com
  23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  24
  25 package org.forester.archaeopteryx;
  26
  27 import java.awt.BorderLayout;
  28 import java.awt.Color;
  29 import java.awt.Component;
  30 import java.awt.Dimension;
  31 import java.awt.Font;
  32 import java.awt.GridBagLayout;
  33 import java.awt.GridLayout;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.ItemEvent;
  37 import java.awt.event.ItemListener;
  38 import java.awt.event.KeyAdapter;
  39 import java.awt.event.KeyEvent;
  40 import java.util.ArrayList;
  41 import java.util.Arrays;
  42 import java.util.Collection;
  43 import java.util.HashMap;
  44 import java.util.HashSet;
  45 import java.util.List;
  46 import java.util.Map;
  47 import java.util.Set;
  48
  49 import javax.swing.BorderFactory;
  50 import javax.swing.DefaultListCellRenderer;
  51 import javax.swing.JButton;
  52 import javax.swing.JCheckBox;
  53 import javax.swing.JComboBox;
  54 import javax.swing.JLabel;
  55 import javax.swing.JList;
  56 import javax.swing.JPanel;
  57 import javax.swing.JScrollBar;
  58 import javax.swing.JTextField;
  59 import javax.swing.ListCellRenderer;
  60
  61 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  62 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  63 import org.forester.phylogeny.Phylogeny;
  64 import org.forester.phylogeny.PhylogenyMethods;
  65 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  66 import org.forester.phylogeny.PhylogenyNode;
  67 import org.forester.phylogeny.data.Sequence;
  68 import org.forester.phylogeny.data.SequenceRelation;
  69 import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE;
  70 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  71 import org.forester.util.ForesterUtil;
  72
  73 final class ControlPanel extends JPanel implements ActionListener {
  74
  75     enum NodeClickAction {
  76         ADD_NEW_NODE,
  77         BLAST,
  78         COLLAPSE,
  79         COLOR_SUBTREE,
  80         COPY_SUBTREE,
  81         CUT_SUBTREE,
  82         DELETE_NODE_OR_SUBTREE,
  83         EDIT_NODE_DATA,
  84         GET_EXT_DESC_DATA,
  85         OPEN_PDB_WEB,
  86         OPEN_SEQ_WEB,
  87         OPEN_TAX_WEB,
  88         PASTE_SUBTREE,
  89         REROOT,
  90         SELECT_NODES,
  91         SHOW_DATA,
  92         SORT_DESCENDENTS,
  93         SUBTREE,
  94         SWAP,
  95         CHANGE_NODE_FONT,
  96         COLOR_NODE_FONT,
  97         UNCOLLAPSE_ALL,
  98         ORDER_SUBTREE;
  99     }
 100     final static Font                         jcb_bold_font             = new Font( Configuration.getDefaultFontFamilyName(),
 101                                                                                     Font.BOLD,
 102                                                                                     9 );
 103     final static Font                         jcb_font                  = new Font( Configuration.getDefaultFontFamilyName(),
 104                                                                                     Font.PLAIN,
 105                                                                                     9 );
 106     final static Font                         js_font                   = new Font( Configuration.getDefaultFontFamilyName(),
 107                                                                                     Font.PLAIN,
 108                                                                                     9 );
 109     private static final String               RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
 110     private static final String               SEARCH_TIP_TEXT           = "Enter text to search for. Use ',' for logical OR and '+' for logical AND (not used in this manner for regular expression searches).";
 111     private static final long                 serialVersionUID          = -8463483932821545633L;
 112     private NodeClickAction                   _action_when_node_clicked;
 113     private int                               _add_new_node_item;
 114     private Map<Integer, String>              _all_click_to_names;
 115     private Map<String, Color>                _annotation_colors;
 116     private int                               _blast_item;
 117     private JComboBox<String>                 _click_to_combobox;
 118     private JLabel                            _click_to_label;
 119     private List<String>                      _click_to_names;
 120     private int                               _collapse_cb_item;
 121     private int                               _uncollapse_all_cb_item;
 122     private int                               _order_subtree_cb_item;
 123
 124
 125     private JCheckBox                         _color_acc_species;
 126     private JCheckBox                         _color_acc_sequence;
 127     private JCheckBox                         _color_according_to_annotation;
 128     private boolean                           _color_branches;
 129     private JCheckBox                         _use_visual_styles_cb;
 130     private int                               _color_subtree_cb_item;
 131     private int                               _change_node_font_item;
 132     // The settings from the conf file
 133     private final Configuration               _configuration;
 134     private int                               _copy_subtree_item;
 135     private int                               _cut_subtree_item;
 136     private JButton                           _decr_domain_structure_evalue_thr;
 137     private int                               _delete_node_or_subtree_item;
 138     private JCheckBox                         _display_as_phylogram_cb;
 139     // Tree checkboxes
 140     private JCheckBox                         _display_internal_data;
 141     private JLabel                            _domain_display_label;
 142     private JTextField                        _domain_structure_evalue_thr_tf;
 143     private List<Boolean>                     _draw_phylogram;
 144     private JCheckBox                         _dynamically_hide_data;
 145     private int                               _edit_node_data_item;
 146     private int                               _get_ext_desc_data;
 147     private JButton                           _incr_domain_structure_evalue_thr;
 148     private final MainPanel                   _mainpanel;
 149     private JCheckBox                         _node_desc_popup_cb;
 150     private int                               _open_pdb_item;
 151     private int                               _open_seq_web_item;
 152     private int                               _open_tax_web_item;
 153     private int                               _color_node_font_item;
 154     private JButton                           _order;
 155     private int                               _paste_subtree_item;
 156     private int                               _reroot_cb_item;
 157     private JButton                           _return_to_super_tree;
 158     // Search
 159     private JLabel                            _search_found_label_0;
 160     private JLabel                            _search_found_label_1;
 161     private JButton                           _search_reset_button_0;
 162     private JButton                           _search_reset_button_1;
 163     private JTextField                        _search_tf_0;
 164     private JTextField                        _search_tf_1;
 165     private int                               _select_nodes_item;
 166     private Sequence                          _selected_query_seq;
 167     private JCheckBox                         _seq_relation_confidence_switch;
 168     private JComboBox<SEQUENCE_RELATION_TYPE> _sequence_relation_type_box;
 169     private JCheckBox                         _show_annotation;
 170     private JCheckBox                         _show_binary_character_counts;
 171     private JCheckBox                         _show_binary_characters;
 172     // Indices for the click-to options in the combo box
 173     private int                               _show_data_item;
 174     private JCheckBox                         _show_domain_architectures;
 175     private JCheckBox                         _show_mol_seqs;
 176     private JCheckBox                         _write_branch_length_values;
 177     private JCheckBox                         _show_events;
 178     private JCheckBox                         _show_gene_names;
 179     private JCheckBox                         _show_node_names;
 180     private JCheckBox                         _show_properties_cb;
 181     private JCheckBox                         _show_seq_names;
 182     private JCheckBox                         _show_seq_symbols;
 183     private JCheckBox                         _show_sequence_acc;
 184     private JComboBox<String>                 _show_sequence_relations;
 185     private JCheckBox                         _show_taxo_code;
 186     private JCheckBox                         _show_taxo_rank;
 187     private JCheckBox                         _show_taxo_common_names;
 188     private JCheckBox                         _show_taxo_images_cb;
 189     private JCheckBox                         _show_taxo_scientific_names;
 190     private JCheckBox                         _show_vector_data_cb;
 191     private JButton                           _show_whole;
 192     private int                               _sort_descendents_item;
 193     private Map<String, Color>                _species_colors;
 194     private Map<String, Color>                _sequence_colors;
 195     private int                               _subtree_cb_item;
 196     private int                               _swap_cb_item;
 197     private JButton                           _uncollapse_all;
 198     private JCheckBox                         _width_branches;
 199     private JCheckBox                         _write_confidence;
 200     private JButton                           _zoom_in_domain_structure;
 201     private JButton                           _zoom_in_x;
 202     private JButton                           _zoom_in_y;
 203     private JLabel                            _zoom_label;
 204     private JButton                           _zoom_out_domain_structure;
 205     private JButton                           _zoom_out_x;
 206     private JButton                           _zoom_out_y;
 207
 208     ControlPanel( final MainPanel ap, final Configuration configuration ) {
 209         init();
 210         _mainpanel = ap;
 211         _configuration = configuration;
 212         if ( !_configuration.isUseNativeUI() ) {
 213             setBackground( getConfiguration().getGuiBackgroundColor() );
 214             setBorder( BorderFactory.createRaisedBevelBorder() );
 215         }
 216         setLayout( new GridLayout( 0, 1, 2, 2 ) );
 217         setupControls();
 218     }
 219
 220     /**
 221      * Handle an action.
 222      */
 223     @Override
 224     public void actionPerformed( final ActionEvent e ) {
 225         try {
 226             if ( e.getSource() == _color_acc_sequence ) {
 227                 if ( _color_acc_species != null ) {
 228                     _color_acc_species.setSelected( false );
 229                 }
 230             }
 231             else if ( e.getSource() == _color_acc_species ) {
 232                 if ( _color_acc_sequence != null ) {
 233                     _color_acc_sequence.setSelected( false );
 234                 }
 235             }
 236             final TreePanel tp = getMainPanel().getCurrentTreePanel();
 237             if ( tp == null ) {
 238                 return;
 239             }
 240             if ( e.getSource() == _click_to_combobox ) {
 241                 setClickToAction( _click_to_combobox.getSelectedIndex() );
 242                 getCurrentTreePanel().repaint();
 243             }
 244             else if ( e.getSource() == _show_binary_characters ) {
 245                 if ( ( _show_binary_character_counts != null ) && _show_binary_characters.isSelected() ) {
 246                     _show_binary_character_counts.setSelected( false );
 247                 }
 248                 displayedPhylogenyMightHaveChanged( true );
 249             }
 250             else if ( e.getSource() == _show_binary_character_counts ) {
 251                 if ( ( _show_binary_characters != null ) && _show_binary_character_counts.isSelected() ) {
 252                     _show_binary_characters.setSelected( false );
 253                 }
 254                 displayedPhylogenyMightHaveChanged( true );
 255             }
 256             else if ( e.getSource() == _show_domain_architectures ) {
 257                 search0();
 258                 search1();
 259                 displayedPhylogenyMightHaveChanged( true );
 260             }
 261             else if ( ( tp != null ) && ( tp.getPhylogeny() != null ) ) {
 262                 if ( e.getSource() == getDisplayAsPhylogramCb() ) {
 263                     setDrawPhylogram( getDisplayAsPhylogramCb().isSelected() );
 264                     showWhole();
 265                 }
 266                 // Zoom buttons
 267                 else if ( e.getSource() == _zoom_in_x ) {
 268                     zoomInX( AptxConstants.BUTTON_ZOOM_IN_FACTOR, AptxConstants.BUTTON_ZOOM_IN_X_CORRECTION_FACTOR );
 269                     displayedPhylogenyMightHaveChanged( false );
 270                 }
 271                 else if ( e.getSource() == _zoom_in_y ) {
 272                     zoomInY( AptxConstants.BUTTON_ZOOM_IN_FACTOR );
 273                     displayedPhylogenyMightHaveChanged( false );
 274                 }
 275                 else if ( e.getSource() == _zoom_out_x ) {
 276                     zoomOutX( AptxConstants.BUTTON_ZOOM_OUT_FACTOR, AptxConstants.BUTTON_ZOOM_OUT_X_CORRECTION_FACTOR );
 277                     displayedPhylogenyMightHaveChanged( false );
 278                 }
 279                 else if ( e.getSource() == _zoom_out_y ) {
 280                     zoomOutY( AptxConstants.BUTTON_ZOOM_OUT_FACTOR );
 281                     displayedPhylogenyMightHaveChanged( false );
 282                 }
 283                 else if ( e.getSource() == _show_whole ) {
 284                     displayedPhylogenyMightHaveChanged( true );
 285                     showWhole();
 286                 }
 287                 else if ( e.getSource() == _return_to_super_tree ) {
 288                     _mainpanel.getCurrentTreePanel().superTree();
 289                     showWhole();
 290                 }
 291                 else if ( e.getSource() == _order ) {
 292                     DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
 293                     if ( isShowTaxonomyScientificNames() || isShowTaxonomyCode() ) {
 294                         pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
 295                     }
 296                     else if ( isShowSeqNames() || isShowSeqSymbols() || isShowGeneNames() ) {
 297                         pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
 298                     }
 299                     PhylogenyMethods.orderAppearanceX( tp.getPhylogeny().getRoot(), true, pri );
 300
 301                     tp.setNodeInPreorderToNull();
 302                     tp.getPhylogeny().externalNodesHaveChanged();
 303                     tp.getPhylogeny().clearHashIdToNodeMap();
 304                     tp.getPhylogeny().recalculateNumberOfExternalDescendants( true );
 305                     tp.resetNodeIdToDistToLeafMap();
 306                     tp.setEdited( true );
 307                     displayedPhylogenyMightHaveChanged( true );
 308                 }
 309                 else if ( e.getSource() == _uncollapse_all ) {
 310                     uncollapseAll( tp );
 311                     displayedPhylogenyMightHaveChanged( false );
 312                 }
 313                 else if ( e.getSource() == _zoom_in_domain_structure ) {
 314                     _mainpanel.getCurrentTreePanel().zoomInDomainStructure();
 315                     displayedPhylogenyMightHaveChanged( true );
 316                 }
 317                 else if ( e.getSource() == _zoom_out_domain_structure ) {
 318                     _mainpanel.getCurrentTreePanel().zoomOutDomainStructure();
 319                     displayedPhylogenyMightHaveChanged( true );
 320                 }
 321                 else if ( e.getSource() == _decr_domain_structure_evalue_thr ) {
 322                     _mainpanel.getCurrentTreePanel().decreaseDomainStructureEvalueThresholdExp();
 323                     search0();
 324                     search1();
 325                     displayedPhylogenyMightHaveChanged( true );
 326                 }
 327                 else if ( e.getSource() == _incr_domain_structure_evalue_thr ) {
 328                     _mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThresholdExp();
 329                     search0();
 330                     search1();
 331                     displayedPhylogenyMightHaveChanged( true );
 332                 }
 333                 else if ( e.getSource() == _search_tf_0 ) {
 334                     search0();
 335                     displayedPhylogenyMightHaveChanged( true );
 336                 }
 337                 else if ( e.getSource() == _search_tf_1 ) {
 338                     search1();
 339                     displayedPhylogenyMightHaveChanged( true );
 340                 }
 341                 else if ( ( _dynamically_hide_data != null ) && ( e.getSource() == _dynamically_hide_data )
 342                         && !_dynamically_hide_data.isSelected() ) {
 343                     setDynamicHidingIsOn( false );
 344                     displayedPhylogenyMightHaveChanged( true );
 345                 }
 346                 else {
 347                     displayedPhylogenyMightHaveChanged( true );
 348                 }
 349             }
 350             tp.requestFocus();
 351             tp.requestFocusInWindow();
 352             tp.requestFocus();
 353         }
 354         catch ( final Exception ex ) {
 355             AptxUtil.unexpectedException( ex );
 356         }
 357         catch ( final Error err ) {
 358             AptxUtil.unexpectedError( err );
 359         }
 360     }
 361
 362     public JCheckBox getColorAccSequenceCb() {
 363         return _color_acc_sequence;
 364     }
 365
 366     public JCheckBox getColorAccSpeciesCb() {
 367         return _color_acc_species;
 368     }
 369
 370     public JCheckBox getDisplayAsPhylogramCb() {
 371         return _display_as_phylogram_cb;
 372     }
 373
 374     public JCheckBox getDynamicallyHideData() {
 375         return _dynamically_hide_data;
 376     }
 377
 378     public JCheckBox getNodeDescPopupCb() {
 379         return _node_desc_popup_cb;
 380     }
 381
 382     public Sequence getSelectedQuerySequence() {
 383         return _selected_query_seq;
 384     }
 385
 386     public JComboBox<String> getSequenceRelationBox() {
 387         if ( _show_sequence_relations == null ) {
 388             _show_sequence_relations = new JComboBox<String>();
 389             _show_sequence_relations.setFocusable( false );
 390             _show_sequence_relations.setMaximumRowCount( 20 );
 391             _show_sequence_relations.setFont( ControlPanel.js_font );
 392             if ( !_configuration.isUseNativeUI() ) {
 393                 _show_sequence_relations.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 394                 _show_sequence_relations.setForeground( getConfiguration().getGuiButtonTextColor() );
 395             }
 396             _show_sequence_relations.addItem( "-----" );
 397             _show_sequence_relations.setToolTipText( "To display orthology information for selected query" );
 398         }
 399         return _show_sequence_relations;
 400     }
 401
 402     /* GUILHEM_BEG */
 403     public JComboBox<SEQUENCE_RELATION_TYPE> getSequenceRelationTypeBox() {
 404         if ( _sequence_relation_type_box == null ) {
 405             _sequence_relation_type_box = new JComboBox<SEQUENCE_RELATION_TYPE>();
 406             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : SequenceRelation.SEQUENCE_RELATION_TYPE.values() ) {
 407                 _sequence_relation_type_box.addItem( type );
 408             }
 409             _sequence_relation_type_box.addActionListener( new ActionListener() {
 410
 411                 @Override
 412                 public void actionPerformed( final ActionEvent e ) {
 413                     if ( _mainpanel.getCurrentPhylogeny() != null ) {
 414                         setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
 415                     }
 416                 }
 417             } );
 418         }
 419         return _sequence_relation_type_box;
 420     }
 421
 422     public JCheckBox getShowEventsCb() {
 423         return _show_events;
 424     }
 425
 426     public JCheckBox getUseVisualStylesCb() {
 427         return _use_visual_styles_cb;
 428     }
 429
 430     public JCheckBox getWriteConfidenceCb() {
 431         return _write_confidence;
 432     }
 433
 434     public boolean isShowMolSequences() {
 435         return ( ( _show_mol_seqs != null ) && _show_mol_seqs.isSelected() );
 436     }
 437
 438     public boolean isShowProperties() {
 439         return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
 440     }
 441
 442     public boolean isShowTaxonomyImages() {
 443         return ( ( _show_taxo_images_cb != null ) && _show_taxo_images_cb.isSelected() );
 444     }
 445
 446     public boolean isShowVectorData() {
 447         return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
 448     }
 449
 450     public void setSequenceRelationQueries( final Collection<Sequence> sequenceRelationQueries ) {
 451         final JComboBox<String> box = getSequenceRelationBox();
 452         while ( box.getItemCount() > 1 ) {
 453             box.removeItemAt( 1 );
 454         }
 455         final HashMap<String, Sequence> sequencesByName = new HashMap<String, Sequence>();
 456         final SequenceRelation.SEQUENCE_RELATION_TYPE relationType = ( SequenceRelation.SEQUENCE_RELATION_TYPE ) _sequence_relation_type_box
 457                 .getSelectedItem();
 458         if ( relationType == null ) {
 459             return;
 460         }
 461         final ArrayList<String> sequenceNamesToAdd = new ArrayList<String>();
 462         for( final Sequence seq : sequenceRelationQueries ) {
 463             if ( seq.isHasSequenceRelations() ) {
 464                 boolean fFoundForCurrentType = false;
 465                 for( final SequenceRelation sq : seq.getSequenceRelations() ) {
 466                     if ( sq.getType().equals( relationType ) ) {
 467                         fFoundForCurrentType = true;
 468                         break;
 469                     }
 470                 }
 471                 if ( fFoundForCurrentType ) {
 472                     sequenceNamesToAdd.add( seq.getName() );
 473                     sequencesByName.put( seq.getName(), seq );
 474                 }
 475             }
 476         }
 477         // sort sequences by name before adding them to the combo
 478         final String[] sequenceNameArray = sequenceNamesToAdd.toArray( new String[ sequenceNamesToAdd.size() ] );
 479         Arrays.sort( sequenceNameArray, String.CASE_INSENSITIVE_ORDER );
 480         for( final String seqName : sequenceNameArray ) {
 481             box.addItem( seqName );
 482         }
 483         for( final ItemListener oldItemListener : box.getItemListeners() ) {
 484             box.removeItemListener( oldItemListener );
 485         }
 486         box.addItemListener( new ItemListener() {
 487
 488             @Override
 489             public void itemStateChanged( final ItemEvent e ) {
 490                 _selected_query_seq = sequencesByName.get( e.getItem() );
 491                 _mainpanel.getCurrentTreePanel().repaint();
 492             }
 493         } );
 494     }
 495
 496     private void addClickToOption( final int which, final String title ) {
 497         _click_to_combobox.addItem( title );
 498         _click_to_names.add( title );
 499         _all_click_to_names.put( new Integer( which ), title );
 500         if ( !_configuration.isUseNativeUI() ) {
 501             _click_to_combobox.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 502             _click_to_combobox.setForeground( getConfiguration().getGuiButtonTextColor() );
 503         }
 504     }
 505
 506     /* GUILHEM_BEG */
 507     private void addSequenceRelationBlock() {
 508         final JLabel spacer = new JLabel( "" );
 509         spacer.setSize( 1, 1 );
 510         add( spacer );
 511         final JLabel mainLabel = new JLabel( "Sequence relations to display" );
 512         final JLabel typeLabel = customizeLabel( new JLabel( "(type) " ), getConfiguration() );
 513         typeLabel.setFont( ControlPanel.js_font.deriveFont( 7 ) );
 514         getSequenceRelationTypeBox().setFocusable( false );
 515         _sequence_relation_type_box.setFont( ControlPanel.js_font );
 516         if ( !_configuration.isUseNativeUI() ) {
 517             _sequence_relation_type_box.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
 518             _sequence_relation_type_box.setForeground( getConfiguration().getGuiButtonTextColor() );
 519         }
 520         _sequence_relation_type_box.setRenderer( new ListCellRenderer<Object>() {
 521
 522             @Override
 523             public Component getListCellRendererComponent( final JList<?> list,
 524                                                            final Object value,
 525                                                            final int index,
 526                                                            final boolean isSelected,
 527                                                            final boolean cellHasFocus ) {
 528                 final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
 529                                                                                                         value,
 530                                                                                                         index,
 531                                                                                                         isSelected,
 532                                                                                                         cellHasFocus );
 533                 if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) {
 534                     ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation
 535                             .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) );
 536                 }
 537                 return component;
 538             }
 539         } );
 540         final GridBagLayout gbl = new GridBagLayout();
 541         _sequence_relation_type_box.setMinimumSize( new Dimension( 115, 17 ) );
 542         _sequence_relation_type_box.setPreferredSize( new Dimension( 115, 20 ) );
 543         final JPanel horizGrid = new JPanel( gbl );
 544         horizGrid.setBackground( getBackground() );
 545         horizGrid.add( typeLabel );
 546         horizGrid.add( _sequence_relation_type_box );
 547         add( customizeLabel( mainLabel, getConfiguration() ) );
 548         add( horizGrid );
 549         add( getSequenceRelationBox() );
 550         if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
 551             addCheckbox( Configuration.show_relation_confidence,
 552                          _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
 553             setCheckbox( Configuration.show_relation_confidence,
 554                          _configuration.doCheckOption( Configuration.show_relation_confidence ) );
 555         }
 556     }// addSequenceRelationBlock
 557
 558     /* GUILHEM_END */
 559
 560     private List<Boolean> getIsDrawPhylogramList() {
 561         return _draw_phylogram;
 562     }
 563
 564     // This takes care of ArchaeopteryxE-issue.
 565     // Can, and will, return null prior to  ArchaeopteryxE initialization completion.
 566     final private MainFrame getMainFrame() {
 567         MainFrame mf = getMainPanel().getMainFrame();
 568         if ( mf == null ) {
 569             // Must be "E" applet version.
 570             final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
 571             if ( e.getMainPanel() == null ) {
 572                 return null;
 573             }
 574             mf = e.getMainPanel().getMainFrame();
 575         }
 576         return mf;
 577     }
 578
 579     private void init() {
 580         _draw_phylogram = new ArrayList<Boolean>();
 581         setSpeciesColors( new HashMap<String, Color>() );
 582         setSequenceColors( new HashMap<String, Color>() );
 583         setAnnotationColors( new HashMap<String, Color>() );
 584     }
 585
 586     private boolean isDrawPhylogram( final int index ) {
 587         return getIsDrawPhylogramList().get( index );
 588     }
 589
 590     private void search0( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
 591         getSearchFoundCountsLabel0().setVisible( true );
 592         getSearchResetButton0().setEnabled( true );
 593         getSearchResetButton0().setVisible( true );
 594         String[] queries = null;
 595         Set<Long> nodes = null;
 596         if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
 597             queries = query_str.split( ",+" );
 598         }
 599         else {
 600             queries = new String[ 1 ];
 601             queries[ 0 ] = query_str.trim();
 602         }
 603         if ( ( queries != null ) && ( queries.length > 0 ) ) {
 604             nodes = new HashSet<Long>();
 605             for( String query : queries ) {
 606                 if ( ForesterUtil.isEmpty( query ) ) {
 607                     continue;
 608                 }
 609                 query = query.trim();
 610                 final TreePanel tp = getMainPanel().getCurrentTreePanel();
 611                 if ( ( query.indexOf( '+' ) > 0 ) && !getOptions().isSearchWithRegex() ) {
 612                     nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
 613                                                                          tree,
 614                                                                          getOptions().isSearchCaseSensitive(),
 615                                                                          !getOptions().isMatchWholeTermsOnly(),
 616                                                                          isShowDomainArchitectures(),
 617                                                                          tp != null ? Math.pow( 10,
 618                                                                                                 tp.getDomainStructureEvalueThresholdExp() )
 619                                                                                                 : 0 ) );
 620                 }
 621                 else {
 622                     nodes.addAll( PhylogenyMethods.searchData( query,
 623                                                                tree,
 624                                                                getOptions().isSearchCaseSensitive(),
 625                                                                !getOptions().isMatchWholeTermsOnly(),
 626                                                                getOptions().isSearchWithRegex(),
 627                                                                isShowDomainArchitectures(),
 628                                                                tp != null ? Math.pow( 10, tp
 629                                                                                       .getDomainStructureEvalueThresholdExp() ) : 0 ) );
 630                 }
 631             }
 632             if ( getOptions().isInverseSearchResult() ) {
 633                 final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
 634                 final Set<Long> temp_nodes = nodes;
 635                 nodes = new HashSet<Long>();
 636                 for( final PhylogenyNode n : all ) {
 637                     if ( (!temp_nodes.contains( n.getId() )) && n.isHasNodeData() ) {
 638                         nodes.add( n.getId() );
 639                     }
 640                 }
 641             }
 642         }
 643         if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
 644             main_panel.getCurrentTreePanel().setFoundNodes0( new HashSet<Long>() );
 645             for( final Long node : nodes ) {
 646                 main_panel.getCurrentTreePanel().getFoundNodes0().add( node );
 647             }
 648             setSearchFoundCountsOnLabel0( nodes.size() );
 649         }
 650         else {
 651             setSearchFoundCountsOnLabel0( 0 );
 652             searchReset0();
 653         }
 654     }
 655
 656     private void search1( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
 657         getSearchFoundCountsLabel1().setVisible( true );
 658         getSearchResetButton1().setEnabled( true );
 659         getSearchResetButton1().setVisible( true );
 660         String[] queries = null;
 661         Set<Long> nodes = null;
 662         if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
 663             queries = query_str.split( ",+" );
 664         }
 665         else {
 666             queries = new String[ 1 ];
 667             queries[ 0 ] = query_str.trim();
 668         }
 669         if ( ( queries != null ) && ( queries.length > 0 ) ) {
 670             nodes = new HashSet<Long>();
 671             for( String query : queries ) {
 672                 if ( ForesterUtil.isEmpty( query ) ) {
 673                     continue;
 674                 }
 675                 query = query.trim();
 676                 final TreePanel tp = getMainPanel().getCurrentTreePanel();
 677                 if ( ( query.indexOf( '+' ) > 0 ) && !getOptions().isSearchWithRegex() ) {
 678                     nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
 679                                                                          tree,
 680                                                                          getOptions().isSearchCaseSensitive(),
 681                                                                          !getOptions().isMatchWholeTermsOnly(),
 682                                                                          isShowDomainArchitectures(),
 683                                                                          tp != null ? Math.pow( 10,
 684                                                                                                 tp.getDomainStructureEvalueThresholdExp() )
 685                                                                                                 : 0 ) );
 686                 }
 687                 else {
 688                     nodes.addAll( PhylogenyMethods.searchData( query,
 689                                                                tree,
 690                                                                getOptions().isSearchCaseSensitive(),
 691                                                                !getOptions().isMatchWholeTermsOnly(),
 692                                                                getOptions().isSearchWithRegex(),
 693                                                                isShowDomainArchitectures(),
 694                                                                tp != null ? Math.pow( 10, tp
 695                                                                                       .getDomainStructureEvalueThresholdExp() ) : 0 ) );
 696                 }
 697             }
 698             if ( getOptions().isInverseSearchResult() ) {
 699                 final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
 700                 final Set<Long> temp_nodes = nodes;
 701                 nodes = new HashSet<Long>();
 702                 for( final PhylogenyNode n : all ) {
 703                     if ( (!temp_nodes.contains( n.getId() )) && n.isHasNodeData() ) {
 704                         nodes.add( n.getId() );
 705                     }
 706                 }
 707             }
 708         }
 709         if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
 710             main_panel.getCurrentTreePanel().setFoundNodes1( new HashSet<Long>() );
 711             for( final Long node : nodes ) {
 712                 main_panel.getCurrentTreePanel().getFoundNodes1().add( node );
 713             }
 714             setSearchFoundCountsOnLabel1( nodes.size() );
 715         }
 716         else {
 717             setSearchFoundCountsOnLabel1( 0 );
 718             searchReset1();
 719         }
 720     }
 721
 722     private void setDrawPhylogram( final int index, final boolean b ) {
 723         getIsDrawPhylogramList().set( index, b );
 724     }
 725
 726     private void setupClickToOptions() {
 727         final int default_option = _configuration.getDefaultDisplayClicktoOption();
 728         int selected_index = 0;
 729         int cb_index = 0;
 730         if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
 731             _show_data_item = cb_index;
 732             addClickToOption( Configuration.display_node_data,
 733                               _configuration.getClickToTitle( Configuration.display_node_data ) );
 734             if ( default_option == Configuration.display_node_data ) {
 735                 selected_index = cb_index;
 736             }
 737             cb_index++;
 738         }
 739         if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
 740             _collapse_cb_item = cb_index;
 741             addClickToOption( Configuration.collapse_uncollapse,
 742                               _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
 743             if ( default_option == Configuration.collapse_uncollapse ) {
 744                 selected_index = cb_index;
 745             }
 746             cb_index++;
 747         }
 748 if ( _configuration.doDisplayClickToOption( Configuration.uncollapse_all ) ) {
 749             _uncollapse_all_cb_item = cb_index;
 750             addClickToOption( Configuration.uncollapse_all,
 751                               _configuration.getClickToTitle( Configuration.uncollapse_all ) );
 752             if ( default_option == Configuration.uncollapse_all ) {
 753                 selected_index = cb_index;
 754             }
 755             cb_index++;
 756 }
 757         if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
 758             _reroot_cb_item = cb_index;
 759             addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
 760             if ( default_option == Configuration.reroot ) {
 761                 selected_index = cb_index;
 762             }
 763             cb_index++;
 764         }
 765         if ( _configuration.doDisplayClickToOption( Configuration.subtree ) ) {
 766             _subtree_cb_item = cb_index;
 767             addClickToOption( Configuration.subtree, _configuration.getClickToTitle( Configuration.subtree ) );
 768             if ( default_option == Configuration.subtree ) {
 769                 selected_index = cb_index;
 770             }
 771             cb_index++;
 772         }
 773         if ( _configuration.doDisplayClickToOption( Configuration.swap ) ) {
 774             _swap_cb_item = cb_index;
 775             addClickToOption( Configuration.swap, _configuration.getClickToTitle( Configuration.swap ) );
 776             if ( default_option == Configuration.swap ) {
 777                 selected_index = cb_index;
 778             }
 779             cb_index++;
 780         }
 781 if ( _configuration.doDisplayClickToOption( Configuration.order_subtree ) ) {
 782             _order_subtree_cb_item = cb_index;
 783             addClickToOption( Configuration.order_subtree,
 784                               _configuration.getClickToTitle( Configuration.order_subtree ) );
 785             if ( default_option == Configuration.order_subtree ) {
 786                 selected_index = cb_index;
 787             }
 788             cb_index++;
 789 }
 790
 791         if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
 792             _sort_descendents_item = cb_index;
 793             addClickToOption( Configuration.sort_descendents,
 794                               _configuration.getClickToTitle( Configuration.sort_descendents ) );
 795             if ( default_option == Configuration.sort_descendents ) {
 796                 selected_index = cb_index;
 797             }
 798             cb_index++;
 799         }
 800         if ( _configuration.doDisplayClickToOption( Configuration.color_node_font ) ) {
 801             _color_node_font_item = cb_index;
 802             addClickToOption( Configuration.color_node_font,
 803                               _configuration.getClickToTitle( Configuration.color_node_font ) );
 804             if ( default_option == Configuration.color_node_font ) {
 805                 selected_index = cb_index;
 806             }
 807             cb_index++;
 808         }
 809         if ( _configuration.doDisplayClickToOption( Configuration.change_node_font ) ) {
 810             _change_node_font_item = cb_index;
 811             addClickToOption( Configuration.change_node_font,
 812                               _configuration.getClickToTitle( Configuration.change_node_font ) );
 813             if ( default_option == Configuration.change_node_font ) {
 814                 selected_index = cb_index;
 815             }
 816             cb_index++;
 817         }
 818         if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
 819             _color_subtree_cb_item = cb_index;
 820             addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
 821             if ( default_option == Configuration.color_subtree ) {
 822                 selected_index = cb_index;
 823             }
 824             cb_index++;
 825         }
 826         if ( _configuration.doDisplayClickToOption( Configuration.open_seq_web ) ) {
 827             _open_seq_web_item = cb_index;
 828             addClickToOption( Configuration.open_seq_web, _configuration.getClickToTitle( Configuration.open_seq_web ) );
 829             if ( default_option == Configuration.open_seq_web ) {
 830                 selected_index = cb_index;
 831             }
 832             cb_index++;
 833         }
 834         if ( _configuration.doDisplayClickToOption( Configuration.open_pdb_web ) ) {
 835             _open_pdb_item = cb_index;
 836             addClickToOption( Configuration.open_pdb_web, _configuration.getClickToTitle( Configuration.open_pdb_web ) );
 837             if ( default_option == Configuration.open_pdb_web ) {
 838                 selected_index = cb_index;
 839             }
 840             cb_index++;
 841         }
 842         if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
 843             _open_tax_web_item = cb_index;
 844             addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
 845             if ( default_option == Configuration.open_tax_web ) {
 846                 selected_index = cb_index;
 847             }
 848             cb_index++;
 849         }
 850         if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
 851             _blast_item = cb_index;
 852             addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
 853             if ( default_option == Configuration.blast ) {
 854                 selected_index = cb_index;
 855             }
 856             cb_index++;
 857         }
 858         if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) {
 859             _select_nodes_item = cb_index;
 860             addClickToOption( Configuration.select_nodes, _configuration.getClickToTitle( Configuration.select_nodes ) );
 861             if ( default_option == Configuration.select_nodes ) {
 862                 selected_index = cb_index;
 863             }
 864             cb_index++;
 865         }
 866         if ( _configuration.doDisplayClickToOption( Configuration.get_ext_desc_data ) ) {
 867             _get_ext_desc_data = cb_index;
 868             if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) {
 869                 addClickToOption( Configuration.get_ext_desc_data, getConfiguration()
 870                                   .getLabelForGetExtDescendentsData() );
 871             }
 872             else {
 873                 addClickToOption( Configuration.get_ext_desc_data,
 874                                   getConfiguration().getClickToTitle( Configuration.get_ext_desc_data ) );
 875             }
 876             if ( default_option == Configuration.get_ext_desc_data ) {
 877                 selected_index = cb_index;
 878             }
 879             cb_index++;
 880         }
 881         if ( getOptions().isEditable() ) {
 882             if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
 883                 _cut_subtree_item = cb_index;
 884                 addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
 885                 if ( default_option == Configuration.cut_subtree ) {
 886                     selected_index = cb_index;
 887                 }
 888                 cb_index++;
 889             }
 890             if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
 891                 _copy_subtree_item = cb_index;
 892                 addClickToOption( Configuration.copy_subtree,
 893                                   _configuration.getClickToTitle( Configuration.copy_subtree ) );
 894                 if ( default_option == Configuration.copy_subtree ) {
 895                     selected_index = cb_index;
 896                 }
 897                 cb_index++;
 898             }
 899             if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
 900                 _paste_subtree_item = cb_index;
 901                 addClickToOption( Configuration.paste_subtree,
 902                                   _configuration.getClickToTitle( Configuration.paste_subtree ) );
 903                 if ( default_option == Configuration.paste_subtree ) {
 904                     selected_index = cb_index;
 905                 }
 906                 cb_index++;
 907             }
 908             if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
 909                 _delete_node_or_subtree_item = cb_index;
 910                 addClickToOption( Configuration.delete_subtree_or_node,
 911                                   _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
 912                 if ( default_option == Configuration.delete_subtree_or_node ) {
 913                     selected_index = cb_index;
 914                 }
 915                 cb_index++;
 916             }
 917             if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
 918                 _add_new_node_item = cb_index;
 919                 addClickToOption( Configuration.add_new_node,
 920                                   _configuration.getClickToTitle( Configuration.add_new_node ) );
 921                 if ( default_option == Configuration.add_new_node ) {
 922                     selected_index = cb_index;
 923                 }
 924                 cb_index++;
 925             }
 926             if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
 927                 _edit_node_data_item = cb_index;
 928                 addClickToOption( Configuration.edit_node_data,
 929                                   _configuration.getClickToTitle( Configuration.edit_node_data ) );
 930                 if ( default_option == Configuration.edit_node_data ) {
 931                     selected_index = cb_index;
 932                 }
 933                 cb_index++;
 934             }
 935         }
 936         // Set default selection and its action
 937         _click_to_combobox.setSelectedIndex( selected_index );
 938         setClickToAction( selected_index );
 939     }
 940
 941     private void setupDisplayCheckboxes() {
 942         if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
 943             addCheckbox( Configuration.display_as_phylogram,
 944                          _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
 945             setCheckbox( Configuration.display_as_phylogram,
 946                          _configuration.doCheckOption( Configuration.display_as_phylogram ) );
 947         }
 948         if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
 949             addCheckbox( Configuration.dynamically_hide_data,
 950                          _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
 951             setCheckbox( Configuration.dynamically_hide_data,
 952                          _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
 953         }
 954         if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
 955             addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
 956             setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
 957         }
 958         if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
 959             addCheckbox( Configuration.display_internal_data,
 960                          _configuration.getDisplayTitle( Configuration.display_internal_data ) );
 961             setCheckbox( Configuration.display_internal_data,
 962                          _configuration.doCheckOption( Configuration.display_internal_data ) );
 963         }
 964         if ( _configuration.doDisplayOption( Configuration.color_according_to_sequence ) ) {
 965             addCheckbox( Configuration.color_according_to_sequence,
 966                          _configuration.getDisplayTitle( Configuration.color_according_to_sequence ) );
 967             setCheckbox( Configuration.color_according_to_sequence,
 968                          _configuration.doCheckOption( Configuration.color_according_to_sequence ) );
 969         }
 970         if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
 971             addCheckbox( Configuration.color_according_to_species,
 972                          _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
 973             setCheckbox( Configuration.color_according_to_species,
 974                          _configuration.doCheckOption( Configuration.color_according_to_species ) );
 975         }
 976         if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
 977             addCheckbox( Configuration.color_according_to_annotation,
 978                          _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
 979             setCheckbox( Configuration.color_according_to_annotation,
 980                          _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
 981         }
 982         if ( _configuration.doDisplayOption( Configuration.use_style ) ) {
 983             addCheckbox( Configuration.use_style, _configuration.getDisplayTitle( Configuration.use_style ) );
 984             setCheckbox( Configuration.use_style, _configuration.doCheckOption( Configuration.use_style ) );
 985         }
 986         if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
 987             addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
 988             setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
 989         }
 990         final JLabel label = new JLabel( "Display Data:" );
 991         label.setFont( ControlPanel.jcb_bold_font );
 992         if ( !getConfiguration().isUseNativeUI() ) {
 993             label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
 994         }
 995         add( label );
 996         if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
 997             addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
 998             setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
 999         }
1000         if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
1001             addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
1002             setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
1003         }
1004         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
1005             addCheckbox( Configuration.show_taxonomy_scientific_names,
1006                          _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
1007             setCheckbox( Configuration.show_taxonomy_scientific_names,
1008                          _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
1009         }
1010         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
1011             addCheckbox( Configuration.show_taxonomy_common_names,
1012                          _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
1013             setCheckbox( Configuration.show_taxonomy_common_names,
1014                          _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
1015         }
1016         if ( _configuration.doDisplayOption( Configuration.show_tax_rank ) ) {
1017             addCheckbox( Configuration.show_tax_rank, _configuration.getDisplayTitle( Configuration.show_tax_rank ) );
1018             setCheckbox( Configuration.show_tax_rank, _configuration.doCheckOption( Configuration.show_tax_rank ) );
1019         }
1020         if ( _configuration.doDisplayOption( Configuration.show_seq_names ) ) {
1021             addCheckbox( Configuration.show_seq_names, _configuration.getDisplayTitle( Configuration.show_seq_names ) );
1022             setCheckbox( Configuration.show_seq_names, _configuration.doCheckOption( Configuration.show_seq_names ) );
1023         }
1024         if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
1025             addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
1026             setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
1027         }
1028         if ( _configuration.doDisplayOption( Configuration.show_seq_symbols ) ) {
1029             addCheckbox( Configuration.show_seq_symbols,
1030                          _configuration.getDisplayTitle( Configuration.show_seq_symbols ) );
1031             setCheckbox( Configuration.show_seq_symbols, _configuration.doCheckOption( Configuration.show_seq_symbols ) );
1032         }
1033         if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
1034             addCheckbox( Configuration.show_sequence_acc,
1035                          _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
1036             setCheckbox( Configuration.show_sequence_acc,
1037                          _configuration.doCheckOption( Configuration.show_sequence_acc ) );
1038         }
1039         if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
1040             addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
1041             setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
1042         }
1043         if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
1044             addCheckbox( Configuration.write_confidence_values,
1045                          _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
1046             setCheckbox( Configuration.write_confidence_values,
1047                          _configuration.doCheckOption( Configuration.write_confidence_values ) );
1048         }
1049         if ( _configuration.doDisplayOption( Configuration.write_branch_length_values ) ) {
1050             addCheckbox( Configuration.write_branch_length_values,
1051                          _configuration.getDisplayTitle( Configuration.write_branch_length_values ) );
1052             setCheckbox( Configuration.write_branch_length_values,
1053                          _configuration.doCheckOption( Configuration.write_branch_length_values ) );
1054         }
1055         if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
1056             addCheckbox( Configuration.show_binary_characters,
1057                          _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
1058             setCheckbox( Configuration.show_binary_characters,
1059                          _configuration.doCheckOption( Configuration.show_binary_characters ) );
1060         }
1061         if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
1062             addCheckbox( Configuration.show_binary_character_counts,
1063                          _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
1064             setCheckbox( Configuration.show_binary_character_counts,
1065                          _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
1066         }
1067         if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
1068             addCheckbox( Configuration.show_domain_architectures,
1069                          _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
1070             setCheckbox( Configuration.show_domain_architectures,
1071                          _configuration.doCheckOption( Configuration.show_domain_architectures ) );
1072         }
1073         if ( _configuration.doDisplayOption( Configuration.show_mol_seqs ) ) {
1074             addCheckbox( Configuration.show_mol_seqs, _configuration.getDisplayTitle( Configuration.show_mol_seqs ) );
1075             setCheckbox( Configuration.show_mol_seqs, _configuration.doCheckOption( Configuration.show_mol_seqs ) );
1076         }
1077         if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
1078             addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
1079             setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
1080         }
1081         if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
1082             addCheckbox( Configuration.show_vector_data,
1083                          _configuration.getDisplayTitle( Configuration.show_vector_data ) );
1084             setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
1085         }
1086         if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
1087             addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
1088             setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
1089         }
1090         if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
1091             addCheckbox( Configuration.show_taxonomy_images,
1092                          _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
1093             setCheckbox( Configuration.show_taxonomy_images,
1094                          _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
1095         }
1096     }
1097
1098     private void setVisibilityOfDomainStrucureControls() {
1099         if ( _zoom_in_domain_structure != null ) {
1100             final MainFrame mf = getMainFrame();
1101             if ( mf != null ) {
1102                 if ( isShowDomainArchitectures() ) {
1103                     _domain_display_label.setVisible( true );
1104                     _zoom_in_domain_structure.setVisible( true );
1105                     _zoom_out_domain_structure.setVisible( true );
1106                     _decr_domain_structure_evalue_thr.setVisible( true );
1107                     _incr_domain_structure_evalue_thr.setVisible( true );
1108                     _domain_structure_evalue_thr_tf.setVisible( true );
1109                     if ( mf._right_line_up_domains_cbmi != null ) {
1110                         mf._right_line_up_domains_cbmi.setVisible( true );
1111                     }
1112                     if ( mf._show_domain_labels != null ) {
1113                         mf._show_domain_labels.setVisible( true );
1114                     }
1115                 }
1116                 else {
1117                     _domain_display_label.setVisible( false );
1118                     _zoom_in_domain_structure.setVisible( false );
1119                     _zoom_out_domain_structure.setVisible( false );
1120                     _decr_domain_structure_evalue_thr.setVisible( false );
1121                     _incr_domain_structure_evalue_thr.setVisible( false );
1122                     _domain_structure_evalue_thr_tf.setVisible( false );
1123                     if ( mf._right_line_up_domains_cbmi != null ) {
1124                         mf._right_line_up_domains_cbmi.setVisible( false );
1125                     }
1126                     if ( mf._show_domain_labels != null ) {
1127                         mf._show_domain_labels.setVisible( false );
1128                     }
1129                 }
1130             }
1131         }
1132     }
1133
1134     void activateButtonToReturnToSuperTree( int index ) {
1135         --index;
1136         if ( index > 0 ) {
1137             _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT + " " + index );
1138         }
1139         else {
1140             _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
1141         }
1142         _return_to_super_tree.setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
1143         _return_to_super_tree.setEnabled( true );
1144     }
1145
1146     /**
1147      * Add zoom and quick edit buttons. (Last modified 8/9/04)
1148      */
1149     void addButtons() {
1150         final JLabel spacer = new JLabel( "" );
1151         spacer.setOpaque( false );
1152         add( spacer );
1153         final JPanel x_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
1154         final JPanel y_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
1155         final JPanel z_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
1156         if ( !getConfiguration().isUseNativeUI() ) {
1157             x_panel.setBackground( getBackground() );
1158             y_panel.setBackground( getBackground() );
1159             z_panel.setBackground( getBackground() );
1160         }
1161         add( _zoom_label = new JLabel( "Zoom:" ) );
1162         customizeLabel( _zoom_label, getConfiguration() );
1163         add( x_panel );
1164         add( y_panel );
1165         add( z_panel );
1166         if ( getConfiguration().isUseNativeUI() ) {
1167             _zoom_in_x = new JButton( "+" );
1168             _zoom_out_x = new JButton( "-" );
1169         }
1170         else {
1171             _zoom_in_x = new JButton( "X+" );
1172             _zoom_out_x = new JButton( "X-" );
1173         }
1174         _zoom_in_y = new JButton( "Y+" );
1175         _zoom_out_y = new JButton( "Y-" );
1176         _show_whole = new JButton( "F" );
1177         _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [F or Home]" );
1178         _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+cursor-right]" );
1179         _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+cursor-up]" );
1180         _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+cursor-left]" );
1181         _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+cursor-down]" );
1182         if ( getConfiguration().isUseNativeUI() && ForesterUtil.isMac() ) {
1183             _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
1184             _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );
1185         }
1186         else {
1187             _zoom_out_x.setPreferredSize( new Dimension( 10, 10 ) );
1188             _zoom_in_x.setPreferredSize( new Dimension( 10, 10 ) );
1189         }
1190         _zoom_out_y.setPreferredSize( new Dimension( 10, 10 ) );
1191         _zoom_in_y.setPreferredSize( new Dimension( 10, 10 ) );
1192         _show_whole.setPreferredSize( new Dimension( 10, 10 ) );
1193         _return_to_super_tree = new JButton( RETURN_TO_SUPER_TREE_TEXT );
1194         _return_to_super_tree.setEnabled( false );
1195         _order = new JButton( "Order Tree" );
1196         _uncollapse_all = new JButton( "Uncollapse All" );
1197
1198         addJButton( _zoom_in_y, x_panel );
1199         addJButton( _zoom_out_x, y_panel );
1200         addJButton( _show_whole, y_panel );
1201         addJButton( _zoom_in_x, y_panel );
1202         addJButton( _zoom_out_y, z_panel );
1203         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
1204             setUpControlsForDomainStrucures();
1205         }
1206         final JLabel spacer2 = new JLabel( "" );
1207         add( spacer2 );
1208         addJButton( _return_to_super_tree, this );
1209         addJButton( _order, this );
1210         addJButton( _uncollapse_all, this );
1211         final JLabel spacer3 = new JLabel( "" );
1212         add( spacer3 );
1213         setVisibilityOfDomainStrucureControls();
1214     }
1215
1216     void addCheckbox( final int which, final String title ) {
1217         final JPanel ch_panel = new JPanel( new BorderLayout( 0, 0 ) );
1218         switch ( which ) {
1219             case Configuration.display_as_phylogram:
1220                 _display_as_phylogram_cb = new JCheckBox( title );
1221                 getDisplayAsPhylogramCb().setToolTipText( "To switch between phylogram and cladogram display" );
1222                 addJCheckBox( getDisplayAsPhylogramCb(), ch_panel );
1223                 add( ch_panel );
1224                 break;
1225             case Configuration.display_internal_data:
1226                 _display_internal_data = new JCheckBox( title );
1227                 _display_internal_data.setToolTipText( "To allow or disallow display of internal labels" );
1228                 addJCheckBox( _display_internal_data, ch_panel );
1229                 add( ch_panel );
1230                 break;
1231             case Configuration.color_according_to_species:
1232                 _color_acc_species = new JCheckBox( title );
1233                 _color_acc_species.setToolTipText( "To colorize node labels as a function of taxonomy" );
1234                 addJCheckBox( _color_acc_species, ch_panel );
1235                 add( ch_panel );
1236                 break;
1237             case Configuration.color_according_to_sequence:
1238                 _color_acc_sequence = new JCheckBox( title );
1239                 _color_acc_sequence.setToolTipText( "To colorize node labels as a function of sequence name" );
1240                 addJCheckBox( _color_acc_sequence, ch_panel );
1241                 add( ch_panel );
1242                 break;
1243             case Configuration.color_according_to_annotation:
1244                 _color_according_to_annotation = new JCheckBox( title );
1245                 _color_according_to_annotation
1246                         .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" );
1247                 addJCheckBox( _color_according_to_annotation, ch_panel );
1248                 add( ch_panel );
1249                 break;
1250             case Configuration.show_node_names:
1251                 _show_node_names = new JCheckBox( title );
1252                 addJCheckBox( _show_node_names, ch_panel );
1253                 add( ch_panel );
1254                 break;
1255             case Configuration.show_taxonomy_scientific_names:
1256                 _show_taxo_scientific_names = new JCheckBox( title );
1257                 addJCheckBox( _show_taxo_scientific_names, ch_panel );
1258                 add( ch_panel );
1259                 break;
1260             case Configuration.show_taxonomy_common_names:
1261                 _show_taxo_common_names = new JCheckBox( title );
1262                 addJCheckBox( _show_taxo_common_names, ch_panel );
1263                 add( ch_panel );
1264                 break;
1265             case Configuration.show_tax_code:
1266                 _show_taxo_code = new JCheckBox( title );
1267                 addJCheckBox( _show_taxo_code, ch_panel );
1268                 add( ch_panel );
1269                 break;
1270             case Configuration.show_tax_rank:
1271                 _show_taxo_rank = new JCheckBox( title );
1272                 addJCheckBox( _show_taxo_rank, ch_panel );
1273                 add( ch_panel );
1274                 break;
1275             case Configuration.show_taxonomy_images:
1276                 _show_taxo_images_cb = new JCheckBox( title );
1277                 addJCheckBox( _show_taxo_images_cb, ch_panel );
1278                 add( ch_panel );
1279                 break;
1280             case Configuration.show_binary_characters:
1281                 _show_binary_characters = new JCheckBox( title );
1282                 addJCheckBox( _show_binary_characters, ch_panel );
1283                 add( ch_panel );
1284                 break;
1285             case Configuration.show_annotation:
1286                 _show_annotation = new JCheckBox( title );
1287                 addJCheckBox( _show_annotation, ch_panel );
1288                 add( ch_panel );
1289                 break;
1290             case Configuration.show_binary_character_counts:
1291                 _show_binary_character_counts = new JCheckBox( title );
1292                 addJCheckBox( _show_binary_character_counts, ch_panel );
1293                 add( ch_panel );
1294                 break;
1295             case Configuration.write_confidence_values:
1296                 _write_confidence = new JCheckBox( title );
1297                 addJCheckBox( getWriteConfidenceCb(), ch_panel );
1298                 add( ch_panel );
1299                 break;
1300             case Configuration.write_events:
1301                 _show_events = new JCheckBox( title );
1302                 addJCheckBox( getShowEventsCb(), ch_panel );
1303                 add( ch_panel );
1304                 break;
1305             case Configuration.use_style:
1306                 _use_visual_styles_cb = new JCheckBox( title );
1307                 getUseVisualStylesCb()
1308                         .setToolTipText( "To use visual styles (node colors, fonts) and branch colors, if present" );
1309                 addJCheckBox( getUseVisualStylesCb(), ch_panel );
1310                 add( ch_panel );
1311                 break;
1312             case Configuration.width_branches:
1313                 _width_branches = new JCheckBox( title );
1314                 _width_branches.setToolTipText( "To use branch width values, if present" );
1315                 addJCheckBox( _width_branches, ch_panel );
1316                 add( ch_panel );
1317                 break;
1318             case Configuration.write_branch_length_values:
1319                 _write_branch_length_values = new JCheckBox( title );
1320                 addJCheckBox( _write_branch_length_values, ch_panel );
1321                 add( ch_panel );
1322                 break;
1323             case Configuration.show_domain_architectures:
1324                 _show_domain_architectures = new JCheckBox( title );
1325                 addJCheckBox( _show_domain_architectures, ch_panel );
1326                 add( ch_panel );
1327                 break;
1328             case Configuration.show_mol_seqs:
1329                 _show_mol_seqs = new JCheckBox( title );
1330                 addJCheckBox( _show_mol_seqs, ch_panel );
1331                 add( ch_panel );
1332                 break;
1333             case Configuration.show_seq_names:
1334                 _show_seq_names = new JCheckBox( title );
1335                 addJCheckBox( _show_seq_names, ch_panel );
1336                 add( ch_panel );
1337                 break;
1338             case Configuration.show_gene_names:
1339                 _show_gene_names = new JCheckBox( title );
1340                 addJCheckBox( _show_gene_names, ch_panel );
1341                 add( ch_panel );
1342                 break;
1343             case Configuration.show_seq_symbols:
1344                 _show_seq_symbols = new JCheckBox( title );
1345                 addJCheckBox( _show_seq_symbols, ch_panel );
1346                 add( ch_panel );
1347                 break;
1348             case Configuration.show_sequence_acc:
1349                 _show_sequence_acc = new JCheckBox( title );
1350                 addJCheckBox( _show_sequence_acc, ch_panel );
1351                 add( ch_panel );
1352                 break;
1353             case Configuration.dynamically_hide_data:
1354                 _dynamically_hide_data = new JCheckBox( title );
1355                 getDynamicallyHideData().setToolTipText( "To hide labels depending on expected visibility" );
1356                 addJCheckBox( getDynamicallyHideData(), ch_panel );
1357                 add( ch_panel );
1358                 break;
1359             case Configuration.node_data_popup:
1360                 _node_desc_popup_cb = new JCheckBox( title );
1361                 getNodeDescPopupCb().setToolTipText( "To enable mouse rollover display of basic node data" );
1362                 addJCheckBox( getNodeDescPopupCb(), ch_panel );
1363                 add( ch_panel );
1364                 break;
1365             case Configuration.show_relation_confidence:
1366                 _seq_relation_confidence_switch = new JCheckBox( title );
1367                 addJCheckBox( _seq_relation_confidence_switch, ch_panel );
1368                 add( ch_panel );
1369                 break;
1370             case Configuration.show_vector_data:
1371                 _show_vector_data_cb = new JCheckBox( title );
1372                 addJCheckBox( _show_vector_data_cb, ch_panel );
1373                 add( ch_panel );
1374                 break;
1375             case Configuration.show_properties:
1376                 _show_properties_cb = new JCheckBox( title );
1377                 addJCheckBox( _show_properties_cb, ch_panel );
1378                 add( ch_panel );
1379                 break;
1380             default:
1381                 throw new RuntimeException( "unknown checkbox: " + which );
1382         }
1383     }// addCheckbox
1384
1385     void addJButton( final JButton jb, final JPanel p ) {
1386         jb.setFocusPainted( false );
1387         jb.setFont( ControlPanel.jcb_font );
1388         if ( !_configuration.isUseNativeUI() ) {
1389             jb.setBorder( BorderFactory.createLineBorder( getConfiguration().getGuiButtonBorderColor() ) );
1390             jb.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
1391             jb.setForeground( getConfiguration().getGuiButtonTextColor() );
1392         }
1393         p.add( jb );
1394         jb.addActionListener( this );
1395     }
1396
1397     void addJCheckBox( final JCheckBox jcb, final JPanel p ) {
1398         jcb.setFocusPainted( false );
1399         jcb.setFont( ControlPanel.jcb_font );
1400         if ( !_configuration.isUseNativeUI() ) {
1401             jcb.setBackground( getConfiguration().getGuiBackgroundColor() );
1402             jcb.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1403         }
1404         p.add( jcb, "Center" );
1405         jcb.addActionListener( this );
1406     }
1407
1408     void addJTextField( final JTextField tf, final JPanel p ) {
1409         if ( !_configuration.isUseNativeUI() ) {
1410             tf.setForeground( getConfiguration().getGuiBackgroundColor() );
1411             tf.setFont( ControlPanel.jcb_font );
1412         }
1413         p.add( tf );
1414         tf.addActionListener( this );
1415     }
1416
1417     void deactivateButtonToReturnToSuperTree() {
1418         _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
1419         _return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
1420         _return_to_super_tree.setEnabled( false );
1421     }
1422
1423     void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
1424         if ( ( _mainpanel != null )
1425                 && ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
1426
1427             if ( recalc_longest_ext_node_info ) {
1428                 _mainpanel.getCurrentTreePanel().initNodeData();
1429                 _mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
1430             }
1431             if ( getOptions().isShowOverview() ) {
1432                 _mainpanel.getCurrentTreePanel().updateOvSizes();
1433             }
1434             _mainpanel.getCurrentTreePanel().recalculateMaxDistanceToRoot();
1435             setVisibilityOfDomainStrucureControls();
1436             updateDomainStructureEvaluethresholdDisplay();
1437             _mainpanel.getCurrentTreePanel().calculateScaleDistance();
1438             _mainpanel.getCurrentTreePanel().calcMaxDepth();
1439             _mainpanel.adjustJScrollPane();
1440
1441             _mainpanel.getCurrentTreePanel().repaint();
1442             // _mainpanel.getCurrentTreePanel().setUpUrtFactor();
1443         }
1444     }
1445
1446     void endClickToOptions() {
1447         _click_to_combobox.addActionListener( this );
1448     }
1449
1450     /**
1451      * Indicates what action should be execute when a node is clicked
1452      *
1453      * @return the click-on action
1454      */
1455     NodeClickAction getActionWhenNodeClicked() {
1456         return _action_when_node_clicked;
1457     }
1458
1459     Map<Integer, String> getAllClickToItems() {
1460         return _all_click_to_names;
1461     }
1462
1463     Map<String, Color> getAnnotationColors() {
1464         return _annotation_colors;
1465     }
1466
1467     Configuration getConfiguration() {
1468         return _configuration;
1469     }
1470
1471     TreePanel getCurrentTreePanel() {
1472         return getMainPanel().getCurrentTreePanel();
1473     }
1474
1475     MainPanel getMainPanel() {
1476         return _mainpanel;
1477     }
1478
1479     Options getOptions() {
1480         return getMainPanel().getOptions();
1481     }
1482
1483     JLabel getSearchFoundCountsLabel0() {
1484         return _search_found_label_0;
1485     }
1486
1487     JLabel getSearchFoundCountsLabel1() {
1488         return _search_found_label_1;
1489     }
1490
1491     JButton getSearchResetButton0() {
1492         return _search_reset_button_0;
1493     }
1494
1495     JButton getSearchResetButton1() {
1496         return _search_reset_button_1;
1497     }
1498
1499     JTextField getSearchTextField0() {
1500         return _search_tf_0;
1501     }
1502
1503     JTextField getSearchTextField1() {
1504         return _search_tf_1;
1505     }
1506
1507     Map<String, Color> getSequenceColors() {
1508         return _sequence_colors;
1509     }
1510
1511     List<String> getSingleClickToNames() {
1512         return _click_to_names;
1513     }
1514
1515     Map<String, Color> getSpeciesColors() {
1516         return _species_colors;
1517     }
1518
1519     boolean isAntialiasScreenText() {
1520         return true;
1521     }
1522
1523     boolean isColorAccordingToAnnotation() {
1524         return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
1525     }
1526
1527     boolean isColorAccordingToSequence() {
1528         return ( ( _color_acc_sequence != null ) && _color_acc_sequence.isSelected() );
1529     }
1530
1531     boolean isColorAccordingToTaxonomy() {
1532         return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
1533     }
1534
1535     boolean isDrawPhylogram() {
1536         return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
1537     }
1538
1539     boolean isDynamicallyHideData() {
1540         return ( ( getDynamicallyHideData() != null ) && getDynamicallyHideData().isSelected() );
1541     }
1542
1543     boolean isEvents() {
1544         return ( ( getShowEventsCb() != null ) && getShowEventsCb().isSelected() );
1545     }
1546
1547     boolean isNodeDescPopup() {
1548         return ( ( getNodeDescPopupCb() != null ) && getNodeDescPopupCb().isSelected() );
1549     }
1550
1551     boolean isShowAnnotation() {
1552         return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
1553     }
1554
1555     boolean isShowBinaryCharacterCounts() {
1556         return ( ( _show_binary_character_counts != null ) && _show_binary_character_counts.isSelected() );
1557     }
1558
1559     boolean isShowBinaryCharacters() {
1560         return ( ( _show_binary_characters != null ) && _show_binary_characters.isSelected() );
1561     }
1562
1563     boolean isShowConfidenceValues() {
1564         return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
1565     }
1566
1567     boolean isShowDomainArchitectures() {
1568         return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
1569     }
1570
1571     boolean isShowGeneNames() {
1572         return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
1573     }
1574
1575     boolean isShowInternalData() {
1576         return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() );
1577     }
1578
1579     boolean isShowNodeNames() {
1580         return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
1581     }
1582
1583     boolean isShowSeqNames() {
1584         return ( ( _show_seq_names != null ) && _show_seq_names.isSelected() );
1585     }
1586
1587     boolean isShowSeqSymbols() {
1588         return ( ( _show_seq_symbols != null ) && _show_seq_symbols.isSelected() );
1589     }
1590
1591     boolean isShowSequenceAcc() {
1592         return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
1593     }
1594
1595     boolean isShowSequenceRelationConfidence() {
1596         return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
1597     }
1598
1599     boolean isShowSequenceRelations() {
1600         return ( ( _show_sequence_relations != null ) && ( _show_sequence_relations.getSelectedIndex() > 0 ) );
1601     }
1602
1603     boolean isShowTaxonomyCode() {
1604         return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
1605     }
1606
1607     boolean isShowTaxonomyRank() {
1608         return ( ( _show_taxo_rank != null ) && _show_taxo_rank.isSelected() );
1609     }
1610
1611     boolean isShowTaxonomyCommonNames() {
1612         return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
1613     }
1614
1615     boolean isShowTaxonomyScientificNames() {
1616         return ( ( _show_taxo_scientific_names != null ) && _show_taxo_scientific_names.isSelected() );
1617     }
1618
1619     boolean isUseVisualStyles() {
1620         return ( ( ( getUseVisualStylesCb() != null ) && getUseVisualStylesCb().isSelected() ) || ( ( getUseVisualStylesCb() == null ) && _color_branches ) );
1621     }
1622
1623     boolean isWidthBranches() {
1624         return ( ( _width_branches != null ) && _width_branches.isSelected() );
1625     }
1626
1627     boolean isWriteBranchLengthValues() {
1628         return ( ( _write_branch_length_values != null ) && _write_branch_length_values.isSelected() );
1629     }
1630
1631     void phylogenyAdded( final Configuration configuration ) {
1632         getIsDrawPhylogramList().add( configuration.isDrawAsPhylogram() );
1633     }
1634
1635     void phylogenyRemoved( final int index ) {
1636         getIsDrawPhylogramList().remove( index );
1637     }
1638
1639     void search0() {
1640         final MainPanel main_panel = getMainPanel();
1641         final Phylogeny tree = main_panel.getCurrentPhylogeny();
1642         if ( ( tree == null ) || tree.isEmpty() ) {
1643             return;
1644         }
1645         String query = getSearchTextField0().getText();
1646         if ( query != null ) {
1647             query = query.trim();
1648         }
1649         if ( !ForesterUtil.isEmpty( query ) ) {
1650             search0( main_panel, tree, query );
1651         }
1652         else {
1653             getSearchFoundCountsLabel0().setVisible( false );
1654             getSearchResetButton0().setEnabled( false );
1655             getSearchResetButton0().setVisible( false );
1656             searchReset0();
1657         }
1658     }
1659
1660     void search1() {
1661         final MainPanel main_panel = getMainPanel();
1662         final Phylogeny tree = main_panel.getCurrentPhylogeny();
1663         if ( ( tree == null ) || tree.isEmpty() ) {
1664             return;
1665         }
1666         String query = getSearchTextField1().getText();
1667         if ( query != null ) {
1668             query = query.trim();
1669         }
1670         if ( !ForesterUtil.isEmpty( query ) ) {
1671             search1( main_panel, tree, query );
1672         }
1673         else {
1674             getSearchFoundCountsLabel1().setVisible( false );
1675             getSearchResetButton1().setEnabled( false );
1676             getSearchResetButton1().setVisible( false );
1677             searchReset1();
1678         }
1679     }
1680
1681     void searchReset0() {
1682         if ( getMainPanel().getCurrentTreePanel() != null ) {
1683             getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
1684         }
1685     }
1686
1687     void searchReset1() {
1688         if ( getMainPanel().getCurrentTreePanel() != null ) {
1689             getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
1690         }
1691     }
1692
1693     void setActionWhenNodeClicked( final NodeClickAction action ) {
1694         _action_when_node_clicked = action;
1695     }
1696
1697     void setAnnotationColors( final Map<String, Color> annotation_colors ) {
1698         _annotation_colors = annotation_colors;
1699     }
1700
1701     void setCheckbox( final int which, final boolean state ) {
1702         switch ( which ) {
1703             case Configuration.display_as_phylogram:
1704                 if ( getDisplayAsPhylogramCb() != null ) {
1705                     getDisplayAsPhylogramCb().setSelected( state );
1706                 }
1707                 break;
1708             case Configuration.display_internal_data:
1709                 if ( _display_internal_data != null ) {
1710                     _display_internal_data.setSelected( state );
1711                 }
1712                 break;
1713             case Configuration.color_according_to_species:
1714                 if ( _color_acc_species != null ) {
1715                     _color_acc_species.setSelected( state );
1716                 }
1717                 break;
1718             case Configuration.color_according_to_sequence:
1719                 if ( _color_acc_sequence != null ) {
1720                     _color_acc_sequence.setSelected( state );
1721                 }
1722                 break;
1723             case Configuration.color_according_to_annotation:
1724                 if ( _color_according_to_annotation != null ) {
1725                     _color_according_to_annotation.setSelected( state );
1726                 }
1727                 break;
1728             case Configuration.show_node_names:
1729                 if ( _show_node_names != null ) {
1730                     _show_node_names.setSelected( state );
1731                 }
1732                 break;
1733             case Configuration.show_taxonomy_scientific_names:
1734                 if ( _show_taxo_scientific_names != null ) {
1735                     _show_taxo_scientific_names.setSelected( state );
1736                 }
1737                 break;
1738             case Configuration.show_taxonomy_common_names:
1739                 if ( _show_taxo_common_names != null ) {
1740                     _show_taxo_common_names.setSelected( state );
1741                 }
1742                 break;
1743             case Configuration.show_tax_code:
1744                 if ( _show_taxo_code != null ) {
1745                     _show_taxo_code.setSelected( state );
1746                 }
1747                 break;
1748             case Configuration.show_tax_rank:
1749                 if ( _show_taxo_rank != null ) {
1750                     _show_taxo_rank.setSelected( state );
1751                 }
1752                 break;
1753             case Configuration.show_taxonomy_images:
1754                 if ( _show_taxo_images_cb != null ) {
1755                     _show_taxo_images_cb.setSelected( state );
1756                 }
1757                 break;
1758             case Configuration.show_annotation:
1759                 if ( _show_annotation != null ) {
1760                     _show_annotation.setSelected( state );
1761                 }
1762                 break;
1763             case Configuration.show_binary_characters:
1764                 if ( _show_binary_characters != null ) {
1765                     _show_binary_characters.setSelected( state );
1766                 }
1767                 break;
1768             case Configuration.show_binary_character_counts:
1769                 if ( _show_binary_character_counts != null ) {
1770                     _show_binary_character_counts.setSelected( state );
1771                 }
1772                 break;
1773             case Configuration.write_confidence_values:
1774                 if ( getWriteConfidenceCb() != null ) {
1775                     getWriteConfidenceCb().setSelected( state );
1776                 }
1777                 break;
1778             case Configuration.write_events:
1779                 if ( getShowEventsCb() != null ) {
1780                     getShowEventsCb().setSelected( state );
1781                 }
1782                 break;
1783             case Configuration.use_style:
1784                 if ( getUseVisualStylesCb() != null ) {
1785                     getUseVisualStylesCb().setSelected( state );
1786                 }
1787                 break;
1788             case Configuration.width_branches:
1789                 if ( _width_branches != null ) {
1790                     _width_branches.setSelected( state );
1791                 }
1792                 break;
1793             case Configuration.show_domain_architectures:
1794                 if ( _show_domain_architectures != null ) {
1795                     _show_domain_architectures.setSelected( state );
1796                 }
1797                 break;
1798             case Configuration.write_branch_length_values:
1799                 if ( _write_branch_length_values != null ) {
1800                     _write_branch_length_values.setSelected( state );
1801                 }
1802                 break;
1803             case Configuration.show_mol_seqs:
1804                 if ( _show_mol_seqs != null ) {
1805                     _show_mol_seqs.setSelected( state );
1806                 }
1807                 break;
1808             case Configuration.show_seq_names:
1809                 if ( _show_seq_names != null ) {
1810                     _show_seq_names.setSelected( state );
1811                 }
1812                 break;
1813             case Configuration.show_gene_names:
1814                 if ( _show_gene_names != null ) {
1815                     _show_gene_names.setSelected( state );
1816                 }
1817                 break;
1818             case Configuration.show_seq_symbols:
1819                 if ( _show_seq_symbols != null ) {
1820                     _show_seq_symbols.setSelected( state );
1821                 }
1822                 break;
1823             case Configuration.show_vector_data:
1824                 if ( _show_vector_data_cb != null ) {
1825                     _show_vector_data_cb.setSelected( state );
1826                 }
1827                 break;
1828             case Configuration.show_properties:
1829                 if ( _show_properties_cb != null ) {
1830                     _show_properties_cb.setSelected( state );
1831                 }
1832                 break;
1833             case Configuration.show_sequence_acc:
1834                 if ( _show_sequence_acc != null ) {
1835                     _show_sequence_acc.setSelected( state );
1836                 }
1837                 break;
1838             case Configuration.dynamically_hide_data:
1839                 if ( getDynamicallyHideData() != null ) {
1840                     getDynamicallyHideData().setSelected( state );
1841                 }
1842                 break;
1843             case Configuration.node_data_popup:
1844                 if ( getNodeDescPopupCb() != null ) {
1845                     getNodeDescPopupCb().setSelected( state );
1846                 }
1847                 break;
1848             /* GUILHEM_BEG */
1849             case Configuration.show_relation_confidence:
1850                 if ( _seq_relation_confidence_switch != null ) {
1851                     _seq_relation_confidence_switch.setSelected( state );
1852                 }
1853                 break;
1854             /* GUILHEM_END */
1855             default:
1856                 throw new AssertionError( "unknown checkbox: " + which );
1857         }
1858     }
1859
1860     /**
1861      * Set this checkbox state. Not all checkboxes have been instantiated
1862      * depending on the config.
1863      */
1864     void setCheckbox( final JCheckBox cb, final boolean state ) {
1865         if ( cb != null ) {
1866             cb.setSelected( state );
1867         }
1868     }
1869
1870     void setClickToAction( final int action ) {
1871         // Set click-to action
1872         if ( action == _show_data_item ) {
1873             setActionWhenNodeClicked( NodeClickAction.SHOW_DATA );
1874         }
1875         else if ( action == _collapse_cb_item ) {
1876             setActionWhenNodeClicked( NodeClickAction.COLLAPSE );
1877         }
1878         else if ( action == _reroot_cb_item ) {
1879             setActionWhenNodeClicked( NodeClickAction.REROOT );
1880         }
1881         else if ( action == _subtree_cb_item ) {
1882             setActionWhenNodeClicked( NodeClickAction.SUBTREE );
1883         }
1884         else if ( action == _swap_cb_item ) {
1885             setActionWhenNodeClicked( NodeClickAction.SWAP );
1886         }
1887         else if ( action == _color_subtree_cb_item ) {
1888             setActionWhenNodeClicked( NodeClickAction.COLOR_SUBTREE );
1889         }
1890         else if ( action == _open_seq_web_item ) {
1891             setActionWhenNodeClicked( NodeClickAction.OPEN_SEQ_WEB );
1892         }
1893         else if ( action == _sort_descendents_item ) {
1894             setActionWhenNodeClicked( NodeClickAction.SORT_DESCENDENTS );
1895         }
1896         else if ( action == _blast_item ) {
1897             setActionWhenNodeClicked( NodeClickAction.BLAST );
1898         }
1899         else if ( action == _open_tax_web_item ) {
1900             setActionWhenNodeClicked( NodeClickAction.OPEN_TAX_WEB );
1901         }
1902         else if ( action == _cut_subtree_item ) {
1903             setActionWhenNodeClicked( NodeClickAction.CUT_SUBTREE );
1904         }
1905         else if ( action == _copy_subtree_item ) {
1906             setActionWhenNodeClicked( NodeClickAction.COPY_SUBTREE );
1907         }
1908         else if ( action == _delete_node_or_subtree_item ) {
1909             setActionWhenNodeClicked( NodeClickAction.DELETE_NODE_OR_SUBTREE );
1910         }
1911         else if ( action == _paste_subtree_item ) {
1912             setActionWhenNodeClicked( NodeClickAction.PASTE_SUBTREE );
1913         }
1914         else if ( action == _add_new_node_item ) {
1915             setActionWhenNodeClicked( NodeClickAction.ADD_NEW_NODE );
1916         }
1917         else if ( action == _edit_node_data_item ) {
1918             setActionWhenNodeClicked( NodeClickAction.EDIT_NODE_DATA );
1919         }
1920         else if ( action == _select_nodes_item ) {
1921             setActionWhenNodeClicked( NodeClickAction.SELECT_NODES );
1922         }
1923         else if ( action == _get_ext_desc_data ) {
1924             setActionWhenNodeClicked( NodeClickAction.GET_EXT_DESC_DATA );
1925         }
1926         else if ( action == _open_pdb_item ) {
1927             setActionWhenNodeClicked( NodeClickAction.OPEN_PDB_WEB );
1928         }
1929         else if ( action == _color_node_font_item ) {
1930             setActionWhenNodeClicked( NodeClickAction.COLOR_NODE_FONT );
1931         }
1932         else if ( action == _change_node_font_item ) {
1933             setActionWhenNodeClicked( NodeClickAction.CHANGE_NODE_FONT );
1934         }
1935         else if ( action == _uncollapse_all_cb_item ) {
1936             setActionWhenNodeClicked( NodeClickAction.UNCOLLAPSE_ALL );
1937         }
1938         else if ( action == _order_subtree_cb_item ) {
1939             setActionWhenNodeClicked( NodeClickAction.ORDER_SUBTREE );
1940         }
1941         else {
1942             throw new RuntimeException( "unknown action: " + action );
1943         }
1944         // make sure drop down is displaying the correct action
1945         // in case this was called from outside the class
1946         _click_to_combobox.setSelectedIndex( action );
1947     }
1948
1949     void setColorBranches( final boolean color_branches ) {
1950         _color_branches = color_branches;
1951     }
1952
1953     void setDrawPhylogram( final boolean b ) {
1954         getDisplayAsPhylogramCb().setSelected( b );
1955         setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
1956     }
1957
1958     void setDrawPhylogramEnabled( final boolean b ) {
1959         getDisplayAsPhylogramCb().setEnabled( b );
1960     }
1961
1962     void setDynamicHidingIsOn( final boolean is_on ) {
1963         if ( is_on ) {
1964             getDynamicallyHideData().setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
1965         }
1966         else {
1967             if ( !_configuration.isUseNativeUI() ) {
1968                 getDynamicallyHideData().setForeground( getConfiguration().getGuiButtonTextColor() );
1969             }
1970             else {
1971                 getDynamicallyHideData().setForeground( Color.BLACK );
1972             }
1973         }
1974     }
1975
1976     void setSearchFoundCountsOnLabel0( final int counts ) {
1977         getSearchFoundCountsLabel0().setText( "Found: " + counts );
1978     }
1979
1980     void setSearchFoundCountsOnLabel1( final int counts ) {
1981         getSearchFoundCountsLabel1().setText( "Found: " + counts );
1982     }
1983
1984     void setSequenceColors( final Map<String, Color> sequence_colors ) {
1985         _sequence_colors = sequence_colors;
1986     }
1987
1988     void setShowEvents( final boolean show_events ) {
1989         if ( getShowEventsCb() == null ) {
1990             _show_events = new JCheckBox( "" );
1991         }
1992         getShowEventsCb().setSelected( show_events );
1993     }
1994
1995     void setSpeciesColors( final Map<String, Color> species_colors ) {
1996         _species_colors = species_colors;
1997     }
1998
1999     void setupControls() {
2000         // The tree display options:
2001         setupDisplayCheckboxes();
2002         /* GUILHEM_BEG */
2003         // The sequence relation query selection combo-box
2004         if ( _configuration.displaySequenceRelations() ) {
2005             addSequenceRelationBlock();
2006         }
2007         /* GUILHEM_END */
2008         // Click-to options
2009         startClickToOptions();
2010         setupClickToOptions();
2011         endClickToOptions();
2012         // Zoom and quick edit buttons
2013         addButtons();
2014         setupSearchTools0();
2015         setupSearchTools1();
2016     }
2017
2018     void setUpControlsForDomainStrucures() {
2019         _domain_display_label = new JLabel( "Domain Architectures:" );
2020         add( customizeLabel( _domain_display_label, getConfiguration() ) );
2021         add( _domain_display_label );
2022         _zoom_in_domain_structure = new JButton( "d+" );
2023         _zoom_out_domain_structure = new JButton( "d-" );
2024         _decr_domain_structure_evalue_thr = new JButton( "-" );
2025         _incr_domain_structure_evalue_thr = new JButton( "+" );
2026         _zoom_in_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
2027         _zoom_out_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
2028         _decr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
2029         _incr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
2030         _incr_domain_structure_evalue_thr.setToolTipText( "Increase the E-value threshold by a factor of 10" );
2031         _decr_domain_structure_evalue_thr.setToolTipText( "Decrease the E-value threshold by a factor of 10" );
2032         _domain_structure_evalue_thr_tf = new JTextField( 3 );
2033         _domain_structure_evalue_thr_tf.setEditable( false );
2034         if ( !getConfiguration().isUseNativeUI() ) {
2035             _domain_structure_evalue_thr_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
2036             _domain_structure_evalue_thr_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
2037             _domain_structure_evalue_thr_tf.setBorder( null );
2038         }
2039         final JPanel d1_panel = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
2040         final JPanel d2_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
2041         if ( !_configuration.isUseNativeUI() ) {
2042             d1_panel.setBackground( getBackground() );
2043             d2_panel.setBackground( getBackground() );
2044         }
2045         add( d1_panel );
2046         add( d2_panel );
2047         addJButton( _zoom_out_domain_structure, d1_panel );
2048         addJButton( _zoom_in_domain_structure, d1_panel );
2049         addJButton( _decr_domain_structure_evalue_thr, d2_panel );
2050         addJTextField( _domain_structure_evalue_thr_tf, d2_panel );
2051         addJButton( _incr_domain_structure_evalue_thr, d2_panel );
2052     }
2053
2054     void setupSearchTools0() {
2055         final JLabel search_label = new JLabel( "Search (A):" );
2056         search_label.setFont( ControlPanel.jcb_bold_font );
2057         if ( !getConfiguration().isUseNativeUI() ) {
2058             search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
2059         }
2060         add( search_label );
2061         search_label.setToolTipText( SEARCH_TIP_TEXT );
2062         _search_found_label_0 = new JLabel();
2063         getSearchFoundCountsLabel0().setVisible( false );
2064         _search_found_label_0.setFont( ControlPanel.jcb_bold_font );
2065         if ( !getConfiguration().isUseNativeUI() ) {
2066             _search_found_label_0.setForeground( getConfiguration().getGuiCheckboxTextColor() );
2067         }
2068         _search_tf_0 = new JTextField( 3 );
2069         _search_tf_0.setToolTipText( SEARCH_TIP_TEXT );
2070         _search_tf_0.setEditable( true );
2071         if ( !getConfiguration().isUseNativeUI() ) {
2072             _search_tf_0.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
2073             _search_tf_0.setBackground( getConfiguration().getGuiCheckboxTextColor() );
2074             _search_tf_0.setBorder( null );
2075         }
2076         _search_reset_button_0 = new JButton();
2077         getSearchResetButton0().setText( "Reset" );
2078         getSearchResetButton0().setEnabled( false );
2079         getSearchResetButton0().setVisible( false );
2080         final JPanel s_panel_1 = new JPanel( new BorderLayout() );
2081         final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
2082         s_panel_1.setBackground( getBackground() );
2083         add( s_panel_1 );
2084         s_panel_2.setBackground( getBackground() );
2085         add( s_panel_2 );
2086         final KeyAdapter key_adapter = new KeyAdapter() {
2087
2088             @Override
2089             public void keyReleased( final KeyEvent key_event ) {
2090                 search0();
2091                 displayedPhylogenyMightHaveChanged( true );
2092             }
2093         };
2094         final ActionListener action_listener = new ActionListener() {
2095
2096             @Override
2097             public void actionPerformed( final ActionEvent e ) {
2098                 searchReset0();
2099                 setSearchFoundCountsOnLabel0( 0 );
2100                 getSearchFoundCountsLabel0().setVisible( false );
2101                 getSearchTextField0().setText( "" );
2102                 getSearchResetButton0().setEnabled( false );
2103                 getSearchResetButton0().setVisible( false );
2104                 displayedPhylogenyMightHaveChanged( true );
2105             }
2106         };
2107         _search_reset_button_0.addActionListener( action_listener );
2108         _search_tf_0.addKeyListener( key_adapter );
2109         addJTextField( _search_tf_0, s_panel_1 );
2110         s_panel_2.add( _search_found_label_0 );
2111         addJButton( _search_reset_button_0, s_panel_2 );
2112     }
2113
2114     void setupSearchTools1() {
2115         final JLabel search_label = new JLabel( "Search (B):" );
2116         search_label.setFont( ControlPanel.jcb_bold_font );
2117         if ( !getConfiguration().isUseNativeUI() ) {
2118             search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
2119         }
2120         add( search_label );
2121         search_label.setToolTipText( SEARCH_TIP_TEXT );
2122         _search_found_label_1 = new JLabel();
2123         getSearchFoundCountsLabel1().setVisible( false );
2124         _search_found_label_1.setFont( ControlPanel.jcb_bold_font );
2125         if ( !getConfiguration().isUseNativeUI() ) {
2126             _search_found_label_1.setForeground( getConfiguration().getGuiCheckboxTextColor() );
2127         }
2128         _search_tf_1 = new JTextField( 3 );
2129         _search_tf_1.setToolTipText( SEARCH_TIP_TEXT );
2130         _search_tf_1.setEditable( true );
2131         if ( !getConfiguration().isUseNativeUI() ) {
2132             _search_tf_1.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
2133             _search_tf_1.setBackground( getConfiguration().getGuiCheckboxTextColor() );
2134             _search_tf_1.setBorder( null );
2135         }
2136         _search_reset_button_1 = new JButton();
2137         getSearchResetButton1().setText( "Reset" );
2138         getSearchResetButton1().setEnabled( false );
2139         getSearchResetButton1().setVisible( false );
2140         final JPanel s_panel_1 = new JPanel( new BorderLayout() );
2141         final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
2142         s_panel_1.setBackground( getBackground() );
2143         add( s_panel_1 );
2144         s_panel_2.setBackground( getBackground() );
2145         add( s_panel_2 );
2146         final KeyAdapter key_adapter = new KeyAdapter() {
2147
2148             @Override
2149             public void keyReleased( final KeyEvent key_event ) {
2150                 search1();
2151                 displayedPhylogenyMightHaveChanged( true );
2152             }
2153         };
2154         final ActionListener action_listener = new ActionListener() {
2155
2156             @Override
2157             public void actionPerformed( final ActionEvent e ) {
2158                 searchReset1();
2159                 setSearchFoundCountsOnLabel1( 0 );
2160                 getSearchFoundCountsLabel1().setVisible( false );
2161                 getSearchTextField1().setText( "" );
2162                 getSearchResetButton1().setEnabled( false );
2163                 getSearchResetButton1().setVisible( false );
2164                 displayedPhylogenyMightHaveChanged( true );
2165             }
2166         };
2167         _search_reset_button_1.addActionListener( action_listener );
2168         _search_tf_1.addKeyListener( key_adapter );
2169         addJTextField( _search_tf_1, s_panel_1 );
2170         s_panel_2.add( _search_found_label_1 );
2171         addJButton( _search_reset_button_1, s_panel_2 );
2172     }
2173
2174     void setVisibilityOfDomainStrucureCB() {
2175         try {
2176             if ( ( getCurrentTreePanel() != null )
2177                     && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
2178                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
2179                 if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
2180                     getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false );
2181                 }
2182                 if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
2183                     getMainPanel().getMainFrame()._show_domain_labels.setVisible( false );
2184                 }
2185             }
2186             else if ( isShowDomainArchitectures() ) {
2187                 if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
2188                     getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( true );
2189                 }
2190                 if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
2191                     getMainPanel().getMainFrame()._show_domain_labels.setVisible( true );
2192                 }
2193             }
2194             else {
2195                 if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
2196                     getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false );
2197                 }
2198                 if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
2199                     getMainPanel().getMainFrame()._show_domain_labels.setVisible( false );
2200                 }
2201             }
2202         }
2203         catch ( final Exception ignore ) {
2204             //not important...
2205         }
2206     }
2207
2208     void setVisibilityOfX() {
2209         final MainFrame mf = getMainFrame();
2210         if ( mf != null ) {
2211             if ( ( getCurrentTreePanel() != null ) && ( getCurrentTreePanel().getPhylogeny() != null ) ) {
2212                 if ( AptxUtil.isHasAtLeastOneBranchWithSupportSD( getCurrentTreePanel().getPhylogeny() ) ) {
2213                     if ( mf._show_confidence_stddev_cbmi != null ) {
2214                         mf._show_confidence_stddev_cbmi.setVisible( true );
2215                     }
2216                 }
2217                 else {
2218                     if ( mf._show_confidence_stddev_cbmi != null ) {
2219                         mf._show_confidence_stddev_cbmi.setVisible( false );
2220                     }
2221                 }
2222                 if ( AptxUtil.isHasAtLeastOneNodeWithScientificName( getCurrentTreePanel().getPhylogeny() ) ) {
2223                     if ( mf._abbreviate_scientific_names != null ) {
2224                         mf._abbreviate_scientific_names.setVisible( true );
2225                     }
2226                 }
2227                 else {
2228                     if ( mf._abbreviate_scientific_names != null ) {
2229                         mf._abbreviate_scientific_names.setVisible( false );
2230                     }
2231                 }
2232                 if ( AptxUtil.isHasAtLeastOneNodeWithSequenceAnnotation( getCurrentTreePanel().getPhylogeny() ) ) {
2233                     if ( mf._show_annotation_ref_source != null ) {
2234                         mf._show_annotation_ref_source.setVisible( true );
2235                     }
2236                 }
2237                 else {
2238                     if ( mf._show_annotation_ref_source != null ) {
2239                         mf._show_annotation_ref_source.setVisible( false );
2240                     }
2241                 }
2242             }
2243             if ( isDrawPhylogram()
2244                     || ( ( getCurrentTreePanel() != null ) && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
2245                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) ) {
2246                 if ( mf._non_lined_up_cladograms_rbmi != null ) {
2247                     mf._non_lined_up_cladograms_rbmi.setVisible( false );
2248                 }
2249                 if ( mf._uniform_cladograms_rbmi != null ) {
2250                     mf._uniform_cladograms_rbmi.setVisible( false );
2251                 }
2252                 if ( mf._ext_node_dependent_cladogram_rbmi != null ) {
2253                     mf._ext_node_dependent_cladogram_rbmi.setVisible( false );
2254                 }
2255             }
2256             else {
2257                 if ( mf._non_lined_up_cladograms_rbmi != null ) {
2258                     mf._non_lined_up_cladograms_rbmi.setVisible( true );
2259                 }
2260                 if ( mf._uniform_cladograms_rbmi != null ) {
2261                     mf._uniform_cladograms_rbmi.setVisible( true );
2262                 }
2263                 if ( mf._ext_node_dependent_cladogram_rbmi != null ) {
2264                     mf._ext_node_dependent_cladogram_rbmi.setVisible( true );
2265                 }
2266             }
2267             if ( isDrawPhylogram() ) {
2268                 if ( mf._show_scale_cbmi != null ) {
2269                     mf._show_scale_cbmi.setVisible( true );
2270                 }
2271             }
2272             else {
2273                 if ( mf._show_scale_cbmi != null ) {
2274                     mf._show_scale_cbmi.setVisible( false );
2275                 }
2276             }
2277             if ( getCurrentTreePanel() != null ) {
2278                 if ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
2279                         || ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
2280                     if ( mf._label_direction_cbmi != null ) {
2281                         mf._label_direction_cbmi.setVisible( true );
2282                     }
2283                 }
2284                 else {
2285                     if ( mf._label_direction_cbmi != null ) {
2286                         mf._label_direction_cbmi.setVisible( false );
2287                     }
2288                 }
2289             }
2290         }
2291     }
2292
2293     void showAnnotations() {
2294         if ( _show_annotation != null ) {
2295             _show_annotation.setSelected( true );
2296         }
2297         if ( _color_according_to_annotation != null ) {
2298             _color_according_to_annotation.setSelected( true );
2299         }
2300         if ( _color_acc_species != null ) {
2301             _color_acc_species.setSelected( false );
2302         }
2303         if ( _color_acc_sequence != null ) {
2304             _color_acc_sequence.setSelected( false );
2305         }
2306         _mainpanel.getCurrentTreePanel().repaint();
2307     }
2308
2309     /**
2310      * Fit entire tree into window.
2311      */
2312     void showWhole() {
2313         if ( ( _mainpanel.getCurrentScrollPane() == null ) || _mainpanel.getCurrentTreePanel().getPhylogeny().isEmpty() ) {
2314             return;
2315         }
2316         getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
2317         displayedPhylogenyMightHaveChanged( true );
2318         _mainpanel.getCurrentTreePanel().updateOvSettings();
2319         _mainpanel.getCurrentTreePanel().validate();
2320         _mainpanel.validate();
2321         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
2322                                                                     _mainpanel.getSizeOfViewport().height );
2323         _mainpanel.getCurrentTreePanel().resetPreferredSize();
2324         _mainpanel.adjustJScrollPane();
2325         _mainpanel.getCurrentTreePanel().repaint();
2326         _mainpanel.getCurrentTreePanel().validate();
2327         _mainpanel.validate();
2328         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
2329                                                                     _mainpanel.getSizeOfViewport().height );
2330         _mainpanel.getCurrentTreePanel().resetPreferredSize();
2331         _mainpanel.adjustJScrollPane();
2332         _mainpanel.getCurrentTreePanel().repaint();
2333         _mainpanel.getCurrentTreePanel().updateOvSizes();
2334     }
2335
2336     void showWholeAll() {
2337         for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
2338             if ( tree_panel != null ) {
2339                 tree_panel.validate();
2340                 tree_panel.calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
2341                                                       _mainpanel.getSizeOfViewport().height );
2342                 tree_panel.resetPreferredSize();
2343                 tree_panel.repaint();
2344             }
2345         }
2346     }
2347
2348     // Create header for click-to combo box.
2349     void startClickToOptions() {
2350         final JLabel spacer = new JLabel( "" );
2351         spacer.setFont( ControlPanel.jcb_font );
2352         add( spacer );
2353         _click_to_label = new JLabel( "Click on Node to:" );
2354         add( customizeLabel( _click_to_label, getConfiguration() ) );
2355         _click_to_combobox = new JComboBox<String>();
2356         _click_to_combobox.setFocusable( false );
2357         _click_to_combobox.setMaximumRowCount( 14 );
2358         _click_to_combobox.setFont( ControlPanel.js_font );
2359         if ( !_configuration.isUseNativeUI() ) {
2360             _click_to_combobox.setBackground( getConfiguration().getGuiBackgroundColor() );
2361         }
2362         // don't add listener until all items are set (or each one will trigger
2363         // an event)
2364         // click_to_list.addActionListener(this);
2365         add( _click_to_combobox );
2366         // Correlates option names to titles
2367         _all_click_to_names = new HashMap<Integer, String>();
2368         _click_to_names = new ArrayList<String>();
2369     }
2370
2371     void tabChanged() {
2372         if ( getMainPanel().getTabbedPane().getTabCount() > 0 ) {
2373             if ( getCurrentTreePanel().isPhyHasBranchLengths()
2374                     && ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
2375                 setDrawPhylogramEnabled( true );
2376                 setDrawPhylogram( isDrawPhylogram() );
2377             }
2378             else {
2379                 setDrawPhylogramEnabled( false );
2380                 setDrawPhylogram( false );
2381             }
2382             if ( getMainPanel().getMainFrame() == null ) {
2383                 // Must be "E" applet version.
2384                 final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
2385                 e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() );
2386             }
2387             else {
2388                 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel()
2389                         .getPhylogenyGraphicsType() );
2390             }
2391             getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
2392             getMainPanel().getControlPanel().search0();
2393             getMainPanel().getControlPanel().search1();
2394             getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
2395             getSequenceRelationTypeBox().removeAllItems();
2396             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
2397                     .getRelevantSequenceRelationTypes() ) {
2398                 _sequence_relation_type_box.addItem( type );
2399             }
2400             getMainPanel().getCurrentTreePanel().repaint();
2401             //setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
2402             // according to GUILHEM the line above can be removed.
2403         }
2404     }
2405
2406     /**
2407      * Uncollapse all nodes.
2408      */
2409     void uncollapseAll( final TreePanel tp ) {
2410         final Phylogeny t = tp.getPhylogeny();
2411         if ( ( t != null ) && !t.isEmpty() ) {
2412             for( final PhylogenyNodeIterator iter = t.iteratorPreorder(); iter.hasNext(); ) {
2413                 final PhylogenyNode node = iter.next();
2414                 node.setCollapse( false );
2415             }
2416             tp.resetNodeIdToDistToLeafMap();
2417             tp.updateSetOfCollapsedExternalNodes();
2418             t.recalculateNumberOfExternalDescendants( false );
2419             tp.setNodeInPreorderToNull();
2420             t.clearHashIdToNodeMap();
2421             showWhole();
2422         }
2423     }
2424
2425     void updateDomainStructureEvaluethresholdDisplay() {
2426         if ( _domain_structure_evalue_thr_tf != null ) {
2427             _domain_structure_evalue_thr_tf.setText( "10^"
2428                     + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThresholdExp() );
2429         }
2430     }
2431
2432     void zoomInX( final float factor, final float x_correction_factor ) {
2433         final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
2434         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
2435         treepanel.multiplyUrtFactor( 1f );
2436         if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
2437                 || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
2438                 || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
2439                 || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
2440             final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
2441             treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
2442             treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
2443             getMainPanel().adjustJScrollPane();
2444             treepanel.resetPreferredSize();
2445             getMainPanel().getCurrentScrollPane().getViewport().validate();
2446             sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
2447                     - ( sb.getVisibleAmount() / 2.0 ) ) );
2448         }
2449         else {
2450             final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
2451             treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
2452             treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
2453             getMainPanel().adjustJScrollPane();
2454             treepanel.resetPreferredSize();
2455             getMainPanel().getCurrentScrollPane().getViewport().validate();
2456             sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
2457         }
2458         treepanel.resetPreferredSize();
2459         treepanel.updateOvSizes();
2460     }
2461
2462     void zoomInY( final float factor ) {
2463         final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
2464         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
2465         treepanel.multiplyUrtFactor( 1.1f );
2466         final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
2467         treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
2468         getMainPanel().adjustJScrollPane();
2469         treepanel.resetPreferredSize();
2470         getMainPanel().getCurrentScrollPane().getViewport().validate();
2471         sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
2472                 - ( sb.getVisibleAmount() / 2.0 ) ) );
2473         treepanel.resetPreferredSize();
2474         treepanel.updateOvSizes();
2475     }
2476
2477     void zoomOutX( final float factor, final float x_correction_factor ) {
2478         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
2479         treepanel.multiplyUrtFactor( 1f );
2480         if ( ( treepanel.getXdistance() * factor ) > 0.0 ) {
2481             final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
2482             if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
2483                     || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
2484                     || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
2485                     || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
2486                 getMainPanel().adjustJScrollPane();
2487                 treepanel.resetPreferredSize();
2488                 getMainPanel().getCurrentScrollPane().getViewport().validate();
2489                 final double x = ( sb.getMaximum() - sb.getMinimum() )
2490                         / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
2491                 treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
2492                 treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
2493                 getMainPanel().adjustJScrollPane();
2494                 treepanel.resetPreferredSize();
2495                 getMainPanel().getCurrentScrollPane().getViewport().validate();
2496                 sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
2497                         - ( sb.getVisibleAmount() / 2.0 ) ) );
2498             }
2499             else {
2500                 final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
2501                 treepanel.setXdistance( treepanel.getXdistance() * factor );
2502                 treepanel.setXcorrectionFactor( treepanel.getXcorrectionFactor() * x_correction_factor );
2503                 if ( x > 0 ) {
2504                     getMainPanel().adjustJScrollPane();
2505                     treepanel.resetPreferredSize();
2506                     getMainPanel().getCurrentScrollPane().getViewport().validate();
2507                     sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
2508                 }
2509             }
2510             treepanel.resetPreferredSize();
2511             treepanel.updateOvSizes();
2512         }
2513     }
2514
2515     void zoomOutY( final float factor ) {
2516         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
2517         treepanel.multiplyUrtFactor( 0.9f );
2518         if ( ( treepanel.getYdistance() * factor ) > 0.0 ) {
2519             final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
2520             final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
2521             treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
2522             getMainPanel().adjustJScrollPane();
2523             treepanel.resetPreferredSize();
2524             getMainPanel().getCurrentScrollPane().getViewport().validate();
2525             sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
2526                     - ( sb.getVisibleAmount() / 2.0 ) ) );
2527             treepanel.resetPreferredSize();
2528             treepanel.updateOvSizes();
2529         }
2530     }
2531
2532     static JLabel customizeLabel( final JLabel label, final Configuration configuration ) {
2533         label.setFont( ControlPanel.jcb_bold_font );
2534         if ( !configuration.isUseNativeUI() ) {
2535             label.setForeground( configuration.getGuiCheckboxTextColor() );
2536             label.setBackground( configuration.getGuiBackgroundColor() );
2537         }
2538         return label;
2539     }
2540
2541     public JCheckBox getUseBranchWidthsCb() {
2542         return _width_branches;
2543     }
2544 }