2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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.
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.
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
22 // Contact: phylosoft @ gmail . com
23 // WWW: www.phylosoft.org/forester
25 package org.forester.archaeopteryx;
27 import java.awt.BorderLayout;
28 import java.awt.Color;
29 import java.awt.Component;
30 import java.awt.Dimension;
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;
48 import javax.swing.BorderFactory;
49 import javax.swing.DefaultListCellRenderer;
50 import javax.swing.JButton;
51 import javax.swing.JCheckBox;
52 import javax.swing.JComboBox;
53 import javax.swing.JLabel;
54 import javax.swing.JList;
55 import javax.swing.JPanel;
56 import javax.swing.JScrollBar;
57 import javax.swing.JTextField;
58 import javax.swing.ListCellRenderer;
60 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
61 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
62 import org.forester.phylogeny.Phylogeny;
63 import org.forester.phylogeny.PhylogenyMethods;
64 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
65 import org.forester.phylogeny.PhylogenyNode;
66 import org.forester.phylogeny.data.Sequence;
67 import org.forester.phylogeny.data.SequenceRelation;
68 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
69 import org.forester.util.ForesterUtil;
71 final class ControlPanel extends JPanel implements ActionListener {
73 private static final String RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
74 final static Font jcb_font = new Font( Configuration.getDefaultFontFamilyName(),
77 final static Font js_font = new Font( Configuration.getDefaultFontFamilyName(),
80 final static Font jcb_bold_font = new Font( Configuration.getDefaultFontFamilyName(),
83 private static final long serialVersionUID = -8463483932821545633L;
84 private final MainPanel _mainpanel;
85 // The settings from the conf file
86 private final Configuration _configuration;
88 private JCheckBox _display_internal_data;
89 private JCheckBox _show_node_names;
90 private JCheckBox _show_taxo_code;
91 private JCheckBox _write_confidence;
92 private JCheckBox _show_events;
93 private JCheckBox _color_acc_species;
94 private JCheckBox _color_branches_cb;
95 private JCheckBox _width_branches;
96 private JCheckBox _show_domain_architectures;
97 private JCheckBox _show_annotation;
98 private JCheckBox _show_binary_characters;
99 private JCheckBox _show_binary_character_counts;
100 private JCheckBox _show_gene_names;
101 private JCheckBox _show_gene_symbols;
102 private JCheckBox _show_sequence_acc;
103 private JCheckBox _node_desc_popup_cb;
104 private JCheckBox _dynamically_hide_data;
105 private JCheckBox _show_taxo_scientific_names;
106 private JCheckBox _show_taxo_common_names;
107 private JCheckBox _show_taxo_images_cb;
108 private JCheckBox _color_according_to_annotation;
109 private JCheckBox _display_as_phylogram_cb;
110 private JCheckBox _seq_relation_confidence_switch;
111 private JComboBox _show_sequence_relations;
112 private JComboBox _sequence_relation_type_box;
113 private JCheckBox _show_vector_data_cb;
114 private JCheckBox _show_properties_cb;
115 private JLabel _click_to_label;
116 private JLabel _zoom_label;
117 private JLabel _domain_display_label;
118 private JComboBox _click_to_combobox;
119 private Map<Integer, String> _all_click_to_names;
120 private List<String> _click_to_names;
121 // Indices for the click-to options in the combo box
122 private int _show_data_item;
123 private int _collapse_cb_item;
124 private int _reroot_cb_item;
125 private int _swap_cb_item;
126 private int _subtree_cb_item;
127 private int _color_subtree_cb_item;
128 private int _open_seq_web_item;
129 private int _sort_descendents_item;
130 private int _open_tax_web_item;
131 private int _cut_subtree_item;
132 private int _copy_subtree_item;
133 private int _delete_node_or_subtree_item;
134 private int _paste_subtree_item;
135 private int _add_new_node_item;
136 private int _edit_node_data_item;
137 private int _blast_item;
138 // zooming and quick tree manipulation buttons:
139 private JButton _zoom_in_x;
140 private JButton _zoom_in_y;
141 private JButton _zoom_out_x;
142 private JButton _zoom_out_y;
143 private JButton _show_whole;
144 private JButton _order;
145 private JButton _uncollapse_all;
146 private JButton _zoom_in_domain_structure;
147 private JButton _zoom_out_domain_structure;
148 private JButton _decr_domain_structure_evalue_thr;
149 private JButton _incr_domain_structure_evalue_thr;
150 private JButton _return_to_super_tree;
151 private JTextField _domain_structure_evalue_thr_tf;
152 private JTextField _search_tf;
153 private boolean _order_of_appearance;
154 private boolean _color_branches;
155 private NodeClickAction _action_when_node_clicked;
156 private List<Boolean> _draw_phylogram;
157 private Map<String, Color> _annotation_colors;
158 private Map<String, Color> _species_colors;
159 private JButton _search_reset_button;
160 private JLabel _search_found_label;
161 private Sequence _selected_query_seq;
163 ControlPanel( final MainPanel ap, final Configuration configuration ) {
166 _configuration = configuration;
167 if ( !_configuration.isUseNativeUI() ) {
168 setBackground( getConfiguration().getGuiBackgroundColor() );
169 setBorder( BorderFactory.createRaisedBevelBorder() );
171 setLayout( new GridLayout( 0, 1, 2, 2 ) );
172 _order_of_appearance = true;
180 public void actionPerformed( final ActionEvent e ) {
182 final TreePanel tp = getMainPanel().getCurrentTreePanel();
186 if ( e.getSource() == _click_to_combobox ) {
187 setClickToAction( _click_to_combobox.getSelectedIndex() );
188 getCurrentTreePanel().repaint();
190 else if ( e.getSource() == _show_binary_characters ) {
191 if ( ( _show_binary_character_counts != null ) && _show_binary_characters.isSelected() ) {
192 _show_binary_character_counts.setSelected( false );
194 displayedPhylogenyMightHaveChanged( true );
196 else if ( e.getSource() == _show_binary_character_counts ) {
197 if ( ( _show_binary_characters != null ) && _show_binary_character_counts.isSelected() ) {
198 _show_binary_characters.setSelected( false );
200 displayedPhylogenyMightHaveChanged( true );
202 else if ( e.getSource() == _color_according_to_annotation ) {
203 if ( ( _show_annotation != null ) && _color_according_to_annotation.isSelected() ) {
204 _show_annotation.setSelected( true );
206 displayedPhylogenyMightHaveChanged( false );
208 else if ( e.getSource() == _show_annotation ) {
209 if ( ( _color_according_to_annotation != null ) && !_show_annotation.isSelected() ) {
210 _color_according_to_annotation.setSelected( false );
212 displayedPhylogenyMightHaveChanged( false );
214 else if ( ( tp != null ) && ( tp.getPhylogeny() != null ) ) {
215 if ( e.getSource() == getDisplayAsPhylogramCb() ) {
216 setDrawPhylogram( getDisplayAsPhylogramCb().isSelected() );
220 else if ( e.getSource() == _zoom_in_x ) {
221 zoomInX( Constants.BUTTON_ZOOM_IN_FACTOR, Constants.BUTTON_ZOOM_IN_X_CORRECTION_FACTOR );
222 displayedPhylogenyMightHaveChanged( false );
224 else if ( e.getSource() == _zoom_in_y ) {
225 zoomInY( Constants.BUTTON_ZOOM_IN_FACTOR );
226 displayedPhylogenyMightHaveChanged( false );
228 else if ( e.getSource() == _zoom_out_x ) {
229 zoomOutX( Constants.BUTTON_ZOOM_OUT_FACTOR, Constants.BUTTON_ZOOM_OUT_X_CORRECTION_FACTOR );
230 displayedPhylogenyMightHaveChanged( false );
232 else if ( e.getSource() == _zoom_out_y ) {
233 zoomOutY( Constants.BUTTON_ZOOM_OUT_FACTOR );
234 displayedPhylogenyMightHaveChanged( false );
236 else if ( e.getSource() == _show_whole ) {
239 else if ( e.getSource() == _return_to_super_tree ) {
240 _mainpanel.getCurrentTreePanel().superTree();
243 else if ( e.getSource() == _order ) {
244 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
245 if ( ( !isShowTaxonomyScientificNames() && !isShowTaxonomyCode() && !isShowTaxonomyCommonNames() ) ) {
246 if ( ( isShowSequenceAcc() || isShowGeneNames() || isShowGeneSymbols() ) ) {
247 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
249 else if ( isShowNodeNames() ) {
250 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
253 PhylogenyMethods.orderAppearance( tp.getPhylogeny().getRoot(), _order_of_appearance, true, pri );
254 _order_of_appearance = !_order_of_appearance;
255 tp.setNodeInPreorderToNull();
256 tp.getPhylogeny().externalNodesHaveChanged();
257 tp.getPhylogeny().hashIDs();
258 tp.getPhylogeny().recalculateNumberOfExternalDescendants( true );
259 tp.resetNodeIdToDistToLeafMap();
260 tp.setEdited( true );
261 displayedPhylogenyMightHaveChanged( false );
263 else if ( e.getSource() == _uncollapse_all ) {
265 displayedPhylogenyMightHaveChanged( false );
267 else if ( e.getSource() == _zoom_in_domain_structure ) {
268 _mainpanel.getCurrentTreePanel().zoomInDomainStructure();
269 displayedPhylogenyMightHaveChanged( true );
271 else if ( e.getSource() == _zoom_out_domain_structure ) {
272 _mainpanel.getCurrentTreePanel().zoomOutDomainStructure();
273 displayedPhylogenyMightHaveChanged( true );
275 else if ( e.getSource() == _decr_domain_structure_evalue_thr ) {
276 _mainpanel.getCurrentTreePanel().decreaseDomainStructureEvalueThreshold();
277 displayedPhylogenyMightHaveChanged( true );
279 else if ( e.getSource() == _incr_domain_structure_evalue_thr ) {
280 _mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThreshold();
281 displayedPhylogenyMightHaveChanged( true );
283 else if ( e.getSource() == _search_tf ) {
285 displayedPhylogenyMightHaveChanged( true );
288 displayedPhylogenyMightHaveChanged( true );
292 tp.requestFocusInWindow();
295 catch ( final Exception ex ) {
296 AptxUtil.unexpectedException( ex );
298 catch ( final Error err ) {
299 AptxUtil.unexpectedError( err );
303 void activateButtonToReturnToSuperTree( int index ) {
306 _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT + " " + index );
309 _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
311 _return_to_super_tree.setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
312 _return_to_super_tree.setEnabled( true );
316 * Add zoom and quick edit buttons. (Last modified 8/9/04)
319 final JLabel spacer = new JLabel( "" );
320 spacer.setOpaque( false );
322 final JPanel x_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
323 final JPanel y_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
324 final JPanel z_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
325 if ( !getConfiguration().isUseNativeUI() ) {
326 x_panel.setBackground( getBackground() );
327 y_panel.setBackground( getBackground() );
328 z_panel.setBackground( getBackground() );
330 add( _zoom_label = new JLabel( "Zoom:" ) );
331 customizeLabel( _zoom_label, getConfiguration() );
335 if ( getConfiguration().isUseNativeUI() ) {
336 _zoom_in_x = new JButton( "+" );
337 _zoom_out_x = new JButton( "-" );
340 _zoom_in_x = new JButton( "X+" );
341 _zoom_out_x = new JButton( "X-" );
343 _zoom_in_y = new JButton( "Y+" );
344 _zoom_out_y = new JButton( "Y-" );
345 _show_whole = new JButton( "F" );
346 _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [Backspace]" );
347 _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+Right]" );
348 _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+Up]" );
349 _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+Left]" );
350 _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+Down]" );
351 if ( getConfiguration().isUseNativeUI() && AptxUtil.isMac() ) {
352 _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
353 _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );
356 _zoom_out_x.setPreferredSize( new Dimension( 10, 10 ) );
357 _zoom_in_x.setPreferredSize( new Dimension( 10, 10 ) );
359 _zoom_out_y.setPreferredSize( new Dimension( 10, 10 ) );
360 _zoom_in_y.setPreferredSize( new Dimension( 10, 10 ) );
361 _show_whole.setPreferredSize( new Dimension( 10, 10 ) );
362 _return_to_super_tree = new JButton( RETURN_TO_SUPER_TREE_TEXT );
363 _return_to_super_tree.setEnabled( false );
364 _order = new JButton( "Order Subtrees" );
365 _uncollapse_all = new JButton( "Uncollapse All" );
366 addJButton( _zoom_in_y, x_panel );
367 addJButton( _zoom_out_x, y_panel );
368 addJButton( _show_whole, y_panel );
369 addJButton( _zoom_in_x, y_panel );
370 addJButton( _zoom_out_y, z_panel );
371 if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
372 setUpControlsForDomainStrucures();
374 final JLabel spacer2 = new JLabel( "" );
376 addJButton( _return_to_super_tree, this );
377 addJButton( _order, this );
378 addJButton( _uncollapse_all, this );
379 final JLabel spacer3 = new JLabel( "" );
381 setVisibilityOfDomainStrucureControls();
384 void addCheckbox( final int which, final String title ) {
385 final JPanel ch_panel = new JPanel( new BorderLayout( 0, 0 ) );
387 case Configuration.display_as_phylogram:
388 _display_as_phylogram_cb = new JCheckBox( title );
389 getDisplayAsPhylogramCb().setToolTipText( "To switch between phylogram and cladogram display" );
390 addJCheckBox( getDisplayAsPhylogramCb(), ch_panel );
393 case Configuration.display_internal_data:
394 _display_internal_data = new JCheckBox( title );
395 _display_internal_data.setToolTipText( "To allow or disallow display of internal labels" );
396 addJCheckBox( _display_internal_data, ch_panel );
399 case Configuration.color_according_to_species:
400 _color_acc_species = new JCheckBox( title );
402 .setToolTipText( "To colorize taxonomy and sequence labels as a function of taxonomy" );
403 addJCheckBox( _color_acc_species, ch_panel );
406 case Configuration.color_according_to_annotation:
407 _color_according_to_annotation = new JCheckBox( title );
408 _color_according_to_annotation
409 .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" );
410 addJCheckBox( _color_according_to_annotation, ch_panel );
413 case Configuration.show_node_names:
414 _show_node_names = new JCheckBox( title );
415 addJCheckBox( _show_node_names, ch_panel );
418 case Configuration.show_taxonomy_scientific_names:
419 _show_taxo_scientific_names = new JCheckBox( title );
420 addJCheckBox( _show_taxo_scientific_names, ch_panel );
423 case Configuration.show_taxonomy_common_names:
424 _show_taxo_common_names = new JCheckBox( title );
425 addJCheckBox( _show_taxo_common_names, ch_panel );
428 case Configuration.show_tax_code:
429 _show_taxo_code = new JCheckBox( title );
430 addJCheckBox( _show_taxo_code, ch_panel );
433 case Configuration.show_taxonomy_images:
434 _show_taxo_images_cb = new JCheckBox( title );
435 addJCheckBox( _show_taxo_images_cb, ch_panel );
438 case Configuration.show_binary_characters:
439 _show_binary_characters = new JCheckBox( title );
440 addJCheckBox( _show_binary_characters, ch_panel );
443 case Configuration.show_annotation:
444 _show_annotation = new JCheckBox( title );
445 addJCheckBox( _show_annotation, ch_panel );
448 case Configuration.show_binary_character_counts:
449 _show_binary_character_counts = new JCheckBox( title );
450 addJCheckBox( _show_binary_character_counts, ch_panel );
453 case Configuration.write_confidence_values:
454 _write_confidence = new JCheckBox( title );
455 addJCheckBox( getWriteConfidenceCb(), ch_panel );
458 case Configuration.write_events:
459 _show_events = new JCheckBox( title );
460 addJCheckBox( getShowEventsCb(), ch_panel );
463 case Configuration.color_branches:
464 _color_branches_cb = new JCheckBox( title );
465 getColorBranchesCb().setToolTipText( "To use branch color values, if present" );
466 addJCheckBox( getColorBranchesCb(), ch_panel );
469 case Configuration.width_branches:
470 _width_branches = new JCheckBox( title );
471 _width_branches.setToolTipText( "To use branch width values, if present" );
472 addJCheckBox( _width_branches, ch_panel );
475 case Configuration.show_domain_architectures:
476 _show_domain_architectures = new JCheckBox( title );
477 addJCheckBox( _show_domain_architectures, ch_panel );
480 case Configuration.show_gene_names:
481 _show_gene_names = new JCheckBox( title );
482 addJCheckBox( _show_gene_names, ch_panel );
485 case Configuration.show_gene_symbols:
486 _show_gene_symbols = new JCheckBox( title );
487 addJCheckBox( _show_gene_symbols, ch_panel );
490 case Configuration.show_sequence_acc:
491 _show_sequence_acc = new JCheckBox( title );
492 addJCheckBox( _show_sequence_acc, ch_panel );
495 case Configuration.dynamically_hide_data:
496 _dynamically_hide_data = new JCheckBox( title );
497 getDynamicallyHideData().setToolTipText( "To hide labels depending on likely visibility" );
498 addJCheckBox( getDynamicallyHideData(), ch_panel );
501 case Configuration.node_data_popup:
502 _node_desc_popup_cb = new JCheckBox( title );
503 getNodeDescPopupCb().setToolTipText( "To enable mouse rollover display of basic node data" );
504 addJCheckBox( getNodeDescPopupCb(), ch_panel );
507 case Configuration.show_relation_confidence:
508 _seq_relation_confidence_switch = new JCheckBox( title );
509 addJCheckBox( _seq_relation_confidence_switch, ch_panel );
512 case Configuration.show_vector_data:
513 _show_vector_data_cb = new JCheckBox( title );
514 addJCheckBox( _show_vector_data_cb, ch_panel );
517 case Configuration.show_properties:
518 _show_properties_cb = new JCheckBox( title );
519 addJCheckBox( _show_properties_cb, ch_panel );
523 throw new RuntimeException( "unknown checkbox: " + which );
527 private void addClickToOption( final int which, final String title ) {
528 _click_to_combobox.addItem( title );
529 _click_to_names.add( title );
530 _all_click_to_names.put( new Integer( which ), title );
531 if ( !_configuration.isUseNativeUI() ) {
532 _click_to_combobox.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
533 _click_to_combobox.setForeground( getConfiguration().getGuiButtonTextColor() );
537 void addJButton( final JButton jb, final JPanel p ) {
538 jb.setFocusPainted( false );
539 jb.setFont( ControlPanel.jcb_font );
540 if ( !_configuration.isUseNativeUI() ) {
541 jb.setBorder( BorderFactory.createLineBorder( getConfiguration().getGuiButtonBorderColor() ) );
542 jb.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
543 jb.setForeground( getConfiguration().getGuiButtonTextColor() );
546 jb.addActionListener( this );
549 void addJCheckBox( final JCheckBox jcb, final JPanel p ) {
550 jcb.setFocusPainted( false );
551 jcb.setFont( ControlPanel.jcb_font );
552 if ( !_configuration.isUseNativeUI() ) {
553 jcb.setBackground( getConfiguration().getGuiBackgroundColor() );
554 jcb.setForeground( getConfiguration().getGuiCheckboxTextColor() );
556 p.add( jcb, "Center" );
557 jcb.addActionListener( this );
560 void addJTextField( final JTextField tf, final JPanel p ) {
561 if ( !_configuration.isUseNativeUI() ) {
562 tf.setForeground( getConfiguration().getGuiBackgroundColor() );
563 tf.setFont( ControlPanel.jcb_font );
566 tf.addActionListener( this );
570 private void addSequenceRelationBlock() {
571 final JLabel spacer = new JLabel( "" );
572 spacer.setSize( 1, 1 );
574 final JLabel mainLabel = new JLabel( "Sequence relations to display" );
575 final JLabel typeLabel = customizeLabel( new JLabel( "(type) " ), getConfiguration() );
576 typeLabel.setFont( ControlPanel.js_font.deriveFont( 7 ) );
577 getSequenceRelationTypeBox().setFocusable( false );
578 _sequence_relation_type_box.setFont( ControlPanel.js_font );
579 if ( !_configuration.isUseNativeUI() ) {
580 _sequence_relation_type_box.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
581 _sequence_relation_type_box.setForeground( getConfiguration().getGuiButtonTextColor() );
583 _sequence_relation_type_box.setRenderer( new ListCellRenderer() {
586 public Component getListCellRendererComponent( final JList list,
589 final boolean isSelected,
590 final boolean cellHasFocus ) {
591 final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
596 if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) {
597 ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation
598 .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) );
603 final GridBagLayout gbl = new GridBagLayout();
604 _sequence_relation_type_box.setMinimumSize( new Dimension( 115, 17 ) );
605 _sequence_relation_type_box.setPreferredSize( new Dimension( 115, 20 ) );
606 final JPanel horizGrid = new JPanel( gbl );
607 horizGrid.setBackground( getBackground() );
608 horizGrid.add( typeLabel );
609 horizGrid.add( _sequence_relation_type_box );
610 add( customizeLabel( mainLabel, getConfiguration() ) );
612 add( getSequenceRelationBox() );
613 if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
614 addCheckbox( Configuration.show_relation_confidence,
615 _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
616 setCheckbox( Configuration.show_relation_confidence,
617 _configuration.doCheckOption( Configuration.show_relation_confidence ) );
619 }// addSequenceRelationBlock
621 void deactivateButtonToReturnToSuperTree() {
622 _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
623 _return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
624 _return_to_super_tree.setEnabled( false );
627 void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
628 if ( ( _mainpanel != null ) && ( _mainpanel.getCurrentPhylogeny() != null ) ) {
629 if ( getOptions().isShowOverview() ) {
630 _mainpanel.getCurrentTreePanel().updateOvSizes();
632 _mainpanel.getCurrentTreePanel().recalculateMaxDistanceToRoot();
633 setVisibilityOfDomainStrucureControls();
634 updateDomainStructureEvaluethresholdDisplay();
635 _mainpanel.getCurrentTreePanel().calculateScaleDistance();
636 _mainpanel.getCurrentTreePanel().calcMaxDepth();
637 _mainpanel.adjustJScrollPane();
638 if ( recalc_longest_ext_node_info ) {
639 _mainpanel.getCurrentTreePanel().initNodeData();
640 _mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
642 _mainpanel.getCurrentTreePanel().repaint();
643 // _mainpanel.getCurrentTreePanel().setUpUrtFactors();
647 void endClickToOptions() {
648 _click_to_combobox.addActionListener( this );
652 * Indicates what action should be execute when a node is clicked
654 * @return the click-on action
656 NodeClickAction getActionWhenNodeClicked() {
657 return _action_when_node_clicked;
660 Map<Integer, String> getAllClickToItems() {
661 return _all_click_to_names;
664 Map<String, Color> getAnnotationColors() {
665 return _annotation_colors;
668 public JCheckBox getColorBranchesCb() {
669 return _color_branches_cb;
672 public JCheckBox getColorAccSpeciesCb() {
673 return _color_acc_species;
676 Configuration getConfiguration() {
677 return _configuration;
680 TreePanel getCurrentTreePanel() {
681 return getMainPanel().getCurrentTreePanel();
684 public JCheckBox getDisplayAsPhylogramCb() {
685 return _display_as_phylogram_cb;
688 public JCheckBox getDynamicallyHideData() {
689 return _dynamically_hide_data;
693 private List<Boolean> getIsDrawPhylogramList() {
694 return _draw_phylogram;
697 MainPanel getMainPanel() {
701 public JCheckBox getNodeDescPopupCb() {
702 return _node_desc_popup_cb;
705 Options getOptions() {
706 return getMainPanel().getOptions();
709 private JLabel getSearchFoundCountsLabel() {
710 return _search_found_label;
713 private JButton getSearchResetButton() {
714 return _search_reset_button;
717 JTextField getSearchTextField() {
721 public Sequence getSelectedQuerySequence() {
722 return _selected_query_seq;
725 public JComboBox getSequenceRelationBox() {
726 if ( _show_sequence_relations == null ) {
727 _show_sequence_relations = new JComboBox();
728 _show_sequence_relations.setFocusable( false );
729 _show_sequence_relations.setMaximumRowCount( 20 );
730 _show_sequence_relations.setFont( ControlPanel.js_font );
731 if ( !_configuration.isUseNativeUI() ) {
732 _show_sequence_relations.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
733 _show_sequence_relations.setForeground( getConfiguration().getGuiButtonTextColor() );
735 _show_sequence_relations.addItem( "-----" );
736 _show_sequence_relations.setToolTipText( "To display orthology information for selected query" );
738 return _show_sequence_relations;
742 public JComboBox getSequenceRelationTypeBox() {
743 if ( _sequence_relation_type_box == null ) {
744 _sequence_relation_type_box = new JComboBox();
745 for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : SequenceRelation.SEQUENCE_RELATION_TYPE.values() ) {
746 _sequence_relation_type_box.addItem( type );
748 _sequence_relation_type_box.addActionListener( new ActionListener() {
751 public void actionPerformed( final ActionEvent e ) {
752 if ( _mainpanel.getCurrentPhylogeny() != null ) {
753 setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
758 return _sequence_relation_type_box;
761 public JCheckBox getShowEventsCb() {
765 List<String> getSingleClickToNames() {
766 return _click_to_names;
769 Map<String, Color> getSpeciesColors() {
770 return _species_colors;
773 public JCheckBox getWriteConfidenceCb() {
774 return _write_confidence;
777 private void init() {
778 _draw_phylogram = new ArrayList<Boolean>();
779 setSpeciesColors( new HashMap<String, Color>() );
780 setAnnotationColors( new HashMap<String, Color>() );
783 boolean isAntialiasScreenText() {
787 boolean isColorAccordingToAnnotation() {
788 return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
791 boolean isColorAccordingToTaxonomy() {
792 return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
795 boolean isColorBranches() {
796 return ( ( ( getColorBranchesCb() != null ) && getColorBranchesCb().isSelected() ) || ( ( getColorBranchesCb() == null ) && _color_branches ) );
799 boolean isDrawPhylogram() {
800 return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
803 private boolean isDrawPhylogram( final int index ) {
804 return getIsDrawPhylogramList().get( index );
807 boolean isDynamicallyHideData() {
808 return ( ( getDynamicallyHideData() != null ) && getDynamicallyHideData().isSelected() );
812 return ( ( getShowEventsCb() != null ) && getShowEventsCb().isSelected() );
815 boolean isNodeDescPopup() {
816 return ( ( getNodeDescPopupCb() != null ) && getNodeDescPopupCb().isSelected() );
819 boolean isShowAnnotation() {
820 return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
823 boolean isShowBinaryCharacterCounts() {
824 return ( ( _show_binary_character_counts != null ) && _show_binary_character_counts.isSelected() );
827 boolean isShowBinaryCharacters() {
828 return ( ( _show_binary_characters != null ) && _show_binary_characters.isSelected() );
831 boolean isShowConfidenceValues() {
832 return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
835 boolean isShowDomainArchitectures() {
836 return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
839 boolean isShowGeneNames() {
840 return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
843 public boolean isShowVectorData() {
844 return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
847 public boolean isShowProperties() {
848 return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
851 boolean isShowGeneSymbols() {
852 return ( ( _show_gene_symbols != null ) && _show_gene_symbols.isSelected() );
855 boolean isShowInternalData() {
856 return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() );
859 boolean isShowNodeNames() {
860 return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
863 boolean isShowSequenceAcc() {
864 return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
867 boolean isShowSequenceRelationConfidence() {
868 return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
871 boolean isShowSequenceRelations() {
872 return ( ( _show_sequence_relations != null ) && ( _show_sequence_relations.getSelectedIndex() > 0 ) );
875 boolean isShowTaxonomyCode() {
876 return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
879 public boolean isShowTaxonomyImages() {
880 return ( ( _show_taxo_images_cb != null ) && _show_taxo_images_cb.isSelected() );
883 boolean isShowTaxonomyCommonNames() {
884 return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
887 boolean isShowTaxonomyScientificNames() {
888 return ( ( _show_taxo_scientific_names != null ) && _show_taxo_scientific_names.isSelected() );
891 boolean isWidthBranches() {
892 return ( ( _width_branches != null ) && _width_branches.isSelected() );
895 void phylogenyAdded( final Configuration configuration ) {
896 getIsDrawPhylogramList().add( configuration.isDrawAsPhylogram() );
899 void phylogenyRemoved( final int index ) {
900 getIsDrawPhylogramList().remove( index );
904 final MainPanel main_panel = getMainPanel();
905 final Phylogeny tree = main_panel.getCurrentPhylogeny();
906 if ( ( tree == null ) || tree.isEmpty() ) {
909 String query = getSearchTextField().getText();
910 if ( query != null ) {
911 query = query.trim();
914 getSearchFoundCountsLabel().setVisible( false );
915 getSearchResetButton().setEnabled( false );
916 getSearchResetButton().setVisible( false );
919 if ( !ForesterUtil.isEmpty( query ) ) {
920 search( main_panel, tree, query );
923 getSearchFoundCountsLabel().setVisible( false );
924 getSearchResetButton().setEnabled( false );
925 getSearchResetButton().setVisible( false );
930 private void search( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
931 getSearchFoundCountsLabel().setVisible( true );
932 getSearchResetButton().setEnabled( true );
933 getSearchResetButton().setVisible( true );
934 String[] queries = null;
935 List<PhylogenyNode> nodes = null;
936 if ( query_str.indexOf( ',' ) >= 0 ) {
937 queries = query_str.split( ",+" );
940 queries = new String[ 1 ];
941 queries[ 0 ] = query_str.trim();
943 if ( ( queries != null ) && ( queries.length > 0 ) ) {
944 nodes = new ArrayList<PhylogenyNode>();
945 for( String query : queries ) {
946 if ( ForesterUtil.isEmpty( query ) ) {
949 query = query.trim();
950 if ( query.indexOf( '+' ) >= 0 ) {
951 nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ), tree, getOptions()
952 .isSearchCaseSensitive(), !getOptions().isMatchWholeTermsOnly() ) );
955 nodes.addAll( PhylogenyMethods.searchData( query,
957 getOptions().isSearchCaseSensitive(),
958 !getOptions().isMatchWholeTermsOnly() ) );
961 if ( getOptions().isInverseSearchResult() ) {
962 final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
963 all.removeAll( nodes );
967 if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
968 main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Integer>() );
969 for( final PhylogenyNode node : nodes ) {
970 main_panel.getCurrentTreePanel().getFoundNodes().add( node.getId() );
972 setSearchFoundCountsOnLabel( nodes.size() );
975 setSearchFoundCountsOnLabel( 0 );
980 private void searchReset() {
981 if ( getMainPanel().getCurrentTreePanel() != null ) {
982 getMainPanel().getCurrentTreePanel().setFoundNodes( null );
986 void setActionWhenNodeClicked( final NodeClickAction action ) {
987 _action_when_node_clicked = action;
990 void setAnnotationColors( final Map<String, Color> annotation_colors ) {
991 _annotation_colors = annotation_colors;
994 void setCheckbox( final int which, final boolean state ) {
996 case Configuration.display_as_phylogram:
997 if ( getDisplayAsPhylogramCb() != null ) {
998 getDisplayAsPhylogramCb().setSelected( state );
1001 case Configuration.display_internal_data:
1002 if ( _display_internal_data != null ) {
1003 _display_internal_data.setSelected( state );
1006 case Configuration.color_according_to_species:
1007 if ( _color_acc_species != null ) {
1008 _color_acc_species.setSelected( state );
1011 case Configuration.color_according_to_annotation:
1012 if ( _color_according_to_annotation != null ) {
1013 _color_according_to_annotation.setSelected( state );
1016 case Configuration.show_node_names:
1017 if ( _show_node_names != null ) {
1018 _show_node_names.setSelected( state );
1021 case Configuration.show_taxonomy_scientific_names:
1022 if ( _show_taxo_scientific_names != null ) {
1023 _show_taxo_scientific_names.setSelected( state );
1026 case Configuration.show_taxonomy_common_names:
1027 if ( _show_taxo_common_names != null ) {
1028 _show_taxo_common_names.setSelected( state );
1031 case Configuration.show_tax_code:
1032 if ( _show_taxo_code != null ) {
1033 _show_taxo_code.setSelected( state );
1036 case Configuration.show_taxonomy_images:
1037 if ( _show_taxo_images_cb != null ) {
1038 _show_taxo_images_cb.setSelected( state );
1041 case Configuration.show_annotation:
1042 if ( _show_annotation != null ) {
1043 _show_annotation.setSelected( state );
1046 case Configuration.show_binary_characters:
1047 if ( _show_binary_characters != null ) {
1048 _show_binary_characters.setSelected( state );
1051 case Configuration.show_binary_character_counts:
1052 if ( _show_binary_character_counts != null ) {
1053 _show_binary_character_counts.setSelected( state );
1056 case Configuration.write_confidence_values:
1057 if ( getWriteConfidenceCb() != null ) {
1058 getWriteConfidenceCb().setSelected( state );
1061 case Configuration.write_events:
1062 if ( getShowEventsCb() != null ) {
1063 getShowEventsCb().setSelected( state );
1066 case Configuration.color_branches:
1067 if ( getColorBranchesCb() != null ) {
1068 getColorBranchesCb().setSelected( state );
1071 case Configuration.width_branches:
1072 if ( _width_branches != null ) {
1073 _width_branches.setSelected( state );
1076 case Configuration.show_domain_architectures:
1077 if ( _show_domain_architectures != null ) {
1078 _show_domain_architectures.setSelected( state );
1081 case Configuration.show_gene_names:
1082 if ( _show_gene_names != null ) {
1083 _show_gene_names.setSelected( state );
1086 case Configuration.show_gene_symbols:
1087 if ( _show_gene_symbols != null ) {
1088 _show_gene_symbols.setSelected( state );
1091 case Configuration.show_vector_data:
1092 if ( _show_vector_data_cb != null ) {
1093 _show_vector_data_cb.setSelected( state );
1096 case Configuration.show_properties:
1097 if ( _show_properties_cb != null ) {
1098 _show_properties_cb.setSelected( state );
1101 case Configuration.show_sequence_acc:
1102 if ( _show_sequence_acc != null ) {
1103 _show_sequence_acc.setSelected( state );
1106 case Configuration.dynamically_hide_data:
1107 if ( getDynamicallyHideData() != null ) {
1108 getDynamicallyHideData().setSelected( state );
1111 case Configuration.node_data_popup:
1112 if ( getNodeDescPopupCb() != null ) {
1113 getNodeDescPopupCb().setSelected( state );
1117 case Configuration.show_relation_confidence:
1118 if ( _seq_relation_confidence_switch != null ) {
1119 _seq_relation_confidence_switch.setSelected( state );
1124 throw new AssertionError( "unknown checkbox: " + which );
1129 * Set this checkbox state. Not all checkboxes have been instantiated
1130 * depending on the config.
1132 void setCheckbox( final JCheckBox cb, final boolean state ) {
1134 cb.setSelected( state );
1138 void setClickToAction( final int action ) {
1139 // Set click-to action
1140 if ( action == _show_data_item ) {
1141 setActionWhenNodeClicked( NodeClickAction.SHOW_DATA );
1143 else if ( action == _collapse_cb_item ) {
1144 setActionWhenNodeClicked( NodeClickAction.COLLAPSE );
1146 else if ( action == _reroot_cb_item ) {
1147 setActionWhenNodeClicked( NodeClickAction.REROOT );
1149 else if ( action == _subtree_cb_item ) {
1150 setActionWhenNodeClicked( NodeClickAction.SUBTREE );
1152 else if ( action == _swap_cb_item ) {
1153 setActionWhenNodeClicked( NodeClickAction.SWAP );
1155 else if ( action == _color_subtree_cb_item ) {
1156 setActionWhenNodeClicked( NodeClickAction.COLOR_SUBTREE );
1158 else if ( action == _open_seq_web_item ) {
1159 setActionWhenNodeClicked( NodeClickAction.OPEN_SEQ_WEB );
1161 else if ( action == _sort_descendents_item ) {
1162 setActionWhenNodeClicked( NodeClickAction.SORT_DESCENDENTS );
1164 else if ( action == _blast_item ) {
1165 setActionWhenNodeClicked( NodeClickAction.BLAST );
1167 else if ( action == _open_tax_web_item ) {
1168 setActionWhenNodeClicked( NodeClickAction.OPEN_TAX_WEB );
1170 else if ( action == _cut_subtree_item ) {
1171 setActionWhenNodeClicked( NodeClickAction.CUT_SUBTREE );
1173 else if ( action == _copy_subtree_item ) {
1174 setActionWhenNodeClicked( NodeClickAction.COPY_SUBTREE );
1176 else if ( action == _delete_node_or_subtree_item ) {
1177 setActionWhenNodeClicked( NodeClickAction.DELETE_NODE_OR_SUBTREE );
1179 else if ( action == _paste_subtree_item ) {
1180 setActionWhenNodeClicked( NodeClickAction.PASTE_SUBTREE );
1182 else if ( action == _add_new_node_item ) {
1183 setActionWhenNodeClicked( NodeClickAction.ADD_NEW_NODE );
1185 else if ( action == _edit_node_data_item ) {
1186 setActionWhenNodeClicked( NodeClickAction.EDIT_NODE_DATA );
1189 throw new RuntimeException( "unknown action: " + action );
1191 // make sure drop down is displaying the correct action
1192 // in case this was called from outside the class
1193 _click_to_combobox.setSelectedIndex( action );
1196 void setColorBranches( final boolean color_branches ) {
1197 _color_branches = color_branches;
1200 void setDrawPhylogram( final boolean b ) {
1201 getDisplayAsPhylogramCb().setSelected( b );
1202 setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
1205 private void setDrawPhylogram( final int index, final boolean b ) {
1206 getIsDrawPhylogramList().set( index, b );
1209 void setDrawPhylogramEnabled( final boolean b ) {
1210 getDisplayAsPhylogramCb().setEnabled( b );
1213 void setDynamicHidingIsOn( final boolean is_on ) {
1214 // if ( !_configuration.isUseNativeUI() ) {
1216 getDynamicallyHideData().setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
1219 if ( !_configuration.isUseNativeUI() ) {
1220 getDynamicallyHideData().setForeground( getConfiguration().getGuiButtonTextColor() );
1223 getDynamicallyHideData().setForeground( Color.BLACK );
1229 private void setSearchFoundCountsOnLabel( final int counts ) {
1230 getSearchFoundCountsLabel().setText( "Found: " + counts );
1233 public void setSequenceRelationQueries( final Collection<Sequence> sequenceRelationQueries ) {
1234 final JComboBox box = getSequenceRelationBox();
1235 while ( box.getItemCount() > 1 ) {
1236 box.removeItemAt( 1 );
1238 final HashMap<String, Sequence> sequencesByName = new HashMap<String, Sequence>();
1239 final SequenceRelation.SEQUENCE_RELATION_TYPE relationType = ( SequenceRelation.SEQUENCE_RELATION_TYPE ) _sequence_relation_type_box
1241 if ( relationType == null ) {
1244 final ArrayList<String> sequenceNamesToAdd = new ArrayList<String>();
1245 for( final Sequence seq : sequenceRelationQueries ) {
1246 if ( seq.hasSequenceRelations() ) {
1247 boolean fFoundForCurrentType = false;
1248 for( final SequenceRelation sq : seq.getSequenceRelations() ) {
1249 if ( sq.getType().equals( relationType ) ) {
1250 fFoundForCurrentType = true;
1254 if ( fFoundForCurrentType ) {
1255 sequenceNamesToAdd.add( seq.getName() );
1256 sequencesByName.put( seq.getName(), seq );
1260 // sort sequences by name before adding them to the combo
1261 final String[] sequenceNameArray = sequenceNamesToAdd.toArray( new String[ sequenceNamesToAdd.size() ] );
1262 Arrays.sort( sequenceNameArray, String.CASE_INSENSITIVE_ORDER );
1263 for( final String seqName : sequenceNameArray ) {
1264 box.addItem( seqName );
1266 for( final ItemListener oldItemListener : box.getItemListeners() ) {
1267 box.removeItemListener( oldItemListener );
1269 box.addItemListener( new ItemListener() {
1272 public void itemStateChanged( final ItemEvent e ) {
1273 _selected_query_seq = sequencesByName.get( e.getItem() );
1274 _mainpanel.getCurrentTreePanel().repaint();
1279 void setShowEvents( final boolean show_events ) {
1280 if ( getShowEventsCb() == null ) {
1281 _show_events = new JCheckBox( "" );
1283 getShowEventsCb().setSelected( show_events );
1286 void setSpeciesColors( final Map<String, Color> species_colors ) {
1287 _species_colors = species_colors;
1290 private void setupClickToOptions() {
1291 final int default_option = _configuration.getDefaultDisplayClicktoOption();
1292 int selected_index = 0;
1294 if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
1295 _show_data_item = cb_index;
1296 addClickToOption( Configuration.display_node_data,
1297 _configuration.getClickToTitle( Configuration.display_node_data ) );
1298 if ( default_option == Configuration.display_node_data ) {
1299 selected_index = cb_index;
1303 if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
1304 _collapse_cb_item = cb_index;
1305 addClickToOption( Configuration.collapse_uncollapse,
1306 _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
1307 if ( default_option == Configuration.collapse_uncollapse ) {
1308 selected_index = cb_index;
1312 if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
1313 _reroot_cb_item = cb_index;
1314 addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
1315 if ( default_option == Configuration.reroot ) {
1316 selected_index = cb_index;
1320 if ( _configuration.doDisplayClickToOption( Configuration.subtree ) ) {
1321 _subtree_cb_item = cb_index;
1322 addClickToOption( Configuration.subtree, _configuration.getClickToTitle( Configuration.subtree ) );
1323 if ( default_option == Configuration.subtree ) {
1324 selected_index = cb_index;
1328 if ( _configuration.doDisplayClickToOption( Configuration.swap ) ) {
1329 _swap_cb_item = cb_index;
1330 addClickToOption( Configuration.swap, _configuration.getClickToTitle( Configuration.swap ) );
1331 if ( default_option == Configuration.swap ) {
1332 selected_index = cb_index;
1336 if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
1337 _sort_descendents_item = cb_index;
1338 addClickToOption( Configuration.sort_descendents,
1339 _configuration.getClickToTitle( Configuration.sort_descendents ) );
1340 if ( default_option == Configuration.sort_descendents ) {
1341 selected_index = cb_index;
1345 if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
1346 _color_subtree_cb_item = cb_index;
1347 addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
1348 if ( default_option == Configuration.color_subtree ) {
1349 selected_index = cb_index;
1353 if ( _configuration.doDisplayClickToOption( Configuration.open_seq_web ) ) {
1354 _open_seq_web_item = cb_index;
1355 addClickToOption( Configuration.open_seq_web, _configuration.getClickToTitle( Configuration.open_seq_web ) );
1356 if ( default_option == Configuration.open_seq_web ) {
1357 selected_index = cb_index;
1361 if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
1362 _open_tax_web_item = cb_index;
1363 addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
1364 if ( default_option == Configuration.open_tax_web ) {
1365 selected_index = cb_index;
1369 if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
1370 _blast_item = cb_index;
1371 addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
1372 if ( default_option == Configuration.blast ) {
1373 selected_index = cb_index;
1377 if ( getOptions().isEditable() ) {
1378 if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
1379 _cut_subtree_item = cb_index;
1380 addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
1381 if ( default_option == Configuration.cut_subtree ) {
1382 selected_index = cb_index;
1386 if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
1387 _copy_subtree_item = cb_index;
1388 addClickToOption( Configuration.copy_subtree,
1389 _configuration.getClickToTitle( Configuration.copy_subtree ) );
1390 if ( default_option == Configuration.copy_subtree ) {
1391 selected_index = cb_index;
1395 if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
1396 _paste_subtree_item = cb_index;
1397 addClickToOption( Configuration.paste_subtree,
1398 _configuration.getClickToTitle( Configuration.paste_subtree ) );
1399 if ( default_option == Configuration.paste_subtree ) {
1400 selected_index = cb_index;
1404 if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
1405 _delete_node_or_subtree_item = cb_index;
1406 addClickToOption( Configuration.delete_subtree_or_node,
1407 _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
1408 if ( default_option == Configuration.delete_subtree_or_node ) {
1409 selected_index = cb_index;
1413 if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
1414 _add_new_node_item = cb_index;
1415 addClickToOption( Configuration.add_new_node,
1416 _configuration.getClickToTitle( Configuration.add_new_node ) );
1417 if ( default_option == Configuration.add_new_node ) {
1418 selected_index = cb_index;
1422 if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
1423 _edit_node_data_item = cb_index;
1424 addClickToOption( Configuration.edit_node_data,
1425 _configuration.getClickToTitle( Configuration.edit_node_data ) );
1426 if ( default_option == Configuration.edit_node_data ) {
1427 selected_index = cb_index;
1432 // Set default selection and its action
1433 _click_to_combobox.setSelectedIndex( selected_index );
1434 setClickToAction( selected_index );
1439 * Set up the controls from the config settings. 11/26/05
1441 void setupControls() {
1442 // The tree display options:
1443 setupDisplayCheckboxes();
1445 // The sequence relation query selection combo-box
1446 if ( _configuration.displaySequenceRelations() ) {
1447 addSequenceRelationBlock();
1451 startClickToOptions();
1452 setupClickToOptions();
1453 endClickToOptions();
1454 // Zoom and quick edit buttons
1459 void setUpControlsForDomainStrucures() {
1460 _domain_display_label = new JLabel( "Domain Display:" );
1461 add( customizeLabel( _domain_display_label, getConfiguration() ) );
1462 add( _domain_display_label );
1463 _zoom_in_domain_structure = new JButton( "d+" );
1464 _zoom_out_domain_structure = new JButton( "d-" );
1465 _decr_domain_structure_evalue_thr = new JButton( "-" );
1466 _incr_domain_structure_evalue_thr = new JButton( "+" );
1467 _zoom_in_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
1468 _zoom_out_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
1469 _decr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
1470 _incr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
1471 _incr_domain_structure_evalue_thr.setToolTipText( "Increase the E-value threshold by a factor of 10" );
1472 _decr_domain_structure_evalue_thr.setToolTipText( "Decrease the E-value threshold by a factor of 10" );
1473 _domain_structure_evalue_thr_tf = new JTextField( 3 );
1474 _domain_structure_evalue_thr_tf.setEditable( false );
1475 if ( !getConfiguration().isUseNativeUI() ) {
1476 _domain_structure_evalue_thr_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1477 _domain_structure_evalue_thr_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1478 _domain_structure_evalue_thr_tf.setBorder( null );
1480 final JPanel d1_panel = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1481 final JPanel d2_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
1482 if ( !_configuration.isUseNativeUI() ) {
1483 d1_panel.setBackground( getBackground() );
1484 d2_panel.setBackground( getBackground() );
1488 addJButton( _zoom_out_domain_structure, d1_panel );
1489 addJButton( _zoom_in_domain_structure, d1_panel );
1490 addJButton( _decr_domain_structure_evalue_thr, d2_panel );
1491 addJTextField( _domain_structure_evalue_thr_tf, d2_panel );
1492 addJButton( _incr_domain_structure_evalue_thr, d2_panel );
1495 private void setupDisplayCheckboxes() {
1496 if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
1497 addCheckbox( Configuration.display_as_phylogram,
1498 _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
1499 setCheckbox( Configuration.display_as_phylogram,
1500 _configuration.doCheckOption( Configuration.display_as_phylogram ) );
1502 if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
1503 addCheckbox( Configuration.dynamically_hide_data,
1504 _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
1505 setCheckbox( Configuration.dynamically_hide_data,
1506 _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
1508 if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
1509 addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
1510 setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
1512 if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
1513 addCheckbox( Configuration.display_internal_data,
1514 _configuration.getDisplayTitle( Configuration.display_internal_data ) );
1515 setCheckbox( Configuration.display_internal_data,
1516 _configuration.doCheckOption( Configuration.display_internal_data ) );
1518 if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
1519 addCheckbox( Configuration.color_according_to_species,
1520 _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
1521 setCheckbox( Configuration.color_according_to_species,
1522 _configuration.doCheckOption( Configuration.color_according_to_species ) );
1524 if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
1525 addCheckbox( Configuration.color_according_to_annotation,
1526 _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
1527 setCheckbox( Configuration.color_according_to_annotation,
1528 _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
1530 if ( _configuration.doDisplayOption( Configuration.color_branches ) ) {
1531 addCheckbox( Configuration.color_branches, _configuration.getDisplayTitle( Configuration.color_branches ) );
1532 setCheckbox( Configuration.color_branches, _configuration.doCheckOption( Configuration.color_branches ) );
1534 if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
1535 addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
1536 setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
1538 final JLabel label = new JLabel( "Display Data:" );
1539 label.setFont( ControlPanel.jcb_bold_font );
1540 if ( !getConfiguration().isUseNativeUI() ) {
1541 label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1544 if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
1545 addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
1546 setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
1548 if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
1549 addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
1550 setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
1552 if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
1553 addCheckbox( Configuration.show_taxonomy_scientific_names,
1554 _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
1555 setCheckbox( Configuration.show_taxonomy_scientific_names,
1556 _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
1558 if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
1559 addCheckbox( Configuration.show_taxonomy_common_names,
1560 _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
1561 setCheckbox( Configuration.show_taxonomy_common_names,
1562 _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
1564 if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
1565 addCheckbox( Configuration.show_taxonomy_images,
1566 _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
1567 setCheckbox( Configuration.show_taxonomy_images,
1568 _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
1570 if ( _configuration.doDisplayOption( Configuration.show_gene_symbols ) ) {
1571 addCheckbox( Configuration.show_gene_symbols,
1572 _configuration.getDisplayTitle( Configuration.show_gene_symbols ) );
1573 setCheckbox( Configuration.show_gene_symbols,
1574 _configuration.doCheckOption( Configuration.show_gene_symbols ) );
1576 if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
1577 addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
1578 setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
1580 if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
1581 addCheckbox( Configuration.show_sequence_acc,
1582 _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
1583 setCheckbox( Configuration.show_sequence_acc,
1584 _configuration.doCheckOption( Configuration.show_sequence_acc ) );
1586 if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
1587 addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
1588 setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
1590 if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
1591 addCheckbox( Configuration.show_binary_characters,
1592 _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
1593 setCheckbox( Configuration.show_binary_characters,
1594 _configuration.doCheckOption( Configuration.show_binary_characters ) );
1596 if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
1597 addCheckbox( Configuration.show_binary_character_counts,
1598 _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
1599 setCheckbox( Configuration.show_binary_character_counts,
1600 _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
1602 if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
1603 addCheckbox( Configuration.show_domain_architectures,
1604 _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
1605 setCheckbox( Configuration.show_domain_architectures,
1606 _configuration.doCheckOption( Configuration.show_domain_architectures ) );
1608 if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
1609 addCheckbox( Configuration.write_confidence_values,
1610 _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
1611 setCheckbox( Configuration.write_confidence_values,
1612 _configuration.doCheckOption( Configuration.write_confidence_values ) );
1614 if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
1615 addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
1616 setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
1618 if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
1619 addCheckbox( Configuration.show_vector_data,
1620 _configuration.getDisplayTitle( Configuration.show_vector_data ) );
1621 setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
1623 if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
1624 addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
1625 setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
1629 void setupSearchTools() {
1630 final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
1631 final JLabel search_label = new JLabel( "Search:" );
1632 search_label.setFont( ControlPanel.jcb_bold_font );
1633 if ( !getConfiguration().isUseNativeUI() ) {
1634 search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1636 add( search_label );
1637 search_label.setToolTipText( tip );
1638 _search_found_label = new JLabel();
1639 getSearchFoundCountsLabel().setVisible( false );
1640 _search_found_label.setFont( ControlPanel.jcb_bold_font );
1641 if ( !getConfiguration().isUseNativeUI() ) {
1642 _search_found_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
1644 _search_tf = new JTextField( 3 );
1645 _search_tf.setToolTipText( tip );
1646 _search_tf.setEditable( true );
1647 if ( !getConfiguration().isUseNativeUI() ) {
1648 _search_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
1649 _search_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
1650 _search_tf.setBorder( null );
1652 _search_reset_button = new JButton();
1653 getSearchResetButton().setText( "Reset" );
1654 getSearchResetButton().setEnabled( false );
1655 getSearchResetButton().setVisible( false );
1656 final JPanel s_panel_1 = new JPanel( new BorderLayout() );
1657 final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
1658 s_panel_1.setBackground( getBackground() );
1660 s_panel_2.setBackground( getBackground() );
1662 final KeyAdapter key_adapter = new KeyAdapter() {
1665 public void keyReleased( final KeyEvent key_event ) {
1667 displayedPhylogenyMightHaveChanged( true );
1670 final ActionListener action_listener = new ActionListener() {
1673 public void actionPerformed( final ActionEvent e ) {
1675 setSearchFoundCountsOnLabel( 0 );
1676 getSearchFoundCountsLabel().setVisible( false );
1677 getSearchTextField().setText( "" );
1678 getSearchResetButton().setEnabled( false );
1679 getSearchResetButton().setVisible( false );
1680 displayedPhylogenyMightHaveChanged( true );
1683 _search_reset_button.addActionListener( action_listener );
1684 _search_tf.addKeyListener( key_adapter );
1685 addJTextField( _search_tf, s_panel_1 );
1686 s_panel_2.add( _search_found_label );
1687 addJButton( _search_reset_button, s_panel_2 );
1690 private void setVisibilityOfDomainStrucureControls() {
1691 if ( _zoom_in_domain_structure != null ) {
1692 if ( isShowDomainArchitectures() ) {
1693 _domain_display_label.setVisible( true );
1694 _zoom_in_domain_structure.setVisible( true );
1695 _zoom_out_domain_structure.setVisible( true );
1696 _decr_domain_structure_evalue_thr.setVisible( true );
1697 _incr_domain_structure_evalue_thr.setVisible( true );
1698 _domain_structure_evalue_thr_tf.setVisible( true );
1701 _domain_display_label.setVisible( false );
1702 _zoom_in_domain_structure.setVisible( false );
1703 _zoom_out_domain_structure.setVisible( false );
1704 _decr_domain_structure_evalue_thr.setVisible( false );
1705 _incr_domain_structure_evalue_thr.setVisible( false );
1706 _domain_structure_evalue_thr_tf.setVisible( false );
1712 * Fit entire tree into window.
1715 if ( _mainpanel.getCurrentScrollPane() == null ) {
1718 displayedPhylogenyMightHaveChanged( false );
1719 _mainpanel.getCurrentTreePanel().updateOvSettings();
1720 _mainpanel.getCurrentTreePanel().validate();
1721 _mainpanel.validate();
1722 _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
1723 _mainpanel.getSizeOfViewport().height,
1725 _mainpanel.getCurrentTreePanel().resetPreferredSize();
1726 _mainpanel.adjustJScrollPane();
1727 _mainpanel.getCurrentTreePanel().repaint();
1728 _mainpanel.getCurrentTreePanel().validate();
1729 _mainpanel.validate();
1730 _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
1731 _mainpanel.getSizeOfViewport().height,
1733 _mainpanel.getCurrentTreePanel().resetPreferredSize();
1734 _mainpanel.adjustJScrollPane();
1735 _mainpanel.getCurrentTreePanel().repaint();
1736 _mainpanel.getCurrentTreePanel().updateOvSizes();
1739 void showWholeAll() {
1740 for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
1741 if ( tree_panel != null ) {
1742 tree_panel.validate();
1743 tree_panel.setParametersForPainting( _mainpanel.getSizeOfViewport().width,
1744 _mainpanel.getSizeOfViewport().height,
1746 tree_panel.resetPreferredSize();
1747 tree_panel.repaint();
1752 // Create header for click-to combo box.
1753 void startClickToOptions() {
1754 final JLabel spacer = new JLabel( "" );
1755 spacer.setFont( ControlPanel.jcb_font );
1757 _click_to_label = new JLabel( "Click on Node to:" );
1758 add( customizeLabel( _click_to_label, getConfiguration() ) );
1759 _click_to_combobox = new JComboBox();
1760 _click_to_combobox.setFocusable( false );
1761 _click_to_combobox.setMaximumRowCount( 14 );
1762 _click_to_combobox.setFont( ControlPanel.js_font );
1763 if ( !_configuration.isUseNativeUI() ) {
1764 _click_to_combobox.setBackground( getConfiguration().getGuiBackgroundColor() );
1766 // don't add listener until all items are set (or each one will trigger
1768 // click_to_list.addActionListener(this);
1769 add( _click_to_combobox );
1770 // Correlates option names to titles
1771 _all_click_to_names = new HashMap<Integer, String>();
1772 _click_to_names = new ArrayList<String>();
1776 if ( getMainPanel().getTabbedPane().getTabCount() > 0 ) {
1777 if ( getCurrentTreePanel().isPhyHasBranchLengths()
1778 && ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1779 setDrawPhylogramEnabled( true );
1780 setDrawPhylogram( isDrawPhylogram() );
1783 setDrawPhylogramEnabled( false );
1784 setDrawPhylogram( false );
1786 if ( getMainPanel().getMainFrame() == null ) {
1787 // Must be "E" applet version.
1788 final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1789 e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() );
1792 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel()
1793 .getPhylogenyGraphicsType() );
1795 getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
1796 getMainPanel().getControlPanel().search();
1797 getSequenceRelationTypeBox().removeAllItems();
1798 for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
1799 .getRelevantSequenceRelationTypes() ) {
1800 _sequence_relation_type_box.addItem( type );
1802 //setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
1803 // according to GUILHEM the line above can be removed.
1808 * Uncollapse all nodes.
1810 void uncollapseAll( final TreePanel tp ) {
1811 final Phylogeny t = tp.getPhylogeny();
1812 if ( ( t != null ) && !t.isEmpty() ) {
1813 for( final PhylogenyNodeIterator iter = t.iteratorPreorder(); iter.hasNext(); ) {
1814 final PhylogenyNode node = iter.next();
1815 node.setCollapse( false );
1817 tp.resetNodeIdToDistToLeafMap();
1818 tp.updateSetOfCollapsedExternalNodes( t );
1819 t.recalculateNumberOfExternalDescendants( false );
1820 tp.setNodeInPreorderToNull();
1826 void updateDomainStructureEvaluethresholdDisplay() {
1827 if ( _domain_structure_evalue_thr_tf != null ) {
1828 _domain_structure_evalue_thr_tf.setText( "10^"
1829 + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThreshold() );
1833 void zoomInX( final float factor, final float x_correction_factor ) {
1834 final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
1835 final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1836 treepanel.multiplyUrtFactor( 1f );
1837 if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1838 || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1839 || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
1840 || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
1841 final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1842 treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1843 treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1844 getMainPanel().adjustJScrollPane();
1845 treepanel.resetPreferredSize();
1846 getMainPanel().getCurrentScrollPane().getViewport().validate();
1847 sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1848 - ( sb.getVisibleAmount() / 2.0 ) ) );
1851 final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
1852 treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1853 treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1854 getMainPanel().adjustJScrollPane();
1855 treepanel.resetPreferredSize();
1856 getMainPanel().getCurrentScrollPane().getViewport().validate();
1857 sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
1859 treepanel.resetPreferredSize();
1860 treepanel.updateOvSizes();
1863 void zoomInY( final float factor ) {
1864 final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
1865 final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1866 treepanel.multiplyUrtFactor( 1.1f );
1867 final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1868 treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
1869 getMainPanel().adjustJScrollPane();
1870 treepanel.resetPreferredSize();
1871 getMainPanel().getCurrentScrollPane().getViewport().validate();
1872 sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1873 - ( sb.getVisibleAmount() / 2.0 ) ) );
1874 treepanel.resetPreferredSize();
1875 treepanel.updateOvSizes();
1878 void zoomOutX( final float factor, final float x_correction_factor ) {
1879 final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1880 treepanel.multiplyUrtFactor( 1f );
1881 if ( ( treepanel.getXdistance() * factor ) > 0.0 ) {
1882 final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
1883 if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1884 || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1885 || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
1886 || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
1887 getMainPanel().adjustJScrollPane();
1888 treepanel.resetPreferredSize();
1889 getMainPanel().getCurrentScrollPane().getViewport().validate();
1890 final double x = ( sb.getMaximum() - sb.getMinimum() )
1891 / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1892 treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
1893 treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
1894 getMainPanel().adjustJScrollPane();
1895 treepanel.resetPreferredSize();
1896 getMainPanel().getCurrentScrollPane().getViewport().validate();
1897 sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1898 - ( sb.getVisibleAmount() / 2.0 ) ) );
1901 final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
1902 treepanel.setXdistance( treepanel.getXdistance() * factor );
1903 treepanel.setXcorrectionFactor( treepanel.getXcorrectionFactor() * x_correction_factor );
1905 getMainPanel().adjustJScrollPane();
1906 treepanel.resetPreferredSize();
1907 getMainPanel().getCurrentScrollPane().getViewport().validate();
1908 sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
1911 treepanel.resetPreferredSize();
1912 treepanel.updateOvSizes();
1916 void zoomOutY( final float factor ) {
1917 final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
1918 treepanel.multiplyUrtFactor( 0.9f );
1919 if ( ( treepanel.getYdistance() * factor ) > 0.0 ) {
1920 final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
1921 final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
1922 treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
1923 getMainPanel().adjustJScrollPane();
1924 treepanel.resetPreferredSize();
1925 getMainPanel().getCurrentScrollPane().getViewport().validate();
1926 sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
1927 - ( sb.getVisibleAmount() / 2.0 ) ) );
1928 treepanel.resetPreferredSize();
1929 treepanel.updateOvSizes();
1933 static JLabel customizeLabel( final JLabel label, final Configuration configuration ) {
1934 label.setFont( ControlPanel.jcb_bold_font );
1935 if ( !configuration.isUseNativeUI() ) {
1936 label.setForeground( configuration.getGuiCheckboxTextColor() );
1937 label.setBackground( configuration.getGuiBackgroundColor() );
1942 enum NodeClickAction {
1953 DELETE_NODE_OR_SUBTREE,