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
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.archaeopteryx;
28 import java.awt.BasicStroke;
29 import java.awt.Color;
30 import java.awt.Cursor;
31 import java.awt.Dimension;
33 import java.awt.GradientPaint;
34 import java.awt.Graphics;
35 import java.awt.Graphics2D;
36 import java.awt.Point;
37 import java.awt.Rectangle;
38 import java.awt.RenderingHints;
39 import java.awt.Stroke;
40 import java.awt.event.ActionEvent;
41 import java.awt.event.ActionListener;
42 import java.awt.event.FocusAdapter;
43 import java.awt.event.FocusEvent;
44 import java.awt.event.InputEvent;
45 import java.awt.event.KeyAdapter;
46 import java.awt.event.KeyEvent;
47 import java.awt.event.MouseEvent;
48 import java.awt.event.MouseWheelEvent;
49 import java.awt.event.MouseWheelListener;
50 import java.awt.font.FontRenderContext;
51 import java.awt.font.TextLayout;
52 import java.awt.geom.AffineTransform;
53 import java.awt.geom.Arc2D;
54 import java.awt.geom.CubicCurve2D;
55 import java.awt.geom.Ellipse2D;
56 import java.awt.geom.Line2D;
57 import java.awt.geom.Path2D;
58 import java.awt.geom.QuadCurve2D;
59 import java.awt.geom.Rectangle2D;
60 import java.awt.image.BufferedImage;
61 import java.awt.print.PageFormat;
62 import java.awt.print.Printable;
63 import java.awt.print.PrinterException;
65 import java.io.IOException;
66 import java.io.UnsupportedEncodingException;
68 import java.net.URISyntaxException;
69 import java.net.URLEncoder;
70 import java.text.DecimalFormat;
71 import java.text.DecimalFormatSymbols;
72 import java.text.NumberFormat;
73 import java.util.ArrayList;
74 import java.util.Collections;
75 import java.util.HashMap;
76 import java.util.HashSet;
77 import java.util.Hashtable;
78 import java.util.List;
79 import java.util.Map.Entry;
81 import java.util.SortedMap;
82 import java.util.SortedSet;
83 import java.util.TreeMap;
85 import javax.swing.BorderFactory;
86 import javax.swing.JApplet;
87 import javax.swing.JColorChooser;
88 import javax.swing.JDialog;
89 import javax.swing.JMenuItem;
90 import javax.swing.JOptionPane;
91 import javax.swing.JPanel;
92 import javax.swing.JPopupMenu;
93 import javax.swing.JTextArea;
94 import javax.swing.Popup;
95 import javax.swing.PopupFactory;
97 import org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON;
98 import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
99 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
100 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
101 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
102 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
103 import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
104 import org.forester.archaeopteryx.tools.Blast;
105 import org.forester.archaeopteryx.tools.ImageLoader;
106 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
107 import org.forester.io.writers.SequenceWriter;
108 import org.forester.phylogeny.Phylogeny;
109 import org.forester.phylogeny.PhylogenyMethods;
110 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
111 import org.forester.phylogeny.PhylogenyNode;
112 import org.forester.phylogeny.data.Annotation;
113 import org.forester.phylogeny.data.BranchColor;
114 import org.forester.phylogeny.data.Confidence;
115 import org.forester.phylogeny.data.Event;
116 import org.forester.phylogeny.data.NodeData.NODE_DATA;
117 import org.forester.phylogeny.data.NodeVisualization;
118 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
119 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
120 import org.forester.phylogeny.data.PhylogenyDataUtil;
121 import org.forester.phylogeny.data.PropertiesMap;
122 import org.forester.phylogeny.data.Property;
123 import org.forester.phylogeny.data.Sequence;
124 import org.forester.phylogeny.data.SequenceRelation;
125 import org.forester.phylogeny.data.Taxonomy;
126 import org.forester.phylogeny.data.Uri;
127 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
128 import org.forester.phylogeny.iterators.PreorderTreeIterator;
129 import org.forester.util.BasicDescriptiveStatistics;
130 import org.forester.util.DescriptiveStatistics;
131 import org.forester.util.ForesterConstants;
132 import org.forester.util.ForesterUtil;
133 import org.forester.util.SequenceIdParser;
135 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
137 private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
138 private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
139 private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
140 private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
141 private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
142 private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
143 private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
144 private static final float PI = ( float ) ( Math.PI );
145 private static final double TWO_PI = 2 * Math.PI;
146 private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
147 private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
148 private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
149 private static final short OV_BORDER = 10;
150 final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
151 final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
152 final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
153 final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
154 final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
155 private final static long serialVersionUID = -978349745916505029L;
156 private final static int EURO_D = 10;
157 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
158 private final static int MIN_ROOT_LENGTH = 3;
159 private final static int MAX_SUBTREES = 100;
160 private final static int MAX_NODE_FRAMES = 10;
161 private final static int MOVE = 20;
162 private final static NumberFormat FORMATTER_CONFIDENCE;
163 private final static NumberFormat FORMATTER_BRANCH_LENGTH;
164 private final static int WIGGLE = 2;
165 private final static int LIMIT_FOR_HQ_RENDERING = 2000;
166 private final static int CONFIDENCE_LEFT_MARGIN = 4;
167 private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
168 RenderingHints.VALUE_RENDER_DEFAULT );
169 private File _treefile = null;
170 private Configuration _configuration = null;
171 private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
172 private int _node_frame_index = 0;
173 private Phylogeny _phylogeny = null;
174 private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
175 private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
176 private int _subtree_index = 0;
177 private MainPanel _main_panel = null;
178 private Set<Long> _found_nodes = null;
179 private PhylogenyNode _highlight_node = null;
180 private JPopupMenu _node_popup_menu = null;
181 private JMenuItem _node_popup_menu_items[] = null;
182 private int _longest_ext_node_info = 0;
183 private float _x_correction_factor = 0.0f;
184 private float _ov_x_correction_factor = 0.0f;
185 private float _x_distance = 0.0f;
186 private float _y_distance = 0.0f;
187 private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
188 private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
189 private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
190 private float _last_drag_point_x = 0;
191 private float _last_drag_point_y = 0;
192 private ControlPanel _control_panel = null;
193 private int _external_node_index = 0;
194 private final Path2D.Float _polygon = new Path2D.Float();
195 private final StringBuilder _sb = new StringBuilder();
196 private JColorChooser _color_chooser = null;
197 private double _scale_distance = 0.0;
198 private String _scale_label = null;
199 private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
200 private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
201 private final Line2D _line = new Line2D.Float();
202 private final Ellipse2D _ellipse = new Ellipse2D.Float();
203 private final Rectangle2D _rectangle = new Rectangle2D.Float();
204 private Options _options = null;
205 private float _ov_max_width = 0;
206 private float _ov_max_height = 0;
207 private int _ov_x_position = 0;
208 private int _ov_y_position = 0;
209 private int _ov_y_start = 0;
210 private float _ov_y_distance = 0;
211 private float _ov_x_distance = 0;
212 private boolean _ov_on = false;
213 private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
214 private float _urt_factor = 1;
215 private float _urt_factor_ov = 1;
216 private final boolean _phy_has_branch_lengths;
217 private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
218 private boolean _in_ov_rect = false;
219 private boolean _in_ov = false;
220 private final Rectangle _ov_virtual_rectangle = new Rectangle();
221 final private static double _180_OVER_PI = 180.0 / Math.PI;
222 private static final float ROUNDED_D = 8;
223 private int _circ_max_depth;
224 private PhylogenyNode _root;
225 final private Arc2D _arc = new Arc2D.Double();
226 final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
227 final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
228 final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
229 HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
230 private AffineTransform _at;
231 private double _max_distance_to_root = -1;
232 private int _dynamic_hiding_factor = 0;
233 private boolean _edited = false;
234 private Popup _node_desc_popup;
235 private JTextArea _rollover_popup;
236 private final StringBuffer _popup_buffer = new StringBuffer();
237 final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
240 private Sequence _query_sequence = null;
241 private final FontRenderContext _frc = new FontRenderContext( null,
244 // expression values menu:
245 private DescriptiveStatistics _statistics_for_vector_data;
246 private PhylogenyNode[] _nodes_in_preorder = null;
247 private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
248 private int _current_external_nodes_data_buffer_change_counter = 0;
249 private Set<Long> _current_external_nodes = null;
250 // private Image offscreenImage;
251 // private Graphics offscreenGraphics;
252 // private Dimension offscreenDimension;
254 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
255 dfs.setDecimalSeparator( '.' );
256 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
257 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
260 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
261 requestFocusInWindow();
262 addKeyListener( new KeyAdapter() {
265 public void keyPressed( final KeyEvent key_event ) {
266 keyPressedCalls( key_event );
267 requestFocusInWindow();
270 addFocusListener( new FocusAdapter() {
273 public void focusGained( final FocusEvent e ) {
274 requestFocusInWindow();
277 if ( ( t == null ) || t.isEmpty() ) {
278 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
280 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
282 _configuration = configuration;
284 _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
286 // if ( !_phylogeny.isEmpty() ) {
287 _phylogeny.recalculateNumberOfExternalDescendants( true );
288 checkForVectorProperties( _phylogeny );
290 setBackground( getTreeColorSet().getBackgroundColor() );
291 final MouseListener mouse_listener = new MouseListener( this );
292 addMouseListener( mouse_listener );
293 addMouseMotionListener( mouse_listener );
294 addMouseWheelListener( this );
295 calculateScaleDistance();
296 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
297 FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
298 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
302 final public void actionPerformed( final ActionEvent e ) {
303 boolean done = false;
304 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
305 for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
306 // NOTE: index corresponds to the indices of click-to options
307 // in the control panel.
308 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
309 // Set this as the new default click-to action
310 _main_panel.getControlPanel().setClickToAction( index );
311 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
312 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
313 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
318 requestFocusInWindow();
321 public synchronized Hashtable<String, BufferedImage> getImageMap() {
322 return getMainPanel().getImageMap();
325 final public MainPanel getMainPanel() {
330 * Get a pointer to the phylogeny
332 * @return a pointer to the phylogeny
334 public final Phylogeny getPhylogeny() {
339 final public void mouseWheelMoved( final MouseWheelEvent e ) {
340 final int notches = e.getWheelRotation();
341 if ( inOvVirtualRectangle( e ) ) {
342 if ( !isInOvRect() ) {
348 if ( isInOvRect() ) {
349 setInOvRect( false );
353 if ( e.isControlDown() ) {
355 getTreeFontSet().increaseFontSize();
356 getControlPanel().displayedPhylogenyMightHaveChanged( true );
359 getTreeFontSet().decreaseFontSize( 1, false );
360 getControlPanel().displayedPhylogenyMightHaveChanged( true );
363 else if ( e.isShiftDown() ) {
364 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
365 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
367 for( int i = 0; i < ( -notches ); ++i ) {
368 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
369 getControlPanel().displayedPhylogenyMightHaveChanged( false );
373 for( int i = 0; i < notches; ++i ) {
374 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
375 if ( getStartingAngle() < 0 ) {
376 setStartingAngle( TWO_PI + getStartingAngle() );
378 getControlPanel().displayedPhylogenyMightHaveChanged( false );
384 for( int i = 0; i < ( -notches ); ++i ) {
385 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
386 getControlPanel().displayedPhylogenyMightHaveChanged( false );
390 for( int i = 0; i < notches; ++i ) {
391 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
392 getControlPanel().displayedPhylogenyMightHaveChanged( false );
399 for( int i = 0; i < ( -notches ); ++i ) {
400 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
401 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
402 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
403 getControlPanel().displayedPhylogenyMightHaveChanged( false );
407 for( int i = 0; i < notches; ++i ) {
408 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
409 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
410 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
411 getControlPanel().displayedPhylogenyMightHaveChanged( false );
416 requestFocusInWindow();
421 final public void paintComponent( final Graphics g ) {
422 // Dimension currentSize = getSize();
423 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
424 // call the 'java.awt.Component.createImage(...)' method to get an
426 // offscreenImage = createImage( currentSize.width, currentSize.height );
427 // offscreenGraphics = offscreenImage.getGraphics();
428 // offscreenDimension = currentSize;
430 // super.paintComponent( g ); //why?
431 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
432 final Graphics2D g2d = ( Graphics2D ) g;
433 g2d.setRenderingHints( _rendering_hints );
434 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
435 //g.drawImage( offscreenImage, 0, 0, this );
439 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
440 throws PrinterException {
441 if ( page_index > 0 ) {
442 return ( NO_SUCH_PAGE );
445 final Graphics2D g2d = ( Graphics2D ) g;
446 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
447 // Turn off double buffering !?
448 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
449 // Turn double buffering back on !?
450 return ( PAGE_EXISTS );
454 public final void setEdited( final boolean edited ) {
458 public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
459 getMainPanel().setImageMap( image_map );
463 * Set a phylogeny tree.
466 * an instance of a Phylogeny
468 public final void setTree( final Phylogeny t ) {
469 setNodeInPreorderToNull();
473 public final void setWaitCursor() {
474 setCursor( WAIT_CURSOR );
479 public void update( final Graphics g ) {
483 final void calcMaxDepth() {
484 if ( _phylogeny != null ) {
485 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
490 * Set parameters for printing the displayed tree
493 final void calcParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
494 // updateStyle(); not needed?
495 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
497 if ( recalc_longest_ext_node_info ) {
498 calculateLongestExtNodeInfo();
499 if ( getOptions().isAllowFontSizeChange() ) {
500 if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
501 && ( getTreeFontSet().getLargeFont().getSize() > 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
502 while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
503 && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
504 getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(),
506 calculateLongestExtNodeInfo();
510 while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
511 && ( getTreeFontSet().getLargeFont().getSize() <= getTreeFontSet().getLargeFontMemory()
512 .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
513 getMainPanel().getTreeFontSet().increaseFontSize();
514 calculateLongestExtNodeInfo();
519 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
520 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
521 if ( ext_nodes == 1 ) {
522 ext_nodes = max_depth;
523 if ( ext_nodes < 1 ) {
530 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
531 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
532 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
535 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
536 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
538 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
542 if ( ov_xdist < 0.0 ) {
548 setXdistance( xdist );
549 setYdistance( ydist );
550 setOvXDistance( ov_xdist );
551 final double height = _phylogeny.getHeight();
553 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
554 setXcorrectionFactor( corr > 0 ? corr : 0 );
555 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
556 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
559 setXcorrectionFactor( 0 );
560 setOvXcorrectionFactor( 0 );
562 _circ_max_depth = max_depth;
565 if ( getOptions().isAllowFontSizeChange() ) {
566 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
567 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
568 // int dynamic_hiding_factor = calcDynamicHidingFactor();
569 // if ( dynamic_hiding_factor > 1 ) {
570 // while ( dynamic_hiding_factor > 1
571 // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
572 // getTreeFontSet().decreaseFontSize( 1, true );
573 // dynamic_hiding_factor = calcDynamicHidingFactor();
576 // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
577 // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
578 // getTreeFontSet().increaseFontSize();
579 // dynamic_hiding_factor = calcDynamicHidingFactor();
588 final void calculateLongestExtNodeInfo() {
589 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
592 int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
593 * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
594 if ( max_length < 40 ) {
598 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
600 if ( node.isCollapse() ) {
603 if ( getControlPanel().isShowNodeNames() ) {
604 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
606 if ( node.getNodeData().isHasSequence() ) {
607 if ( getControlPanel().isShowSequenceAcc()
608 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
609 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
613 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
614 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
616 if ( getControlPanel().isShowGeneSymbols()
617 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
618 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
620 if ( getControlPanel().isShowAnnotation()
621 && ( node.getNodeData().getSequence().getAnnotations() != null )
622 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
623 sum += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
624 .getNodeData().getSequence().getAnnotations(), getOptions().isShowAnnotationRefSource() )
627 if ( getControlPanel().isShowDomainArchitectures()
628 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
629 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
630 .getRenderingSize().getWidth();
633 if ( node.getNodeData().isHasTaxonomy() ) {
634 final Taxonomy tax = node.getNodeData().getTaxonomy();
635 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
636 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
638 if ( getControlPanel().isShowTaxonomyScientificNames()
639 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
640 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
642 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
643 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
646 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
647 sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
649 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
650 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
651 .getGainedCharactersAsStringBuffer().toString() );
653 if ( sum >= max_length ) {
654 setLongestExtNodeInfo( max_length );
657 if ( sum > longest ) {
661 if ( longest >= max_length ) {
662 setLongestExtNodeInfo( max_length );
665 setLongestExtNodeInfo( longest );
669 final void calculateScaleDistance() {
670 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
673 final double height = getMaxDistanceToRoot();
675 if ( ( height <= 0.5 ) ) {
676 setScaleDistance( 0.01 );
678 else if ( height <= 5.0 ) {
679 setScaleDistance( 0.1 );
681 else if ( height <= 50.0 ) {
682 setScaleDistance( 1 );
684 else if ( height <= 500.0 ) {
685 setScaleDistance( 10 );
688 setScaleDistance( 100 );
692 setScaleDistance( 0.0 );
694 String scale_label = String.valueOf( getScaleDistance() );
695 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
696 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
698 setScaleLabel( scale_label );
701 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
702 if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
703 return getTreeColorSet().getTaxonomyColor();
706 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
707 c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
709 if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
710 c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
713 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
714 c = TreePanelUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
715 getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
718 c = TreePanelUtil.calculateColorFromString( tax.getScientificName(), true );
719 getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
725 void checkForVectorProperties( final Phylogeny phy ) {
726 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
727 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
728 final PhylogenyNode node = iter.next();
729 if ( node.getNodeData().getProperties() != null ) {
730 final PropertiesMap pm = node.getNodeData().getProperties();
731 final double[] vector = new double[ pm.getProperties().size() ];
733 for( final String ref : pm.getProperties().keySet() ) {
734 if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
735 final Property p = pm.getProperty( ref );
736 final String value_str = p.getValue();
737 final String index_str = ref
738 .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
741 d = Double.parseDouble( value_str );
743 catch ( final NumberFormatException e ) {
744 JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
745 + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
750 i = Integer.parseInt( index_str );
752 catch ( final NumberFormatException e ) {
753 JOptionPane.showMessageDialog( this,
754 "Could not parse \"" + index_str
755 + "\" into index for vector data",
756 "Problem with Vector Data",
757 JOptionPane.ERROR_MESSAGE );
761 JOptionPane.showMessageDialog( this,
762 "Attempt to use negative index for vector data",
763 "Problem with Vector Data",
764 JOptionPane.ERROR_MESSAGE );
772 final List<Double> vector_l = new ArrayList<Double>( counter );
773 for( int i = 0; i < counter; ++i ) {
774 vector_l.add( vector[ i ] );
776 node.getNodeData().setVector( vector_l );
779 if ( stats.getN() > 0 ) {
780 _statistics_for_vector_data = stats;
784 void clearCurrentExternalNodesDataBuffer() {
785 setCurrentExternalNodesDataBuffer( new StringBuilder() );
789 * Collapse the tree from the given node
794 final void collapse( final PhylogenyNode node ) {
795 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
796 JOptionPane.showMessageDialog( this,
797 "Cannot collapse in unrooted display type",
798 "Attempt to collapse in unrooted display",
799 JOptionPane.WARNING_MESSAGE );
802 if ( !node.isExternal() && !node.isRoot() ) {
803 final boolean collapse = !node.isCollapse();
804 TreePanelUtil.collapseSubtree( node, collapse );
805 updateSetOfCollapsedExternalNodes();
806 _phylogeny.recalculateNumberOfExternalDescendants( true );
807 resetNodeIdToDistToLeafMap();
808 calculateLongestExtNodeInfo();
809 setNodeInPreorderToNull();
810 _control_panel.displayedPhylogenyMightHaveChanged( true );
811 resetPreferredSize();
813 _main_panel.adjustJScrollPane();
818 final void collapseSpeciesSpecificSubtrees() {
819 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
823 TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
824 updateSetOfCollapsedExternalNodes();
825 _phylogeny.recalculateNumberOfExternalDescendants( true );
826 resetNodeIdToDistToLeafMap();
827 calculateLongestExtNodeInfo();
828 setNodeInPreorderToNull();
829 resetPreferredSize();
830 _main_panel.adjustJScrollPane();
835 final void colorRank( final String rank ) {
836 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
840 AptxUtil.removeBranchColors( _phylogeny );
841 final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
842 if ( colorizations > 0 ) {
843 _control_panel.setColorBranches( true );
844 if ( _control_panel.getColorBranchesCb() != null ) {
845 _control_panel.getColorBranchesCb().setSelected( true );
847 if ( _control_panel.getColorAccSpeciesCb() != null ) {
848 _control_panel.getColorAccSpeciesCb().setSelected( false );
850 _options.setColorLabelsSameAsParentBranch( true );
851 _control_panel.repaint();
855 if ( colorizations > 0 ) {
856 String msg = "Taxonomy colorization via " + rank + " completed:\n";
857 if ( colorizations > 1 ) {
858 msg += "colorized " + colorizations + " subtrees";
861 msg += "colorized one subtree";
864 JOptionPane.showMessageDialog( this,
866 "Taxonomy Colorization Completed (" + rank + ")",
867 JOptionPane.INFORMATION_MESSAGE );
870 String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
871 msg += "Possible solutions (given that suitable taxonomic information is present):\n";
872 msg += "select a different rank (e.g. phylum, genus, ...)\n";
875 msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
876 msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
877 JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
881 final void confColor() {
882 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
886 AptxUtil.removeBranchColors( _phylogeny );
887 TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
888 _control_panel.setColorBranches( true );
889 if ( _control_panel.getColorBranchesCb() != null ) {
890 _control_panel.getColorBranchesCb().setSelected( true );
896 final void decreaseDomainStructureEvalueThreshold() {
897 if ( _domain_structure_e_value_thr_exp > -20 ) {
898 _domain_structure_e_value_thr_exp -= 1;
903 * Find the node, if any, at the given location
907 * @return pointer to the node at x,y, null if not found
909 final PhylogenyNode findNode( final int x, final int y ) {
910 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
913 final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
914 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
915 final PhylogenyNode node = iter.next();
916 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
917 && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
918 && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
919 && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
920 && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
927 final Configuration getConfiguration() {
928 return _configuration;
931 final ControlPanel getControlPanel() {
932 return _control_panel;
935 String getCurrentExternalNodesDataBufferAsString() {
936 return _current_external_nodes_data_buffer.toString();
939 int getCurrentExternalNodesDataBufferChangeCounter() {
940 return _current_external_nodes_data_buffer_change_counter;
943 final int getDomainStructureEvalueThreshold() {
944 return _domain_structure_e_value_thr_exp;
947 final Set<Long> getFoundNodes() {
951 final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
952 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
953 return ( PhylogenyMethods.getBranchColorValue( node ) );
956 return ( getTreeColorSet().getBranchColor() );
960 final int getLongestExtNodeInfo() {
961 return _longest_ext_node_info;
964 final Options getOptions() {
965 if ( _options == null ) {
966 _options = getControlPanel().getOptions();
971 final Rectangle2D getOvRectangle() {
972 return _ov_rectangle;
975 final Rectangle getOvVirtualRectangle() {
976 return _ov_virtual_rectangle;
979 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
980 return _graphics_type;
983 final double getStartingAngle() {
984 return _urt_starting_angle;
987 DescriptiveStatistics getStatisticsForExpressionValues() {
988 return _statistics_for_vector_data;
992 * Find a color for this species name.
995 * @return the species color
997 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
998 if ( node.getNodeData().isHasTaxonomy() ) {
999 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
1001 // return non-colorized color
1002 return getTreeColorSet().getTaxonomyColor();
1006 * @return pointer to colorset for tree drawing
1008 final TreeColorSet getTreeColorSet() {
1009 return getMainPanel().getTreeColorSet();
1012 final File getTreeFile() {
1016 final float getXcorrectionFactor() {
1017 return _x_correction_factor;
1020 final float getXdistance() {
1024 final float getYdistance() {
1028 final void increaseDomainStructureEvalueThreshold() {
1029 if ( _domain_structure_e_value_thr_exp < 3 ) {
1030 _domain_structure_e_value_thr_exp += 1;
1034 final void initNodeData() {
1035 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1038 double max_original_domain_structure_width = 0.0;
1039 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1040 if ( node.getNodeData().isHasSequence()
1041 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1042 RenderableDomainArchitecture rds = null;
1043 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
1044 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1045 getConfiguration() );
1046 node.getNodeData().getSequence().setDomainArchitecture( rds );
1049 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1051 if ( getControlPanel().isShowDomainArchitectures() ) {
1052 final double dsw = rds.getOriginalSize().getWidth();
1053 if ( dsw > max_original_domain_structure_width ) {
1054 max_original_domain_structure_width = dsw;
1059 if ( getControlPanel().isShowDomainArchitectures() ) {
1060 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1061 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1062 if ( node.getNodeData().isHasSequence()
1063 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1064 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1065 .getSequence().getDomainArchitecture();
1066 rds.setRenderingFactorWidth( ds_factor_width );
1067 rds.setParameter( _domain_structure_e_value_thr_exp );
1073 final boolean inOv( final MouseEvent e ) {
1074 return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
1075 && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
1076 && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
1077 + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
1080 final boolean inOvRectangle( final MouseEvent e ) {
1081 return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
1082 && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
1083 && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
1084 + getOvRectangle().getHeight() + 1 ) ) );
1087 final boolean isApplet() {
1088 return getMainPanel() instanceof MainPanelApplets;
1091 final boolean isCanCollapse() {
1092 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1095 final boolean isCanColorSubtree() {
1096 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1099 final boolean isCanCopy() {
1100 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1103 final boolean isCanCut( final PhylogenyNode node ) {
1104 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1108 final boolean isCanDelete() {
1109 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1112 final boolean isCanPaste() {
1113 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1114 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1117 final boolean isCanReroot() {
1118 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1121 final boolean isCanSubtree( final PhylogenyNode node ) {
1122 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1123 .isRoot() || ( _subtree_index > 0 ) ) );
1126 final boolean isCurrentTreeIsSubtree() {
1127 return ( _subtree_index > 0 );
1130 final boolean isEdited() {
1134 final boolean isInOvRect() {
1138 final boolean isOvOn() {
1142 final boolean isPhyHasBranchLengths() {
1143 return _phy_has_branch_lengths;
1146 final void midpointRoot() {
1147 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1150 if ( !_phylogeny.isRerootable() ) {
1151 JOptionPane.showMessageDialog( this,
1152 "This is not rerootable",
1154 JOptionPane.WARNING_MESSAGE );
1157 setNodeInPreorderToNull();
1159 PhylogenyMethods.midpointRoot( _phylogeny );
1160 resetNodeIdToDistToLeafMap();
1166 final void mouseClicked( final MouseEvent e ) {
1167 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1168 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1169 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1170 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
1172 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
1180 final double max_x = getWidth() - getVisibleRect().width;
1181 final double max_y = getHeight() - getVisibleRect().height;
1188 getMainPanel().getCurrentScrollPane().getViewport()
1189 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1190 setInOvRect( true );
1194 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1195 if ( node != null ) {
1196 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1199 _highlight_node = node;
1200 // Check if shift key is down
1201 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1202 // Yes, so add to _found_nodes
1203 if ( getFoundNodes() == null ) {
1204 setFoundNodes( new HashSet<Long>() );
1206 getFoundNodes().add( node.getId() );
1207 // Check if control key is down
1209 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1210 // Yes, so pop-up menu
1211 displayNodePopupMenu( node, e.getX(), e.getY() );
1212 // Handle unadorned click
1215 // Check for right mouse button
1216 if ( e.getModifiers() == 4 ) {
1217 displayNodePopupMenu( node, e.getX(), e.getY() );
1220 // if not in _found_nodes, clear _found_nodes
1221 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1226 // no node was clicked
1227 _highlight_node = null;
1233 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1234 setCursor( MOVE_CURSOR );
1235 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1236 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1237 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1238 if ( scroll_position.x < 0 ) {
1239 scroll_position.x = 0;
1242 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1243 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1244 if ( scroll_position.x > max_x ) {
1245 scroll_position.x = max_x;
1248 if ( scroll_position.y < 0 ) {
1249 scroll_position.y = 0;
1252 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1253 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1254 if ( scroll_position.y > max_y ) {
1255 scroll_position.y = max_y;
1258 if ( isOvOn() || getOptions().isShowScale() ) {
1261 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1264 final void mouseDragInOvRectangle( final MouseEvent e ) {
1265 setCursor( HAND_CURSOR );
1266 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1267 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1268 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1269 double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
1270 double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
1271 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1272 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1273 if ( scroll_position.x <= 0 ) {
1274 scroll_position.x = 0;
1278 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1279 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1280 if ( scroll_position.x >= max_x ) {
1282 scroll_position.x = max_x;
1285 if ( scroll_position.y <= 0 ) {
1287 scroll_position.y = 0;
1290 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1291 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1292 if ( scroll_position.y >= max_y ) {
1294 scroll_position.y = max_y;
1298 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1299 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1300 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1303 final void mouseMoved( final MouseEvent e ) {
1304 requestFocusInWindow();
1305 if ( _current_external_nodes != null ) {
1306 _current_external_nodes = null;
1309 if ( getControlPanel().isNodeDescPopup() ) {
1310 if ( _node_desc_popup != null ) {
1311 _node_desc_popup.hide();
1312 _node_desc_popup = null;
1315 if ( getOptions().isShowOverview() && isOvOn() ) {
1316 if ( inOvVirtualRectangle( e ) ) {
1317 if ( !isInOvRect() ) {
1318 setInOvRect( true );
1323 if ( isInOvRect() ) {
1324 setInOvRect( false );
1329 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
1338 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1339 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
1340 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
1341 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
1342 addToCurrentExternalNodes( n.getId() );
1344 setCursor( HAND_CURSOR );
1347 else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
1348 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
1349 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
1350 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
1351 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
1352 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
1353 setCursor( CUT_CURSOR );
1356 setCursor( HAND_CURSOR );
1357 if ( getControlPanel().isNodeDescPopup() ) {
1358 showNodeDataPopup( e, node );
1363 setCursor( ARROW_CURSOR );
1368 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
1369 setCursor( ARROW_CURSOR );
1372 final void multiplyUrtFactor( final float f ) {
1376 final JApplet obtainApplet() {
1377 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1380 final void paintBranchCircular( final PhylogenyNode p,
1381 final PhylogenyNode c,
1383 final boolean radial_labels,
1384 final boolean to_pdf,
1385 final boolean to_graphics_file ) {
1386 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1387 final double root_x = _root.getXcoord();
1388 final double root_y = _root.getYcoord();
1389 final double dx = root_x - p.getXcoord();
1390 final double dy = root_y - p.getYcoord();
1391 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1392 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1393 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
1394 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
1395 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
1396 final double r2 = 2.0 * parent_radius;
1397 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1399 drawLine( c.getXcoord(),
1401 root_x + ( Math.cos( angle ) * parent_radius ),
1402 root_y + ( Math.sin( angle ) * parent_radius ),
1404 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c )
1405 || isInCurrentExternalNodes( c ) );
1406 if ( c.isExternal() ) {
1407 final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c );
1408 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
1409 && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
1412 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
1416 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
1417 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1418 final double root_x = _root.getXSecondary();
1419 final double root_y = _root.getYSecondary();
1420 final double dx = root_x - p.getXSecondary();
1421 final double dy = root_y - p.getYSecondary();
1422 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1423 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1424 g.setColor( getTreeColorSet().getOvColor() );
1425 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
1426 final double r2 = 2.0 * parent_radius;
1427 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1429 drawLine( c.getXSecondary(),
1431 root_x + ( Math.cos( angle ) * parent_radius ),
1432 root_y + ( Math.sin( angle ) * parent_radius ),
1434 if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
1435 g.setColor( getTreeColorSet().getFoundColor() );
1436 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
1440 final void paintCircular( final Phylogeny phy,
1441 final double starting_angle,
1446 final boolean to_pdf,
1447 final boolean to_graphics_file ) {
1448 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
1449 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
1450 _root = phy.getRoot();
1451 _root.setXcoord( center_x );
1452 _root.setYcoord( center_y );
1453 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1454 double current_angle = starting_angle;
1456 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1457 final PhylogenyNode n = it.next();
1458 if ( !n.isCollapse() ) {
1459 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1460 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1461 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1462 _urt_nodeid_index_map.put( n.getId(), i++ );
1463 current_angle += ( TWO_PI / circ_num_ext_nodes );
1467 System.out.println( "is collapse" + n.getName() );
1470 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
1471 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
1474 final void paintCircularLite( final Phylogeny phy,
1475 final double starting_angle,
1479 final Graphics2D g ) {
1480 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
1481 _root = phy.getRoot();
1482 _root.setXSecondary( center_x );
1483 _root.setYSecondary( center_y );
1484 double current_angle = starting_angle;
1485 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1486 final PhylogenyNode n = it.next();
1487 n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1488 n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1489 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1490 current_angle += ( TWO_PI / circ_num_ext_nodes );
1492 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
1495 final void paintPhylogeny( final Graphics2D g,
1496 final boolean to_pdf,
1497 final boolean to_graphics_file,
1498 final int graphics_file_width,
1499 final int graphics_file_height,
1500 final int graphics_file_x,
1501 final int graphics_file_y ) {
1502 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1505 if ( _control_panel.isShowSequenceRelations() ) {
1506 _query_sequence = _control_panel.getSelectedQuerySequence();
1508 // Color the background
1510 final Rectangle r = getVisibleRect();
1511 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
1512 g.setColor( getTreeColorSet().getBackgroundColor() );
1513 if ( !to_graphics_file ) {
1517 if ( getOptions().isPrintBlackAndWhite() ) {
1518 g.setColor( Color.WHITE );
1520 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1524 if ( !to_graphics_file ) {
1525 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
1526 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
1530 g.setPaint( new GradientPaint( graphics_file_x,
1532 getTreeColorSet().getBackgroundColor(),
1534 graphics_file_y + graphics_file_height,
1535 getTreeColorSet().getBackgroundColorGradientBottom() ) );
1536 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1542 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
1544 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1545 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1546 _external_node_index = 0;
1547 // Position starting X of tree
1548 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
1549 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
1551 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
1552 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
1553 .getDistanceToParent() * getXcorrectionFactor() ) ) );
1556 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
1558 // Position starting Y of tree
1559 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
1560 + ( TreePanel.MOVE / 2.0f ) );
1561 final int dynamic_hiding_factor = calcDynamicHidingFactor();
1562 if ( getControlPanel().isDynamicallyHideData() ) {
1563 if ( dynamic_hiding_factor > 1 ) {
1564 getControlPanel().setDynamicHidingIsOn( true );
1567 getControlPanel().setDynamicHidingIsOn( false );
1570 if ( _nodes_in_preorder == null ) {
1571 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
1573 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1574 _nodes_in_preorder[ i++ ] = it.next();
1577 //final PhylogenyNodeIterator it;
1578 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1579 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
1580 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1582 for( final PhylogenyNode element : _nodes_in_preorder ) {
1583 paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
1584 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1586 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
1587 if ( !( to_graphics_file || to_pdf ) ) {
1590 getVisibleRect().y + getVisibleRect().height,
1595 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1598 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1599 paintPhylogenyLite( g );
1602 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1603 if ( getControlPanel().getDynamicallyHideData() != null ) {
1604 getControlPanel().setDynamicHidingIsOn( false );
1606 final double angle = getStartingAngle();
1607 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1608 _dynamic_hiding_factor = 0;
1609 if ( getControlPanel().isDynamicallyHideData() ) {
1610 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1611 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
1613 if ( getControlPanel().getDynamicallyHideData() != null ) {
1614 if ( _dynamic_hiding_factor > 1 ) {
1615 getControlPanel().setDynamicHidingIsOn( true );
1618 getControlPanel().setDynamicHidingIsOn( false );
1621 paintUnrooted( _phylogeny.getRoot(),
1623 ( float ) ( angle + ( 2 * Math.PI ) ),
1628 if ( getOptions().isShowScale() ) {
1629 if ( !( to_graphics_file || to_pdf ) ) {
1632 getVisibleRect().y + getVisibleRect().height,
1637 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1640 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1641 g.setColor( getTreeColorSet().getOvColor() );
1642 paintUnrootedLite( _phylogeny.getRoot(),
1644 angle + ( 2 * Math.PI ),
1646 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
1647 paintOvRectangle( g );
1650 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1651 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
1652 final int d = radius + MOVE + getLongestExtNodeInfo();
1653 _dynamic_hiding_factor = 0;
1654 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
1655 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1656 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
1658 if ( getControlPanel().getDynamicallyHideData() != null ) {
1659 if ( _dynamic_hiding_factor > 1 ) {
1660 getControlPanel().setDynamicHidingIsOn( true );
1663 getControlPanel().setDynamicHidingIsOn( false );
1666 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
1667 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1668 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
1669 : getOvMaxWidth() / 2 );
1670 double x_scale = 1.0;
1671 double y_scale = 1.0;
1672 int x_pos = getVisibleRect().x + getOvXPosition();
1673 int y_pos = getVisibleRect().y + getOvYPosition();
1674 if ( getWidth() > getHeight() ) {
1675 x_scale = ( double ) getHeight() / getWidth();
1676 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
1679 y_scale = ( double ) getWidth() / getHeight();
1680 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
1682 _at = g.getTransform();
1683 g.scale( x_scale, y_scale );
1684 paintCircularLite( _phylogeny,
1688 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
1691 g.setTransform( _at );
1692 paintOvRectangle( g );
1697 final void recalculateMaxDistanceToRoot() {
1698 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
1702 * Remove all edit-node frames
1704 final void removeAllEditNodeJFrames() {
1705 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
1706 if ( _node_frames[ i ] != null ) {
1707 _node_frames[ i ].dispose();
1708 _node_frames[ i ] = null;
1711 _node_frame_index = 0;
1715 * Remove a node-edit frame.
1717 final void removeEditNodeFrame( final int i ) {
1718 _node_frame_index--;
1719 _node_frames[ i ] = null;
1720 if ( i < _node_frame_index ) {
1721 for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
1722 _node_frames[ j ] = _node_frames[ j + 1 ];
1724 _node_frames[ _node_frame_index ] = null;
1728 final void reRoot( final PhylogenyNode node ) {
1729 if ( !getPhylogeny().isRerootable() ) {
1730 JOptionPane.showMessageDialog( this,
1731 "This is not rerootable",
1733 JOptionPane.WARNING_MESSAGE );
1736 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1737 JOptionPane.showMessageDialog( this,
1738 "Cannot reroot in unrooted display type",
1739 "Attempt to reroot tree in unrooted display",
1740 JOptionPane.WARNING_MESSAGE );
1743 getPhylogeny().reRoot( node );
1744 getPhylogeny().recalculateNumberOfExternalDescendants( true );
1745 resetNodeIdToDistToLeafMap();
1746 setNodeInPreorderToNull();
1747 resetPreferredSize();
1748 getMainPanel().adjustJScrollPane();
1751 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1752 getControlPanel().showWhole();
1756 final void resetNodeIdToDistToLeafMap() {
1757 _nodeid_dist_to_leaf = new HashMap<Long, Short>();
1760 final void resetPreferredSize() {
1761 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
1767 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
1768 if ( getControlPanel().isDrawPhylogram() ) {
1770 + getLongestExtNodeInfo()
1772 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
1775 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
1777 + getLongestExtNodeInfo()
1778 + ForesterUtil.roundToInt( getXdistance()
1779 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
1783 + getLongestExtNodeInfo()
1784 + ForesterUtil.roundToInt( getXdistance()
1785 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
1788 setPreferredSize( new Dimension( x, y ) );
1791 final void selectNode( final PhylogenyNode node ) {
1792 if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
1793 getFoundNodes().remove( node.getId() );
1794 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1795 if ( getFoundNodes().size() < 1 ) {
1796 getControlPanel().searchReset();
1800 getControlPanel().getSearchFoundCountsLabel().setVisible( true );
1801 getControlPanel().getSearchResetButton().setEnabled( true );
1802 getControlPanel().getSearchResetButton().setVisible( true );
1803 if ( getFoundNodes() == null ) {
1804 setFoundNodes( new HashSet<Long>() );
1806 getFoundNodes().add( node.getId() );
1807 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1811 final void setArrowCursor() {
1812 setCursor( ARROW_CURSOR );
1816 final void setControlPanel( final ControlPanel atv_control ) {
1817 _control_panel = atv_control;
1820 void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
1821 increaseCurrentExternalNodesDataBufferChangeCounter();
1822 _current_external_nodes_data_buffer = sb;
1825 final void setFoundNodes( final Set<Long> found_nodes ) {
1826 _found_nodes = found_nodes;
1829 final void setInOvRect( final boolean in_ov_rect ) {
1830 _in_ov_rect = in_ov_rect;
1833 final void setLargeFonts() {
1834 getTreeFontSet().largeFonts();
1837 final void setLastMouseDragPointX( final float x ) {
1838 _last_drag_point_x = x;
1841 final void setLastMouseDragPointY( final float y ) {
1842 _last_drag_point_y = y;
1845 final void setLongestExtNodeInfo( final int i ) {
1846 _longest_ext_node_info = i;
1849 final void setMediumFonts() {
1850 getTreeFontSet().mediumFonts();
1853 final void setNodeInPreorderToNull() {
1854 _nodes_in_preorder = null;
1857 final void setOvOn( final boolean ov_on ) {
1861 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
1862 _graphics_type = graphics_type;
1866 final void setSmallFonts() {
1867 getTreeFontSet().smallFonts();
1870 final void setStartingAngle( final double starting_angle ) {
1871 _urt_starting_angle = starting_angle;
1874 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
1875 _statistics_for_vector_data = statistics_for_expression_values;
1878 final void setSuperTinyFonts() {
1879 getTreeFontSet().superTinyFonts();
1882 final void setTextAntialias() {
1883 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
1884 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
1885 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
1888 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
1891 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
1892 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
1894 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
1896 // catch ( final Throwable e ) {
1897 // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
1901 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
1902 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1906 final void setTinyFonts() {
1907 getTreeFontSet().tinyFonts();
1910 final void setTreeFile( final File treefile ) {
1911 _treefile = treefile;
1914 final void setXcorrectionFactor( final float f ) {
1915 _x_correction_factor = f;
1918 final void setXdistance( final float x ) {
1922 final void setYdistance( final float y ) {
1926 final void sortDescendants( final PhylogenyNode node ) {
1927 if ( !node.isExternal() ) {
1928 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
1929 if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
1930 .isShowTaxonomyCommonNames() ) ) {
1931 if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
1932 .isShowGeneSymbols() ) ) {
1933 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
1935 else if ( getControlPanel().isShowNodeNames() ) {
1936 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
1939 PhylogenyMethods.sortNodeDescendents( node, pri );
1940 setNodeInPreorderToNull();
1941 _phylogeny.externalNodesHaveChanged();
1942 _phylogeny.clearHashIdToNodeMap();
1943 _phylogeny.recalculateNumberOfExternalDescendants( true );
1944 resetNodeIdToDistToLeafMap();
1950 final void subTree( final PhylogenyNode node ) {
1951 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1952 JOptionPane.showMessageDialog( this,
1953 "Cannot get a sub/super tree in unrooted display",
1954 "Attempt to get sub/super tree in unrooted display",
1955 JOptionPane.WARNING_MESSAGE );
1958 if ( node.isExternal() ) {
1959 JOptionPane.showMessageDialog( this,
1960 "Cannot get a subtree of a external node",
1961 "Attempt to get subtree of external node",
1962 JOptionPane.WARNING_MESSAGE );
1965 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
1966 JOptionPane.showMessageDialog( this,
1967 "Cannot get a subtree of the root node",
1968 "Attempt to get subtree of root node",
1969 JOptionPane.WARNING_MESSAGE );
1972 setNodeInPreorderToNull();
1973 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
1974 _sub_phylogenies[ _subtree_index ] = _phylogeny;
1975 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
1977 _phylogeny = TreePanelUtil.subTree( node, _phylogeny );
1978 updateSubSuperTreeButton();
1980 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
1983 _main_panel.getControlPanel().showWhole();
1987 final void superTree() {
1988 setNodeInPreorderToNull();
1989 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
1990 for( final PhylogenyNode n : temp_root.getDescendants() ) {
1991 n.setParent( temp_root );
1993 _sub_phylogenies[ _subtree_index ] = null;
1994 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
1995 _phylogeny = _sub_phylogenies[ --_subtree_index ];
1996 updateSubSuperTreeButton();
1999 final void swap( final PhylogenyNode node ) {
2000 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
2003 if ( node.getNumberOfDescendants() > 2 ) {
2004 JOptionPane.showMessageDialog( this,
2005 "Cannot swap descendants of nodes with more than 2 descendants",
2006 "Cannot swap descendants",
2007 JOptionPane.ERROR_MESSAGE );
2010 if ( !node.isExternal() ) {
2011 node.swapChildren();
2012 setNodeInPreorderToNull();
2013 _phylogeny.externalNodesHaveChanged();
2014 _phylogeny.clearHashIdToNodeMap();
2015 _phylogeny.recalculateNumberOfExternalDescendants( true );
2016 resetNodeIdToDistToLeafMap();
2022 final void taxColor() {
2023 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
2027 TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
2028 _control_panel.setColorBranches( true );
2029 if ( _control_panel.getColorBranchesCb() != null ) {
2030 _control_panel.getColorBranchesCb().setSelected( true );
2037 final void updateOvSettings() {
2038 switch ( getOptions().getOvPlacement() ) {
2040 setOvXPosition( OV_BORDER );
2041 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2042 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2045 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2046 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2047 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2050 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2051 setOvYPosition( OV_BORDER );
2052 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2055 setOvXPosition( OV_BORDER );
2056 setOvYPosition( OV_BORDER );
2057 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2062 final void updateOvSizes() {
2063 if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
2065 float l = getLongestExtNodeInfo();
2066 final float w_ratio = getOvMaxWidth() / getWidth();
2068 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
2069 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
2071 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
2072 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
2075 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
2077 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
2078 if ( ov_xdist < 0.0 ) {
2081 if ( ydist < 0.0 ) {
2084 setOvXDistance( ov_xdist );
2085 final double height = _phylogeny.getHeight();
2087 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
2088 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
2091 setOvXcorrectionFactor( 0 );
2099 void updateSetOfCollapsedExternalNodes() {
2100 final Phylogeny phy = getPhylogeny();
2101 _collapsed_external_nodeid_set.clear();
2102 if ( phy != null ) {
2103 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2104 final PhylogenyNode ext_node = it.next();
2105 PhylogenyNode n = ext_node;
2106 while ( !n.isRoot() ) {
2107 if ( n.isCollapse() ) {
2108 _collapsed_external_nodeid_set.add( ext_node.getId() );
2109 ext_node.setCollapse( true );
2118 final void updateSubSuperTreeButton() {
2119 if ( _subtree_index < 1 ) {
2120 getControlPanel().deactivateButtonToReturnToSuperTree();
2123 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
2127 final void zoomInDomainStructure() {
2128 if ( _domain_structure_width < 2000 ) {
2129 _domain_structure_width *= 1.2;
2133 final void zoomOutDomainStructure() {
2134 if ( _domain_structure_width > 20 ) {
2135 _domain_structure_width *= 0.8;
2139 private void abbreviateScientificName( final String sn ) {
2140 final String[] a = sn.split( "\\s+" );
2141 _sb.append( a[ 0 ].substring( 0, 1 ) );
2142 _sb.append( a[ 1 ].substring( 0, 2 ) );
2143 if ( a.length > 2 ) {
2144 for( int i = 2; i < a.length; i++ ) {
2146 _sb.append( a[ i ] );
2151 final private void addEmptyNode( final PhylogenyNode node ) {
2152 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2153 errorMessageNoCutCopyPasteInUnrootedDisplay();
2156 final String label = createASimpleTextRepresentationOfANode( node );
2158 if ( ForesterUtil.isEmpty( label ) ) {
2159 msg = "How to add the new, empty node?";
2162 msg = "How to add the new, empty node to node" + label + "?";
2164 final Object[] options = { "As sibling", "As descendant", "Cancel" };
2165 final int r = JOptionPane.showOptionDialog( this,
2167 "Addition of Empty New Node",
2168 JOptionPane.CLOSED_OPTION,
2169 JOptionPane.QUESTION_MESSAGE,
2173 boolean add_as_sibling = true;
2175 add_as_sibling = false;
2177 else if ( r != 0 ) {
2180 final Phylogeny phy = new Phylogeny();
2181 phy.setRoot( new PhylogenyNode() );
2182 phy.setRooted( true );
2183 if ( add_as_sibling ) {
2184 if ( node.isRoot() ) {
2185 JOptionPane.showMessageDialog( this,
2186 "Cannot add sibling to root",
2187 "Attempt to add sibling to root",
2188 JOptionPane.ERROR_MESSAGE );
2191 phy.addAsSibling( node );
2194 phy.addAsChild( node );
2196 setNodeInPreorderToNull();
2197 _phylogeny.externalNodesHaveChanged();
2198 _phylogeny.clearHashIdToNodeMap();
2199 _phylogeny.recalculateNumberOfExternalDescendants( true );
2200 resetNodeIdToDistToLeafMap();
2205 final private void addToCurrentExternalNodes( final long i ) {
2206 if ( _current_external_nodes == null ) {
2207 _current_external_nodes = new HashSet<Long>();
2209 _current_external_nodes.add( i );
2212 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
2213 final boolean is_vertical,
2215 final boolean to_pdf,
2216 final boolean to_graphics_file ) {
2217 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
2218 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2219 g.setColor( Color.BLACK );
2221 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
2222 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
2223 && ( getCutOrCopiedTree() != null )
2224 && ( getCopiedAndPastedNodes() != null )
2226 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
2227 g.setColor( getTreeColorSet().getFoundColor() );
2229 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2230 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2232 else if ( to_pdf ) {
2233 g.setColor( getTreeColorSet().getBranchColorForPdf() );
2236 g.setColor( getTreeColorSet().getBranchColor() );
2240 final private void blast( final PhylogenyNode node ) {
2241 if ( !isCanBlast( node ) ) {
2242 JOptionPane.showMessageDialog( this,
2243 "Insufficient information present",
2245 JOptionPane.INFORMATION_MESSAGE );
2249 final String query = Blast.obtainQueryForBlast( node );
2250 System.out.println( "query for BLAST is: " + query );
2252 if ( !ForesterUtil.isEmpty( query ) ) {
2253 if ( node.getNodeData().isHasSequence() ) {
2254 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
2255 if ( node.getNodeData().getSequence().getType().toLowerCase()
2256 .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
2263 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2264 if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2272 if ( type == '?' ) {
2273 if ( SequenceIdParser.isProtein( query ) ) {
2280 JApplet applet = null;
2282 applet = obtainApplet();
2285 Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
2287 catch ( final Exception e ) {
2288 e.printStackTrace();
2290 if ( Constants.ALLOW_DDBJ_BLAST ) {
2292 System.out.println( "trying: " + query );
2293 final Blast s = new Blast();
2294 s.ddbjBlast( query );
2296 catch ( final Exception e ) {
2297 e.printStackTrace();
2304 private final int calcDynamicHidingFactor() {
2305 return ( int ) ( 0.5 + ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ) );
2309 * Calculate the length of the distance between the given node and its
2315 * @return the distance value
2317 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
2318 if ( getControlPanel().isDrawPhylogram() ) {
2319 if ( node.getDistanceToParent() < 0.0 ) {
2322 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
2325 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2326 return getXdistance();
2328 return getXdistance() * factor;
2332 final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
2333 Color c = getTreeColorSet().getAnnotationColor();
2334 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
2335 final StringBuilder sb = new StringBuilder();
2336 for( final Annotation a : ann ) {
2337 sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() );
2339 final String ann_str = sb.toString();
2340 if ( !ForesterUtil.isEmpty( ann_str ) ) {
2341 c = getControlPanel().getAnnotationColors().get( ann_str );
2343 c = TreePanelUtil.calculateColorFromString( ann_str, false );
2344 getControlPanel().getAnnotationColors().put( ann_str, c );
2347 c = getTreeColorSet().getAnnotationColor();
2354 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
2355 if ( getControlPanel().isDrawPhylogram() ) {
2356 if ( node.getDistanceToParent() < 0.0 ) {
2359 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
2362 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2363 return getOvXDistance();
2365 return getOvXDistance() * factor;
2369 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
2370 JOptionPane.showMessageDialog( this,
2371 "Cannot launch web browser for " + type_type + " data of this node",
2372 "Cannot launch web browser",
2373 JOptionPane.WARNING_MESSAGE );
2376 final private void colorizeSubtree( final Color c,
2377 final PhylogenyNode node,
2378 final List<PhylogenyNode> additional_nodes ) {
2379 _control_panel.setColorBranches( true );
2380 if ( _control_panel.getColorBranchesCb() != null ) {
2381 _control_panel.getColorBranchesCb().setSelected( true );
2383 if ( node != null ) {
2384 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
2385 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
2388 if ( additional_nodes != null ) {
2389 for( final PhylogenyNode n : additional_nodes ) {
2390 n.getBranchData().setBranchColor( new BranchColor( c ) );
2396 final private void colorSubtree( final PhylogenyNode node ) {
2397 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2398 JOptionPane.showMessageDialog( this,
2399 "Cannot colorize subtree in unrooted display type",
2400 "Attempt to colorize subtree in unrooted display",
2401 JOptionPane.WARNING_MESSAGE );
2404 _color_chooser.setPreviewPanel( new JPanel() );
2405 SubtreeColorizationActionListener al;
2406 if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
2407 final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
2408 for( final Long id : getFoundNodes() ) {
2409 additional_nodes.add( _phylogeny.getNode( id ) );
2411 al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
2414 al = new SubtreeColorizationActionListener( _color_chooser, node );
2416 final JDialog dialog = JColorChooser
2417 .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
2418 dialog.setVisible( true );
2421 final private void copySubtree( final PhylogenyNode node ) {
2422 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2423 errorMessageNoCutCopyPasteInUnrootedDisplay();
2426 setNodeInPreorderToNull();
2427 setCutOrCopiedTree( _phylogeny.copy( node ) );
2428 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
2429 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
2430 for( final PhylogenyNode n : nodes ) {
2431 node_ids.add( n.getId() );
2433 node_ids.add( node.getId() );
2434 setCopiedAndPastedNodes( node_ids );
2438 final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
2439 final String tax = PhylogenyMethods.getSpecies( node );
2440 String label = node.getName();
2441 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
2442 label = label + " " + tax;
2444 else if ( !ForesterUtil.isEmpty( tax ) ) {
2450 if ( !ForesterUtil.isEmpty( label ) ) {
2451 label = " [" + label + "]";
2456 final private void cutSubtree( final PhylogenyNode node ) {
2457 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2458 errorMessageNoCutCopyPasteInUnrootedDisplay();
2461 if ( node.isRoot() ) {
2462 JOptionPane.showMessageDialog( this,
2463 "Cannot cut entire tree as subtree",
2464 "Attempt to cut entire tree",
2465 JOptionPane.ERROR_MESSAGE );
2468 final String label = createASimpleTextRepresentationOfANode( node );
2469 final int r = JOptionPane.showConfirmDialog( null,
2470 "Cut subtree" + label + "?",
2471 "Confirm Cutting of Subtree",
2472 JOptionPane.YES_NO_OPTION );
2473 if ( r != JOptionPane.OK_OPTION ) {
2476 setNodeInPreorderToNull();
2477 setCopiedAndPastedNodes( null );
2478 setCutOrCopiedTree( _phylogeny.copy( node ) );
2479 _phylogeny.deleteSubtree( node, true );
2480 _phylogeny.clearHashIdToNodeMap();
2481 _phylogeny.recalculateNumberOfExternalDescendants( true );
2482 resetNodeIdToDistToLeafMap();
2487 final private void cycleColors() {
2488 getMainPanel().getTreeColorSet().cycleColorScheme();
2489 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
2490 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
2494 final private void decreaseOvSize() {
2495 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
2496 setOvMaxWidth( getOvMaxWidth() - 5 );
2497 setOvMaxHeight( getOvMaxHeight() - 5 );
2499 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2503 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
2504 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2505 errorMessageNoCutCopyPasteInUnrootedDisplay();
2508 if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
2509 JOptionPane.showMessageDialog( this,
2510 "Cannot delete entire tree",
2511 "Attempt to delete entire tree",
2512 JOptionPane.ERROR_MESSAGE );
2515 final String label = createASimpleTextRepresentationOfANode( node );
2516 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
2517 final int r = JOptionPane.showOptionDialog( this,
2518 "Delete" + label + "?",
2519 "Delete Node/Subtree",
2520 JOptionPane.CLOSED_OPTION,
2521 JOptionPane.QUESTION_MESSAGE,
2525 setNodeInPreorderToNull();
2526 boolean node_only = true;
2530 else if ( r != 0 ) {
2534 PhylogenyMethods.removeNode( node, _phylogeny );
2537 _phylogeny.deleteSubtree( node, true );
2539 _phylogeny.externalNodesHaveChanged();
2540 _phylogeny.clearHashIdToNodeMap();
2541 _phylogeny.recalculateNumberOfExternalDescendants( true );
2542 resetNodeIdToDistToLeafMap();
2547 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
2548 makePopupMenus( node );
2549 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
2550 _node_popup_menu.show( this, x, y );
2553 final private void drawArc( final double x,
2556 final double heigth,
2557 final double start_angle,
2558 final double arc_angle,
2559 final Graphics2D g ) {
2560 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
2564 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
2565 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
2568 _line.setLine( x1, y1, x2, y2 );
2572 final private void drawOval( final double x,
2575 final double heigth,
2576 final Graphics2D g ) {
2577 _ellipse.setFrame( x, y, width, heigth );
2581 final private void drawOvalFilled( final double x,
2584 final double heigth,
2585 final Graphics2D g ) {
2586 _ellipse.setFrame( x, y, width, heigth );
2590 final private void drawOvalGradient( final double x,
2593 final double heigth,
2595 final Color color_1,
2596 final Color color_2,
2597 final Color color_border ) {
2598 _ellipse.setFrame( x, y, width, heigth );
2599 g.setPaint( new GradientPaint( ( float ) x,
2602 ( float ) ( x + width ),
2603 ( float ) ( y + heigth ),
2607 if ( color_border != null ) {
2608 g.setPaint( color_border );
2613 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
2614 _rectangle.setFrame( x, y, width, heigth );
2615 g.draw( _rectangle );
2618 final private void drawRectFilled( final double x,
2621 final double heigth,
2622 final Graphics2D g ) {
2623 _rectangle.setFrame( x, y, width, heigth );
2624 g.fill( _rectangle );
2627 final private void drawRectGradient( final double x,
2630 final double heigth,
2632 final Color color_1,
2633 final Color color_2,
2634 final Color color_border ) {
2635 _rectangle.setFrame( x, y, width, heigth );
2636 g.setPaint( new GradientPaint( ( float ) x,
2639 ( float ) ( x + width ),
2640 ( float ) ( y + heigth ),
2643 g.fill( _rectangle );
2644 if ( color_border != null ) {
2645 g.setPaint( color_border );
2646 g.draw( _rectangle );
2650 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2651 final List<Uri> us = new ArrayList<Uri>();
2652 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2653 for( final Uri uri : t.getUris() ) {
2658 for( final Uri uri : us ) {
2659 if ( uri != null ) {
2660 final String uri_str = uri.getValue().toString().toLowerCase();
2661 if ( getImageMap().containsKey( uri_str ) ) {
2662 final BufferedImage bi = getImageMap().get( uri_str );
2663 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2664 double scaling_factor = 1;
2665 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
2666 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
2667 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
2669 // y = y - ( 0.9 * getYdistance() );
2670 final double hs = bi.getHeight() * scaling_factor;
2671 double ws = ( bi.getWidth() * scaling_factor ) + offset;
2672 final double my_y = y - ( 0.5 * hs );
2673 final int x_w = ( int ) ( x + ws + 0.5 );
2674 final int y_h = ( int ) ( my_y + hs + 0.5 );
2675 if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
2677 ( int ) ( x + 0.5 + offset ),
2678 ( int ) ( my_y + 0.5 ),
2699 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
2700 JOptionPane.showMessageDialog( this,
2701 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
2702 "Attempt to cut/copy/paste/add/delete in unrooted display",
2703 JOptionPane.ERROR_MESSAGE );
2706 final private Set<Long> getCopiedAndPastedNodes() {
2707 return getMainPanel().getCopiedAndPastedNodes();
2710 final private Set<Long> getCurrentExternalNodes() {
2711 return _current_external_nodes;
2714 final private Phylogeny getCutOrCopiedTree() {
2715 return getMainPanel().getCutOrCopiedTree();
2718 final private float getLastDragPointX() {
2719 return _last_drag_point_x;
2722 final private float getLastDragPointY() {
2723 return _last_drag_point_y;
2726 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
2727 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
2728 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
2729 _nodeid_dist_to_leaf.put( node.getId(), m );
2733 return _nodeid_dist_to_leaf.get( node.getId() );
2737 final private double getMaxDistanceToRoot() {
2738 if ( _max_distance_to_root < 0 ) {
2739 recalculateMaxDistanceToRoot();
2741 return _max_distance_to_root;
2744 final private float getOvMaxHeight() {
2745 return _ov_max_height;
2748 final private float getOvMaxWidth() {
2749 return _ov_max_width;
2752 final private float getOvXcorrectionFactor() {
2753 return _ov_x_correction_factor;
2756 final private float getOvXDistance() {
2757 return _ov_x_distance;
2760 final private int getOvXPosition() {
2761 return _ov_x_position;
2764 final private float getOvYDistance() {
2765 return _ov_y_distance;
2768 final private int getOvYPosition() {
2769 return _ov_y_position;
2772 final private int getOvYStart() {
2776 final private double getScaleDistance() {
2777 return _scale_distance;
2780 final private String getScaleLabel() {
2781 return _scale_label;
2784 final private TreeFontSet getTreeFontSet() {
2785 return getMainPanel().getTreeFontSet();
2788 final private float getUrtFactor() {
2792 final private float getUrtFactorOv() {
2793 return _urt_factor_ov;
2796 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
2799 showNodeFrame( node );
2814 colorSubtree( node );
2829 copySubtree( node );
2832 pasteSubtree( node );
2834 case DELETE_NODE_OR_SUBTREE:
2835 deleteNodeOrSubtree( node );
2838 addEmptyNode( node );
2840 case EDIT_NODE_DATA:
2841 showNodeEditFrame( node );
2846 case SORT_DESCENDENTS:
2847 sortDescendants( node );
2849 case GET_EXT_DESC_DATA:
2850 showExtDescNodeData( node );
2853 throw new IllegalArgumentException( "unknown action: " + action );
2857 final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
2858 _current_external_nodes_data_buffer_change_counter++;
2861 final private void increaseOvSize() {
2862 if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
2863 && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
2864 .getHeight() / 2 ) ) ) {
2865 setOvMaxWidth( getOvMaxWidth() + 5 );
2866 setOvMaxHeight( getOvMaxHeight() + 5 );
2868 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2872 final private void init() {
2873 _color_chooser = new JColorChooser();
2874 _rollover_popup = new JTextArea();
2875 _rollover_popup.setFont( POPUP_FONT );
2876 resetNodeIdToDistToLeafMap();
2878 setTreeFile( null );
2880 initializeOvSettings();
2881 setStartingAngle( ( TWO_PI * 3 ) / 4 );
2882 final ImageLoader il = new ImageLoader( this );
2883 new Thread( il ).start();
2886 final private void initializeOvSettings() {
2887 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
2888 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
2891 final private boolean inOvVirtualRectangle( final int x, final int y ) {
2892 return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
2893 && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
2894 && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
2895 + getOvVirtualRectangle().height + 1 ) ) );
2898 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
2899 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
2902 final private boolean isCanBlast( final PhylogenyNode node ) {
2903 if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
2906 return Blast.isContainsQueryForBlast( node );
2909 final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
2910 String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
2911 if ( ForesterUtil.isEmpty( v ) ) {
2912 v = ForesterUtil.extractGenbankAccessor( node );
2914 if ( ForesterUtil.isEmpty( v ) ) {
2915 v = ForesterUtil.extractRefSeqAccessorAccessor( node );
2917 if ( ForesterUtil.isEmpty( v ) ) {
2918 v = ForesterUtil.extractGInumber( node );
2923 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
2924 if ( node.getNodeData().isHasTaxonomy()
2925 && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
2926 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
2927 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
2928 .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
2929 .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
2937 final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
2938 return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
2941 final private boolean isInFoundNodes( final PhylogenyNode node ) {
2942 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
2945 final private boolean isInOv() {
2949 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
2951 if ( getControlPanel().isShowTaxonomyImages() ) {
2952 y_dist = 40 + ( int ) getYdistance();
2954 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
2955 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
2956 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
2959 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
2960 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
2961 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
2962 || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
2963 .getMaxX() + 20 ) ) );
2966 final private boolean isNonLinedUpCladogram() {
2967 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
2970 final private boolean isUniformBranchLengthsForCladogram() {
2971 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
2974 final private void keyPressedCalls( final KeyEvent e ) {
2975 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
2976 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
2977 if ( !isInOvRect() ) {
2978 setInOvRect( true );
2981 else if ( isInOvRect() ) {
2982 setInOvRect( false );
2985 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
2986 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2987 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2988 getMainPanel().getTreeFontSet().mediumFonts();
2989 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2991 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
2992 getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
2993 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2995 else if ( plusPressed( e.getKeyCode() ) ) {
2996 getMainPanel().getTreeFontSet().increaseFontSize();
2997 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
3001 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
3002 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
3003 getControlPanel().showWhole();
3005 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
3006 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
3007 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
3008 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
3009 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3010 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3012 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3013 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3014 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3016 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3017 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3018 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3019 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3021 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3022 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3023 Constants.WHEEL_ZOOM_IN_FACTOR );
3024 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3031 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3034 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3038 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3042 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
3043 scroll_position.x = scroll_position.x + dx;
3044 scroll_position.y = scroll_position.y + dy;
3045 if ( scroll_position.x <= 0 ) {
3046 scroll_position.x = 0;
3049 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
3050 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
3051 if ( scroll_position.x >= max_x ) {
3052 scroll_position.x = max_x;
3055 if ( scroll_position.y <= 0 ) {
3056 scroll_position.y = 0;
3059 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
3060 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
3061 if ( scroll_position.y >= max_y ) {
3062 scroll_position.y = max_y;
3066 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
3069 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3070 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3071 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3072 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3073 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3075 else if ( plusPressed( e.getKeyCode() ) ) {
3076 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3077 Constants.WHEEL_ZOOM_IN_FACTOR );
3078 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3079 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3081 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
3082 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3083 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3084 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
3085 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3088 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
3089 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3090 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3091 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
3092 if ( getStartingAngle() < 0 ) {
3093 setStartingAngle( TWO_PI + getStartingAngle() );
3095 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3098 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
3099 boolean selected = false;
3100 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
3101 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
3105 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
3107 if ( getMainPanel().getMainFrame() == null ) {
3108 // Must be "E" applet version.
3109 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
3110 if ( ae.getlabelDirectionCbmi() != null ) {
3111 ae.getlabelDirectionCbmi().setSelected( selected );
3115 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
3119 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
3120 switchDisplaygetPhylogenyGraphicsType();
3123 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
3127 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
3128 MainFrame.cycleOverview( getOptions(), this );
3131 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
3134 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
3141 final private void makePopupMenus( final PhylogenyNode node ) {
3142 _node_popup_menu = new JPopupMenu();
3143 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
3144 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
3145 for( int i = 0; i < clickto_names.size(); i++ ) {
3146 final String title = clickto_names.get( i );
3147 _node_popup_menu_items[ i ] = new JMenuItem( title );
3148 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
3149 final String id = isCanOpenSeqWeb( node );
3150 if ( !ForesterUtil.isEmpty( id ) ) {
3151 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
3152 _node_popup_menu_items[ i ].setEnabled( true );
3155 _node_popup_menu_items[ i ].setEnabled( false );
3158 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
3159 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
3161 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
3162 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
3164 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
3165 if ( !getOptions().isEditable() ) {
3168 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
3170 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
3171 if ( !getOptions().isEditable() ) {
3174 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
3176 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
3177 if ( !getOptions().isEditable() ) {
3180 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
3182 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
3183 if ( !getOptions().isEditable() ) {
3186 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
3188 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
3189 if ( !getOptions().isEditable() ) {
3193 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
3194 if ( !getOptions().isEditable() ) {
3198 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
3199 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
3201 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
3202 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
3204 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
3205 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
3207 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
3208 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
3210 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
3211 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
3213 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
3214 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
3216 _node_popup_menu_items[ i ].addActionListener( this );
3217 _node_popup_menu.add( _node_popup_menu_items[ i ] );
3221 private final String obtainTitleForExtDescNodeData() {
3222 switch ( getOptions().getExtDescNodeDataToReturn() ) {
3224 return "Node Names";
3226 return "Sequence Names";
3227 case SEQUENCE_SYMBOL:
3228 return "Sequence Symbols";
3229 case SEQUENCE_MOL_SEQ:
3230 return "Molecular Sequences";
3231 case SEQUENCE_MOL_SEQ_FASTA:
3232 return "Molecular Sequences (Fasta)";
3234 return "Sequence Accessors";
3235 case TAXONOMY_SCIENTIFIC_NAME:
3236 return "Scientific Names";
3238 return "Taxonomy Codes";
3239 case TAXONOMY_COMM0N_NAME:
3240 return "Taxonomy Common Names";
3242 return "User Selected Data";
3244 throw new IllegalArgumentException( "unknown data element: "
3245 + getOptions().getExtDescNodeDataToReturn() );
3249 final private void openSeqWeb( final PhylogenyNode node ) {
3250 if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
3251 cannotOpenBrowserWarningMessage( "sequence" );
3254 final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
3255 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3257 AptxUtil.launchWebBrowser( new URI( uri_str ),
3259 isApplet() ? obtainApplet() : null,
3262 catch ( final IOException e ) {
3263 AptxUtil.showErrorMessage( this, e.toString() );
3264 e.printStackTrace();
3266 catch ( final URISyntaxException e ) {
3267 AptxUtil.showErrorMessage( this, e.toString() );
3268 e.printStackTrace();
3272 cannotOpenBrowserWarningMessage( "sequence" );
3276 final private void openTaxWeb( final PhylogenyNode node ) {
3277 if ( !isCanOpenTaxWeb( node ) ) {
3278 cannotOpenBrowserWarningMessage( "taxonomic" );
3281 String uri_str = null;
3282 final Taxonomy tax = node.getNodeData().getTaxonomy();
3283 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3284 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
3286 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
3288 catch ( final URISyntaxException e ) {
3289 AptxUtil.showErrorMessage( this, e.toString() );
3291 e.printStackTrace();
3294 else if ( ( tax.getIdentifier() != null )
3295 && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3296 && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
3297 && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
3298 .equalsIgnoreCase( "uniprot" ) ) ) {
3300 uri_str = "http://www.uniprot.org/taxonomy/"
3301 + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
3303 catch ( final UnsupportedEncodingException e ) {
3304 AptxUtil.showErrorMessage( this, e.toString() );
3305 e.printStackTrace();
3308 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
3310 uri_str = "http://www.uniprot.org/taxonomy/?query="
3311 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
3313 catch ( final UnsupportedEncodingException e ) {
3314 AptxUtil.showErrorMessage( this, e.toString() );
3315 e.printStackTrace();
3318 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
3320 uri_str = "http://www.uniprot.org/taxonomy/?query="
3321 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
3323 catch ( final UnsupportedEncodingException e ) {
3324 AptxUtil.showErrorMessage( this, e.toString() );
3325 e.printStackTrace();
3328 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
3330 uri_str = "http://www.uniprot.org/taxonomy/?query="
3331 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
3333 catch ( final UnsupportedEncodingException e ) {
3334 AptxUtil.showErrorMessage( this, e.toString() );
3335 e.printStackTrace();
3338 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3340 AptxUtil.launchWebBrowser( new URI( uri_str ),
3342 isApplet() ? obtainApplet() : null,
3345 catch ( final IOException e ) {
3346 AptxUtil.showErrorMessage( this, e.toString() );
3347 e.printStackTrace();
3349 catch ( final URISyntaxException e ) {
3350 AptxUtil.showErrorMessage( this, e.toString() );
3351 e.printStackTrace();
3355 cannotOpenBrowserWarningMessage( "taxonomic" );
3359 final private void paintBranchLength( final Graphics2D g,
3360 final PhylogenyNode node,
3361 final boolean to_pdf,
3362 final boolean to_graphics_file ) {
3363 g.setFont( getTreeFontSet().getSmallFont() );
3364 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3365 g.setColor( Color.BLACK );
3368 g.setColor( getTreeColorSet().getBranchLengthColor() );
3370 if ( !node.isRoot() ) {
3371 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3372 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3373 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3375 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3376 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3377 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3380 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3381 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3385 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
3386 - getTreeFontSet()._small_max_descent, g );
3390 final private void paintBranchLite( final Graphics2D g,
3395 final PhylogenyNode node ) {
3396 g.setColor( getTreeColorSet().getOvColor() );
3397 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3398 drawLine( x1, y1, x2, y2, g );
3400 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3401 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3402 ( g ).draw( _quad_curve );
3404 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3405 final float dx = x2 - x1;
3406 final float dy = y2 - y1;
3407 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3408 + ( dy * 0.8f ), x2, y2 );
3409 ( g ).draw( _cubic_curve );
3412 final float x2a = x2;
3413 final float x1a = x1;
3414 // draw the vertical line
3415 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
3416 drawLine( x1, y1, x1, y2, g );
3418 // draw the horizontal line
3419 drawLine( x1a, y2, x2a, y2, g );
3424 * Paint a branch which consists of a vertical and a horizontal bar
3425 * @param is_ind_found_nodes
3427 final private void paintBranchRectangular( final Graphics2D g,
3432 final PhylogenyNode node,
3433 final boolean to_pdf,
3434 final boolean to_graphics_file ) {
3435 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
3436 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3437 drawLine( x1, y1, x2, y2, g );
3439 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3440 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3441 g.draw( _quad_curve );
3443 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3444 final float dx = x2 - x1;
3445 final float dy = y2 - y1;
3446 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3447 + ( dy * 0.8f ), x2, y2 );
3448 g.draw( _cubic_curve );
3451 final float x2a = x2;
3452 final float x1a = x1;
3454 if ( node.isFirstChildNode() || node.isLastChildNode()
3455 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3456 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3457 if ( !to_graphics_file
3459 && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
3460 .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
3464 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3465 float x2c = x1 + EURO_D;
3469 drawLine( x1, y1, x2c, y2, g );
3471 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3473 y2_r = y2 - ROUNDED_D;
3477 drawLine( x1, y1, x1, y2_r, g );
3480 y2_r = y2 + ROUNDED_D;
3484 drawLine( x1, y1, x1, y2_r, g );
3488 drawLine( x1, y1, x1, y2, g );
3492 // draw the horizontal line
3493 if ( !to_graphics_file && !to_pdf
3494 && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
3498 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
3499 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3500 x1_r = x1a + ROUNDED_D;
3502 drawLine( x1_r, y2, x2a, y2, g );
3505 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3506 final float x1c = x1a + EURO_D;
3508 drawLine( x1c, y2, x2a, y2, g );
3512 drawLine( x1a, y2, x2a, y2, g );
3516 final double w = PhylogenyMethods.getBranchWidthValue( node );
3517 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3518 x1_r = x1a + ROUNDED_D;
3520 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
3523 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3524 final float x1c = x1a + EURO_D;
3526 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
3530 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
3533 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3538 final double diff = y2 - y2_r;
3539 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
3542 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
3547 if ( node.isExternal() ) {
3548 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
3549 || isInCurrentExternalNodes( node ) );
3553 final private double paintCirculars( final PhylogenyNode n,
3554 final Phylogeny phy,
3555 final float center_x,
3556 final float center_y,
3557 final double radius,
3558 final boolean radial_labels,
3560 final boolean to_pdf,
3561 final boolean to_graphics_file ) {
3562 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
3563 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
3564 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
3566 return _urt_nodeid_angle_map.get( n.getId() );
3569 final List<PhylogenyNode> descs = n.getDescendants();
3571 for( final PhylogenyNode desc : descs ) {
3572 sum += paintCirculars( desc,
3583 if ( !n.isRoot() ) {
3584 r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3586 final double theta = sum / descs.size();
3587 n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
3588 n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
3589 _urt_nodeid_angle_map.put( n.getId(), theta );
3590 for( final PhylogenyNode desc : descs ) {
3591 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
3597 final private void paintCircularsLite( final PhylogenyNode n,
3598 final Phylogeny phy,
3602 final Graphics2D g ) {
3603 if ( n.isExternal() ) {
3607 final List<PhylogenyNode> descs = n.getDescendants();
3608 for( final PhylogenyNode desc : descs ) {
3609 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
3612 if ( !n.isRoot() ) {
3613 r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3615 final double theta = _urt_nodeid_angle_map.get( n.getId() );
3616 n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
3617 n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
3618 for( final PhylogenyNode desc : descs ) {
3619 paintBranchCircularLite( n, desc, g );
3624 final private void paintCollapsedNode( final Graphics2D g,
3625 final PhylogenyNode node,
3626 final boolean to_graphics_file,
3627 final boolean to_pdf,
3628 final boolean is_in_found_nodes ) {
3630 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3633 else if ( is_in_found_nodes ) {
3634 c = getTreeColorSet().getFoundColor();
3636 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3637 c = getTaxonomyBasedColor( node );
3639 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3640 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3641 c = PhylogenyMethods.getBranchColorValue( node );
3644 c = getTreeColorSet().getCollapseFillColor();
3646 double d = node.getAllExternalDescendants().size();
3648 d = ( 3 * _y_distance ) / 3;
3651 d = ( Math.log10( d ) * _y_distance ) / 2.5;
3653 final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
3654 if ( d < box_size ) {
3657 final float xx = node.getXcoord() - ( 2 * box_size );
3658 final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
3660 _polygon.moveTo( xxx, node.getYcoord() );
3661 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
3662 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
3663 _polygon.closePath();
3664 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3668 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3669 g.setColor( getBackground() );
3674 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3675 g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
3676 .getYcoord() - d ), c, false ) );
3681 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3684 final private void paintConfidenceValues( final Graphics2D g,
3685 final PhylogenyNode node,
3686 final boolean to_pdf,
3687 final boolean to_graphics_file ) {
3688 final List<Confidence> confidences = node.getBranchData().getConfidences();
3689 // if ( confidences.size() == 1 ) {
3690 // final double value = node.getBranchData().getConfidence( 0 ).getValue();
3691 // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
3694 // conf_str = FORMATTER_CONFIDENCE.format( value );
3696 // else if ( confidences.size() > 1 ) {
3697 boolean one_ok = false;
3698 boolean not_first = false;
3699 Collections.sort( confidences );
3700 final StringBuilder sb = new StringBuilder();
3701 String conf_str = "";
3702 for( final Confidence confidence : confidences ) {
3703 final double value = confidence.getValue();
3704 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3705 if ( value >= getOptions().getMinConfidenceValue() ) {
3714 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
3715 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3716 if ( getOptions().isShowConfidenceStddev() ) {
3717 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3719 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
3721 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3728 conf_str = sb.toString();
3731 if ( conf_str.length() > 0 ) {
3732 final double parent_x = node.getParent().getXcoord();
3733 double x = node.getXcoord();
3734 g.setFont( getTreeFontSet().getSmallFont() );
3735 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3738 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3741 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3742 g.setColor( Color.BLACK );
3745 g.setColor( getTreeColorSet().getConfidenceColor() );
3748 .drawString( conf_str,
3750 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
3751 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
3756 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
3757 final int box_size = getOptions().getDefaultNodeShapeSize();
3758 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3759 g.setColor( getTreeColorSet().getFoundColor() );
3760 g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
3763 final private void paintGainedAndLostCharacters( final Graphics2D g,
3764 final PhylogenyNode node,
3765 final String gained,
3766 final String lost ) {
3767 if ( node.getParent() != null ) {
3768 final double parent_x = node.getParent().getXcoord();
3769 final double x = node.getXcoord();
3770 g.setFont( getTreeFontSet().getLargeFont() );
3771 g.setColor( getTreeColorSet().getGainedCharactersColor() );
3772 if ( Constants.SPECIAL_CUSTOM ) {
3773 g.setColor( Color.BLUE );
3776 .drawString( gained,
3777 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
3778 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
3780 g.setColor( getTreeColorSet().getLostCharactersColor() );
3781 TreePanel.drawString( lost,
3782 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
3783 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
3789 * Draw a box at the indicated node.
3796 final private void paintNodeBox( final double x,
3798 final PhylogenyNode node,
3800 final boolean to_pdf,
3801 final boolean to_graphics_file,
3802 final boolean is_in_found_nodes ) {
3803 if ( node.isCollapse() ) {
3806 // if this node should be highlighted, do so
3807 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
3808 g.setColor( getTreeColorSet().getFoundColor() );
3809 drawOval( x - 8, y - 8, 16, 16, g );
3810 drawOval( x - 9, y - 8, 17, 17, g );
3811 drawOval( x - 9, y - 9, 18, 18, g );
3813 if ( is_in_found_nodes ) {
3814 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
3817 Color outline_color = null;
3818 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3819 outline_color = Color.BLACK;
3821 else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
3822 final Event event = node.getNodeData().getEvent();
3823 if ( event.isDuplication() ) {
3824 outline_color = getTreeColorSet().getDuplicationBoxColor();
3826 else if ( event.isSpeciation() ) {
3827 outline_color = getTreeColorSet().getSpecBoxColor();
3829 else if ( event.isSpeciationOrDuplication() ) {
3830 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
3833 else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
3834 outline_color = getTaxonomyBasedColor( node );
3837 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
3838 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
3839 outline_color = getTreeColorSet().getBranchColorForPdf();
3842 final int box_size = getOptions().getDefaultNodeShapeSize();
3843 final int half_box_size = box_size / 2;
3844 if ( ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
3845 || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
3846 || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
3847 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
3848 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3849 drawOvalGradient( x - half_box_size,
3854 to_pdf ? Color.WHITE : outline_color,
3855 to_pdf ? outline_color : getBackground(),
3858 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
3859 Color background = getBackground();
3861 background = Color.WHITE;
3863 drawOvalGradient( x - half_box_size,
3872 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3873 g.setColor( outline_color );
3874 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3877 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
3878 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
3879 drawRectGradient( x - half_box_size,
3884 to_pdf ? Color.WHITE : outline_color,
3885 to_pdf ? outline_color : getBackground(),
3888 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3889 Color background = getBackground();
3891 background = Color.WHITE;
3893 drawRectGradient( x - half_box_size,
3902 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3903 g.setColor( outline_color );
3904 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3911 final private void paintNodeData( final Graphics2D g,
3912 final PhylogenyNode node,
3913 final boolean to_graphics_file,
3914 final boolean to_pdf,
3915 final boolean is_in_found_nodes ) {
3916 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
3919 if ( getOptions().isShowBranchLengthValues()
3920 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3921 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3922 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
3923 paintBranchLength( g, node, to_pdf, to_graphics_file );
3925 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
3930 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3931 if ( getControlPanel().isShowTaxonomyImages()
3932 && ( getImageMap() != null )
3933 && !getImageMap().isEmpty()
3934 && node.getNodeData().isHasTaxonomy()
3935 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
3936 .getUris().isEmpty() ) ) {
3937 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
3939 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3940 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
3941 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
3943 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3944 g.setColor( Color.BLACK );
3946 else if ( is_in_found_nodes ) {
3947 g.setColor( getTreeColorSet().getFoundColor() );
3949 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3950 g.setColor( getTaxonomyBasedColor( node ) );
3952 else if ( getControlPanel().isColorAccordingToAnnotation()
3953 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
3954 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
3955 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
3957 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3958 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3959 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3961 else if ( to_pdf ) {
3962 g.setColor( Color.BLACK );
3965 g.setColor( getTreeColorSet().getSequenceColor() );
3967 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3968 if ( _sb.length() > 0 ) {
3971 _sb.append( node.getAllExternalDescendants().size() );
3978 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3979 if ( _sb.length() > 0 ) {
3982 _sb.append( node.getName() );
3984 if ( node.getNodeData().isHasSequence() ) {
3985 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
3986 if ( _sb.length() > 0 ) {
3989 _sb.append( node.getNodeData().getSequence().getSymbol() );
3991 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3992 if ( _sb.length() > 0 ) {
3995 _sb.append( node.getNodeData().getSequence().getName() );
3997 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3998 if ( _sb.length() > 0 ) {
4001 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4002 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4005 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4008 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
4009 if ( _sb.length() > 0 ) {
4012 _sb.append( propertiesToString( node ) );
4014 g.setFont( getTreeFontSet().getLargeFont() );
4015 if ( is_in_found_nodes ) {
4016 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4018 double down_shift_factor = 3.0;
4019 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
4020 down_shift_factor = 1;
4022 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
4023 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
4024 final String sb_str = _sb.toString();
4025 // GUILHEM_BEG ______________
4026 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
4027 && ( _query_sequence != null ) ) {
4028 int nodeTextBoundsWidth = 0;
4029 if ( sb_str.length() > 0 ) {
4030 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
4031 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
4033 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
4034 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
4035 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
4036 g.setColor( getTreeColorSet().getBackgroundColor() );
4040 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
4041 for( final SequenceRelation seqRelation : seqRelations ) {
4042 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
4043 .getRef1().isEqual( _query_sequence ) )
4044 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
4045 .getSelectedItem() );
4046 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
4047 final double linePosX = node.getXcoord() + 2 + half_box_size;
4048 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
4049 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
4051 if ( sConfidence != null ) {
4052 double confidenceX = pos_x;
4053 if ( sb_str.length() > 0 ) {
4054 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
4055 + CONFIDENCE_LEFT_MARGIN;
4057 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
4058 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
4059 .getBounds().getWidth();
4060 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
4061 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
4064 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
4066 if ( nodeTextBoundsWidth == 0 ) {
4067 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
4070 nodeTextBoundsWidth += 2;
4072 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
4073 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
4080 if ( sb_str.length() > 0 ) {
4081 TreePanel.drawString( sb_str, pos_x, pos_y, g );
4083 // GUILHEM_END _____________
4084 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
4085 // TODO FIXME need to check this one!
4086 //if ( _sb.length() > 0 ) {
4087 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
4088 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4090 // COMMENTED_OUT_BY_GUILHEM_END ________________
4091 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
4092 && ( node.getNodeData().getSequence().getAnnotations() != null )
4093 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4094 if ( _sb.length() > 0 ) {
4095 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4097 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
4098 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4099 g.setColor( Color.BLACK );
4101 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
4102 g.setColor( calculateColorForAnnotation( ann ) );
4104 final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
4105 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
4106 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4108 _sb.append( ann_str );
4110 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4111 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
4112 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
4113 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
4114 && node.getNodeData().isHasBinaryCharacters() ) {
4115 if ( _sb.length() > 0 ) {
4116 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4118 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4119 g.setColor( Color.BLACK );
4122 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
4124 if ( getControlPanel().isShowBinaryCharacters() ) {
4125 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
4126 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
4127 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4128 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
4129 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
4130 .getLostCharactersAsStringBuffer().toString() );
4133 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
4134 node.getXcoord() + x + 4 + half_box_size,
4136 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
4138 paintGainedAndLostCharacters( g, node, "+"
4139 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
4140 + node.getNodeData().getBinaryCharacters().getLostCount() );
4146 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
4147 final PhylogenyNode node,
4148 final boolean to_pdf,
4149 final boolean to_graphics_file,
4150 final boolean radial_labels,
4151 final double ur_angle,
4152 final boolean is_in_found_nodes ) {
4153 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
4156 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4157 g.setColor( Color.BLACK );
4159 else if ( is_in_found_nodes ) {
4160 g.setColor( getTreeColorSet().getFoundColor() );
4162 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4163 g.setColor( getTaxonomyBasedColor( node ) );
4165 else if ( getControlPanel().isColorAccordingToAnnotation()
4166 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4167 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4168 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4171 g.setColor( getTreeColorSet().getSequenceColor() );
4175 if ( node.getNodeData().isHasTaxonomy()
4176 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4177 .isShowTaxonomyCommonNames() ) ) {
4178 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4179 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4180 _sb.append( taxonomy.getTaxonomyCode() );
4183 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4184 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4185 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4186 _sb.append( taxonomy.getScientificName() );
4188 _sb.append( taxonomy.getCommonName() );
4191 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4192 _sb.append( taxonomy.getScientificName() );
4195 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4196 _sb.append( taxonomy.getCommonName() );
4200 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4201 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4202 _sb.append( taxonomy.getScientificName() );
4206 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4207 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4208 _sb.append( taxonomy.getCommonName() );
4213 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4215 _sb.append( node.getAllExternalDescendants().size() );
4218 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4219 if ( _sb.length() > 0 ) {
4222 _sb.append( node.getName() );
4224 if ( node.getNodeData().isHasSequence() ) {
4225 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4226 if ( _sb.length() > 0 ) {
4229 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4230 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4233 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4235 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4236 if ( _sb.length() > 0 ) {
4239 _sb.append( node.getNodeData().getSequence().getName() );
4242 g.setFont( getTreeFontSet().getLargeFont() );
4243 if ( is_in_found_nodes ) {
4244 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4246 if ( _sb.length() > 1 ) {
4247 final String sb_str = _sb.toString();
4249 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4250 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
4253 m = ( float ) ( ur_angle % TWO_PI );
4255 _at = g.getTransform();
4256 boolean need_to_reset = false;
4257 final float x_coord = node.getXcoord();
4258 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
4259 if ( radial_labels ) {
4260 need_to_reset = true;
4261 boolean left = false;
4262 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4266 g.rotate( m, x_coord, node.getYcoord() );
4268 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
4272 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4273 need_to_reset = true;
4274 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
4277 TreePanel.drawString( sb_str, x_coord, y_coord, g );
4278 if ( need_to_reset ) {
4279 g.setTransform( _at );
4284 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
4285 if ( node.isCollapse() ) {
4286 if ( !node.isRoot() && !node.getParent().isCollapse() ) {
4287 paintCollapsedNode( g, node, false, false, false );
4291 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4292 g.setColor( getTreeColorSet().getFoundColor() );
4293 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
4296 if ( !node.isExternal() && !node.isCollapse() ) {
4297 boolean first_child = true;
4299 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4300 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4301 final PhylogenyNode child_node = node.getChildNode( i );
4303 if ( !isUniformBranchLengthsForCladogram() ) {
4304 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4307 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4309 if ( first_child ) {
4310 first_child = false;
4311 y2 = node.getYSecondary()
4312 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
4313 .getNumberOfExternalNodes() ) );
4316 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4318 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
4319 new_x = x2 + node.getXSecondary();
4320 final float diff_y = node.getYSecondary() - y2;
4321 final float diff_x = node.getXSecondary() - new_x;
4322 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
4323 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
4325 child_node.setXSecondary( new_x );
4326 child_node.setYSecondary( y2 );
4327 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4332 final private void paintNodeRectangular( final Graphics2D g,
4333 final PhylogenyNode node,
4334 final boolean to_pdf,
4335 final boolean dynamically_hide,
4336 final int dynamic_hiding_factor,
4337 final boolean to_graphics_file ) {
4338 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
4339 if ( node.isCollapse() ) {
4340 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
4341 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4345 if ( node.isExternal() ) {
4346 ++_external_node_index;
4348 // Confidence values
4349 if ( getControlPanel().isShowConfidenceValues()
4350 && !node.isExternal()
4352 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
4353 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4354 && node.getBranchData().isHasConfidences() ) {
4355 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
4357 // Draw a line to root:
4358 if ( node.isRoot() && _phylogeny.isRooted() ) {
4359 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
4362 float new_x_min = Float.MAX_VALUE;
4363 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
4364 float min_dist = 1.5f;
4365 if ( !disallow_shortcutting ) {
4366 // System.out.println( dynamic_hiding_factor );
4367 if ( dynamic_hiding_factor > 4000 ) {
4370 else if ( dynamic_hiding_factor > 1000 ) {
4373 else if ( dynamic_hiding_factor > 100 ) {
4377 if ( !node.isExternal() && !node.isCollapse() ) {
4378 boolean first_child = true;
4380 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4381 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4382 final PhylogenyNode child_node = node.getChildNode( i );
4384 if ( !isUniformBranchLengthsForCladogram() ) {
4385 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4388 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4390 if ( first_child ) {
4391 first_child = false;
4392 y2 = node.getYcoord()
4393 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
4396 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4398 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
4399 new_x = x2 + node.getXcoord();
4400 if ( dynamically_hide && ( x2 < new_x_min ) ) {
4403 final float diff_y = node.getYcoord() - y2;
4404 final float diff_x = node.getXcoord() - new_x;
4405 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
4406 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
4407 paintBranchRectangular( g,
4416 child_node.setXcoord( new_x );
4417 child_node.setYcoord( y2 );
4418 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4420 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
4421 || isInCurrentExternalNodes( node ) );
4423 if ( dynamically_hide
4424 && !is_in_found_nodes
4425 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
4426 .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
4427 .getHeight() ) ) ) ) ) {
4430 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4431 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
4434 final private void paintNodeWithRenderableData( final Graphics2D g,
4435 final PhylogenyNode node,
4436 final boolean to_graphics_file,
4437 final boolean to_pdf ) {
4438 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
4441 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
4444 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4445 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4446 RenderableDomainArchitecture rds = null;
4447 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
4449 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
4451 catch ( final ClassCastException cce ) {
4452 cce.printStackTrace();
4454 if ( rds != null ) {
4455 rds.setRenderingHeight( 6 );
4457 if ( node.getNodeData().isHasTaxonomy() ) {
4458 if ( getControlPanel().isShowTaxonomyCode()
4459 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
4460 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4464 if ( getControlPanel().isShowTaxonomyScientificNames()
4465 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
4466 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4467 .getScientificName()
4470 if ( getControlPanel().isShowTaxonomyCommonNames()
4471 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
4472 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4477 if ( node.getNodeData().isHasSequence() ) {
4478 if ( getControlPanel().isShowGeneNames()
4479 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
4480 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
4483 if ( getControlPanel().isShowGeneSymbols()
4484 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
4485 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
4488 if ( getControlPanel().isShowSequenceAcc()
4489 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4490 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
4491 .getAccession().toString()
4494 if ( getControlPanel().isShowAnnotation()
4495 && ( node.getNodeData().getSequence().getAnnotations() != null )
4496 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4497 x += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
4498 .getNodeData().getSequence().getAnnotations(), getOptions()
4499 .isShowAnnotationRefSource() )
4503 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
4504 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
4506 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
4511 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4512 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
4513 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
4514 getStatisticsForExpressionValues(),
4515 getConfiguration() );
4518 PhylogenyNode my_node = node;
4519 if ( !getControlPanel().isDrawPhylogram() ) {
4520 my_node = getPhylogeny().getFirstExternalNode();
4522 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
4523 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
4525 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
4526 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
4528 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
4534 final private void paintOvRectangle( final Graphics2D g ) {
4535 final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
4536 final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
4537 final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
4538 final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
4539 final float width = getOvMaxWidth() / w_ratio;
4540 final float height = getOvMaxHeight() / h_ratio;
4541 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
4542 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
4543 g.setColor( getTreeColorSet().getFoundColor() );
4544 getOvRectangle().setRect( x, y, width, height );
4545 final Stroke s = g.getStroke();
4546 g.setStroke( STROKE_1 );
4547 if ( ( width < 6 ) && ( height < 6 ) ) {
4548 drawRectFilled( x, y, 6, 6, g );
4549 getOvVirtualRectangle().setRect( x, y, 6, 6 );
4551 else if ( width < 6 ) {
4552 drawRectFilled( x, y, 6, height, g );
4553 getOvVirtualRectangle().setRect( x, y, 6, height );
4555 else if ( height < 6 ) {
4556 drawRectFilled( x, y, width, 6, g );
4557 getOvVirtualRectangle().setRect( x, y, width, 6 );
4560 drawRect( x, y, width, height, g );
4561 if ( isInOvRect() ) {
4562 drawRect( x + 1, y + 1, width - 2, height - 2, g );
4564 getOvVirtualRectangle().setRect( x, y, width, height );
4569 final private void paintPhylogenyLite( final Graphics2D g ) {
4572 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
4573 .getWidth() ) ) ) );
4574 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
4575 final Stroke s = g.getStroke();
4576 g.setStroke( STROKE_05 );
4577 for( final PhylogenyNode element : _nodes_in_preorder ) {
4578 paintNodeLite( g, element );
4581 paintOvRectangle( g );
4585 * Paint the root branch. (Differs from others because it will always be a
4586 * single horizontal line).
4587 * @param to_graphics_file
4589 * @return new x1 value
4591 final private void paintRootBranch( final Graphics2D g,
4594 final PhylogenyNode root,
4595 final boolean to_pdf,
4596 final boolean to_graphics_file ) {
4597 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
4598 float d = getXdistance();
4599 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
4600 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
4602 if ( d < MIN_ROOT_LENGTH ) {
4603 d = MIN_ROOT_LENGTH;
4605 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
4606 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
4609 final double w = PhylogenyMethods.getBranchWidthValue( root );
4610 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
4612 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
4615 final private void paintScale( final Graphics2D g,
4618 final boolean to_pdf,
4619 final boolean to_graphics_file ) {
4621 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
4623 final int y2 = y1 - 8;
4624 final int y3 = y1 - 4;
4625 g.setFont( getTreeFontSet().getSmallFont() );
4626 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4627 g.setColor( Color.BLACK );
4630 g.setColor( getTreeColorSet().getBranchLengthColor() );
4632 final Stroke s = g.getStroke();
4633 g.setStroke( STROKE_1 );
4634 drawLine( x1, y1, x1, y2, g );
4635 drawLine( x2, y1, x2, y2, g );
4636 drawLine( x1, y3, x2, y3, g );
4637 if ( getScaleLabel() != null ) {
4638 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
4643 final private int paintTaxonomy( final Graphics2D g,
4644 final PhylogenyNode node,
4645 final boolean is_in_found_nodes,
4646 final boolean to_pdf,
4647 final boolean to_graphics_file,
4648 final double x_shift ) {
4649 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4650 g.setFont( getTreeFontSet().getLargeItalicFont() );
4651 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4652 g.setColor( Color.BLACK );
4654 else if ( is_in_found_nodes ) {
4655 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
4656 g.setColor( getTreeColorSet().getFoundColor() );
4658 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4659 g.setColor( getTaxonomyBasedColor( node ) );
4661 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4662 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4663 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4665 else if ( to_pdf ) {
4666 g.setColor( Color.BLACK );
4669 g.setColor( getTreeColorSet().getTaxonomyColor() );
4671 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4672 final double start_y = node.getYcoord()
4673 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4675 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4676 _sb.append( taxonomy.getTaxonomyCode() );
4679 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4680 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4681 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4682 if ( getOptions().isAbbreviateScientificTaxonNames()
4683 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4684 abbreviateScientificName( taxonomy.getScientificName() );
4687 _sb.append( taxonomy.getScientificName() );
4690 _sb.append( taxonomy.getCommonName() );
4693 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4694 if ( getOptions().isAbbreviateScientificTaxonNames()
4695 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4696 abbreviateScientificName( taxonomy.getScientificName() );
4699 _sb.append( taxonomy.getScientificName() );
4703 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4704 _sb.append( taxonomy.getCommonName() );
4708 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4709 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4710 if ( getOptions().isAbbreviateScientificTaxonNames()
4711 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4712 abbreviateScientificName( taxonomy.getScientificName() );
4715 _sb.append( taxonomy.getScientificName() );
4720 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4721 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4722 _sb.append( taxonomy.getCommonName() );
4726 final String label = _sb.toString();
4728 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4729 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4730 // invert font color and background color to show that this is the query sequence
4731 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4735 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4736 g.setColor( getTreeColorSet().getBackgroundColor() );
4739 TreePanel.drawString( label, start_x, start_y, g );
4740 if ( is_in_found_nodes ) {
4741 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4744 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4748 final private void paintUnrooted( final PhylogenyNode n,
4749 final double low_angle,
4750 final double high_angle,
4751 final boolean radial_labels,
4753 final boolean to_pdf,
4754 final boolean to_graphics_file ) {
4756 n.setXcoord( getWidth() / 2 );
4757 n.setYcoord( getHeight() / 2 );
4759 if ( n.isExternal() ) {
4760 paintNodeDataUnrootedCirc( g,
4765 ( high_angle + low_angle ) / 2,
4766 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
4769 final float num_enclosed = n.getNumberOfExternalNodes();
4770 final float x = n.getXcoord();
4771 final float y = n.getYcoord();
4772 double current_angle = low_angle;
4773 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4774 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4775 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4776 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4777 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4778 final PhylogenyNode desc = n.getChildNode( i );
4779 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4780 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4781 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4782 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4785 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4788 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4791 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4792 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4794 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4795 if ( desc.getDistanceToParent() < 0 ) {
4799 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4803 length = getUrtFactor();
4805 final double mid_angle = current_angle + ( arc_size / 2 );
4806 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4807 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4808 desc.setXcoord( new_x );
4809 desc.setYcoord( new_y );
4810 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4811 current_angle += arc_size;
4812 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4813 drawLine( x, y, new_x, new_y, g );
4814 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc )
4815 || isInCurrentExternalNodes( desc ) );
4818 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
4822 final private void paintUnrootedLite( final PhylogenyNode n,
4823 final double low_angle,
4824 final double high_angle,
4826 final float urt_ov_factor ) {
4828 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
4829 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
4830 n.setXSecondary( x_pos );
4831 n.setYSecondary( y_pos );
4833 if ( n.isExternal() ) {
4836 final float num_enclosed = n.getNumberOfExternalNodes();
4837 final float x = n.getXSecondary();
4838 final float y = n.getYSecondary();
4839 double current_angle = low_angle;
4840 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4841 final PhylogenyNode desc = n.getChildNode( i );
4842 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4843 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4845 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4846 if ( desc.getDistanceToParent() < 0 ) {
4850 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
4854 length = urt_ov_factor;
4856 final double mid_angle = current_angle + ( arc_size / 2 );
4857 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4858 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4859 desc.setXSecondary( new_x );
4860 desc.setYSecondary( new_y );
4861 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
4862 g.setColor( getTreeColorSet().getFoundColor() );
4863 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
4864 g.setColor( getTreeColorSet().getOvColor() );
4866 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4867 current_angle += arc_size;
4868 drawLine( x, y, new_x, new_y, g );
4872 final private void pasteSubtree( final PhylogenyNode node ) {
4873 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4874 errorMessageNoCutCopyPasteInUnrootedDisplay();
4877 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
4878 JOptionPane.showMessageDialog( this,
4879 "No tree in buffer (need to copy or cut a subtree first)",
4880 "Attempt to paste with empty buffer",
4881 JOptionPane.ERROR_MESSAGE );
4884 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
4885 final Object[] options = { "As sibling", "As descendant", "Cancel" };
4886 final int r = JOptionPane.showOptionDialog( this,
4887 "How to paste subtree" + label + "?",
4889 JOptionPane.CLOSED_OPTION,
4890 JOptionPane.QUESTION_MESSAGE,
4894 boolean paste_as_sibling = true;
4896 paste_as_sibling = false;
4898 else if ( r != 0 ) {
4901 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
4902 buffer_phy.setAllNodesToNotCollapse();
4903 PhylogenyMethods.preOrderReId( buffer_phy );
4904 buffer_phy.setRooted( true );
4905 boolean need_to_show_whole = false;
4906 if ( paste_as_sibling ) {
4907 if ( node.isRoot() ) {
4908 JOptionPane.showMessageDialog( this,
4909 "Cannot paste sibling to root",
4910 "Attempt to paste sibling to root",
4911 JOptionPane.ERROR_MESSAGE );
4914 buffer_phy.addAsSibling( node );
4917 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
4918 need_to_show_whole = true;
4919 _phylogeny = buffer_phy;
4922 buffer_phy.addAsChild( node );
4925 if ( getCopiedAndPastedNodes() == null ) {
4926 setCopiedAndPastedNodes( new HashSet<Long>() );
4928 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
4929 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
4930 for( final PhylogenyNode n : nodes ) {
4931 node_ids.add( n.getId() );
4933 node_ids.add( node.getId() );
4934 getCopiedAndPastedNodes().addAll( node_ids );
4935 setNodeInPreorderToNull();
4936 _phylogeny.externalNodesHaveChanged();
4937 _phylogeny.clearHashIdToNodeMap();
4938 _phylogeny.recalculateNumberOfExternalDescendants( true );
4939 resetNodeIdToDistToLeafMap();
4941 if ( need_to_show_whole ) {
4942 getControlPanel().showWhole();
4947 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
4948 final PropertiesMap properties = node.getNodeData().getProperties();
4949 final StringBuffer sb = new StringBuffer();
4950 boolean first = true;
4951 for( final String ref : properties.getPropertyRefs() ) {
4958 final Property p = properties.getProperty( ref );
4959 sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
4961 sb.append( p.getValue() );
4962 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
4963 sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
4969 final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
4970 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4973 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4974 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4977 final private void setInOv( final boolean in_ov ) {
4981 final private void setOvMaxHeight( final float ov_max_height ) {
4982 _ov_max_height = ov_max_height;
4985 final private void setOvMaxWidth( final float ov_max_width ) {
4986 _ov_max_width = ov_max_width;
4989 final private void setOvXcorrectionFactor( final float f ) {
4990 _ov_x_correction_factor = f;
4993 final private void setOvXDistance( final float ov_x_distance ) {
4994 _ov_x_distance = ov_x_distance;
4997 final private void setOvXPosition( final int ov_x_position ) {
4998 _ov_x_position = ov_x_position;
5001 final private void setOvYDistance( final float ov_y_distance ) {
5002 _ov_y_distance = ov_y_distance;
5005 final private void setOvYPosition( final int ov_y_position ) {
5006 _ov_y_position = ov_y_position;
5009 final private void setOvYStart( final int ov_y_start ) {
5010 _ov_y_start = ov_y_start;
5013 final private void setScaleDistance( final double scale_distance ) {
5014 _scale_distance = scale_distance;
5017 final private void setScaleLabel( final String scale_label ) {
5018 _scale_label = scale_label;
5021 private final void setupStroke( final Graphics2D g ) {
5022 if ( getYdistance() < 0.001 ) {
5023 g.setStroke( STROKE_005 );
5025 else if ( getYdistance() < 0.01 ) {
5026 g.setStroke( STROKE_01 );
5028 else if ( getYdistance() < 0.5 ) {
5029 g.setStroke( STROKE_025 );
5031 else if ( getYdistance() < 1 ) {
5032 g.setStroke( STROKE_05 );
5034 else if ( getYdistance() < 2 ) {
5035 g.setStroke( STROKE_075 );
5037 else if ( getYdistance() < 20 ) {
5038 g.setStroke( STROKE_1 );
5041 g.setStroke( STROKE_2 );
5045 final private void setUpUrtFactor() {
5046 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
5047 : getVisibleRect().height;
5048 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
5049 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
5052 final int max_depth = _circ_max_depth;
5053 if ( max_depth > 0 ) {
5054 setUrtFactor( d / ( 2 * max_depth ) );
5057 setUrtFactor( d / 2 );
5060 setUrtFactorOv( getUrtFactor() );
5063 final private void setUrtFactor( final float urt_factor ) {
5064 _urt_factor = urt_factor;
5067 final private void setUrtFactorOv( final float urt_factor_ov ) {
5068 _urt_factor_ov = urt_factor_ov;
5071 private void showExtDescNodeData( final PhylogenyNode node ) {
5072 final List<String> data = new ArrayList<String>();
5073 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
5074 switch ( getOptions().getExtDescNodeDataToReturn() ) {
5076 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
5077 data.add( n.getName() );
5081 if ( n.getNodeData().isHasSequence()
5082 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5083 data.add( n.getNodeData().getSequence().getName() );
5086 case SEQUENCE_SYMBOL:
5087 if ( n.getNodeData().isHasSequence()
5088 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5089 data.add( n.getNodeData().getSequence().getSymbol() );
5092 case SEQUENCE_MOL_SEQ:
5093 if ( n.getNodeData().isHasSequence()
5094 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5095 data.add( n.getNodeData().getSequence().getMolecularSequence() );
5098 case SEQUENCE_MOL_SEQ_FASTA:
5099 final StringBuilder sb = new StringBuilder();
5100 if ( n.getNodeData().isHasSequence()
5101 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5102 final StringBuilder ann = new StringBuilder();
5103 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
5104 ann.append( n.getName() );
5107 if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5108 ann.append( "SYM=" );
5109 ann.append( n.getNodeData().getSequence().getSymbol() );
5112 if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5113 ann.append( "NAME=" );
5114 ann.append( n.getNodeData().getSequence().getName() );
5117 if ( n.getNodeData().getSequence().getAccession() != null ) {
5118 ann.append( "ACC=" );
5119 ann.append( n.getNodeData().getSequence().getAccession().asText() );
5122 if ( n.getNodeData().isHasTaxonomy() ) {
5123 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5124 ann.append( "TAXID=" );
5125 ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5128 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5129 ann.append( "SN=" );
5130 ann.append( n.getNodeData().getTaxonomy().getScientificName() );
5134 String ann_str = ann.toString().trim();
5135 if ( ann_str.endsWith( "|" ) ) {
5136 ann_str = ann_str.substring( 0, ann_str.length() - 1 );
5138 sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
5139 .getMolecularSequence(), 60 ) );
5140 data.add( sb.toString() );
5144 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
5145 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
5146 data.add( n.getNodeData().getSequence().getAccession().toString() );
5149 case TAXONOMY_SCIENTIFIC_NAME:
5150 if ( n.getNodeData().isHasTaxonomy()
5151 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5152 data.add( n.getNodeData().getTaxonomy().getScientificName() );
5155 case TAXONOMY_COMM0N_NAME:
5156 if ( n.getNodeData().isHasTaxonomy()
5157 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
5158 data.add( n.getNodeData().getTaxonomy().getCommonName() );
5162 if ( n.getNodeData().isHasTaxonomy()
5163 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5164 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5168 TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
5171 throw new IllegalArgumentException( "unknown data element: "
5172 + getOptions().getExtDescNodeDataToReturn() );
5175 final StringBuilder sb = new StringBuilder();
5176 final int size = makeSB( data, getOptions(), sb );
5177 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
5178 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
5179 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
5180 System.out.println( sb );
5182 if ( sb.length() < 1 ) {
5183 clearCurrentExternalNodesDataBuffer();
5186 setCurrentExternalNodesDataBuffer( sb );
5189 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
5190 if ( sb.length() < 1 ) {
5191 TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData()
5192 + ")", "Descendants of selected node do not contain selected data" );
5193 clearCurrentExternalNodesDataBuffer();
5196 setCurrentExternalNodesDataBuffer( sb );
5197 final String title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5198 : obtainTitleForExtDescNodeData() )
5202 + node.getNumberOfExternalNodes()
5203 + " external descendats of node "
5205 + ", unique entries: " + size;
5206 final String s = sb.toString().trim();
5207 if ( getMainPanel().getMainFrame() == null ) {
5208 // Must be "E" applet version.
5209 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
5210 ae.showTextFrame( s, title );
5213 getMainPanel().getMainFrame().showTextFrame( s, title );
5219 private int makeSB( final List<String> data, final Options optz, final StringBuilder sb ) {
5220 final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
5221 if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
5222 && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
5223 for( final String d : data ) {
5224 if ( !ForesterUtil.isEmpty( d ) ) {
5225 if ( map.containsKey( d ) ) {
5226 map.put( d, map.get( d ) + 1 );
5235 if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
5236 && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
5237 for( final Entry<String, Integer> e : map.entrySet() ) {
5238 final String v = e.getKey();
5239 final Object c = e.getValue();
5243 sb.append( ForesterUtil.LINE_SEPARATOR );
5248 for( final String d : data ) {
5249 if ( !ForesterUtil.isEmpty( d ) ) {
5251 sb.append( ForesterUtil.LINE_SEPARATOR );
5259 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
5261 if ( ( node.getName().length() > 0 )
5262 || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData()
5264 || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData()
5265 .getSequence() ) ) || ( node.getNodeData().isHasDate() )
5266 || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) {
5267 _popup_buffer.setLength( 0 );
5269 if ( node.getName().length() > 0 ) {
5271 _popup_buffer.append( node.getName() );
5273 if ( node.getNodeData().isHasTaxonomy()
5274 && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
5276 boolean enc_data = false;
5277 final Taxonomy tax = node.getNodeData().getTaxonomy();
5278 if ( _popup_buffer.length() > 0 ) {
5279 _popup_buffer.append( "\n" );
5281 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
5282 _popup_buffer.append( "[" );
5283 _popup_buffer.append( tax.getTaxonomyCode() );
5284 _popup_buffer.append( "]" );
5287 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
5289 _popup_buffer.append( " " );
5291 _popup_buffer.append( tax.getScientificName() );
5294 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
5296 _popup_buffer.append( " (" );
5299 _popup_buffer.append( "(" );
5301 _popup_buffer.append( tax.getCommonName() );
5302 _popup_buffer.append( ")" );
5305 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
5307 _popup_buffer.append( " (" );
5310 _popup_buffer.append( "(" );
5312 _popup_buffer.append( tax.getAuthority() );
5313 _popup_buffer.append( ")" );
5316 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
5318 _popup_buffer.append( " [" );
5321 _popup_buffer.append( "[" );
5323 _popup_buffer.append( tax.getRank() );
5324 _popup_buffer.append( "]" );
5327 if ( tax.getSynonyms().size() > 0 ) {
5329 _popup_buffer.append( " " );
5331 _popup_buffer.append( "[" );
5333 for( final String syn : tax.getSynonyms() ) {
5334 if ( !ForesterUtil.isEmpty( syn ) ) {
5336 _popup_buffer.append( syn );
5337 if ( counter < tax.getSynonyms().size() ) {
5338 _popup_buffer.append( ", " );
5343 _popup_buffer.append( "]" );
5346 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
5347 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
5348 _popup_buffer.append( "[" );
5349 _popup_buffer.append( tax.getIdentifier().getProvider() );
5350 _popup_buffer.append( "] " );
5352 _popup_buffer.append( tax.getIdentifier().getValue() );
5356 if ( node.getNodeData().isHasSequence()
5357 && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
5359 boolean enc_data = false;
5360 if ( _popup_buffer.length() > 0 ) {
5361 _popup_buffer.append( "\n" );
5363 final Sequence seq = node.getNodeData().getSequence();
5364 if ( seq.getAccession() != null ) {
5365 _popup_buffer.append( "[" );
5366 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
5367 _popup_buffer.append( seq.getAccession().getSource() );
5368 _popup_buffer.append( ":" );
5370 _popup_buffer.append( seq.getAccession().getValue() );
5371 _popup_buffer.append( "]" );
5374 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
5376 _popup_buffer.append( " [" );
5379 _popup_buffer.append( "[" );
5381 _popup_buffer.append( seq.getSymbol() );
5382 _popup_buffer.append( "]" );
5385 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
5387 _popup_buffer.append( " " );
5389 _popup_buffer.append( seq.getName() );
5392 if ( node.getNodeData().isHasDate() ) {
5394 if ( _popup_buffer.length() > 0 ) {
5395 _popup_buffer.append( "\n" );
5397 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
5399 if ( node.getNodeData().isHasDistribution() ) {
5401 if ( _popup_buffer.length() > 0 ) {
5402 _popup_buffer.append( "\n" );
5404 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
5406 if ( node.getBranchData().isHasConfidences() ) {
5407 final List<Confidence> confs = node.getBranchData().getConfidences();
5408 for( final Confidence confidence : confs ) {
5410 if ( _popup_buffer.length() > 0 ) {
5411 _popup_buffer.append( "\n" );
5413 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
5414 _popup_buffer.append( "[" );
5415 _popup_buffer.append( confidence.getType() );
5416 _popup_buffer.append( "] " );
5419 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
5421 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5422 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5423 _popup_buffer.append( " (sd=" );
5424 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
5425 .getStandardDeviation(), getOptions()
5426 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5427 _popup_buffer.append( ")" );
5431 if ( node.getNodeData().isHasProperties() ) {
5432 final PropertiesMap properties = node.getNodeData().getProperties();
5433 for( final String ref : properties.getPropertyRefs() ) {
5434 _popup_buffer.append( "\n" );
5435 final Property p = properties.getProperty( ref );
5436 _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
5437 _popup_buffer.append( "=" );
5438 _popup_buffer.append( p.getValue() );
5439 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5440 _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
5444 if ( _popup_buffer.length() > 0 ) {
5445 if ( !getConfiguration().isUseNativeUI() ) {
5447 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
5448 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
5449 if ( isInFoundNodes( node ) ) {
5450 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
5452 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
5453 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
5456 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
5460 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
5462 _rollover_popup.setText( _popup_buffer.toString() );
5463 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
5465 e.getLocationOnScreen().x + 10,
5466 e.getLocationOnScreen().y
5468 _node_desc_popup.show();
5472 catch ( final Exception ex ) {
5477 final private void showNodeEditFrame( final PhylogenyNode n ) {
5478 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5479 // pop up edit box for single node
5480 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
5481 _node_frame_index++;
5484 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5488 final private void showNodeFrame( final PhylogenyNode n ) {
5489 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5490 // pop up edit box for single node
5491 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
5492 _node_frame_index++;
5495 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5499 final private void switchDisplaygetPhylogenyGraphicsType() {
5500 switch ( getPhylogenyGraphicsType() ) {
5502 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5503 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5506 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5507 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5510 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5511 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5514 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5515 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5518 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5519 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5522 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5523 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5526 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5527 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5530 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5531 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5534 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5536 if ( getControlPanel().getDynamicallyHideData() != null ) {
5537 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5538 getControlPanel().getDynamicallyHideData().setEnabled( false );
5541 getControlPanel().getDynamicallyHideData().setEnabled( true );
5544 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5545 getControlPanel().setDrawPhylogramEnabled( true );
5548 getControlPanel().setDrawPhylogramEnabled( false );
5550 if ( getMainPanel().getMainFrame() == null ) {
5551 // Must be "E" applet version.
5552 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5553 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5556 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5560 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5561 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5564 final private static boolean plusPressed( final int key_code ) {
5565 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5566 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5569 final private class SubtreeColorizationActionListener implements ActionListener {
5571 JColorChooser _chooser = null;
5572 PhylogenyNode _node = null;
5573 List<PhylogenyNode> _additional_nodes = null;
5575 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5580 SubtreeColorizationActionListener( final JColorChooser chooser,
5581 final PhylogenyNode node,
5582 final List<PhylogenyNode> additional_nodes ) {
5585 _additional_nodes = additional_nodes;
5589 public void actionPerformed( final ActionEvent e ) {
5590 final Color c = _chooser.getColor();
5592 colorizeSubtree( c, _node, _additional_nodes );