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;
80 import java.util.SortedSet;
82 import javax.swing.BorderFactory;
83 import javax.swing.JApplet;
84 import javax.swing.JColorChooser;
85 import javax.swing.JDialog;
86 import javax.swing.JMenuItem;
87 import javax.swing.JOptionPane;
88 import javax.swing.JPanel;
89 import javax.swing.JPopupMenu;
90 import javax.swing.JTextArea;
91 import javax.swing.Popup;
92 import javax.swing.PopupFactory;
94 import org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON;
95 import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
96 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
97 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
98 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
99 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
100 import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
101 import org.forester.archaeopteryx.tools.Blast;
102 import org.forester.archaeopteryx.tools.ImageLoader;
103 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
104 import org.forester.io.writers.SequenceWriter;
105 import org.forester.phylogeny.Phylogeny;
106 import org.forester.phylogeny.PhylogenyMethods;
107 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
108 import org.forester.phylogeny.PhylogenyNode;
109 import org.forester.phylogeny.data.Annotation;
110 import org.forester.phylogeny.data.BranchColor;
111 import org.forester.phylogeny.data.Confidence;
112 import org.forester.phylogeny.data.Event;
113 import org.forester.phylogeny.data.NodeData.NODE_DATA;
114 import org.forester.phylogeny.data.NodeVisualization;
115 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
116 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
117 import org.forester.phylogeny.data.PhylogenyDataUtil;
118 import org.forester.phylogeny.data.PropertiesMap;
119 import org.forester.phylogeny.data.Property;
120 import org.forester.phylogeny.data.Sequence;
121 import org.forester.phylogeny.data.SequenceRelation;
122 import org.forester.phylogeny.data.Taxonomy;
123 import org.forester.phylogeny.data.Uri;
124 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
125 import org.forester.phylogeny.iterators.PreorderTreeIterator;
126 import org.forester.util.BasicDescriptiveStatistics;
127 import org.forester.util.DescriptiveStatistics;
128 import org.forester.util.ForesterConstants;
129 import org.forester.util.ForesterUtil;
130 import org.forester.util.SequenceIdParser;
132 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
134 private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
135 private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
136 private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
137 private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
138 private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
139 private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
140 private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
141 private static final float PI = ( float ) ( Math.PI );
142 private static final double TWO_PI = 2 * Math.PI;
143 private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
144 private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
145 private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
146 private static final short OV_BORDER = 10;
147 final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
148 final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
149 final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
150 final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
151 final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
152 private final static long serialVersionUID = -978349745916505029L;
153 private final static int EURO_D = 10;
154 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
155 private final static int MIN_ROOT_LENGTH = 3;
156 private final static int MAX_SUBTREES = 100;
157 private final static int MAX_NODE_FRAMES = 10;
158 private final static int MOVE = 20;
159 private final static NumberFormat FORMATTER_CONFIDENCE;
160 private final static NumberFormat FORMATTER_BRANCH_LENGTH;
161 private final static int WIGGLE = 2;
162 private final static int LIMIT_FOR_HQ_RENDERING = 2000;
163 private final static int CONFIDENCE_LEFT_MARGIN = 4;
164 private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
165 RenderingHints.VALUE_RENDER_DEFAULT );
166 private File _treefile = null;
167 private Configuration _configuration = null;
168 private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
169 private int _node_frame_index = 0;
170 private Phylogeny _phylogeny = null;
171 private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
172 private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
173 private int _subtree_index = 0;
174 private MainPanel _main_panel = null;
175 private Set<Long> _found_nodes = null;
176 private PhylogenyNode _highlight_node = null;
177 private JPopupMenu _node_popup_menu = null;
178 private JMenuItem _node_popup_menu_items[] = null;
179 private int _longest_ext_node_info = 0;
180 private float _x_correction_factor = 0.0f;
181 private float _ov_x_correction_factor = 0.0f;
182 private float _x_distance = 0.0f;
183 private float _y_distance = 0.0f;
184 private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
185 private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
186 private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
187 private float _last_drag_point_x = 0;
188 private float _last_drag_point_y = 0;
189 private ControlPanel _control_panel = null;
190 private int _external_node_index = 0;
191 private final Path2D.Float _polygon = new Path2D.Float();
192 private final StringBuilder _sb = new StringBuilder();
193 private JColorChooser _color_chooser = null;
194 private double _scale_distance = 0.0;
195 private String _scale_label = null;
196 private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
197 private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
198 private final Line2D _line = new Line2D.Float();
199 private final Ellipse2D _ellipse = new Ellipse2D.Float();
200 private final Rectangle2D _rectangle = new Rectangle2D.Float();
201 private Options _options = null;
202 private float _ov_max_width = 0;
203 private float _ov_max_height = 0;
204 private int _ov_x_position = 0;
205 private int _ov_y_position = 0;
206 private int _ov_y_start = 0;
207 private float _ov_y_distance = 0;
208 private float _ov_x_distance = 0;
209 private boolean _ov_on = false;
210 private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
211 private float _urt_factor = 1;
212 private float _urt_factor_ov = 1;
213 private final boolean _phy_has_branch_lengths;
214 private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
215 private boolean _in_ov_rect = false;
216 private boolean _in_ov = false;
217 private final Rectangle _ov_virtual_rectangle = new Rectangle();
218 final private static double _180_OVER_PI = 180.0 / Math.PI;
219 private static final float ROUNDED_D = 8;
220 private int _circ_max_depth;
221 private PhylogenyNode _root;
222 final private Arc2D _arc = new Arc2D.Double();
223 final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
224 final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
225 final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
226 HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
227 private AffineTransform _at;
228 private double _max_distance_to_root = -1;
229 private int _dynamic_hiding_factor = 0;
230 private boolean _edited = false;
231 private Popup _node_desc_popup;
232 private JTextArea _rollover_popup;
233 private final StringBuffer _popup_buffer = new StringBuffer();
234 final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
237 private Sequence _query_sequence = null;
238 private final FontRenderContext _frc = new FontRenderContext( null,
241 // expression values menu:
242 private DescriptiveStatistics _statistics_for_vector_data;
243 private PhylogenyNode[] _nodes_in_preorder = null;
244 private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
245 private int _current_external_nodes_data_buffer_change_counter = 0;
246 private Set<Long> _current_external_nodes = null;
247 // private Image offscreenImage;
248 // private Graphics offscreenGraphics;
249 // private Dimension offscreenDimension;
251 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
252 dfs.setDecimalSeparator( '.' );
253 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
254 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
257 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
258 requestFocusInWindow();
259 addKeyListener( new KeyAdapter() {
262 public void keyPressed( final KeyEvent key_event ) {
263 keyPressedCalls( key_event );
264 requestFocusInWindow();
267 addFocusListener( new FocusAdapter() {
270 public void focusGained( final FocusEvent e ) {
271 requestFocusInWindow();
274 if ( ( t == null ) || t.isEmpty() ) {
275 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
277 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
279 _configuration = configuration;
281 _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
283 // if ( !_phylogeny.isEmpty() ) {
284 _phylogeny.recalculateNumberOfExternalDescendants( true );
285 checkForVectorProperties( _phylogeny );
287 setBackground( getTreeColorSet().getBackgroundColor() );
288 final MouseListener mouse_listener = new MouseListener( this );
289 addMouseListener( mouse_listener );
290 addMouseMotionListener( mouse_listener );
291 addMouseWheelListener( this );
292 calculateScaleDistance();
293 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
294 FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
295 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
299 final public void actionPerformed( final ActionEvent e ) {
300 boolean done = false;
301 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
302 for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
303 // NOTE: index corresponds to the indices of click-to options
304 // in the control panel.
305 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
306 // Set this as the new default click-to action
307 _main_panel.getControlPanel().setClickToAction( index );
308 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
309 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
310 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
315 requestFocusInWindow();
318 public synchronized Hashtable<String, BufferedImage> getImageMap() {
319 return getMainPanel().getImageMap();
322 final public MainPanel getMainPanel() {
327 * Get a pointer to the phylogeny
329 * @return a pointer to the phylogeny
331 public final Phylogeny getPhylogeny() {
336 final public void mouseWheelMoved( final MouseWheelEvent e ) {
337 final int notches = e.getWheelRotation();
338 if ( inOvVirtualRectangle( e ) ) {
339 if ( !isInOvRect() ) {
345 if ( isInOvRect() ) {
346 setInOvRect( false );
350 if ( e.isControlDown() ) {
352 getTreeFontSet().increaseFontSize();
353 getControlPanel().displayedPhylogenyMightHaveChanged( true );
356 getTreeFontSet().decreaseFontSize( 1, false );
357 getControlPanel().displayedPhylogenyMightHaveChanged( true );
360 else if ( e.isShiftDown() ) {
361 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
362 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
364 for( int i = 0; i < ( -notches ); ++i ) {
365 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
366 getControlPanel().displayedPhylogenyMightHaveChanged( false );
370 for( int i = 0; i < notches; ++i ) {
371 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
372 if ( getStartingAngle() < 0 ) {
373 setStartingAngle( TWO_PI + getStartingAngle() );
375 getControlPanel().displayedPhylogenyMightHaveChanged( false );
381 for( int i = 0; i < ( -notches ); ++i ) {
382 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
383 getControlPanel().displayedPhylogenyMightHaveChanged( false );
387 for( int i = 0; i < notches; ++i ) {
388 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
389 getControlPanel().displayedPhylogenyMightHaveChanged( false );
396 for( int i = 0; i < ( -notches ); ++i ) {
397 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
398 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
399 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
400 getControlPanel().displayedPhylogenyMightHaveChanged( false );
404 for( int i = 0; i < notches; ++i ) {
405 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
406 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
407 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
408 getControlPanel().displayedPhylogenyMightHaveChanged( false );
413 requestFocusInWindow();
418 final public void paintComponent( final Graphics g ) {
419 // Dimension currentSize = getSize();
420 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
421 // call the 'java.awt.Component.createImage(...)' method to get an
423 // offscreenImage = createImage( currentSize.width, currentSize.height );
424 // offscreenGraphics = offscreenImage.getGraphics();
425 // offscreenDimension = currentSize;
427 // super.paintComponent( g ); //why?
428 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
429 final Graphics2D g2d = ( Graphics2D ) g;
430 g2d.setRenderingHints( _rendering_hints );
431 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
432 //g.drawImage( offscreenImage, 0, 0, this );
436 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
437 throws PrinterException {
438 if ( page_index > 0 ) {
439 return ( NO_SUCH_PAGE );
442 final Graphics2D g2d = ( Graphics2D ) g;
443 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
444 // Turn off double buffering !?
445 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
446 // Turn double buffering back on !?
447 return ( PAGE_EXISTS );
451 public final void setEdited( final boolean edited ) {
455 public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
456 getMainPanel().setImageMap( image_map );
460 * Set a phylogeny tree.
463 * an instance of a Phylogeny
465 public final void setTree( final Phylogeny t ) {
466 setNodeInPreorderToNull();
470 public final void setWaitCursor() {
471 setCursor( WAIT_CURSOR );
476 public void update( final Graphics g ) {
480 final void calcMaxDepth() {
481 if ( _phylogeny != null ) {
482 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
487 * Set parameters for printing the displayed tree
490 final void calcParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
491 // updateStyle(); not needed?
492 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
494 if ( recalc_longest_ext_node_info ) {
495 calculateLongestExtNodeInfo();
496 if ( getOptions().isAllowFontSizeChange() ) {
497 if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
498 && ( getTreeFontSet().getLargeFont().getSize() > 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
499 while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
500 && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
501 getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(),
503 calculateLongestExtNodeInfo();
507 while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
508 && ( getTreeFontSet().getLargeFont().getSize() <= getTreeFontSet().getLargeFontMemory()
509 .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
510 getMainPanel().getTreeFontSet().increaseFontSize();
511 calculateLongestExtNodeInfo();
516 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
517 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
518 if ( ext_nodes == 1 ) {
519 ext_nodes = max_depth;
520 if ( ext_nodes < 1 ) {
527 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
528 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
529 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
532 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
533 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
535 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
539 if ( ov_xdist < 0.0 ) {
545 setXdistance( xdist );
546 setYdistance( ydist );
547 setOvXDistance( ov_xdist );
548 final double height = _phylogeny.getHeight();
550 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
551 setXcorrectionFactor( corr > 0 ? corr : 0 );
552 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
553 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
556 setXcorrectionFactor( 0 );
557 setOvXcorrectionFactor( 0 );
559 _circ_max_depth = max_depth;
562 if ( getOptions().isAllowFontSizeChange() ) {
563 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
564 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
565 // int dynamic_hiding_factor = calcDynamicHidingFactor();
566 // if ( dynamic_hiding_factor > 1 ) {
567 // while ( dynamic_hiding_factor > 1
568 // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
569 // getTreeFontSet().decreaseFontSize( 1, true );
570 // dynamic_hiding_factor = calcDynamicHidingFactor();
573 // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
574 // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
575 // getTreeFontSet().increaseFontSize();
576 // dynamic_hiding_factor = calcDynamicHidingFactor();
585 final void calculateLongestExtNodeInfo() {
586 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
589 int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
590 * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
591 if ( max_length < 40 ) {
595 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
597 if ( node.isCollapse() ) {
600 if ( getControlPanel().isShowNodeNames() ) {
601 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
603 if ( node.getNodeData().isHasSequence() ) {
604 if ( getControlPanel().isShowSequenceAcc()
605 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
606 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
610 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
611 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
613 if ( getControlPanel().isShowGeneSymbols()
614 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
615 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
617 if ( getControlPanel().isShowAnnotation()
618 && ( node.getNodeData().getSequence().getAnnotations() != null )
619 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
620 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
624 if ( getControlPanel().isShowDomainArchitectures()
625 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
626 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
627 .getRenderingSize().getWidth();
630 if ( node.getNodeData().isHasTaxonomy() ) {
631 final Taxonomy tax = node.getNodeData().getTaxonomy();
632 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
633 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
635 if ( getControlPanel().isShowTaxonomyScientificNames()
636 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
637 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
639 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
640 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
643 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
644 sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
646 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
647 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
648 .getGainedCharactersAsStringBuffer().toString() );
650 if ( sum >= max_length ) {
651 setLongestExtNodeInfo( max_length );
654 if ( sum > longest ) {
658 if ( longest >= max_length ) {
659 setLongestExtNodeInfo( max_length );
662 setLongestExtNodeInfo( longest );
666 final void calculateScaleDistance() {
667 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
670 final double height = getMaxDistanceToRoot();
672 if ( ( height <= 0.5 ) ) {
673 setScaleDistance( 0.01 );
675 else if ( height <= 5.0 ) {
676 setScaleDistance( 0.1 );
678 else if ( height <= 50.0 ) {
679 setScaleDistance( 1 );
681 else if ( height <= 500.0 ) {
682 setScaleDistance( 10 );
685 setScaleDistance( 100 );
689 setScaleDistance( 0.0 );
691 String scale_label = String.valueOf( getScaleDistance() );
692 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
693 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
695 setScaleLabel( scale_label );
698 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
699 if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
700 return getTreeColorSet().getTaxonomyColor();
703 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
704 c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
706 if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
707 c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
710 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
711 c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode() );
712 getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
715 c = AptxUtil.calculateColorFromString( tax.getScientificName() );
716 getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
722 void checkForVectorProperties( final Phylogeny phy ) {
723 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
724 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
725 final PhylogenyNode node = iter.next();
726 if ( node.getNodeData().getProperties() != null ) {
727 final PropertiesMap pm = node.getNodeData().getProperties();
728 final double[] vector = new double[ pm.getProperties().size() ];
730 for( final String ref : pm.getProperties().keySet() ) {
731 if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
732 final Property p = pm.getProperty( ref );
733 final String value_str = p.getValue();
734 final String index_str = ref
735 .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
738 d = Double.parseDouble( value_str );
740 catch ( final NumberFormatException e ) {
741 JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
742 + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
747 i = Integer.parseInt( index_str );
749 catch ( final NumberFormatException e ) {
750 JOptionPane.showMessageDialog( this,
751 "Could not parse \"" + index_str
752 + "\" into index for vector data",
753 "Problem with Vector Data",
754 JOptionPane.ERROR_MESSAGE );
758 JOptionPane.showMessageDialog( this,
759 "Attempt to use negative index for vector data",
760 "Problem with Vector Data",
761 JOptionPane.ERROR_MESSAGE );
769 final List<Double> vector_l = new ArrayList<Double>( counter );
770 for( int i = 0; i < counter; ++i ) {
771 vector_l.add( vector[ i ] );
773 node.getNodeData().setVector( vector_l );
776 if ( stats.getN() > 0 ) {
777 _statistics_for_vector_data = stats;
781 void clearCurrentExternalNodesDataBuffer() {
782 setCurrentExternalNodesDataBuffer( new StringBuilder() );
786 * Collapse the tree from the given node
791 final void collapse( final PhylogenyNode node ) {
792 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
793 JOptionPane.showMessageDialog( this,
794 "Cannot collapse in unrooted display type",
795 "Attempt to collapse in unrooted display",
796 JOptionPane.WARNING_MESSAGE );
799 if ( !node.isExternal() && !node.isRoot() ) {
800 final boolean collapse = !node.isCollapse();
801 AptxUtil.collapseSubtree( node, collapse );
802 updateSetOfCollapsedExternalNodes();
803 _phylogeny.recalculateNumberOfExternalDescendants( true );
804 resetNodeIdToDistToLeafMap();
805 calculateLongestExtNodeInfo();
806 setNodeInPreorderToNull();
807 _control_panel.displayedPhylogenyMightHaveChanged( true );
808 resetPreferredSize();
810 _main_panel.adjustJScrollPane();
815 final void collapseSpeciesSpecificSubtrees() {
816 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
820 AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
821 updateSetOfCollapsedExternalNodes();
822 _phylogeny.recalculateNumberOfExternalDescendants( true );
823 resetNodeIdToDistToLeafMap();
824 calculateLongestExtNodeInfo();
825 setNodeInPreorderToNull();
826 resetPreferredSize();
827 _main_panel.adjustJScrollPane();
832 final void colorRank( final String rank ) {
833 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
837 AptxUtil.removeBranchColors( _phylogeny );
838 final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
839 if ( colorizations > 0 ) {
840 _control_panel.setColorBranches( true );
841 if ( _control_panel.getColorBranchesCb() != null ) {
842 _control_panel.getColorBranchesCb().setSelected( true );
844 if ( _control_panel.getColorAccSpeciesCb() != null ) {
845 _control_panel.getColorAccSpeciesCb().setSelected( false );
847 _options.setColorLabelsSameAsParentBranch( true );
848 _control_panel.repaint();
852 if ( colorizations > 0 ) {
853 String msg = "Taxonomy colorization via " + rank + " completed:\n";
854 if ( colorizations > 1 ) {
855 msg += "colorized " + colorizations + " subtrees";
858 msg += "colorized one subtree";
861 JOptionPane.showMessageDialog( this,
863 "Taxonomy Colorization Completed (" + rank + ")",
864 JOptionPane.INFORMATION_MESSAGE );
867 String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
868 msg += "Possible solutions (given that suitable taxonomic information is present):\n";
869 msg += "select a different rank (e.g. phylum, genus, ...)\n";
872 msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
873 msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
874 JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
878 final void confColor() {
879 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
883 AptxUtil.removeBranchColors( _phylogeny );
884 AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
885 _control_panel.setColorBranches( true );
886 if ( _control_panel.getColorBranchesCb() != null ) {
887 _control_panel.getColorBranchesCb().setSelected( true );
893 final void decreaseDomainStructureEvalueThreshold() {
894 if ( _domain_structure_e_value_thr_exp > -20 ) {
895 _domain_structure_e_value_thr_exp -= 1;
900 * Find the node, if any, at the given location
904 * @return pointer to the node at x,y, null if not found
906 final PhylogenyNode findNode( final int x, final int y ) {
907 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
910 final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
911 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
912 final PhylogenyNode node = iter.next();
913 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
914 && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
915 && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
916 && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
917 && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
924 final Configuration getConfiguration() {
925 return _configuration;
928 final ControlPanel getControlPanel() {
929 return _control_panel;
932 String getCurrentExternalNodesDataBufferAsString() {
933 return _current_external_nodes_data_buffer.toString();
936 int getCurrentExternalNodesDataBufferChangeCounter() {
937 return _current_external_nodes_data_buffer_change_counter;
940 final int getDomainStructureEvalueThreshold() {
941 return _domain_structure_e_value_thr_exp;
944 final Set<Long> getFoundNodes() {
948 final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
949 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
950 return ( PhylogenyMethods.getBranchColorValue( node ) );
953 return ( getTreeColorSet().getBranchColor() );
957 final int getLongestExtNodeInfo() {
958 return _longest_ext_node_info;
961 final Options getOptions() {
962 if ( _options == null ) {
963 _options = getControlPanel().getOptions();
968 final Rectangle2D getOvRectangle() {
969 return _ov_rectangle;
972 final Rectangle getOvVirtualRectangle() {
973 return _ov_virtual_rectangle;
976 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
977 return _graphics_type;
980 final double getStartingAngle() {
981 return _urt_starting_angle;
984 DescriptiveStatistics getStatisticsForExpressionValues() {
985 return _statistics_for_vector_data;
989 * Find a color for this species name.
992 * @return the species color
994 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
995 if ( node.getNodeData().isHasTaxonomy() ) {
996 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
998 // return non-colorized color
999 return getTreeColorSet().getTaxonomyColor();
1003 * @return pointer to colorset for tree drawing
1005 final TreeColorSet getTreeColorSet() {
1006 return getMainPanel().getTreeColorSet();
1009 final File getTreeFile() {
1013 final float getXcorrectionFactor() {
1014 return _x_correction_factor;
1017 final float getXdistance() {
1021 final float getYdistance() {
1025 final void increaseDomainStructureEvalueThreshold() {
1026 if ( _domain_structure_e_value_thr_exp < 3 ) {
1027 _domain_structure_e_value_thr_exp += 1;
1031 final void initNodeData() {
1032 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1035 double max_original_domain_structure_width = 0.0;
1036 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1037 if ( node.getNodeData().isHasSequence()
1038 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1039 RenderableDomainArchitecture rds = null;
1040 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
1041 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1042 getConfiguration() );
1043 node.getNodeData().getSequence().setDomainArchitecture( rds );
1046 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1048 if ( getControlPanel().isShowDomainArchitectures() ) {
1049 final double dsw = rds.getOriginalSize().getWidth();
1050 if ( dsw > max_original_domain_structure_width ) {
1051 max_original_domain_structure_width = dsw;
1056 if ( getControlPanel().isShowDomainArchitectures() ) {
1057 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1058 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1059 if ( node.getNodeData().isHasSequence()
1060 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1061 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1062 .getSequence().getDomainArchitecture();
1063 rds.setRenderingFactorWidth( ds_factor_width );
1064 rds.setParameter( _domain_structure_e_value_thr_exp );
1070 final boolean inOv( final MouseEvent e ) {
1071 return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
1072 && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
1073 && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
1074 + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
1077 final boolean inOvRectangle( final MouseEvent e ) {
1078 return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
1079 && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
1080 && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
1081 + getOvRectangle().getHeight() + 1 ) ) );
1084 final boolean isApplet() {
1085 return getMainPanel() instanceof MainPanelApplets;
1088 final boolean isCanCollapse() {
1089 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1092 final boolean isCanColorSubtree() {
1093 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1096 final boolean isCanCopy() {
1097 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1100 final boolean isCanCut( final PhylogenyNode node ) {
1101 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1105 final boolean isCanDelete() {
1106 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1109 final boolean isCanPaste() {
1110 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1111 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1114 final boolean isCanReroot() {
1115 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1118 final boolean isCanSubtree( final PhylogenyNode node ) {
1119 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1120 .isRoot() || ( _subtree_index > 0 ) ) );
1123 final boolean isCurrentTreeIsSubtree() {
1124 return ( _subtree_index > 0 );
1127 final boolean isEdited() {
1131 final boolean isInOvRect() {
1135 final boolean isOvOn() {
1139 final boolean isPhyHasBranchLengths() {
1140 return _phy_has_branch_lengths;
1143 final void midpointRoot() {
1144 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1147 if ( !_phylogeny.isRerootable() ) {
1148 JOptionPane.showMessageDialog( this,
1149 "This is not rerootable",
1151 JOptionPane.WARNING_MESSAGE );
1154 setNodeInPreorderToNull();
1156 PhylogenyMethods.midpointRoot( _phylogeny );
1157 resetNodeIdToDistToLeafMap();
1163 final void mouseClicked( final MouseEvent e ) {
1164 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1165 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1166 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1167 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
1169 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
1177 final double max_x = getWidth() - getVisibleRect().width;
1178 final double max_y = getHeight() - getVisibleRect().height;
1185 getMainPanel().getCurrentScrollPane().getViewport()
1186 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1187 setInOvRect( true );
1191 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1192 if ( node != null ) {
1193 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1196 _highlight_node = node;
1197 // Check if shift key is down
1198 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1199 // Yes, so add to _found_nodes
1200 if ( getFoundNodes() == null ) {
1201 setFoundNodes( new HashSet<Long>() );
1203 getFoundNodes().add( node.getId() );
1204 // Check if control key is down
1206 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1207 // Yes, so pop-up menu
1208 displayNodePopupMenu( node, e.getX(), e.getY() );
1209 // Handle unadorned click
1212 // Check for right mouse button
1213 if ( e.getModifiers() == 4 ) {
1214 displayNodePopupMenu( node, e.getX(), e.getY() );
1217 // if not in _found_nodes, clear _found_nodes
1218 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1223 // no node was clicked
1224 _highlight_node = null;
1230 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1231 setCursor( MOVE_CURSOR );
1232 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1233 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1234 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1235 if ( scroll_position.x < 0 ) {
1236 scroll_position.x = 0;
1239 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1240 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1241 if ( scroll_position.x > max_x ) {
1242 scroll_position.x = max_x;
1245 if ( scroll_position.y < 0 ) {
1246 scroll_position.y = 0;
1249 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1250 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1251 if ( scroll_position.y > max_y ) {
1252 scroll_position.y = max_y;
1255 if ( isOvOn() || getOptions().isShowScale() ) {
1258 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1261 final void mouseDragInOvRectangle( final MouseEvent e ) {
1262 setCursor( HAND_CURSOR );
1263 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1264 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1265 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1266 double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
1267 double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
1268 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1269 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1270 if ( scroll_position.x <= 0 ) {
1271 scroll_position.x = 0;
1275 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1276 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1277 if ( scroll_position.x >= max_x ) {
1279 scroll_position.x = max_x;
1282 if ( scroll_position.y <= 0 ) {
1284 scroll_position.y = 0;
1287 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1288 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1289 if ( scroll_position.y >= max_y ) {
1291 scroll_position.y = max_y;
1295 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1296 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1297 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1300 final void mouseMoved( final MouseEvent e ) {
1301 requestFocusInWindow();
1302 if ( _current_external_nodes != null ) {
1303 _current_external_nodes = null;
1306 if ( getControlPanel().isNodeDescPopup() ) {
1307 if ( _node_desc_popup != null ) {
1308 _node_desc_popup.hide();
1309 _node_desc_popup = null;
1312 if ( getOptions().isShowOverview() && isOvOn() ) {
1313 if ( inOvVirtualRectangle( e ) ) {
1314 if ( !isInOvRect() ) {
1315 setInOvRect( true );
1320 if ( isInOvRect() ) {
1321 setInOvRect( false );
1326 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
1335 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1336 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
1337 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
1338 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
1339 addToCurrentExternalNodes( n.getId() );
1341 setCursor( HAND_CURSOR );
1344 else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
1345 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
1346 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
1347 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
1348 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
1349 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
1350 setCursor( CUT_CURSOR );
1353 setCursor( HAND_CURSOR );
1354 if ( getControlPanel().isNodeDescPopup() ) {
1355 showNodeDataPopup( e, node );
1360 setCursor( ARROW_CURSOR );
1365 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
1366 setCursor( ARROW_CURSOR );
1369 final void multiplyUrtFactor( final float f ) {
1373 final JApplet obtainApplet() {
1374 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1377 final void paintBranchCircular( final PhylogenyNode p,
1378 final PhylogenyNode c,
1380 final boolean radial_labels,
1381 final boolean to_pdf,
1382 final boolean to_graphics_file ) {
1383 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1384 final double root_x = _root.getXcoord();
1385 final double root_y = _root.getYcoord();
1386 final double dx = root_x - p.getXcoord();
1387 final double dy = root_y - p.getYcoord();
1388 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1389 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1390 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
1391 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
1392 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
1393 final double r2 = 2.0 * parent_radius;
1394 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1396 drawLine( c.getXcoord(),
1398 root_x + ( Math.cos( angle ) * parent_radius ),
1399 root_y + ( Math.sin( angle ) * parent_radius ),
1401 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c )
1402 || isInCurrentExternalNodes( c ) );
1403 if ( c.isExternal() ) {
1404 final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c );
1405 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
1406 && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
1409 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
1413 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
1414 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1415 final double root_x = _root.getXSecondary();
1416 final double root_y = _root.getYSecondary();
1417 final double dx = root_x - p.getXSecondary();
1418 final double dy = root_y - p.getYSecondary();
1419 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1420 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1421 g.setColor( getTreeColorSet().getOvColor() );
1422 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
1423 final double r2 = 2.0 * parent_radius;
1424 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1426 drawLine( c.getXSecondary(),
1428 root_x + ( Math.cos( angle ) * parent_radius ),
1429 root_y + ( Math.sin( angle ) * parent_radius ),
1431 if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
1432 g.setColor( getTreeColorSet().getFoundColor() );
1433 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
1437 final void paintCircular( final Phylogeny phy,
1438 final double starting_angle,
1443 final boolean to_pdf,
1444 final boolean to_graphics_file ) {
1445 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
1446 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
1447 _root = phy.getRoot();
1448 _root.setXcoord( center_x );
1449 _root.setYcoord( center_y );
1450 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1451 double current_angle = starting_angle;
1453 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1454 final PhylogenyNode n = it.next();
1455 if ( !n.isCollapse() ) {
1456 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1457 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1458 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1459 _urt_nodeid_index_map.put( n.getId(), i++ );
1460 current_angle += ( TWO_PI / circ_num_ext_nodes );
1464 System.out.println( "is collapse" + n.getName() );
1467 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
1468 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
1471 final void paintCircularLite( final Phylogeny phy,
1472 final double starting_angle,
1476 final Graphics2D g ) {
1477 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
1478 _root = phy.getRoot();
1479 _root.setXSecondary( center_x );
1480 _root.setYSecondary( center_y );
1481 double current_angle = starting_angle;
1482 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1483 final PhylogenyNode n = it.next();
1484 n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1485 n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1486 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1487 current_angle += ( TWO_PI / circ_num_ext_nodes );
1489 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
1492 final void paintPhylogeny( final Graphics2D g,
1493 final boolean to_pdf,
1494 final boolean to_graphics_file,
1495 final int graphics_file_width,
1496 final int graphics_file_height,
1497 final int graphics_file_x,
1498 final int graphics_file_y ) {
1499 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1502 if ( _control_panel.isShowSequenceRelations() ) {
1503 _query_sequence = _control_panel.getSelectedQuerySequence();
1505 // Color the background
1507 final Rectangle r = getVisibleRect();
1508 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
1509 g.setColor( getTreeColorSet().getBackgroundColor() );
1510 if ( !to_graphics_file ) {
1514 if ( getOptions().isPrintBlackAndWhite() ) {
1515 g.setColor( Color.WHITE );
1517 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1521 if ( !to_graphics_file ) {
1522 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
1523 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
1527 g.setPaint( new GradientPaint( graphics_file_x,
1529 getTreeColorSet().getBackgroundColor(),
1531 graphics_file_y + graphics_file_height,
1532 getTreeColorSet().getBackgroundColorGradientBottom() ) );
1533 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1539 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
1541 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1542 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1543 _external_node_index = 0;
1544 // Position starting X of tree
1545 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
1546 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
1548 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
1549 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
1550 .getDistanceToParent() * getXcorrectionFactor() ) ) );
1553 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
1555 // Position starting Y of tree
1556 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
1557 + ( TreePanel.MOVE / 2.0f ) );
1558 final int dynamic_hiding_factor = calcDynamicHidingFactor();
1559 if ( getControlPanel().isDynamicallyHideData() ) {
1560 if ( dynamic_hiding_factor > 1 ) {
1561 getControlPanel().setDynamicHidingIsOn( true );
1564 getControlPanel().setDynamicHidingIsOn( false );
1567 if ( _nodes_in_preorder == null ) {
1568 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
1570 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1571 _nodes_in_preorder[ i++ ] = it.next();
1574 //final PhylogenyNodeIterator it;
1575 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1576 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
1577 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1579 for( final PhylogenyNode element : _nodes_in_preorder ) {
1580 paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
1581 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1583 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
1584 if ( !( to_graphics_file || to_pdf ) ) {
1587 getVisibleRect().y + getVisibleRect().height,
1592 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1595 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1596 paintPhylogenyLite( g );
1599 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1600 if ( getControlPanel().getDynamicallyHideData() != null ) {
1601 getControlPanel().setDynamicHidingIsOn( false );
1603 final double angle = getStartingAngle();
1604 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1605 _dynamic_hiding_factor = 0;
1606 if ( getControlPanel().isDynamicallyHideData() ) {
1607 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1608 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
1610 if ( getControlPanel().getDynamicallyHideData() != null ) {
1611 if ( _dynamic_hiding_factor > 1 ) {
1612 getControlPanel().setDynamicHidingIsOn( true );
1615 getControlPanel().setDynamicHidingIsOn( false );
1618 paintUnrooted( _phylogeny.getRoot(),
1620 ( float ) ( angle + ( 2 * Math.PI ) ),
1625 if ( getOptions().isShowScale() ) {
1626 if ( !( to_graphics_file || to_pdf ) ) {
1629 getVisibleRect().y + getVisibleRect().height,
1634 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1637 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1638 g.setColor( getTreeColorSet().getOvColor() );
1639 paintUnrootedLite( _phylogeny.getRoot(),
1641 angle + ( 2 * Math.PI ),
1643 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
1644 paintOvRectangle( g );
1647 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1648 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
1649 final int d = radius + MOVE + getLongestExtNodeInfo();
1650 _dynamic_hiding_factor = 0;
1651 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
1652 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1653 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
1655 if ( getControlPanel().getDynamicallyHideData() != null ) {
1656 if ( _dynamic_hiding_factor > 1 ) {
1657 getControlPanel().setDynamicHidingIsOn( true );
1660 getControlPanel().setDynamicHidingIsOn( false );
1663 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
1664 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1665 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
1666 : getOvMaxWidth() / 2 );
1667 double x_scale = 1.0;
1668 double y_scale = 1.0;
1669 int x_pos = getVisibleRect().x + getOvXPosition();
1670 int y_pos = getVisibleRect().y + getOvYPosition();
1671 if ( getWidth() > getHeight() ) {
1672 x_scale = ( double ) getHeight() / getWidth();
1673 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
1676 y_scale = ( double ) getWidth() / getHeight();
1677 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
1679 _at = g.getTransform();
1680 g.scale( x_scale, y_scale );
1681 paintCircularLite( _phylogeny,
1685 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
1688 g.setTransform( _at );
1689 paintOvRectangle( g );
1694 final void recalculateMaxDistanceToRoot() {
1695 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
1699 * Remove all edit-node frames
1701 final void removeAllEditNodeJFrames() {
1702 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
1703 if ( _node_frames[ i ] != null ) {
1704 _node_frames[ i ].dispose();
1705 _node_frames[ i ] = null;
1708 _node_frame_index = 0;
1712 * Remove a node-edit frame.
1714 final void removeEditNodeFrame( final int i ) {
1715 _node_frame_index--;
1716 _node_frames[ i ] = null;
1717 if ( i < _node_frame_index ) {
1718 for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
1719 _node_frames[ j ] = _node_frames[ j + 1 ];
1721 _node_frames[ _node_frame_index ] = null;
1725 final void reRoot( final PhylogenyNode node ) {
1726 if ( !getPhylogeny().isRerootable() ) {
1727 JOptionPane.showMessageDialog( this,
1728 "This is not rerootable",
1730 JOptionPane.WARNING_MESSAGE );
1733 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1734 JOptionPane.showMessageDialog( this,
1735 "Cannot reroot in unrooted display type",
1736 "Attempt to reroot tree in unrooted display",
1737 JOptionPane.WARNING_MESSAGE );
1740 getPhylogeny().reRoot( node );
1741 getPhylogeny().recalculateNumberOfExternalDescendants( true );
1742 resetNodeIdToDistToLeafMap();
1743 setNodeInPreorderToNull();
1744 resetPreferredSize();
1745 getMainPanel().adjustJScrollPane();
1748 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1749 getControlPanel().showWhole();
1753 final void resetNodeIdToDistToLeafMap() {
1754 _nodeid_dist_to_leaf = new HashMap<Long, Short>();
1757 final void resetPreferredSize() {
1758 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
1764 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
1765 if ( getControlPanel().isDrawPhylogram() ) {
1767 + getLongestExtNodeInfo()
1769 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
1772 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
1774 + getLongestExtNodeInfo()
1775 + ForesterUtil.roundToInt( getXdistance()
1776 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
1780 + getLongestExtNodeInfo()
1781 + ForesterUtil.roundToInt( getXdistance()
1782 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
1785 setPreferredSize( new Dimension( x, y ) );
1788 final void selectNode( final PhylogenyNode node ) {
1789 if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
1790 getFoundNodes().remove( node.getId() );
1791 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1792 if ( getFoundNodes().size() < 1 ) {
1793 getControlPanel().searchReset();
1797 getControlPanel().getSearchFoundCountsLabel().setVisible( true );
1798 getControlPanel().getSearchResetButton().setEnabled( true );
1799 getControlPanel().getSearchResetButton().setVisible( true );
1800 if ( getFoundNodes() == null ) {
1801 setFoundNodes( new HashSet<Long>() );
1803 getFoundNodes().add( node.getId() );
1804 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1808 final void setArrowCursor() {
1809 setCursor( ARROW_CURSOR );
1813 final void setControlPanel( final ControlPanel atv_control ) {
1814 _control_panel = atv_control;
1817 void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
1818 increaseCurrentExternalNodesDataBufferChangeCounter();
1819 _current_external_nodes_data_buffer = sb;
1822 final void setFoundNodes( final Set<Long> found_nodes ) {
1823 _found_nodes = found_nodes;
1826 final void setInOvRect( final boolean in_ov_rect ) {
1827 _in_ov_rect = in_ov_rect;
1830 final void setLargeFonts() {
1831 getTreeFontSet().largeFonts();
1834 final void setLastMouseDragPointX( final float x ) {
1835 _last_drag_point_x = x;
1838 final void setLastMouseDragPointY( final float y ) {
1839 _last_drag_point_y = y;
1842 final void setLongestExtNodeInfo( final int i ) {
1843 _longest_ext_node_info = i;
1846 final void setMediumFonts() {
1847 getTreeFontSet().mediumFonts();
1850 final void setNodeInPreorderToNull() {
1851 _nodes_in_preorder = null;
1854 final void setOvOn( final boolean ov_on ) {
1858 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
1859 _graphics_type = graphics_type;
1863 final void setSmallFonts() {
1864 getTreeFontSet().smallFonts();
1867 final void setStartingAngle( final double starting_angle ) {
1868 _urt_starting_angle = starting_angle;
1871 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
1872 _statistics_for_vector_data = statistics_for_expression_values;
1875 final void setSuperTinyFonts() {
1876 getTreeFontSet().superTinyFonts();
1879 final void setTextAntialias() {
1880 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
1881 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
1882 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
1885 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
1888 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
1889 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
1891 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
1893 // catch ( final Throwable e ) {
1894 // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
1898 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
1899 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1903 final void setTinyFonts() {
1904 getTreeFontSet().tinyFonts();
1907 final void setTreeFile( final File treefile ) {
1908 _treefile = treefile;
1911 final void setXcorrectionFactor( final float f ) {
1912 _x_correction_factor = f;
1915 final void setXdistance( final float x ) {
1919 final void setYdistance( final float y ) {
1923 final void sortDescendants( final PhylogenyNode node ) {
1924 if ( !node.isExternal() ) {
1925 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
1926 if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
1927 .isShowTaxonomyCommonNames() ) ) {
1928 if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
1929 .isShowGeneSymbols() ) ) {
1930 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
1932 else if ( getControlPanel().isShowNodeNames() ) {
1933 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
1936 PhylogenyMethods.sortNodeDescendents( node, pri );
1937 setNodeInPreorderToNull();
1938 _phylogeny.externalNodesHaveChanged();
1939 _phylogeny.clearHashIdToNodeMap();
1940 _phylogeny.recalculateNumberOfExternalDescendants( true );
1941 resetNodeIdToDistToLeafMap();
1947 final void subTree( final PhylogenyNode node ) {
1948 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1949 JOptionPane.showMessageDialog( this,
1950 "Cannot get a sub/super tree in unrooted display",
1951 "Attempt to get sub/super tree in unrooted display",
1952 JOptionPane.WARNING_MESSAGE );
1955 if ( node.isExternal() ) {
1956 JOptionPane.showMessageDialog( this,
1957 "Cannot get a subtree of a external node",
1958 "Attempt to get subtree of external node",
1959 JOptionPane.WARNING_MESSAGE );
1962 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
1963 JOptionPane.showMessageDialog( this,
1964 "Cannot get a subtree of the root node",
1965 "Attempt to get subtree of root node",
1966 JOptionPane.WARNING_MESSAGE );
1969 setNodeInPreorderToNull();
1970 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
1971 _sub_phylogenies[ _subtree_index ] = _phylogeny;
1972 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
1974 _phylogeny = subTree( node, _phylogeny );
1975 updateSubSuperTreeButton();
1977 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
1980 _main_panel.getControlPanel().showWhole();
1984 final void superTree() {
1985 setNodeInPreorderToNull();
1986 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
1987 for( final PhylogenyNode n : temp_root.getDescendants() ) {
1988 n.setParent( temp_root );
1990 _sub_phylogenies[ _subtree_index ] = null;
1991 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
1992 _phylogeny = _sub_phylogenies[ --_subtree_index ];
1993 updateSubSuperTreeButton();
1996 final void swap( final PhylogenyNode node ) {
1997 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
2000 if ( node.getNumberOfDescendants() > 2 ) {
2001 JOptionPane.showMessageDialog( this,
2002 "Cannot swap descendants of nodes with more than 2 descendants",
2003 "Cannot swap descendants",
2004 JOptionPane.ERROR_MESSAGE );
2007 if ( !node.isExternal() ) {
2008 node.swapChildren();
2009 setNodeInPreorderToNull();
2010 _phylogeny.externalNodesHaveChanged();
2011 _phylogeny.clearHashIdToNodeMap();
2012 _phylogeny.recalculateNumberOfExternalDescendants( true );
2013 resetNodeIdToDistToLeafMap();
2019 final void taxColor() {
2020 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
2024 AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
2025 _control_panel.setColorBranches( true );
2026 if ( _control_panel.getColorBranchesCb() != null ) {
2027 _control_panel.getColorBranchesCb().setSelected( true );
2034 final void updateOvSettings() {
2035 switch ( getOptions().getOvPlacement() ) {
2037 setOvXPosition( OV_BORDER );
2038 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2039 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2042 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2043 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2044 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2047 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2048 setOvYPosition( OV_BORDER );
2049 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2052 setOvXPosition( OV_BORDER );
2053 setOvYPosition( OV_BORDER );
2054 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2059 final void updateOvSizes() {
2060 if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
2062 float l = getLongestExtNodeInfo();
2063 final float w_ratio = getOvMaxWidth() / getWidth();
2065 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
2066 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
2068 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
2069 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
2072 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
2074 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
2075 if ( ov_xdist < 0.0 ) {
2078 if ( ydist < 0.0 ) {
2081 setOvXDistance( ov_xdist );
2082 final double height = _phylogeny.getHeight();
2084 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
2085 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
2088 setOvXcorrectionFactor( 0 );
2096 void updateSetOfCollapsedExternalNodes() {
2097 final Phylogeny phy = getPhylogeny();
2098 _collapsed_external_nodeid_set.clear();
2099 if ( phy != null ) {
2100 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2101 final PhylogenyNode ext_node = it.next();
2102 PhylogenyNode n = ext_node;
2103 while ( !n.isRoot() ) {
2104 if ( n.isCollapse() ) {
2105 _collapsed_external_nodeid_set.add( ext_node.getId() );
2106 ext_node.setCollapse( true );
2115 final void updateSubSuperTreeButton() {
2116 if ( _subtree_index < 1 ) {
2117 getControlPanel().deactivateButtonToReturnToSuperTree();
2120 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
2124 final void zoomInDomainStructure() {
2125 if ( _domain_structure_width < 2000 ) {
2126 _domain_structure_width *= 1.2;
2130 final void zoomOutDomainStructure() {
2131 if ( _domain_structure_width > 20 ) {
2132 _domain_structure_width *= 0.8;
2136 private void abbreviateScientificName( final String sn ) {
2137 final String[] a = sn.split( "\\s+" );
2138 _sb.append( a[ 0 ].substring( 0, 1 ) );
2139 _sb.append( a[ 1 ].substring( 0, 2 ) );
2140 if ( a.length > 2 ) {
2141 for( int i = 2; i < a.length; i++ ) {
2143 _sb.append( a[ i ] );
2148 final private void addEmptyNode( final PhylogenyNode node ) {
2149 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2150 errorMessageNoCutCopyPasteInUnrootedDisplay();
2153 final String label = createASimpleTextRepresentationOfANode( node );
2155 if ( ForesterUtil.isEmpty( label ) ) {
2156 msg = "How to add the new, empty node?";
2159 msg = "How to add the new, empty node to node" + label + "?";
2161 final Object[] options = { "As sibling", "As descendant", "Cancel" };
2162 final int r = JOptionPane.showOptionDialog( this,
2164 "Addition of Empty New Node",
2165 JOptionPane.CLOSED_OPTION,
2166 JOptionPane.QUESTION_MESSAGE,
2170 boolean add_as_sibling = true;
2172 add_as_sibling = false;
2174 else if ( r != 0 ) {
2177 final Phylogeny phy = new Phylogeny();
2178 phy.setRoot( new PhylogenyNode() );
2179 phy.setRooted( true );
2180 if ( add_as_sibling ) {
2181 if ( node.isRoot() ) {
2182 JOptionPane.showMessageDialog( this,
2183 "Cannot add sibling to root",
2184 "Attempt to add sibling to root",
2185 JOptionPane.ERROR_MESSAGE );
2188 phy.addAsSibling( node );
2191 phy.addAsChild( node );
2193 setNodeInPreorderToNull();
2194 _phylogeny.externalNodesHaveChanged();
2195 _phylogeny.clearHashIdToNodeMap();
2196 _phylogeny.recalculateNumberOfExternalDescendants( true );
2197 resetNodeIdToDistToLeafMap();
2202 final private void addToCurrentExternalNodes( final long i ) {
2203 if ( _current_external_nodes == null ) {
2204 _current_external_nodes = new HashSet<Long>();
2206 _current_external_nodes.add( i );
2209 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
2210 final boolean is_vertical,
2212 final boolean to_pdf,
2213 final boolean to_graphics_file ) {
2214 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
2215 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2216 g.setColor( Color.BLACK );
2218 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
2219 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
2220 && ( getCutOrCopiedTree() != null )
2221 && ( getCopiedAndPastedNodes() != null )
2223 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
2224 g.setColor( getTreeColorSet().getFoundColor() );
2226 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2227 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2229 else if ( to_pdf ) {
2230 g.setColor( getTreeColorSet().getBranchColorForPdf() );
2233 g.setColor( getTreeColorSet().getBranchColor() );
2237 final private void blast( final PhylogenyNode node ) {
2238 if ( !isCanBlast( node ) ) {
2239 JOptionPane.showMessageDialog( this,
2240 "Insufficient information present",
2242 JOptionPane.INFORMATION_MESSAGE );
2246 final String query = Blast.obtainQueryForBlast( node );
2247 System.out.println( "query for BLAST is: " + query );
2249 if ( !ForesterUtil.isEmpty( query ) ) {
2250 if ( node.getNodeData().isHasSequence() ) {
2251 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
2252 if ( node.getNodeData().getSequence().getType().toLowerCase()
2253 .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
2260 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2261 if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2269 if ( type == '?' ) {
2270 if ( SequenceIdParser.isProtein( query ) ) {
2277 JApplet applet = null;
2279 applet = obtainApplet();
2282 Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
2284 catch ( final Exception e ) {
2285 e.printStackTrace();
2287 if ( Constants.ALLOW_DDBJ_BLAST ) {
2289 System.out.println( "trying: " + query );
2290 final Blast s = new Blast();
2291 s.ddbjBlast( query );
2293 catch ( final Exception e ) {
2294 e.printStackTrace();
2301 private final int calcDynamicHidingFactor() {
2302 return ( int ) ( 0.5 + ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ) );
2306 * Calculate the length of the distance between the given node and its
2312 * @return the distance value
2314 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
2315 if ( getControlPanel().isDrawPhylogram() ) {
2316 if ( node.getDistanceToParent() < 0.0 ) {
2319 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
2322 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2323 return getXdistance();
2325 return getXdistance() * factor;
2329 final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
2330 Color c = getTreeColorSet().getAnnotationColor();
2331 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
2332 final StringBuilder sb = new StringBuilder();
2333 for( final Annotation a : ann ) {
2334 sb.append( !ForesterUtil.isEmpty( a.getRef() ) ? a.getRef() : a.getDesc() );
2336 final String ann_str = sb.toString();
2337 if ( !ForesterUtil.isEmpty( ann_str ) ) {
2338 c = getControlPanel().getAnnotationColors().get( ann_str );
2340 c = AptxUtil.calculateColorFromString( ann_str );
2341 getControlPanel().getAnnotationColors().put( ann_str, c );
2344 c = getTreeColorSet().getAnnotationColor();
2351 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
2352 if ( getControlPanel().isDrawPhylogram() ) {
2353 if ( node.getDistanceToParent() < 0.0 ) {
2356 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
2359 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2360 return getOvXDistance();
2362 return getOvXDistance() * factor;
2366 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
2367 JOptionPane.showMessageDialog( this,
2368 "Cannot launch web browser for " + type_type + " data of this node",
2369 "Cannot launch web browser",
2370 JOptionPane.WARNING_MESSAGE );
2373 final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
2374 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2375 JOptionPane.showMessageDialog( this,
2376 "Cannot colorize subtree in unrooted display type",
2377 "Attempt to colorize subtree in unrooted display",
2378 JOptionPane.WARNING_MESSAGE );
2381 _control_panel.setColorBranches( true );
2382 if ( _control_panel.getColorBranchesCb() != null ) {
2383 _control_panel.getColorBranchesCb().setSelected( true );
2385 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
2386 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
2391 final private void colorSubtree( final PhylogenyNode node ) {
2392 Color intitial_color = null;
2393 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
2394 && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
2395 intitial_color = PhylogenyMethods.getBranchColorValue( node );
2398 intitial_color = getTreeColorSet().getBranchColor();
2400 _color_chooser.setColor( intitial_color );
2401 _color_chooser.setPreviewPanel( new JPanel() );
2402 final JDialog dialog = JColorChooser
2403 .createDialog( this,
2404 "Subtree colorization",
2407 new SubtreeColorizationActionListener( _color_chooser, node ),
2409 dialog.setVisible( true );
2412 final private void copySubtree( final PhylogenyNode node ) {
2413 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2414 errorMessageNoCutCopyPasteInUnrootedDisplay();
2417 setNodeInPreorderToNull();
2418 setCutOrCopiedTree( _phylogeny.copy( node ) );
2419 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
2420 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
2421 for( final PhylogenyNode n : nodes ) {
2422 node_ids.add( n.getId() );
2424 node_ids.add( node.getId() );
2425 setCopiedAndPastedNodes( node_ids );
2429 private String createAnnotationString( final SortedSet<Annotation> ann ) {
2430 final StringBuilder sb = new StringBuilder();
2431 boolean first = true;
2432 for( final Annotation a : ann ) {
2439 sb.append( a.asSimpleText() );
2441 final String ann_str = sb.toString();
2445 final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
2446 final String tax = PhylogenyMethods.getSpecies( node );
2447 String label = node.getName();
2448 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
2449 label = label + " " + tax;
2451 else if ( !ForesterUtil.isEmpty( tax ) ) {
2457 if ( !ForesterUtil.isEmpty( label ) ) {
2458 label = " [" + label + "]";
2463 final private void cutSubtree( final PhylogenyNode node ) {
2464 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2465 errorMessageNoCutCopyPasteInUnrootedDisplay();
2468 if ( node.isRoot() ) {
2469 JOptionPane.showMessageDialog( this,
2470 "Cannot cut entire tree as subtree",
2471 "Attempt to cut entire tree",
2472 JOptionPane.ERROR_MESSAGE );
2475 final String label = createASimpleTextRepresentationOfANode( node );
2476 final int r = JOptionPane.showConfirmDialog( null,
2477 "Cut subtree" + label + "?",
2478 "Confirm Cutting of Subtree",
2479 JOptionPane.YES_NO_OPTION );
2480 if ( r != JOptionPane.OK_OPTION ) {
2483 setNodeInPreorderToNull();
2484 setCopiedAndPastedNodes( null );
2485 setCutOrCopiedTree( _phylogeny.copy( node ) );
2486 _phylogeny.deleteSubtree( node, true );
2487 _phylogeny.clearHashIdToNodeMap();
2488 _phylogeny.recalculateNumberOfExternalDescendants( true );
2489 resetNodeIdToDistToLeafMap();
2494 final private void cycleColors() {
2495 getMainPanel().getTreeColorSet().cycleColorScheme();
2496 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
2497 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
2501 final private void decreaseOvSize() {
2502 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
2503 setOvMaxWidth( getOvMaxWidth() - 5 );
2504 setOvMaxHeight( getOvMaxHeight() - 5 );
2506 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2510 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
2511 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2512 errorMessageNoCutCopyPasteInUnrootedDisplay();
2515 if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
2516 JOptionPane.showMessageDialog( this,
2517 "Cannot delete entire tree",
2518 "Attempt to delete entire tree",
2519 JOptionPane.ERROR_MESSAGE );
2522 final String label = createASimpleTextRepresentationOfANode( node );
2523 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
2524 final int r = JOptionPane.showOptionDialog( this,
2525 "Delete" + label + "?",
2526 "Delete Node/Subtree",
2527 JOptionPane.CLOSED_OPTION,
2528 JOptionPane.QUESTION_MESSAGE,
2532 setNodeInPreorderToNull();
2533 boolean node_only = true;
2537 else if ( r != 0 ) {
2541 PhylogenyMethods.removeNode( node, _phylogeny );
2544 _phylogeny.deleteSubtree( node, true );
2546 _phylogeny.externalNodesHaveChanged();
2547 _phylogeny.clearHashIdToNodeMap();
2548 _phylogeny.recalculateNumberOfExternalDescendants( true );
2549 resetNodeIdToDistToLeafMap();
2554 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
2555 makePopupMenus( node );
2556 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
2557 _node_popup_menu.show( this, x, y );
2560 final private void drawArc( final double x,
2563 final double heigth,
2564 final double start_angle,
2565 final double arc_angle,
2566 final Graphics2D g ) {
2567 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
2571 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
2572 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
2575 _line.setLine( x1, y1, x2, y2 );
2579 final private void drawOval( final double x,
2582 final double heigth,
2583 final Graphics2D g ) {
2584 _ellipse.setFrame( x, y, width, heigth );
2588 final private void drawOvalFilled( final double x,
2591 final double heigth,
2592 final Graphics2D g ) {
2593 _ellipse.setFrame( x, y, width, heigth );
2597 final private void drawOvalGradient( final double x,
2600 final double heigth,
2602 final Color color_1,
2603 final Color color_2,
2604 final Color color_border ) {
2605 _ellipse.setFrame( x, y, width, heigth );
2606 g.setPaint( new GradientPaint( ( float ) x,
2609 ( float ) ( x + width ),
2610 ( float ) ( y + heigth ),
2614 if ( color_border != null ) {
2615 g.setPaint( color_border );
2620 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
2621 _rectangle.setFrame( x, y, width, heigth );
2622 g.draw( _rectangle );
2625 final private void drawRectFilled( final double x,
2628 final double heigth,
2629 final Graphics2D g ) {
2630 _rectangle.setFrame( x, y, width, heigth );
2631 g.fill( _rectangle );
2634 final private void drawRectGradient( final double x,
2637 final double heigth,
2639 final Color color_1,
2640 final Color color_2,
2641 final Color color_border ) {
2642 _rectangle.setFrame( x, y, width, heigth );
2643 g.setPaint( new GradientPaint( ( float ) x,
2646 ( float ) ( x + width ),
2647 ( float ) ( y + heigth ),
2650 g.fill( _rectangle );
2651 if ( color_border != null ) {
2652 g.setPaint( color_border );
2653 g.draw( _rectangle );
2657 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2658 final List<Uri> us = new ArrayList<Uri>();
2659 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2660 for( final Uri uri : t.getUris() ) {
2665 for( final Uri uri : us ) {
2666 if ( uri != null ) {
2667 final String uri_str = uri.getValue().toString().toLowerCase();
2668 if ( getImageMap().containsKey( uri_str ) ) {
2669 final BufferedImage bi = getImageMap().get( uri_str );
2670 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2671 double scaling_factor = 1;
2672 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
2673 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
2674 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
2676 // y = y - ( 0.9 * getYdistance() );
2677 final double hs = bi.getHeight() * scaling_factor;
2678 double ws = ( bi.getWidth() * scaling_factor ) + offset;
2679 final double my_y = y - ( 0.5 * hs );
2680 final int x_w = ( int ) ( x + ws + 0.5 );
2681 final int y_h = ( int ) ( my_y + hs + 0.5 );
2682 if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
2684 ( int ) ( x + 0.5 + offset ),
2685 ( int ) ( my_y + 0.5 ),
2706 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
2707 JOptionPane.showMessageDialog( this,
2708 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
2709 "Attempt to cut/copy/paste/add/delete in unrooted display",
2710 JOptionPane.ERROR_MESSAGE );
2713 final private Set<Long> getCopiedAndPastedNodes() {
2714 return getMainPanel().getCopiedAndPastedNodes();
2717 final private Set<Long> getCurrentExternalNodes() {
2718 return _current_external_nodes;
2721 final private Phylogeny getCutOrCopiedTree() {
2722 return getMainPanel().getCutOrCopiedTree();
2725 final private float getLastDragPointX() {
2726 return _last_drag_point_x;
2729 final private float getLastDragPointY() {
2730 return _last_drag_point_y;
2733 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
2734 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
2735 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
2736 _nodeid_dist_to_leaf.put( node.getId(), m );
2740 return _nodeid_dist_to_leaf.get( node.getId() );
2744 final private double getMaxDistanceToRoot() {
2745 if ( _max_distance_to_root < 0 ) {
2746 recalculateMaxDistanceToRoot();
2748 return _max_distance_to_root;
2751 final private float getOvMaxHeight() {
2752 return _ov_max_height;
2755 final private float getOvMaxWidth() {
2756 return _ov_max_width;
2759 final private float getOvXcorrectionFactor() {
2760 return _ov_x_correction_factor;
2763 final private float getOvXDistance() {
2764 return _ov_x_distance;
2767 final private int getOvXPosition() {
2768 return _ov_x_position;
2771 final private float getOvYDistance() {
2772 return _ov_y_distance;
2775 final private int getOvYPosition() {
2776 return _ov_y_position;
2779 final private int getOvYStart() {
2783 final private double getScaleDistance() {
2784 return _scale_distance;
2787 final private String getScaleLabel() {
2788 return _scale_label;
2791 final private TreeFontSet getTreeFontSet() {
2792 return getMainPanel().getTreeFontSet();
2795 final private float getUrtFactor() {
2799 final private float getUrtFactorOv() {
2800 return _urt_factor_ov;
2803 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
2806 showNodeFrame( node );
2821 colorSubtree( node );
2836 copySubtree( node );
2839 pasteSubtree( node );
2841 case DELETE_NODE_OR_SUBTREE:
2842 deleteNodeOrSubtree( node );
2845 addEmptyNode( node );
2847 case EDIT_NODE_DATA:
2848 showNodeEditFrame( node );
2853 case SORT_DESCENDENTS:
2854 sortDescendants( node );
2856 case GET_EXT_DESC_DATA:
2857 showExtDescNodeData( node );
2860 throw new IllegalArgumentException( "unknown action: " + action );
2864 final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
2865 _current_external_nodes_data_buffer_change_counter++;
2868 final private void increaseOvSize() {
2869 if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
2870 && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
2871 .getHeight() / 2 ) ) ) {
2872 setOvMaxWidth( getOvMaxWidth() + 5 );
2873 setOvMaxHeight( getOvMaxHeight() + 5 );
2875 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2879 final private void init() {
2880 _color_chooser = new JColorChooser();
2881 _rollover_popup = new JTextArea();
2882 _rollover_popup.setFont( POPUP_FONT );
2883 resetNodeIdToDistToLeafMap();
2885 setTreeFile( null );
2887 initializeOvSettings();
2888 setStartingAngle( ( TWO_PI * 3 ) / 4 );
2889 final ImageLoader il = new ImageLoader( this );
2890 new Thread( il ).start();
2893 final private void initializeOvSettings() {
2894 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
2895 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
2898 final private boolean inOvVirtualRectangle( final int x, final int y ) {
2899 return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
2900 && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
2901 && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
2902 + getOvVirtualRectangle().height + 1 ) ) );
2905 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
2906 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
2909 final private boolean isCanBlast( final PhylogenyNode node ) {
2910 if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
2913 return Blast.isContainsQueryForBlast( node );
2916 final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
2917 String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
2918 if ( ForesterUtil.isEmpty( v ) ) {
2919 v = ForesterUtil.extractGenbankAccessor( node );
2921 if ( ForesterUtil.isEmpty( v ) ) {
2922 v = ForesterUtil.extractRefSeqAccessorAccessor( node );
2924 if ( ForesterUtil.isEmpty( v ) ) {
2925 v = ForesterUtil.extractGInumber( node );
2930 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
2931 if ( node.getNodeData().isHasTaxonomy()
2932 && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
2933 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
2934 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
2935 .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
2936 .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
2944 final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
2945 return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
2948 final private boolean isInFoundNodes( final PhylogenyNode node ) {
2949 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
2952 final private boolean isInOv() {
2956 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
2958 if ( getControlPanel().isShowTaxonomyImages() ) {
2959 y_dist = 40 + ( int ) getYdistance();
2961 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
2962 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
2963 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
2966 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
2967 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
2968 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
2969 || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
2970 .getMaxX() + 20 ) ) );
2973 final private boolean isNonLinedUpCladogram() {
2974 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
2977 final private boolean isUniformBranchLengthsForCladogram() {
2978 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
2981 final private void keyPressedCalls( final KeyEvent e ) {
2982 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
2983 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
2984 if ( !isInOvRect() ) {
2985 setInOvRect( true );
2988 else if ( isInOvRect() ) {
2989 setInOvRect( false );
2992 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
2993 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2994 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2995 getMainPanel().getTreeFontSet().mediumFonts();
2996 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2998 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
2999 getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
3000 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
3002 else if ( plusPressed( e.getKeyCode() ) ) {
3003 getMainPanel().getTreeFontSet().increaseFontSize();
3004 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
3008 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
3009 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
3010 getControlPanel().showWhole();
3012 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
3013 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
3014 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
3015 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
3016 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3017 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3019 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3020 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3021 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3023 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3024 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3025 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3026 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3028 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3029 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3030 Constants.WHEEL_ZOOM_IN_FACTOR );
3031 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3038 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3041 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3045 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3049 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
3050 scroll_position.x = scroll_position.x + dx;
3051 scroll_position.y = scroll_position.y + dy;
3052 if ( scroll_position.x <= 0 ) {
3053 scroll_position.x = 0;
3056 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
3057 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
3058 if ( scroll_position.x >= max_x ) {
3059 scroll_position.x = max_x;
3062 if ( scroll_position.y <= 0 ) {
3063 scroll_position.y = 0;
3066 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
3067 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
3068 if ( scroll_position.y >= max_y ) {
3069 scroll_position.y = max_y;
3073 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
3076 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3077 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3078 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3079 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3080 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3082 else if ( plusPressed( e.getKeyCode() ) ) {
3083 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3084 Constants.WHEEL_ZOOM_IN_FACTOR );
3085 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3086 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3088 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
3089 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3090 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3091 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
3092 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3095 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
3096 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3097 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3098 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
3099 if ( getStartingAngle() < 0 ) {
3100 setStartingAngle( TWO_PI + getStartingAngle() );
3102 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3105 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
3106 boolean selected = false;
3107 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
3108 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
3112 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
3114 if ( getMainPanel().getMainFrame() == null ) {
3115 // Must be "E" applet version.
3116 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
3117 if ( ae.getlabelDirectionCbmi() != null ) {
3118 ae.getlabelDirectionCbmi().setSelected( selected );
3122 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
3126 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
3127 switchDisplaygetPhylogenyGraphicsType();
3130 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
3134 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
3135 MainFrame.cycleOverview( getOptions(), this );
3138 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
3141 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
3148 final private void makePopupMenus( final PhylogenyNode node ) {
3149 _node_popup_menu = new JPopupMenu();
3150 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
3151 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
3152 for( int i = 0; i < clickto_names.size(); i++ ) {
3153 final String title = clickto_names.get( i );
3154 _node_popup_menu_items[ i ] = new JMenuItem( title );
3155 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
3156 final String id = isCanOpenSeqWeb( node );
3157 if ( !ForesterUtil.isEmpty( id ) ) {
3158 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
3159 _node_popup_menu_items[ i ].setEnabled( true );
3162 _node_popup_menu_items[ i ].setEnabled( false );
3165 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
3166 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
3168 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
3169 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
3171 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
3172 if ( !getOptions().isEditable() ) {
3175 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
3177 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
3178 if ( !getOptions().isEditable() ) {
3181 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
3183 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
3184 if ( !getOptions().isEditable() ) {
3187 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
3189 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
3190 if ( !getOptions().isEditable() ) {
3193 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
3195 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
3196 if ( !getOptions().isEditable() ) {
3200 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
3201 if ( !getOptions().isEditable() ) {
3205 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
3206 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
3208 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
3209 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
3211 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
3212 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
3214 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
3215 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
3217 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
3218 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
3220 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
3221 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
3223 _node_popup_menu_items[ i ].addActionListener( this );
3224 _node_popup_menu.add( _node_popup_menu_items[ i ] );
3228 private final String obtainTitleForExtDescNodeData() {
3229 switch ( getOptions().getExtDescNodeDataToReturn() ) {
3231 return "Node Names";
3233 return "Sequence Names";
3234 case SEQUENCE_SYMBOL:
3235 return "Sequence Symbols";
3236 case SEQUENCE_MOL_SEQ:
3237 return "Molecular Sequences";
3238 case SEQUENCE_MOL_SEQ_FASTA:
3239 return "Molecular Sequences (Fasta)";
3241 return "Sequence Accessors";
3242 case TAXONOMY_SCIENTIFIC_NAME:
3243 return "Scientific Names";
3245 return "Taxonomy Codes";
3247 return "User Selected Data";
3249 throw new IllegalArgumentException( "unknown data element: "
3250 + getOptions().getExtDescNodeDataToReturn() );
3254 final private void openSeqWeb( final PhylogenyNode node ) {
3255 if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
3256 cannotOpenBrowserWarningMessage( "sequence" );
3259 final String uri_str = AptxUtil.createUriForSeqWeb( node, getConfiguration(), this );
3260 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3262 AptxUtil.launchWebBrowser( new URI( uri_str ),
3264 isApplet() ? obtainApplet() : null,
3267 catch ( final IOException e ) {
3268 AptxUtil.showErrorMessage( this, e.toString() );
3269 e.printStackTrace();
3271 catch ( final URISyntaxException e ) {
3272 AptxUtil.showErrorMessage( this, e.toString() );
3273 e.printStackTrace();
3277 cannotOpenBrowserWarningMessage( "sequence" );
3281 final private void openTaxWeb( final PhylogenyNode node ) {
3282 if ( !isCanOpenTaxWeb( node ) ) {
3283 cannotOpenBrowserWarningMessage( "taxonomic" );
3286 String uri_str = null;
3287 final Taxonomy tax = node.getNodeData().getTaxonomy();
3288 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3289 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
3291 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
3293 catch ( final URISyntaxException e ) {
3294 AptxUtil.showErrorMessage( this, e.toString() );
3296 e.printStackTrace();
3299 else if ( ( tax.getIdentifier() != null )
3300 && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3301 && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
3302 && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
3303 .equalsIgnoreCase( "uniprot" ) ) ) {
3305 uri_str = "http://www.uniprot.org/taxonomy/"
3306 + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
3308 catch ( final UnsupportedEncodingException e ) {
3309 AptxUtil.showErrorMessage( this, e.toString() );
3310 e.printStackTrace();
3313 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
3315 uri_str = "http://www.uniprot.org/taxonomy/?query="
3316 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
3318 catch ( final UnsupportedEncodingException e ) {
3319 AptxUtil.showErrorMessage( this, e.toString() );
3320 e.printStackTrace();
3323 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
3325 uri_str = "http://www.uniprot.org/taxonomy/?query="
3326 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
3328 catch ( final UnsupportedEncodingException e ) {
3329 AptxUtil.showErrorMessage( this, e.toString() );
3330 e.printStackTrace();
3333 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
3335 uri_str = "http://www.uniprot.org/taxonomy/?query="
3336 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
3338 catch ( final UnsupportedEncodingException e ) {
3339 AptxUtil.showErrorMessage( this, e.toString() );
3340 e.printStackTrace();
3343 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3345 AptxUtil.launchWebBrowser( new URI( uri_str ),
3347 isApplet() ? obtainApplet() : null,
3350 catch ( final IOException e ) {
3351 AptxUtil.showErrorMessage( this, e.toString() );
3352 e.printStackTrace();
3354 catch ( final URISyntaxException e ) {
3355 AptxUtil.showErrorMessage( this, e.toString() );
3356 e.printStackTrace();
3360 cannotOpenBrowserWarningMessage( "taxonomic" );
3364 final private void paintBranchLength( final Graphics2D g,
3365 final PhylogenyNode node,
3366 final boolean to_pdf,
3367 final boolean to_graphics_file ) {
3368 g.setFont( getTreeFontSet().getSmallFont() );
3369 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3370 g.setColor( Color.BLACK );
3373 g.setColor( getTreeColorSet().getBranchLengthColor() );
3375 if ( !node.isRoot() ) {
3376 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3377 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3378 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3380 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3381 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3382 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3385 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3386 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3390 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
3391 - getTreeFontSet()._small_max_descent, g );
3395 final private void paintBranchLite( final Graphics2D g,
3400 final PhylogenyNode node ) {
3401 g.setColor( getTreeColorSet().getOvColor() );
3402 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3403 drawLine( x1, y1, x2, y2, g );
3405 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3406 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3407 ( g ).draw( _quad_curve );
3409 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3410 final float dx = x2 - x1;
3411 final float dy = y2 - y1;
3412 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3413 + ( dy * 0.8f ), x2, y2 );
3414 ( g ).draw( _cubic_curve );
3417 final float x2a = x2;
3418 final float x1a = x1;
3419 // draw the vertical line
3420 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
3421 drawLine( x1, y1, x1, y2, g );
3423 // draw the horizontal line
3424 drawLine( x1a, y2, x2a, y2, g );
3429 * Paint a branch which consists of a vertical and a horizontal bar
3430 * @param is_ind_found_nodes
3432 final private void paintBranchRectangular( final Graphics2D g,
3437 final PhylogenyNode node,
3438 final boolean to_pdf,
3439 final boolean to_graphics_file ) {
3440 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
3441 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3442 drawLine( x1, y1, x2, y2, g );
3444 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3445 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3446 g.draw( _quad_curve );
3448 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3449 final float dx = x2 - x1;
3450 final float dy = y2 - y1;
3451 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3452 + ( dy * 0.8f ), x2, y2 );
3453 g.draw( _cubic_curve );
3456 final float x2a = x2;
3457 final float x1a = x1;
3459 if ( node.isFirstChildNode() || node.isLastChildNode()
3460 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3461 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3462 if ( !to_graphics_file
3464 && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
3465 .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
3469 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3470 float x2c = x1 + EURO_D;
3474 drawLine( x1, y1, x2c, y2, g );
3476 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3478 y2_r = y2 - ROUNDED_D;
3482 drawLine( x1, y1, x1, y2_r, g );
3485 y2_r = y2 + ROUNDED_D;
3489 drawLine( x1, y1, x1, y2_r, g );
3493 drawLine( x1, y1, x1, y2, g );
3497 // draw the horizontal line
3498 if ( !to_graphics_file && !to_pdf
3499 && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
3503 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
3504 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3505 x1_r = x1a + ROUNDED_D;
3507 drawLine( x1_r, y2, x2a, y2, g );
3510 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3511 final float x1c = x1a + EURO_D;
3513 drawLine( x1c, y2, x2a, y2, g );
3517 drawLine( x1a, y2, x2a, y2, g );
3521 final double w = PhylogenyMethods.getBranchWidthValue( node );
3522 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3523 x1_r = x1a + ROUNDED_D;
3525 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
3528 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3529 final float x1c = x1a + EURO_D;
3531 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
3535 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
3538 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3543 final double diff = y2 - y2_r;
3544 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
3547 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
3552 if ( node.isExternal() ) {
3553 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
3554 || isInCurrentExternalNodes( node ) );
3558 final private double paintCirculars( final PhylogenyNode n,
3559 final Phylogeny phy,
3560 final float center_x,
3561 final float center_y,
3562 final double radius,
3563 final boolean radial_labels,
3565 final boolean to_pdf,
3566 final boolean to_graphics_file ) {
3567 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
3568 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
3569 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
3571 return _urt_nodeid_angle_map.get( n.getId() );
3574 final List<PhylogenyNode> descs = n.getDescendants();
3576 for( final PhylogenyNode desc : descs ) {
3577 sum += paintCirculars( desc,
3588 if ( !n.isRoot() ) {
3589 r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3591 final double theta = sum / descs.size();
3592 n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
3593 n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
3594 _urt_nodeid_angle_map.put( n.getId(), theta );
3595 for( final PhylogenyNode desc : descs ) {
3596 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
3602 final private void paintCircularsLite( final PhylogenyNode n,
3603 final Phylogeny phy,
3607 final Graphics2D g ) {
3608 if ( n.isExternal() ) {
3612 final List<PhylogenyNode> descs = n.getDescendants();
3613 for( final PhylogenyNode desc : descs ) {
3614 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
3617 if ( !n.isRoot() ) {
3618 r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3620 final double theta = _urt_nodeid_angle_map.get( n.getId() );
3621 n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
3622 n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
3623 for( final PhylogenyNode desc : descs ) {
3624 paintBranchCircularLite( n, desc, g );
3629 final private void paintCollapsedNode( final Graphics2D g,
3630 final PhylogenyNode node,
3631 final boolean to_graphics_file,
3632 final boolean to_pdf,
3633 final boolean is_in_found_nodes ) {
3635 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3638 else if ( is_in_found_nodes ) {
3639 c = getTreeColorSet().getFoundColor();
3641 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3642 c = getTaxonomyBasedColor( node );
3644 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3645 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3646 c = PhylogenyMethods.getBranchColorValue( node );
3649 c = getTreeColorSet().getCollapseFillColor();
3651 double d = node.getAllExternalDescendants().size();
3653 d = ( 3 * _y_distance ) / 3;
3656 d = ( Math.log10( d ) * _y_distance ) / 2.5;
3658 final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
3659 if ( d < box_size ) {
3662 final float xx = node.getXcoord() - ( 2 * box_size );
3663 final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
3665 _polygon.moveTo( xxx, node.getYcoord() );
3666 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
3667 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
3668 _polygon.closePath();
3669 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3673 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3674 g.setColor( getBackground() );
3679 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3680 g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
3681 .getYcoord() - d ), c, false ) );
3686 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3689 final private void paintConfidenceValues( final Graphics2D g,
3690 final PhylogenyNode node,
3691 final boolean to_pdf,
3692 final boolean to_graphics_file ) {
3693 final List<Confidence> confidences = node.getBranchData().getConfidences();
3694 // if ( confidences.size() == 1 ) {
3695 // final double value = node.getBranchData().getConfidence( 0 ).getValue();
3696 // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
3699 // conf_str = FORMATTER_CONFIDENCE.format( value );
3701 // else if ( confidences.size() > 1 ) {
3702 boolean one_ok = false;
3703 boolean not_first = false;
3704 Collections.sort( confidences );
3705 final StringBuilder sb = new StringBuilder();
3706 String conf_str = "";
3707 for( final Confidence confidence : confidences ) {
3708 final double value = confidence.getValue();
3709 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3710 if ( value >= getOptions().getMinConfidenceValue() ) {
3719 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
3720 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3721 if ( getOptions().isShowConfidenceStddev() ) {
3722 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3724 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
3726 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3733 conf_str = sb.toString();
3736 if ( conf_str.length() > 0 ) {
3737 final double parent_x = node.getParent().getXcoord();
3738 double x = node.getXcoord();
3739 g.setFont( getTreeFontSet().getSmallFont() );
3740 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3743 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3746 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3747 g.setColor( Color.BLACK );
3750 g.setColor( getTreeColorSet().getConfidenceColor() );
3753 .drawString( conf_str,
3755 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
3756 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
3761 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
3762 final int box_size = getOptions().getDefaultNodeShapeSize();
3763 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3764 g.setColor( getTreeColorSet().getFoundColor() );
3765 g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
3768 final private void paintGainedAndLostCharacters( final Graphics2D g,
3769 final PhylogenyNode node,
3770 final String gained,
3771 final String lost ) {
3772 if ( node.getParent() != null ) {
3773 final double parent_x = node.getParent().getXcoord();
3774 final double x = node.getXcoord();
3775 g.setFont( getTreeFontSet().getLargeFont() );
3776 g.setColor( getTreeColorSet().getGainedCharactersColor() );
3777 if ( Constants.SPECIAL_CUSTOM ) {
3778 g.setColor( Color.BLUE );
3781 .drawString( gained,
3782 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
3783 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
3785 g.setColor( getTreeColorSet().getLostCharactersColor() );
3786 TreePanel.drawString( lost,
3787 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
3788 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
3794 * Draw a box at the indicated node.
3801 final private void paintNodeBox( final double x,
3803 final PhylogenyNode node,
3805 final boolean to_pdf,
3806 final boolean to_graphics_file,
3807 final boolean is_in_found_nodes ) {
3808 if ( node.isCollapse() ) {
3811 // if this node should be highlighted, do so
3812 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
3813 g.setColor( getTreeColorSet().getFoundColor() );
3814 drawOval( x - 8, y - 8, 16, 16, g );
3815 drawOval( x - 9, y - 8, 17, 17, g );
3816 drawOval( x - 9, y - 9, 18, 18, g );
3818 if ( is_in_found_nodes ) {
3819 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
3822 Color outline_color = null;
3823 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3824 outline_color = Color.BLACK;
3826 else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
3827 final Event event = node.getNodeData().getEvent();
3828 if ( event.isDuplication() ) {
3829 outline_color = getTreeColorSet().getDuplicationBoxColor();
3831 else if ( event.isSpeciation() ) {
3832 outline_color = getTreeColorSet().getSpecBoxColor();
3834 else if ( event.isSpeciationOrDuplication() ) {
3835 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
3838 else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
3839 outline_color = getTaxonomyBasedColor( node );
3842 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
3843 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
3844 outline_color = getTreeColorSet().getBranchColorForPdf();
3847 final int box_size = getOptions().getDefaultNodeShapeSize();
3848 final int half_box_size = box_size / 2;
3849 if ( ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
3850 || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
3851 || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
3852 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
3853 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3854 drawOvalGradient( x - half_box_size,
3859 to_pdf ? Color.WHITE : outline_color,
3860 to_pdf ? outline_color : getBackground(),
3863 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
3864 Color background = getBackground();
3866 background = Color.WHITE;
3868 drawOvalGradient( x - half_box_size,
3877 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3878 g.setColor( outline_color );
3879 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3882 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
3883 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
3884 drawRectGradient( x - half_box_size,
3889 to_pdf ? Color.WHITE : outline_color,
3890 to_pdf ? outline_color : getBackground(),
3893 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3894 Color background = getBackground();
3896 background = Color.WHITE;
3898 drawRectGradient( x - half_box_size,
3907 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3908 g.setColor( outline_color );
3909 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3916 final private void paintNodeData( final Graphics2D g,
3917 final PhylogenyNode node,
3918 final boolean to_graphics_file,
3919 final boolean to_pdf,
3920 final boolean is_in_found_nodes ) {
3921 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
3924 if ( getOptions().isShowBranchLengthValues()
3925 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3926 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3927 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
3928 paintBranchLength( g, node, to_pdf, to_graphics_file );
3930 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
3935 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3936 if ( getControlPanel().isShowTaxonomyImages()
3937 && ( getImageMap() != null )
3938 && !getImageMap().isEmpty()
3939 && node.getNodeData().isHasTaxonomy()
3940 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
3941 .getUris().isEmpty() ) ) {
3942 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
3944 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3945 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
3946 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
3948 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3949 g.setColor( Color.BLACK );
3951 else if ( is_in_found_nodes ) {
3952 g.setColor( getTreeColorSet().getFoundColor() );
3954 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3955 g.setColor( getTaxonomyBasedColor( node ) );
3957 else if ( getControlPanel().isColorAccordingToAnnotation()
3958 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
3959 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
3960 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
3962 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3963 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3964 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3966 else if ( to_pdf ) {
3967 g.setColor( Color.BLACK );
3970 g.setColor( getTreeColorSet().getSequenceColor() );
3972 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3973 if ( _sb.length() > 0 ) {
3976 _sb.append( node.getAllExternalDescendants().size() );
3983 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3984 if ( _sb.length() > 0 ) {
3987 _sb.append( node.getName() );
3989 if ( node.getNodeData().isHasSequence() ) {
3990 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
3991 if ( _sb.length() > 0 ) {
3994 _sb.append( node.getNodeData().getSequence().getSymbol() );
3996 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3997 if ( _sb.length() > 0 ) {
4000 _sb.append( node.getNodeData().getSequence().getName() );
4002 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4003 if ( _sb.length() > 0 ) {
4006 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4007 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4010 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4013 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
4014 if ( _sb.length() > 0 ) {
4017 _sb.append( propertiesToString( node ) );
4019 g.setFont( getTreeFontSet().getLargeFont() );
4020 if ( is_in_found_nodes ) {
4021 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4023 double down_shift_factor = 3.0;
4024 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
4025 down_shift_factor = 1;
4027 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
4028 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
4029 final String sb_str = _sb.toString();
4030 // GUILHEM_BEG ______________
4031 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
4032 && ( _query_sequence != null ) ) {
4033 int nodeTextBoundsWidth = 0;
4034 if ( sb_str.length() > 0 ) {
4035 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
4036 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
4038 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
4039 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
4040 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
4041 g.setColor( getTreeColorSet().getBackgroundColor() );
4045 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
4046 for( final SequenceRelation seqRelation : seqRelations ) {
4047 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
4048 .getRef1().isEqual( _query_sequence ) )
4049 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
4050 .getSelectedItem() );
4051 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
4052 final double linePosX = node.getXcoord() + 2 + half_box_size;
4053 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
4054 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
4056 if ( sConfidence != null ) {
4057 double confidenceX = pos_x;
4058 if ( sb_str.length() > 0 ) {
4059 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
4060 + CONFIDENCE_LEFT_MARGIN;
4062 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
4063 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
4064 .getBounds().getWidth();
4065 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
4066 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
4069 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
4071 if ( nodeTextBoundsWidth == 0 ) {
4072 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
4075 nodeTextBoundsWidth += 2;
4077 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
4078 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
4085 if ( sb_str.length() > 0 ) {
4086 TreePanel.drawString( sb_str, pos_x, pos_y, g );
4088 // GUILHEM_END _____________
4089 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
4090 // TODO FIXME need to check this one!
4091 //if ( _sb.length() > 0 ) {
4092 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
4093 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4095 // COMMENTED_OUT_BY_GUILHEM_END ________________
4096 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
4097 && ( node.getNodeData().getSequence().getAnnotations() != null )
4098 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4099 if ( _sb.length() > 0 ) {
4100 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4102 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
4103 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4104 g.setColor( Color.BLACK );
4106 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
4107 g.setColor( calculateColorForAnnotation( ann ) );
4109 final String ann_str = createAnnotationString( ann );
4110 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
4111 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4113 _sb.append( ann_str );
4115 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4116 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
4117 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
4118 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
4119 && node.getNodeData().isHasBinaryCharacters() ) {
4120 if ( _sb.length() > 0 ) {
4121 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4123 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4124 g.setColor( Color.BLACK );
4127 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
4129 if ( getControlPanel().isShowBinaryCharacters() ) {
4130 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
4131 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
4132 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4133 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
4134 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
4135 .getLostCharactersAsStringBuffer().toString() );
4138 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
4139 node.getXcoord() + x + 4 + half_box_size,
4141 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
4143 paintGainedAndLostCharacters( g, node, "+"
4144 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
4145 + node.getNodeData().getBinaryCharacters().getLostCount() );
4151 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
4152 final PhylogenyNode node,
4153 final boolean to_pdf,
4154 final boolean to_graphics_file,
4155 final boolean radial_labels,
4156 final double ur_angle,
4157 final boolean is_in_found_nodes ) {
4158 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
4161 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4162 g.setColor( Color.BLACK );
4164 else if ( is_in_found_nodes ) {
4165 g.setColor( getTreeColorSet().getFoundColor() );
4167 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4168 g.setColor( getTaxonomyBasedColor( node ) );
4170 else if ( getControlPanel().isColorAccordingToAnnotation()
4171 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4172 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4173 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4176 g.setColor( getTreeColorSet().getSequenceColor() );
4180 if ( node.getNodeData().isHasTaxonomy()
4181 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4182 .isShowTaxonomyCommonNames() ) ) {
4183 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4184 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4185 _sb.append( taxonomy.getTaxonomyCode() );
4188 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4189 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4190 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4191 _sb.append( taxonomy.getScientificName() );
4193 _sb.append( taxonomy.getCommonName() );
4196 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4197 _sb.append( taxonomy.getScientificName() );
4200 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4201 _sb.append( taxonomy.getCommonName() );
4205 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4206 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4207 _sb.append( taxonomy.getScientificName() );
4211 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4212 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4213 _sb.append( taxonomy.getCommonName() );
4218 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4220 _sb.append( node.getAllExternalDescendants().size() );
4223 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4224 if ( _sb.length() > 0 ) {
4227 _sb.append( node.getName() );
4229 if ( node.getNodeData().isHasSequence() ) {
4230 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4231 if ( _sb.length() > 0 ) {
4234 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4235 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4238 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4240 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4241 if ( _sb.length() > 0 ) {
4244 _sb.append( node.getNodeData().getSequence().getName() );
4247 g.setFont( getTreeFontSet().getLargeFont() );
4248 if ( is_in_found_nodes ) {
4249 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4251 if ( _sb.length() > 1 ) {
4252 final String sb_str = _sb.toString();
4254 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4255 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
4258 m = ( float ) ( ur_angle % TWO_PI );
4260 _at = g.getTransform();
4261 boolean need_to_reset = false;
4262 final float x_coord = node.getXcoord();
4263 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
4264 if ( radial_labels ) {
4265 need_to_reset = true;
4266 boolean left = false;
4267 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4271 g.rotate( m, x_coord, node.getYcoord() );
4273 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
4277 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4278 need_to_reset = true;
4279 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
4282 TreePanel.drawString( sb_str, x_coord, y_coord, g );
4283 if ( need_to_reset ) {
4284 g.setTransform( _at );
4289 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
4290 if ( node.isCollapse() ) {
4291 if ( !node.isRoot() && !node.getParent().isCollapse() ) {
4292 paintCollapsedNode( g, node, false, false, false );
4296 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4297 g.setColor( getTreeColorSet().getFoundColor() );
4298 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
4301 if ( !node.isExternal() && !node.isCollapse() ) {
4302 boolean first_child = true;
4304 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4305 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4306 final PhylogenyNode child_node = node.getChildNode( i );
4308 if ( !isUniformBranchLengthsForCladogram() ) {
4309 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4312 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4314 if ( first_child ) {
4315 first_child = false;
4316 y2 = node.getYSecondary()
4317 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
4318 .getNumberOfExternalNodes() ) );
4321 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4323 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
4324 new_x = x2 + node.getXSecondary();
4325 final float diff_y = node.getYSecondary() - y2;
4326 final float diff_x = node.getXSecondary() - new_x;
4327 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
4328 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
4330 child_node.setXSecondary( new_x );
4331 child_node.setYSecondary( y2 );
4332 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4337 final private void paintNodeRectangular( final Graphics2D g,
4338 final PhylogenyNode node,
4339 final boolean to_pdf,
4340 final boolean dynamically_hide,
4341 final int dynamic_hiding_factor,
4342 final boolean to_graphics_file ) {
4343 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
4344 if ( node.isCollapse() ) {
4345 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
4346 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4350 if ( node.isExternal() ) {
4351 ++_external_node_index;
4353 // Confidence values
4354 if ( getControlPanel().isShowConfidenceValues()
4355 && !node.isExternal()
4357 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
4358 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4359 && node.getBranchData().isHasConfidences() ) {
4360 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
4362 // Draw a line to root:
4363 if ( node.isRoot() && _phylogeny.isRooted() ) {
4364 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
4367 float new_x_min = Float.MAX_VALUE;
4368 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
4369 float min_dist = 1.5f;
4370 if ( !disallow_shortcutting ) {
4371 // System.out.println( dynamic_hiding_factor );
4372 if ( dynamic_hiding_factor > 4000 ) {
4375 else if ( dynamic_hiding_factor > 1000 ) {
4378 else if ( dynamic_hiding_factor > 100 ) {
4382 if ( !node.isExternal() && !node.isCollapse() ) {
4383 boolean first_child = true;
4385 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4386 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4387 final PhylogenyNode child_node = node.getChildNode( i );
4389 if ( !isUniformBranchLengthsForCladogram() ) {
4390 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4393 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4395 if ( first_child ) {
4396 first_child = false;
4397 y2 = node.getYcoord()
4398 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
4401 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4403 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
4404 new_x = x2 + node.getXcoord();
4405 if ( dynamically_hide && ( x2 < new_x_min ) ) {
4408 final float diff_y = node.getYcoord() - y2;
4409 final float diff_x = node.getXcoord() - new_x;
4410 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
4411 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
4412 paintBranchRectangular( g,
4421 child_node.setXcoord( new_x );
4422 child_node.setYcoord( y2 );
4423 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4425 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
4426 || isInCurrentExternalNodes( node ) );
4428 if ( dynamically_hide
4429 && !is_in_found_nodes
4430 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
4431 .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
4432 .getHeight() ) ) ) ) ) {
4435 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4436 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
4439 final private void paintNodeWithRenderableData( final Graphics2D g,
4440 final PhylogenyNode node,
4441 final boolean to_graphics_file,
4442 final boolean to_pdf ) {
4443 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
4446 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
4449 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4450 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4451 RenderableDomainArchitecture rds = null;
4452 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
4454 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
4456 catch ( final ClassCastException cce ) {
4457 cce.printStackTrace();
4459 if ( rds != null ) {
4460 rds.setRenderingHeight( 6 );
4462 if ( node.getNodeData().isHasTaxonomy() ) {
4463 if ( getControlPanel().isShowTaxonomyCode()
4464 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
4465 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4469 if ( getControlPanel().isShowTaxonomyScientificNames()
4470 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
4471 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4472 .getScientificName()
4475 if ( getControlPanel().isShowTaxonomyCommonNames()
4476 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
4477 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4482 if ( node.getNodeData().isHasSequence() ) {
4483 if ( getControlPanel().isShowGeneNames()
4484 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
4485 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
4488 if ( getControlPanel().isShowGeneSymbols()
4489 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
4490 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
4493 if ( getControlPanel().isShowSequenceAcc()
4494 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4495 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
4496 .getAccession().toString()
4500 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
4501 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
4503 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
4508 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4509 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
4510 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
4511 getStatisticsForExpressionValues(),
4512 getConfiguration() );
4515 PhylogenyNode my_node = node;
4516 if ( !getControlPanel().isDrawPhylogram() ) {
4517 my_node = getPhylogeny().getFirstExternalNode();
4519 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
4520 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
4522 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
4523 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
4525 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
4531 final private void paintOvRectangle( final Graphics2D g ) {
4532 final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
4533 final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
4534 final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
4535 final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
4536 final float width = getOvMaxWidth() / w_ratio;
4537 final float height = getOvMaxHeight() / h_ratio;
4538 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
4539 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
4540 g.setColor( getTreeColorSet().getFoundColor() );
4541 getOvRectangle().setRect( x, y, width, height );
4542 final Stroke s = g.getStroke();
4543 g.setStroke( STROKE_1 );
4544 if ( ( width < 6 ) && ( height < 6 ) ) {
4545 drawRectFilled( x, y, 6, 6, g );
4546 getOvVirtualRectangle().setRect( x, y, 6, 6 );
4548 else if ( width < 6 ) {
4549 drawRectFilled( x, y, 6, height, g );
4550 getOvVirtualRectangle().setRect( x, y, 6, height );
4552 else if ( height < 6 ) {
4553 drawRectFilled( x, y, width, 6, g );
4554 getOvVirtualRectangle().setRect( x, y, width, 6 );
4557 drawRect( x, y, width, height, g );
4558 if ( isInOvRect() ) {
4559 drawRect( x + 1, y + 1, width - 2, height - 2, g );
4561 getOvVirtualRectangle().setRect( x, y, width, height );
4566 final private void paintPhylogenyLite( final Graphics2D g ) {
4569 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
4570 .getWidth() ) ) ) );
4571 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
4572 final Stroke s = g.getStroke();
4573 g.setStroke( STROKE_05 );
4574 for( final PhylogenyNode element : _nodes_in_preorder ) {
4575 paintNodeLite( g, element );
4578 paintOvRectangle( g );
4582 * Paint the root branch. (Differs from others because it will always be a
4583 * single horizontal line).
4584 * @param to_graphics_file
4586 * @return new x1 value
4588 final private void paintRootBranch( final Graphics2D g,
4591 final PhylogenyNode root,
4592 final boolean to_pdf,
4593 final boolean to_graphics_file ) {
4594 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
4595 float d = getXdistance();
4596 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
4597 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
4599 if ( d < MIN_ROOT_LENGTH ) {
4600 d = MIN_ROOT_LENGTH;
4602 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
4603 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
4606 final double w = PhylogenyMethods.getBranchWidthValue( root );
4607 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
4609 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
4612 final private void paintScale( final Graphics2D g,
4615 final boolean to_pdf,
4616 final boolean to_graphics_file ) {
4618 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
4620 final int y2 = y1 - 8;
4621 final int y3 = y1 - 4;
4622 g.setFont( getTreeFontSet().getSmallFont() );
4623 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4624 g.setColor( Color.BLACK );
4627 g.setColor( getTreeColorSet().getBranchLengthColor() );
4629 final Stroke s = g.getStroke();
4630 g.setStroke( STROKE_1 );
4631 drawLine( x1, y1, x1, y2, g );
4632 drawLine( x2, y1, x2, y2, g );
4633 drawLine( x1, y3, x2, y3, g );
4634 if ( getScaleLabel() != null ) {
4635 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
4640 final private int paintTaxonomy( final Graphics2D g,
4641 final PhylogenyNode node,
4642 final boolean is_in_found_nodes,
4643 final boolean to_pdf,
4644 final boolean to_graphics_file,
4645 final double x_shift ) {
4646 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4647 g.setFont( getTreeFontSet().getLargeItalicFont() );
4648 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4649 g.setColor( Color.BLACK );
4651 else if ( is_in_found_nodes ) {
4652 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
4653 g.setColor( getTreeColorSet().getFoundColor() );
4655 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4656 g.setColor( getTaxonomyBasedColor( node ) );
4658 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4659 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4660 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4662 else if ( to_pdf ) {
4663 g.setColor( Color.BLACK );
4666 g.setColor( getTreeColorSet().getTaxonomyColor() );
4668 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4669 final double start_y = node.getYcoord()
4670 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4672 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4673 _sb.append( taxonomy.getTaxonomyCode() );
4676 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4677 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4678 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4679 if ( getOptions().isAbbreviateScientificTaxonNames()
4680 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4681 abbreviateScientificName( taxonomy.getScientificName() );
4684 _sb.append( taxonomy.getScientificName() );
4687 _sb.append( taxonomy.getCommonName() );
4690 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4691 if ( getOptions().isAbbreviateScientificTaxonNames()
4692 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4693 abbreviateScientificName( taxonomy.getScientificName() );
4696 _sb.append( taxonomy.getScientificName() );
4700 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4701 _sb.append( taxonomy.getCommonName() );
4705 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4706 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4707 if ( getOptions().isAbbreviateScientificTaxonNames()
4708 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4709 abbreviateScientificName( taxonomy.getScientificName() );
4712 _sb.append( taxonomy.getScientificName() );
4717 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4718 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4719 _sb.append( taxonomy.getCommonName() );
4723 final String label = _sb.toString();
4725 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4726 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4727 // invert font color and background color to show that this is the query sequence
4728 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4732 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4733 g.setColor( getTreeColorSet().getBackgroundColor() );
4736 TreePanel.drawString( label, start_x, start_y, g );
4737 if ( is_in_found_nodes ) {
4738 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4741 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4745 final private void paintUnrooted( final PhylogenyNode n,
4746 final double low_angle,
4747 final double high_angle,
4748 final boolean radial_labels,
4750 final boolean to_pdf,
4751 final boolean to_graphics_file ) {
4753 n.setXcoord( getWidth() / 2 );
4754 n.setYcoord( getHeight() / 2 );
4756 if ( n.isExternal() ) {
4757 paintNodeDataUnrootedCirc( g,
4762 ( high_angle + low_angle ) / 2,
4763 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
4766 final float num_enclosed = n.getNumberOfExternalNodes();
4767 final float x = n.getXcoord();
4768 final float y = n.getYcoord();
4769 double current_angle = low_angle;
4770 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4771 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4772 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4773 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4774 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4775 final PhylogenyNode desc = n.getChildNode( i );
4776 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4777 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4778 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4779 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4782 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4785 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4788 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4789 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4791 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4792 if ( desc.getDistanceToParent() < 0 ) {
4796 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4800 length = getUrtFactor();
4802 final double mid_angle = current_angle + ( arc_size / 2 );
4803 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4804 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4805 desc.setXcoord( new_x );
4806 desc.setYcoord( new_y );
4807 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4808 current_angle += arc_size;
4809 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4810 drawLine( x, y, new_x, new_y, g );
4811 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc )
4812 || isInCurrentExternalNodes( desc ) );
4815 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
4819 final private void paintUnrootedLite( final PhylogenyNode n,
4820 final double low_angle,
4821 final double high_angle,
4823 final float urt_ov_factor ) {
4825 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
4826 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
4827 n.setXSecondary( x_pos );
4828 n.setYSecondary( y_pos );
4830 if ( n.isExternal() ) {
4833 final float num_enclosed = n.getNumberOfExternalNodes();
4834 final float x = n.getXSecondary();
4835 final float y = n.getYSecondary();
4836 double current_angle = low_angle;
4837 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4838 final PhylogenyNode desc = n.getChildNode( i );
4839 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4840 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4842 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4843 if ( desc.getDistanceToParent() < 0 ) {
4847 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
4851 length = urt_ov_factor;
4853 final double mid_angle = current_angle + ( arc_size / 2 );
4854 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4855 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4856 desc.setXSecondary( new_x );
4857 desc.setYSecondary( new_y );
4858 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
4859 g.setColor( getTreeColorSet().getFoundColor() );
4860 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
4861 g.setColor( getTreeColorSet().getOvColor() );
4863 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4864 current_angle += arc_size;
4865 drawLine( x, y, new_x, new_y, g );
4869 final private void pasteSubtree( final PhylogenyNode node ) {
4870 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4871 errorMessageNoCutCopyPasteInUnrootedDisplay();
4874 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
4875 JOptionPane.showMessageDialog( this,
4876 "No tree in buffer (need to copy or cut a subtree first)",
4877 "Attempt to paste with empty buffer",
4878 JOptionPane.ERROR_MESSAGE );
4881 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
4882 final Object[] options = { "As sibling", "As descendant", "Cancel" };
4883 final int r = JOptionPane.showOptionDialog( this,
4884 "How to paste subtree" + label + "?",
4886 JOptionPane.CLOSED_OPTION,
4887 JOptionPane.QUESTION_MESSAGE,
4891 boolean paste_as_sibling = true;
4893 paste_as_sibling = false;
4895 else if ( r != 0 ) {
4898 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
4899 buffer_phy.setAllNodesToNotCollapse();
4900 PhylogenyMethods.preOrderReId( buffer_phy );
4901 buffer_phy.setRooted( true );
4902 boolean need_to_show_whole = false;
4903 if ( paste_as_sibling ) {
4904 if ( node.isRoot() ) {
4905 JOptionPane.showMessageDialog( this,
4906 "Cannot paste sibling to root",
4907 "Attempt to paste sibling to root",
4908 JOptionPane.ERROR_MESSAGE );
4911 buffer_phy.addAsSibling( node );
4914 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
4915 need_to_show_whole = true;
4916 _phylogeny = buffer_phy;
4919 buffer_phy.addAsChild( node );
4922 if ( getCopiedAndPastedNodes() == null ) {
4923 setCopiedAndPastedNodes( new HashSet<Long>() );
4925 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
4926 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
4927 for( final PhylogenyNode n : nodes ) {
4928 node_ids.add( n.getId() );
4930 node_ids.add( node.getId() );
4931 getCopiedAndPastedNodes().addAll( node_ids );
4932 setNodeInPreorderToNull();
4933 _phylogeny.externalNodesHaveChanged();
4934 _phylogeny.clearHashIdToNodeMap();
4935 _phylogeny.recalculateNumberOfExternalDescendants( true );
4936 resetNodeIdToDistToLeafMap();
4938 if ( need_to_show_whole ) {
4939 getControlPanel().showWhole();
4944 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
4945 final PropertiesMap properties = node.getNodeData().getProperties();
4946 final StringBuffer sb = new StringBuffer();
4947 boolean first = true;
4948 for( final String ref : properties.getPropertyRefs() ) {
4955 final Property p = properties.getProperty( ref );
4956 sb.append( getPartAfterColon( p.getRef() ) );
4958 sb.append( p.getValue() );
4959 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
4960 sb.append( getPartAfterColon( p.getUnit() ) );
4966 final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
4967 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4970 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4971 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4974 final private void setInOv( final boolean in_ov ) {
4978 final private void setOvMaxHeight( final float ov_max_height ) {
4979 _ov_max_height = ov_max_height;
4982 final private void setOvMaxWidth( final float ov_max_width ) {
4983 _ov_max_width = ov_max_width;
4986 final private void setOvXcorrectionFactor( final float f ) {
4987 _ov_x_correction_factor = f;
4990 final private void setOvXDistance( final float ov_x_distance ) {
4991 _ov_x_distance = ov_x_distance;
4994 final private void setOvXPosition( final int ov_x_position ) {
4995 _ov_x_position = ov_x_position;
4998 final private void setOvYDistance( final float ov_y_distance ) {
4999 _ov_y_distance = ov_y_distance;
5002 final private void setOvYPosition( final int ov_y_position ) {
5003 _ov_y_position = ov_y_position;
5006 final private void setOvYStart( final int ov_y_start ) {
5007 _ov_y_start = ov_y_start;
5010 final private void setScaleDistance( final double scale_distance ) {
5011 _scale_distance = scale_distance;
5014 final private void setScaleLabel( final String scale_label ) {
5015 _scale_label = scale_label;
5018 private final void setupStroke( final Graphics2D g ) {
5019 if ( getYdistance() < 0.001 ) {
5020 g.setStroke( STROKE_005 );
5022 else if ( getYdistance() < 0.01 ) {
5023 g.setStroke( STROKE_01 );
5025 else if ( getYdistance() < 0.5 ) {
5026 g.setStroke( STROKE_025 );
5028 else if ( getYdistance() < 1 ) {
5029 g.setStroke( STROKE_05 );
5031 else if ( getYdistance() < 2 ) {
5032 g.setStroke( STROKE_075 );
5034 else if ( getYdistance() < 20 ) {
5035 g.setStroke( STROKE_1 );
5038 g.setStroke( STROKE_2 );
5042 final private void setUpUrtFactor() {
5043 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
5044 : getVisibleRect().height;
5045 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
5046 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
5049 final int max_depth = _circ_max_depth;
5050 if ( max_depth > 0 ) {
5051 setUrtFactor( d / ( 2 * max_depth ) );
5054 setUrtFactor( d / 2 );
5057 setUrtFactorOv( getUrtFactor() );
5060 final private void setUrtFactor( final float urt_factor ) {
5061 _urt_factor = urt_factor;
5064 final private void setUrtFactorOv( final float urt_factor_ov ) {
5065 _urt_factor_ov = urt_factor_ov;
5068 private void showExtDescNodeData( final PhylogenyNode node ) {
5069 final List<String> data = new ArrayList<String>();
5070 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
5071 switch ( getOptions().getExtDescNodeDataToReturn() ) {
5073 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
5074 data.add( n.getName() );
5078 if ( n.getNodeData().isHasSequence()
5079 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5080 data.add( n.getNodeData().getSequence().getName() );
5083 case SEQUENCE_SYMBOL:
5084 if ( n.getNodeData().isHasSequence()
5085 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5086 data.add( n.getNodeData().getSequence().getSymbol() );
5089 case SEQUENCE_MOL_SEQ:
5090 if ( n.getNodeData().isHasSequence()
5091 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5092 data.add( n.getNodeData().getSequence().getMolecularSequence() );
5095 case SEQUENCE_MOL_SEQ_FASTA:
5096 final StringBuilder sb = new StringBuilder();
5097 if ( n.getNodeData().isHasSequence()
5098 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5099 if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5100 sb.append( SequenceWriter.toFasta( n.getNodeData().getSequence().getName(), n.getNodeData()
5101 .getSequence().getMolecularSequence(), 60 ) );
5104 sb.append( SequenceWriter.toFasta( n.getName(), n.getNodeData().getSequence()
5105 .getMolecularSequence(), 60 ) );
5107 data.add( sb.toString() );
5111 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
5112 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
5113 data.add( n.getNodeData().getSequence().getAccession().toString() );
5116 case TAXONOMY_SCIENTIFIC_NAME:
5117 if ( n.getNodeData().isHasTaxonomy()
5118 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5119 data.add( n.getNodeData().getTaxonomy().getScientificName() );
5123 if ( n.getNodeData().isHasTaxonomy()
5124 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5125 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5129 AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
5132 throw new IllegalArgumentException( "unknown data element: "
5133 + getOptions().getExtDescNodeDataToReturn() );
5136 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
5137 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
5138 final StringBuilder sb = new StringBuilder();
5139 for( final String d : data ) {
5140 if ( !ForesterUtil.isEmpty( d ) ) {
5141 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
5142 System.out.println( d );
5145 sb.append( ForesterUtil.LINE_SEPARATOR );
5148 if ( sb.length() < 1 ) {
5149 clearCurrentExternalNodesDataBuffer();
5152 setCurrentExternalNodesDataBuffer( sb );
5155 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
5156 final StringBuilder sb = new StringBuilder();
5157 for( final String d : data ) {
5158 if ( !ForesterUtil.isEmpty( d ) ) {
5160 sb.append( ForesterUtil.LINE_SEPARATOR );
5163 if ( sb.length() < 1 ) {
5164 AptxUtil.showInformationMessage( this,
5165 "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
5166 "Descendants of selected node do not contain selected data" );
5167 clearCurrentExternalNodesDataBuffer();
5170 setCurrentExternalNodesDataBuffer( sb );
5171 final String title = "External Descendants "
5172 + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5173 : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
5174 + node.getNumberOfExternalNodes() + ") For Node " + node;
5175 final String s = sb.toString().trim();
5176 if ( getMainPanel().getMainFrame() == null ) {
5177 // Must be "E" applet version.
5178 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
5179 ae.showTextFrame( s, title );
5182 getMainPanel().getMainFrame().showTextFrame( s, title );
5188 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
5190 if ( ( node.getName().length() > 0 )
5191 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
5192 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
5193 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
5194 || node.getBranchData().isHasConfidences() ) {
5195 _popup_buffer.setLength( 0 );
5197 if ( node.getName().length() > 0 ) {
5199 _popup_buffer.append( node.getName() );
5201 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
5203 boolean enc_data = false;
5204 final Taxonomy tax = node.getNodeData().getTaxonomy();
5205 if ( _popup_buffer.length() > 0 ) {
5206 _popup_buffer.append( "\n" );
5208 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
5209 _popup_buffer.append( "[" );
5210 _popup_buffer.append( tax.getTaxonomyCode() );
5211 _popup_buffer.append( "]" );
5214 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
5216 _popup_buffer.append( " " );
5218 _popup_buffer.append( tax.getScientificName() );
5221 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
5223 _popup_buffer.append( " (" );
5226 _popup_buffer.append( "(" );
5228 _popup_buffer.append( tax.getCommonName() );
5229 _popup_buffer.append( ")" );
5232 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
5234 _popup_buffer.append( " (" );
5237 _popup_buffer.append( "(" );
5239 _popup_buffer.append( tax.getAuthority() );
5240 _popup_buffer.append( ")" );
5243 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
5245 _popup_buffer.append( " [" );
5248 _popup_buffer.append( "[" );
5250 _popup_buffer.append( tax.getRank() );
5251 _popup_buffer.append( "]" );
5254 if ( tax.getSynonyms().size() > 0 ) {
5256 _popup_buffer.append( " " );
5258 _popup_buffer.append( "[" );
5260 for( final String syn : tax.getSynonyms() ) {
5261 if ( !ForesterUtil.isEmpty( syn ) ) {
5263 _popup_buffer.append( syn );
5264 if ( counter < tax.getSynonyms().size() ) {
5265 _popup_buffer.append( ", " );
5270 _popup_buffer.append( "]" );
5273 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
5274 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
5275 _popup_buffer.append( "[" );
5276 _popup_buffer.append( tax.getIdentifier().getProvider() );
5277 _popup_buffer.append( "] " );
5279 _popup_buffer.append( tax.getIdentifier().getValue() );
5283 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
5285 boolean enc_data = false;
5286 if ( _popup_buffer.length() > 0 ) {
5287 _popup_buffer.append( "\n" );
5289 final Sequence seq = node.getNodeData().getSequence();
5290 if ( seq.getAccession() != null ) {
5291 _popup_buffer.append( "[" );
5292 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
5293 _popup_buffer.append( seq.getAccession().getSource() );
5294 _popup_buffer.append( ":" );
5296 _popup_buffer.append( seq.getAccession().getValue() );
5297 _popup_buffer.append( "]" );
5300 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
5302 _popup_buffer.append( " [" );
5305 _popup_buffer.append( "[" );
5307 _popup_buffer.append( seq.getSymbol() );
5308 _popup_buffer.append( "]" );
5311 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
5313 _popup_buffer.append( " " );
5315 _popup_buffer.append( seq.getName() );
5318 if ( node.getNodeData().isHasDate() ) {
5320 if ( _popup_buffer.length() > 0 ) {
5321 _popup_buffer.append( "\n" );
5323 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
5325 if ( node.getNodeData().isHasDistribution() ) {
5327 if ( _popup_buffer.length() > 0 ) {
5328 _popup_buffer.append( "\n" );
5330 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
5332 if ( node.getBranchData().isHasConfidences() ) {
5333 final List<Confidence> confs = node.getBranchData().getConfidences();
5334 for( final Confidence confidence : confs ) {
5336 if ( _popup_buffer.length() > 0 ) {
5337 _popup_buffer.append( "\n" );
5339 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
5340 _popup_buffer.append( "[" );
5341 _popup_buffer.append( confidence.getType() );
5342 _popup_buffer.append( "] " );
5345 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
5347 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5348 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5349 _popup_buffer.append( " (sd=" );
5350 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
5351 .getStandardDeviation(), getOptions()
5352 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5353 _popup_buffer.append( ")" );
5357 if ( node.getNodeData().isHasProperties() ) {
5358 final PropertiesMap properties = node.getNodeData().getProperties();
5359 for( final String ref : properties.getPropertyRefs() ) {
5360 _popup_buffer.append( "\n" );
5361 final Property p = properties.getProperty( ref );
5362 _popup_buffer.append( getPartAfterColon( p.getRef() ) );
5363 _popup_buffer.append( "=" );
5364 _popup_buffer.append( p.getValue() );
5365 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5366 _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
5370 if ( _popup_buffer.length() > 0 ) {
5371 if ( !getConfiguration().isUseNativeUI() ) {
5373 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
5374 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
5375 if ( isInFoundNodes( node ) ) {
5376 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
5378 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
5379 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
5382 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
5386 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
5388 _rollover_popup.setText( _popup_buffer.toString() );
5389 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
5391 e.getLocationOnScreen().x + 10,
5392 e.getLocationOnScreen().y
5394 _node_desc_popup.show();
5398 catch ( final Exception ex ) {
5403 final private void showNodeEditFrame( final PhylogenyNode n ) {
5404 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5405 // pop up edit box for single node
5406 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
5407 _node_frame_index++;
5410 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5414 final private void showNodeFrame( final PhylogenyNode n ) {
5415 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5416 // pop up edit box for single node
5417 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
5418 _node_frame_index++;
5421 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5425 final private void switchDisplaygetPhylogenyGraphicsType() {
5426 switch ( getPhylogenyGraphicsType() ) {
5428 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5429 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5432 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5433 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5436 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5437 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5440 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5441 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5444 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5445 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5448 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5449 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5452 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5453 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5456 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5457 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5460 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5462 if ( getControlPanel().getDynamicallyHideData() != null ) {
5463 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5464 getControlPanel().getDynamicallyHideData().setEnabled( false );
5467 getControlPanel().getDynamicallyHideData().setEnabled( true );
5470 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5471 getControlPanel().setDrawPhylogramEnabled( true );
5474 getControlPanel().setDrawPhylogramEnabled( false );
5476 if ( getMainPanel().getMainFrame() == null ) {
5477 // Must be "E" applet version.
5478 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5479 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5482 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5486 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
5487 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5490 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5491 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5494 final private static String getPartAfterColon( final String s ) {
5495 final int i = s.indexOf( ':' );
5496 if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
5499 return s.substring( i + 1, s.length() );
5502 final private static boolean isSequenceEmpty( final Sequence seq ) {
5503 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
5504 && ForesterUtil.isEmpty( seq.getSymbol() );
5507 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
5508 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
5509 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
5510 .getSynonyms().isEmpty() );
5513 final private static boolean plusPressed( final int key_code ) {
5514 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5515 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5518 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
5519 final Phylogeny new_phy = new Phylogeny();
5520 new_phy.setRooted( true );
5521 new_phy.setName( source_phy.getName() );
5522 new_phy.setDescription( source_phy.getDescription() );
5523 new_phy.setType( source_phy.getType() );
5524 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
5525 new_phy.setConfidence( source_phy.getConfidence() );
5526 new_phy.setIdentifier( source_phy.getIdentifier() );
5527 new_phy.setRoot( new_root.copyNodeDataShallow() );
5529 for( final PhylogenyNode n : new_root.getDescendants() ) {
5530 new_phy.getRoot().setChildNode( i++, n );
5535 final private class SubtreeColorizationActionListener implements ActionListener {
5537 JColorChooser _chooser;
5538 PhylogenyNode _node;
5540 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5546 public void actionPerformed( final ActionEvent e ) {
5547 final Color c = _chooser.getColor();
5549 colorizeSubtree( c, _node );