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
27 package org.forester.archaeopteryx;
29 import java.awt.BasicStroke;
30 import java.awt.Color;
31 import java.awt.Cursor;
32 import java.awt.Dimension;
34 import java.awt.GradientPaint;
35 import java.awt.Graphics;
36 import java.awt.Graphics2D;
37 import java.awt.Point;
38 import java.awt.Polygon;
39 import java.awt.Rectangle;
40 import java.awt.RenderingHints;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.awt.event.FocusAdapter;
44 import java.awt.event.FocusEvent;
45 import java.awt.event.InputEvent;
46 import java.awt.event.KeyAdapter;
47 import java.awt.event.KeyEvent;
48 import java.awt.event.MouseEvent;
49 import java.awt.event.MouseWheelEvent;
50 import java.awt.event.MouseWheelListener;
51 import java.awt.font.FontRenderContext;
52 import java.awt.font.TextLayout;
53 import java.awt.geom.AffineTransform;
54 import java.awt.geom.Arc2D;
55 import java.awt.geom.CubicCurve2D;
56 import java.awt.geom.Ellipse2D;
57 import java.awt.geom.Line2D;
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.phylogeny.Phylogeny;
105 import org.forester.phylogeny.PhylogenyMethods;
106 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
107 import org.forester.phylogeny.PhylogenyNode;
108 import org.forester.phylogeny.data.Annotation;
109 import org.forester.phylogeny.data.BranchColor;
110 import org.forester.phylogeny.data.Confidence;
111 import org.forester.phylogeny.data.Event;
112 import org.forester.phylogeny.data.NodeData.NODE_DATA;
113 import org.forester.phylogeny.data.NodeVisualization;
114 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
115 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
116 import org.forester.phylogeny.data.PhylogenyDataUtil;
117 import org.forester.phylogeny.data.PropertiesMap;
118 import org.forester.phylogeny.data.Property;
119 import org.forester.phylogeny.data.Sequence;
120 import org.forester.phylogeny.data.SequenceRelation;
121 import org.forester.phylogeny.data.Taxonomy;
122 import org.forester.phylogeny.data.Uri;
123 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
124 import org.forester.phylogeny.iterators.PreorderTreeIterator;
125 import org.forester.util.BasicDescriptiveStatistics;
126 import org.forester.util.DescriptiveStatistics;
127 import org.forester.util.ForesterConstants;
128 import org.forester.util.ForesterUtil;
129 import org.forester.util.SequenceIdParser;
131 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
133 private static final float PI = ( float ) ( Math.PI );
134 private static final double TWO_PI = 2 * Math.PI;
135 private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
136 private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
137 private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
138 private static final short OV_BORDER = 10;
139 final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
140 final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
141 final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
142 final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
143 final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
144 private final static long serialVersionUID = -978349745916505029L;
145 private final static int EURO_D = 10;
146 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
147 private final static int MIN_ROOT_LENGTH = 3;
148 private final static int MAX_SUBTREES = 100;
149 private final static int MAX_NODE_FRAMES = 10;
150 private final static int MOVE = 20;
151 private final static NumberFormat FORMATTER_CONFIDENCE;
152 private final static NumberFormat FORMATTER_BRANCH_LENGTH;
153 private final static int WIGGLE = 2;
154 private final static int LIMIT_FOR_HQ_RENDERING = 1000;
155 private final static int CONFIDENCE_LEFT_MARGIN = 4;
156 private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
157 RenderingHints.VALUE_RENDER_DEFAULT );
158 private File _treefile = null;
159 private Configuration _configuration = null;
160 private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
161 private int _node_frame_index = 0;
162 private Phylogeny _phylogeny = null;
163 private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
164 private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
165 private int _subtree_index = 0;
166 private MainPanel _main_panel = null;
167 private Set<Integer> _found_nodes = null;
168 private PhylogenyNode _highlight_node = null;
169 private JPopupMenu _node_popup_menu = null;
170 private JMenuItem _node_popup_menu_items[] = null;
171 private int _longest_ext_node_info = 0;
172 private float _x_correction_factor = 0.0f;
173 private float _ov_x_correction_factor = 0.0f;
174 private float _x_distance = 0.0f;
175 private float _y_distance = 0.0f;
176 private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
177 private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
178 private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
179 private float _last_drag_point_x = 0;
180 private float _last_drag_point_y = 0;
181 private ControlPanel _control_panel = null;
182 private int _external_node_index = 0;
183 private final Polygon _polygon = new Polygon();
184 private final StringBuilder _sb = new StringBuilder();
185 private JColorChooser _color_chooser = null;
186 private double _scale_distance = 0.0;
187 private String _scale_label = null;
188 private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
189 private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
190 private final Line2D _line = new Line2D.Float();
191 private final Ellipse2D _ellipse = new Ellipse2D.Float();
192 private final Rectangle2D _rectangle = new Rectangle2D.Float();
193 private Options _options = null;
194 private float _ov_max_width = 0;
195 private float _ov_max_height = 0;
196 private int _ov_x_position = 0;
197 private int _ov_y_position = 0;
198 private int _ov_y_start = 0;
199 private float _ov_y_distance = 0;
200 private float _ov_x_distance = 0;
201 private boolean _ov_on = false;
202 private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
203 private float _urt_factor = 1;
204 private float _urt_factor_ov = 1;
205 private final boolean _phy_has_branch_lengths;
206 private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
207 private boolean _in_ov_rect = false;
208 private boolean _in_ov = false;
209 private final Rectangle _ov_virtual_rectangle = new Rectangle();
210 final private static double _180_OVER_PI = 180.0 / Math.PI;
211 private static final float ROUNDED_D = 8;
212 private int _circ_max_depth;
213 private PhylogenyNode _root;
214 final private Arc2D _arc = new Arc2D.Double();
215 final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
216 final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
217 final private Set<Integer> _collapsed_external_nodeid_set = new HashSet<Integer>();
218 HashMap<Integer, Short> _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
219 private AffineTransform _at;
220 private double _max_distance_to_root = -1;
221 private int _dynamic_hiding_factor = 0;
222 private boolean _edited = false;
223 private Popup _node_desc_popup;
224 private JTextArea _rollover_popup;
225 private final StringBuffer _popup_buffer = new StringBuffer();
226 final private static Font POPUP_FONT = new Font( Configuration
227 .getDefaultFontFamilyName(),
230 private Sequence _query_sequence = null;
231 private final FontRenderContext _frc = new FontRenderContext( null,
234 // expression values menu:
235 private DescriptiveStatistics _statistics_for_vector_data;
236 private PhylogenyNode[] _nodes_in_preorder = null;
237 private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
238 private int _current_external_nodes_data_buffer_change_counter = 0;
239 private Set<Integer> _current_external_nodes = null;
240 // private Image offscreenImage;
241 // private Graphics offscreenGraphics;
242 // private Dimension offscreenDimension;
244 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
245 dfs.setDecimalSeparator( '.' );
246 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
247 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
250 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
251 requestFocusInWindow();
252 addKeyListener( new KeyAdapter() {
255 public void keyPressed( final KeyEvent key_event ) {
256 keyPressedCalls( key_event );
257 requestFocusInWindow();
260 addFocusListener( new FocusAdapter() {
263 public void focusGained( final FocusEvent e ) {
264 requestFocusInWindow();
267 if ( ( t == null ) || t.isEmpty() ) {
268 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
270 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
272 _configuration = configuration;
274 _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
276 // if ( !_phylogeny.isEmpty() ) {
277 _phylogeny.recalculateNumberOfExternalDescendants( true );
278 checkForVectorProperties( _phylogeny );
280 setBackground( getTreeColorSet().getBackgroundColor() );
281 final MouseListener mouse_listener = new MouseListener( this );
282 addMouseListener( mouse_listener );
283 addMouseMotionListener( mouse_listener );
284 addMouseWheelListener( this );
285 calculateScaleDistance();
286 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
287 FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
288 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
292 final public void actionPerformed( final ActionEvent e ) {
293 boolean done = false;
294 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
295 for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
296 // NOTE: index corresponds to the indices of click-to options
297 // in the control panel.
298 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
299 // Set this as the new default click-to action
300 _main_panel.getControlPanel().setClickToAction( index );
301 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
302 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
303 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
308 requestFocusInWindow();
311 public void checkForVectorProperties( final Phylogeny phy ) {
312 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
313 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
314 final PhylogenyNode node = iter.next();
315 if ( node.getNodeData().getProperties() != null ) {
316 final PropertiesMap pm = node.getNodeData().getProperties();
317 final double[] vector = new double[ pm.getProperties().size() ];
319 for( final String ref : pm.getProperties().keySet() ) {
320 if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
321 final Property p = pm.getProperty( ref );
322 final String value_str = p.getValue();
323 final String index_str = ref
324 .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
327 d = Double.parseDouble( value_str );
329 catch ( final NumberFormatException e ) {
330 JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
331 + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
336 i = Integer.parseInt( index_str );
338 catch ( final NumberFormatException e ) {
339 JOptionPane.showMessageDialog( this,
340 "Could not parse \"" + index_str
341 + "\" into index for vector data",
342 "Problem with Vector Data",
343 JOptionPane.ERROR_MESSAGE );
347 JOptionPane.showMessageDialog( this,
348 "Attempt to use negative index for vector data",
349 "Problem with Vector Data",
350 JOptionPane.ERROR_MESSAGE );
358 final List<Double> vector_l = new ArrayList<Double>( counter );
359 for( int i = 0; i < counter; ++i ) {
360 vector_l.add( vector[ i ] );
362 node.getNodeData().setVector( vector_l );
365 if ( stats.getN() > 0 ) {
366 _statistics_for_vector_data = stats;
370 public synchronized Hashtable<String, BufferedImage> getImageMap() {
371 return getMainPanel().getImageMap();
374 final public MainPanel getMainPanel() {
379 * Get a pointer to the phylogeny
381 * @return a pointer to the phylogeny
383 public final Phylogeny getPhylogeny() {
388 final public void mouseWheelMoved( final MouseWheelEvent e ) {
389 final int notches = e.getWheelRotation();
390 if ( inOvVirtualRectangle( e ) ) {
391 if ( !isInOvRect() ) {
397 if ( isInOvRect() ) {
398 setInOvRect( false );
402 if ( e.isControlDown() ) {
404 getTreeFontSet().increaseFontSize();
405 getControlPanel().displayedPhylogenyMightHaveChanged( true );
408 getTreeFontSet().decreaseFontSize();
409 getControlPanel().displayedPhylogenyMightHaveChanged( true );
412 else if ( e.isShiftDown() ) {
413 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
414 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
416 for( int i = 0; i < ( -notches ); ++i ) {
417 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
418 getControlPanel().displayedPhylogenyMightHaveChanged( false );
422 for( int i = 0; i < notches; ++i ) {
423 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
424 if ( getStartingAngle() < 0 ) {
425 setStartingAngle( TWO_PI + getStartingAngle() );
427 getControlPanel().displayedPhylogenyMightHaveChanged( false );
433 for( int i = 0; i < ( -notches ); ++i ) {
434 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
435 getControlPanel().displayedPhylogenyMightHaveChanged( false );
439 for( int i = 0; i < notches; ++i ) {
440 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
441 getControlPanel().displayedPhylogenyMightHaveChanged( false );
448 for( int i = 0; i < ( -notches ); ++i ) {
449 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
450 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
451 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
452 getControlPanel().displayedPhylogenyMightHaveChanged( false );
456 for( int i = 0; i < notches; ++i ) {
457 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
458 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
459 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
460 getControlPanel().displayedPhylogenyMightHaveChanged( false );
465 requestFocusInWindow();
470 final public void paintComponent( final Graphics g ) {
471 // Dimension currentSize = getSize();
472 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
473 // call the 'java.awt.Component.createImage(...)' method to get an
475 // offscreenImage = createImage( currentSize.width, currentSize.height );
476 // offscreenGraphics = offscreenImage.getGraphics();
477 // offscreenDimension = currentSize;
479 // super.paintComponent( g ); //why?
480 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
481 final Graphics2D g2d = ( Graphics2D ) g;
482 g2d.setRenderingHints( _rendering_hints );
483 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
484 //g.drawImage( offscreenImage, 0, 0, this );
488 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
489 throws PrinterException {
490 if ( page_index > 0 ) {
491 return ( NO_SUCH_PAGE );
494 final Graphics2D g2d = ( Graphics2D ) g;
495 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
496 // Turn off double buffering !?
497 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
498 // Turn double buffering back on !?
499 return ( PAGE_EXISTS );
503 public final void setArrowCursor() {
504 setCursor( ARROW_CURSOR );
508 public final void setEdited( final boolean edited ) {
512 public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
513 getMainPanel().setImageMap( image_map );
517 * Set parameters for printing the displayed tree
522 public final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
523 // updateStyle(); not needed?
524 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
526 if ( recalc_longest_ext_node_info ) {
527 calculateLongestExtNodeInfo();
528 while ( ( getLongestExtNodeInfo() > y / 2 ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
529 getMainPanel().getTreeFontSet().decreaseFontSize();
530 calculateLongestExtNodeInfo();
533 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
534 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
535 if ( ext_nodes == 1 ) {
536 ext_nodes = max_depth;
537 if ( ext_nodes < 1 ) {
544 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
545 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
546 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
549 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
550 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
552 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
556 if ( ov_xdist < 0.0 ) {
562 setXdistance( xdist );
563 setYdistance( ydist );
564 setOvXDistance( ov_xdist );
565 final double height = _phylogeny.getHeight();
567 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
568 setXcorrectionFactor( corr > 0 ? corr : 0 );
569 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
570 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
573 setXcorrectionFactor( 0 );
574 setOvXcorrectionFactor( 0 );
576 _circ_max_depth = max_depth;
582 * Set a phylogeny tree.
585 * an instance of a Phylogeny
587 public final void setTree( final Phylogeny t ) {
588 setNodeInPreorderToNull();
592 public final void setWaitCursor() {
593 setCursor( WAIT_CURSOR );
598 public void update( final Graphics g ) {
602 final void calcMaxDepth() {
603 if ( _phylogeny != null ) {
604 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
608 final void calculateLongestExtNodeInfo() {
609 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
612 int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
613 * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
614 if ( max_length < 40 ) {
618 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
620 if ( node.isCollapse() ) {
623 if ( getControlPanel().isShowNodeNames() ) {
624 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
626 if ( node.getNodeData().isHasSequence() ) {
627 if ( getControlPanel().isShowSequenceAcc()
628 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
629 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
633 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
634 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
636 if ( getControlPanel().isShowGeneSymbols()
637 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
638 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
640 if ( getControlPanel().isShowAnnotation()
641 && ( node.getNodeData().getSequence().getAnnotations() != null )
642 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
643 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
647 if ( getControlPanel().isShowDomainArchitectures()
648 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
649 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
650 .getRenderingSize().getWidth();
653 if ( node.getNodeData().isHasTaxonomy() ) {
654 final Taxonomy tax = node.getNodeData().getTaxonomy();
655 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
656 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
658 if ( getControlPanel().isShowTaxonomyScientificNames()
659 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
660 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
662 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
663 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
666 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
667 sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
669 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
670 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
671 .getGainedCharactersAsStringBuffer().toString() );
673 if ( sum >= max_length ) {
674 setLongestExtNodeInfo( max_length );
677 if ( sum > longest ) {
681 if ( longest >= max_length ) {
682 setLongestExtNodeInfo( max_length );
685 setLongestExtNodeInfo( longest );
689 final void calculateScaleDistance() {
690 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
693 final double height = getMaxDistanceToRoot();
695 if ( ( height <= 0.5 ) ) {
696 setScaleDistance( 0.01 );
698 else if ( height <= 5.0 ) {
699 setScaleDistance( 0.1 );
701 else if ( height <= 50.0 ) {
702 setScaleDistance( 1 );
704 else if ( height <= 500.0 ) {
705 setScaleDistance( 10 );
708 setScaleDistance( 100 );
712 setScaleDistance( 0.0 );
714 String scale_label = String.valueOf( getScaleDistance() );
715 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
716 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
718 setScaleLabel( scale_label );
721 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
722 String species = tax.getTaxonomyCode();
723 if ( ForesterUtil.isEmpty( species ) ) {
724 species = tax.getScientificName();
725 if ( ForesterUtil.isEmpty( species ) ) {
726 species = tax.getCommonName();
729 if ( ForesterUtil.isEmpty( species ) ) {
730 return getTreeColorSet().getTaxonomyColor();
732 // Look in species hash
733 Color c = getControlPanel().getSpeciesColors().get( species );
735 c = AptxUtil.calculateColorFromString( species );
736 getControlPanel().getSpeciesColors().put( species, c );
741 void clearCurrentExternalNodesDataBuffer() {
742 setCurrentExternalNodesDataBuffer( new StringBuilder() );
746 * Collapse the tree from the given node
751 final void collapse( final PhylogenyNode node ) {
752 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
753 JOptionPane.showMessageDialog( this,
754 "Cannot collapse in unrooted display type",
755 "Attempt to collapse in unrooted display",
756 JOptionPane.WARNING_MESSAGE );
759 if ( !node.isExternal() && !node.isRoot() ) {
760 final boolean collapse = !node.isCollapse();
761 AptxUtil.collapseSubtree( node, collapse );
762 updateSetOfCollapsedExternalNodes();
763 _phylogeny.recalculateNumberOfExternalDescendants( true );
764 resetNodeIdToDistToLeafMap();
765 calculateLongestExtNodeInfo();
766 setNodeInPreorderToNull();
767 _control_panel.displayedPhylogenyMightHaveChanged( true );
768 resetPreferredSize();
770 _main_panel.adjustJScrollPane();
775 final void collapseSpeciesSpecificSubtrees() {
776 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
780 AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
781 updateSetOfCollapsedExternalNodes();
782 _phylogeny.recalculateNumberOfExternalDescendants( true );
783 resetNodeIdToDistToLeafMap();
784 calculateLongestExtNodeInfo();
785 setNodeInPreorderToNull();
786 resetPreferredSize();
787 _main_panel.adjustJScrollPane();
792 final void colorRank( final String rank ) {
793 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
797 AptxUtil.removeBranchColors( _phylogeny );
798 final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
799 if ( colorizations > 0 ) {
800 _control_panel.setColorBranches( true );
801 if ( _control_panel.getColorBranchesCb() != null ) {
802 _control_panel.getColorBranchesCb().setSelected( true );
804 if ( _control_panel.getColorAccSpeciesCb() != null ) {
805 _control_panel.getColorAccSpeciesCb().setSelected( false );
807 _options.setColorLabelsSameAsParentBranch( true );
808 _control_panel.repaint();
812 if ( colorizations > 0 ) {
813 String msg = "Taxonomy colorization via " + rank + " completed:\n";
814 if ( colorizations > 1 ) {
815 msg += "colorized " + colorizations + " subtrees";
818 msg += "colorized one subtree";
820 JOptionPane.showMessageDialog( this,
822 "Taxonomy Colorization Completed (" + rank + ")",
823 JOptionPane.INFORMATION_MESSAGE );
826 String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
827 msg += "Possible solutions (given that suitable taxonomic information is present):\n";
828 msg += "select a different rank (e.g. phylum, genus, ...)\n";
831 msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
832 msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
833 JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
837 final void confColor() {
838 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
842 AptxUtil.removeBranchColors( _phylogeny );
843 AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
844 _control_panel.setColorBranches( true );
845 if ( _control_panel.getColorBranchesCb() != null ) {
846 _control_panel.getColorBranchesCb().setSelected( true );
852 final void decreaseDomainStructureEvalueThreshold() {
853 if ( _domain_structure_e_value_thr_exp > -20 ) {
854 _domain_structure_e_value_thr_exp -= 1;
859 * Find the node, if any, at the given location
863 * @return pointer to the node at x,y, null if not found
865 final PhylogenyNode findNode( final int x, final int y ) {
866 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
869 final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
870 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
871 final PhylogenyNode node = iter.next();
872 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
873 && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
874 && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
875 && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
876 && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
883 final Configuration getConfiguration() {
884 return _configuration;
887 final ControlPanel getControlPanel() {
888 return _control_panel;
891 String getCurrentExternalNodesDataBufferAsString() {
892 return _current_external_nodes_data_buffer.toString();
895 int getCurrentExternalNodesDataBufferChangeCounter() {
896 return _current_external_nodes_data_buffer_change_counter;
899 final int getDomainStructureEvalueThreshold() {
900 return _domain_structure_e_value_thr_exp;
903 final Set<Integer> getFoundNodes() {
907 final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
908 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
909 return ( PhylogenyMethods.getBranchColorValue( node ) );
912 return ( getTreeColorSet().getBranchColor() );
916 final int getLongestExtNodeInfo() {
917 return _longest_ext_node_info;
920 final Options getOptions() {
921 if ( _options == null ) {
922 _options = getControlPanel().getOptions();
927 final Rectangle2D getOvRectangle() {
928 return _ov_rectangle;
931 final Rectangle getOvVirtualRectangle() {
932 return _ov_virtual_rectangle;
935 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
936 return _graphics_type;
939 final double getStartingAngle() {
940 return _urt_starting_angle;
943 DescriptiveStatistics getStatisticsForExpressionValues() {
944 return _statistics_for_vector_data;
948 * Find a color for this species name.
951 * @return the species color
953 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
954 if ( node.getNodeData().isHasTaxonomy() ) {
955 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
957 // return non-colorized color
958 return getTreeColorSet().getTaxonomyColor();
962 * @return pointer to colorset for tree drawing
964 final TreeColorSet getTreeColorSet() {
965 return getMainPanel().getTreeColorSet();
968 final File getTreeFile() {
972 final float getXcorrectionFactor() {
973 return _x_correction_factor;
976 final float getXdistance() {
980 final float getYdistance() {
984 final void increaseDomainStructureEvalueThreshold() {
985 if ( _domain_structure_e_value_thr_exp < 3 ) {
986 _domain_structure_e_value_thr_exp += 1;
990 final void initNodeData() {
991 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
994 double max_original_domain_structure_width = 0.0;
995 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
996 if ( node.getNodeData().isHasSequence()
997 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
998 RenderableDomainArchitecture rds = null;
999 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
1000 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1001 getConfiguration() );
1002 node.getNodeData().getSequence().setDomainArchitecture( rds );
1005 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1007 if ( getControlPanel().isShowDomainArchitectures() ) {
1008 final double dsw = rds.getOriginalSize().getWidth();
1009 if ( dsw > max_original_domain_structure_width ) {
1010 max_original_domain_structure_width = dsw;
1015 if ( getControlPanel().isShowDomainArchitectures() ) {
1016 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1017 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1018 if ( node.getNodeData().isHasSequence()
1019 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1020 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1021 .getSequence().getDomainArchitecture();
1022 rds.setRenderingFactorWidth( ds_factor_width );
1023 rds.setParameter( _domain_structure_e_value_thr_exp );
1029 final boolean inOv( final MouseEvent e ) {
1030 return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
1031 && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
1032 && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
1033 + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
1036 final boolean inOvRectangle( final MouseEvent e ) {
1037 return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
1038 && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
1039 && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
1040 + getOvRectangle().getHeight() + 1 ) ) );
1043 final boolean isApplet() {
1044 return getMainPanel() instanceof MainPanelApplets;
1047 final boolean isCanCollapse() {
1048 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1051 final boolean isCanColorSubtree() {
1052 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1055 final boolean isCanCopy() {
1056 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1059 final boolean isCanCut( final PhylogenyNode node ) {
1060 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1064 final boolean isCanDelete() {
1065 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1068 final boolean isCanPaste() {
1069 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1070 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1073 final boolean isCanReroot() {
1074 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1077 final boolean isCanSubtree( final PhylogenyNode node ) {
1078 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1079 .isRoot() || ( _subtree_index > 0 ) ) );
1082 final boolean isCurrentTreeIsSubtree() {
1083 return ( _subtree_index > 0 );
1086 final boolean isEdited() {
1090 final boolean isInOvRect() {
1094 final boolean isOvOn() {
1098 final boolean isPhyHasBranchLengths() {
1099 return _phy_has_branch_lengths;
1102 final void midpointRoot() {
1103 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1106 if ( !_phylogeny.isRerootable() ) {
1107 JOptionPane.showMessageDialog( this,
1108 "This is not rerootable",
1110 JOptionPane.WARNING_MESSAGE );
1113 setNodeInPreorderToNull();
1115 PhylogenyMethods.midpointRoot( _phylogeny );
1116 resetNodeIdToDistToLeafMap();
1121 final void mouseClicked( final MouseEvent e ) {
1122 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1123 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1124 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1125 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
1127 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
1135 final double max_x = getWidth() - getVisibleRect().width;
1136 final double max_y = getHeight() - getVisibleRect().height;
1143 getMainPanel().getCurrentScrollPane().getViewport()
1144 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1145 setInOvRect( true );
1149 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1150 if ( node != null ) {
1151 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1154 _highlight_node = node;
1155 // Check if shift key is down
1156 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1157 // Yes, so add to _found_nodes
1158 if ( getFoundNodes() == null ) {
1159 setFoundNodes( new HashSet<Integer>() );
1161 getFoundNodes().add( node.getId() );
1162 // Check if control key is down
1164 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1165 // Yes, so pop-up menu
1166 displayNodePopupMenu( node, e.getX(), e.getY() );
1167 // Handle unadorned click
1170 // Check for right mouse button
1171 if ( e.getModifiers() == 4 ) {
1172 displayNodePopupMenu( node, e.getX(), e.getY() );
1175 // if not in _found_nodes, clear _found_nodes
1176 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1181 // no node was clicked
1182 _highlight_node = null;
1188 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1189 setCursor( MOVE_CURSOR );
1190 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1191 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1192 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1193 if ( scroll_position.x < 0 ) {
1194 scroll_position.x = 0;
1197 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1198 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1199 if ( scroll_position.x > max_x ) {
1200 scroll_position.x = max_x;
1203 if ( scroll_position.y < 0 ) {
1204 scroll_position.y = 0;
1207 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1208 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1209 if ( scroll_position.y > max_y ) {
1210 scroll_position.y = max_y;
1213 if ( isOvOn() || getOptions().isShowScale() ) {
1216 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1219 final void mouseDragInOvRectangle( final MouseEvent e ) {
1220 setCursor( HAND_CURSOR );
1221 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1222 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1223 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1224 double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
1225 double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
1226 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1227 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1228 if ( scroll_position.x <= 0 ) {
1229 scroll_position.x = 0;
1233 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1234 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1235 if ( scroll_position.x >= max_x ) {
1237 scroll_position.x = max_x;
1240 if ( scroll_position.y <= 0 ) {
1242 scroll_position.y = 0;
1245 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1246 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1247 if ( scroll_position.y >= max_y ) {
1249 scroll_position.y = max_y;
1253 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1254 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1255 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1258 final void mouseMoved( final MouseEvent e ) {
1259 requestFocusInWindow();
1260 if ( _current_external_nodes != null ) {
1261 _current_external_nodes = null;
1264 if ( getControlPanel().isNodeDescPopup() ) {
1265 if ( _node_desc_popup != null ) {
1266 _node_desc_popup.hide();
1267 _node_desc_popup = null;
1270 if ( getOptions().isShowOverview() && isOvOn() ) {
1271 if ( inOvVirtualRectangle( e ) ) {
1272 if ( !isInOvRect() ) {
1273 setInOvRect( true );
1278 if ( isInOvRect() ) {
1279 setInOvRect( false );
1284 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
1293 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1294 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
1295 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
1296 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
1297 addToCurrentExternalNodes( n.getId() );
1299 setCursor( HAND_CURSOR );
1302 else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
1303 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
1304 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
1305 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
1306 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
1307 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
1308 setCursor( CUT_CURSOR );
1311 setCursor( HAND_CURSOR );
1312 if ( getControlPanel().isNodeDescPopup() ) {
1313 showNodeDataPopup( e, node );
1318 setCursor( ARROW_CURSOR );
1323 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
1324 setCursor( ARROW_CURSOR );
1327 final void multiplyUrtFactor( final float f ) {
1331 final JApplet obtainApplet() {
1332 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1335 final void paintBranchCircular( final PhylogenyNode p,
1336 final PhylogenyNode c,
1338 final boolean radial_labels,
1339 final boolean to_pdf,
1340 final boolean to_graphics_file ) {
1341 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1342 final double root_x = _root.getXcoord();
1343 final double root_y = _root.getYcoord();
1344 final double dx = root_x - p.getXcoord();
1345 final double dy = root_y - p.getYcoord();
1346 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1347 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1348 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
1349 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
1350 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
1351 final double r2 = 2.0 * parent_radius;
1352 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1354 drawLine( c.getXcoord(),
1356 root_x + ( Math.cos( angle ) * parent_radius ),
1357 root_y + ( Math.sin( angle ) * parent_radius ),
1359 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c )
1360 || isInCurrentExternalNodes( c ) );
1361 if ( c.isExternal() ) {
1362 final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c );
1363 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
1364 && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
1367 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
1371 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
1372 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1373 final double root_x = _root.getXSecondary();
1374 final double root_y = _root.getYSecondary();
1375 final double dx = root_x - p.getXSecondary();
1376 final double dy = root_y - p.getYSecondary();
1377 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1378 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1379 g.setColor( getTreeColorSet().getOvColor() );
1380 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
1381 final double r2 = 2.0 * parent_radius;
1382 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1384 drawLine( c.getXSecondary(),
1386 root_x + ( Math.cos( angle ) * parent_radius ),
1387 root_y + ( Math.sin( angle ) * parent_radius ),
1389 if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
1390 g.setColor( getTreeColorSet().getFoundColor() );
1391 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
1395 final void paintCircular( final Phylogeny phy,
1396 final double starting_angle,
1401 final boolean to_pdf,
1402 final boolean to_graphics_file ) {
1403 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
1404 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
1405 _root = phy.getRoot();
1406 _root.setXcoord( center_x );
1407 _root.setYcoord( center_y );
1408 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1409 double current_angle = starting_angle;
1411 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1412 final PhylogenyNode n = it.next();
1413 if ( !n.isCollapse() ) {
1414 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1415 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1416 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1417 _urt_nodeid_index_map.put( n.getId(), i++ );
1418 current_angle += ( TWO_PI / circ_num_ext_nodes );
1422 System.out.println( "is collapse" + n.getName() );
1425 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
1426 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
1429 final void paintCircularLite( final Phylogeny phy,
1430 final double starting_angle,
1434 final Graphics2D g ) {
1435 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
1436 _root = phy.getRoot();
1437 _root.setXSecondary( center_x );
1438 _root.setYSecondary( center_y );
1439 double current_angle = starting_angle;
1440 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1441 final PhylogenyNode n = it.next();
1442 n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1443 n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1444 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1445 current_angle += ( TWO_PI / circ_num_ext_nodes );
1447 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
1450 final void paintPhylogeny( final Graphics2D g,
1451 final boolean to_pdf,
1452 final boolean to_graphics_file,
1453 final int graphics_file_width,
1454 final int graphics_file_height,
1455 final int graphics_file_x,
1456 final int graphics_file_y ) {
1457 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1460 if ( _control_panel.isShowSequenceRelations() ) {
1461 _query_sequence = _control_panel.getSelectedQuerySequence();
1463 // Color the background
1465 final Rectangle r = getVisibleRect();
1466 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
1467 g.setColor( getTreeColorSet().getBackgroundColor() );
1468 if ( !to_graphics_file ) {
1472 if ( getOptions().isPrintBlackAndWhite() ) {
1473 g.setColor( Color.WHITE );
1475 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1479 if ( !to_graphics_file ) {
1480 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
1481 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
1485 g.setPaint( new GradientPaint( graphics_file_x,
1487 getTreeColorSet().getBackgroundColor(),
1489 graphics_file_y + graphics_file_height,
1490 getTreeColorSet().getBackgroundColorGradientBottom() ) );
1491 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1494 g.setStroke( new BasicStroke( 1 ) );
1497 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
1499 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1500 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1501 _external_node_index = 0;
1502 // Position starting X of tree
1503 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
1504 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
1506 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
1507 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
1508 .getDistanceToParent() * getXcorrectionFactor() ) ) );
1511 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
1513 // Position starting Y of tree
1514 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
1515 + ( TreePanel.MOVE / 2.0f ) );
1516 final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) );
1517 if ( getControlPanel().isDynamicallyHideData() ) {
1518 if ( dynamic_hiding_factor > 1 ) {
1519 getControlPanel().setDynamicHidingIsOn( true );
1522 getControlPanel().setDynamicHidingIsOn( false );
1525 if ( _nodes_in_preorder == null ) {
1526 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
1528 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1529 _nodes_in_preorder[ i++ ] = it.next();
1532 //final PhylogenyNodeIterator it;
1533 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1534 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
1535 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1537 for( final PhylogenyNode element : _nodes_in_preorder ) {
1538 paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
1539 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1541 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
1542 if ( !( to_graphics_file || to_pdf ) ) {
1545 getVisibleRect().y + getVisibleRect().height,
1550 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1553 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1554 paintPhylogenyLite( g );
1557 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1558 if ( getControlPanel().getDynamicallyHideData() != null ) {
1559 getControlPanel().setDynamicHidingIsOn( false );
1561 final double angle = getStartingAngle();
1562 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1563 _dynamic_hiding_factor = 0;
1564 if ( getControlPanel().isDynamicallyHideData() ) {
1565 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1566 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
1568 if ( getControlPanel().getDynamicallyHideData() != null ) {
1569 if ( _dynamic_hiding_factor > 1 ) {
1570 getControlPanel().setDynamicHidingIsOn( true );
1573 getControlPanel().setDynamicHidingIsOn( false );
1576 paintUnrooted( _phylogeny.getRoot(),
1578 ( float ) ( angle + ( 2 * Math.PI ) ),
1583 if ( getOptions().isShowScale() ) {
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 g.setColor( getTreeColorSet().getOvColor() );
1597 paintUnrootedLite( _phylogeny.getRoot(),
1599 angle + ( 2 * Math.PI ),
1601 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
1602 paintOvRectangle( g );
1605 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1606 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
1607 final int d = radius + MOVE + getLongestExtNodeInfo();
1608 _dynamic_hiding_factor = 0;
1609 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
1610 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1611 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
1613 if ( getControlPanel().getDynamicallyHideData() != null ) {
1614 if ( _dynamic_hiding_factor > 1 ) {
1615 getControlPanel().setDynamicHidingIsOn( true );
1618 getControlPanel().setDynamicHidingIsOn( false );
1621 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
1622 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1623 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
1624 : getOvMaxWidth() / 2 );
1625 double x_scale = 1.0;
1626 double y_scale = 1.0;
1627 int x_pos = getVisibleRect().x + getOvXPosition();
1628 int y_pos = getVisibleRect().y + getOvYPosition();
1629 if ( getWidth() > getHeight() ) {
1630 x_scale = ( double ) getHeight() / getWidth();
1631 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
1634 y_scale = ( double ) getWidth() / getHeight();
1635 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
1637 _at = g.getTransform();
1638 g.scale( x_scale, y_scale );
1639 paintCircularLite( _phylogeny,
1643 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
1646 g.setTransform( _at );
1647 paintOvRectangle( g );
1652 final void recalculateMaxDistanceToRoot() {
1653 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
1657 * Remove all edit-node frames
1659 final void removeAllEditNodeJFrames() {
1660 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
1661 if ( _node_frames[ i ] != null ) {
1662 _node_frames[ i ].dispose();
1663 _node_frames[ i ] = null;
1666 _node_frame_index = 0;
1670 * Remove a node-edit frame.
1672 final void removeEditNodeFrame( final int i ) {
1673 _node_frame_index--;
1674 _node_frames[ i ] = null;
1675 if ( i < _node_frame_index ) {
1676 for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
1677 _node_frames[ j ] = _node_frames[ j + 1 ];
1679 _node_frames[ _node_frame_index ] = null;
1683 final void reRoot( final PhylogenyNode node ) {
1684 if ( !getPhylogeny().isRerootable() ) {
1685 JOptionPane.showMessageDialog( this,
1686 "This is not rerootable",
1688 JOptionPane.WARNING_MESSAGE );
1691 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1692 JOptionPane.showMessageDialog( this,
1693 "Cannot reroot in unrooted display type",
1694 "Attempt to reroot tree in unrooted display",
1695 JOptionPane.WARNING_MESSAGE );
1698 getPhylogeny().reRoot( node );
1699 getPhylogeny().recalculateNumberOfExternalDescendants( true );
1700 resetNodeIdToDistToLeafMap();
1701 setNodeInPreorderToNull();
1702 resetPreferredSize();
1703 getMainPanel().adjustJScrollPane();
1705 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1706 getControlPanel().showWhole();
1710 final void resetNodeIdToDistToLeafMap() {
1711 _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
1714 final void resetPreferredSize() {
1715 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
1721 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
1722 if ( getControlPanel().isDrawPhylogram() ) {
1724 + getLongestExtNodeInfo()
1726 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
1729 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
1731 + getLongestExtNodeInfo()
1732 + ForesterUtil.roundToInt( getXdistance()
1733 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
1737 + getLongestExtNodeInfo()
1738 + ForesterUtil.roundToInt( getXdistance()
1739 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
1742 setPreferredSize( new Dimension( x, y ) );
1745 final void selectNode( final PhylogenyNode node ) {
1746 if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
1747 getFoundNodes().remove( node.getId() );
1748 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1749 if ( getFoundNodes().size() < 1 ) {
1750 getControlPanel().searchReset();
1754 getControlPanel().getSearchFoundCountsLabel().setVisible( true );
1755 getControlPanel().getSearchResetButton().setEnabled( true );
1756 getControlPanel().getSearchResetButton().setVisible( true );
1757 if ( getFoundNodes() == null ) {
1758 setFoundNodes( new HashSet<Integer>() );
1760 getFoundNodes().add( node.getId() );
1761 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1765 final void setControlPanel( final ControlPanel atv_control ) {
1766 _control_panel = atv_control;
1769 void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
1770 increaseCurrentExternalNodesDataBufferChangeCounter();
1771 _current_external_nodes_data_buffer = sb;
1774 final void setFoundNodes( final Set<Integer> found_nodes ) {
1775 _found_nodes = found_nodes;
1778 final void setInOvRect( final boolean in_ov_rect ) {
1779 _in_ov_rect = in_ov_rect;
1782 final void setLargeFonts() {
1783 getTreeFontSet().largeFonts();
1786 final void setLastMouseDragPointX( final float x ) {
1787 _last_drag_point_x = x;
1790 final void setLastMouseDragPointY( final float y ) {
1791 _last_drag_point_y = y;
1794 final void setLongestExtNodeInfo( final int i ) {
1795 _longest_ext_node_info = i;
1798 final void setMediumFonts() {
1799 getTreeFontSet().mediumFonts();
1802 final void setNodeInPreorderToNull() {
1803 _nodes_in_preorder = null;
1806 final void setOvOn( final boolean ov_on ) {
1810 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
1811 _graphics_type = graphics_type;
1815 final void setSmallFonts() {
1816 getTreeFontSet().smallFonts();
1819 final void setStartingAngle( final double starting_angle ) {
1820 _urt_starting_angle = starting_angle;
1823 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
1824 _statistics_for_vector_data = statistics_for_expression_values;
1827 final void setSuperTinyFonts() {
1828 getTreeFontSet().superTinyFonts();
1831 final void setTextAntialias() {
1832 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
1833 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
1834 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
1837 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
1840 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
1841 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
1842 && !getMainPanel().getOptions().isShowDefaultNodeShapes()
1843 && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
1844 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1847 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
1850 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
1851 RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
1853 catch ( final Throwable e ) {
1854 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
1858 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
1859 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1863 final void setTinyFonts() {
1864 getTreeFontSet().tinyFonts();
1867 final void setTreeFile( final File treefile ) {
1868 _treefile = treefile;
1871 final void setXcorrectionFactor( final float f ) {
1872 _x_correction_factor = f;
1875 final void setXdistance( final float x ) {
1879 final void setYdistance( final float y ) {
1883 final void sortDescendants( final PhylogenyNode node ) {
1884 if ( !node.isExternal() ) {
1885 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
1886 if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
1887 .isShowTaxonomyCommonNames() ) ) {
1888 if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
1889 .isShowGeneSymbols() ) ) {
1890 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
1892 else if ( getControlPanel().isShowNodeNames() ) {
1893 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
1896 PhylogenyMethods.sortNodeDescendents( node, pri );
1897 setNodeInPreorderToNull();
1898 _phylogeny.externalNodesHaveChanged();
1899 _phylogeny.clearHashIdToNodeMap();
1900 _phylogeny.recalculateNumberOfExternalDescendants( true );
1901 resetNodeIdToDistToLeafMap();
1907 final void subTree( final PhylogenyNode node ) {
1908 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1909 JOptionPane.showMessageDialog( this,
1910 "Cannot get a sub/super tree in unrooted display",
1911 "Attempt to get sub/super tree in unrooted display",
1912 JOptionPane.WARNING_MESSAGE );
1915 if ( node.isExternal() ) {
1916 JOptionPane.showMessageDialog( this,
1917 "Cannot get a subtree of a external node",
1918 "Attempt to get subtree of external node",
1919 JOptionPane.WARNING_MESSAGE );
1922 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
1923 JOptionPane.showMessageDialog( this,
1924 "Cannot get a subtree of the root node",
1925 "Attempt to get subtree of root node",
1926 JOptionPane.WARNING_MESSAGE );
1929 setNodeInPreorderToNull();
1930 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
1931 _sub_phylogenies[ _subtree_index ] = _phylogeny;
1932 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
1934 _phylogeny = subTree( node, _phylogeny );
1935 updateSubSuperTreeButton();
1937 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
1940 _main_panel.getControlPanel().showWhole();
1944 final void superTree() {
1945 setNodeInPreorderToNull();
1946 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
1947 for( final PhylogenyNode n : temp_root.getDescendants() ) {
1948 n.setParent( temp_root );
1950 _sub_phylogenies[ _subtree_index ] = null;
1951 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
1952 _phylogeny = _sub_phylogenies[ --_subtree_index ];
1953 updateSubSuperTreeButton();
1956 final void swap( final PhylogenyNode node ) {
1957 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
1960 if ( node.getNumberOfDescendants() > 2 ) {
1961 JOptionPane.showMessageDialog( this,
1962 "Cannot swap descendants of nodes with more than 2 descendants",
1963 "Cannot swap descendants",
1964 JOptionPane.ERROR_MESSAGE );
1967 if ( !node.isExternal() ) {
1968 node.swapChildren();
1969 setNodeInPreorderToNull();
1970 _phylogeny.externalNodesHaveChanged();
1971 _phylogeny.clearHashIdToNodeMap();
1972 _phylogeny.recalculateNumberOfExternalDescendants( true );
1973 resetNodeIdToDistToLeafMap();
1979 final void taxColor() {
1980 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1984 AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
1985 _control_panel.setColorBranches( true );
1986 if ( _control_panel.getColorBranchesCb() != null ) {
1987 _control_panel.getColorBranchesCb().setSelected( true );
1993 final void updateOvSettings() {
1994 switch ( getOptions().getOvPlacement() ) {
1996 setOvXPosition( OV_BORDER );
1997 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
1998 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2001 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2002 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2003 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2006 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2007 setOvYPosition( OV_BORDER );
2008 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2011 setOvXPosition( OV_BORDER );
2012 setOvYPosition( OV_BORDER );
2013 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2018 final void updateOvSizes() {
2019 if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
2021 float l = getLongestExtNodeInfo();
2022 final float w_ratio = getOvMaxWidth() / getWidth();
2024 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
2025 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
2027 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
2028 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
2031 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
2033 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
2034 if ( ov_xdist < 0.0 ) {
2037 if ( ydist < 0.0 ) {
2040 setOvXDistance( ov_xdist );
2041 final double height = _phylogeny.getHeight();
2043 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
2044 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
2047 setOvXcorrectionFactor( 0 );
2055 void updateSetOfCollapsedExternalNodes() {
2056 final Phylogeny phy = getPhylogeny();
2057 _collapsed_external_nodeid_set.clear();
2058 if ( phy != null ) {
2059 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2060 final PhylogenyNode ext_node = it.next();
2061 PhylogenyNode n = ext_node;
2062 while ( !n.isRoot() ) {
2063 if ( n.isCollapse() ) {
2064 _collapsed_external_nodeid_set.add( ext_node.getId() );
2065 ext_node.setCollapse( true );
2074 final void updateSubSuperTreeButton() {
2075 if ( _subtree_index < 1 ) {
2076 getControlPanel().deactivateButtonToReturnToSuperTree();
2079 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
2083 final void zoomInDomainStructure() {
2084 if ( _domain_structure_width < 2000 ) {
2085 _domain_structure_width *= 1.2;
2089 final void zoomOutDomainStructure() {
2090 if ( _domain_structure_width > 20 ) {
2091 _domain_structure_width *= 0.8;
2095 private void abbreviateScientificName( final String sn ) {
2096 final String[] a = sn.split( "\\s+" );
2097 _sb.append( a[ 0 ].substring( 0, 1 ) );
2098 _sb.append( a[ 1 ].substring( 0, 2 ) );
2099 if ( a.length > 2 ) {
2100 for( int i = 2; i < a.length; i++ ) {
2102 _sb.append( a[ i ] );
2107 final private void addEmptyNode( final PhylogenyNode node ) {
2108 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2109 errorMessageNoCutCopyPasteInUnrootedDisplay();
2112 final String label = createASimpleTextRepresentationOfANode( node );
2114 if ( ForesterUtil.isEmpty( label ) ) {
2115 msg = "How to add the new, empty node?";
2118 msg = "How to add the new, empty node to node" + label + "?";
2120 final Object[] options = { "As sibling", "As descendant", "Cancel" };
2121 final int r = JOptionPane.showOptionDialog( this,
2123 "Addition of Empty New Node",
2124 JOptionPane.CLOSED_OPTION,
2125 JOptionPane.QUESTION_MESSAGE,
2129 boolean add_as_sibling = true;
2131 add_as_sibling = false;
2133 else if ( r != 0 ) {
2136 final Phylogeny phy = new Phylogeny();
2137 phy.setRoot( new PhylogenyNode() );
2138 phy.setRooted( true );
2139 if ( add_as_sibling ) {
2140 if ( node.isRoot() ) {
2141 JOptionPane.showMessageDialog( this,
2142 "Cannot add sibling to root",
2143 "Attempt to add sibling to root",
2144 JOptionPane.ERROR_MESSAGE );
2147 phy.addAsSibling( node );
2150 phy.addAsChild( node );
2152 setNodeInPreorderToNull();
2153 _phylogeny.externalNodesHaveChanged();
2154 _phylogeny.clearHashIdToNodeMap();
2155 _phylogeny.recalculateNumberOfExternalDescendants( true );
2156 resetNodeIdToDistToLeafMap();
2161 final private void addToCurrentExternalNodes( final int i ) {
2162 if ( _current_external_nodes == null ) {
2163 _current_external_nodes = new HashSet<Integer>();
2165 _current_external_nodes.add( i );
2168 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
2169 final boolean is_vertical,
2171 final boolean to_pdf,
2172 final boolean to_graphics_file ) {
2173 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
2174 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2175 g.setColor( Color.BLACK );
2177 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
2178 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
2179 && ( getCutOrCopiedTree() != null )
2180 && ( getCopiedAndPastedNodes() != null )
2182 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
2183 g.setColor( getTreeColorSet().getFoundColor() );
2185 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2186 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2188 else if ( to_pdf ) {
2189 g.setColor( getTreeColorSet().getBranchColorForPdf() );
2192 g.setColor( getTreeColorSet().getBranchColor() );
2196 final private void blast( final PhylogenyNode node ) {
2197 if ( !isCanBlast( node ) ) {
2198 JOptionPane.showMessageDialog( this,
2199 "Insufficient information present",
2201 JOptionPane.INFORMATION_MESSAGE );
2205 final String query = Blast.obtainQueryForBlast( node );
2206 System.out.println( "query for BLAST is: " + query );
2208 if ( !ForesterUtil.isEmpty( query ) ) {
2209 if ( node.getNodeData().isHasSequence() ) {
2210 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
2211 if ( node.getNodeData().getSequence().getType().toLowerCase()
2212 .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
2219 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2220 if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2228 if ( type == '?' ) {
2229 if ( SequenceIdParser.isProtein( query ) ) {
2236 JApplet applet = null;
2238 applet = obtainApplet();
2241 Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
2243 catch ( final Exception e ) {
2244 e.printStackTrace();
2246 if ( Constants.ALLOW_DDBJ_BLAST ) {
2248 System.out.println( "trying: " + query );
2249 final Blast s = new Blast();
2250 s.ddbjBlast( query );
2252 catch ( final Exception e ) {
2253 e.printStackTrace();
2261 * Calculate the length of the distance between the given node and its
2267 * @return the distance value
2269 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
2270 if ( getControlPanel().isDrawPhylogram() ) {
2271 if ( node.getDistanceToParent() < 0.0 ) {
2274 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
2277 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2278 return getXdistance();
2280 return getXdistance() * factor;
2284 final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
2285 Color c = getTreeColorSet().getAnnotationColor();
2286 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
2287 final StringBuilder sb = new StringBuilder();
2288 for( final Annotation a : ann ) {
2289 sb.append( !ForesterUtil.isEmpty( a.getRef() ) ? a.getRef() : a.getDesc() );
2291 final String ann_str = sb.toString();
2292 if ( !ForesterUtil.isEmpty( ann_str ) ) {
2293 c = getControlPanel().getAnnotationColors().get( ann_str );
2295 c = AptxUtil.calculateColorFromString( ann_str );
2296 getControlPanel().getAnnotationColors().put( ann_str, c );
2299 c = getTreeColorSet().getAnnotationColor();
2306 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
2307 if ( getControlPanel().isDrawPhylogram() ) {
2308 if ( node.getDistanceToParent() < 0.0 ) {
2311 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
2314 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2315 return getOvXDistance();
2317 return getOvXDistance() * factor;
2321 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
2322 JOptionPane.showMessageDialog( this,
2323 "Cannot launch web browser for " + type_type + " data of this node",
2324 "Cannot launch web browser",
2325 JOptionPane.WARNING_MESSAGE );
2328 final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
2329 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2330 JOptionPane.showMessageDialog( this,
2331 "Cannot colorize subtree in unrooted display type",
2332 "Attempt to colorize subtree in unrooted display",
2333 JOptionPane.WARNING_MESSAGE );
2336 _control_panel.setColorBranches( true );
2337 if ( _control_panel.getColorBranchesCb() != null ) {
2338 _control_panel.getColorBranchesCb().setSelected( true );
2340 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
2341 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
2346 final private void colorSubtree( final PhylogenyNode node ) {
2347 Color intitial_color = null;
2348 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
2349 && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
2350 intitial_color = PhylogenyMethods.getBranchColorValue( node );
2353 intitial_color = getTreeColorSet().getBranchColor();
2355 _color_chooser.setColor( intitial_color );
2356 _color_chooser.setPreviewPanel( new JPanel() );
2357 final JDialog dialog = JColorChooser
2358 .createDialog( this,
2359 "Subtree colorization",
2362 new SubtreeColorizationActionListener( _color_chooser, node ),
2364 dialog.setVisible( true );
2367 final private void copySubtree( final PhylogenyNode node ) {
2368 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2369 errorMessageNoCutCopyPasteInUnrootedDisplay();
2372 setNodeInPreorderToNull();
2373 setCutOrCopiedTree( _phylogeny.copy( node ) );
2374 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
2375 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
2376 for( final PhylogenyNode n : nodes ) {
2377 node_ids.add( n.getId() );
2379 node_ids.add( node.getId() );
2380 setCopiedAndPastedNodes( node_ids );
2384 private String createAnnotationString( final SortedSet<Annotation> ann ) {
2385 final StringBuilder sb = new StringBuilder();
2386 boolean first = true;
2387 for( final Annotation a : ann ) {
2394 sb.append( a.asSimpleText() );
2396 final String ann_str = sb.toString();
2400 final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
2401 final String tax = PhylogenyMethods.getSpecies( node );
2402 String label = node.getName();
2403 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
2404 label = label + " " + tax;
2406 else if ( !ForesterUtil.isEmpty( tax ) ) {
2412 if ( !ForesterUtil.isEmpty( label ) ) {
2413 label = " [" + label + "]";
2418 final private void cutSubtree( final PhylogenyNode node ) {
2419 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2420 errorMessageNoCutCopyPasteInUnrootedDisplay();
2423 if ( node.isRoot() ) {
2424 JOptionPane.showMessageDialog( this,
2425 "Cannot cut entire tree as subtree",
2426 "Attempt to cut entire tree",
2427 JOptionPane.ERROR_MESSAGE );
2430 final String label = createASimpleTextRepresentationOfANode( node );
2431 final int r = JOptionPane.showConfirmDialog( null,
2432 "Cut subtree" + label + "?",
2433 "Confirm Cutting of Subtree",
2434 JOptionPane.YES_NO_OPTION );
2435 if ( r != JOptionPane.OK_OPTION ) {
2438 setNodeInPreorderToNull();
2439 setCopiedAndPastedNodes( null );
2440 setCutOrCopiedTree( _phylogeny.copy( node ) );
2441 _phylogeny.deleteSubtree( node, true );
2442 _phylogeny.clearHashIdToNodeMap();
2443 _phylogeny.recalculateNumberOfExternalDescendants( true );
2444 resetNodeIdToDistToLeafMap();
2449 final private void cycleColors() {
2450 getMainPanel().getTreeColorSet().cycleColorScheme();
2451 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
2452 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
2456 final private void decreaseOvSize() {
2457 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
2458 setOvMaxWidth( getOvMaxWidth() - 5 );
2459 setOvMaxHeight( getOvMaxHeight() - 5 );
2461 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2465 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
2466 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2467 errorMessageNoCutCopyPasteInUnrootedDisplay();
2470 if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
2471 JOptionPane.showMessageDialog( this,
2472 "Cannot delete entire tree",
2473 "Attempt to delete entire tree",
2474 JOptionPane.ERROR_MESSAGE );
2477 final String label = createASimpleTextRepresentationOfANode( node );
2478 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
2479 final int r = JOptionPane.showOptionDialog( this,
2480 "Delete" + label + "?",
2481 "Delete Node/Subtree",
2482 JOptionPane.CLOSED_OPTION,
2483 JOptionPane.QUESTION_MESSAGE,
2487 setNodeInPreorderToNull();
2488 boolean node_only = true;
2492 else if ( r != 0 ) {
2496 PhylogenyMethods.removeNode( node, _phylogeny );
2499 _phylogeny.deleteSubtree( node, true );
2501 _phylogeny.externalNodesHaveChanged();
2502 _phylogeny.clearHashIdToNodeMap();
2503 _phylogeny.recalculateNumberOfExternalDescendants( true );
2504 resetNodeIdToDistToLeafMap();
2509 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
2510 makePopupMenus( node );
2511 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
2512 _node_popup_menu.show( this, x, y );
2515 final private void drawArc( final double x,
2518 final double heigth,
2519 final double start_angle,
2520 final double arc_angle,
2521 final Graphics2D g ) {
2522 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
2526 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
2527 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
2530 _line.setLine( x1, y1, x2, y2 );
2534 final private void drawOval( final double x,
2537 final double heigth,
2538 final Graphics2D g ) {
2539 _ellipse.setFrame( x, y, width, heigth );
2543 final private void drawOvalFilled( final double x,
2546 final double heigth,
2547 final Graphics2D g ) {
2548 _ellipse.setFrame( x, y, width, heigth );
2552 final private void drawOvalGradient( final double x,
2555 final double heigth,
2557 final Color color_1,
2558 final Color color_2,
2559 final Color color_border ) {
2560 _ellipse.setFrame( x, y, width, heigth );
2561 g.setPaint( new GradientPaint( ( float ) x,
2564 ( float ) ( x + width ),
2565 ( float ) ( y + heigth ),
2569 if ( color_border != null ) {
2570 g.setPaint( color_border );
2575 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
2576 _rectangle.setFrame( x, y, width, heigth );
2577 g.draw( _rectangle );
2580 final private void drawRectFilled( final double x,
2583 final double heigth,
2584 final Graphics2D g ) {
2585 _rectangle.setFrame( x, y, width, heigth );
2586 g.fill( _rectangle );
2589 final private void drawRectGradient( final double x,
2592 final double heigth,
2594 final Color color_1,
2595 final Color color_2,
2596 final Color color_border ) {
2597 _rectangle.setFrame( x, y, width, heigth );
2598 g.setPaint( new GradientPaint( ( float ) x,
2601 ( float ) ( x + width ),
2602 ( float ) ( y + heigth ),
2605 g.fill( _rectangle );
2606 if ( color_border != null ) {
2607 g.setPaint( color_border );
2608 g.draw( _rectangle );
2612 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2613 final List<Uri> us = new ArrayList<Uri>();
2614 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2615 for( final Uri uri : t.getUris() ) {
2620 for( final Uri uri : us ) {
2621 if ( uri != null ) {
2622 final String uri_str = uri.getValue().toString().toLowerCase();
2623 if ( getImageMap().containsKey( uri_str ) ) {
2624 final BufferedImage bi = getImageMap().get( uri_str );
2625 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2626 double scaling_factor = 1;
2627 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
2628 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
2629 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
2631 // y = y - ( 0.9 * getYdistance() );
2632 final double hs = bi.getHeight() * scaling_factor;
2633 double ws = ( bi.getWidth() * scaling_factor ) + offset;
2634 final double my_y = y - ( 0.5 * hs );
2635 final int x_w = ( int ) ( x + ws + 0.5 );
2636 final int y_h = ( int ) ( my_y + hs + 0.5 );
2637 if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
2639 ( int ) ( x + 0.5 + offset ),
2640 ( int ) ( my_y + 0.5 ),
2661 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
2662 JOptionPane.showMessageDialog( this,
2663 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
2664 "Attempt to cut/copy/paste/add/delete in unrooted display",
2665 JOptionPane.ERROR_MESSAGE );
2668 final private Set<Integer> getCopiedAndPastedNodes() {
2669 return getMainPanel().getCopiedAndPastedNodes();
2672 final private Set<Integer> getCurrentExternalNodes() {
2673 return _current_external_nodes;
2676 final private Phylogeny getCutOrCopiedTree() {
2677 return getMainPanel().getCutOrCopiedTree();
2680 final private float getLastDragPointX() {
2681 return _last_drag_point_x;
2684 final private float getLastDragPointY() {
2685 return _last_drag_point_y;
2688 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
2689 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
2690 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
2691 _nodeid_dist_to_leaf.put( node.getId(), m );
2695 return _nodeid_dist_to_leaf.get( node.getId() );
2699 final private double getMaxDistanceToRoot() {
2700 if ( _max_distance_to_root < 0 ) {
2701 recalculateMaxDistanceToRoot();
2703 return _max_distance_to_root;
2706 final private float getOvMaxHeight() {
2707 return _ov_max_height;
2710 final private float getOvMaxWidth() {
2711 return _ov_max_width;
2714 final private float getOvXcorrectionFactor() {
2715 return _ov_x_correction_factor;
2718 final private float getOvXDistance() {
2719 return _ov_x_distance;
2722 final private int getOvXPosition() {
2723 return _ov_x_position;
2726 final private float getOvYDistance() {
2727 return _ov_y_distance;
2730 final private int getOvYPosition() {
2731 return _ov_y_position;
2734 final private int getOvYStart() {
2738 final private double getScaleDistance() {
2739 return _scale_distance;
2742 final private String getScaleLabel() {
2743 return _scale_label;
2746 final private TreeFontSet getTreeFontSet() {
2747 return getMainPanel().getTreeFontSet();
2750 final private float getUrtFactor() {
2754 final private float getUrtFactorOv() {
2755 return _urt_factor_ov;
2758 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
2761 showNodeFrame( node );
2776 colorSubtree( node );
2791 copySubtree( node );
2794 pasteSubtree( node );
2796 case DELETE_NODE_OR_SUBTREE:
2797 deleteNodeOrSubtree( node );
2800 addEmptyNode( node );
2802 case EDIT_NODE_DATA:
2803 showNodeEditFrame( node );
2808 case SORT_DESCENDENTS:
2809 sortDescendants( node );
2811 case GET_EXT_DESC_DATA:
2812 showExtDescNodeData( node );
2815 throw new IllegalArgumentException( "unknown action: " + action );
2819 final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
2820 _current_external_nodes_data_buffer_change_counter++;
2823 final private void increaseOvSize() {
2824 if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
2825 && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
2826 .getHeight() / 2 ) ) ) {
2827 setOvMaxWidth( getOvMaxWidth() + 5 );
2828 setOvMaxHeight( getOvMaxHeight() + 5 );
2830 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2834 final private void init() {
2835 _color_chooser = new JColorChooser();
2836 _rollover_popup = new JTextArea();
2837 _rollover_popup.setFont( POPUP_FONT );
2838 resetNodeIdToDistToLeafMap();
2840 setTreeFile( null );
2842 initializeOvSettings();
2843 setStartingAngle( ( TWO_PI * 3 ) / 4 );
2844 final ImageLoader il = new ImageLoader( this );
2845 new Thread( il ).start();
2848 final private void initializeOvSettings() {
2849 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
2850 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
2853 final private boolean inOvVirtualRectangle( final int x, final int y ) {
2854 return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
2855 && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
2856 && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
2857 + getOvVirtualRectangle().height + 1 ) ) );
2860 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
2861 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
2864 final private boolean isCanBlast( final PhylogenyNode node ) {
2865 if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
2868 return Blast.isContainsQueryForBlast( node );
2871 final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
2872 if ( node.getNodeData().isHasSequence()
2873 && ( node.getNodeData().getSequence().getAccession() != null )
2874 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
2875 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
2876 && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
2877 .toLowerCase() ) ) {
2883 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
2884 if ( node.getNodeData().isHasTaxonomy()
2885 && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
2886 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
2887 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
2888 .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
2889 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
2890 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
2891 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
2892 .getNodeData().getTaxonomy().getIdentifier() != null )
2893 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
2894 .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
2902 final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
2903 return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
2906 final private boolean isInFoundNodes( final PhylogenyNode node ) {
2907 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
2910 final private boolean isInOv() {
2914 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
2916 if ( getControlPanel().isShowTaxonomyImages() ) {
2917 y_dist = 40 + ( int ) getYdistance();
2919 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
2920 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
2921 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
2924 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
2925 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
2926 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
2927 || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
2928 .getMaxX() + 20 ) ) );
2931 final private boolean isNonLinedUpCladogram() {
2932 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
2935 final private boolean isUniformBranchLengthsForCladogram() {
2936 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
2939 final private void keyPressedCalls( final KeyEvent e ) {
2940 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
2941 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
2942 if ( !isInOvRect() ) {
2943 setInOvRect( true );
2946 else if ( isInOvRect() ) {
2947 setInOvRect( false );
2950 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
2951 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2952 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2953 getMainPanel().getTreeFontSet().mediumFonts();
2954 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2956 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
2957 getMainPanel().getTreeFontSet().decreaseFontSize();
2958 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2960 else if ( plusPressed( e.getKeyCode() ) ) {
2961 getMainPanel().getTreeFontSet().increaseFontSize();
2962 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2966 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2967 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2968 getControlPanel().showWhole();
2970 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
2971 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
2972 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
2973 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
2974 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
2975 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2977 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
2978 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
2979 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2981 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
2982 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
2983 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
2984 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2986 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
2987 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
2988 Constants.WHEEL_ZOOM_IN_FACTOR );
2989 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2996 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
2999 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3003 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3007 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
3008 scroll_position.x = scroll_position.x + dx;
3009 scroll_position.y = scroll_position.y + dy;
3010 if ( scroll_position.x <= 0 ) {
3011 scroll_position.x = 0;
3014 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
3015 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
3016 if ( scroll_position.x >= max_x ) {
3017 scroll_position.x = max_x;
3020 if ( scroll_position.y <= 0 ) {
3021 scroll_position.y = 0;
3024 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
3025 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
3026 if ( scroll_position.y >= max_y ) {
3027 scroll_position.y = max_y;
3031 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
3034 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3035 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3036 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3037 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3038 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3040 else if ( plusPressed( e.getKeyCode() ) ) {
3041 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3042 Constants.WHEEL_ZOOM_IN_FACTOR );
3043 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3044 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3046 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
3047 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3048 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3049 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
3050 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3053 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
3054 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3055 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3056 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
3057 if ( getStartingAngle() < 0 ) {
3058 setStartingAngle( TWO_PI + getStartingAngle() );
3060 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3063 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
3064 boolean selected = false;
3065 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
3066 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
3070 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
3072 if ( getMainPanel().getMainFrame() == null ) {
3073 // Must be "E" applet version.
3074 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
3075 if ( ae.getlabelDirectionCbmi() != null ) {
3076 ae.getlabelDirectionCbmi().setSelected( selected );
3080 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
3084 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
3085 switchDisplaygetPhylogenyGraphicsType();
3088 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
3092 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
3093 MainFrame.cycleOverview( getOptions(), this );
3096 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
3099 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
3106 final private void makePopupMenus( final PhylogenyNode node ) {
3107 _node_popup_menu = new JPopupMenu();
3108 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
3109 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
3110 for( int i = 0; i < clickto_names.size(); i++ ) {
3111 final String title = clickto_names.get( i );
3112 _node_popup_menu_items[ i ] = new JMenuItem( title );
3113 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
3114 _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
3116 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
3117 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
3119 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
3120 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
3122 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
3123 if ( !getOptions().isEditable() ) {
3126 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
3128 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
3129 if ( !getOptions().isEditable() ) {
3132 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
3134 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
3135 if ( !getOptions().isEditable() ) {
3138 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
3140 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
3141 if ( !getOptions().isEditable() ) {
3144 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
3146 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
3147 if ( !getOptions().isEditable() ) {
3151 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
3152 if ( !getOptions().isEditable() ) {
3156 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
3157 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
3159 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
3160 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
3162 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
3163 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
3165 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
3166 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
3168 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
3169 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
3171 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
3172 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
3174 _node_popup_menu_items[ i ].addActionListener( this );
3175 _node_popup_menu.add( _node_popup_menu_items[ i ] );
3179 private final String obtainTitleForExtDescNodeData() {
3180 switch ( getOptions().getExtDescNodeDataToReturn() ) {
3182 return "Node Names";
3184 return "Sequence Names";
3185 case SEQUENCE_SYMBOL:
3186 return "Sequence Symbols";
3187 case SEQUENCE_MOL_SEQ:
3188 return "Molecular Sequences";
3190 return "Sequence Accessors";
3191 case TAXONOMY_SCIENTIFIC_NAME:
3192 return "Scientific Names";
3194 return "Taxonomy Codes";
3196 return "User Selected Data";
3198 throw new IllegalArgumentException( "unknown data element: "
3199 + getOptions().getExtDescNodeDataToReturn() );
3203 final private void openSeqWeb( final PhylogenyNode node ) {
3204 if ( !isCanOpenSeqWeb( node ) ) {
3205 cannotOpenBrowserWarningMessage( "sequence" );
3208 String uri_str = null;
3209 final Sequence seq = node.getNodeData().getSequence();
3210 final String source = seq.getAccession().getSource().toLowerCase();
3212 if ( source.toLowerCase().equals( "ncbi" ) ) {
3213 url = Constants.NCBI_ALL_DATABASE_SEARCH;
3216 final WebLink weblink = getConfiguration().getWebLink( source );
3217 url = weblink.getUrl().toString();
3220 uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
3222 catch ( final UnsupportedEncodingException e ) {
3223 AptxUtil.showErrorMessage( this, e.toString() );
3224 e.printStackTrace();
3226 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3228 JApplet applet = null;
3230 applet = obtainApplet();
3232 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
3234 catch ( final IOException e ) {
3235 AptxUtil.showErrorMessage( this, e.toString() );
3236 e.printStackTrace();
3238 catch ( final URISyntaxException e ) {
3239 AptxUtil.showErrorMessage( this, e.toString() );
3240 e.printStackTrace();
3244 cannotOpenBrowserWarningMessage( "sequence" );
3248 final private void openTaxWeb( final PhylogenyNode node ) {
3249 if ( !isCanOpenTaxWeb( node ) ) {
3250 cannotOpenBrowserWarningMessage( "taxonomic" );
3253 String uri_str = null;
3254 final Taxonomy tax = node.getNodeData().getTaxonomy();
3255 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
3256 && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
3257 final String type = tax.getIdentifier().getProvider().toLowerCase();
3258 final WebLink weblink = getConfiguration().getWebLink( type );
3260 uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
3262 catch ( final UnsupportedEncodingException e ) {
3263 AptxUtil.showErrorMessage( this, e.toString() );
3264 e.printStackTrace();
3267 else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3268 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
3270 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
3272 catch ( final URISyntaxException e ) {
3273 AptxUtil.showErrorMessage( this, e.toString() );
3275 e.printStackTrace();
3278 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
3280 uri_str = "http://www.eol.org/search?q="
3281 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
3283 catch ( final UnsupportedEncodingException e ) {
3284 AptxUtil.showErrorMessage( this, e.toString() );
3285 e.printStackTrace();
3288 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
3290 uri_str = "http://www.uniprot.org/taxonomy/?query="
3291 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
3293 catch ( final UnsupportedEncodingException e ) {
3294 AptxUtil.showErrorMessage( this, e.toString() );
3295 e.printStackTrace();
3298 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
3300 uri_str = "http://www.eol.org/search?q="
3301 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
3303 catch ( final UnsupportedEncodingException e ) {
3304 AptxUtil.showErrorMessage( this, e.toString() );
3305 e.printStackTrace();
3308 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3310 JApplet applet = null;
3312 applet = obtainApplet();
3314 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
3316 catch ( final IOException e ) {
3317 AptxUtil.showErrorMessage( this, e.toString() );
3318 e.printStackTrace();
3320 catch ( final URISyntaxException e ) {
3321 AptxUtil.showErrorMessage( this, e.toString() );
3322 e.printStackTrace();
3326 cannotOpenBrowserWarningMessage( "taxonomic" );
3330 final private void paintBranchLength( final Graphics2D g,
3331 final PhylogenyNode node,
3332 final boolean to_pdf,
3333 final boolean to_graphics_file ) {
3334 g.setFont( getTreeFontSet().getSmallFont() );
3335 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3336 g.setColor( Color.BLACK );
3339 g.setColor( getTreeColorSet().getBranchLengthColor() );
3341 if ( !node.isRoot() ) {
3342 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3343 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3344 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3346 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3347 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3348 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3351 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3352 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3356 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
3357 - getTreeFontSet()._small_max_descent, g );
3361 final private void paintBranchLite( final Graphics2D g,
3366 final PhylogenyNode node ) {
3367 g.setColor( getTreeColorSet().getOvColor() );
3368 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3369 drawLine( x1, y1, x2, y2, g );
3371 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3372 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3373 ( g ).draw( _quad_curve );
3375 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3376 final float dx = x2 - x1;
3377 final float dy = y2 - y1;
3378 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3379 + ( dy * 0.8f ), x2, y2 );
3380 ( g ).draw( _cubic_curve );
3383 final float x2a = x2;
3384 final float x1a = x1;
3385 // draw the vertical line
3386 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
3387 drawLine( x1, y1, x1, y2, g );
3389 // draw the horizontal line
3390 drawLine( x1a, y2, x2a, y2, g );
3395 * Paint a branch which consists of a vertical and a horizontal bar
3396 * @param is_ind_found_nodes
3398 final private void paintBranchRectangular( final Graphics2D g,
3403 final PhylogenyNode node,
3404 final boolean to_pdf,
3405 final boolean to_graphics_file ) {
3406 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
3407 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3408 drawLine( x1, y1, x2, y2, g );
3410 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3411 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3412 g.draw( _quad_curve );
3414 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3415 final float dx = x2 - x1;
3416 final float dy = y2 - y1;
3417 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3418 + ( dy * 0.8f ), x2, y2 );
3419 g.draw( _cubic_curve );
3422 final float x2a = x2;
3423 final float x1a = x1;
3425 if ( node.isFirstChildNode() || node.isLastChildNode()
3426 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3427 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3428 if ( !to_graphics_file
3430 && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
3431 .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
3435 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3436 float x2c = x1 + EURO_D;
3440 drawLine( x1, y1, x2c, y2, g );
3442 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3444 y2_r = y2 - ROUNDED_D;
3448 drawLine( x1, y1, x1, y2_r, g );
3451 y2_r = y2 + ROUNDED_D;
3455 drawLine( x1, y1, x1, y2_r, g );
3459 drawLine( x1, y1, x1, y2, g );
3463 // draw the horizontal line
3464 if ( !to_graphics_file && !to_pdf
3465 && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
3469 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
3470 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3471 x1_r = x1a + ROUNDED_D;
3473 drawLine( x1_r, y2, x2a, y2, g );
3476 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3477 final float x1c = x1a + EURO_D;
3479 drawLine( x1c, y2, x2a, y2, g );
3483 drawLine( x1a, y2, x2a, y2, g );
3487 final double w = PhylogenyMethods.getBranchWidthValue( node );
3488 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3489 x1_r = x1a + ROUNDED_D;
3491 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
3494 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3495 final float x1c = x1a + EURO_D;
3497 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
3501 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
3504 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3509 final double diff = y2 - y2_r;
3510 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
3513 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
3518 if ( node.isExternal() ) {
3519 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
3520 || isInCurrentExternalNodes( node ) );
3524 final private double paintCirculars( final PhylogenyNode n,
3525 final Phylogeny phy,
3526 final float center_x,
3527 final float center_y,
3528 final double radius,
3529 final boolean radial_labels,
3531 final boolean to_pdf,
3532 final boolean to_graphics_file ) {
3533 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
3534 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
3535 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
3537 return _urt_nodeid_angle_map.get( n.getId() );
3540 final List<PhylogenyNode> descs = n.getDescendants();
3542 for( final PhylogenyNode desc : descs ) {
3543 sum += paintCirculars( desc,
3554 if ( !n.isRoot() ) {
3555 r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3557 final double theta = sum / descs.size();
3558 n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
3559 n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
3560 _urt_nodeid_angle_map.put( n.getId(), theta );
3561 for( final PhylogenyNode desc : descs ) {
3562 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
3568 final private void paintCircularsLite( final PhylogenyNode n,
3569 final Phylogeny phy,
3573 final Graphics2D g ) {
3574 if ( n.isExternal() ) {
3578 final List<PhylogenyNode> descs = n.getDescendants();
3579 for( final PhylogenyNode desc : descs ) {
3580 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
3583 if ( !n.isRoot() ) {
3584 r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3586 final double theta = _urt_nodeid_angle_map.get( n.getId() );
3587 n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
3588 n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
3589 for( final PhylogenyNode desc : descs ) {
3590 paintBranchCircularLite( n, desc, g );
3595 final private void paintCollapsedNode( final Graphics2D g,
3596 final PhylogenyNode node,
3597 final boolean to_graphics_file,
3598 final boolean to_pdf,
3599 final boolean is_in_found_nodes ) {
3601 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3604 else if ( is_in_found_nodes ) {
3605 c = getTreeColorSet().getFoundColor();
3607 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3608 c = getTaxonomyBasedColor( node );
3610 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3611 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3612 c = PhylogenyMethods.getBranchColorValue( node );
3615 c = getTreeColorSet().getCollapseFillColor();
3617 double d = node.getAllExternalDescendants().size();
3619 d = ( 3 * _y_distance ) / 3;
3622 d = ( Math.log10( d ) * _y_distance ) / 2.5;
3624 final int box_size = getOptions().getDefaultNodeShapeSize();
3625 if ( d < box_size ) {
3629 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
3630 ForesterUtil.roundToInt( node.getYcoord() ) );
3631 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
3632 ForesterUtil.roundToInt( node.getYcoord() - d ) );
3633 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
3634 ForesterUtil.roundToInt( node.getYcoord() + d ) );
3635 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3637 g.fillPolygon( _polygon );
3639 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3640 g.setColor( getBackground() );
3641 g.fillPolygon( _polygon );
3643 g.drawPolygon( _polygon );
3645 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3646 g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
3647 .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
3652 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3655 final private void paintConfidenceValues( final Graphics2D g,
3656 final PhylogenyNode node,
3657 final boolean to_pdf,
3658 final boolean to_graphics_file ) {
3659 final List<Confidence> confidences = node.getBranchData().getConfidences();
3660 // if ( confidences.size() == 1 ) {
3661 // final double value = node.getBranchData().getConfidence( 0 ).getValue();
3662 // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
3665 // conf_str = FORMATTER_CONFIDENCE.format( value );
3667 // else if ( confidences.size() > 1 ) {
3668 boolean one_ok = false;
3669 boolean not_first = false;
3670 Collections.sort( confidences );
3671 final StringBuilder sb = new StringBuilder();
3672 String conf_str = "";
3673 for( final Confidence confidence : confidences ) {
3674 final double value = confidence.getValue();
3675 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3676 if ( value >= getOptions().getMinConfidenceValue() ) {
3685 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
3686 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3687 if ( getOptions().isShowConfidenceStddev() ) {
3688 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3690 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
3692 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3699 conf_str = sb.toString();
3702 if ( conf_str.length() > 0 ) {
3703 final double parent_x = node.getParent().getXcoord();
3704 double x = node.getXcoord();
3705 g.setFont( getTreeFontSet().getSmallFont() );
3706 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3709 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3712 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3713 g.setColor( Color.BLACK );
3716 g.setColor( getTreeColorSet().getConfidenceColor() );
3719 .drawString( conf_str,
3721 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
3722 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
3727 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
3728 final int box_size = getOptions().getDefaultNodeShapeSize();
3729 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3730 g.setColor( getTreeColorSet().getFoundColor() );
3731 g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
3734 final private void paintGainedAndLostCharacters( final Graphics2D g,
3735 final PhylogenyNode node,
3736 final String gained,
3737 final String lost ) {
3738 if ( node.getParent() != null ) {
3739 final double parent_x = node.getParent().getXcoord();
3740 final double x = node.getXcoord();
3741 g.setFont( getTreeFontSet().getLargeFont() );
3742 g.setColor( getTreeColorSet().getGainedCharactersColor() );
3743 if ( Constants.SPECIAL_CUSTOM ) {
3744 g.setColor( Color.BLUE );
3747 .drawString( gained,
3748 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
3749 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
3751 g.setColor( getTreeColorSet().getLostCharactersColor() );
3752 TreePanel.drawString( lost,
3753 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
3754 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
3760 * Draw a box at the indicated node.
3767 final private void paintNodeBox( final double x,
3769 final PhylogenyNode node,
3771 final boolean to_pdf,
3772 final boolean to_graphics_file,
3773 final boolean is_in_found_nodes ) {
3774 if ( node.isCollapse() ) {
3777 // if this node should be highlighted, do so
3778 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
3779 g.setColor( getTreeColorSet().getFoundColor() );
3780 drawOval( x - 8, y - 8, 16, 16, g );
3781 drawOval( x - 9, y - 8, 17, 17, g );
3782 drawOval( x - 9, y - 9, 18, 18, g );
3784 if ( is_in_found_nodes ) {
3785 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
3788 Color outline_color = null;
3789 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3790 outline_color = Color.BLACK;
3792 else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
3793 final Event event = node.getNodeData().getEvent();
3794 if ( event.isDuplication() ) {
3795 outline_color = getTreeColorSet().getDuplicationBoxColor();
3797 else if ( event.isSpeciation() ) {
3798 outline_color = getTreeColorSet().getSpecBoxColor();
3800 else if ( event.isSpeciationOrDuplication() ) {
3801 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
3804 else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
3805 outline_color = getTaxonomyBasedColor( node );
3808 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
3809 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
3810 outline_color = getTreeColorSet().getBranchColorForPdf();
3813 final int box_size = getOptions().getDefaultNodeShapeSize();
3814 final int half_box_size = box_size / 2;
3815 if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
3816 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
3817 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3818 drawOvalGradient( x - half_box_size,
3823 to_pdf ? Color.WHITE : outline_color,
3824 to_pdf ? outline_color : getBackground(),
3827 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
3828 Color background = getBackground();
3830 background = Color.WHITE;
3832 drawOvalGradient( x - half_box_size,
3841 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3842 g.setColor( outline_color );
3843 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3846 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
3847 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
3848 drawRectGradient( x - half_box_size,
3853 to_pdf ? Color.WHITE : outline_color,
3854 to_pdf ? outline_color : getBackground(),
3857 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3858 Color background = getBackground();
3860 background = Color.WHITE;
3862 drawRectGradient( x - half_box_size,
3871 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3872 g.setColor( outline_color );
3873 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3880 final private void paintNodeData( final Graphics2D g,
3881 final PhylogenyNode node,
3882 final boolean to_graphics_file,
3883 final boolean to_pdf,
3884 final boolean is_in_found_nodes ) {
3885 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
3888 if ( getOptions().isShowBranchLengthValues()
3889 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3890 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3891 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
3892 paintBranchLength( g, node, to_pdf, to_graphics_file );
3894 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
3898 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3899 if ( getControlPanel().isShowTaxonomyImages()
3900 && ( getImageMap() != null )
3901 && !getImageMap().isEmpty()
3902 && node.getNodeData().isHasTaxonomy()
3903 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
3904 .getUris().isEmpty() ) ) {
3905 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
3907 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3908 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
3909 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
3911 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3912 g.setColor( Color.BLACK );
3914 else if ( is_in_found_nodes ) {
3915 g.setColor( getTreeColorSet().getFoundColor() );
3917 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3918 g.setColor( getTaxonomyBasedColor( node ) );
3920 else if ( getControlPanel().isColorAccordingToAnnotation()
3921 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
3922 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
3923 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
3925 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3926 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3927 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3929 else if ( to_pdf ) {
3930 g.setColor( Color.BLACK );
3933 g.setColor( getTreeColorSet().getSequenceColor() );
3936 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3938 _sb.append( node.getAllExternalDescendants().size() );
3941 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3942 if ( _sb.length() > 0 ) {
3945 _sb.append( node.getName() );
3947 if ( node.getNodeData().isHasSequence() ) {
3948 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
3949 if ( _sb.length() > 0 ) {
3952 _sb.append( node.getNodeData().getSequence().getSymbol() );
3954 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3955 if ( _sb.length() > 0 ) {
3958 _sb.append( node.getNodeData().getSequence().getName() );
3960 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3961 if ( _sb.length() > 0 ) {
3964 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3965 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3968 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3971 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
3972 if ( _sb.length() > 0 ) {
3975 _sb.append( propertiesToString( node ) );
3977 g.setFont( getTreeFontSet().getLargeFont() );
3978 if ( is_in_found_nodes ) {
3979 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3981 double down_shift_factor = 3.0;
3982 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
3983 down_shift_factor = 1;
3985 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
3986 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
3987 final String sb_str = _sb.toString();
3988 // GUILHEM_BEG ______________
3989 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
3990 && ( _query_sequence != null ) ) {
3991 int nodeTextBoundsWidth = 0;
3992 if ( sb_str.length() > 0 ) {
3993 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
3994 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
3996 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
3997 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
3998 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
3999 g.setColor( getTreeColorSet().getBackgroundColor() );
4003 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
4004 for( final SequenceRelation seqRelation : seqRelations ) {
4005 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
4006 .getRef1().isEqual( _query_sequence ) )
4007 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
4008 .getSelectedItem() );
4009 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
4010 final double linePosX = node.getXcoord() + 2 + half_box_size;
4011 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
4012 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
4014 if ( sConfidence != null ) {
4015 double confidenceX = pos_x;
4016 if ( sb_str.length() > 0 ) {
4017 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
4018 + CONFIDENCE_LEFT_MARGIN;
4020 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
4021 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
4022 .getBounds().getWidth();
4023 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
4024 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
4027 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
4029 if ( nodeTextBoundsWidth == 0 ) {
4030 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
4033 nodeTextBoundsWidth += 2;
4035 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
4036 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
4043 if ( sb_str.length() > 0 ) {
4044 TreePanel.drawString( sb_str, pos_x, pos_y, g );
4046 // GUILHEM_END _____________
4047 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
4048 // TODO FIXME need to check this one!
4049 //if ( _sb.length() > 0 ) {
4050 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
4051 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4053 // COMMENTED_OUT_BY_GUILHEM_END ________________
4054 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
4055 && ( node.getNodeData().getSequence().getAnnotations() != null )
4056 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4057 if ( _sb.length() > 0 ) {
4058 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4060 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
4061 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4062 g.setColor( Color.BLACK );
4064 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
4065 g.setColor( calculateColorForAnnotation( ann ) );
4067 final String ann_str = createAnnotationString( ann );
4068 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
4069 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4071 _sb.append( ann_str );
4073 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4074 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
4075 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
4076 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
4077 && node.getNodeData().isHasBinaryCharacters() ) {
4078 if ( _sb.length() > 0 ) {
4079 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4081 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4082 g.setColor( Color.BLACK );
4085 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
4087 if ( getControlPanel().isShowBinaryCharacters() ) {
4088 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
4089 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
4090 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4091 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
4092 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
4093 .getLostCharactersAsStringBuffer().toString() );
4096 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
4097 node.getXcoord() + x + 4 + half_box_size,
4099 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
4101 paintGainedAndLostCharacters( g, node, "+"
4102 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
4103 + node.getNodeData().getBinaryCharacters().getLostCount() );
4109 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
4110 final PhylogenyNode node,
4111 final boolean to_pdf,
4112 final boolean to_graphics_file,
4113 final boolean radial_labels,
4114 final double ur_angle,
4115 final boolean is_in_found_nodes ) {
4116 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
4119 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4120 g.setColor( Color.BLACK );
4122 else if ( is_in_found_nodes ) {
4123 g.setColor( getTreeColorSet().getFoundColor() );
4125 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4126 g.setColor( getTaxonomyBasedColor( node ) );
4128 else if ( getControlPanel().isColorAccordingToAnnotation()
4129 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4130 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4131 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4134 g.setColor( getTreeColorSet().getSequenceColor() );
4138 if ( node.getNodeData().isHasTaxonomy()
4139 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4140 .isShowTaxonomyCommonNames() ) ) {
4141 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4142 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4143 _sb.append( taxonomy.getTaxonomyCode() );
4146 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4147 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4148 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4149 _sb.append( taxonomy.getScientificName() );
4151 _sb.append( taxonomy.getCommonName() );
4154 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4155 _sb.append( taxonomy.getScientificName() );
4158 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4159 _sb.append( taxonomy.getCommonName() );
4163 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4164 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4165 _sb.append( taxonomy.getScientificName() );
4169 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4170 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4171 _sb.append( taxonomy.getCommonName() );
4176 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4178 _sb.append( node.getAllExternalDescendants().size() );
4181 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4182 if ( _sb.length() > 0 ) {
4185 _sb.append( node.getName() );
4187 if ( node.getNodeData().isHasSequence() ) {
4188 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4189 if ( _sb.length() > 0 ) {
4192 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4193 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4196 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4198 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4199 if ( _sb.length() > 0 ) {
4202 _sb.append( node.getNodeData().getSequence().getName() );
4205 g.setFont( getTreeFontSet().getLargeFont() );
4206 if ( is_in_found_nodes ) {
4207 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4209 if ( _sb.length() > 1 ) {
4210 final String sb_str = _sb.toString();
4212 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4213 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
4216 m = ( float ) ( ur_angle % TWO_PI );
4218 _at = g.getTransform();
4219 boolean need_to_reset = false;
4220 final float x_coord = node.getXcoord();
4221 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
4222 if ( radial_labels ) {
4223 need_to_reset = true;
4224 boolean left = false;
4225 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4229 g.rotate( m, x_coord, node.getYcoord() );
4231 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
4235 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4236 need_to_reset = true;
4237 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
4240 TreePanel.drawString( sb_str, x_coord, y_coord, g );
4241 if ( need_to_reset ) {
4242 g.setTransform( _at );
4247 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
4248 if ( node.isCollapse() ) {
4249 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
4250 paintCollapsedNode( g, node, false, false, false );
4254 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4255 g.setColor( getTreeColorSet().getFoundColor() );
4256 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
4259 if ( !node.isExternal() && !node.isCollapse() ) {
4260 boolean first_child = true;
4262 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4263 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4264 final PhylogenyNode child_node = node.getChildNode( i );
4266 if ( !isUniformBranchLengthsForCladogram() ) {
4267 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4270 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4272 if ( first_child ) {
4273 first_child = false;
4274 y2 = node.getYSecondary()
4275 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
4276 .getNumberOfExternalNodes() ) );
4279 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4281 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
4282 new_x = x2 + node.getXSecondary();
4283 final float diff_y = node.getYSecondary() - y2;
4284 final float diff_x = node.getXSecondary() - new_x;
4285 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
4286 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
4288 child_node.setXSecondary( new_x );
4289 child_node.setYSecondary( y2 );
4290 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4295 final private void paintNodeRectangular( final Graphics2D g,
4296 final PhylogenyNode node,
4297 final boolean to_pdf,
4298 final boolean dynamically_hide,
4299 final int dynamic_hiding_factor,
4300 final boolean to_graphics_file ) {
4301 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
4302 if ( node.isCollapse() ) {
4303 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
4304 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4308 if ( node.isExternal() ) {
4309 ++_external_node_index;
4311 // Confidence values
4312 if ( getControlPanel().isShowConfidenceValues()
4313 && !node.isExternal()
4315 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
4316 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4317 && node.getBranchData().isHasConfidences() ) {
4318 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
4320 // Draw a line to root:
4321 if ( node.isRoot() && _phylogeny.isRooted() ) {
4322 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
4325 float new_x_min = Float.MAX_VALUE;
4326 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
4327 float min_dist = 1.5f;
4328 if ( !disallow_shortcutting ) {
4329 // System.out.println( dynamic_hiding_factor );
4330 if ( dynamic_hiding_factor > 4000 ) {
4333 else if ( dynamic_hiding_factor > 1000 ) {
4336 else if ( dynamic_hiding_factor > 100 ) {
4340 if ( !node.isExternal() && !node.isCollapse() ) {
4341 boolean first_child = true;
4343 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4344 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4345 final PhylogenyNode child_node = node.getChildNode( i );
4347 if ( !isUniformBranchLengthsForCladogram() ) {
4348 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4351 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4353 if ( first_child ) {
4354 first_child = false;
4355 y2 = node.getYcoord()
4356 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
4359 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4361 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
4362 new_x = x2 + node.getXcoord();
4363 if ( dynamically_hide && ( x2 < new_x_min ) ) {
4366 final float diff_y = node.getYcoord() - y2;
4367 final float diff_x = node.getXcoord() - new_x;
4368 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
4369 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
4370 paintBranchRectangular( g,
4379 child_node.setXcoord( new_x );
4380 child_node.setYcoord( y2 );
4381 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4383 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
4384 || isInCurrentExternalNodes( node ) );
4386 if ( dynamically_hide
4387 && !is_in_found_nodes
4388 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
4389 .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
4390 .getHeight() ) ) ) ) ) {
4393 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4394 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
4397 final private void paintNodeWithRenderableData( final Graphics2D g,
4398 final PhylogenyNode node,
4399 final boolean to_graphics_file,
4400 final boolean to_pdf ) {
4401 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
4404 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
4407 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4408 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4409 RenderableDomainArchitecture rds = null;
4410 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
4412 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
4414 catch ( final ClassCastException cce ) {
4415 cce.printStackTrace();
4417 if ( rds != null ) {
4418 rds.setRenderingHeight( 6 );
4420 if ( node.getNodeData().isHasTaxonomy() ) {
4421 if ( getControlPanel().isShowTaxonomyCode()
4422 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
4423 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4427 if ( getControlPanel().isShowTaxonomyScientificNames()
4428 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
4429 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4430 .getScientificName()
4433 if ( getControlPanel().isShowTaxonomyCommonNames()
4434 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
4435 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4440 if ( node.getNodeData().isHasSequence() ) {
4441 if ( getControlPanel().isShowGeneNames()
4442 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
4443 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
4446 if ( getControlPanel().isShowGeneSymbols()
4447 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
4448 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
4451 if ( getControlPanel().isShowSequenceAcc()
4452 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4453 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
4454 .getAccession().toString()
4458 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
4459 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
4461 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
4466 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4467 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
4468 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
4469 getStatisticsForExpressionValues(),
4470 getConfiguration() );
4473 PhylogenyNode my_node = node;
4474 if ( !getControlPanel().isDrawPhylogram() ) {
4475 my_node = getPhylogeny().getFirstExternalNode();
4477 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
4478 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
4480 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
4481 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
4483 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
4489 final private void paintOvRectangle( final Graphics2D g ) {
4490 final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
4491 final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
4492 final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
4493 final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
4494 final float width = getOvMaxWidth() / w_ratio;
4495 final float height = getOvMaxHeight() / h_ratio;
4496 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
4497 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
4498 g.setColor( getTreeColorSet().getFoundColor() );
4499 getOvRectangle().setRect( x, y, width, height );
4500 if ( ( width < 6 ) && ( height < 6 ) ) {
4501 drawRectFilled( x, y, 6, 6, g );
4502 getOvVirtualRectangle().setRect( x, y, 6, 6 );
4504 else if ( width < 6 ) {
4505 drawRectFilled( x, y, 6, height, g );
4506 getOvVirtualRectangle().setRect( x, y, 6, height );
4508 else if ( height < 6 ) {
4509 drawRectFilled( x, y, width, 6, g );
4510 getOvVirtualRectangle().setRect( x, y, width, 6 );
4513 drawRect( x, y, width, height, g );
4514 if ( isInOvRect() ) {
4515 drawRect( x + 1, y + 1, width - 2, height - 2, g );
4517 getOvVirtualRectangle().setRect( x, y, width, height );
4521 final private void paintPhylogenyLite( final Graphics2D g ) {
4524 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
4525 .getWidth() ) ) ) );
4526 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
4527 for( final PhylogenyNode element : _nodes_in_preorder ) {
4528 paintNodeLite( g, element );
4530 paintOvRectangle( g );
4534 * Paint the root branch. (Differs from others because it will always be a
4535 * single horizontal line).
4536 * @param to_graphics_file
4538 * @return new x1 value
4540 final private void paintRootBranch( final Graphics2D g,
4543 final PhylogenyNode root,
4544 final boolean to_pdf,
4545 final boolean to_graphics_file ) {
4546 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
4547 float d = getXdistance();
4548 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
4549 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
4551 if ( d < MIN_ROOT_LENGTH ) {
4552 d = MIN_ROOT_LENGTH;
4554 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
4555 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
4558 final double w = PhylogenyMethods.getBranchWidthValue( root );
4559 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
4561 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
4564 final private void paintScale( final Graphics2D g,
4567 final boolean to_pdf,
4568 final boolean to_graphics_file ) {
4570 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
4572 final int y2 = y1 - 8;
4573 final int y3 = y1 - 4;
4574 g.setFont( getTreeFontSet().getSmallFont() );
4575 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4576 g.setColor( Color.BLACK );
4579 g.setColor( getTreeColorSet().getBranchLengthColor() );
4581 drawLine( x1, y1, x1, y2, g );
4582 drawLine( x2, y1, x2, y2, g );
4583 drawLine( x1, y3, x2, y3, g );
4584 if ( getScaleLabel() != null ) {
4585 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
4589 final private int paintTaxonomy( final Graphics2D g,
4590 final PhylogenyNode node,
4591 final boolean is_in_found_nodes,
4592 final boolean to_pdf,
4593 final boolean to_graphics_file,
4594 final double x_shift ) {
4595 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4596 g.setFont( getTreeFontSet().getLargeItalicFont() );
4597 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4598 g.setColor( Color.BLACK );
4600 else if ( is_in_found_nodes ) {
4601 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
4602 g.setColor( getTreeColorSet().getFoundColor() );
4604 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4605 g.setColor( getTaxonomyBasedColor( node ) );
4607 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4608 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4609 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4611 else if ( to_pdf ) {
4612 g.setColor( Color.BLACK );
4615 g.setColor( getTreeColorSet().getTaxonomyColor() );
4617 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4618 final double start_y = node.getYcoord()
4619 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4621 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4622 _sb.append( taxonomy.getTaxonomyCode() );
4625 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4626 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4627 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4628 if ( getOptions().isAbbreviateScientificTaxonNames()
4629 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4630 abbreviateScientificName( taxonomy.getScientificName() );
4633 _sb.append( taxonomy.getScientificName() );
4636 _sb.append( taxonomy.getCommonName() );
4639 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4640 if ( getOptions().isAbbreviateScientificTaxonNames()
4641 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4642 abbreviateScientificName( taxonomy.getScientificName() );
4645 _sb.append( taxonomy.getScientificName() );
4649 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4650 _sb.append( taxonomy.getCommonName() );
4654 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4655 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4656 if ( getOptions().isAbbreviateScientificTaxonNames()
4657 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4658 abbreviateScientificName( taxonomy.getScientificName() );
4661 _sb.append( taxonomy.getScientificName() );
4666 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4667 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4668 _sb.append( taxonomy.getCommonName() );
4672 final String label = _sb.toString();
4674 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4675 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4676 // invert font color and background color to show that this is the query sequence
4677 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4681 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4682 g.setColor( getTreeColorSet().getBackgroundColor() );
4685 TreePanel.drawString( label, start_x, start_y, g );
4686 if ( is_in_found_nodes ) {
4687 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4690 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4694 final private void paintUnrooted( final PhylogenyNode n,
4695 final double low_angle,
4696 final double high_angle,
4697 final boolean radial_labels,
4699 final boolean to_pdf,
4700 final boolean to_graphics_file ) {
4702 n.setXcoord( getWidth() / 2 );
4703 n.setYcoord( getHeight() / 2 );
4705 if ( n.isExternal() ) {
4706 paintNodeDataUnrootedCirc( g,
4711 ( high_angle + low_angle ) / 2,
4712 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
4715 final float num_enclosed = n.getNumberOfExternalNodes();
4716 final float x = n.getXcoord();
4717 final float y = n.getYcoord();
4718 double current_angle = low_angle;
4719 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4720 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4721 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4722 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4723 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4724 final PhylogenyNode desc = n.getChildNode( i );
4725 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4726 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4727 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4728 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4731 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4734 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4737 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4738 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4740 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4741 if ( desc.getDistanceToParent() < 0 ) {
4745 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4749 length = getUrtFactor();
4751 final double mid_angle = current_angle + ( arc_size / 2 );
4752 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4753 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4754 desc.setXcoord( new_x );
4755 desc.setYcoord( new_y );
4756 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4757 current_angle += arc_size;
4758 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4759 drawLine( x, y, new_x, new_y, g );
4760 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc )
4761 || isInCurrentExternalNodes( desc ) );
4764 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
4768 final private void paintUnrootedLite( final PhylogenyNode n,
4769 final double low_angle,
4770 final double high_angle,
4772 final float urt_ov_factor ) {
4774 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
4775 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
4776 n.setXSecondary( x_pos );
4777 n.setYSecondary( y_pos );
4779 if ( n.isExternal() ) {
4782 final float num_enclosed = n.getNumberOfExternalNodes();
4783 final float x = n.getXSecondary();
4784 final float y = n.getYSecondary();
4785 double current_angle = low_angle;
4786 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4787 final PhylogenyNode desc = n.getChildNode( i );
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() * urt_ov_factor );
4800 length = urt_ov_factor;
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.setXSecondary( new_x );
4806 desc.setYSecondary( new_y );
4807 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
4808 g.setColor( getTreeColorSet().getFoundColor() );
4809 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
4810 g.setColor( getTreeColorSet().getOvColor() );
4812 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4813 current_angle += arc_size;
4814 drawLine( x, y, new_x, new_y, g );
4818 final private void pasteSubtree( final PhylogenyNode node ) {
4819 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4820 errorMessageNoCutCopyPasteInUnrootedDisplay();
4823 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
4824 JOptionPane.showMessageDialog( this,
4825 "No tree in buffer (need to copy or cut a subtree first)",
4826 "Attempt to paste with empty buffer",
4827 JOptionPane.ERROR_MESSAGE );
4830 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
4831 final Object[] options = { "As sibling", "As descendant", "Cancel" };
4832 final int r = JOptionPane.showOptionDialog( this,
4833 "How to paste subtree" + label + "?",
4835 JOptionPane.CLOSED_OPTION,
4836 JOptionPane.QUESTION_MESSAGE,
4840 boolean paste_as_sibling = true;
4842 paste_as_sibling = false;
4844 else if ( r != 0 ) {
4847 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
4848 buffer_phy.setAllNodesToNotCollapse();
4849 PhylogenyMethods.preOrderReId( buffer_phy );
4850 buffer_phy.setRooted( true );
4851 boolean need_to_show_whole = false;
4852 if ( paste_as_sibling ) {
4853 if ( node.isRoot() ) {
4854 JOptionPane.showMessageDialog( this,
4855 "Cannot paste sibling to root",
4856 "Attempt to paste sibling to root",
4857 JOptionPane.ERROR_MESSAGE );
4860 buffer_phy.addAsSibling( node );
4863 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
4864 need_to_show_whole = true;
4865 _phylogeny = buffer_phy;
4868 buffer_phy.addAsChild( node );
4871 if ( getCopiedAndPastedNodes() == null ) {
4872 setCopiedAndPastedNodes( new HashSet<Integer>() );
4874 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
4875 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
4876 for( final PhylogenyNode n : nodes ) {
4877 node_ids.add( n.getId() );
4879 node_ids.add( node.getId() );
4880 getCopiedAndPastedNodes().addAll( node_ids );
4881 setNodeInPreorderToNull();
4882 _phylogeny.externalNodesHaveChanged();
4883 _phylogeny.clearHashIdToNodeMap();
4884 _phylogeny.recalculateNumberOfExternalDescendants( true );
4885 resetNodeIdToDistToLeafMap();
4887 if ( need_to_show_whole ) {
4888 getControlPanel().showWhole();
4893 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
4894 final PropertiesMap properties = node.getNodeData().getProperties();
4895 final StringBuffer sb = new StringBuffer();
4896 boolean first = true;
4897 for( final String ref : properties.getPropertyRefs() ) {
4904 final Property p = properties.getProperty( ref );
4905 sb.append( getPartAfterColon( p.getRef() ) );
4907 sb.append( p.getValue() );
4908 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
4909 sb.append( getPartAfterColon( p.getUnit() ) );
4915 final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
4916 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4919 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4920 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4923 final private void setInOv( final boolean in_ov ) {
4927 final private void setOvMaxHeight( final float ov_max_height ) {
4928 _ov_max_height = ov_max_height;
4931 final private void setOvMaxWidth( final float ov_max_width ) {
4932 _ov_max_width = ov_max_width;
4935 final private void setOvXcorrectionFactor( final float f ) {
4936 _ov_x_correction_factor = f;
4939 final private void setOvXDistance( final float ov_x_distance ) {
4940 _ov_x_distance = ov_x_distance;
4943 final private void setOvXPosition( final int ov_x_position ) {
4944 _ov_x_position = ov_x_position;
4947 final private void setOvYDistance( final float ov_y_distance ) {
4948 _ov_y_distance = ov_y_distance;
4951 final private void setOvYPosition( final int ov_y_position ) {
4952 _ov_y_position = ov_y_position;
4955 final private void setOvYStart( final int ov_y_start ) {
4956 _ov_y_start = ov_y_start;
4959 final private void setScaleDistance( final double scale_distance ) {
4960 _scale_distance = scale_distance;
4963 final private void setScaleLabel( final String scale_label ) {
4964 _scale_label = scale_label;
4967 final private void setUpUrtFactor() {
4968 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
4969 : getVisibleRect().height;
4970 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4971 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
4974 final int max_depth = _circ_max_depth;
4975 if ( max_depth > 0 ) {
4976 setUrtFactor( d / ( 2 * max_depth ) );
4979 setUrtFactor( d / 2 );
4982 setUrtFactorOv( getUrtFactor() );
4985 final private void setUrtFactor( final float urt_factor ) {
4986 _urt_factor = urt_factor;
4989 final private void setUrtFactorOv( final float urt_factor_ov ) {
4990 _urt_factor_ov = urt_factor_ov;
4993 private void showExtDescNodeData( final PhylogenyNode node ) {
4994 final List<String> data = new ArrayList<String>();
4995 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
4996 switch ( getOptions().getExtDescNodeDataToReturn() ) {
4998 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
4999 data.add( n.getName() );
5003 if ( n.getNodeData().isHasSequence()
5004 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5005 data.add( n.getNodeData().getSequence().getName() );
5008 case SEQUENCE_SYMBOL:
5009 if ( n.getNodeData().isHasSequence()
5010 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5011 data.add( n.getNodeData().getSequence().getSymbol() );
5014 case SEQUENCE_MOL_SEQ:
5015 if ( n.getNodeData().isHasSequence()
5016 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5017 data.add( n.getNodeData().getSequence().getMolecularSequence() );
5021 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
5022 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
5023 data.add( n.getNodeData().getSequence().getAccession().toString() );
5026 case TAXONOMY_SCIENTIFIC_NAME:
5027 if ( n.getNodeData().isHasTaxonomy()
5028 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5029 data.add( n.getNodeData().getTaxonomy().getScientificName() );
5033 if ( n.getNodeData().isHasTaxonomy()
5034 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5035 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5039 AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
5042 throw new IllegalArgumentException( "unknown data element: "
5043 + getOptions().getExtDescNodeDataToReturn() );
5046 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
5047 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
5048 final StringBuilder sb = new StringBuilder();
5049 for( final String d : data ) {
5050 if ( !ForesterUtil.isEmpty( d ) ) {
5051 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
5052 System.out.println( d );
5055 sb.append( ForesterUtil.LINE_SEPARATOR );
5058 if ( sb.length() < 1 ) {
5059 clearCurrentExternalNodesDataBuffer();
5062 setCurrentExternalNodesDataBuffer( sb );
5065 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
5066 final StringBuilder sb = new StringBuilder();
5067 for( final String d : data ) {
5068 if ( !ForesterUtil.isEmpty( d ) ) {
5070 sb.append( ForesterUtil.LINE_SEPARATOR );
5073 if ( sb.length() < 1 ) {
5074 AptxUtil.showInformationMessage( this,
5075 "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
5076 "Descendants of selected node do not contain selected data" );
5077 clearCurrentExternalNodesDataBuffer();
5080 setCurrentExternalNodesDataBuffer( sb );
5081 final String title = "External Descendants "
5082 + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5083 : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
5084 + node.getNumberOfExternalNodes() + ") For Node " + node;
5085 final String s = sb.toString().trim();
5086 if ( getMainPanel().getMainFrame() == null ) {
5087 // Must be "E" applet version.
5088 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
5089 ae.showTextFrame( s, title );
5092 getMainPanel().getMainFrame().showTextFrame( s, title );
5098 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
5100 if ( ( node.getName().length() > 0 )
5101 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
5102 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
5103 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
5104 || node.getBranchData().isHasConfidences() ) {
5105 _popup_buffer.setLength( 0 );
5107 if ( node.getName().length() > 0 ) {
5109 _popup_buffer.append( node.getName() );
5111 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
5113 boolean enc_data = false;
5114 final Taxonomy tax = node.getNodeData().getTaxonomy();
5115 if ( _popup_buffer.length() > 0 ) {
5116 _popup_buffer.append( "\n" );
5118 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
5119 _popup_buffer.append( "[" );
5120 _popup_buffer.append( tax.getTaxonomyCode() );
5121 _popup_buffer.append( "]" );
5124 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
5126 _popup_buffer.append( " " );
5128 _popup_buffer.append( tax.getScientificName() );
5131 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
5133 _popup_buffer.append( " (" );
5136 _popup_buffer.append( "(" );
5138 _popup_buffer.append( tax.getCommonName() );
5139 _popup_buffer.append( ")" );
5142 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
5144 _popup_buffer.append( " (" );
5147 _popup_buffer.append( "(" );
5149 _popup_buffer.append( tax.getAuthority() );
5150 _popup_buffer.append( ")" );
5153 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
5155 _popup_buffer.append( " [" );
5158 _popup_buffer.append( "[" );
5160 _popup_buffer.append( tax.getRank() );
5161 _popup_buffer.append( "]" );
5164 if ( tax.getSynonyms().size() > 0 ) {
5166 _popup_buffer.append( " " );
5168 _popup_buffer.append( "[" );
5170 for( final String syn : tax.getSynonyms() ) {
5171 if ( !ForesterUtil.isEmpty( syn ) ) {
5173 _popup_buffer.append( syn );
5174 if ( counter < tax.getSynonyms().size() ) {
5175 _popup_buffer.append( ", " );
5180 _popup_buffer.append( "]" );
5183 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
5184 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
5185 _popup_buffer.append( "[" );
5186 _popup_buffer.append( tax.getIdentifier().getProvider() );
5187 _popup_buffer.append( "] " );
5189 _popup_buffer.append( tax.getIdentifier().getValue() );
5193 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
5195 boolean enc_data = false;
5196 if ( _popup_buffer.length() > 0 ) {
5197 _popup_buffer.append( "\n" );
5199 final Sequence seq = node.getNodeData().getSequence();
5200 if ( seq.getAccession() != null ) {
5201 _popup_buffer.append( "[" );
5202 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
5203 _popup_buffer.append( seq.getAccession().getSource() );
5204 _popup_buffer.append( ":" );
5206 _popup_buffer.append( seq.getAccession().getValue() );
5207 _popup_buffer.append( "]" );
5210 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
5212 _popup_buffer.append( " [" );
5215 _popup_buffer.append( "[" );
5217 _popup_buffer.append( seq.getSymbol() );
5218 _popup_buffer.append( "]" );
5221 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
5223 _popup_buffer.append( " " );
5225 _popup_buffer.append( seq.getName() );
5228 if ( node.getNodeData().isHasDate() ) {
5230 if ( _popup_buffer.length() > 0 ) {
5231 _popup_buffer.append( "\n" );
5233 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
5235 if ( node.getNodeData().isHasDistribution() ) {
5237 if ( _popup_buffer.length() > 0 ) {
5238 _popup_buffer.append( "\n" );
5240 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
5242 if ( node.getBranchData().isHasConfidences() ) {
5243 final List<Confidence> confs = node.getBranchData().getConfidences();
5244 for( final Confidence confidence : confs ) {
5246 if ( _popup_buffer.length() > 0 ) {
5247 _popup_buffer.append( "\n" );
5249 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
5250 _popup_buffer.append( "[" );
5251 _popup_buffer.append( confidence.getType() );
5252 _popup_buffer.append( "] " );
5255 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
5257 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5258 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5259 _popup_buffer.append( " (sd=" );
5260 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
5261 .getStandardDeviation(), getOptions()
5262 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5263 _popup_buffer.append( ")" );
5267 if ( node.getNodeData().isHasProperties() ) {
5268 final PropertiesMap properties = node.getNodeData().getProperties();
5269 for( final String ref : properties.getPropertyRefs() ) {
5270 _popup_buffer.append( "\n" );
5271 final Property p = properties.getProperty( ref );
5272 _popup_buffer.append( getPartAfterColon( p.getRef() ) );
5273 _popup_buffer.append( "=" );
5274 _popup_buffer.append( p.getValue() );
5275 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5276 _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
5280 if ( _popup_buffer.length() > 0 ) {
5281 if ( !getConfiguration().isUseNativeUI() ) {
5283 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
5284 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
5285 if ( isInFoundNodes( node ) ) {
5286 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
5288 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
5289 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
5292 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
5296 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
5298 _rollover_popup.setText( _popup_buffer.toString() );
5299 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
5301 e.getLocationOnScreen().x + 10,
5302 e.getLocationOnScreen().y
5304 _node_desc_popup.show();
5308 catch ( final Exception ex ) {
5313 final private void showNodeEditFrame( final PhylogenyNode n ) {
5314 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5315 // pop up edit box for single node
5316 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
5317 _node_frame_index++;
5320 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5324 final private void showNodeFrame( final PhylogenyNode n ) {
5325 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5326 // pop up edit box for single node
5327 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
5328 _node_frame_index++;
5331 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5335 final private void switchDisplaygetPhylogenyGraphicsType() {
5336 switch ( getPhylogenyGraphicsType() ) {
5338 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5339 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5342 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5343 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5346 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5347 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5350 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5351 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5354 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5355 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5358 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5359 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5362 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5363 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5366 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5367 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5370 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5372 if ( getControlPanel().getDynamicallyHideData() != null ) {
5373 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5374 getControlPanel().getDynamicallyHideData().setEnabled( false );
5377 getControlPanel().getDynamicallyHideData().setEnabled( true );
5380 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5381 getControlPanel().setDrawPhylogramEnabled( true );
5384 getControlPanel().setDrawPhylogramEnabled( false );
5386 if ( getMainPanel().getMainFrame() == null ) {
5387 // Must be "E" applet version.
5388 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5389 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5392 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5396 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
5397 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5400 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5401 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5404 final private static String getPartAfterColon( final String s ) {
5405 final int i = s.indexOf( ':' );
5406 if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
5409 return s.substring( i + 1, s.length() );
5412 final private static boolean isSequenceEmpty( final Sequence seq ) {
5413 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
5414 && ForesterUtil.isEmpty( seq.getSymbol() );
5417 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
5418 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
5419 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
5420 .getSynonyms().isEmpty() );
5423 final private static boolean plusPressed( final int key_code ) {
5424 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5425 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5428 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
5429 final Phylogeny new_phy = new Phylogeny();
5430 new_phy.setRooted( true );
5431 new_phy.setName( source_phy.getName() );
5432 new_phy.setDescription( source_phy.getDescription() );
5433 new_phy.setType( source_phy.getType() );
5434 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
5435 new_phy.setConfidence( source_phy.getConfidence() );
5436 new_phy.setIdentifier( source_phy.getIdentifier() );
5437 new_phy.setRoot( new_root.copyNodeDataShallow() );
5439 for( final PhylogenyNode n : new_root.getDescendants() ) {
5440 new_phy.getRoot().setChildNode( i++, n );
5445 final private class SubtreeColorizationActionListener implements ActionListener {
5447 JColorChooser _chooser;
5448 PhylogenyNode _node;
5450 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5456 public void actionPerformed( final ActionEvent e ) {
5457 final Color c = _chooser.getColor();
5459 colorizeSubtree( c, _node );