2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.archaeopteryx;
28 import java.awt.BasicStroke;
29 import java.awt.Color;
30 import java.awt.Cursor;
31 import java.awt.Dimension;
33 import java.awt.GradientPaint;
34 import java.awt.Graphics;
35 import java.awt.Graphics2D;
36 import java.awt.Point;
37 import java.awt.Polygon;
38 import java.awt.Rectangle;
39 import java.awt.RenderingHints;
40 import java.awt.event.ActionEvent;
41 import java.awt.event.ActionListener;
42 import java.awt.event.FocusAdapter;
43 import java.awt.event.FocusEvent;
44 import java.awt.event.InputEvent;
45 import java.awt.event.KeyAdapter;
46 import java.awt.event.KeyEvent;
47 import java.awt.event.MouseEvent;
48 import java.awt.event.MouseWheelEvent;
49 import java.awt.event.MouseWheelListener;
50 import java.awt.font.FontRenderContext;
51 import java.awt.font.TextLayout;
52 import java.awt.geom.AffineTransform;
53 import java.awt.geom.Arc2D;
54 import java.awt.geom.CubicCurve2D;
55 import java.awt.geom.Ellipse2D;
56 import java.awt.geom.Line2D;
57 import java.awt.geom.QuadCurve2D;
58 import java.awt.geom.Rectangle2D;
59 import java.awt.image.BufferedImage;
60 import java.awt.print.PageFormat;
61 import java.awt.print.Printable;
62 import java.awt.print.PrinterException;
64 import java.io.IOException;
65 import java.io.UnsupportedEncodingException;
67 import java.net.URISyntaxException;
68 import java.net.URLEncoder;
69 import java.text.DecimalFormat;
70 import java.text.DecimalFormatSymbols;
71 import java.text.NumberFormat;
72 import java.util.ArrayList;
73 import java.util.Collections;
74 import java.util.HashMap;
75 import java.util.HashSet;
76 import java.util.Hashtable;
77 import java.util.List;
79 import java.util.SortedSet;
81 import javax.swing.BorderFactory;
82 import javax.swing.JApplet;
83 import javax.swing.JColorChooser;
84 import javax.swing.JDialog;
85 import javax.swing.JMenuItem;
86 import javax.swing.JOptionPane;
87 import javax.swing.JPanel;
88 import javax.swing.JPopupMenu;
89 import javax.swing.JTextArea;
90 import javax.swing.Popup;
91 import javax.swing.PopupFactory;
93 import org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON;
94 import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
95 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
96 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
97 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
98 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
99 import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
100 import org.forester.archaeopteryx.tools.Blast;
101 import org.forester.archaeopteryx.tools.ImageLoader;
102 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
103 import org.forester.phylogeny.Phylogeny;
104 import org.forester.phylogeny.PhylogenyMethods;
105 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
106 import org.forester.phylogeny.PhylogenyNode;
107 import org.forester.phylogeny.data.Annotation;
108 import org.forester.phylogeny.data.BranchColor;
109 import org.forester.phylogeny.data.Confidence;
110 import org.forester.phylogeny.data.Event;
111 import org.forester.phylogeny.data.NodeData.NODE_DATA;
112 import org.forester.phylogeny.data.NodeVisualization;
113 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
114 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
115 import org.forester.phylogeny.data.PhylogenyDataUtil;
116 import org.forester.phylogeny.data.PropertiesMap;
117 import org.forester.phylogeny.data.Property;
118 import org.forester.phylogeny.data.Sequence;
119 import org.forester.phylogeny.data.SequenceRelation;
120 import org.forester.phylogeny.data.Taxonomy;
121 import org.forester.phylogeny.data.Uri;
122 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
123 import org.forester.phylogeny.iterators.PreorderTreeIterator;
124 import org.forester.util.BasicDescriptiveStatistics;
125 import org.forester.util.DescriptiveStatistics;
126 import org.forester.util.ForesterConstants;
127 import org.forester.util.ForesterUtil;
128 import org.forester.util.SequenceIdParser;
130 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
132 private static final float PI = ( float ) ( Math.PI );
133 private static final double TWO_PI = 2 * Math.PI;
134 private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
135 private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
136 private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
137 private static final short OV_BORDER = 10;
138 final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
139 final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
140 final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
141 final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
142 final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
143 private final static long serialVersionUID = -978349745916505029L;
144 private final static int EURO_D = 10;
145 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
146 private final static int MIN_ROOT_LENGTH = 3;
147 private final static int MAX_SUBTREES = 100;
148 private final static int MAX_NODE_FRAMES = 10;
149 private final static int MOVE = 20;
150 private final static NumberFormat FORMATTER_CONFIDENCE;
151 private final static NumberFormat FORMATTER_BRANCH_LENGTH;
152 private final static int WIGGLE = 2;
153 private final static int LIMIT_FOR_HQ_RENDERING = 1000;
154 private final static int CONFIDENCE_LEFT_MARGIN = 4;
155 private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
156 RenderingHints.VALUE_RENDER_DEFAULT );
157 private File _treefile = null;
158 private Configuration _configuration = null;
159 private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
160 private int _node_frame_index = 0;
161 private Phylogeny _phylogeny = null;
162 private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
163 private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
164 private int _subtree_index = 0;
165 private MainPanel _main_panel = null;
166 private Set<Integer> _found_nodes = null;
167 private PhylogenyNode _highlight_node = null;
168 private JPopupMenu _node_popup_menu = null;
169 private JMenuItem _node_popup_menu_items[] = null;
170 private int _longest_ext_node_info = 0;
171 private float _x_correction_factor = 0.0f;
172 private float _ov_x_correction_factor = 0.0f;
173 private float _x_distance = 0.0f;
174 private float _y_distance = 0.0f;
175 private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
176 private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
177 private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
178 private float _last_drag_point_x = 0;
179 private float _last_drag_point_y = 0;
180 private ControlPanel _control_panel = null;
181 private int _external_node_index = 0;
182 private final Polygon _polygon = new Polygon();
183 private final StringBuilder _sb = new StringBuilder();
184 private JColorChooser _color_chooser = null;
185 private double _scale_distance = 0.0;
186 private String _scale_label = null;
187 private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
188 private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
189 private final Line2D _line = new Line2D.Float();
190 private final Ellipse2D _ellipse = new Ellipse2D.Float();
191 private final Rectangle2D _rectangle = new Rectangle2D.Float();
192 private Options _options = null;
193 private float _ov_max_width = 0;
194 private float _ov_max_height = 0;
195 private int _ov_x_position = 0;
196 private int _ov_y_position = 0;
197 private int _ov_y_start = 0;
198 private float _ov_y_distance = 0;
199 private float _ov_x_distance = 0;
200 private boolean _ov_on = false;
201 private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
202 private float _urt_factor = 1;
203 private float _urt_factor_ov = 1;
204 private final boolean _phy_has_branch_lengths;
205 private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
206 private boolean _in_ov_rect = false;
207 private boolean _in_ov = false;
208 private final Rectangle _ov_virtual_rectangle = new Rectangle();
209 final private static double _180_OVER_PI = 180.0 / Math.PI;
210 private static final float ROUNDED_D = 8;
211 private int _circ_max_depth;
212 private PhylogenyNode _root;
213 final private Arc2D _arc = new Arc2D.Double();
214 final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
215 final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
216 final private Set<Integer> _collapsed_external_nodeid_set = new HashSet<Integer>();
217 HashMap<Integer, Short> _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
218 private AffineTransform _at;
219 private double _max_distance_to_root = -1;
220 private int _dynamic_hiding_factor = 0;
221 private boolean _edited = false;
222 private Popup _node_desc_popup;
223 private JTextArea _rollover_popup;
224 private final StringBuffer _popup_buffer = new StringBuffer();
225 final private static Font POPUP_FONT = new Font( Configuration
226 .getDefaultFontFamilyName(),
229 private Sequence _query_sequence = null;
230 private final FontRenderContext _frc = new FontRenderContext( null,
233 // expression values menu:
234 private DescriptiveStatistics _statistics_for_vector_data;
235 private PhylogenyNode[] _nodes_in_preorder = null;
236 private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
237 private int _current_external_nodes_data_buffer_change_counter = 0;
238 private Set<Integer> _current_external_nodes = null;
239 // private Image offscreenImage;
240 // private Graphics offscreenGraphics;
241 // private Dimension offscreenDimension;
243 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
244 dfs.setDecimalSeparator( '.' );
245 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
246 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
249 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
250 requestFocusInWindow();
251 addKeyListener( new KeyAdapter() {
254 public void keyPressed( final KeyEvent key_event ) {
255 keyPressedCalls( key_event );
256 requestFocusInWindow();
259 addFocusListener( new FocusAdapter() {
262 public void focusGained( final FocusEvent e ) {
263 requestFocusInWindow();
266 if ( ( t == null ) || t.isEmpty() ) {
267 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
269 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
271 _configuration = configuration;
273 _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
275 // if ( !_phylogeny.isEmpty() ) {
276 _phylogeny.recalculateNumberOfExternalDescendants( true );
277 checkForVectorProperties( _phylogeny );
279 setBackground( getTreeColorSet().getBackgroundColor() );
280 final MouseListener mouse_listener = new MouseListener( this );
281 addMouseListener( mouse_listener );
282 addMouseMotionListener( mouse_listener );
283 addMouseWheelListener( this );
284 calculateScaleDistance();
285 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
286 FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
287 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
291 final public void actionPerformed( final ActionEvent e ) {
292 boolean done = false;
293 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
294 for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
295 // NOTE: index corresponds to the indices of click-to options
296 // in the control panel.
297 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
298 // Set this as the new default click-to action
299 _main_panel.getControlPanel().setClickToAction( index );
300 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
301 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
302 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
307 requestFocusInWindow();
310 public void checkForVectorProperties( final Phylogeny phy ) {
311 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
312 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
313 final PhylogenyNode node = iter.next();
314 if ( node.getNodeData().getProperties() != null ) {
315 final PropertiesMap pm = node.getNodeData().getProperties();
316 final double[] vector = new double[ pm.getProperties().size() ];
318 for( final String ref : pm.getProperties().keySet() ) {
319 if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
320 final Property p = pm.getProperty( ref );
321 final String value_str = p.getValue();
322 final String index_str = ref
323 .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
326 d = Double.parseDouble( value_str );
328 catch ( final NumberFormatException e ) {
329 JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
330 + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
335 i = Integer.parseInt( index_str );
337 catch ( final NumberFormatException e ) {
338 JOptionPane.showMessageDialog( this,
339 "Could not parse \"" + index_str
340 + "\" into index for vector data",
341 "Problem with Vector Data",
342 JOptionPane.ERROR_MESSAGE );
346 JOptionPane.showMessageDialog( this,
347 "Attempt to use negative index for vector data",
348 "Problem with Vector Data",
349 JOptionPane.ERROR_MESSAGE );
357 final List<Double> vector_l = new ArrayList<Double>( counter );
358 for( int i = 0; i < counter; ++i ) {
359 vector_l.add( vector[ i ] );
361 node.getNodeData().setVector( vector_l );
364 if ( stats.getN() > 0 ) {
365 _statistics_for_vector_data = stats;
369 public synchronized Hashtable<String, BufferedImage> getImageMap() {
370 return getMainPanel().getImageMap();
373 final public MainPanel getMainPanel() {
378 * Get a pointer to the phylogeny
380 * @return a pointer to the phylogeny
382 public final Phylogeny getPhylogeny() {
387 final public void mouseWheelMoved( final MouseWheelEvent e ) {
388 final int notches = e.getWheelRotation();
389 if ( inOvVirtualRectangle( e ) ) {
390 if ( !isInOvRect() ) {
396 if ( isInOvRect() ) {
397 setInOvRect( false );
401 if ( e.isControlDown() ) {
403 getTreeFontSet().increaseFontSize();
404 getControlPanel().displayedPhylogenyMightHaveChanged( true );
407 getTreeFontSet().decreaseFontSize();
408 getControlPanel().displayedPhylogenyMightHaveChanged( true );
411 else if ( e.isShiftDown() ) {
412 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
413 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
415 for( int i = 0; i < ( -notches ); ++i ) {
416 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
417 getControlPanel().displayedPhylogenyMightHaveChanged( false );
421 for( int i = 0; i < notches; ++i ) {
422 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
423 if ( getStartingAngle() < 0 ) {
424 setStartingAngle( TWO_PI + getStartingAngle() );
426 getControlPanel().displayedPhylogenyMightHaveChanged( false );
432 for( int i = 0; i < ( -notches ); ++i ) {
433 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
434 getControlPanel().displayedPhylogenyMightHaveChanged( false );
438 for( int i = 0; i < notches; ++i ) {
439 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
440 getControlPanel().displayedPhylogenyMightHaveChanged( false );
447 for( int i = 0; i < ( -notches ); ++i ) {
448 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
449 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
450 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
451 getControlPanel().displayedPhylogenyMightHaveChanged( false );
455 for( int i = 0; i < notches; ++i ) {
456 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
457 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
458 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
459 getControlPanel().displayedPhylogenyMightHaveChanged( false );
464 requestFocusInWindow();
469 final public void paintComponent( final Graphics g ) {
470 // Dimension currentSize = getSize();
471 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
472 // call the 'java.awt.Component.createImage(...)' method to get an
474 // offscreenImage = createImage( currentSize.width, currentSize.height );
475 // offscreenGraphics = offscreenImage.getGraphics();
476 // offscreenDimension = currentSize;
478 // super.paintComponent( g ); //why?
479 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
480 final Graphics2D g2d = ( Graphics2D ) g;
481 g2d.setRenderingHints( _rendering_hints );
482 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
483 //g.drawImage( offscreenImage, 0, 0, this );
487 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
488 throws PrinterException {
489 if ( page_index > 0 ) {
490 return ( NO_SUCH_PAGE );
493 final Graphics2D g2d = ( Graphics2D ) g;
494 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
495 // Turn off double buffering !?
496 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
497 // Turn double buffering back on !?
498 return ( PAGE_EXISTS );
502 public final void setArrowCursor() {
503 setCursor( ARROW_CURSOR );
507 public final void setEdited( final boolean edited ) {
511 public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
512 getMainPanel().setImageMap( image_map );
516 * Set parameters for printing the displayed tree
521 public final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
522 // updateStyle(); not needed?
523 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
525 if ( recalc_longest_ext_node_info ) {
526 calculateLongestExtNodeInfo();
527 while ( ( getLongestExtNodeInfo() > ( x * 0.67 ) ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
528 getMainPanel().getTreeFontSet().decreaseFontSize();
529 calculateLongestExtNodeInfo();
532 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
533 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
534 if ( ext_nodes == 1 ) {
535 ext_nodes = max_depth;
536 if ( ext_nodes < 1 ) {
543 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
544 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
545 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
548 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
549 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
551 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
555 if ( ov_xdist < 0.0 ) {
561 setXdistance( xdist );
562 setYdistance( ydist );
563 setOvXDistance( ov_xdist );
564 final double height = _phylogeny.getHeight();
566 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
567 setXcorrectionFactor( corr > 0 ? corr : 0 );
568 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
569 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
572 setXcorrectionFactor( 0 );
573 setOvXcorrectionFactor( 0 );
575 _circ_max_depth = max_depth;
581 * Set a phylogeny tree.
584 * an instance of a Phylogeny
586 public final void setTree( final Phylogeny t ) {
587 setNodeInPreorderToNull();
591 public final void setWaitCursor() {
592 setCursor( WAIT_CURSOR );
597 public void update( final Graphics g ) {
601 final void calcMaxDepth() {
602 if ( _phylogeny != null ) {
603 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
607 final void calculateLongestExtNodeInfo() {
608 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
611 int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
612 * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
613 if ( max_length < 40 ) {
617 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
619 if ( node.isCollapse() ) {
622 if ( getControlPanel().isShowNodeNames() ) {
623 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
625 if ( node.getNodeData().isHasSequence() ) {
626 if ( getControlPanel().isShowSequenceAcc()
627 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
628 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
632 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
633 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
635 if ( getControlPanel().isShowGeneSymbols()
636 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
637 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
639 if ( getControlPanel().isShowAnnotation()
640 && ( node.getNodeData().getSequence().getAnnotations() != null )
641 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
642 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
646 if ( getControlPanel().isShowDomainArchitectures()
647 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
648 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
649 .getRenderingSize().getWidth();
652 if ( node.getNodeData().isHasTaxonomy() ) {
653 final Taxonomy tax = node.getNodeData().getTaxonomy();
654 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
655 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
657 if ( getControlPanel().isShowTaxonomyScientificNames()
658 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
659 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
661 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
662 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
665 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
666 sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
668 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
669 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
670 .getGainedCharactersAsStringBuffer().toString() );
672 if ( sum >= max_length ) {
673 setLongestExtNodeInfo( max_length );
676 if ( sum > longest ) {
680 if ( longest >= max_length ) {
681 setLongestExtNodeInfo( max_length );
684 setLongestExtNodeInfo( longest );
688 final void calculateScaleDistance() {
689 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
692 final double height = getMaxDistanceToRoot();
694 if ( ( height <= 0.5 ) ) {
695 setScaleDistance( 0.01 );
697 else if ( height <= 5.0 ) {
698 setScaleDistance( 0.1 );
700 else if ( height <= 50.0 ) {
701 setScaleDistance( 1 );
703 else if ( height <= 500.0 ) {
704 setScaleDistance( 10 );
707 setScaleDistance( 100 );
711 setScaleDistance( 0.0 );
713 String scale_label = String.valueOf( getScaleDistance() );
714 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
715 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
717 setScaleLabel( scale_label );
720 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
721 String species = tax.getTaxonomyCode();
722 if ( ForesterUtil.isEmpty( species ) ) {
723 species = tax.getScientificName();
724 if ( ForesterUtil.isEmpty( species ) ) {
725 species = tax.getCommonName();
728 if ( ForesterUtil.isEmpty( species ) ) {
729 return getTreeColorSet().getTaxonomyColor();
731 // Look in species hash
732 Color c = getControlPanel().getSpeciesColors().get( species );
734 c = AptxUtil.calculateColorFromString( species );
735 getControlPanel().getSpeciesColors().put( species, c );
740 void clearCurrentExternalNodesDataBuffer() {
741 setCurrentExternalNodesDataBuffer( new StringBuilder() );
745 * Collapse the tree from the given node
750 final void collapse( final PhylogenyNode node ) {
751 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
752 JOptionPane.showMessageDialog( this,
753 "Cannot collapse in unrooted display type",
754 "Attempt to collapse in unrooted display",
755 JOptionPane.WARNING_MESSAGE );
758 if ( !node.isExternal() && !node.isRoot() ) {
759 final boolean collapse = !node.isCollapse();
760 AptxUtil.collapseSubtree( node, collapse );
761 updateSetOfCollapsedExternalNodes();
762 _phylogeny.recalculateNumberOfExternalDescendants( true );
763 resetNodeIdToDistToLeafMap();
764 calculateLongestExtNodeInfo();
765 setNodeInPreorderToNull();
766 _control_panel.displayedPhylogenyMightHaveChanged( true );
767 resetPreferredSize();
769 _main_panel.adjustJScrollPane();
774 final void collapseSpeciesSpecificSubtrees() {
775 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
779 AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
780 updateSetOfCollapsedExternalNodes();
781 _phylogeny.recalculateNumberOfExternalDescendants( true );
782 resetNodeIdToDistToLeafMap();
783 calculateLongestExtNodeInfo();
784 setNodeInPreorderToNull();
785 resetPreferredSize();
786 _main_panel.adjustJScrollPane();
791 final void colorRank( final String rank ) {
792 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
796 AptxUtil.removeBranchColors( _phylogeny );
797 final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
798 if ( colorizations > 0 ) {
799 _control_panel.setColorBranches( true );
800 if ( _control_panel.getColorBranchesCb() != null ) {
801 _control_panel.getColorBranchesCb().setSelected( true );
803 if ( _control_panel.getColorAccSpeciesCb() != null ) {
804 _control_panel.getColorAccSpeciesCb().setSelected( false );
806 _options.setColorLabelsSameAsParentBranch( true );
807 _control_panel.repaint();
811 if ( colorizations > 0 ) {
812 String msg = "Taxonomy colorization via " + rank + " completed:\n";
813 if ( colorizations > 1 ) {
814 msg += "colorized " + colorizations + " subtrees";
817 msg += "colorized one subtree";
819 JOptionPane.showMessageDialog( this,
821 "Taxonomy Colorization Completed (" + rank + ")",
822 JOptionPane.INFORMATION_MESSAGE );
825 String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
826 msg += "Possible solutions (given that suitable taxonomic information is present):\n";
827 msg += "select a different rank (e.g. phylum, genus, ...)\n";
830 msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
831 msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
832 JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
836 final void confColor() {
837 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
841 AptxUtil.removeBranchColors( _phylogeny );
842 AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
843 _control_panel.setColorBranches( true );
844 if ( _control_panel.getColorBranchesCb() != null ) {
845 _control_panel.getColorBranchesCb().setSelected( true );
851 final void decreaseDomainStructureEvalueThreshold() {
852 if ( _domain_structure_e_value_thr_exp > -20 ) {
853 _domain_structure_e_value_thr_exp -= 1;
858 * Find the node, if any, at the given location
862 * @return pointer to the node at x,y, null if not found
864 final PhylogenyNode findNode( final int x, final int y ) {
865 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
868 final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
869 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
870 final PhylogenyNode node = iter.next();
871 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
872 && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
873 && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
874 && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
875 && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
882 final Configuration getConfiguration() {
883 return _configuration;
886 final ControlPanel getControlPanel() {
887 return _control_panel;
890 String getCurrentExternalNodesDataBufferAsString() {
891 return _current_external_nodes_data_buffer.toString();
894 int getCurrentExternalNodesDataBufferChangeCounter() {
895 return _current_external_nodes_data_buffer_change_counter;
898 final int getDomainStructureEvalueThreshold() {
899 return _domain_structure_e_value_thr_exp;
902 final Set<Integer> getFoundNodes() {
906 final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
907 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
908 return ( PhylogenyMethods.getBranchColorValue( node ) );
911 return ( getTreeColorSet().getBranchColor() );
915 final int getLongestExtNodeInfo() {
916 return _longest_ext_node_info;
919 final Options getOptions() {
920 if ( _options == null ) {
921 _options = getControlPanel().getOptions();
926 final Rectangle2D getOvRectangle() {
927 return _ov_rectangle;
930 final Rectangle getOvVirtualRectangle() {
931 return _ov_virtual_rectangle;
934 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
935 return _graphics_type;
938 final double getStartingAngle() {
939 return _urt_starting_angle;
942 DescriptiveStatistics getStatisticsForExpressionValues() {
943 return _statistics_for_vector_data;
947 * Find a color for this species name.
950 * @return the species color
952 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
953 if ( node.getNodeData().isHasTaxonomy() ) {
954 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
956 // return non-colorized color
957 return getTreeColorSet().getTaxonomyColor();
961 * @return pointer to colorset for tree drawing
963 final TreeColorSet getTreeColorSet() {
964 return getMainPanel().getTreeColorSet();
967 final File getTreeFile() {
971 final float getXcorrectionFactor() {
972 return _x_correction_factor;
975 final float getXdistance() {
979 final float getYdistance() {
983 final void increaseDomainStructureEvalueThreshold() {
984 if ( _domain_structure_e_value_thr_exp < 3 ) {
985 _domain_structure_e_value_thr_exp += 1;
989 final void initNodeData() {
990 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
993 double max_original_domain_structure_width = 0.0;
994 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
995 if ( node.getNodeData().isHasSequence()
996 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
997 RenderableDomainArchitecture rds = null;
998 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
999 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1000 getConfiguration() );
1001 node.getNodeData().getSequence().setDomainArchitecture( rds );
1004 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1006 if ( getControlPanel().isShowDomainArchitectures() ) {
1007 final double dsw = rds.getOriginalSize().getWidth();
1008 if ( dsw > max_original_domain_structure_width ) {
1009 max_original_domain_structure_width = dsw;
1014 if ( getControlPanel().isShowDomainArchitectures() ) {
1015 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1016 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1017 if ( node.getNodeData().isHasSequence()
1018 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1019 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1020 .getSequence().getDomainArchitecture();
1021 rds.setRenderingFactorWidth( ds_factor_width );
1022 rds.setParameter( _domain_structure_e_value_thr_exp );
1028 final boolean inOv( final MouseEvent e ) {
1029 return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
1030 && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
1031 && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
1032 + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
1035 final boolean inOvRectangle( final MouseEvent e ) {
1036 return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
1037 && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
1038 && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
1039 + getOvRectangle().getHeight() + 1 ) ) );
1042 final boolean isApplet() {
1043 return getMainPanel() instanceof MainPanelApplets;
1046 final boolean isCanCollapse() {
1047 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1050 final boolean isCanColorSubtree() {
1051 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1054 final boolean isCanCopy() {
1055 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1058 final boolean isCanCut( final PhylogenyNode node ) {
1059 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1063 final boolean isCanDelete() {
1064 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1067 final boolean isCanPaste() {
1068 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1069 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1072 final boolean isCanReroot() {
1073 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1076 final boolean isCanSubtree( final PhylogenyNode node ) {
1077 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1078 .isRoot() || ( _subtree_index > 0 ) ) );
1081 final boolean isCurrentTreeIsSubtree() {
1082 return ( _subtree_index > 0 );
1085 final boolean isEdited() {
1089 final boolean isInOvRect() {
1093 final boolean isOvOn() {
1097 final boolean isPhyHasBranchLengths() {
1098 return _phy_has_branch_lengths;
1101 final void midpointRoot() {
1102 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1105 if ( !_phylogeny.isRerootable() ) {
1106 JOptionPane.showMessageDialog( this,
1107 "This is not rerootable",
1109 JOptionPane.WARNING_MESSAGE );
1112 setNodeInPreorderToNull();
1114 PhylogenyMethods.midpointRoot( _phylogeny );
1115 resetNodeIdToDistToLeafMap();
1120 final void mouseClicked( final MouseEvent e ) {
1121 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1122 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1123 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1124 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
1126 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
1134 final double max_x = getWidth() - getVisibleRect().width;
1135 final double max_y = getHeight() - getVisibleRect().height;
1142 getMainPanel().getCurrentScrollPane().getViewport()
1143 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1144 setInOvRect( true );
1148 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1149 if ( node != null ) {
1150 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1153 _highlight_node = node;
1154 // Check if shift key is down
1155 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1156 // Yes, so add to _found_nodes
1157 if ( getFoundNodes() == null ) {
1158 setFoundNodes( new HashSet<Integer>() );
1160 getFoundNodes().add( node.getId() );
1161 // Check if control key is down
1163 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1164 // Yes, so pop-up menu
1165 displayNodePopupMenu( node, e.getX(), e.getY() );
1166 // Handle unadorned click
1169 // Check for right mouse button
1170 if ( e.getModifiers() == 4 ) {
1171 displayNodePopupMenu( node, e.getX(), e.getY() );
1174 // if not in _found_nodes, clear _found_nodes
1175 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1180 // no node was clicked
1181 _highlight_node = null;
1187 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1188 setCursor( MOVE_CURSOR );
1189 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1190 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1191 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1192 if ( scroll_position.x < 0 ) {
1193 scroll_position.x = 0;
1196 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1197 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1198 if ( scroll_position.x > max_x ) {
1199 scroll_position.x = max_x;
1202 if ( scroll_position.y < 0 ) {
1203 scroll_position.y = 0;
1206 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1207 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1208 if ( scroll_position.y > max_y ) {
1209 scroll_position.y = max_y;
1212 if ( isOvOn() || getOptions().isShowScale() ) {
1215 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1218 final void mouseDragInOvRectangle( final MouseEvent e ) {
1219 setCursor( HAND_CURSOR );
1220 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1221 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1222 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1223 double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
1224 double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
1225 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1226 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1227 if ( scroll_position.x <= 0 ) {
1228 scroll_position.x = 0;
1232 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1233 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1234 if ( scroll_position.x >= max_x ) {
1236 scroll_position.x = max_x;
1239 if ( scroll_position.y <= 0 ) {
1241 scroll_position.y = 0;
1244 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1245 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1246 if ( scroll_position.y >= max_y ) {
1248 scroll_position.y = max_y;
1252 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1253 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1254 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1257 final void mouseMoved( final MouseEvent e ) {
1258 requestFocusInWindow();
1259 if ( _current_external_nodes != null ) {
1260 _current_external_nodes = null;
1263 if ( getControlPanel().isNodeDescPopup() ) {
1264 if ( _node_desc_popup != null ) {
1265 _node_desc_popup.hide();
1266 _node_desc_popup = null;
1269 if ( getOptions().isShowOverview() && isOvOn() ) {
1270 if ( inOvVirtualRectangle( e ) ) {
1271 if ( !isInOvRect() ) {
1272 setInOvRect( true );
1277 if ( isInOvRect() ) {
1278 setInOvRect( false );
1283 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
1292 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1293 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
1294 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
1295 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
1296 addToCurrentExternalNodes( n.getId() );
1298 setCursor( HAND_CURSOR );
1301 else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
1302 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
1303 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
1304 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
1305 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
1306 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
1307 setCursor( CUT_CURSOR );
1310 setCursor( HAND_CURSOR );
1311 if ( getControlPanel().isNodeDescPopup() ) {
1312 showNodeDataPopup( e, node );
1317 setCursor( ARROW_CURSOR );
1322 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
1323 setCursor( ARROW_CURSOR );
1326 final void multiplyUrtFactor( final float f ) {
1330 final JApplet obtainApplet() {
1331 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1334 final void paintBranchCircular( final PhylogenyNode p,
1335 final PhylogenyNode c,
1337 final boolean radial_labels,
1338 final boolean to_pdf,
1339 final boolean to_graphics_file ) {
1340 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1341 final double root_x = _root.getXcoord();
1342 final double root_y = _root.getYcoord();
1343 final double dx = root_x - p.getXcoord();
1344 final double dy = root_y - p.getYcoord();
1345 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1346 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1347 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
1348 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
1349 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
1350 final double r2 = 2.0 * parent_radius;
1351 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1353 drawLine( c.getXcoord(),
1355 root_x + ( Math.cos( angle ) * parent_radius ),
1356 root_y + ( Math.sin( angle ) * parent_radius ),
1358 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c )
1359 || isInCurrentExternalNodes( c ) );
1360 if ( c.isExternal() ) {
1361 final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c );
1362 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
1363 && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
1366 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
1370 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
1371 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1372 final double root_x = _root.getXSecondary();
1373 final double root_y = _root.getYSecondary();
1374 final double dx = root_x - p.getXSecondary();
1375 final double dy = root_y - p.getYSecondary();
1376 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1377 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1378 g.setColor( getTreeColorSet().getOvColor() );
1379 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
1380 final double r2 = 2.0 * parent_radius;
1381 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1383 drawLine( c.getXSecondary(),
1385 root_x + ( Math.cos( angle ) * parent_radius ),
1386 root_y + ( Math.sin( angle ) * parent_radius ),
1388 if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
1389 g.setColor( getTreeColorSet().getFoundColor() );
1390 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
1394 final void paintCircular( final Phylogeny phy,
1395 final double starting_angle,
1400 final boolean to_pdf,
1401 final boolean to_graphics_file ) {
1402 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
1403 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
1404 _root = phy.getRoot();
1405 _root.setXcoord( center_x );
1406 _root.setYcoord( center_y );
1407 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1408 double current_angle = starting_angle;
1410 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1411 final PhylogenyNode n = it.next();
1412 if ( !n.isCollapse() ) {
1413 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1414 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1415 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1416 _urt_nodeid_index_map.put( n.getId(), i++ );
1417 current_angle += ( TWO_PI / circ_num_ext_nodes );
1421 System.out.println( "is collapse" + n.getName() );
1424 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
1425 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
1428 final void paintCircularLite( final Phylogeny phy,
1429 final double starting_angle,
1433 final Graphics2D g ) {
1434 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
1435 _root = phy.getRoot();
1436 _root.setXSecondary( center_x );
1437 _root.setYSecondary( center_y );
1438 double current_angle = starting_angle;
1439 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1440 final PhylogenyNode n = it.next();
1441 n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1442 n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1443 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1444 current_angle += ( TWO_PI / circ_num_ext_nodes );
1446 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
1449 final void paintPhylogeny( final Graphics2D g,
1450 final boolean to_pdf,
1451 final boolean to_graphics_file,
1452 final int graphics_file_width,
1453 final int graphics_file_height,
1454 final int graphics_file_x,
1455 final int graphics_file_y ) {
1456 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1459 if ( _control_panel.isShowSequenceRelations() ) {
1460 _query_sequence = _control_panel.getSelectedQuerySequence();
1462 // Color the background
1464 final Rectangle r = getVisibleRect();
1465 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
1466 g.setColor( getTreeColorSet().getBackgroundColor() );
1467 if ( !to_graphics_file ) {
1471 if ( getOptions().isPrintBlackAndWhite() ) {
1472 g.setColor( Color.WHITE );
1474 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1478 if ( !to_graphics_file ) {
1479 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
1480 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
1484 g.setPaint( new GradientPaint( graphics_file_x,
1486 getTreeColorSet().getBackgroundColor(),
1488 graphics_file_y + graphics_file_height,
1489 getTreeColorSet().getBackgroundColorGradientBottom() ) );
1490 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1493 g.setStroke( new BasicStroke( 1 ) );
1496 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
1498 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1499 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1500 _external_node_index = 0;
1501 // Position starting X of tree
1502 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
1503 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
1505 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
1506 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
1507 .getDistanceToParent() * getXcorrectionFactor() ) ) );
1510 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
1512 // Position starting Y of tree
1513 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
1514 + ( TreePanel.MOVE / 2.0f ) );
1515 final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) );
1516 if ( getControlPanel().isDynamicallyHideData() ) {
1517 if ( dynamic_hiding_factor > 1 ) {
1518 getControlPanel().setDynamicHidingIsOn( true );
1521 getControlPanel().setDynamicHidingIsOn( false );
1524 if ( _nodes_in_preorder == null ) {
1525 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
1527 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1528 _nodes_in_preorder[ i++ ] = it.next();
1531 //final PhylogenyNodeIterator it;
1532 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1533 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
1534 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1536 for( final PhylogenyNode element : _nodes_in_preorder ) {
1537 paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
1538 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1540 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
1541 if ( !( to_graphics_file || to_pdf ) ) {
1544 getVisibleRect().y + getVisibleRect().height,
1549 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1552 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1553 paintPhylogenyLite( g );
1556 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1557 if ( getControlPanel().getDynamicallyHideData() != null ) {
1558 getControlPanel().setDynamicHidingIsOn( false );
1560 final double angle = getStartingAngle();
1561 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1562 _dynamic_hiding_factor = 0;
1563 if ( getControlPanel().isDynamicallyHideData() ) {
1564 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1565 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
1567 if ( getControlPanel().getDynamicallyHideData() != null ) {
1568 if ( _dynamic_hiding_factor > 1 ) {
1569 getControlPanel().setDynamicHidingIsOn( true );
1572 getControlPanel().setDynamicHidingIsOn( false );
1575 paintUnrooted( _phylogeny.getRoot(),
1577 ( float ) ( angle + ( 2 * Math.PI ) ),
1582 if ( getOptions().isShowScale() ) {
1583 if ( !( to_graphics_file || to_pdf ) ) {
1586 getVisibleRect().y + getVisibleRect().height,
1591 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1594 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1595 g.setColor( getTreeColorSet().getOvColor() );
1596 paintUnrootedLite( _phylogeny.getRoot(),
1598 angle + ( 2 * Math.PI ),
1600 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
1601 paintOvRectangle( g );
1604 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1605 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
1606 final int d = radius + MOVE + getLongestExtNodeInfo();
1607 _dynamic_hiding_factor = 0;
1608 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
1609 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1610 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
1612 if ( getControlPanel().getDynamicallyHideData() != null ) {
1613 if ( _dynamic_hiding_factor > 1 ) {
1614 getControlPanel().setDynamicHidingIsOn( true );
1617 getControlPanel().setDynamicHidingIsOn( false );
1620 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
1621 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1622 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
1623 : getOvMaxWidth() / 2 );
1624 double x_scale = 1.0;
1625 double y_scale = 1.0;
1626 int x_pos = getVisibleRect().x + getOvXPosition();
1627 int y_pos = getVisibleRect().y + getOvYPosition();
1628 if ( getWidth() > getHeight() ) {
1629 x_scale = ( double ) getHeight() / getWidth();
1630 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
1633 y_scale = ( double ) getWidth() / getHeight();
1634 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
1636 _at = g.getTransform();
1637 g.scale( x_scale, y_scale );
1638 paintCircularLite( _phylogeny,
1642 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
1645 g.setTransform( _at );
1646 paintOvRectangle( g );
1651 final void recalculateMaxDistanceToRoot() {
1652 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
1656 * Remove all edit-node frames
1658 final void removeAllEditNodeJFrames() {
1659 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
1660 if ( _node_frames[ i ] != null ) {
1661 _node_frames[ i ].dispose();
1662 _node_frames[ i ] = null;
1665 _node_frame_index = 0;
1669 * Remove a node-edit frame.
1671 final void removeEditNodeFrame( final int i ) {
1672 _node_frame_index--;
1673 _node_frames[ i ] = null;
1674 if ( i < _node_frame_index ) {
1675 for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
1676 _node_frames[ j ] = _node_frames[ j + 1 ];
1678 _node_frames[ _node_frame_index ] = null;
1682 final void reRoot( final PhylogenyNode node ) {
1683 if ( !getPhylogeny().isRerootable() ) {
1684 JOptionPane.showMessageDialog( this,
1685 "This is not rerootable",
1687 JOptionPane.WARNING_MESSAGE );
1690 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1691 JOptionPane.showMessageDialog( this,
1692 "Cannot reroot in unrooted display type",
1693 "Attempt to reroot tree in unrooted display",
1694 JOptionPane.WARNING_MESSAGE );
1697 getPhylogeny().reRoot( node );
1698 getPhylogeny().recalculateNumberOfExternalDescendants( true );
1699 resetNodeIdToDistToLeafMap();
1700 setNodeInPreorderToNull();
1701 resetPreferredSize();
1702 getMainPanel().adjustJScrollPane();
1704 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1705 getControlPanel().showWhole();
1709 final void resetNodeIdToDistToLeafMap() {
1710 _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
1713 final void resetPreferredSize() {
1714 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
1720 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
1721 if ( getControlPanel().isDrawPhylogram() ) {
1723 + getLongestExtNodeInfo()
1725 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
1728 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
1730 + getLongestExtNodeInfo()
1731 + ForesterUtil.roundToInt( getXdistance()
1732 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
1736 + getLongestExtNodeInfo()
1737 + ForesterUtil.roundToInt( getXdistance()
1738 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
1741 setPreferredSize( new Dimension( x, y ) );
1744 final void selectNode( final PhylogenyNode node ) {
1745 if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
1746 getFoundNodes().remove( node.getId() );
1747 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1748 if ( getFoundNodes().size() < 1 ) {
1749 getControlPanel().searchReset();
1753 getControlPanel().getSearchFoundCountsLabel().setVisible( true );
1754 getControlPanel().getSearchResetButton().setEnabled( true );
1755 getControlPanel().getSearchResetButton().setVisible( true );
1756 if ( getFoundNodes() == null ) {
1757 setFoundNodes( new HashSet<Integer>() );
1759 getFoundNodes().add( node.getId() );
1760 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1764 final void setControlPanel( final ControlPanel atv_control ) {
1765 _control_panel = atv_control;
1768 void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
1769 increaseCurrentExternalNodesDataBufferChangeCounter();
1770 _current_external_nodes_data_buffer = sb;
1773 final void setFoundNodes( final Set<Integer> found_nodes ) {
1774 _found_nodes = found_nodes;
1777 final void setInOvRect( final boolean in_ov_rect ) {
1778 _in_ov_rect = in_ov_rect;
1781 final void setLargeFonts() {
1782 getTreeFontSet().largeFonts();
1785 final void setLastMouseDragPointX( final float x ) {
1786 _last_drag_point_x = x;
1789 final void setLastMouseDragPointY( final float y ) {
1790 _last_drag_point_y = y;
1793 final void setLongestExtNodeInfo( final int i ) {
1794 _longest_ext_node_info = i;
1797 final void setMediumFonts() {
1798 getTreeFontSet().mediumFonts();
1801 final void setNodeInPreorderToNull() {
1802 _nodes_in_preorder = null;
1805 final void setOvOn( final boolean ov_on ) {
1809 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
1810 _graphics_type = graphics_type;
1814 final void setSmallFonts() {
1815 getTreeFontSet().smallFonts();
1818 final void setStartingAngle( final double starting_angle ) {
1819 _urt_starting_angle = starting_angle;
1822 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
1823 _statistics_for_vector_data = statistics_for_expression_values;
1826 final void setSuperTinyFonts() {
1827 getTreeFontSet().superTinyFonts();
1830 final void setTextAntialias() {
1831 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
1832 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
1833 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
1836 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
1839 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
1840 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
1841 && !getMainPanel().getOptions().isShowDefaultNodeShapesInternal()
1842 && !getMainPanel().getOptions().isShowDefaultNodeShapesExternal()
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().isShowDefaultNodeShapesExternal() && node.isExternal() )
3816 || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
3817 || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
3818 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
3819 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3820 drawOvalGradient( x - half_box_size,
3825 to_pdf ? Color.WHITE : outline_color,
3826 to_pdf ? outline_color : getBackground(),
3829 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
3830 Color background = getBackground();
3832 background = Color.WHITE;
3834 drawOvalGradient( x - half_box_size,
3843 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3844 g.setColor( outline_color );
3845 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3848 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
3849 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
3850 drawRectGradient( x - half_box_size,
3855 to_pdf ? Color.WHITE : outline_color,
3856 to_pdf ? outline_color : getBackground(),
3859 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3860 Color background = getBackground();
3862 background = Color.WHITE;
3864 drawRectGradient( x - half_box_size,
3873 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3874 g.setColor( outline_color );
3875 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3882 final private void paintNodeData( final Graphics2D g,
3883 final PhylogenyNode node,
3884 final boolean to_graphics_file,
3885 final boolean to_pdf,
3886 final boolean is_in_found_nodes ) {
3887 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
3890 if ( getOptions().isShowBranchLengthValues()
3891 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3892 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3893 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
3894 paintBranchLength( g, node, to_pdf, to_graphics_file );
3896 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
3900 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3901 if ( getControlPanel().isShowTaxonomyImages()
3902 && ( getImageMap() != null )
3903 && !getImageMap().isEmpty()
3904 && node.getNodeData().isHasTaxonomy()
3905 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
3906 .getUris().isEmpty() ) ) {
3907 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
3909 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3910 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
3911 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
3913 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3914 g.setColor( Color.BLACK );
3916 else if ( is_in_found_nodes ) {
3917 g.setColor( getTreeColorSet().getFoundColor() );
3919 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3920 g.setColor( getTaxonomyBasedColor( node ) );
3922 else if ( getControlPanel().isColorAccordingToAnnotation()
3923 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
3924 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
3925 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
3927 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3928 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3929 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3931 else if ( to_pdf ) {
3932 g.setColor( Color.BLACK );
3935 g.setColor( getTreeColorSet().getSequenceColor() );
3938 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3940 _sb.append( node.getAllExternalDescendants().size() );
3943 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3944 if ( _sb.length() > 0 ) {
3947 _sb.append( node.getName() );
3949 if ( node.getNodeData().isHasSequence() ) {
3950 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
3951 if ( _sb.length() > 0 ) {
3954 _sb.append( node.getNodeData().getSequence().getSymbol() );
3956 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3957 if ( _sb.length() > 0 ) {
3960 _sb.append( node.getNodeData().getSequence().getName() );
3962 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3963 if ( _sb.length() > 0 ) {
3966 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3967 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3970 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3973 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
3974 if ( _sb.length() > 0 ) {
3977 _sb.append( propertiesToString( node ) );
3979 g.setFont( getTreeFontSet().getLargeFont() );
3980 if ( is_in_found_nodes ) {
3981 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3983 double down_shift_factor = 3.0;
3984 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
3985 down_shift_factor = 1;
3987 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
3988 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
3989 final String sb_str = _sb.toString();
3990 // GUILHEM_BEG ______________
3991 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
3992 && ( _query_sequence != null ) ) {
3993 int nodeTextBoundsWidth = 0;
3994 if ( sb_str.length() > 0 ) {
3995 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
3996 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
3998 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
3999 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
4000 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
4001 g.setColor( getTreeColorSet().getBackgroundColor() );
4005 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
4006 for( final SequenceRelation seqRelation : seqRelations ) {
4007 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
4008 .getRef1().isEqual( _query_sequence ) )
4009 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
4010 .getSelectedItem() );
4011 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
4012 final double linePosX = node.getXcoord() + 2 + half_box_size;
4013 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
4014 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
4016 if ( sConfidence != null ) {
4017 double confidenceX = pos_x;
4018 if ( sb_str.length() > 0 ) {
4019 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
4020 + CONFIDENCE_LEFT_MARGIN;
4022 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
4023 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
4024 .getBounds().getWidth();
4025 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
4026 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
4029 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
4031 if ( nodeTextBoundsWidth == 0 ) {
4032 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
4035 nodeTextBoundsWidth += 2;
4037 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
4038 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
4045 if ( sb_str.length() > 0 ) {
4046 TreePanel.drawString( sb_str, pos_x, pos_y, g );
4048 // GUILHEM_END _____________
4049 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
4050 // TODO FIXME need to check this one!
4051 //if ( _sb.length() > 0 ) {
4052 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
4053 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4055 // COMMENTED_OUT_BY_GUILHEM_END ________________
4056 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
4057 && ( node.getNodeData().getSequence().getAnnotations() != null )
4058 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4059 if ( _sb.length() > 0 ) {
4060 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4062 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
4063 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4064 g.setColor( Color.BLACK );
4066 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
4067 g.setColor( calculateColorForAnnotation( ann ) );
4069 final String ann_str = createAnnotationString( ann );
4070 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
4071 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4073 _sb.append( ann_str );
4075 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4076 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
4077 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
4078 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
4079 && node.getNodeData().isHasBinaryCharacters() ) {
4080 if ( _sb.length() > 0 ) {
4081 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4083 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4084 g.setColor( Color.BLACK );
4087 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
4089 if ( getControlPanel().isShowBinaryCharacters() ) {
4090 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
4091 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
4092 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4093 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
4094 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
4095 .getLostCharactersAsStringBuffer().toString() );
4098 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
4099 node.getXcoord() + x + 4 + half_box_size,
4101 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
4103 paintGainedAndLostCharacters( g, node, "+"
4104 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
4105 + node.getNodeData().getBinaryCharacters().getLostCount() );
4111 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
4112 final PhylogenyNode node,
4113 final boolean to_pdf,
4114 final boolean to_graphics_file,
4115 final boolean radial_labels,
4116 final double ur_angle,
4117 final boolean is_in_found_nodes ) {
4118 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
4121 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4122 g.setColor( Color.BLACK );
4124 else if ( is_in_found_nodes ) {
4125 g.setColor( getTreeColorSet().getFoundColor() );
4127 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4128 g.setColor( getTaxonomyBasedColor( node ) );
4130 else if ( getControlPanel().isColorAccordingToAnnotation()
4131 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4132 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4133 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4136 g.setColor( getTreeColorSet().getSequenceColor() );
4140 if ( node.getNodeData().isHasTaxonomy()
4141 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4142 .isShowTaxonomyCommonNames() ) ) {
4143 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4144 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4145 _sb.append( taxonomy.getTaxonomyCode() );
4148 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4149 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4150 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4151 _sb.append( taxonomy.getScientificName() );
4153 _sb.append( taxonomy.getCommonName() );
4156 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4157 _sb.append( taxonomy.getScientificName() );
4160 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4161 _sb.append( taxonomy.getCommonName() );
4165 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4166 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4167 _sb.append( taxonomy.getScientificName() );
4171 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4172 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4173 _sb.append( taxonomy.getCommonName() );
4178 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4180 _sb.append( node.getAllExternalDescendants().size() );
4183 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4184 if ( _sb.length() > 0 ) {
4187 _sb.append( node.getName() );
4189 if ( node.getNodeData().isHasSequence() ) {
4190 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4191 if ( _sb.length() > 0 ) {
4194 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4195 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4198 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4200 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4201 if ( _sb.length() > 0 ) {
4204 _sb.append( node.getNodeData().getSequence().getName() );
4207 g.setFont( getTreeFontSet().getLargeFont() );
4208 if ( is_in_found_nodes ) {
4209 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4211 if ( _sb.length() > 1 ) {
4212 final String sb_str = _sb.toString();
4214 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4215 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
4218 m = ( float ) ( ur_angle % TWO_PI );
4220 _at = g.getTransform();
4221 boolean need_to_reset = false;
4222 final float x_coord = node.getXcoord();
4223 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
4224 if ( radial_labels ) {
4225 need_to_reset = true;
4226 boolean left = false;
4227 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4231 g.rotate( m, x_coord, node.getYcoord() );
4233 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
4237 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4238 need_to_reset = true;
4239 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
4242 TreePanel.drawString( sb_str, x_coord, y_coord, g );
4243 if ( need_to_reset ) {
4244 g.setTransform( _at );
4249 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
4250 if ( node.isCollapse() ) {
4251 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
4252 paintCollapsedNode( g, node, false, false, false );
4256 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4257 g.setColor( getTreeColorSet().getFoundColor() );
4258 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
4261 if ( !node.isExternal() && !node.isCollapse() ) {
4262 boolean first_child = true;
4264 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4265 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4266 final PhylogenyNode child_node = node.getChildNode( i );
4268 if ( !isUniformBranchLengthsForCladogram() ) {
4269 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4272 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4274 if ( first_child ) {
4275 first_child = false;
4276 y2 = node.getYSecondary()
4277 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
4278 .getNumberOfExternalNodes() ) );
4281 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4283 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
4284 new_x = x2 + node.getXSecondary();
4285 final float diff_y = node.getYSecondary() - y2;
4286 final float diff_x = node.getXSecondary() - new_x;
4287 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
4288 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
4290 child_node.setXSecondary( new_x );
4291 child_node.setYSecondary( y2 );
4292 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4297 final private void paintNodeRectangular( final Graphics2D g,
4298 final PhylogenyNode node,
4299 final boolean to_pdf,
4300 final boolean dynamically_hide,
4301 final int dynamic_hiding_factor,
4302 final boolean to_graphics_file ) {
4303 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
4304 if ( node.isCollapse() ) {
4305 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
4306 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4310 if ( node.isExternal() ) {
4311 ++_external_node_index;
4313 // Confidence values
4314 if ( getControlPanel().isShowConfidenceValues()
4315 && !node.isExternal()
4317 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
4318 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4319 && node.getBranchData().isHasConfidences() ) {
4320 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
4322 // Draw a line to root:
4323 if ( node.isRoot() && _phylogeny.isRooted() ) {
4324 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
4327 float new_x_min = Float.MAX_VALUE;
4328 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
4329 float min_dist = 1.5f;
4330 if ( !disallow_shortcutting ) {
4331 // System.out.println( dynamic_hiding_factor );
4332 if ( dynamic_hiding_factor > 4000 ) {
4335 else if ( dynamic_hiding_factor > 1000 ) {
4338 else if ( dynamic_hiding_factor > 100 ) {
4342 if ( !node.isExternal() && !node.isCollapse() ) {
4343 boolean first_child = true;
4345 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4346 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4347 final PhylogenyNode child_node = node.getChildNode( i );
4349 if ( !isUniformBranchLengthsForCladogram() ) {
4350 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4353 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4355 if ( first_child ) {
4356 first_child = false;
4357 y2 = node.getYcoord()
4358 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
4361 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4363 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
4364 new_x = x2 + node.getXcoord();
4365 if ( dynamically_hide && ( x2 < new_x_min ) ) {
4368 final float diff_y = node.getYcoord() - y2;
4369 final float diff_x = node.getXcoord() - new_x;
4370 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
4371 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
4372 paintBranchRectangular( g,
4381 child_node.setXcoord( new_x );
4382 child_node.setYcoord( y2 );
4383 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4385 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
4386 || isInCurrentExternalNodes( node ) );
4388 if ( dynamically_hide
4389 && !is_in_found_nodes
4390 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
4391 .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
4392 .getHeight() ) ) ) ) ) {
4395 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4396 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
4399 final private void paintNodeWithRenderableData( final Graphics2D g,
4400 final PhylogenyNode node,
4401 final boolean to_graphics_file,
4402 final boolean to_pdf ) {
4403 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
4406 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
4409 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4410 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4411 RenderableDomainArchitecture rds = null;
4412 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
4414 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
4416 catch ( final ClassCastException cce ) {
4417 cce.printStackTrace();
4419 if ( rds != null ) {
4420 rds.setRenderingHeight( 6 );
4422 if ( node.getNodeData().isHasTaxonomy() ) {
4423 if ( getControlPanel().isShowTaxonomyCode()
4424 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
4425 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4429 if ( getControlPanel().isShowTaxonomyScientificNames()
4430 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
4431 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4432 .getScientificName()
4435 if ( getControlPanel().isShowTaxonomyCommonNames()
4436 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
4437 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4442 if ( node.getNodeData().isHasSequence() ) {
4443 if ( getControlPanel().isShowGeneNames()
4444 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
4445 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
4448 if ( getControlPanel().isShowGeneSymbols()
4449 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
4450 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
4453 if ( getControlPanel().isShowSequenceAcc()
4454 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4455 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
4456 .getAccession().toString()
4460 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
4461 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
4463 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
4468 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4469 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
4470 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
4471 getStatisticsForExpressionValues(),
4472 getConfiguration() );
4475 PhylogenyNode my_node = node;
4476 if ( !getControlPanel().isDrawPhylogram() ) {
4477 my_node = getPhylogeny().getFirstExternalNode();
4479 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
4480 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
4482 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
4483 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
4485 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
4491 final private void paintOvRectangle( final Graphics2D g ) {
4492 final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
4493 final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
4494 final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
4495 final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
4496 final float width = getOvMaxWidth() / w_ratio;
4497 final float height = getOvMaxHeight() / h_ratio;
4498 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
4499 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
4500 g.setColor( getTreeColorSet().getFoundColor() );
4501 getOvRectangle().setRect( x, y, width, height );
4502 if ( ( width < 6 ) && ( height < 6 ) ) {
4503 drawRectFilled( x, y, 6, 6, g );
4504 getOvVirtualRectangle().setRect( x, y, 6, 6 );
4506 else if ( width < 6 ) {
4507 drawRectFilled( x, y, 6, height, g );
4508 getOvVirtualRectangle().setRect( x, y, 6, height );
4510 else if ( height < 6 ) {
4511 drawRectFilled( x, y, width, 6, g );
4512 getOvVirtualRectangle().setRect( x, y, width, 6 );
4515 drawRect( x, y, width, height, g );
4516 if ( isInOvRect() ) {
4517 drawRect( x + 1, y + 1, width - 2, height - 2, g );
4519 getOvVirtualRectangle().setRect( x, y, width, height );
4523 final private void paintPhylogenyLite( final Graphics2D g ) {
4526 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
4527 .getWidth() ) ) ) );
4528 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
4529 for( final PhylogenyNode element : _nodes_in_preorder ) {
4530 paintNodeLite( g, element );
4532 paintOvRectangle( g );
4536 * Paint the root branch. (Differs from others because it will always be a
4537 * single horizontal line).
4538 * @param to_graphics_file
4540 * @return new x1 value
4542 final private void paintRootBranch( final Graphics2D g,
4545 final PhylogenyNode root,
4546 final boolean to_pdf,
4547 final boolean to_graphics_file ) {
4548 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
4549 float d = getXdistance();
4550 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
4551 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
4553 if ( d < MIN_ROOT_LENGTH ) {
4554 d = MIN_ROOT_LENGTH;
4556 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
4557 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
4560 final double w = PhylogenyMethods.getBranchWidthValue( root );
4561 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
4563 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
4566 final private void paintScale( final Graphics2D g,
4569 final boolean to_pdf,
4570 final boolean to_graphics_file ) {
4572 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
4574 final int y2 = y1 - 8;
4575 final int y3 = y1 - 4;
4576 g.setFont( getTreeFontSet().getSmallFont() );
4577 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4578 g.setColor( Color.BLACK );
4581 g.setColor( getTreeColorSet().getBranchLengthColor() );
4583 drawLine( x1, y1, x1, y2, g );
4584 drawLine( x2, y1, x2, y2, g );
4585 drawLine( x1, y3, x2, y3, g );
4586 if ( getScaleLabel() != null ) {
4587 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
4591 final private int paintTaxonomy( final Graphics2D g,
4592 final PhylogenyNode node,
4593 final boolean is_in_found_nodes,
4594 final boolean to_pdf,
4595 final boolean to_graphics_file,
4596 final double x_shift ) {
4597 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4598 g.setFont( getTreeFontSet().getLargeItalicFont() );
4599 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4600 g.setColor( Color.BLACK );
4602 else if ( is_in_found_nodes ) {
4603 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
4604 g.setColor( getTreeColorSet().getFoundColor() );
4606 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4607 g.setColor( getTaxonomyBasedColor( node ) );
4609 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4610 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4611 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4613 else if ( to_pdf ) {
4614 g.setColor( Color.BLACK );
4617 g.setColor( getTreeColorSet().getTaxonomyColor() );
4619 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4620 final double start_y = node.getYcoord()
4621 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4623 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4624 _sb.append( taxonomy.getTaxonomyCode() );
4627 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4628 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4629 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4630 if ( getOptions().isAbbreviateScientificTaxonNames()
4631 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4632 abbreviateScientificName( taxonomy.getScientificName() );
4635 _sb.append( taxonomy.getScientificName() );
4638 _sb.append( taxonomy.getCommonName() );
4641 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4642 if ( getOptions().isAbbreviateScientificTaxonNames()
4643 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4644 abbreviateScientificName( taxonomy.getScientificName() );
4647 _sb.append( taxonomy.getScientificName() );
4651 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4652 _sb.append( taxonomy.getCommonName() );
4656 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4657 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4658 if ( getOptions().isAbbreviateScientificTaxonNames()
4659 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4660 abbreviateScientificName( taxonomy.getScientificName() );
4663 _sb.append( taxonomy.getScientificName() );
4668 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4669 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4670 _sb.append( taxonomy.getCommonName() );
4674 final String label = _sb.toString();
4676 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4677 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4678 // invert font color and background color to show that this is the query sequence
4679 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4683 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4684 g.setColor( getTreeColorSet().getBackgroundColor() );
4687 TreePanel.drawString( label, start_x, start_y, g );
4688 if ( is_in_found_nodes ) {
4689 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4692 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4696 final private void paintUnrooted( final PhylogenyNode n,
4697 final double low_angle,
4698 final double high_angle,
4699 final boolean radial_labels,
4701 final boolean to_pdf,
4702 final boolean to_graphics_file ) {
4704 n.setXcoord( getWidth() / 2 );
4705 n.setYcoord( getHeight() / 2 );
4707 if ( n.isExternal() ) {
4708 paintNodeDataUnrootedCirc( g,
4713 ( high_angle + low_angle ) / 2,
4714 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
4717 final float num_enclosed = n.getNumberOfExternalNodes();
4718 final float x = n.getXcoord();
4719 final float y = n.getYcoord();
4720 double current_angle = low_angle;
4721 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4722 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4723 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4724 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4725 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4726 final PhylogenyNode desc = n.getChildNode( i );
4727 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4728 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4729 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4730 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4733 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4736 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4739 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4740 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4742 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4743 if ( desc.getDistanceToParent() < 0 ) {
4747 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4751 length = getUrtFactor();
4753 final double mid_angle = current_angle + ( arc_size / 2 );
4754 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4755 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4756 desc.setXcoord( new_x );
4757 desc.setYcoord( new_y );
4758 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4759 current_angle += arc_size;
4760 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4761 drawLine( x, y, new_x, new_y, g );
4762 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc )
4763 || isInCurrentExternalNodes( desc ) );
4766 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
4770 final private void paintUnrootedLite( final PhylogenyNode n,
4771 final double low_angle,
4772 final double high_angle,
4774 final float urt_ov_factor ) {
4776 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
4777 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
4778 n.setXSecondary( x_pos );
4779 n.setYSecondary( y_pos );
4781 if ( n.isExternal() ) {
4784 final float num_enclosed = n.getNumberOfExternalNodes();
4785 final float x = n.getXSecondary();
4786 final float y = n.getYSecondary();
4787 double current_angle = low_angle;
4788 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4789 final PhylogenyNode desc = n.getChildNode( i );
4790 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4791 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4793 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4794 if ( desc.getDistanceToParent() < 0 ) {
4798 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
4802 length = urt_ov_factor;
4804 final double mid_angle = current_angle + ( arc_size / 2 );
4805 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4806 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4807 desc.setXSecondary( new_x );
4808 desc.setYSecondary( new_y );
4809 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
4810 g.setColor( getTreeColorSet().getFoundColor() );
4811 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
4812 g.setColor( getTreeColorSet().getOvColor() );
4814 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4815 current_angle += arc_size;
4816 drawLine( x, y, new_x, new_y, g );
4820 final private void pasteSubtree( final PhylogenyNode node ) {
4821 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4822 errorMessageNoCutCopyPasteInUnrootedDisplay();
4825 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
4826 JOptionPane.showMessageDialog( this,
4827 "No tree in buffer (need to copy or cut a subtree first)",
4828 "Attempt to paste with empty buffer",
4829 JOptionPane.ERROR_MESSAGE );
4832 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
4833 final Object[] options = { "As sibling", "As descendant", "Cancel" };
4834 final int r = JOptionPane.showOptionDialog( this,
4835 "How to paste subtree" + label + "?",
4837 JOptionPane.CLOSED_OPTION,
4838 JOptionPane.QUESTION_MESSAGE,
4842 boolean paste_as_sibling = true;
4844 paste_as_sibling = false;
4846 else if ( r != 0 ) {
4849 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
4850 buffer_phy.setAllNodesToNotCollapse();
4851 PhylogenyMethods.preOrderReId( buffer_phy );
4852 buffer_phy.setRooted( true );
4853 boolean need_to_show_whole = false;
4854 if ( paste_as_sibling ) {
4855 if ( node.isRoot() ) {
4856 JOptionPane.showMessageDialog( this,
4857 "Cannot paste sibling to root",
4858 "Attempt to paste sibling to root",
4859 JOptionPane.ERROR_MESSAGE );
4862 buffer_phy.addAsSibling( node );
4865 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
4866 need_to_show_whole = true;
4867 _phylogeny = buffer_phy;
4870 buffer_phy.addAsChild( node );
4873 if ( getCopiedAndPastedNodes() == null ) {
4874 setCopiedAndPastedNodes( new HashSet<Integer>() );
4876 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
4877 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
4878 for( final PhylogenyNode n : nodes ) {
4879 node_ids.add( n.getId() );
4881 node_ids.add( node.getId() );
4882 getCopiedAndPastedNodes().addAll( node_ids );
4883 setNodeInPreorderToNull();
4884 _phylogeny.externalNodesHaveChanged();
4885 _phylogeny.clearHashIdToNodeMap();
4886 _phylogeny.recalculateNumberOfExternalDescendants( true );
4887 resetNodeIdToDistToLeafMap();
4889 if ( need_to_show_whole ) {
4890 getControlPanel().showWhole();
4895 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
4896 final PropertiesMap properties = node.getNodeData().getProperties();
4897 final StringBuffer sb = new StringBuffer();
4898 boolean first = true;
4899 for( final String ref : properties.getPropertyRefs() ) {
4906 final Property p = properties.getProperty( ref );
4907 sb.append( getPartAfterColon( p.getRef() ) );
4909 sb.append( p.getValue() );
4910 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
4911 sb.append( getPartAfterColon( p.getUnit() ) );
4917 final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
4918 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4921 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4922 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4925 final private void setInOv( final boolean in_ov ) {
4929 final private void setOvMaxHeight( final float ov_max_height ) {
4930 _ov_max_height = ov_max_height;
4933 final private void setOvMaxWidth( final float ov_max_width ) {
4934 _ov_max_width = ov_max_width;
4937 final private void setOvXcorrectionFactor( final float f ) {
4938 _ov_x_correction_factor = f;
4941 final private void setOvXDistance( final float ov_x_distance ) {
4942 _ov_x_distance = ov_x_distance;
4945 final private void setOvXPosition( final int ov_x_position ) {
4946 _ov_x_position = ov_x_position;
4949 final private void setOvYDistance( final float ov_y_distance ) {
4950 _ov_y_distance = ov_y_distance;
4953 final private void setOvYPosition( final int ov_y_position ) {
4954 _ov_y_position = ov_y_position;
4957 final private void setOvYStart( final int ov_y_start ) {
4958 _ov_y_start = ov_y_start;
4961 final private void setScaleDistance( final double scale_distance ) {
4962 _scale_distance = scale_distance;
4965 final private void setScaleLabel( final String scale_label ) {
4966 _scale_label = scale_label;
4969 final private void setUpUrtFactor() {
4970 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
4971 : getVisibleRect().height;
4972 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4973 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
4976 final int max_depth = _circ_max_depth;
4977 if ( max_depth > 0 ) {
4978 setUrtFactor( d / ( 2 * max_depth ) );
4981 setUrtFactor( d / 2 );
4984 setUrtFactorOv( getUrtFactor() );
4987 final private void setUrtFactor( final float urt_factor ) {
4988 _urt_factor = urt_factor;
4991 final private void setUrtFactorOv( final float urt_factor_ov ) {
4992 _urt_factor_ov = urt_factor_ov;
4995 private void showExtDescNodeData( final PhylogenyNode node ) {
4996 final List<String> data = new ArrayList<String>();
4997 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
4998 switch ( getOptions().getExtDescNodeDataToReturn() ) {
5000 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
5001 data.add( n.getName() );
5005 if ( n.getNodeData().isHasSequence()
5006 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5007 data.add( n.getNodeData().getSequence().getName() );
5010 case SEQUENCE_SYMBOL:
5011 if ( n.getNodeData().isHasSequence()
5012 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5013 data.add( n.getNodeData().getSequence().getSymbol() );
5016 case SEQUENCE_MOL_SEQ:
5017 if ( n.getNodeData().isHasSequence()
5018 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5019 data.add( n.getNodeData().getSequence().getMolecularSequence() );
5023 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
5024 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
5025 data.add( n.getNodeData().getSequence().getAccession().toString() );
5028 case TAXONOMY_SCIENTIFIC_NAME:
5029 if ( n.getNodeData().isHasTaxonomy()
5030 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5031 data.add( n.getNodeData().getTaxonomy().getScientificName() );
5035 if ( n.getNodeData().isHasTaxonomy()
5036 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5037 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5041 AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
5044 throw new IllegalArgumentException( "unknown data element: "
5045 + getOptions().getExtDescNodeDataToReturn() );
5048 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
5049 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
5050 final StringBuilder sb = new StringBuilder();
5051 for( final String d : data ) {
5052 if ( !ForesterUtil.isEmpty( d ) ) {
5053 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
5054 System.out.println( d );
5057 sb.append( ForesterUtil.LINE_SEPARATOR );
5060 if ( sb.length() < 1 ) {
5061 clearCurrentExternalNodesDataBuffer();
5064 setCurrentExternalNodesDataBuffer( sb );
5067 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
5068 final StringBuilder sb = new StringBuilder();
5069 for( final String d : data ) {
5070 if ( !ForesterUtil.isEmpty( d ) ) {
5072 sb.append( ForesterUtil.LINE_SEPARATOR );
5075 if ( sb.length() < 1 ) {
5076 AptxUtil.showInformationMessage( this,
5077 "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
5078 "Descendants of selected node do not contain selected data" );
5079 clearCurrentExternalNodesDataBuffer();
5082 setCurrentExternalNodesDataBuffer( sb );
5083 final String title = "External Descendants "
5084 + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5085 : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
5086 + node.getNumberOfExternalNodes() + ") For Node " + node;
5087 final String s = sb.toString().trim();
5088 if ( getMainPanel().getMainFrame() == null ) {
5089 // Must be "E" applet version.
5090 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
5091 ae.showTextFrame( s, title );
5094 getMainPanel().getMainFrame().showTextFrame( s, title );
5100 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
5102 if ( ( node.getName().length() > 0 )
5103 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
5104 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
5105 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
5106 || node.getBranchData().isHasConfidences() ) {
5107 _popup_buffer.setLength( 0 );
5109 if ( node.getName().length() > 0 ) {
5111 _popup_buffer.append( node.getName() );
5113 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
5115 boolean enc_data = false;
5116 final Taxonomy tax = node.getNodeData().getTaxonomy();
5117 if ( _popup_buffer.length() > 0 ) {
5118 _popup_buffer.append( "\n" );
5120 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
5121 _popup_buffer.append( "[" );
5122 _popup_buffer.append( tax.getTaxonomyCode() );
5123 _popup_buffer.append( "]" );
5126 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
5128 _popup_buffer.append( " " );
5130 _popup_buffer.append( tax.getScientificName() );
5133 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
5135 _popup_buffer.append( " (" );
5138 _popup_buffer.append( "(" );
5140 _popup_buffer.append( tax.getCommonName() );
5141 _popup_buffer.append( ")" );
5144 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
5146 _popup_buffer.append( " (" );
5149 _popup_buffer.append( "(" );
5151 _popup_buffer.append( tax.getAuthority() );
5152 _popup_buffer.append( ")" );
5155 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
5157 _popup_buffer.append( " [" );
5160 _popup_buffer.append( "[" );
5162 _popup_buffer.append( tax.getRank() );
5163 _popup_buffer.append( "]" );
5166 if ( tax.getSynonyms().size() > 0 ) {
5168 _popup_buffer.append( " " );
5170 _popup_buffer.append( "[" );
5172 for( final String syn : tax.getSynonyms() ) {
5173 if ( !ForesterUtil.isEmpty( syn ) ) {
5175 _popup_buffer.append( syn );
5176 if ( counter < tax.getSynonyms().size() ) {
5177 _popup_buffer.append( ", " );
5182 _popup_buffer.append( "]" );
5185 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
5186 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
5187 _popup_buffer.append( "[" );
5188 _popup_buffer.append( tax.getIdentifier().getProvider() );
5189 _popup_buffer.append( "] " );
5191 _popup_buffer.append( tax.getIdentifier().getValue() );
5195 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
5197 boolean enc_data = false;
5198 if ( _popup_buffer.length() > 0 ) {
5199 _popup_buffer.append( "\n" );
5201 final Sequence seq = node.getNodeData().getSequence();
5202 if ( seq.getAccession() != null ) {
5203 _popup_buffer.append( "[" );
5204 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
5205 _popup_buffer.append( seq.getAccession().getSource() );
5206 _popup_buffer.append( ":" );
5208 _popup_buffer.append( seq.getAccession().getValue() );
5209 _popup_buffer.append( "]" );
5212 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
5214 _popup_buffer.append( " [" );
5217 _popup_buffer.append( "[" );
5219 _popup_buffer.append( seq.getSymbol() );
5220 _popup_buffer.append( "]" );
5223 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
5225 _popup_buffer.append( " " );
5227 _popup_buffer.append( seq.getName() );
5230 if ( node.getNodeData().isHasDate() ) {
5232 if ( _popup_buffer.length() > 0 ) {
5233 _popup_buffer.append( "\n" );
5235 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
5237 if ( node.getNodeData().isHasDistribution() ) {
5239 if ( _popup_buffer.length() > 0 ) {
5240 _popup_buffer.append( "\n" );
5242 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
5244 if ( node.getBranchData().isHasConfidences() ) {
5245 final List<Confidence> confs = node.getBranchData().getConfidences();
5246 for( final Confidence confidence : confs ) {
5248 if ( _popup_buffer.length() > 0 ) {
5249 _popup_buffer.append( "\n" );
5251 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
5252 _popup_buffer.append( "[" );
5253 _popup_buffer.append( confidence.getType() );
5254 _popup_buffer.append( "] " );
5257 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
5259 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5260 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5261 _popup_buffer.append( " (sd=" );
5262 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
5263 .getStandardDeviation(), getOptions()
5264 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5265 _popup_buffer.append( ")" );
5269 if ( node.getNodeData().isHasProperties() ) {
5270 final PropertiesMap properties = node.getNodeData().getProperties();
5271 for( final String ref : properties.getPropertyRefs() ) {
5272 _popup_buffer.append( "\n" );
5273 final Property p = properties.getProperty( ref );
5274 _popup_buffer.append( getPartAfterColon( p.getRef() ) );
5275 _popup_buffer.append( "=" );
5276 _popup_buffer.append( p.getValue() );
5277 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5278 _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
5282 if ( _popup_buffer.length() > 0 ) {
5283 if ( !getConfiguration().isUseNativeUI() ) {
5285 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
5286 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
5287 if ( isInFoundNodes( node ) ) {
5288 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
5290 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
5291 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
5294 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
5298 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
5300 _rollover_popup.setText( _popup_buffer.toString() );
5301 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
5303 e.getLocationOnScreen().x + 10,
5304 e.getLocationOnScreen().y
5306 _node_desc_popup.show();
5310 catch ( final Exception ex ) {
5315 final private void showNodeEditFrame( final PhylogenyNode n ) {
5316 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5317 // pop up edit box for single node
5318 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
5319 _node_frame_index++;
5322 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5326 final private void showNodeFrame( final PhylogenyNode n ) {
5327 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5328 // pop up edit box for single node
5329 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
5330 _node_frame_index++;
5333 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5337 final private void switchDisplaygetPhylogenyGraphicsType() {
5338 switch ( getPhylogenyGraphicsType() ) {
5340 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5341 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5344 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5345 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5348 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5349 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5352 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5353 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5356 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5357 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5360 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5361 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5364 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5365 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5368 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5369 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5372 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5374 if ( getControlPanel().getDynamicallyHideData() != null ) {
5375 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5376 getControlPanel().getDynamicallyHideData().setEnabled( false );
5379 getControlPanel().getDynamicallyHideData().setEnabled( true );
5382 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5383 getControlPanel().setDrawPhylogramEnabled( true );
5386 getControlPanel().setDrawPhylogramEnabled( false );
5388 if ( getMainPanel().getMainFrame() == null ) {
5389 // Must be "E" applet version.
5390 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5391 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5394 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5398 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
5399 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5402 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5403 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5406 final private static String getPartAfterColon( final String s ) {
5407 final int i = s.indexOf( ':' );
5408 if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
5411 return s.substring( i + 1, s.length() );
5414 final private static boolean isSequenceEmpty( final Sequence seq ) {
5415 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
5416 && ForesterUtil.isEmpty( seq.getSymbol() );
5419 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
5420 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
5421 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
5422 .getSynonyms().isEmpty() );
5425 final private static boolean plusPressed( final int key_code ) {
5426 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5427 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5430 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
5431 final Phylogeny new_phy = new Phylogeny();
5432 new_phy.setRooted( true );
5433 new_phy.setName( source_phy.getName() );
5434 new_phy.setDescription( source_phy.getDescription() );
5435 new_phy.setType( source_phy.getType() );
5436 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
5437 new_phy.setConfidence( source_phy.getConfidence() );
5438 new_phy.setIdentifier( source_phy.getIdentifier() );
5439 new_phy.setRoot( new_root.copyNodeDataShallow() );
5441 for( final PhylogenyNode n : new_root.getDescendants() ) {
5442 new_phy.getRoot().setChildNode( i++, n );
5447 final private class SubtreeColorizationActionListener implements ActionListener {
5449 JColorChooser _chooser;
5450 PhylogenyNode _node;
5452 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5458 public void actionPerformed( final ActionEvent e ) {
5459 final Color c = _chooser.getColor();
5461 colorizeSubtree( c, _node );