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() > y / 2 ) && ( 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().isShowDefaultNodeShapes()
1842 && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
1843 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1846 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
1849 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
1850 RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
1852 catch ( final Throwable e ) {
1853 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
1857 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
1858 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1862 final void setTinyFonts() {
1863 getTreeFontSet().tinyFonts();
1866 final void setTreeFile( final File treefile ) {
1867 _treefile = treefile;
1870 final void setXcorrectionFactor( final float f ) {
1871 _x_correction_factor = f;
1874 final void setXdistance( final float x ) {
1878 final void setYdistance( final float y ) {
1882 final void sortDescendants( final PhylogenyNode node ) {
1883 if ( !node.isExternal() ) {
1884 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
1885 if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
1886 .isShowTaxonomyCommonNames() ) ) {
1887 if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
1888 .isShowGeneSymbols() ) ) {
1889 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
1891 else if ( getControlPanel().isShowNodeNames() ) {
1892 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
1895 PhylogenyMethods.sortNodeDescendents( node, pri );
1896 setNodeInPreorderToNull();
1897 _phylogeny.externalNodesHaveChanged();
1898 _phylogeny.clearHashIdToNodeMap();
1899 _phylogeny.recalculateNumberOfExternalDescendants( true );
1900 resetNodeIdToDistToLeafMap();
1906 final void subTree( final PhylogenyNode node ) {
1907 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1908 JOptionPane.showMessageDialog( this,
1909 "Cannot get a sub/super tree in unrooted display",
1910 "Attempt to get sub/super tree in unrooted display",
1911 JOptionPane.WARNING_MESSAGE );
1914 if ( node.isExternal() ) {
1915 JOptionPane.showMessageDialog( this,
1916 "Cannot get a subtree of a external node",
1917 "Attempt to get subtree of external node",
1918 JOptionPane.WARNING_MESSAGE );
1921 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
1922 JOptionPane.showMessageDialog( this,
1923 "Cannot get a subtree of the root node",
1924 "Attempt to get subtree of root node",
1925 JOptionPane.WARNING_MESSAGE );
1928 setNodeInPreorderToNull();
1929 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
1930 _sub_phylogenies[ _subtree_index ] = _phylogeny;
1931 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
1933 _phylogeny = subTree( node, _phylogeny );
1934 updateSubSuperTreeButton();
1936 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
1939 _main_panel.getControlPanel().showWhole();
1943 final void superTree() {
1944 setNodeInPreorderToNull();
1945 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
1946 for( final PhylogenyNode n : temp_root.getDescendants() ) {
1947 n.setParent( temp_root );
1949 _sub_phylogenies[ _subtree_index ] = null;
1950 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
1951 _phylogeny = _sub_phylogenies[ --_subtree_index ];
1952 updateSubSuperTreeButton();
1955 final void swap( final PhylogenyNode node ) {
1956 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
1959 if ( node.getNumberOfDescendants() > 2 ) {
1960 JOptionPane.showMessageDialog( this,
1961 "Cannot swap descendants of nodes with more than 2 descendants",
1962 "Cannot swap descendants",
1963 JOptionPane.ERROR_MESSAGE );
1966 if ( !node.isExternal() ) {
1967 node.swapChildren();
1968 setNodeInPreorderToNull();
1969 _phylogeny.externalNodesHaveChanged();
1970 _phylogeny.clearHashIdToNodeMap();
1971 _phylogeny.recalculateNumberOfExternalDescendants( true );
1972 resetNodeIdToDistToLeafMap();
1978 final void taxColor() {
1979 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1983 AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
1984 _control_panel.setColorBranches( true );
1985 if ( _control_panel.getColorBranchesCb() != null ) {
1986 _control_panel.getColorBranchesCb().setSelected( true );
1992 final void updateOvSettings() {
1993 switch ( getOptions().getOvPlacement() ) {
1995 setOvXPosition( OV_BORDER );
1996 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
1997 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2000 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2001 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2002 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2005 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2006 setOvYPosition( OV_BORDER );
2007 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2010 setOvXPosition( OV_BORDER );
2011 setOvYPosition( OV_BORDER );
2012 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2017 final void updateOvSizes() {
2018 if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
2020 float l = getLongestExtNodeInfo();
2021 final float w_ratio = getOvMaxWidth() / getWidth();
2023 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
2024 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
2026 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
2027 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
2030 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
2032 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
2033 if ( ov_xdist < 0.0 ) {
2036 if ( ydist < 0.0 ) {
2039 setOvXDistance( ov_xdist );
2040 final double height = _phylogeny.getHeight();
2042 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
2043 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
2046 setOvXcorrectionFactor( 0 );
2054 void updateSetOfCollapsedExternalNodes() {
2055 final Phylogeny phy = getPhylogeny();
2056 _collapsed_external_nodeid_set.clear();
2057 if ( phy != null ) {
2058 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2059 final PhylogenyNode ext_node = it.next();
2060 PhylogenyNode n = ext_node;
2061 while ( !n.isRoot() ) {
2062 if ( n.isCollapse() ) {
2063 _collapsed_external_nodeid_set.add( ext_node.getId() );
2064 ext_node.setCollapse( true );
2073 final void updateSubSuperTreeButton() {
2074 if ( _subtree_index < 1 ) {
2075 getControlPanel().deactivateButtonToReturnToSuperTree();
2078 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
2082 final void zoomInDomainStructure() {
2083 if ( _domain_structure_width < 2000 ) {
2084 _domain_structure_width *= 1.2;
2088 final void zoomOutDomainStructure() {
2089 if ( _domain_structure_width > 20 ) {
2090 _domain_structure_width *= 0.8;
2094 private void abbreviateScientificName( final String sn ) {
2095 final String[] a = sn.split( "\\s+" );
2096 _sb.append( a[ 0 ].substring( 0, 1 ) );
2097 _sb.append( a[ 1 ].substring( 0, 2 ) );
2098 if ( a.length > 2 ) {
2099 for( int i = 2; i < a.length; i++ ) {
2101 _sb.append( a[ i ] );
2106 final private void addEmptyNode( final PhylogenyNode node ) {
2107 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2108 errorMessageNoCutCopyPasteInUnrootedDisplay();
2111 final String label = createASimpleTextRepresentationOfANode( node );
2113 if ( ForesterUtil.isEmpty( label ) ) {
2114 msg = "How to add the new, empty node?";
2117 msg = "How to add the new, empty node to node" + label + "?";
2119 final Object[] options = { "As sibling", "As descendant", "Cancel" };
2120 final int r = JOptionPane.showOptionDialog( this,
2122 "Addition of Empty New Node",
2123 JOptionPane.CLOSED_OPTION,
2124 JOptionPane.QUESTION_MESSAGE,
2128 boolean add_as_sibling = true;
2130 add_as_sibling = false;
2132 else if ( r != 0 ) {
2135 final Phylogeny phy = new Phylogeny();
2136 phy.setRoot( new PhylogenyNode() );
2137 phy.setRooted( true );
2138 if ( add_as_sibling ) {
2139 if ( node.isRoot() ) {
2140 JOptionPane.showMessageDialog( this,
2141 "Cannot add sibling to root",
2142 "Attempt to add sibling to root",
2143 JOptionPane.ERROR_MESSAGE );
2146 phy.addAsSibling( node );
2149 phy.addAsChild( node );
2151 setNodeInPreorderToNull();
2152 _phylogeny.externalNodesHaveChanged();
2153 _phylogeny.clearHashIdToNodeMap();
2154 _phylogeny.recalculateNumberOfExternalDescendants( true );
2155 resetNodeIdToDistToLeafMap();
2160 final private void addToCurrentExternalNodes( final int i ) {
2161 if ( _current_external_nodes == null ) {
2162 _current_external_nodes = new HashSet<Integer>();
2164 _current_external_nodes.add( i );
2167 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
2168 final boolean is_vertical,
2170 final boolean to_pdf,
2171 final boolean to_graphics_file ) {
2172 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
2173 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2174 g.setColor( Color.BLACK );
2176 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
2177 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
2178 && ( getCutOrCopiedTree() != null )
2179 && ( getCopiedAndPastedNodes() != null )
2181 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
2182 g.setColor( getTreeColorSet().getFoundColor() );
2184 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2185 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2187 else if ( to_pdf ) {
2188 g.setColor( getTreeColorSet().getBranchColorForPdf() );
2191 g.setColor( getTreeColorSet().getBranchColor() );
2195 final private void blast( final PhylogenyNode node ) {
2196 if ( !isCanBlast( node ) ) {
2197 JOptionPane.showMessageDialog( this,
2198 "Insufficient information present",
2200 JOptionPane.INFORMATION_MESSAGE );
2204 final String query = Blast.obtainQueryForBlast( node );
2205 System.out.println( "query for BLAST is: " + query );
2207 if ( !ForesterUtil.isEmpty( query ) ) {
2208 if ( node.getNodeData().isHasSequence() ) {
2209 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
2210 if ( node.getNodeData().getSequence().getType().toLowerCase()
2211 .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
2218 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2219 if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2227 if ( type == '?' ) {
2228 if ( SequenceIdParser.isProtein( query ) ) {
2235 JApplet applet = null;
2237 applet = obtainApplet();
2240 Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
2242 catch ( final Exception e ) {
2243 e.printStackTrace();
2245 if ( Constants.ALLOW_DDBJ_BLAST ) {
2247 System.out.println( "trying: " + query );
2248 final Blast s = new Blast();
2249 s.ddbjBlast( query );
2251 catch ( final Exception e ) {
2252 e.printStackTrace();
2260 * Calculate the length of the distance between the given node and its
2266 * @return the distance value
2268 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
2269 if ( getControlPanel().isDrawPhylogram() ) {
2270 if ( node.getDistanceToParent() < 0.0 ) {
2273 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
2276 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2277 return getXdistance();
2279 return getXdistance() * factor;
2283 final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
2284 Color c = getTreeColorSet().getAnnotationColor();
2285 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
2286 final StringBuilder sb = new StringBuilder();
2287 for( final Annotation a : ann ) {
2288 sb.append( !ForesterUtil.isEmpty( a.getRef() ) ? a.getRef() : a.getDesc() );
2290 final String ann_str = sb.toString();
2291 if ( !ForesterUtil.isEmpty( ann_str ) ) {
2292 c = getControlPanel().getAnnotationColors().get( ann_str );
2294 c = AptxUtil.calculateColorFromString( ann_str );
2295 getControlPanel().getAnnotationColors().put( ann_str, c );
2298 c = getTreeColorSet().getAnnotationColor();
2305 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
2306 if ( getControlPanel().isDrawPhylogram() ) {
2307 if ( node.getDistanceToParent() < 0.0 ) {
2310 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
2313 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2314 return getOvXDistance();
2316 return getOvXDistance() * factor;
2320 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
2321 JOptionPane.showMessageDialog( this,
2322 "Cannot launch web browser for " + type_type + " data of this node",
2323 "Cannot launch web browser",
2324 JOptionPane.WARNING_MESSAGE );
2327 final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
2328 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2329 JOptionPane.showMessageDialog( this,
2330 "Cannot colorize subtree in unrooted display type",
2331 "Attempt to colorize subtree in unrooted display",
2332 JOptionPane.WARNING_MESSAGE );
2335 _control_panel.setColorBranches( true );
2336 if ( _control_panel.getColorBranchesCb() != null ) {
2337 _control_panel.getColorBranchesCb().setSelected( true );
2339 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
2340 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
2345 final private void colorSubtree( final PhylogenyNode node ) {
2346 Color intitial_color = null;
2347 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
2348 && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
2349 intitial_color = PhylogenyMethods.getBranchColorValue( node );
2352 intitial_color = getTreeColorSet().getBranchColor();
2354 _color_chooser.setColor( intitial_color );
2355 _color_chooser.setPreviewPanel( new JPanel() );
2356 final JDialog dialog = JColorChooser
2357 .createDialog( this,
2358 "Subtree colorization",
2361 new SubtreeColorizationActionListener( _color_chooser, node ),
2363 dialog.setVisible( true );
2366 final private void copySubtree( final PhylogenyNode node ) {
2367 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2368 errorMessageNoCutCopyPasteInUnrootedDisplay();
2371 setNodeInPreorderToNull();
2372 setCutOrCopiedTree( _phylogeny.copy( node ) );
2373 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
2374 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
2375 for( final PhylogenyNode n : nodes ) {
2376 node_ids.add( n.getId() );
2378 node_ids.add( node.getId() );
2379 setCopiedAndPastedNodes( node_ids );
2383 private String createAnnotationString( final SortedSet<Annotation> ann ) {
2384 final StringBuilder sb = new StringBuilder();
2385 boolean first = true;
2386 for( final Annotation a : ann ) {
2393 sb.append( a.asSimpleText() );
2395 final String ann_str = sb.toString();
2399 final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
2400 final String tax = PhylogenyMethods.getSpecies( node );
2401 String label = node.getName();
2402 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
2403 label = label + " " + tax;
2405 else if ( !ForesterUtil.isEmpty( tax ) ) {
2411 if ( !ForesterUtil.isEmpty( label ) ) {
2412 label = " [" + label + "]";
2417 final private void cutSubtree( final PhylogenyNode node ) {
2418 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2419 errorMessageNoCutCopyPasteInUnrootedDisplay();
2422 if ( node.isRoot() ) {
2423 JOptionPane.showMessageDialog( this,
2424 "Cannot cut entire tree as subtree",
2425 "Attempt to cut entire tree",
2426 JOptionPane.ERROR_MESSAGE );
2429 final String label = createASimpleTextRepresentationOfANode( node );
2430 final int r = JOptionPane.showConfirmDialog( null,
2431 "Cut subtree" + label + "?",
2432 "Confirm Cutting of Subtree",
2433 JOptionPane.YES_NO_OPTION );
2434 if ( r != JOptionPane.OK_OPTION ) {
2437 setNodeInPreorderToNull();
2438 setCopiedAndPastedNodes( null );
2439 setCutOrCopiedTree( _phylogeny.copy( node ) );
2440 _phylogeny.deleteSubtree( node, true );
2441 _phylogeny.clearHashIdToNodeMap();
2442 _phylogeny.recalculateNumberOfExternalDescendants( true );
2443 resetNodeIdToDistToLeafMap();
2448 final private void cycleColors() {
2449 getMainPanel().getTreeColorSet().cycleColorScheme();
2450 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
2451 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
2455 final private void decreaseOvSize() {
2456 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
2457 setOvMaxWidth( getOvMaxWidth() - 5 );
2458 setOvMaxHeight( getOvMaxHeight() - 5 );
2460 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2464 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
2465 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2466 errorMessageNoCutCopyPasteInUnrootedDisplay();
2469 if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
2470 JOptionPane.showMessageDialog( this,
2471 "Cannot delete entire tree",
2472 "Attempt to delete entire tree",
2473 JOptionPane.ERROR_MESSAGE );
2476 final String label = createASimpleTextRepresentationOfANode( node );
2477 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
2478 final int r = JOptionPane.showOptionDialog( this,
2479 "Delete" + label + "?",
2480 "Delete Node/Subtree",
2481 JOptionPane.CLOSED_OPTION,
2482 JOptionPane.QUESTION_MESSAGE,
2486 setNodeInPreorderToNull();
2487 boolean node_only = true;
2491 else if ( r != 0 ) {
2495 PhylogenyMethods.removeNode( node, _phylogeny );
2498 _phylogeny.deleteSubtree( node, true );
2500 _phylogeny.externalNodesHaveChanged();
2501 _phylogeny.clearHashIdToNodeMap();
2502 _phylogeny.recalculateNumberOfExternalDescendants( true );
2503 resetNodeIdToDistToLeafMap();
2508 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
2509 makePopupMenus( node );
2510 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
2511 _node_popup_menu.show( this, x, y );
2514 final private void drawArc( final double x,
2517 final double heigth,
2518 final double start_angle,
2519 final double arc_angle,
2520 final Graphics2D g ) {
2521 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
2525 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
2526 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
2529 _line.setLine( x1, y1, x2, y2 );
2533 final private void drawOval( final double x,
2536 final double heigth,
2537 final Graphics2D g ) {
2538 _ellipse.setFrame( x, y, width, heigth );
2542 final private void drawOvalFilled( final double x,
2545 final double heigth,
2546 final Graphics2D g ) {
2547 _ellipse.setFrame( x, y, width, heigth );
2551 final private void drawOvalGradient( final double x,
2554 final double heigth,
2556 final Color color_1,
2557 final Color color_2,
2558 final Color color_border ) {
2559 _ellipse.setFrame( x, y, width, heigth );
2560 g.setPaint( new GradientPaint( ( float ) x,
2563 ( float ) ( x + width ),
2564 ( float ) ( y + heigth ),
2568 if ( color_border != null ) {
2569 g.setPaint( color_border );
2574 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
2575 _rectangle.setFrame( x, y, width, heigth );
2576 g.draw( _rectangle );
2579 final private void drawRectFilled( final double x,
2582 final double heigth,
2583 final Graphics2D g ) {
2584 _rectangle.setFrame( x, y, width, heigth );
2585 g.fill( _rectangle );
2588 final private void drawRectGradient( final double x,
2591 final double heigth,
2593 final Color color_1,
2594 final Color color_2,
2595 final Color color_border ) {
2596 _rectangle.setFrame( x, y, width, heigth );
2597 g.setPaint( new GradientPaint( ( float ) x,
2600 ( float ) ( x + width ),
2601 ( float ) ( y + heigth ),
2604 g.fill( _rectangle );
2605 if ( color_border != null ) {
2606 g.setPaint( color_border );
2607 g.draw( _rectangle );
2611 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2612 final List<Uri> us = new ArrayList<Uri>();
2613 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2614 for( final Uri uri : t.getUris() ) {
2619 for( final Uri uri : us ) {
2620 if ( uri != null ) {
2621 final String uri_str = uri.getValue().toString().toLowerCase();
2622 if ( getImageMap().containsKey( uri_str ) ) {
2623 final BufferedImage bi = getImageMap().get( uri_str );
2624 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2625 double scaling_factor = 1;
2626 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
2627 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
2628 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
2630 // y = y - ( 0.9 * getYdistance() );
2631 final double hs = bi.getHeight() * scaling_factor;
2632 double ws = ( bi.getWidth() * scaling_factor ) + offset;
2633 final double my_y = y - ( 0.5 * hs );
2634 final int x_w = ( int ) ( x + ws + 0.5 );
2635 final int y_h = ( int ) ( my_y + hs + 0.5 );
2636 if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
2638 ( int ) ( x + 0.5 + offset ),
2639 ( int ) ( my_y + 0.5 ),
2660 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
2661 JOptionPane.showMessageDialog( this,
2662 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
2663 "Attempt to cut/copy/paste/add/delete in unrooted display",
2664 JOptionPane.ERROR_MESSAGE );
2667 final private Set<Integer> getCopiedAndPastedNodes() {
2668 return getMainPanel().getCopiedAndPastedNodes();
2671 final private Set<Integer> getCurrentExternalNodes() {
2672 return _current_external_nodes;
2675 final private Phylogeny getCutOrCopiedTree() {
2676 return getMainPanel().getCutOrCopiedTree();
2679 final private float getLastDragPointX() {
2680 return _last_drag_point_x;
2683 final private float getLastDragPointY() {
2684 return _last_drag_point_y;
2687 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
2688 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
2689 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
2690 _nodeid_dist_to_leaf.put( node.getId(), m );
2694 return _nodeid_dist_to_leaf.get( node.getId() );
2698 final private double getMaxDistanceToRoot() {
2699 if ( _max_distance_to_root < 0 ) {
2700 recalculateMaxDistanceToRoot();
2702 return _max_distance_to_root;
2705 final private float getOvMaxHeight() {
2706 return _ov_max_height;
2709 final private float getOvMaxWidth() {
2710 return _ov_max_width;
2713 final private float getOvXcorrectionFactor() {
2714 return _ov_x_correction_factor;
2717 final private float getOvXDistance() {
2718 return _ov_x_distance;
2721 final private int getOvXPosition() {
2722 return _ov_x_position;
2725 final private float getOvYDistance() {
2726 return _ov_y_distance;
2729 final private int getOvYPosition() {
2730 return _ov_y_position;
2733 final private int getOvYStart() {
2737 final private double getScaleDistance() {
2738 return _scale_distance;
2741 final private String getScaleLabel() {
2742 return _scale_label;
2745 final private TreeFontSet getTreeFontSet() {
2746 return getMainPanel().getTreeFontSet();
2749 final private float getUrtFactor() {
2753 final private float getUrtFactorOv() {
2754 return _urt_factor_ov;
2757 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
2760 showNodeFrame( node );
2775 colorSubtree( node );
2790 copySubtree( node );
2793 pasteSubtree( node );
2795 case DELETE_NODE_OR_SUBTREE:
2796 deleteNodeOrSubtree( node );
2799 addEmptyNode( node );
2801 case EDIT_NODE_DATA:
2802 showNodeEditFrame( node );
2807 case SORT_DESCENDENTS:
2808 sortDescendants( node );
2810 case GET_EXT_DESC_DATA:
2811 showExtDescNodeData( node );
2814 throw new IllegalArgumentException( "unknown action: " + action );
2818 final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
2819 _current_external_nodes_data_buffer_change_counter++;
2822 final private void increaseOvSize() {
2823 if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
2824 && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
2825 .getHeight() / 2 ) ) ) {
2826 setOvMaxWidth( getOvMaxWidth() + 5 );
2827 setOvMaxHeight( getOvMaxHeight() + 5 );
2829 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2833 final private void init() {
2834 _color_chooser = new JColorChooser();
2835 _rollover_popup = new JTextArea();
2836 _rollover_popup.setFont( POPUP_FONT );
2837 resetNodeIdToDistToLeafMap();
2839 setTreeFile( null );
2841 initializeOvSettings();
2842 setStartingAngle( ( TWO_PI * 3 ) / 4 );
2843 final ImageLoader il = new ImageLoader( this );
2844 new Thread( il ).start();
2847 final private void initializeOvSettings() {
2848 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
2849 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
2852 final private boolean inOvVirtualRectangle( final int x, final int y ) {
2853 return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
2854 && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
2855 && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
2856 + getOvVirtualRectangle().height + 1 ) ) );
2859 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
2860 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
2863 final private boolean isCanBlast( final PhylogenyNode node ) {
2864 if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
2867 return Blast.isContainsQueryForBlast( node );
2870 final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
2871 if ( node.getNodeData().isHasSequence()
2872 && ( node.getNodeData().getSequence().getAccession() != null )
2873 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
2874 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
2875 && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
2876 .toLowerCase() ) ) {
2882 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
2883 if ( node.getNodeData().isHasTaxonomy()
2884 && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
2885 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
2886 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
2887 .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
2888 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
2889 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
2890 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
2891 .getNodeData().getTaxonomy().getIdentifier() != null )
2892 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
2893 .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
2901 final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
2902 return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
2905 final private boolean isInFoundNodes( final PhylogenyNode node ) {
2906 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
2909 final private boolean isInOv() {
2913 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
2915 if ( getControlPanel().isShowTaxonomyImages() ) {
2916 y_dist = 40 + ( int ) getYdistance();
2918 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
2919 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
2920 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
2923 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
2924 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
2925 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
2926 || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
2927 .getMaxX() + 20 ) ) );
2930 final private boolean isNonLinedUpCladogram() {
2931 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
2934 final private boolean isUniformBranchLengthsForCladogram() {
2935 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
2938 final private void keyPressedCalls( final KeyEvent e ) {
2939 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
2940 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
2941 if ( !isInOvRect() ) {
2942 setInOvRect( true );
2945 else if ( isInOvRect() ) {
2946 setInOvRect( false );
2949 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
2950 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2951 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2952 getMainPanel().getTreeFontSet().mediumFonts();
2953 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2955 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
2956 getMainPanel().getTreeFontSet().decreaseFontSize();
2957 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2959 else if ( plusPressed( e.getKeyCode() ) ) {
2960 getMainPanel().getTreeFontSet().increaseFontSize();
2961 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2965 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2966 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2967 getControlPanel().showWhole();
2969 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
2970 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
2971 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
2972 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
2973 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
2974 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2976 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
2977 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
2978 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2980 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
2981 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
2982 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
2983 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2985 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
2986 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
2987 Constants.WHEEL_ZOOM_IN_FACTOR );
2988 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2995 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
2998 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3002 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3006 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
3007 scroll_position.x = scroll_position.x + dx;
3008 scroll_position.y = scroll_position.y + dy;
3009 if ( scroll_position.x <= 0 ) {
3010 scroll_position.x = 0;
3013 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
3014 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
3015 if ( scroll_position.x >= max_x ) {
3016 scroll_position.x = max_x;
3019 if ( scroll_position.y <= 0 ) {
3020 scroll_position.y = 0;
3023 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
3024 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
3025 if ( scroll_position.y >= max_y ) {
3026 scroll_position.y = max_y;
3030 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
3033 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3034 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3035 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3036 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3037 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3039 else if ( plusPressed( e.getKeyCode() ) ) {
3040 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3041 Constants.WHEEL_ZOOM_IN_FACTOR );
3042 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3043 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3045 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
3046 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3047 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3048 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
3049 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3052 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
3053 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3054 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3055 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
3056 if ( getStartingAngle() < 0 ) {
3057 setStartingAngle( TWO_PI + getStartingAngle() );
3059 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3062 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
3063 boolean selected = false;
3064 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
3065 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
3069 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
3071 if ( getMainPanel().getMainFrame() == null ) {
3072 // Must be "E" applet version.
3073 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
3074 if ( ae.getlabelDirectionCbmi() != null ) {
3075 ae.getlabelDirectionCbmi().setSelected( selected );
3079 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
3083 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
3084 switchDisplaygetPhylogenyGraphicsType();
3087 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
3091 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
3092 MainFrame.cycleOverview( getOptions(), this );
3095 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
3098 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
3105 final private void makePopupMenus( final PhylogenyNode node ) {
3106 _node_popup_menu = new JPopupMenu();
3107 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
3108 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
3109 for( int i = 0; i < clickto_names.size(); i++ ) {
3110 final String title = clickto_names.get( i );
3111 _node_popup_menu_items[ i ] = new JMenuItem( title );
3112 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
3113 _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
3115 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
3116 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
3118 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
3119 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
3121 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
3122 if ( !getOptions().isEditable() ) {
3125 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
3127 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
3128 if ( !getOptions().isEditable() ) {
3131 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
3133 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
3134 if ( !getOptions().isEditable() ) {
3137 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
3139 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
3140 if ( !getOptions().isEditable() ) {
3143 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
3145 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
3146 if ( !getOptions().isEditable() ) {
3150 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
3151 if ( !getOptions().isEditable() ) {
3155 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
3156 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
3158 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
3159 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
3161 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
3162 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
3164 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
3165 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
3167 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
3168 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
3170 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
3171 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
3173 _node_popup_menu_items[ i ].addActionListener( this );
3174 _node_popup_menu.add( _node_popup_menu_items[ i ] );
3178 private final String obtainTitleForExtDescNodeData() {
3179 switch ( getOptions().getExtDescNodeDataToReturn() ) {
3181 return "Node Names";
3183 return "Sequence Names";
3184 case SEQUENCE_SYMBOL:
3185 return "Sequence Symbols";
3186 case SEQUENCE_MOL_SEQ:
3187 return "Molecular Sequences";
3189 return "Sequence Accessors";
3190 case TAXONOMY_SCIENTIFIC_NAME:
3191 return "Scientific Names";
3193 return "Taxonomy Codes";
3195 return "User Selected Data";
3197 throw new IllegalArgumentException( "unknown data element: "
3198 + getOptions().getExtDescNodeDataToReturn() );
3202 final private void openSeqWeb( final PhylogenyNode node ) {
3203 if ( !isCanOpenSeqWeb( node ) ) {
3204 cannotOpenBrowserWarningMessage( "sequence" );
3207 String uri_str = null;
3208 final Sequence seq = node.getNodeData().getSequence();
3209 final String source = seq.getAccession().getSource().toLowerCase();
3211 if ( source.toLowerCase().equals( "ncbi" ) ) {
3212 url = Constants.NCBI_ALL_DATABASE_SEARCH;
3215 final WebLink weblink = getConfiguration().getWebLink( source );
3216 url = weblink.getUrl().toString();
3219 uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
3221 catch ( final UnsupportedEncodingException e ) {
3222 AptxUtil.showErrorMessage( this, e.toString() );
3223 e.printStackTrace();
3225 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3227 JApplet applet = null;
3229 applet = obtainApplet();
3231 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
3233 catch ( final IOException e ) {
3234 AptxUtil.showErrorMessage( this, e.toString() );
3235 e.printStackTrace();
3237 catch ( final URISyntaxException e ) {
3238 AptxUtil.showErrorMessage( this, e.toString() );
3239 e.printStackTrace();
3243 cannotOpenBrowserWarningMessage( "sequence" );
3247 final private void openTaxWeb( final PhylogenyNode node ) {
3248 if ( !isCanOpenTaxWeb( node ) ) {
3249 cannotOpenBrowserWarningMessage( "taxonomic" );
3252 String uri_str = null;
3253 final Taxonomy tax = node.getNodeData().getTaxonomy();
3254 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
3255 && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
3256 final String type = tax.getIdentifier().getProvider().toLowerCase();
3257 final WebLink weblink = getConfiguration().getWebLink( type );
3259 uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
3261 catch ( final UnsupportedEncodingException e ) {
3262 AptxUtil.showErrorMessage( this, e.toString() );
3263 e.printStackTrace();
3266 else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3267 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
3269 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
3271 catch ( final URISyntaxException e ) {
3272 AptxUtil.showErrorMessage( this, e.toString() );
3274 e.printStackTrace();
3277 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
3279 uri_str = "http://www.eol.org/search?q="
3280 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
3282 catch ( final UnsupportedEncodingException e ) {
3283 AptxUtil.showErrorMessage( this, e.toString() );
3284 e.printStackTrace();
3287 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
3289 uri_str = "http://www.uniprot.org/taxonomy/?query="
3290 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
3292 catch ( final UnsupportedEncodingException e ) {
3293 AptxUtil.showErrorMessage( this, e.toString() );
3294 e.printStackTrace();
3297 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
3299 uri_str = "http://www.eol.org/search?q="
3300 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
3302 catch ( final UnsupportedEncodingException e ) {
3303 AptxUtil.showErrorMessage( this, e.toString() );
3304 e.printStackTrace();
3307 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3309 JApplet applet = null;
3311 applet = obtainApplet();
3313 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
3315 catch ( final IOException e ) {
3316 AptxUtil.showErrorMessage( this, e.toString() );
3317 e.printStackTrace();
3319 catch ( final URISyntaxException e ) {
3320 AptxUtil.showErrorMessage( this, e.toString() );
3321 e.printStackTrace();
3325 cannotOpenBrowserWarningMessage( "taxonomic" );
3329 final private void paintBranchLength( final Graphics2D g,
3330 final PhylogenyNode node,
3331 final boolean to_pdf,
3332 final boolean to_graphics_file ) {
3333 g.setFont( getTreeFontSet().getSmallFont() );
3334 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3335 g.setColor( Color.BLACK );
3338 g.setColor( getTreeColorSet().getBranchLengthColor() );
3340 if ( !node.isRoot() ) {
3341 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3342 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3343 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3345 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3346 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3347 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3350 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3351 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3355 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
3356 - getTreeFontSet()._small_max_descent, g );
3360 final private void paintBranchLite( final Graphics2D g,
3365 final PhylogenyNode node ) {
3366 g.setColor( getTreeColorSet().getOvColor() );
3367 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3368 drawLine( x1, y1, x2, y2, g );
3370 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3371 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3372 ( g ).draw( _quad_curve );
3374 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3375 final float dx = x2 - x1;
3376 final float dy = y2 - y1;
3377 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3378 + ( dy * 0.8f ), x2, y2 );
3379 ( g ).draw( _cubic_curve );
3382 final float x2a = x2;
3383 final float x1a = x1;
3384 // draw the vertical line
3385 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
3386 drawLine( x1, y1, x1, y2, g );
3388 // draw the horizontal line
3389 drawLine( x1a, y2, x2a, y2, g );
3394 * Paint a branch which consists of a vertical and a horizontal bar
3395 * @param is_ind_found_nodes
3397 final private void paintBranchRectangular( final Graphics2D g,
3402 final PhylogenyNode node,
3403 final boolean to_pdf,
3404 final boolean to_graphics_file ) {
3405 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
3406 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3407 drawLine( x1, y1, x2, y2, g );
3409 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3410 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3411 g.draw( _quad_curve );
3413 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3414 final float dx = x2 - x1;
3415 final float dy = y2 - y1;
3416 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3417 + ( dy * 0.8f ), x2, y2 );
3418 g.draw( _cubic_curve );
3421 final float x2a = x2;
3422 final float x1a = x1;
3424 if ( node.isFirstChildNode() || node.isLastChildNode()
3425 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3426 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3427 if ( !to_graphics_file
3429 && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
3430 .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
3434 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3435 float x2c = x1 + EURO_D;
3439 drawLine( x1, y1, x2c, y2, g );
3441 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3443 y2_r = y2 - ROUNDED_D;
3447 drawLine( x1, y1, x1, y2_r, g );
3450 y2_r = y2 + ROUNDED_D;
3454 drawLine( x1, y1, x1, y2_r, g );
3458 drawLine( x1, y1, x1, y2, g );
3462 // draw the horizontal line
3463 if ( !to_graphics_file && !to_pdf
3464 && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
3468 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
3469 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3470 x1_r = x1a + ROUNDED_D;
3472 drawLine( x1_r, y2, x2a, y2, g );
3475 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3476 final float x1c = x1a + EURO_D;
3478 drawLine( x1c, y2, x2a, y2, g );
3482 drawLine( x1a, y2, x2a, y2, g );
3486 final double w = PhylogenyMethods.getBranchWidthValue( node );
3487 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3488 x1_r = x1a + ROUNDED_D;
3490 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
3493 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3494 final float x1c = x1a + EURO_D;
3496 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
3500 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
3503 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3508 final double diff = y2 - y2_r;
3509 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
3512 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
3517 if ( node.isExternal() ) {
3518 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
3519 || isInCurrentExternalNodes( node ) );
3523 final private double paintCirculars( final PhylogenyNode n,
3524 final Phylogeny phy,
3525 final float center_x,
3526 final float center_y,
3527 final double radius,
3528 final boolean radial_labels,
3530 final boolean to_pdf,
3531 final boolean to_graphics_file ) {
3532 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
3533 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
3534 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
3536 return _urt_nodeid_angle_map.get( n.getId() );
3539 final List<PhylogenyNode> descs = n.getDescendants();
3541 for( final PhylogenyNode desc : descs ) {
3542 sum += paintCirculars( desc,
3553 if ( !n.isRoot() ) {
3554 r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3556 final double theta = sum / descs.size();
3557 n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
3558 n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
3559 _urt_nodeid_angle_map.put( n.getId(), theta );
3560 for( final PhylogenyNode desc : descs ) {
3561 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
3567 final private void paintCircularsLite( final PhylogenyNode n,
3568 final Phylogeny phy,
3572 final Graphics2D g ) {
3573 if ( n.isExternal() ) {
3577 final List<PhylogenyNode> descs = n.getDescendants();
3578 for( final PhylogenyNode desc : descs ) {
3579 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
3582 if ( !n.isRoot() ) {
3583 r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3585 final double theta = _urt_nodeid_angle_map.get( n.getId() );
3586 n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
3587 n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
3588 for( final PhylogenyNode desc : descs ) {
3589 paintBranchCircularLite( n, desc, g );
3594 final private void paintCollapsedNode( final Graphics2D g,
3595 final PhylogenyNode node,
3596 final boolean to_graphics_file,
3597 final boolean to_pdf,
3598 final boolean is_in_found_nodes ) {
3600 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3603 else if ( is_in_found_nodes ) {
3604 c = getTreeColorSet().getFoundColor();
3606 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3607 c = getTaxonomyBasedColor( node );
3609 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3610 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3611 c = PhylogenyMethods.getBranchColorValue( node );
3614 c = getTreeColorSet().getCollapseFillColor();
3616 double d = node.getAllExternalDescendants().size();
3618 d = ( 3 * _y_distance ) / 3;
3621 d = ( Math.log10( d ) * _y_distance ) / 2.5;
3623 final int box_size = getOptions().getDefaultNodeShapeSize();
3624 if ( d < box_size ) {
3628 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
3629 ForesterUtil.roundToInt( node.getYcoord() ) );
3630 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
3631 ForesterUtil.roundToInt( node.getYcoord() - d ) );
3632 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
3633 ForesterUtil.roundToInt( node.getYcoord() + d ) );
3634 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3636 g.fillPolygon( _polygon );
3638 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3639 g.setColor( getBackground() );
3640 g.fillPolygon( _polygon );
3642 g.drawPolygon( _polygon );
3644 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3645 g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
3646 .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
3651 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3654 final private void paintConfidenceValues( final Graphics2D g,
3655 final PhylogenyNode node,
3656 final boolean to_pdf,
3657 final boolean to_graphics_file ) {
3658 final List<Confidence> confidences = node.getBranchData().getConfidences();
3659 // if ( confidences.size() == 1 ) {
3660 // final double value = node.getBranchData().getConfidence( 0 ).getValue();
3661 // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
3664 // conf_str = FORMATTER_CONFIDENCE.format( value );
3666 // else if ( confidences.size() > 1 ) {
3667 boolean one_ok = false;
3668 boolean not_first = false;
3669 Collections.sort( confidences );
3670 final StringBuilder sb = new StringBuilder();
3671 String conf_str = "";
3672 for( final Confidence confidence : confidences ) {
3673 final double value = confidence.getValue();
3674 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3675 if ( value >= getOptions().getMinConfidenceValue() ) {
3684 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
3685 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3686 if ( getOptions().isShowConfidenceStddev() ) {
3687 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3689 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
3691 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3698 conf_str = sb.toString();
3701 if ( conf_str.length() > 0 ) {
3702 final double parent_x = node.getParent().getXcoord();
3703 double x = node.getXcoord();
3704 g.setFont( getTreeFontSet().getSmallFont() );
3705 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3708 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3711 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3712 g.setColor( Color.BLACK );
3715 g.setColor( getTreeColorSet().getConfidenceColor() );
3718 .drawString( conf_str,
3720 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
3721 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
3726 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
3727 final int box_size = getOptions().getDefaultNodeShapeSize();
3728 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3729 g.setColor( getTreeColorSet().getFoundColor() );
3730 g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
3733 final private void paintGainedAndLostCharacters( final Graphics2D g,
3734 final PhylogenyNode node,
3735 final String gained,
3736 final String lost ) {
3737 if ( node.getParent() != null ) {
3738 final double parent_x = node.getParent().getXcoord();
3739 final double x = node.getXcoord();
3740 g.setFont( getTreeFontSet().getLargeFont() );
3741 g.setColor( getTreeColorSet().getGainedCharactersColor() );
3742 if ( Constants.SPECIAL_CUSTOM ) {
3743 g.setColor( Color.BLUE );
3746 .drawString( gained,
3747 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
3748 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
3750 g.setColor( getTreeColorSet().getLostCharactersColor() );
3751 TreePanel.drawString( lost,
3752 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
3753 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
3759 * Draw a box at the indicated node.
3766 final private void paintNodeBox( final double x,
3768 final PhylogenyNode node,
3770 final boolean to_pdf,
3771 final boolean to_graphics_file,
3772 final boolean is_in_found_nodes ) {
3773 if ( node.isCollapse() ) {
3776 // if this node should be highlighted, do so
3777 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
3778 g.setColor( getTreeColorSet().getFoundColor() );
3779 drawOval( x - 8, y - 8, 16, 16, g );
3780 drawOval( x - 9, y - 8, 17, 17, g );
3781 drawOval( x - 9, y - 9, 18, 18, g );
3783 if ( is_in_found_nodes ) {
3784 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
3787 Color outline_color = null;
3788 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3789 outline_color = Color.BLACK;
3791 else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
3792 final Event event = node.getNodeData().getEvent();
3793 if ( event.isDuplication() ) {
3794 outline_color = getTreeColorSet().getDuplicationBoxColor();
3796 else if ( event.isSpeciation() ) {
3797 outline_color = getTreeColorSet().getSpecBoxColor();
3799 else if ( event.isSpeciationOrDuplication() ) {
3800 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
3803 else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
3804 outline_color = getTaxonomyBasedColor( node );
3807 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
3808 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
3809 outline_color = getTreeColorSet().getBranchColorForPdf();
3812 final int box_size = getOptions().getDefaultNodeShapeSize();
3813 final int half_box_size = box_size / 2;
3814 if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
3815 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
3816 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3817 drawOvalGradient( x - half_box_size,
3822 to_pdf ? Color.WHITE : outline_color,
3823 to_pdf ? outline_color : getBackground(),
3826 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
3827 Color background = getBackground();
3829 background = Color.WHITE;
3831 drawOvalGradient( x - half_box_size,
3840 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3841 g.setColor( outline_color );
3842 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3845 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
3846 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
3847 drawRectGradient( x - half_box_size,
3852 to_pdf ? Color.WHITE : outline_color,
3853 to_pdf ? outline_color : getBackground(),
3856 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3857 Color background = getBackground();
3859 background = Color.WHITE;
3861 drawRectGradient( x - half_box_size,
3870 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3871 g.setColor( outline_color );
3872 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3879 final private void paintNodeData( final Graphics2D g,
3880 final PhylogenyNode node,
3881 final boolean to_graphics_file,
3882 final boolean to_pdf,
3883 final boolean is_in_found_nodes ) {
3884 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
3887 if ( getOptions().isShowBranchLengthValues()
3888 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3889 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3890 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
3891 paintBranchLength( g, node, to_pdf, to_graphics_file );
3893 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
3897 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3898 if ( getControlPanel().isShowTaxonomyImages()
3899 && ( getImageMap() != null )
3900 && !getImageMap().isEmpty()
3901 && node.getNodeData().isHasTaxonomy()
3902 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
3903 .getUris().isEmpty() ) ) {
3904 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
3906 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3907 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
3908 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
3910 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3911 g.setColor( Color.BLACK );
3913 else if ( is_in_found_nodes ) {
3914 g.setColor( getTreeColorSet().getFoundColor() );
3916 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3917 g.setColor( getTaxonomyBasedColor( node ) );
3919 else if ( getControlPanel().isColorAccordingToAnnotation()
3920 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
3921 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
3922 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
3924 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3925 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3926 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3928 else if ( to_pdf ) {
3929 g.setColor( Color.BLACK );
3932 g.setColor( getTreeColorSet().getSequenceColor() );
3935 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3937 _sb.append( node.getAllExternalDescendants().size() );
3940 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3941 if ( _sb.length() > 0 ) {
3944 _sb.append( node.getName() );
3946 if ( node.getNodeData().isHasSequence() ) {
3947 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
3948 if ( _sb.length() > 0 ) {
3951 _sb.append( node.getNodeData().getSequence().getSymbol() );
3953 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3954 if ( _sb.length() > 0 ) {
3957 _sb.append( node.getNodeData().getSequence().getName() );
3959 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3960 if ( _sb.length() > 0 ) {
3963 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3964 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3967 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3970 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
3971 if ( _sb.length() > 0 ) {
3974 _sb.append( propertiesToString( node ) );
3976 g.setFont( getTreeFontSet().getLargeFont() );
3977 if ( is_in_found_nodes ) {
3978 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3980 double down_shift_factor = 3.0;
3981 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
3982 down_shift_factor = 1;
3984 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
3985 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
3986 final String sb_str = _sb.toString();
3987 // GUILHEM_BEG ______________
3988 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
3989 && ( _query_sequence != null ) ) {
3990 int nodeTextBoundsWidth = 0;
3991 if ( sb_str.length() > 0 ) {
3992 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
3993 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
3995 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
3996 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
3997 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
3998 g.setColor( getTreeColorSet().getBackgroundColor() );
4002 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
4003 for( final SequenceRelation seqRelation : seqRelations ) {
4004 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
4005 .getRef1().isEqual( _query_sequence ) )
4006 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
4007 .getSelectedItem() );
4008 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
4009 final double linePosX = node.getXcoord() + 2 + half_box_size;
4010 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
4011 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
4013 if ( sConfidence != null ) {
4014 double confidenceX = pos_x;
4015 if ( sb_str.length() > 0 ) {
4016 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
4017 + CONFIDENCE_LEFT_MARGIN;
4019 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
4020 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
4021 .getBounds().getWidth();
4022 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
4023 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
4026 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
4028 if ( nodeTextBoundsWidth == 0 ) {
4029 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
4032 nodeTextBoundsWidth += 2;
4034 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
4035 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
4042 if ( sb_str.length() > 0 ) {
4043 TreePanel.drawString( sb_str, pos_x, pos_y, g );
4045 // GUILHEM_END _____________
4046 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
4047 // TODO FIXME need to check this one!
4048 //if ( _sb.length() > 0 ) {
4049 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
4050 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4052 // COMMENTED_OUT_BY_GUILHEM_END ________________
4053 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
4054 && ( node.getNodeData().getSequence().getAnnotations() != null )
4055 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4056 if ( _sb.length() > 0 ) {
4057 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4059 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
4060 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4061 g.setColor( Color.BLACK );
4063 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
4064 g.setColor( calculateColorForAnnotation( ann ) );
4066 final String ann_str = createAnnotationString( ann );
4067 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
4068 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4070 _sb.append( ann_str );
4072 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4073 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
4074 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
4075 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
4076 && node.getNodeData().isHasBinaryCharacters() ) {
4077 if ( _sb.length() > 0 ) {
4078 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4080 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4081 g.setColor( Color.BLACK );
4084 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
4086 if ( getControlPanel().isShowBinaryCharacters() ) {
4087 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
4088 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
4089 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4090 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
4091 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
4092 .getLostCharactersAsStringBuffer().toString() );
4095 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
4096 node.getXcoord() + x + 4 + half_box_size,
4098 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
4100 paintGainedAndLostCharacters( g, node, "+"
4101 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
4102 + node.getNodeData().getBinaryCharacters().getLostCount() );
4108 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
4109 final PhylogenyNode node,
4110 final boolean to_pdf,
4111 final boolean to_graphics_file,
4112 final boolean radial_labels,
4113 final double ur_angle,
4114 final boolean is_in_found_nodes ) {
4115 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
4118 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4119 g.setColor( Color.BLACK );
4121 else if ( is_in_found_nodes ) {
4122 g.setColor( getTreeColorSet().getFoundColor() );
4124 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4125 g.setColor( getTaxonomyBasedColor( node ) );
4127 else if ( getControlPanel().isColorAccordingToAnnotation()
4128 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4129 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4130 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4133 g.setColor( getTreeColorSet().getSequenceColor() );
4137 if ( node.getNodeData().isHasTaxonomy()
4138 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4139 .isShowTaxonomyCommonNames() ) ) {
4140 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4141 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4142 _sb.append( taxonomy.getTaxonomyCode() );
4145 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4146 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4147 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4148 _sb.append( taxonomy.getScientificName() );
4150 _sb.append( taxonomy.getCommonName() );
4153 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4154 _sb.append( taxonomy.getScientificName() );
4157 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4158 _sb.append( taxonomy.getCommonName() );
4162 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4163 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4164 _sb.append( taxonomy.getScientificName() );
4168 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4169 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4170 _sb.append( taxonomy.getCommonName() );
4175 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4177 _sb.append( node.getAllExternalDescendants().size() );
4180 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4181 if ( _sb.length() > 0 ) {
4184 _sb.append( node.getName() );
4186 if ( node.getNodeData().isHasSequence() ) {
4187 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4188 if ( _sb.length() > 0 ) {
4191 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4192 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4195 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4197 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4198 if ( _sb.length() > 0 ) {
4201 _sb.append( node.getNodeData().getSequence().getName() );
4204 g.setFont( getTreeFontSet().getLargeFont() );
4205 if ( is_in_found_nodes ) {
4206 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4208 if ( _sb.length() > 1 ) {
4209 final String sb_str = _sb.toString();
4211 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4212 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
4215 m = ( float ) ( ur_angle % TWO_PI );
4217 _at = g.getTransform();
4218 boolean need_to_reset = false;
4219 final float x_coord = node.getXcoord();
4220 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
4221 if ( radial_labels ) {
4222 need_to_reset = true;
4223 boolean left = false;
4224 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4228 g.rotate( m, x_coord, node.getYcoord() );
4230 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
4234 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4235 need_to_reset = true;
4236 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
4239 TreePanel.drawString( sb_str, x_coord, y_coord, g );
4240 if ( need_to_reset ) {
4241 g.setTransform( _at );
4246 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
4247 if ( node.isCollapse() ) {
4248 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
4249 paintCollapsedNode( g, node, false, false, false );
4253 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4254 g.setColor( getTreeColorSet().getFoundColor() );
4255 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
4258 if ( !node.isExternal() && !node.isCollapse() ) {
4259 boolean first_child = true;
4261 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4262 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4263 final PhylogenyNode child_node = node.getChildNode( i );
4265 if ( !isUniformBranchLengthsForCladogram() ) {
4266 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4269 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4271 if ( first_child ) {
4272 first_child = false;
4273 y2 = node.getYSecondary()
4274 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
4275 .getNumberOfExternalNodes() ) );
4278 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4280 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
4281 new_x = x2 + node.getXSecondary();
4282 final float diff_y = node.getYSecondary() - y2;
4283 final float diff_x = node.getXSecondary() - new_x;
4284 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
4285 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
4287 child_node.setXSecondary( new_x );
4288 child_node.setYSecondary( y2 );
4289 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4294 final private void paintNodeRectangular( final Graphics2D g,
4295 final PhylogenyNode node,
4296 final boolean to_pdf,
4297 final boolean dynamically_hide,
4298 final int dynamic_hiding_factor,
4299 final boolean to_graphics_file ) {
4300 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
4301 if ( node.isCollapse() ) {
4302 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
4303 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4307 if ( node.isExternal() ) {
4308 ++_external_node_index;
4310 // Confidence values
4311 if ( getControlPanel().isShowConfidenceValues()
4312 && !node.isExternal()
4314 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
4315 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4316 && node.getBranchData().isHasConfidences() ) {
4317 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
4319 // Draw a line to root:
4320 if ( node.isRoot() && _phylogeny.isRooted() ) {
4321 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
4324 float new_x_min = Float.MAX_VALUE;
4325 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
4326 float min_dist = 1.5f;
4327 if ( !disallow_shortcutting ) {
4328 // System.out.println( dynamic_hiding_factor );
4329 if ( dynamic_hiding_factor > 4000 ) {
4332 else if ( dynamic_hiding_factor > 1000 ) {
4335 else if ( dynamic_hiding_factor > 100 ) {
4339 if ( !node.isExternal() && !node.isCollapse() ) {
4340 boolean first_child = true;
4342 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4343 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4344 final PhylogenyNode child_node = node.getChildNode( i );
4346 if ( !isUniformBranchLengthsForCladogram() ) {
4347 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4350 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4352 if ( first_child ) {
4353 first_child = false;
4354 y2 = node.getYcoord()
4355 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
4358 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4360 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
4361 new_x = x2 + node.getXcoord();
4362 if ( dynamically_hide && ( x2 < new_x_min ) ) {
4365 final float diff_y = node.getYcoord() - y2;
4366 final float diff_x = node.getXcoord() - new_x;
4367 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
4368 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
4369 paintBranchRectangular( g,
4378 child_node.setXcoord( new_x );
4379 child_node.setYcoord( y2 );
4380 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4382 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
4383 || isInCurrentExternalNodes( node ) );
4385 if ( dynamically_hide
4386 && !is_in_found_nodes
4387 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
4388 .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
4389 .getHeight() ) ) ) ) ) {
4392 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4393 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
4396 final private void paintNodeWithRenderableData( final Graphics2D g,
4397 final PhylogenyNode node,
4398 final boolean to_graphics_file,
4399 final boolean to_pdf ) {
4400 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
4403 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
4406 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4407 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4408 RenderableDomainArchitecture rds = null;
4409 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
4411 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
4413 catch ( final ClassCastException cce ) {
4414 cce.printStackTrace();
4416 if ( rds != null ) {
4417 rds.setRenderingHeight( 6 );
4419 if ( node.getNodeData().isHasTaxonomy() ) {
4420 if ( getControlPanel().isShowTaxonomyCode()
4421 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
4422 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4426 if ( getControlPanel().isShowTaxonomyScientificNames()
4427 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
4428 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4429 .getScientificName()
4432 if ( getControlPanel().isShowTaxonomyCommonNames()
4433 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
4434 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4439 if ( node.getNodeData().isHasSequence() ) {
4440 if ( getControlPanel().isShowGeneNames()
4441 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
4442 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
4445 if ( getControlPanel().isShowGeneSymbols()
4446 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
4447 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
4450 if ( getControlPanel().isShowSequenceAcc()
4451 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4452 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
4453 .getAccession().toString()
4457 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
4458 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
4460 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
4465 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4466 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
4467 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
4468 getStatisticsForExpressionValues(),
4469 getConfiguration() );
4472 PhylogenyNode my_node = node;
4473 if ( !getControlPanel().isDrawPhylogram() ) {
4474 my_node = getPhylogeny().getFirstExternalNode();
4476 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
4477 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
4479 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
4480 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
4482 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
4488 final private void paintOvRectangle( final Graphics2D g ) {
4489 final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
4490 final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
4491 final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
4492 final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
4493 final float width = getOvMaxWidth() / w_ratio;
4494 final float height = getOvMaxHeight() / h_ratio;
4495 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
4496 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
4497 g.setColor( getTreeColorSet().getFoundColor() );
4498 getOvRectangle().setRect( x, y, width, height );
4499 if ( ( width < 6 ) && ( height < 6 ) ) {
4500 drawRectFilled( x, y, 6, 6, g );
4501 getOvVirtualRectangle().setRect( x, y, 6, 6 );
4503 else if ( width < 6 ) {
4504 drawRectFilled( x, y, 6, height, g );
4505 getOvVirtualRectangle().setRect( x, y, 6, height );
4507 else if ( height < 6 ) {
4508 drawRectFilled( x, y, width, 6, g );
4509 getOvVirtualRectangle().setRect( x, y, width, 6 );
4512 drawRect( x, y, width, height, g );
4513 if ( isInOvRect() ) {
4514 drawRect( x + 1, y + 1, width - 2, height - 2, g );
4516 getOvVirtualRectangle().setRect( x, y, width, height );
4520 final private void paintPhylogenyLite( final Graphics2D g ) {
4523 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
4524 .getWidth() ) ) ) );
4525 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
4526 for( final PhylogenyNode element : _nodes_in_preorder ) {
4527 paintNodeLite( g, element );
4529 paintOvRectangle( g );
4533 * Paint the root branch. (Differs from others because it will always be a
4534 * single horizontal line).
4535 * @param to_graphics_file
4537 * @return new x1 value
4539 final private void paintRootBranch( final Graphics2D g,
4542 final PhylogenyNode root,
4543 final boolean to_pdf,
4544 final boolean to_graphics_file ) {
4545 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
4546 float d = getXdistance();
4547 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
4548 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
4550 if ( d < MIN_ROOT_LENGTH ) {
4551 d = MIN_ROOT_LENGTH;
4553 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
4554 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
4557 final double w = PhylogenyMethods.getBranchWidthValue( root );
4558 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
4560 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
4563 final private void paintScale( final Graphics2D g,
4566 final boolean to_pdf,
4567 final boolean to_graphics_file ) {
4569 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
4571 final int y2 = y1 - 8;
4572 final int y3 = y1 - 4;
4573 g.setFont( getTreeFontSet().getSmallFont() );
4574 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4575 g.setColor( Color.BLACK );
4578 g.setColor( getTreeColorSet().getBranchLengthColor() );
4580 drawLine( x1, y1, x1, y2, g );
4581 drawLine( x2, y1, x2, y2, g );
4582 drawLine( x1, y3, x2, y3, g );
4583 if ( getScaleLabel() != null ) {
4584 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
4588 final private int paintTaxonomy( final Graphics2D g,
4589 final PhylogenyNode node,
4590 final boolean is_in_found_nodes,
4591 final boolean to_pdf,
4592 final boolean to_graphics_file,
4593 final double x_shift ) {
4594 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4595 g.setFont( getTreeFontSet().getLargeItalicFont() );
4596 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4597 g.setColor( Color.BLACK );
4599 else if ( is_in_found_nodes ) {
4600 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
4601 g.setColor( getTreeColorSet().getFoundColor() );
4603 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4604 g.setColor( getTaxonomyBasedColor( node ) );
4606 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4607 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4608 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4610 else if ( to_pdf ) {
4611 g.setColor( Color.BLACK );
4614 g.setColor( getTreeColorSet().getTaxonomyColor() );
4616 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4617 final double start_y = node.getYcoord()
4618 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4620 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4621 _sb.append( taxonomy.getTaxonomyCode() );
4624 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4625 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4626 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4627 if ( getOptions().isAbbreviateScientificTaxonNames()
4628 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4629 abbreviateScientificName( taxonomy.getScientificName() );
4632 _sb.append( taxonomy.getScientificName() );
4635 _sb.append( taxonomy.getCommonName() );
4638 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4639 if ( getOptions().isAbbreviateScientificTaxonNames()
4640 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4641 abbreviateScientificName( taxonomy.getScientificName() );
4644 _sb.append( taxonomy.getScientificName() );
4648 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4649 _sb.append( taxonomy.getCommonName() );
4653 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4654 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4655 if ( getOptions().isAbbreviateScientificTaxonNames()
4656 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4657 abbreviateScientificName( taxonomy.getScientificName() );
4660 _sb.append( taxonomy.getScientificName() );
4665 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4666 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4667 _sb.append( taxonomy.getCommonName() );
4671 final String label = _sb.toString();
4673 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4674 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4675 // invert font color and background color to show that this is the query sequence
4676 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4680 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4681 g.setColor( getTreeColorSet().getBackgroundColor() );
4684 TreePanel.drawString( label, start_x, start_y, g );
4685 if ( is_in_found_nodes ) {
4686 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4689 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4693 final private void paintUnrooted( final PhylogenyNode n,
4694 final double low_angle,
4695 final double high_angle,
4696 final boolean radial_labels,
4698 final boolean to_pdf,
4699 final boolean to_graphics_file ) {
4701 n.setXcoord( getWidth() / 2 );
4702 n.setYcoord( getHeight() / 2 );
4704 if ( n.isExternal() ) {
4705 paintNodeDataUnrootedCirc( g,
4710 ( high_angle + low_angle ) / 2,
4711 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
4714 final float num_enclosed = n.getNumberOfExternalNodes();
4715 final float x = n.getXcoord();
4716 final float y = n.getYcoord();
4717 double current_angle = low_angle;
4718 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4719 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4720 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4721 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4722 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4723 final PhylogenyNode desc = n.getChildNode( i );
4724 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4725 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4726 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4727 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4730 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4733 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4736 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4737 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4739 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4740 if ( desc.getDistanceToParent() < 0 ) {
4744 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4748 length = getUrtFactor();
4750 final double mid_angle = current_angle + ( arc_size / 2 );
4751 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4752 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4753 desc.setXcoord( new_x );
4754 desc.setYcoord( new_y );
4755 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4756 current_angle += arc_size;
4757 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4758 drawLine( x, y, new_x, new_y, g );
4759 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc )
4760 || isInCurrentExternalNodes( desc ) );
4763 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
4767 final private void paintUnrootedLite( final PhylogenyNode n,
4768 final double low_angle,
4769 final double high_angle,
4771 final float urt_ov_factor ) {
4773 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
4774 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
4775 n.setXSecondary( x_pos );
4776 n.setYSecondary( y_pos );
4778 if ( n.isExternal() ) {
4781 final float num_enclosed = n.getNumberOfExternalNodes();
4782 final float x = n.getXSecondary();
4783 final float y = n.getYSecondary();
4784 double current_angle = low_angle;
4785 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4786 final PhylogenyNode desc = n.getChildNode( i );
4787 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4788 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4790 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4791 if ( desc.getDistanceToParent() < 0 ) {
4795 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
4799 length = urt_ov_factor;
4801 final double mid_angle = current_angle + ( arc_size / 2 );
4802 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4803 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4804 desc.setXSecondary( new_x );
4805 desc.setYSecondary( new_y );
4806 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
4807 g.setColor( getTreeColorSet().getFoundColor() );
4808 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
4809 g.setColor( getTreeColorSet().getOvColor() );
4811 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4812 current_angle += arc_size;
4813 drawLine( x, y, new_x, new_y, g );
4817 final private void pasteSubtree( final PhylogenyNode node ) {
4818 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4819 errorMessageNoCutCopyPasteInUnrootedDisplay();
4822 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
4823 JOptionPane.showMessageDialog( this,
4824 "No tree in buffer (need to copy or cut a subtree first)",
4825 "Attempt to paste with empty buffer",
4826 JOptionPane.ERROR_MESSAGE );
4829 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
4830 final Object[] options = { "As sibling", "As descendant", "Cancel" };
4831 final int r = JOptionPane.showOptionDialog( this,
4832 "How to paste subtree" + label + "?",
4834 JOptionPane.CLOSED_OPTION,
4835 JOptionPane.QUESTION_MESSAGE,
4839 boolean paste_as_sibling = true;
4841 paste_as_sibling = false;
4843 else if ( r != 0 ) {
4846 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
4847 buffer_phy.setAllNodesToNotCollapse();
4848 PhylogenyMethods.preOrderReId( buffer_phy );
4849 buffer_phy.setRooted( true );
4850 boolean need_to_show_whole = false;
4851 if ( paste_as_sibling ) {
4852 if ( node.isRoot() ) {
4853 JOptionPane.showMessageDialog( this,
4854 "Cannot paste sibling to root",
4855 "Attempt to paste sibling to root",
4856 JOptionPane.ERROR_MESSAGE );
4859 buffer_phy.addAsSibling( node );
4862 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
4863 need_to_show_whole = true;
4864 _phylogeny = buffer_phy;
4867 buffer_phy.addAsChild( node );
4870 if ( getCopiedAndPastedNodes() == null ) {
4871 setCopiedAndPastedNodes( new HashSet<Integer>() );
4873 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
4874 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
4875 for( final PhylogenyNode n : nodes ) {
4876 node_ids.add( n.getId() );
4878 node_ids.add( node.getId() );
4879 getCopiedAndPastedNodes().addAll( node_ids );
4880 setNodeInPreorderToNull();
4881 _phylogeny.externalNodesHaveChanged();
4882 _phylogeny.clearHashIdToNodeMap();
4883 _phylogeny.recalculateNumberOfExternalDescendants( true );
4884 resetNodeIdToDistToLeafMap();
4886 if ( need_to_show_whole ) {
4887 getControlPanel().showWhole();
4892 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
4893 final PropertiesMap properties = node.getNodeData().getProperties();
4894 final StringBuffer sb = new StringBuffer();
4895 boolean first = true;
4896 for( final String ref : properties.getPropertyRefs() ) {
4903 final Property p = properties.getProperty( ref );
4904 sb.append( getPartAfterColon( p.getRef() ) );
4906 sb.append( p.getValue() );
4907 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
4908 sb.append( getPartAfterColon( p.getUnit() ) );
4914 final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
4915 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4918 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4919 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4922 final private void setInOv( final boolean in_ov ) {
4926 final private void setOvMaxHeight( final float ov_max_height ) {
4927 _ov_max_height = ov_max_height;
4930 final private void setOvMaxWidth( final float ov_max_width ) {
4931 _ov_max_width = ov_max_width;
4934 final private void setOvXcorrectionFactor( final float f ) {
4935 _ov_x_correction_factor = f;
4938 final private void setOvXDistance( final float ov_x_distance ) {
4939 _ov_x_distance = ov_x_distance;
4942 final private void setOvXPosition( final int ov_x_position ) {
4943 _ov_x_position = ov_x_position;
4946 final private void setOvYDistance( final float ov_y_distance ) {
4947 _ov_y_distance = ov_y_distance;
4950 final private void setOvYPosition( final int ov_y_position ) {
4951 _ov_y_position = ov_y_position;
4954 final private void setOvYStart( final int ov_y_start ) {
4955 _ov_y_start = ov_y_start;
4958 final private void setScaleDistance( final double scale_distance ) {
4959 _scale_distance = scale_distance;
4962 final private void setScaleLabel( final String scale_label ) {
4963 _scale_label = scale_label;
4966 final private void setUpUrtFactor() {
4967 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
4968 : getVisibleRect().height;
4969 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4970 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
4973 final int max_depth = _circ_max_depth;
4974 if ( max_depth > 0 ) {
4975 setUrtFactor( d / ( 2 * max_depth ) );
4978 setUrtFactor( d / 2 );
4981 setUrtFactorOv( getUrtFactor() );
4984 final private void setUrtFactor( final float urt_factor ) {
4985 _urt_factor = urt_factor;
4988 final private void setUrtFactorOv( final float urt_factor_ov ) {
4989 _urt_factor_ov = urt_factor_ov;
4992 private void showExtDescNodeData( final PhylogenyNode node ) {
4993 final List<String> data = new ArrayList<String>();
4994 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
4995 switch ( getOptions().getExtDescNodeDataToReturn() ) {
4997 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
4998 data.add( n.getName() );
5002 if ( n.getNodeData().isHasSequence()
5003 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5004 data.add( n.getNodeData().getSequence().getName() );
5007 case SEQUENCE_SYMBOL:
5008 if ( n.getNodeData().isHasSequence()
5009 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5010 data.add( n.getNodeData().getSequence().getSymbol() );
5013 case SEQUENCE_MOL_SEQ:
5014 if ( n.getNodeData().isHasSequence()
5015 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5016 data.add( n.getNodeData().getSequence().getMolecularSequence() );
5020 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
5021 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
5022 data.add( n.getNodeData().getSequence().getAccession().toString() );
5025 case TAXONOMY_SCIENTIFIC_NAME:
5026 if ( n.getNodeData().isHasTaxonomy()
5027 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5028 data.add( n.getNodeData().getTaxonomy().getScientificName() );
5032 if ( n.getNodeData().isHasTaxonomy()
5033 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5034 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5038 AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
5041 throw new IllegalArgumentException( "unknown data element: "
5042 + getOptions().getExtDescNodeDataToReturn() );
5045 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
5046 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
5047 final StringBuilder sb = new StringBuilder();
5048 for( final String d : data ) {
5049 if ( !ForesterUtil.isEmpty( d ) ) {
5050 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
5051 System.out.println( d );
5054 sb.append( ForesterUtil.LINE_SEPARATOR );
5057 if ( sb.length() < 1 ) {
5058 clearCurrentExternalNodesDataBuffer();
5061 setCurrentExternalNodesDataBuffer( sb );
5064 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
5065 final StringBuilder sb = new StringBuilder();
5066 for( final String d : data ) {
5067 if ( !ForesterUtil.isEmpty( d ) ) {
5069 sb.append( ForesterUtil.LINE_SEPARATOR );
5072 if ( sb.length() < 1 ) {
5073 AptxUtil.showInformationMessage( this,
5074 "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
5075 "Descendants of selected node do not contain selected data" );
5076 clearCurrentExternalNodesDataBuffer();
5079 setCurrentExternalNodesDataBuffer( sb );
5080 final String title = "External Descendants "
5081 + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5082 : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
5083 + node.getNumberOfExternalNodes() + ") For Node " + node;
5084 final String s = sb.toString().trim();
5085 if ( getMainPanel().getMainFrame() == null ) {
5086 // Must be "E" applet version.
5087 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
5088 ae.showTextFrame( s, title );
5091 getMainPanel().getMainFrame().showTextFrame( s, title );
5097 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
5099 if ( ( node.getName().length() > 0 )
5100 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
5101 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
5102 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
5103 || node.getBranchData().isHasConfidences() ) {
5104 _popup_buffer.setLength( 0 );
5106 if ( node.getName().length() > 0 ) {
5108 _popup_buffer.append( node.getName() );
5110 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
5112 boolean enc_data = false;
5113 final Taxonomy tax = node.getNodeData().getTaxonomy();
5114 if ( _popup_buffer.length() > 0 ) {
5115 _popup_buffer.append( "\n" );
5117 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
5118 _popup_buffer.append( "[" );
5119 _popup_buffer.append( tax.getTaxonomyCode() );
5120 _popup_buffer.append( "]" );
5123 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
5125 _popup_buffer.append( " " );
5127 _popup_buffer.append( tax.getScientificName() );
5130 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
5132 _popup_buffer.append( " (" );
5135 _popup_buffer.append( "(" );
5137 _popup_buffer.append( tax.getCommonName() );
5138 _popup_buffer.append( ")" );
5141 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
5143 _popup_buffer.append( " (" );
5146 _popup_buffer.append( "(" );
5148 _popup_buffer.append( tax.getAuthority() );
5149 _popup_buffer.append( ")" );
5152 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
5154 _popup_buffer.append( " [" );
5157 _popup_buffer.append( "[" );
5159 _popup_buffer.append( tax.getRank() );
5160 _popup_buffer.append( "]" );
5163 if ( tax.getSynonyms().size() > 0 ) {
5165 _popup_buffer.append( " " );
5167 _popup_buffer.append( "[" );
5169 for( final String syn : tax.getSynonyms() ) {
5170 if ( !ForesterUtil.isEmpty( syn ) ) {
5172 _popup_buffer.append( syn );
5173 if ( counter < tax.getSynonyms().size() ) {
5174 _popup_buffer.append( ", " );
5179 _popup_buffer.append( "]" );
5182 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
5183 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
5184 _popup_buffer.append( "[" );
5185 _popup_buffer.append( tax.getIdentifier().getProvider() );
5186 _popup_buffer.append( "] " );
5188 _popup_buffer.append( tax.getIdentifier().getValue() );
5192 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
5194 boolean enc_data = false;
5195 if ( _popup_buffer.length() > 0 ) {
5196 _popup_buffer.append( "\n" );
5198 final Sequence seq = node.getNodeData().getSequence();
5199 if ( seq.getAccession() != null ) {
5200 _popup_buffer.append( "[" );
5201 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
5202 _popup_buffer.append( seq.getAccession().getSource() );
5203 _popup_buffer.append( ":" );
5205 _popup_buffer.append( seq.getAccession().getValue() );
5206 _popup_buffer.append( "]" );
5209 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
5211 _popup_buffer.append( " [" );
5214 _popup_buffer.append( "[" );
5216 _popup_buffer.append( seq.getSymbol() );
5217 _popup_buffer.append( "]" );
5220 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
5222 _popup_buffer.append( " " );
5224 _popup_buffer.append( seq.getName() );
5227 if ( node.getNodeData().isHasDate() ) {
5229 if ( _popup_buffer.length() > 0 ) {
5230 _popup_buffer.append( "\n" );
5232 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
5234 if ( node.getNodeData().isHasDistribution() ) {
5236 if ( _popup_buffer.length() > 0 ) {
5237 _popup_buffer.append( "\n" );
5239 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
5241 if ( node.getBranchData().isHasConfidences() ) {
5242 final List<Confidence> confs = node.getBranchData().getConfidences();
5243 for( final Confidence confidence : confs ) {
5245 if ( _popup_buffer.length() > 0 ) {
5246 _popup_buffer.append( "\n" );
5248 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
5249 _popup_buffer.append( "[" );
5250 _popup_buffer.append( confidence.getType() );
5251 _popup_buffer.append( "] " );
5254 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
5256 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5257 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5258 _popup_buffer.append( " (sd=" );
5259 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
5260 .getStandardDeviation(), getOptions()
5261 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5262 _popup_buffer.append( ")" );
5266 if ( node.getNodeData().isHasProperties() ) {
5267 final PropertiesMap properties = node.getNodeData().getProperties();
5268 for( final String ref : properties.getPropertyRefs() ) {
5269 _popup_buffer.append( "\n" );
5270 final Property p = properties.getProperty( ref );
5271 _popup_buffer.append( getPartAfterColon( p.getRef() ) );
5272 _popup_buffer.append( "=" );
5273 _popup_buffer.append( p.getValue() );
5274 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5275 _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
5279 if ( _popup_buffer.length() > 0 ) {
5280 if ( !getConfiguration().isUseNativeUI() ) {
5282 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
5283 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
5284 if ( isInFoundNodes( node ) ) {
5285 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
5287 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
5288 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
5291 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
5295 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
5297 _rollover_popup.setText( _popup_buffer.toString() );
5298 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
5300 e.getLocationOnScreen().x + 10,
5301 e.getLocationOnScreen().y
5303 _node_desc_popup.show();
5307 catch ( final Exception ex ) {
5312 final private void showNodeEditFrame( final PhylogenyNode n ) {
5313 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5314 // pop up edit box for single node
5315 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
5316 _node_frame_index++;
5319 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5323 final private void showNodeFrame( final PhylogenyNode n ) {
5324 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5325 // pop up edit box for single node
5326 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
5327 _node_frame_index++;
5330 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5334 final private void switchDisplaygetPhylogenyGraphicsType() {
5335 switch ( getPhylogenyGraphicsType() ) {
5337 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5338 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5341 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5342 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5345 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5346 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5349 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5350 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5353 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5354 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5357 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5358 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5361 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5362 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5365 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5366 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5369 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5371 if ( getControlPanel().getDynamicallyHideData() != null ) {
5372 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5373 getControlPanel().getDynamicallyHideData().setEnabled( false );
5376 getControlPanel().getDynamicallyHideData().setEnabled( true );
5379 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5380 getControlPanel().setDrawPhylogramEnabled( true );
5383 getControlPanel().setDrawPhylogramEnabled( false );
5385 if ( getMainPanel().getMainFrame() == null ) {
5386 // Must be "E" applet version.
5387 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5388 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5391 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5395 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
5396 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5399 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5400 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5403 final private static String getPartAfterColon( final String s ) {
5404 final int i = s.indexOf( ':' );
5405 if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
5408 return s.substring( i + 1, s.length() );
5411 final private static boolean isSequenceEmpty( final Sequence seq ) {
5412 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
5413 && ForesterUtil.isEmpty( seq.getSymbol() );
5416 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
5417 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
5418 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
5419 .getSynonyms().isEmpty() );
5422 final private static boolean plusPressed( final int key_code ) {
5423 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5424 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5427 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
5428 final Phylogeny new_phy = new Phylogeny();
5429 new_phy.setRooted( true );
5430 new_phy.setName( source_phy.getName() );
5431 new_phy.setDescription( source_phy.getDescription() );
5432 new_phy.setType( source_phy.getType() );
5433 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
5434 new_phy.setConfidence( source_phy.getConfidence() );
5435 new_phy.setIdentifier( source_phy.getIdentifier() );
5436 new_phy.setRoot( new_root.copyNodeDataShallow() );
5438 for( final PhylogenyNode n : new_root.getDescendants() ) {
5439 new_phy.getRoot().setChildNode( i++, n );
5444 final private class SubtreeColorizationActionListener implements ActionListener {
5446 JColorChooser _chooser;
5447 PhylogenyNode _node;
5449 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5455 public void actionPerformed( final ActionEvent e ) {
5456 final Color c = _chooser.getColor();
5458 colorizeSubtree( c, _node );