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: www.phylosoft.org/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();
528 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
529 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
530 if ( ext_nodes == 1 ) {
531 ext_nodes = max_depth;
532 if ( ext_nodes < 1 ) {
539 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
540 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
541 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
544 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
545 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
547 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
551 if ( ov_xdist < 0.0 ) {
557 setXdistance( xdist );
558 setYdistance( ydist );
559 setOvXDistance( ov_xdist );
560 final double height = _phylogeny.getHeight();
562 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
563 setXcorrectionFactor( corr > 0 ? corr : 0 );
564 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
565 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
568 setXcorrectionFactor( 0 );
569 setOvXcorrectionFactor( 0 );
571 _circ_max_depth = max_depth;
577 * Set a phylogeny tree.
580 * an instance of a Phylogeny
582 public final void setTree( final Phylogeny t ) {
583 setNodeInPreorderToNull();
587 public final void setWaitCursor() {
588 setCursor( WAIT_CURSOR );
593 public void update( final Graphics g ) {
597 final void calcMaxDepth() {
598 if ( _phylogeny != null ) {
599 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
603 final void calculateLongestExtNodeInfo() {
604 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
607 int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
608 * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
609 if ( max_length < 40 ) {
613 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
615 if ( node.isCollapse() ) {
618 if ( getControlPanel().isShowNodeNames() ) {
619 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
621 if ( node.getNodeData().isHasSequence() ) {
622 if ( getControlPanel().isShowSequenceAcc()
623 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
624 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
628 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
629 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
631 if ( getControlPanel().isShowGeneSymbols()
632 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
633 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
635 if ( getControlPanel().isShowAnnotation()
636 && ( node.getNodeData().getSequence().getAnnotations() != null )
637 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
638 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
642 if ( getControlPanel().isShowDomainArchitectures()
643 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
644 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
645 .getRenderingSize().getWidth();
648 if ( node.getNodeData().isHasTaxonomy() ) {
649 final Taxonomy tax = node.getNodeData().getTaxonomy();
650 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
651 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
653 if ( getControlPanel().isShowTaxonomyScientificNames()
654 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
655 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
657 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
658 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
661 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
662 sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
664 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
665 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
666 .getGainedCharactersAsStringBuffer().toString() );
668 if ( sum >= max_length ) {
669 setLongestExtNodeInfo( max_length );
672 if ( sum > longest ) {
676 if ( longest >= max_length ) {
677 setLongestExtNodeInfo( max_length );
680 setLongestExtNodeInfo( longest );
684 final void calculateScaleDistance() {
685 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
688 final double height = getMaxDistanceToRoot();
690 if ( ( height <= 0.5 ) ) {
691 setScaleDistance( 0.01 );
693 else if ( height <= 5.0 ) {
694 setScaleDistance( 0.1 );
696 else if ( height <= 50.0 ) {
697 setScaleDistance( 1 );
699 else if ( height <= 500.0 ) {
700 setScaleDistance( 10 );
703 setScaleDistance( 100 );
707 setScaleDistance( 0.0 );
709 String scale_label = String.valueOf( getScaleDistance() );
710 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
711 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
713 setScaleLabel( scale_label );
716 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
717 String species = tax.getTaxonomyCode();
718 if ( ForesterUtil.isEmpty( species ) ) {
719 species = tax.getScientificName();
720 if ( ForesterUtil.isEmpty( species ) ) {
721 species = tax.getCommonName();
724 if ( ForesterUtil.isEmpty( species ) ) {
725 return getTreeColorSet().getTaxonomyColor();
727 // Look in species hash
728 Color c = getControlPanel().getSpeciesColors().get( species );
730 c = AptxUtil.calculateColorFromString( species );
731 getControlPanel().getSpeciesColors().put( species, c );
736 void clearCurrentExternalNodesDataBuffer() {
737 setCurrentExternalNodesDataBuffer( new StringBuilder() );
741 * Collapse the tree from the given node
746 final void collapse( final PhylogenyNode node ) {
747 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
748 JOptionPane.showMessageDialog( this,
749 "Cannot collapse in unrooted display type",
750 "Attempt to collapse in unrooted display",
751 JOptionPane.WARNING_MESSAGE );
754 if ( !node.isExternal() && !node.isRoot() ) {
755 final boolean collapse = !node.isCollapse();
756 AptxUtil.collapseSubtree( node, collapse );
757 updateSetOfCollapsedExternalNodes();
758 _phylogeny.recalculateNumberOfExternalDescendants( true );
759 resetNodeIdToDistToLeafMap();
760 calculateLongestExtNodeInfo();
761 setNodeInPreorderToNull();
762 _control_panel.displayedPhylogenyMightHaveChanged( true );
763 resetPreferredSize();
765 _main_panel.adjustJScrollPane();
770 final void collapseSpeciesSpecificSubtrees() {
771 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
775 AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
776 updateSetOfCollapsedExternalNodes();
777 _phylogeny.recalculateNumberOfExternalDescendants( true );
778 resetNodeIdToDistToLeafMap();
779 calculateLongestExtNodeInfo();
780 setNodeInPreorderToNull();
781 resetPreferredSize();
782 _main_panel.adjustJScrollPane();
787 final void colorRank( final String rank ) {
788 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
792 AptxUtil.removeBranchColors( _phylogeny );
793 final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
794 if ( colorizations > 0 ) {
795 _control_panel.setColorBranches( true );
796 if ( _control_panel.getColorBranchesCb() != null ) {
797 _control_panel.getColorBranchesCb().setSelected( true );
799 if ( _control_panel.getColorAccSpeciesCb() != null ) {
800 _control_panel.getColorAccSpeciesCb().setSelected( false );
802 _options.setColorLabelsSameAsParentBranch( true );
803 _control_panel.repaint();
807 if ( colorizations > 0 ) {
808 String msg = "Taxonomy colorization via " + rank + " completed:\n";
809 if ( colorizations > 1 ) {
810 msg += "colorized " + colorizations + " subtrees";
813 msg += "colorized one subtree";
815 JOptionPane.showMessageDialog( this,
817 "Taxonomy Colorization Completed (" + rank + ")",
818 JOptionPane.INFORMATION_MESSAGE );
821 String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
822 msg += "Possible solutions (given that suitable taxonomic information is present):\n";
823 msg += "select a different rank (e.g. phylum, genus, ...)\n";
826 msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
827 msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
828 JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
832 final void confColor() {
833 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
837 AptxUtil.removeBranchColors( _phylogeny );
838 AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
839 _control_panel.setColorBranches( true );
840 if ( _control_panel.getColorBranchesCb() != null ) {
841 _control_panel.getColorBranchesCb().setSelected( true );
847 final void decreaseDomainStructureEvalueThreshold() {
848 if ( _domain_structure_e_value_thr_exp > -20 ) {
849 _domain_structure_e_value_thr_exp -= 1;
854 * Find the node, if any, at the given location
858 * @return pointer to the node at x,y, null if not found
860 final PhylogenyNode findNode( final int x, final int y ) {
861 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
864 final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
865 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
866 final PhylogenyNode node = iter.next();
867 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
868 && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
869 && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
870 && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
871 && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
878 final Configuration getConfiguration() {
879 return _configuration;
882 final ControlPanel getControlPanel() {
883 return _control_panel;
886 String getCurrentExternalNodesDataBufferAsString() {
887 return _current_external_nodes_data_buffer.toString();
890 int getCurrentExternalNodesDataBufferChangeCounter() {
891 return _current_external_nodes_data_buffer_change_counter;
894 final int getDomainStructureEvalueThreshold() {
895 return _domain_structure_e_value_thr_exp;
898 final Set<Integer> getFoundNodes() {
902 final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
903 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
904 return ( PhylogenyMethods.getBranchColorValue( node ) );
907 return ( getTreeColorSet().getBranchColor() );
911 final int getLongestExtNodeInfo() {
912 return _longest_ext_node_info;
915 final Options getOptions() {
916 if ( _options == null ) {
917 _options = getControlPanel().getOptions();
922 final Rectangle2D getOvRectangle() {
923 return _ov_rectangle;
926 final Rectangle getOvVirtualRectangle() {
927 return _ov_virtual_rectangle;
930 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
931 return _graphics_type;
934 final double getStartingAngle() {
935 return _urt_starting_angle;
938 DescriptiveStatistics getStatisticsForExpressionValues() {
939 return _statistics_for_vector_data;
943 * Find a color for this species name.
946 * @return the species color
948 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
949 if ( node.getNodeData().isHasTaxonomy() ) {
950 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
952 // return non-colorized color
953 return getTreeColorSet().getTaxonomyColor();
957 * @return pointer to colorset for tree drawing
959 final TreeColorSet getTreeColorSet() {
960 return getMainPanel().getTreeColorSet();
963 final File getTreeFile() {
967 final float getXcorrectionFactor() {
968 return _x_correction_factor;
971 final float getXdistance() {
975 final float getYdistance() {
979 final void increaseDomainStructureEvalueThreshold() {
980 if ( _domain_structure_e_value_thr_exp < 3 ) {
981 _domain_structure_e_value_thr_exp += 1;
985 final void initNodeData() {
986 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
989 double max_original_domain_structure_width = 0.0;
990 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
991 if ( node.getNodeData().isHasSequence()
992 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
993 RenderableDomainArchitecture rds = null;
994 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
995 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
996 getConfiguration() );
997 node.getNodeData().getSequence().setDomainArchitecture( rds );
1000 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1002 if ( getControlPanel().isShowDomainArchitectures() ) {
1003 final double dsw = rds.getOriginalSize().getWidth();
1004 if ( dsw > max_original_domain_structure_width ) {
1005 max_original_domain_structure_width = dsw;
1010 if ( getControlPanel().isShowDomainArchitectures() ) {
1011 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1012 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1013 if ( node.getNodeData().isHasSequence()
1014 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1015 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1016 .getSequence().getDomainArchitecture();
1017 rds.setRenderingFactorWidth( ds_factor_width );
1018 rds.setParameter( _domain_structure_e_value_thr_exp );
1024 final boolean inOv( final MouseEvent e ) {
1025 return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
1026 && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
1027 && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
1028 + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
1031 final boolean inOvRectangle( final MouseEvent e ) {
1032 return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
1033 && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
1034 && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
1035 + getOvRectangle().getHeight() + 1 ) ) );
1038 final boolean isApplet() {
1039 return getMainPanel() instanceof MainPanelApplets;
1042 final boolean isCanCollapse() {
1043 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1046 final boolean isCanColorSubtree() {
1047 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1050 final boolean isCanCopy() {
1051 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1054 final boolean isCanCut( final PhylogenyNode node ) {
1055 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1059 final boolean isCanDelete() {
1060 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1063 final boolean isCanPaste() {
1064 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1065 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1068 final boolean isCanReroot() {
1069 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1072 final boolean isCanSubtree( final PhylogenyNode node ) {
1073 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1074 .isRoot() || ( _subtree_index > 0 ) ) );
1077 final boolean isCurrentTreeIsSubtree() {
1078 return ( _subtree_index > 0 );
1081 final boolean isEdited() {
1085 final boolean isInOvRect() {
1089 final boolean isOvOn() {
1093 final boolean isPhyHasBranchLengths() {
1094 return _phy_has_branch_lengths;
1097 final void midpointRoot() {
1098 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1101 if ( !_phylogeny.isRerootable() ) {
1102 JOptionPane.showMessageDialog( this,
1103 "This is not rerootable",
1105 JOptionPane.WARNING_MESSAGE );
1108 setNodeInPreorderToNull();
1110 PhylogenyMethods.midpointRoot( _phylogeny );
1111 resetNodeIdToDistToLeafMap();
1116 final void mouseClicked( final MouseEvent e ) {
1117 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1118 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1119 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1120 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
1122 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
1130 final double max_x = getWidth() - getVisibleRect().width;
1131 final double max_y = getHeight() - getVisibleRect().height;
1138 getMainPanel().getCurrentScrollPane().getViewport()
1139 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1140 setInOvRect( true );
1144 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1145 if ( node != null ) {
1146 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1149 _highlight_node = node;
1150 // Check if shift key is down
1151 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1152 // Yes, so add to _found_nodes
1153 if ( getFoundNodes() == null ) {
1154 setFoundNodes( new HashSet<Integer>() );
1156 getFoundNodes().add( node.getId() );
1157 // Check if control key is down
1159 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1160 // Yes, so pop-up menu
1161 displayNodePopupMenu( node, e.getX(), e.getY() );
1162 // Handle unadorned click
1165 // Check for right mouse button
1166 if ( e.getModifiers() == 4 ) {
1167 displayNodePopupMenu( node, e.getX(), e.getY() );
1170 // if not in _found_nodes, clear _found_nodes
1171 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1176 // no node was clicked
1177 _highlight_node = null;
1183 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1184 setCursor( MOVE_CURSOR );
1185 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1186 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1187 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1188 if ( scroll_position.x < 0 ) {
1189 scroll_position.x = 0;
1192 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1193 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1194 if ( scroll_position.x > max_x ) {
1195 scroll_position.x = max_x;
1198 if ( scroll_position.y < 0 ) {
1199 scroll_position.y = 0;
1202 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1203 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1204 if ( scroll_position.y > max_y ) {
1205 scroll_position.y = max_y;
1208 if ( isOvOn() || getOptions().isShowScale() ) {
1211 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1214 final void mouseDragInOvRectangle( final MouseEvent e ) {
1215 setCursor( HAND_CURSOR );
1216 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1217 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1218 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1219 double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
1220 double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
1221 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1222 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1223 if ( scroll_position.x <= 0 ) {
1224 scroll_position.x = 0;
1228 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1229 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1230 if ( scroll_position.x >= max_x ) {
1232 scroll_position.x = max_x;
1235 if ( scroll_position.y <= 0 ) {
1237 scroll_position.y = 0;
1240 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1241 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1242 if ( scroll_position.y >= max_y ) {
1244 scroll_position.y = max_y;
1248 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1249 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1250 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1253 final void mouseMoved( final MouseEvent e ) {
1254 requestFocusInWindow();
1255 if ( _current_external_nodes != null ) {
1256 _current_external_nodes = null;
1259 if ( getControlPanel().isNodeDescPopup() ) {
1260 if ( _node_desc_popup != null ) {
1261 _node_desc_popup.hide();
1262 _node_desc_popup = null;
1265 if ( getOptions().isShowOverview() && isOvOn() ) {
1266 if ( inOvVirtualRectangle( e ) ) {
1267 if ( !isInOvRect() ) {
1268 setInOvRect( true );
1273 if ( isInOvRect() ) {
1274 setInOvRect( false );
1279 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
1288 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1289 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
1290 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
1291 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
1292 addToCurrentExternalNodes( n.getId() );
1294 setCursor( HAND_CURSOR );
1297 else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
1298 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
1299 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
1300 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
1301 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
1302 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
1303 setCursor( CUT_CURSOR );
1306 setCursor( HAND_CURSOR );
1307 if ( getControlPanel().isNodeDescPopup() ) {
1308 showNodeDataPopup( e, node );
1313 setCursor( ARROW_CURSOR );
1318 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
1319 setCursor( ARROW_CURSOR );
1322 final void multiplyUrtFactor( final float f ) {
1326 final JApplet obtainApplet() {
1327 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1330 final void paintBranchCircular( final PhylogenyNode p,
1331 final PhylogenyNode c,
1333 final boolean radial_labels,
1334 final boolean to_pdf,
1335 final boolean to_graphics_file ) {
1336 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1337 final double root_x = _root.getXcoord();
1338 final double root_y = _root.getYcoord();
1339 final double dx = root_x - p.getXcoord();
1340 final double dy = root_y - p.getYcoord();
1341 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1342 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1343 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
1344 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
1345 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
1346 final double r2 = 2.0 * parent_radius;
1347 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1349 drawLine( c.getXcoord(),
1351 root_x + ( Math.cos( angle ) * parent_radius ),
1352 root_y + ( Math.sin( angle ) * parent_radius ),
1354 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c )
1355 || isInCurrentExternalNodes( c ) );
1356 if ( c.isExternal() ) {
1357 final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c );
1358 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
1359 && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
1362 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
1366 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
1367 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1368 final double root_x = _root.getXSecondary();
1369 final double root_y = _root.getYSecondary();
1370 final double dx = root_x - p.getXSecondary();
1371 final double dy = root_y - p.getYSecondary();
1372 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1373 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1374 g.setColor( getTreeColorSet().getOvColor() );
1375 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
1376 final double r2 = 2.0 * parent_radius;
1377 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1379 drawLine( c.getXSecondary(),
1381 root_x + ( Math.cos( angle ) * parent_radius ),
1382 root_y + ( Math.sin( angle ) * parent_radius ),
1384 if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
1385 g.setColor( getTreeColorSet().getFoundColor() );
1386 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
1390 final void paintCircular( final Phylogeny phy,
1391 final double starting_angle,
1396 final boolean to_pdf,
1397 final boolean to_graphics_file ) {
1398 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
1399 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
1400 _root = phy.getRoot();
1401 _root.setXcoord( center_x );
1402 _root.setYcoord( center_y );
1403 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1404 double current_angle = starting_angle;
1406 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1407 final PhylogenyNode n = it.next();
1408 if ( !n.isCollapse() ) {
1409 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1410 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1411 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1412 _urt_nodeid_index_map.put( n.getId(), i++ );
1413 current_angle += ( TWO_PI / circ_num_ext_nodes );
1417 System.out.println( "is collapse" + n.getName() );
1420 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
1421 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
1424 final void paintCircularLite( final Phylogeny phy,
1425 final double starting_angle,
1429 final Graphics2D g ) {
1430 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
1431 _root = phy.getRoot();
1432 _root.setXSecondary( center_x );
1433 _root.setYSecondary( center_y );
1434 double current_angle = starting_angle;
1435 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1436 final PhylogenyNode n = it.next();
1437 n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1438 n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1439 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1440 current_angle += ( TWO_PI / circ_num_ext_nodes );
1442 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
1445 final void paintPhylogeny( final Graphics2D g,
1446 final boolean to_pdf,
1447 final boolean to_graphics_file,
1448 final int graphics_file_width,
1449 final int graphics_file_height,
1450 final int graphics_file_x,
1451 final int graphics_file_y ) {
1452 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1455 if ( _control_panel.isShowSequenceRelations() ) {
1456 _query_sequence = _control_panel.getSelectedQuerySequence();
1458 // Color the background
1460 final Rectangle r = getVisibleRect();
1461 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
1462 g.setColor( getTreeColorSet().getBackgroundColor() );
1463 if ( !to_graphics_file ) {
1467 if ( getOptions().isPrintBlackAndWhite() ) {
1468 g.setColor( Color.WHITE );
1470 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1474 if ( !to_graphics_file ) {
1475 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
1476 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
1480 g.setPaint( new GradientPaint( graphics_file_x,
1482 getTreeColorSet().getBackgroundColor(),
1484 graphics_file_y + graphics_file_height,
1485 getTreeColorSet().getBackgroundColorGradientBottom() ) );
1486 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1489 g.setStroke( new BasicStroke( 1 ) );
1492 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
1494 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1495 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1496 _external_node_index = 0;
1497 // Position starting X of tree
1498 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
1499 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
1501 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
1502 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
1503 .getDistanceToParent() * getXcorrectionFactor() ) ) );
1506 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
1508 // Position starting Y of tree
1509 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
1510 + ( TreePanel.MOVE / 2.0f ) );
1511 final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) );
1512 if ( getControlPanel().isDynamicallyHideData() ) {
1513 if ( dynamic_hiding_factor > 1 ) {
1514 getControlPanel().setDynamicHidingIsOn( true );
1517 getControlPanel().setDynamicHidingIsOn( false );
1520 if ( _nodes_in_preorder == null ) {
1521 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
1523 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1524 _nodes_in_preorder[ i++ ] = it.next();
1527 //final PhylogenyNodeIterator it;
1528 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1529 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
1530 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1532 for( final PhylogenyNode element : _nodes_in_preorder ) {
1533 paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
1534 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1536 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
1537 if ( !( to_graphics_file || to_pdf ) ) {
1540 getVisibleRect().y + getVisibleRect().height,
1545 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1548 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1549 paintPhylogenyLite( g );
1552 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1553 if ( getControlPanel().getDynamicallyHideData() != null ) {
1554 getControlPanel().setDynamicHidingIsOn( false );
1556 final double angle = getStartingAngle();
1557 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1558 _dynamic_hiding_factor = 0;
1559 if ( getControlPanel().isDynamicallyHideData() ) {
1560 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1561 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
1563 if ( getControlPanel().getDynamicallyHideData() != null ) {
1564 if ( _dynamic_hiding_factor > 1 ) {
1565 getControlPanel().setDynamicHidingIsOn( true );
1568 getControlPanel().setDynamicHidingIsOn( false );
1571 paintUnrooted( _phylogeny.getRoot(),
1573 ( float ) ( angle + ( 2 * Math.PI ) ),
1578 if ( getOptions().isShowScale() ) {
1579 if ( !( to_graphics_file || to_pdf ) ) {
1582 getVisibleRect().y + getVisibleRect().height,
1587 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1590 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1591 g.setColor( getTreeColorSet().getOvColor() );
1592 paintUnrootedLite( _phylogeny.getRoot(),
1594 angle + ( 2 * Math.PI ),
1596 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
1597 paintOvRectangle( g );
1600 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1601 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
1602 final int d = radius + MOVE + getLongestExtNodeInfo();
1603 _dynamic_hiding_factor = 0;
1604 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
1605 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1606 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
1608 if ( getControlPanel().getDynamicallyHideData() != null ) {
1609 if ( _dynamic_hiding_factor > 1 ) {
1610 getControlPanel().setDynamicHidingIsOn( true );
1613 getControlPanel().setDynamicHidingIsOn( false );
1616 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
1617 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1618 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
1619 : getOvMaxWidth() / 2 );
1620 double x_scale = 1.0;
1621 double y_scale = 1.0;
1622 int x_pos = getVisibleRect().x + getOvXPosition();
1623 int y_pos = getVisibleRect().y + getOvYPosition();
1624 if ( getWidth() > getHeight() ) {
1625 x_scale = ( double ) getHeight() / getWidth();
1626 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
1629 y_scale = ( double ) getWidth() / getHeight();
1630 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
1632 _at = g.getTransform();
1633 g.scale( x_scale, y_scale );
1634 paintCircularLite( _phylogeny,
1638 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
1641 g.setTransform( _at );
1642 paintOvRectangle( g );
1647 final void recalculateMaxDistanceToRoot() {
1648 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
1652 * Remove all edit-node frames
1654 final void removeAllEditNodeJFrames() {
1655 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
1656 if ( _node_frames[ i ] != null ) {
1657 _node_frames[ i ].dispose();
1658 _node_frames[ i ] = null;
1661 _node_frame_index = 0;
1665 * Remove a node-edit frame.
1667 final void removeEditNodeFrame( final int i ) {
1668 _node_frame_index--;
1669 _node_frames[ i ] = null;
1670 if ( i < _node_frame_index ) {
1671 for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
1672 _node_frames[ j ] = _node_frames[ j + 1 ];
1674 _node_frames[ _node_frame_index ] = null;
1678 final void reRoot( final PhylogenyNode node ) {
1679 if ( !getPhylogeny().isRerootable() ) {
1680 JOptionPane.showMessageDialog( this,
1681 "This is not rerootable",
1683 JOptionPane.WARNING_MESSAGE );
1686 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1687 JOptionPane.showMessageDialog( this,
1688 "Cannot reroot in unrooted display type",
1689 "Attempt to reroot tree in unrooted display",
1690 JOptionPane.WARNING_MESSAGE );
1693 getPhylogeny().reRoot( node );
1694 getPhylogeny().recalculateNumberOfExternalDescendants( true );
1695 resetNodeIdToDistToLeafMap();
1696 setNodeInPreorderToNull();
1697 resetPreferredSize();
1698 getMainPanel().adjustJScrollPane();
1700 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1701 getControlPanel().showWhole();
1705 final void resetNodeIdToDistToLeafMap() {
1706 _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
1709 final void resetPreferredSize() {
1710 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
1716 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
1717 if ( getControlPanel().isDrawPhylogram() ) {
1719 + getLongestExtNodeInfo()
1721 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
1724 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
1726 + getLongestExtNodeInfo()
1727 + ForesterUtil.roundToInt( getXdistance()
1728 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
1732 + getLongestExtNodeInfo()
1733 + ForesterUtil.roundToInt( getXdistance()
1734 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
1737 setPreferredSize( new Dimension( x, y ) );
1740 final void selectNode( final PhylogenyNode node ) {
1741 if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
1742 getFoundNodes().remove( node.getId() );
1743 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1744 if ( getFoundNodes().size() < 1 ) {
1745 getControlPanel().searchReset();
1749 getControlPanel().getSearchFoundCountsLabel().setVisible( true );
1750 getControlPanel().getSearchResetButton().setEnabled( true );
1751 getControlPanel().getSearchResetButton().setVisible( true );
1752 if ( getFoundNodes() == null ) {
1753 setFoundNodes( new HashSet<Integer>() );
1755 getFoundNodes().add( node.getId() );
1756 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1760 final void setControlPanel( final ControlPanel atv_control ) {
1761 _control_panel = atv_control;
1764 void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
1765 increaseCurrentExternalNodesDataBufferChangeCounter();
1766 _current_external_nodes_data_buffer = sb;
1769 final void setFoundNodes( final Set<Integer> found_nodes ) {
1770 _found_nodes = found_nodes;
1773 final void setInOvRect( final boolean in_ov_rect ) {
1774 _in_ov_rect = in_ov_rect;
1777 final void setLargeFonts() {
1778 getTreeFontSet().largeFonts();
1781 final void setLastMouseDragPointX( final float x ) {
1782 _last_drag_point_x = x;
1785 final void setLastMouseDragPointY( final float y ) {
1786 _last_drag_point_y = y;
1789 final void setLongestExtNodeInfo( final int i ) {
1790 _longest_ext_node_info = i;
1793 final void setMediumFonts() {
1794 getTreeFontSet().mediumFonts();
1797 final void setNodeInPreorderToNull() {
1798 _nodes_in_preorder = null;
1801 final void setOvOn( final boolean ov_on ) {
1805 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
1806 _graphics_type = graphics_type;
1810 final void setSmallFonts() {
1811 getTreeFontSet().smallFonts();
1814 final void setStartingAngle( final double starting_angle ) {
1815 _urt_starting_angle = starting_angle;
1818 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
1819 _statistics_for_vector_data = statistics_for_expression_values;
1822 final void setSuperTinyFonts() {
1823 getTreeFontSet().superTinyFonts();
1826 final void setTextAntialias() {
1827 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
1828 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
1829 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
1832 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
1835 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
1836 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
1837 && !getMainPanel().getOptions().isShowDefaultNodeShapes()
1838 && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
1839 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1842 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
1845 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
1846 RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
1848 catch ( final Throwable e ) {
1849 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
1853 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
1854 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1858 final void setTinyFonts() {
1859 getTreeFontSet().tinyFonts();
1862 final void setTreeFile( final File treefile ) {
1863 _treefile = treefile;
1866 final void setXcorrectionFactor( final float f ) {
1867 _x_correction_factor = f;
1870 final void setXdistance( final float x ) {
1874 final void setYdistance( final float y ) {
1878 final void sortDescendants( final PhylogenyNode node ) {
1879 if ( !node.isExternal() ) {
1880 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
1881 if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
1882 .isShowTaxonomyCommonNames() ) ) {
1883 if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
1884 .isShowGeneSymbols() ) ) {
1885 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
1887 else if ( getControlPanel().isShowNodeNames() ) {
1888 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
1891 PhylogenyMethods.sortNodeDescendents( node, pri );
1892 setNodeInPreorderToNull();
1893 _phylogeny.externalNodesHaveChanged();
1894 _phylogeny.clearHashIdToNodeMap();
1895 _phylogeny.recalculateNumberOfExternalDescendants( true );
1896 resetNodeIdToDistToLeafMap();
1902 final void subTree( final PhylogenyNode node ) {
1903 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1904 JOptionPane.showMessageDialog( this,
1905 "Cannot get a sub/super tree in unrooted display",
1906 "Attempt to get sub/super tree in unrooted display",
1907 JOptionPane.WARNING_MESSAGE );
1910 if ( node.isExternal() ) {
1911 JOptionPane.showMessageDialog( this,
1912 "Cannot get a subtree of a external node",
1913 "Attempt to get subtree of external node",
1914 JOptionPane.WARNING_MESSAGE );
1917 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
1918 JOptionPane.showMessageDialog( this,
1919 "Cannot get a subtree of the root node",
1920 "Attempt to get subtree of root node",
1921 JOptionPane.WARNING_MESSAGE );
1924 setNodeInPreorderToNull();
1925 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
1926 _sub_phylogenies[ _subtree_index ] = _phylogeny;
1927 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
1929 _phylogeny = subTree( node, _phylogeny );
1930 updateSubSuperTreeButton();
1932 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
1935 _main_panel.getControlPanel().showWhole();
1939 final void superTree() {
1940 setNodeInPreorderToNull();
1941 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
1942 for( final PhylogenyNode n : temp_root.getDescendants() ) {
1943 n.setParent( temp_root );
1945 _sub_phylogenies[ _subtree_index ] = null;
1946 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
1947 _phylogeny = _sub_phylogenies[ --_subtree_index ];
1948 updateSubSuperTreeButton();
1951 final void swap( final PhylogenyNode node ) {
1952 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
1955 if ( node.getNumberOfDescendants() > 2 ) {
1956 JOptionPane.showMessageDialog( this,
1957 "Cannot swap descendants of nodes with more than 2 descendants",
1958 "Cannot swap descendants",
1959 JOptionPane.ERROR_MESSAGE );
1962 if ( !node.isExternal() ) {
1963 node.swapChildren();
1964 setNodeInPreorderToNull();
1965 _phylogeny.externalNodesHaveChanged();
1966 _phylogeny.clearHashIdToNodeMap();
1967 _phylogeny.recalculateNumberOfExternalDescendants( true );
1968 resetNodeIdToDistToLeafMap();
1974 final void taxColor() {
1975 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1979 AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
1980 _control_panel.setColorBranches( true );
1981 if ( _control_panel.getColorBranchesCb() != null ) {
1982 _control_panel.getColorBranchesCb().setSelected( true );
1988 final void updateOvSettings() {
1989 switch ( getOptions().getOvPlacement() ) {
1991 setOvXPosition( OV_BORDER );
1992 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
1993 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
1996 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
1997 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
1998 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2001 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2002 setOvYPosition( OV_BORDER );
2003 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2006 setOvXPosition( OV_BORDER );
2007 setOvYPosition( OV_BORDER );
2008 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2013 final void updateOvSizes() {
2014 if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
2016 float l = getLongestExtNodeInfo();
2017 final float w_ratio = getOvMaxWidth() / getWidth();
2019 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
2020 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
2022 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
2023 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
2026 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
2028 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
2029 if ( ov_xdist < 0.0 ) {
2032 if ( ydist < 0.0 ) {
2035 setOvXDistance( ov_xdist );
2036 final double height = _phylogeny.getHeight();
2038 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
2039 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
2042 setOvXcorrectionFactor( 0 );
2050 void updateSetOfCollapsedExternalNodes() {
2051 final Phylogeny phy = getPhylogeny();
2052 _collapsed_external_nodeid_set.clear();
2053 if ( phy != null ) {
2054 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2055 final PhylogenyNode ext_node = it.next();
2056 PhylogenyNode n = ext_node;
2057 while ( !n.isRoot() ) {
2058 if ( n.isCollapse() ) {
2059 _collapsed_external_nodeid_set.add( ext_node.getId() );
2060 ext_node.setCollapse( true );
2069 final void updateSubSuperTreeButton() {
2070 if ( _subtree_index < 1 ) {
2071 getControlPanel().deactivateButtonToReturnToSuperTree();
2074 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
2078 final void zoomInDomainStructure() {
2079 if ( _domain_structure_width < 2000 ) {
2080 _domain_structure_width *= 1.2;
2084 final void zoomOutDomainStructure() {
2085 if ( _domain_structure_width > 20 ) {
2086 _domain_structure_width *= 0.8;
2090 private void abbreviateScientificName( final String sn ) {
2091 final String[] a = sn.split( "\\s+" );
2092 _sb.append( a[ 0 ].substring( 0, 1 ) );
2093 _sb.append( a[ 1 ].substring( 0, 2 ) );
2094 if ( a.length > 2 ) {
2095 for( int i = 2; i < a.length; i++ ) {
2097 _sb.append( a[ i ] );
2102 final private void addEmptyNode( final PhylogenyNode node ) {
2103 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2104 errorMessageNoCutCopyPasteInUnrootedDisplay();
2107 final String label = createASimpleTextRepresentationOfANode( node );
2109 if ( ForesterUtil.isEmpty( label ) ) {
2110 msg = "How to add the new, empty node?";
2113 msg = "How to add the new, empty node to node" + label + "?";
2115 final Object[] options = { "As sibling", "As descendant", "Cancel" };
2116 final int r = JOptionPane.showOptionDialog( this,
2118 "Addition of Empty New Node",
2119 JOptionPane.CLOSED_OPTION,
2120 JOptionPane.QUESTION_MESSAGE,
2124 boolean add_as_sibling = true;
2126 add_as_sibling = false;
2128 else if ( r != 0 ) {
2131 final Phylogeny phy = new Phylogeny();
2132 phy.setRoot( new PhylogenyNode() );
2133 phy.setRooted( true );
2134 if ( add_as_sibling ) {
2135 if ( node.isRoot() ) {
2136 JOptionPane.showMessageDialog( this,
2137 "Cannot add sibling to root",
2138 "Attempt to add sibling to root",
2139 JOptionPane.ERROR_MESSAGE );
2142 phy.addAsSibling( node );
2145 phy.addAsChild( node );
2147 setNodeInPreorderToNull();
2148 _phylogeny.externalNodesHaveChanged();
2149 _phylogeny.clearHashIdToNodeMap();
2150 _phylogeny.recalculateNumberOfExternalDescendants( true );
2151 resetNodeIdToDistToLeafMap();
2156 final private void addToCurrentExternalNodes( final int i ) {
2157 if ( _current_external_nodes == null ) {
2158 _current_external_nodes = new HashSet<Integer>();
2160 _current_external_nodes.add( i );
2163 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
2164 final boolean is_vertical,
2166 final boolean to_pdf,
2167 final boolean to_graphics_file ) {
2168 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
2169 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2170 g.setColor( Color.BLACK );
2172 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
2173 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
2174 && ( getCutOrCopiedTree() != null )
2175 && ( getCopiedAndPastedNodes() != null )
2177 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
2178 g.setColor( getTreeColorSet().getFoundColor() );
2180 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2181 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2183 else if ( to_pdf ) {
2184 g.setColor( getTreeColorSet().getBranchColorForPdf() );
2187 g.setColor( getTreeColorSet().getBranchColor() );
2191 final private void blast( final PhylogenyNode node ) {
2192 if ( !isCanBlast( node ) ) {
2193 JOptionPane.showMessageDialog( this,
2194 "Insufficient information present",
2196 JOptionPane.INFORMATION_MESSAGE );
2200 final String query = Blast.obtainQueryForBlast( node );
2201 System.out.println( "query for BLAST is: " + query );
2203 if ( !ForesterUtil.isEmpty( query ) ) {
2204 if ( node.getNodeData().isHasSequence() ) {
2205 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
2206 if ( node.getNodeData().getSequence().getType().toLowerCase()
2207 .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
2214 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2215 if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2223 if ( type == '?' ) {
2224 if ( SequenceIdParser.isProtein( query ) ) {
2231 JApplet applet = null;
2233 applet = obtainApplet();
2236 Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
2238 catch ( final Exception e ) {
2239 e.printStackTrace();
2241 if ( Constants.ALLOW_DDBJ_BLAST ) {
2243 System.out.println( "trying: " + query );
2244 final Blast s = new Blast();
2245 s.ddbjBlast( query );
2247 catch ( final Exception e ) {
2248 e.printStackTrace();
2256 * Calculate the length of the distance between the given node and its
2262 * @return the distance value
2264 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
2265 if ( getControlPanel().isDrawPhylogram() ) {
2266 if ( node.getDistanceToParent() < 0.0 ) {
2269 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
2272 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2273 return getXdistance();
2275 return getXdistance() * factor;
2279 final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
2280 Color c = getTreeColorSet().getAnnotationColor();
2281 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
2282 final StringBuilder sb = new StringBuilder();
2283 for( final Annotation a : ann ) {
2284 sb.append( !ForesterUtil.isEmpty( a.getRef() ) ? a.getRef() : a.getDesc() );
2286 final String ann_str = sb.toString();
2287 if ( !ForesterUtil.isEmpty( ann_str ) ) {
2288 c = getControlPanel().getAnnotationColors().get( ann_str );
2290 c = AptxUtil.calculateColorFromString( ann_str );
2291 getControlPanel().getAnnotationColors().put( ann_str, c );
2294 c = getTreeColorSet().getAnnotationColor();
2301 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
2302 if ( getControlPanel().isDrawPhylogram() ) {
2303 if ( node.getDistanceToParent() < 0.0 ) {
2306 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
2309 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2310 return getOvXDistance();
2312 return getOvXDistance() * factor;
2316 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
2317 JOptionPane.showMessageDialog( this,
2318 "Cannot launch web browser for " + type_type + " data of this node",
2319 "Cannot launch web browser",
2320 JOptionPane.WARNING_MESSAGE );
2323 final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
2324 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2325 JOptionPane.showMessageDialog( this,
2326 "Cannot colorize subtree in unrooted display type",
2327 "Attempt to colorize subtree in unrooted display",
2328 JOptionPane.WARNING_MESSAGE );
2331 _control_panel.setColorBranches( true );
2332 if ( _control_panel.getColorBranchesCb() != null ) {
2333 _control_panel.getColorBranchesCb().setSelected( true );
2335 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
2336 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
2341 final private void colorSubtree( final PhylogenyNode node ) {
2342 Color intitial_color = null;
2343 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
2344 && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
2345 intitial_color = PhylogenyMethods.getBranchColorValue( node );
2348 intitial_color = getTreeColorSet().getBranchColor();
2350 _color_chooser.setColor( intitial_color );
2351 _color_chooser.setPreviewPanel( new JPanel() );
2352 final JDialog dialog = JColorChooser
2353 .createDialog( this,
2354 "Subtree colorization",
2357 new SubtreeColorizationActionListener( _color_chooser, node ),
2359 dialog.setVisible( true );
2362 final private void copySubtree( final PhylogenyNode node ) {
2363 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2364 errorMessageNoCutCopyPasteInUnrootedDisplay();
2367 setNodeInPreorderToNull();
2368 setCutOrCopiedTree( _phylogeny.copy( node ) );
2369 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
2370 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
2371 for( final PhylogenyNode n : nodes ) {
2372 node_ids.add( n.getId() );
2374 node_ids.add( node.getId() );
2375 setCopiedAndPastedNodes( node_ids );
2379 private String createAnnotationString( final SortedSet<Annotation> ann ) {
2380 final StringBuilder sb = new StringBuilder();
2381 boolean first = true;
2382 for( final Annotation a : ann ) {
2389 sb.append( a.asSimpleText() );
2391 final String ann_str = sb.toString();
2395 final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
2396 final String tax = PhylogenyMethods.getSpecies( node );
2397 String label = node.getName();
2398 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
2399 label = label + " " + tax;
2401 else if ( !ForesterUtil.isEmpty( tax ) ) {
2407 if ( !ForesterUtil.isEmpty( label ) ) {
2408 label = " [" + label + "]";
2413 final private void cutSubtree( final PhylogenyNode node ) {
2414 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2415 errorMessageNoCutCopyPasteInUnrootedDisplay();
2418 if ( node.isRoot() ) {
2419 JOptionPane.showMessageDialog( this,
2420 "Cannot cut entire tree as subtree",
2421 "Attempt to cut entire tree",
2422 JOptionPane.ERROR_MESSAGE );
2425 final String label = createASimpleTextRepresentationOfANode( node );
2426 final int r = JOptionPane.showConfirmDialog( null,
2427 "Cut subtree" + label + "?",
2428 "Confirm Cutting of Subtree",
2429 JOptionPane.YES_NO_OPTION );
2430 if ( r != JOptionPane.OK_OPTION ) {
2433 setNodeInPreorderToNull();
2434 setCopiedAndPastedNodes( null );
2435 setCutOrCopiedTree( _phylogeny.copy( node ) );
2436 _phylogeny.deleteSubtree( node, true );
2437 _phylogeny.clearHashIdToNodeMap();
2438 _phylogeny.recalculateNumberOfExternalDescendants( true );
2439 resetNodeIdToDistToLeafMap();
2444 final private void cycleColors() {
2445 getMainPanel().getTreeColorSet().cycleColorScheme();
2446 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
2447 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
2451 final private void decreaseOvSize() {
2452 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
2453 setOvMaxWidth( getOvMaxWidth() - 5 );
2454 setOvMaxHeight( getOvMaxHeight() - 5 );
2456 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2460 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
2461 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2462 errorMessageNoCutCopyPasteInUnrootedDisplay();
2465 if ( node.isRoot() ) {
2466 JOptionPane.showMessageDialog( this,
2467 "Cannot delete entire tree",
2468 "Attempt to delete entire tree",
2469 JOptionPane.ERROR_MESSAGE );
2472 final String label = createASimpleTextRepresentationOfANode( node );
2473 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
2474 final int r = JOptionPane.showOptionDialog( this,
2475 "Delete" + label + "?",
2476 "Delete Node/Subtree",
2477 JOptionPane.CLOSED_OPTION,
2478 JOptionPane.QUESTION_MESSAGE,
2482 setNodeInPreorderToNull();
2483 boolean node_only = true;
2487 else if ( r != 0 ) {
2491 PhylogenyMethods.removeNode( node, _phylogeny );
2494 _phylogeny.deleteSubtree( node, true );
2496 _phylogeny.externalNodesHaveChanged();
2497 _phylogeny.clearHashIdToNodeMap();
2498 _phylogeny.recalculateNumberOfExternalDescendants( true );
2499 resetNodeIdToDistToLeafMap();
2504 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
2505 makePopupMenus( node );
2506 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
2507 _node_popup_menu.show( this, x, y );
2510 final private void drawArc( final double x,
2513 final double heigth,
2514 final double start_angle,
2515 final double arc_angle,
2516 final Graphics2D g ) {
2517 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
2521 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
2522 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
2525 _line.setLine( x1, y1, x2, y2 );
2529 final private void drawOval( final double x,
2532 final double heigth,
2533 final Graphics2D g ) {
2534 _ellipse.setFrame( x, y, width, heigth );
2538 final private void drawOvalFilled( final double x,
2541 final double heigth,
2542 final Graphics2D g ) {
2543 _ellipse.setFrame( x, y, width, heigth );
2547 final private void drawOvalGradient( final double x,
2550 final double heigth,
2552 final Color color_1,
2553 final Color color_2,
2554 final Color color_border ) {
2555 _ellipse.setFrame( x, y, width, heigth );
2556 g.setPaint( new GradientPaint( ( float ) x,
2559 ( float ) ( x + width ),
2560 ( float ) ( y + heigth ),
2564 if ( color_border != null ) {
2565 g.setPaint( color_border );
2570 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
2571 _rectangle.setFrame( x, y, width, heigth );
2572 g.draw( _rectangle );
2575 final private void drawRectFilled( final double x,
2578 final double heigth,
2579 final Graphics2D g ) {
2580 _rectangle.setFrame( x, y, width, heigth );
2581 g.fill( _rectangle );
2584 final private void drawRectGradient( final double x,
2587 final double heigth,
2589 final Color color_1,
2590 final Color color_2,
2591 final Color color_border ) {
2592 _rectangle.setFrame( x, y, width, heigth );
2593 g.setPaint( new GradientPaint( ( float ) x,
2596 ( float ) ( x + width ),
2597 ( float ) ( y + heigth ),
2600 g.fill( _rectangle );
2601 if ( color_border != null ) {
2602 g.setPaint( color_border );
2603 g.draw( _rectangle );
2607 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2608 final List<Uri> us = new ArrayList<Uri>();
2609 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2610 for( final Uri uri : t.getUris() ) {
2615 for( final Uri uri : us ) {
2616 if ( uri != null ) {
2617 final String uri_str = uri.getValue().toString().toLowerCase();
2618 if ( getImageMap().containsKey( uri_str ) ) {
2619 final BufferedImage bi = getImageMap().get( uri_str );
2620 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2621 double scaling_factor = 1;
2622 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
2623 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
2624 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
2626 // y = y - ( 0.9 * getYdistance() );
2627 final double hs = bi.getHeight() * scaling_factor;
2628 double ws = ( bi.getWidth() * scaling_factor ) + offset;
2629 final double my_y = y - ( 0.5 * hs );
2630 final int x_w = ( int ) ( x + ws + 0.5 );
2631 final int y_h = ( int ) ( my_y + hs + 0.5 );
2632 if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
2634 ( int ) ( x + 0.5 + offset ),
2635 ( int ) ( my_y + 0.5 ),
2656 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
2657 JOptionPane.showMessageDialog( this,
2658 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
2659 "Attempt to cut/copy/paste/add/delete in unrooted display",
2660 JOptionPane.ERROR_MESSAGE );
2663 final private Set<Integer> getCopiedAndPastedNodes() {
2664 return getMainPanel().getCopiedAndPastedNodes();
2667 final private Set<Integer> getCurrentExternalNodes() {
2668 return _current_external_nodes;
2671 final private Phylogeny getCutOrCopiedTree() {
2672 return getMainPanel().getCutOrCopiedTree();
2675 final private float getLastDragPointX() {
2676 return _last_drag_point_x;
2679 final private float getLastDragPointY() {
2680 return _last_drag_point_y;
2683 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
2684 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
2685 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
2686 _nodeid_dist_to_leaf.put( node.getId(), m );
2690 return _nodeid_dist_to_leaf.get( node.getId() );
2694 final private double getMaxDistanceToRoot() {
2695 if ( _max_distance_to_root < 0 ) {
2696 recalculateMaxDistanceToRoot();
2698 return _max_distance_to_root;
2701 final private float getOvMaxHeight() {
2702 return _ov_max_height;
2705 final private float getOvMaxWidth() {
2706 return _ov_max_width;
2709 final private float getOvXcorrectionFactor() {
2710 return _ov_x_correction_factor;
2713 final private float getOvXDistance() {
2714 return _ov_x_distance;
2717 final private int getOvXPosition() {
2718 return _ov_x_position;
2721 final private float getOvYDistance() {
2722 return _ov_y_distance;
2725 final private int getOvYPosition() {
2726 return _ov_y_position;
2729 final private int getOvYStart() {
2733 final private double getScaleDistance() {
2734 return _scale_distance;
2737 final private String getScaleLabel() {
2738 return _scale_label;
2741 final private TreeFontSet getTreeFontSet() {
2742 return getMainPanel().getTreeFontSet();
2745 final private float getUrtFactor() {
2749 final private float getUrtFactorOv() {
2750 return _urt_factor_ov;
2753 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
2756 showNodeFrame( node );
2771 colorSubtree( node );
2786 copySubtree( node );
2789 pasteSubtree( node );
2791 case DELETE_NODE_OR_SUBTREE:
2792 deleteNodeOrSubtree( node );
2795 addEmptyNode( node );
2797 case EDIT_NODE_DATA:
2798 showNodeEditFrame( node );
2803 case SORT_DESCENDENTS:
2804 sortDescendants( node );
2806 case GET_EXT_DESC_DATA:
2807 showExtDescNodeData( node );
2810 throw new IllegalArgumentException( "unknown action: " + action );
2814 final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
2815 _current_external_nodes_data_buffer_change_counter++;
2818 final private void increaseOvSize() {
2819 if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
2820 && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
2821 .getHeight() / 2 ) ) ) {
2822 setOvMaxWidth( getOvMaxWidth() + 5 );
2823 setOvMaxHeight( getOvMaxHeight() + 5 );
2825 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2829 final private void init() {
2830 _color_chooser = new JColorChooser();
2831 _rollover_popup = new JTextArea();
2832 _rollover_popup.setFont( POPUP_FONT );
2833 resetNodeIdToDistToLeafMap();
2835 setTreeFile( null );
2837 initializeOvSettings();
2838 setStartingAngle( ( TWO_PI * 3 ) / 4 );
2839 final ImageLoader il = new ImageLoader( this );
2840 new Thread( il ).start();
2843 final private void initializeOvSettings() {
2844 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
2845 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
2848 final private boolean inOvVirtualRectangle( final int x, final int y ) {
2849 return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
2850 && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
2851 && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
2852 + getOvVirtualRectangle().height + 1 ) ) );
2855 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
2856 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
2859 final private boolean isCanBlast( final PhylogenyNode node ) {
2860 if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
2863 return Blast.isContainsQueryForBlast( node );
2866 final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
2867 if ( node.getNodeData().isHasSequence()
2868 && ( node.getNodeData().getSequence().getAccession() != null )
2869 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
2870 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
2871 && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
2872 .toLowerCase() ) ) {
2878 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
2879 if ( node.getNodeData().isHasTaxonomy()
2880 && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
2881 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
2882 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
2883 .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
2884 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
2885 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
2886 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
2887 .getNodeData().getTaxonomy().getIdentifier() != null )
2888 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
2889 .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
2897 final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
2898 return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
2901 final private boolean isInFoundNodes( final PhylogenyNode node ) {
2902 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
2905 final private boolean isInOv() {
2909 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
2911 if ( getControlPanel().isShowTaxonomyImages() ) {
2912 y_dist = 40 + ( int ) getYdistance();
2914 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
2915 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
2916 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
2919 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
2920 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
2921 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
2922 || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
2923 .getMaxX() + 20 ) ) );
2926 final private boolean isNonLinedUpCladogram() {
2927 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
2930 final private boolean isUniformBranchLengthsForCladogram() {
2931 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
2934 final private void keyPressedCalls( final KeyEvent e ) {
2935 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
2936 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
2937 if ( !isInOvRect() ) {
2938 setInOvRect( true );
2941 else if ( isInOvRect() ) {
2942 setInOvRect( false );
2945 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
2946 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2947 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2948 getMainPanel().getTreeFontSet().mediumFonts();
2949 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2951 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
2952 getMainPanel().getTreeFontSet().decreaseFontSize();
2953 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2955 else if ( plusPressed( e.getKeyCode() ) ) {
2956 getMainPanel().getTreeFontSet().increaseFontSize();
2957 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2961 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2962 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2963 getControlPanel().showWhole();
2965 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
2966 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
2967 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
2968 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
2969 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
2970 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2972 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
2973 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
2974 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2976 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
2977 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
2978 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
2979 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2981 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
2982 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
2983 Constants.WHEEL_ZOOM_IN_FACTOR );
2984 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2991 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
2994 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
2998 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3002 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
3003 scroll_position.x = scroll_position.x + dx;
3004 scroll_position.y = scroll_position.y + dy;
3005 if ( scroll_position.x <= 0 ) {
3006 scroll_position.x = 0;
3009 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
3010 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
3011 if ( scroll_position.x >= max_x ) {
3012 scroll_position.x = max_x;
3015 if ( scroll_position.y <= 0 ) {
3016 scroll_position.y = 0;
3019 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
3020 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
3021 if ( scroll_position.y >= max_y ) {
3022 scroll_position.y = max_y;
3026 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
3029 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3030 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3031 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3032 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3033 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3035 else if ( plusPressed( e.getKeyCode() ) ) {
3036 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3037 Constants.WHEEL_ZOOM_IN_FACTOR );
3038 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3039 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3041 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
3042 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3043 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3044 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
3045 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3048 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
3049 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3050 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3051 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
3052 if ( getStartingAngle() < 0 ) {
3053 setStartingAngle( TWO_PI + getStartingAngle() );
3055 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3058 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
3059 boolean selected = false;
3060 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
3061 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
3065 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
3067 if ( getMainPanel().getMainFrame() == null ) {
3068 // Must be "E" applet version.
3069 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
3070 if ( ae.getlabelDirectionCbmi() != null ) {
3071 ae.getlabelDirectionCbmi().setSelected( selected );
3075 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
3079 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
3080 switchDisplaygetPhylogenyGraphicsType();
3083 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
3087 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
3088 MainFrame.cycleOverview( getOptions(), this );
3091 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
3094 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
3101 final private void makePopupMenus( final PhylogenyNode node ) {
3102 _node_popup_menu = new JPopupMenu();
3103 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
3104 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
3105 for( int i = 0; i < clickto_names.size(); i++ ) {
3106 final String title = clickto_names.get( i );
3107 _node_popup_menu_items[ i ] = new JMenuItem( title );
3108 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
3109 _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
3111 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
3112 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
3114 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
3115 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
3117 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
3118 if ( !getOptions().isEditable() ) {
3121 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
3123 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
3124 if ( !getOptions().isEditable() ) {
3127 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
3129 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
3130 if ( !getOptions().isEditable() ) {
3133 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
3135 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
3136 if ( !getOptions().isEditable() ) {
3139 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
3141 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
3142 if ( !getOptions().isEditable() ) {
3146 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
3147 if ( !getOptions().isEditable() ) {
3151 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
3152 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
3154 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
3155 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
3157 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
3158 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
3160 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
3161 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
3163 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
3164 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
3166 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
3167 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
3169 _node_popup_menu_items[ i ].addActionListener( this );
3170 _node_popup_menu.add( _node_popup_menu_items[ i ] );
3174 private final String obtainTitleForExtDescNodeData() {
3175 switch ( getOptions().getExtDescNodeDataToReturn() ) {
3177 return "Node Names";
3179 return "Sequence Names";
3180 case SEQUENCE_SYMBOL:
3181 return "Sequence Symbols";
3182 case SEQUENCE_MOL_SEQ:
3183 return "Molecular Sequences";
3185 return "Sequence Accessors";
3186 case TAXONOMY_SCIENTIFIC_NAME:
3187 return "Scientific Names";
3189 return "Taxonomy Codes";
3191 return "User Selected Data";
3193 throw new IllegalArgumentException( "unknown data element: "
3194 + getOptions().getExtDescNodeDataToReturn() );
3198 final private void openSeqWeb( final PhylogenyNode node ) {
3199 if ( !isCanOpenSeqWeb( node ) ) {
3200 cannotOpenBrowserWarningMessage( "sequence" );
3203 String uri_str = null;
3204 final Sequence seq = node.getNodeData().getSequence();
3205 final String source = seq.getAccession().getSource().toLowerCase();
3207 if ( source.toLowerCase().equals( "ncbi" ) ) {
3208 url = Constants.NCBI_ALL_DATABASE_SEARCH;
3211 final WebLink weblink = getConfiguration().getWebLink( source );
3212 url = weblink.getUrl().toString();
3215 uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
3217 catch ( final UnsupportedEncodingException e ) {
3218 AptxUtil.showErrorMessage( this, e.toString() );
3219 e.printStackTrace();
3221 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3223 JApplet applet = null;
3225 applet = obtainApplet();
3227 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
3229 catch ( final IOException e ) {
3230 AptxUtil.showErrorMessage( this, e.toString() );
3231 e.printStackTrace();
3233 catch ( final URISyntaxException e ) {
3234 AptxUtil.showErrorMessage( this, e.toString() );
3235 e.printStackTrace();
3239 cannotOpenBrowserWarningMessage( "sequence" );
3243 final private void openTaxWeb( final PhylogenyNode node ) {
3244 if ( !isCanOpenTaxWeb( node ) ) {
3245 cannotOpenBrowserWarningMessage( "taxonomic" );
3248 String uri_str = null;
3249 final Taxonomy tax = node.getNodeData().getTaxonomy();
3250 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
3251 && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
3252 final String type = tax.getIdentifier().getProvider().toLowerCase();
3253 final WebLink weblink = getConfiguration().getWebLink( type );
3255 uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
3257 catch ( final UnsupportedEncodingException e ) {
3258 AptxUtil.showErrorMessage( this, e.toString() );
3259 e.printStackTrace();
3262 else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3263 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
3265 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
3267 catch ( final URISyntaxException e ) {
3268 AptxUtil.showErrorMessage( this, e.toString() );
3270 e.printStackTrace();
3273 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
3275 uri_str = "http://www.eol.org/search?q="
3276 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
3278 catch ( final UnsupportedEncodingException e ) {
3279 AptxUtil.showErrorMessage( this, e.toString() );
3280 e.printStackTrace();
3283 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
3285 uri_str = "http://www.uniprot.org/taxonomy/?query="
3286 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
3288 catch ( final UnsupportedEncodingException e ) {
3289 AptxUtil.showErrorMessage( this, e.toString() );
3290 e.printStackTrace();
3293 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
3295 uri_str = "http://www.eol.org/search?q="
3296 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
3298 catch ( final UnsupportedEncodingException e ) {
3299 AptxUtil.showErrorMessage( this, e.toString() );
3300 e.printStackTrace();
3303 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3305 JApplet applet = null;
3307 applet = obtainApplet();
3309 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
3311 catch ( final IOException e ) {
3312 AptxUtil.showErrorMessage( this, e.toString() );
3313 e.printStackTrace();
3315 catch ( final URISyntaxException e ) {
3316 AptxUtil.showErrorMessage( this, e.toString() );
3317 e.printStackTrace();
3321 cannotOpenBrowserWarningMessage( "taxonomic" );
3325 final private void paintBranchLength( final Graphics2D g,
3326 final PhylogenyNode node,
3327 final boolean to_pdf,
3328 final boolean to_graphics_file ) {
3329 g.setFont( getTreeFontSet().getSmallFont() );
3330 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3331 g.setColor( Color.BLACK );
3334 g.setColor( getTreeColorSet().getBranchLengthColor() );
3336 if ( !node.isRoot() ) {
3337 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3338 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3339 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3341 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3342 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3343 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3346 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3347 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3351 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
3352 - getTreeFontSet()._small_max_descent, g );
3356 final private void paintBranchLite( final Graphics2D g,
3361 final PhylogenyNode node ) {
3362 g.setColor( getTreeColorSet().getOvColor() );
3363 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3364 drawLine( x1, y1, x2, y2, g );
3366 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3367 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3368 ( g ).draw( _quad_curve );
3370 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3371 final float dx = x2 - x1;
3372 final float dy = y2 - y1;
3373 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3374 + ( dy * 0.8f ), x2, y2 );
3375 ( g ).draw( _cubic_curve );
3378 final float x2a = x2;
3379 final float x1a = x1;
3380 // draw the vertical line
3381 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
3382 drawLine( x1, y1, x1, y2, g );
3384 // draw the horizontal line
3385 drawLine( x1a, y2, x2a, y2, g );
3390 * Paint a branch which consists of a vertical and a horizontal bar
3391 * @param is_ind_found_nodes
3393 final private void paintBranchRectangular( final Graphics2D g,
3398 final PhylogenyNode node,
3399 final boolean to_pdf,
3400 final boolean to_graphics_file ) {
3401 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
3402 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3403 drawLine( x1, y1, x2, y2, g );
3405 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3406 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3407 g.draw( _quad_curve );
3409 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3410 final float dx = x2 - x1;
3411 final float dy = y2 - y1;
3412 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3413 + ( dy * 0.8f ), x2, y2 );
3414 g.draw( _cubic_curve );
3417 final float x2a = x2;
3418 final float x1a = x1;
3420 if ( node.isFirstChildNode() || node.isLastChildNode()
3421 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3422 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3423 if ( !to_graphics_file
3425 && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
3426 .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
3430 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3431 float x2c = x1 + EURO_D;
3435 drawLine( x1, y1, x2c, y2, g );
3437 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3439 y2_r = y2 - ROUNDED_D;
3443 drawLine( x1, y1, x1, y2_r, g );
3446 y2_r = y2 + ROUNDED_D;
3450 drawLine( x1, y1, x1, y2_r, g );
3454 drawLine( x1, y1, x1, y2, g );
3458 // draw the horizontal line
3459 if ( !to_graphics_file && !to_pdf
3460 && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
3464 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
3465 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3466 x1_r = x1a + ROUNDED_D;
3468 drawLine( x1_r, y2, x2a, y2, g );
3471 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3472 final float x1c = x1a + EURO_D;
3474 drawLine( x1c, y2, x2a, y2, g );
3478 drawLine( x1a, y2, x2a, y2, g );
3482 final double w = PhylogenyMethods.getBranchWidthValue( node );
3483 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3484 x1_r = x1a + ROUNDED_D;
3486 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
3489 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3490 final float x1c = x1a + EURO_D;
3492 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
3496 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
3499 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3504 final double diff = y2 - y2_r;
3505 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
3508 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
3513 if ( node.isExternal() ) {
3514 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
3515 || isInCurrentExternalNodes( node ) );
3519 final private double paintCirculars( final PhylogenyNode n,
3520 final Phylogeny phy,
3521 final float center_x,
3522 final float center_y,
3523 final double radius,
3524 final boolean radial_labels,
3526 final boolean to_pdf,
3527 final boolean to_graphics_file ) {
3528 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
3529 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
3530 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
3532 return _urt_nodeid_angle_map.get( n.getId() );
3535 final List<PhylogenyNode> descs = n.getDescendants();
3537 for( final PhylogenyNode desc : descs ) {
3538 sum += paintCirculars( desc,
3549 if ( !n.isRoot() ) {
3550 r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3552 final double theta = sum / descs.size();
3553 n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
3554 n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
3555 _urt_nodeid_angle_map.put( n.getId(), theta );
3556 for( final PhylogenyNode desc : descs ) {
3557 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
3563 final private void paintCircularsLite( final PhylogenyNode n,
3564 final Phylogeny phy,
3568 final Graphics2D g ) {
3569 if ( n.isExternal() ) {
3573 final List<PhylogenyNode> descs = n.getDescendants();
3574 for( final PhylogenyNode desc : descs ) {
3575 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
3578 if ( !n.isRoot() ) {
3579 r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3581 final double theta = _urt_nodeid_angle_map.get( n.getId() );
3582 n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
3583 n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
3584 for( final PhylogenyNode desc : descs ) {
3585 paintBranchCircularLite( n, desc, g );
3590 final private void paintCollapsedNode( final Graphics2D g,
3591 final PhylogenyNode node,
3592 final boolean to_graphics_file,
3593 final boolean to_pdf,
3594 final boolean is_in_found_nodes ) {
3596 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3599 else if ( is_in_found_nodes ) {
3600 c = getTreeColorSet().getFoundColor();
3602 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3603 c = getTaxonomyBasedColor( node );
3605 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3606 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3607 c = PhylogenyMethods.getBranchColorValue( node );
3610 c = getTreeColorSet().getCollapseFillColor();
3612 double d = node.getAllExternalDescendants().size();
3614 d = ( 3 * _y_distance ) / 3;
3617 d = ( Math.log10( d ) * _y_distance ) / 2.5;
3619 final int box_size = getOptions().getDefaultNodeShapeSize();
3620 if ( d < box_size ) {
3624 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
3625 ForesterUtil.roundToInt( node.getYcoord() ) );
3626 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
3627 ForesterUtil.roundToInt( node.getYcoord() - d ) );
3628 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
3629 ForesterUtil.roundToInt( node.getYcoord() + d ) );
3630 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3632 g.fillPolygon( _polygon );
3634 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3635 g.setColor( getBackground() );
3636 g.fillPolygon( _polygon );
3638 g.drawPolygon( _polygon );
3640 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3641 g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
3642 .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
3647 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3650 final private void paintConfidenceValues( final Graphics2D g,
3651 final PhylogenyNode node,
3652 final boolean to_pdf,
3653 final boolean to_graphics_file ) {
3654 final List<Confidence> confidences = node.getBranchData().getConfidences();
3655 // if ( confidences.size() == 1 ) {
3656 // final double value = node.getBranchData().getConfidence( 0 ).getValue();
3657 // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
3660 // conf_str = FORMATTER_CONFIDENCE.format( value );
3662 // else if ( confidences.size() > 1 ) {
3663 boolean one_ok = false;
3664 boolean not_first = false;
3665 Collections.sort( confidences );
3666 final StringBuilder sb = new StringBuilder();
3667 String conf_str = "";
3668 for( final Confidence confidence : confidences ) {
3669 final double value = confidence.getValue();
3670 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3671 if ( value >= getOptions().getMinConfidenceValue() ) {
3680 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
3681 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3682 if ( getOptions().isShowConfidenceStddev() ) {
3683 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3685 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
3687 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3694 conf_str = sb.toString();
3697 if ( conf_str.length() > 0 ) {
3698 final double parent_x = node.getParent().getXcoord();
3699 double x = node.getXcoord();
3700 g.setFont( getTreeFontSet().getSmallFont() );
3701 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3704 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3707 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3708 g.setColor( Color.BLACK );
3711 g.setColor( getTreeColorSet().getConfidenceColor() );
3714 .drawString( conf_str,
3716 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
3717 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
3722 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
3723 final int box_size = getOptions().getDefaultNodeShapeSize();
3724 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3725 g.setColor( getTreeColorSet().getFoundColor() );
3726 g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
3729 final private void paintGainedAndLostCharacters( final Graphics2D g,
3730 final PhylogenyNode node,
3731 final String gained,
3732 final String lost ) {
3733 if ( node.getParent() != null ) {
3734 final double parent_x = node.getParent().getXcoord();
3735 final double x = node.getXcoord();
3736 g.setFont( getTreeFontSet().getLargeFont() );
3737 g.setColor( getTreeColorSet().getGainedCharactersColor() );
3738 if ( Constants.SPECIAL_CUSTOM ) {
3739 g.setColor( Color.BLUE );
3742 .drawString( gained,
3743 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
3744 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
3746 g.setColor( getTreeColorSet().getLostCharactersColor() );
3747 TreePanel.drawString( lost,
3748 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
3749 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
3755 * Draw a box at the indicated node.
3762 final private void paintNodeBox( final double x,
3764 final PhylogenyNode node,
3766 final boolean to_pdf,
3767 final boolean to_graphics_file,
3768 final boolean is_in_found_nodes ) {
3769 if ( node.isCollapse() ) {
3772 // if this node should be highlighted, do so
3773 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
3774 g.setColor( getTreeColorSet().getFoundColor() );
3775 drawOval( x - 8, y - 8, 16, 16, g );
3776 drawOval( x - 9, y - 8, 17, 17, g );
3777 drawOval( x - 9, y - 9, 18, 18, g );
3779 if ( is_in_found_nodes ) {
3780 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
3783 Color outline_color = null;
3784 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3785 outline_color = Color.BLACK;
3787 else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
3788 final Event event = node.getNodeData().getEvent();
3789 if ( event.isDuplication() ) {
3790 outline_color = getTreeColorSet().getDuplicationBoxColor();
3792 else if ( event.isSpeciation() ) {
3793 outline_color = getTreeColorSet().getSpecBoxColor();
3795 else if ( event.isSpeciationOrDuplication() ) {
3796 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
3799 else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
3800 outline_color = getTaxonomyBasedColor( node );
3803 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
3804 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
3805 outline_color = getTreeColorSet().getBranchColorForPdf();
3808 final int box_size = getOptions().getDefaultNodeShapeSize();
3809 final int half_box_size = box_size / 2;
3810 if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
3811 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
3812 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3813 drawOvalGradient( x - half_box_size,
3818 to_pdf ? Color.WHITE : outline_color,
3819 to_pdf ? outline_color : getBackground(),
3822 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
3823 Color background = getBackground();
3825 background = Color.WHITE;
3827 drawOvalGradient( x - half_box_size,
3836 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3837 g.setColor( outline_color );
3838 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3841 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
3842 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
3843 drawRectGradient( x - half_box_size,
3848 to_pdf ? Color.WHITE : outline_color,
3849 to_pdf ? outline_color : getBackground(),
3852 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3853 Color background = getBackground();
3855 background = Color.WHITE;
3857 drawRectGradient( x - half_box_size,
3866 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3867 g.setColor( outline_color );
3868 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3875 final private void paintNodeData( final Graphics2D g,
3876 final PhylogenyNode node,
3877 final boolean to_graphics_file,
3878 final boolean to_pdf,
3879 final boolean is_in_found_nodes ) {
3880 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
3883 if ( getOptions().isShowBranchLengthValues()
3884 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3885 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3886 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
3887 paintBranchLength( g, node, to_pdf, to_graphics_file );
3889 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
3893 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3894 if ( getControlPanel().isShowTaxonomyImages()
3895 && ( getImageMap() != null )
3896 && !getImageMap().isEmpty()
3897 && node.getNodeData().isHasTaxonomy()
3898 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
3899 .getUris().isEmpty() ) ) {
3900 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
3902 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3903 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
3904 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
3906 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3907 g.setColor( Color.BLACK );
3909 else if ( is_in_found_nodes ) {
3910 g.setColor( getTreeColorSet().getFoundColor() );
3912 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3913 g.setColor( getTaxonomyBasedColor( node ) );
3915 else if ( getControlPanel().isColorAccordingToAnnotation()
3916 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
3917 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
3918 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
3920 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3921 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3922 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3924 else if ( to_pdf ) {
3925 g.setColor( Color.BLACK );
3928 g.setColor( getTreeColorSet().getSequenceColor() );
3931 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3933 _sb.append( node.getAllExternalDescendants().size() );
3936 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3937 if ( _sb.length() > 0 ) {
3940 _sb.append( node.getName() );
3942 if ( node.getNodeData().isHasSequence() ) {
3943 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
3944 if ( _sb.length() > 0 ) {
3947 _sb.append( node.getNodeData().getSequence().getSymbol() );
3949 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3950 if ( _sb.length() > 0 ) {
3953 _sb.append( node.getNodeData().getSequence().getName() );
3955 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3956 if ( _sb.length() > 0 ) {
3959 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3960 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3963 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3966 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
3967 if ( _sb.length() > 0 ) {
3970 _sb.append( propertiesToString( node ) );
3972 g.setFont( getTreeFontSet().getLargeFont() );
3973 if ( is_in_found_nodes ) {
3974 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3976 double down_shift_factor = 3.0;
3977 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
3978 down_shift_factor = 1;
3980 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
3981 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
3982 final String sb_str = _sb.toString();
3983 // GUILHEM_BEG ______________
3984 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
3985 && ( _query_sequence != null ) ) {
3986 int nodeTextBoundsWidth = 0;
3987 if ( sb_str.length() > 0 ) {
3988 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
3989 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
3991 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
3992 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
3993 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
3994 g.setColor( getTreeColorSet().getBackgroundColor() );
3998 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
3999 for( final SequenceRelation seqRelation : seqRelations ) {
4000 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
4001 .getRef1().isEqual( _query_sequence ) )
4002 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
4003 .getSelectedItem() );
4004 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
4005 final double linePosX = node.getXcoord() + 2 + half_box_size;
4006 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
4007 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
4009 if ( sConfidence != null ) {
4010 double confidenceX = pos_x;
4011 if ( sb_str.length() > 0 ) {
4012 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
4013 + CONFIDENCE_LEFT_MARGIN;
4015 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
4016 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
4017 .getBounds().getWidth();
4018 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
4019 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
4022 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
4024 if ( nodeTextBoundsWidth == 0 ) {
4025 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
4028 nodeTextBoundsWidth += 2;
4030 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
4031 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
4038 if ( sb_str.length() > 0 ) {
4039 TreePanel.drawString( sb_str, pos_x, pos_y, g );
4041 // GUILHEM_END _____________
4042 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
4043 // TODO FIXME need to check this one!
4044 //if ( _sb.length() > 0 ) {
4045 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
4046 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4048 // COMMENTED_OUT_BY_GUILHEM_END ________________
4049 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
4050 && ( node.getNodeData().getSequence().getAnnotations() != null )
4051 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4052 if ( _sb.length() > 0 ) {
4053 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4055 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
4056 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4057 g.setColor( Color.BLACK );
4059 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
4060 g.setColor( calculateColorForAnnotation( ann ) );
4062 final String ann_str = createAnnotationString( ann );
4063 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
4064 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4066 _sb.append( ann_str );
4068 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4069 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
4070 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
4071 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
4072 && node.getNodeData().isHasBinaryCharacters() ) {
4073 if ( _sb.length() > 0 ) {
4074 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4076 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4077 g.setColor( Color.BLACK );
4080 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
4082 if ( getControlPanel().isShowBinaryCharacters() ) {
4083 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
4084 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
4085 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4086 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
4087 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
4088 .getLostCharactersAsStringBuffer().toString() );
4091 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
4092 node.getXcoord() + x + 4 + half_box_size,
4094 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
4096 paintGainedAndLostCharacters( g, node, "+"
4097 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
4098 + node.getNodeData().getBinaryCharacters().getLostCount() );
4104 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
4105 final PhylogenyNode node,
4106 final boolean to_pdf,
4107 final boolean to_graphics_file,
4108 final boolean radial_labels,
4109 final double ur_angle,
4110 final boolean is_in_found_nodes ) {
4111 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
4114 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4115 g.setColor( Color.BLACK );
4117 else if ( is_in_found_nodes ) {
4118 g.setColor( getTreeColorSet().getFoundColor() );
4120 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4121 g.setColor( getTaxonomyBasedColor( node ) );
4123 else if ( getControlPanel().isColorAccordingToAnnotation()
4124 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4125 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4126 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4129 g.setColor( getTreeColorSet().getSequenceColor() );
4133 if ( node.getNodeData().isHasTaxonomy()
4134 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4135 .isShowTaxonomyCommonNames() ) ) {
4136 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4137 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4138 _sb.append( taxonomy.getTaxonomyCode() );
4141 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4142 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4143 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4144 _sb.append( taxonomy.getScientificName() );
4146 _sb.append( taxonomy.getCommonName() );
4149 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4150 _sb.append( taxonomy.getScientificName() );
4153 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4154 _sb.append( taxonomy.getCommonName() );
4158 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4159 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4160 _sb.append( taxonomy.getScientificName() );
4164 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4165 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4166 _sb.append( taxonomy.getCommonName() );
4171 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4173 _sb.append( node.getAllExternalDescendants().size() );
4176 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4177 if ( _sb.length() > 0 ) {
4180 _sb.append( node.getName() );
4182 if ( node.getNodeData().isHasSequence() ) {
4183 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4184 if ( _sb.length() > 0 ) {
4187 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4188 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4191 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4193 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4194 if ( _sb.length() > 0 ) {
4197 _sb.append( node.getNodeData().getSequence().getName() );
4200 g.setFont( getTreeFontSet().getLargeFont() );
4201 if ( is_in_found_nodes ) {
4202 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4204 if ( _sb.length() > 1 ) {
4205 final String sb_str = _sb.toString();
4207 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4208 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
4211 m = ( float ) ( ur_angle % TWO_PI );
4213 _at = g.getTransform();
4214 boolean need_to_reset = false;
4215 final float x_coord = node.getXcoord();
4216 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
4217 if ( radial_labels ) {
4218 need_to_reset = true;
4219 boolean left = false;
4220 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4224 g.rotate( m, x_coord, node.getYcoord() );
4226 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
4230 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4231 need_to_reset = true;
4232 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
4235 TreePanel.drawString( sb_str, x_coord, y_coord, g );
4236 if ( need_to_reset ) {
4237 g.setTransform( _at );
4242 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
4243 if ( node.isCollapse() ) {
4244 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
4245 paintCollapsedNode( g, node, false, false, false );
4249 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4250 g.setColor( getTreeColorSet().getFoundColor() );
4251 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
4254 if ( !node.isExternal() && !node.isCollapse() ) {
4255 boolean first_child = true;
4257 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4258 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4259 final PhylogenyNode child_node = node.getChildNode( i );
4261 if ( !isUniformBranchLengthsForCladogram() ) {
4262 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4265 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4267 if ( first_child ) {
4268 first_child = false;
4269 y2 = node.getYSecondary()
4270 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
4271 .getNumberOfExternalNodes() ) );
4274 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4276 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
4277 new_x = x2 + node.getXSecondary();
4278 final float diff_y = node.getYSecondary() - y2;
4279 final float diff_x = node.getXSecondary() - new_x;
4280 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
4281 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
4283 child_node.setXSecondary( new_x );
4284 child_node.setYSecondary( y2 );
4285 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4290 final private void paintNodeRectangular( final Graphics2D g,
4291 final PhylogenyNode node,
4292 final boolean to_pdf,
4293 final boolean dynamically_hide,
4294 final int dynamic_hiding_factor,
4295 final boolean to_graphics_file ) {
4296 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
4297 if ( node.isCollapse() ) {
4298 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
4299 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4303 if ( node.isExternal() ) {
4304 ++_external_node_index;
4306 // Confidence values
4307 if ( getControlPanel().isShowConfidenceValues()
4308 && !node.isExternal()
4310 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
4311 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4312 && node.getBranchData().isHasConfidences() ) {
4313 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
4315 // Draw a line to root:
4316 if ( node.isRoot() && _phylogeny.isRooted() ) {
4317 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
4320 float new_x_min = Float.MAX_VALUE;
4321 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
4322 float min_dist = 1.5f;
4323 if ( !disallow_shortcutting ) {
4324 // System.out.println( dynamic_hiding_factor );
4325 if ( dynamic_hiding_factor > 4000 ) {
4328 else if ( dynamic_hiding_factor > 1000 ) {
4331 else if ( dynamic_hiding_factor > 100 ) {
4335 if ( !node.isExternal() && !node.isCollapse() ) {
4336 boolean first_child = true;
4338 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4339 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4340 final PhylogenyNode child_node = node.getChildNode( i );
4342 if ( !isUniformBranchLengthsForCladogram() ) {
4343 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4346 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4348 if ( first_child ) {
4349 first_child = false;
4350 y2 = node.getYcoord()
4351 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
4354 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4356 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
4357 new_x = x2 + node.getXcoord();
4358 if ( dynamically_hide && ( x2 < new_x_min ) ) {
4361 final float diff_y = node.getYcoord() - y2;
4362 final float diff_x = node.getXcoord() - new_x;
4363 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
4364 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
4365 paintBranchRectangular( g,
4374 child_node.setXcoord( new_x );
4375 child_node.setYcoord( y2 );
4376 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4378 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
4379 || isInCurrentExternalNodes( node ) );
4381 if ( dynamically_hide
4382 && !is_in_found_nodes
4383 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
4384 .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
4385 .getHeight() ) ) ) ) ) {
4388 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4389 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
4392 final private void paintNodeWithRenderableData( final Graphics2D g,
4393 final PhylogenyNode node,
4394 final boolean to_graphics_file,
4395 final boolean to_pdf ) {
4396 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
4399 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
4402 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4403 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4404 RenderableDomainArchitecture rds = null;
4405 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
4407 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
4409 catch ( final ClassCastException cce ) {
4410 cce.printStackTrace();
4412 if ( rds != null ) {
4413 rds.setRenderingHeight( 6 );
4415 if ( node.getNodeData().isHasTaxonomy() ) {
4416 if ( getControlPanel().isShowTaxonomyCode()
4417 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
4418 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4422 if ( getControlPanel().isShowTaxonomyScientificNames()
4423 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
4424 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4425 .getScientificName()
4428 if ( getControlPanel().isShowTaxonomyCommonNames()
4429 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
4430 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4435 if ( node.getNodeData().isHasSequence() ) {
4436 if ( getControlPanel().isShowGeneNames()
4437 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
4438 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
4441 if ( getControlPanel().isShowGeneSymbols()
4442 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
4443 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
4446 if ( getControlPanel().isShowSequenceAcc()
4447 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4448 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
4449 .getAccession().toString()
4453 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
4454 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
4456 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
4461 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4462 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
4463 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
4464 getStatisticsForExpressionValues(),
4465 getConfiguration() );
4468 PhylogenyNode my_node = node;
4469 if ( !getControlPanel().isDrawPhylogram() ) {
4470 my_node = getPhylogeny().getFirstExternalNode();
4472 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
4473 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
4475 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
4476 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
4478 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
4484 final private void paintOvRectangle( final Graphics2D g ) {
4485 final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
4486 final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
4487 final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
4488 final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
4489 final float width = getOvMaxWidth() / w_ratio;
4490 final float height = getOvMaxHeight() / h_ratio;
4491 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
4492 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
4493 g.setColor( getTreeColorSet().getFoundColor() );
4494 getOvRectangle().setRect( x, y, width, height );
4495 if ( ( width < 6 ) && ( height < 6 ) ) {
4496 drawRectFilled( x, y, 6, 6, g );
4497 getOvVirtualRectangle().setRect( x, y, 6, 6 );
4499 else if ( width < 6 ) {
4500 drawRectFilled( x, y, 6, height, g );
4501 getOvVirtualRectangle().setRect( x, y, 6, height );
4503 else if ( height < 6 ) {
4504 drawRectFilled( x, y, width, 6, g );
4505 getOvVirtualRectangle().setRect( x, y, width, 6 );
4508 drawRect( x, y, width, height, g );
4509 if ( isInOvRect() ) {
4510 drawRect( x + 1, y + 1, width - 2, height - 2, g );
4512 getOvVirtualRectangle().setRect( x, y, width, height );
4516 final private void paintPhylogenyLite( final Graphics2D g ) {
4519 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
4520 .getWidth() ) ) ) );
4521 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
4522 for( final PhylogenyNode element : _nodes_in_preorder ) {
4523 paintNodeLite( g, element );
4525 paintOvRectangle( g );
4529 * Paint the root branch. (Differs from others because it will always be a
4530 * single horizontal line).
4531 * @param to_graphics_file
4533 * @return new x1 value
4535 final private void paintRootBranch( final Graphics2D g,
4538 final PhylogenyNode root,
4539 final boolean to_pdf,
4540 final boolean to_graphics_file ) {
4541 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
4542 float d = getXdistance();
4543 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
4544 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
4546 if ( d < MIN_ROOT_LENGTH ) {
4547 d = MIN_ROOT_LENGTH;
4549 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
4550 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
4553 final double w = PhylogenyMethods.getBranchWidthValue( root );
4554 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
4556 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
4559 final private void paintScale( final Graphics2D g,
4562 final boolean to_pdf,
4563 final boolean to_graphics_file ) {
4565 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
4567 final int y2 = y1 - 8;
4568 final int y3 = y1 - 4;
4569 g.setFont( getTreeFontSet().getSmallFont() );
4570 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4571 g.setColor( Color.BLACK );
4574 g.setColor( getTreeColorSet().getBranchLengthColor() );
4576 drawLine( x1, y1, x1, y2, g );
4577 drawLine( x2, y1, x2, y2, g );
4578 drawLine( x1, y3, x2, y3, g );
4579 if ( getScaleLabel() != null ) {
4580 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
4584 final private int paintTaxonomy( final Graphics2D g,
4585 final PhylogenyNode node,
4586 final boolean is_in_found_nodes,
4587 final boolean to_pdf,
4588 final boolean to_graphics_file,
4589 final double x_shift ) {
4590 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4591 g.setFont( getTreeFontSet().getLargeItalicFont() );
4592 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4593 g.setColor( Color.BLACK );
4595 else if ( is_in_found_nodes ) {
4596 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
4597 g.setColor( getTreeColorSet().getFoundColor() );
4599 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4600 g.setColor( getTaxonomyBasedColor( node ) );
4602 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4603 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4604 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4606 else if ( to_pdf ) {
4607 g.setColor( Color.BLACK );
4610 g.setColor( getTreeColorSet().getTaxonomyColor() );
4612 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4613 final double start_y = node.getYcoord()
4614 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4616 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4617 _sb.append( taxonomy.getTaxonomyCode() );
4620 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4621 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4622 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4623 if ( getOptions().isAbbreviateScientificTaxonNames()
4624 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4625 abbreviateScientificName( taxonomy.getScientificName() );
4628 _sb.append( taxonomy.getScientificName() );
4631 _sb.append( taxonomy.getCommonName() );
4634 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4635 if ( getOptions().isAbbreviateScientificTaxonNames()
4636 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4637 abbreviateScientificName( taxonomy.getScientificName() );
4640 _sb.append( taxonomy.getScientificName() );
4644 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4645 _sb.append( taxonomy.getCommonName() );
4649 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4650 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4651 if ( getOptions().isAbbreviateScientificTaxonNames()
4652 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4653 abbreviateScientificName( taxonomy.getScientificName() );
4656 _sb.append( taxonomy.getScientificName() );
4661 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4662 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4663 _sb.append( taxonomy.getCommonName() );
4667 final String label = _sb.toString();
4669 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4670 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4671 // invert font color and background color to show that this is the query sequence
4672 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4676 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4677 g.setColor( getTreeColorSet().getBackgroundColor() );
4680 TreePanel.drawString( label, start_x, start_y, g );
4681 if ( is_in_found_nodes ) {
4682 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4685 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4689 final private void paintUnrooted( final PhylogenyNode n,
4690 final double low_angle,
4691 final double high_angle,
4692 final boolean radial_labels,
4694 final boolean to_pdf,
4695 final boolean to_graphics_file ) {
4697 n.setXcoord( getWidth() / 2 );
4698 n.setYcoord( getHeight() / 2 );
4700 if ( n.isExternal() ) {
4701 paintNodeDataUnrootedCirc( g,
4706 ( high_angle + low_angle ) / 2,
4707 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
4710 final float num_enclosed = n.getNumberOfExternalNodes();
4711 final float x = n.getXcoord();
4712 final float y = n.getYcoord();
4713 double current_angle = low_angle;
4714 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4715 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4716 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4717 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4718 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4719 final PhylogenyNode desc = n.getChildNode( i );
4720 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4721 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4722 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4723 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4726 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4729 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4732 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4733 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4735 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4736 if ( desc.getDistanceToParent() < 0 ) {
4740 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4744 length = getUrtFactor();
4746 final double mid_angle = current_angle + ( arc_size / 2 );
4747 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4748 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4749 desc.setXcoord( new_x );
4750 desc.setYcoord( new_y );
4751 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4752 current_angle += arc_size;
4753 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4754 drawLine( x, y, new_x, new_y, g );
4755 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc )
4756 || isInCurrentExternalNodes( desc ) );
4759 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
4763 final private void paintUnrootedLite( final PhylogenyNode n,
4764 final double low_angle,
4765 final double high_angle,
4767 final float urt_ov_factor ) {
4769 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
4770 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
4771 n.setXSecondary( x_pos );
4772 n.setYSecondary( y_pos );
4774 if ( n.isExternal() ) {
4777 final float num_enclosed = n.getNumberOfExternalNodes();
4778 final float x = n.getXSecondary();
4779 final float y = n.getYSecondary();
4780 double current_angle = low_angle;
4781 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4782 final PhylogenyNode desc = n.getChildNode( i );
4783 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4784 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4786 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4787 if ( desc.getDistanceToParent() < 0 ) {
4791 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
4795 length = urt_ov_factor;
4797 final double mid_angle = current_angle + ( arc_size / 2 );
4798 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4799 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4800 desc.setXSecondary( new_x );
4801 desc.setYSecondary( new_y );
4802 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
4803 g.setColor( getTreeColorSet().getFoundColor() );
4804 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
4805 g.setColor( getTreeColorSet().getOvColor() );
4807 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4808 current_angle += arc_size;
4809 drawLine( x, y, new_x, new_y, g );
4813 final private void pasteSubtree( final PhylogenyNode node ) {
4814 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4815 errorMessageNoCutCopyPasteInUnrootedDisplay();
4818 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
4819 JOptionPane.showMessageDialog( this,
4820 "No tree in buffer (need to copy or cut a subtree first)",
4821 "Attempt to paste with empty buffer",
4822 JOptionPane.ERROR_MESSAGE );
4825 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
4826 final Object[] options = { "As sibling", "As descendant", "Cancel" };
4827 final int r = JOptionPane.showOptionDialog( this,
4828 "How to paste subtree" + label + "?",
4830 JOptionPane.CLOSED_OPTION,
4831 JOptionPane.QUESTION_MESSAGE,
4835 boolean paste_as_sibling = true;
4837 paste_as_sibling = false;
4839 else if ( r != 0 ) {
4842 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
4843 buffer_phy.setAllNodesToNotCollapse();
4844 PhylogenyMethods.preOrderReId( buffer_phy );
4845 buffer_phy.setRooted( true );
4846 boolean need_to_show_whole = false;
4847 if ( paste_as_sibling ) {
4848 if ( node.isRoot() ) {
4849 JOptionPane.showMessageDialog( this,
4850 "Cannot paste sibling to root",
4851 "Attempt to paste sibling to root",
4852 JOptionPane.ERROR_MESSAGE );
4855 buffer_phy.addAsSibling( node );
4858 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
4859 need_to_show_whole = true;
4860 _phylogeny = buffer_phy;
4863 buffer_phy.addAsChild( node );
4866 if ( getCopiedAndPastedNodes() == null ) {
4867 setCopiedAndPastedNodes( new HashSet<Integer>() );
4869 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
4870 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
4871 for( final PhylogenyNode n : nodes ) {
4872 node_ids.add( n.getId() );
4874 node_ids.add( node.getId() );
4875 getCopiedAndPastedNodes().addAll( node_ids );
4876 setNodeInPreorderToNull();
4877 _phylogeny.externalNodesHaveChanged();
4878 _phylogeny.clearHashIdToNodeMap();
4879 _phylogeny.recalculateNumberOfExternalDescendants( true );
4880 resetNodeIdToDistToLeafMap();
4882 if ( need_to_show_whole ) {
4883 getControlPanel().showWhole();
4888 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
4889 final PropertiesMap properties = node.getNodeData().getProperties();
4890 final StringBuffer sb = new StringBuffer();
4891 boolean first = true;
4892 for( final String ref : properties.getPropertyRefs() ) {
4899 final Property p = properties.getProperty( ref );
4900 sb.append( getPartAfterColon( p.getRef() ) );
4902 sb.append( p.getValue() );
4903 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
4904 sb.append( getPartAfterColon( p.getUnit() ) );
4910 final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
4911 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4914 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4915 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4918 final private void setInOv( final boolean in_ov ) {
4922 final private void setOvMaxHeight( final float ov_max_height ) {
4923 _ov_max_height = ov_max_height;
4926 final private void setOvMaxWidth( final float ov_max_width ) {
4927 _ov_max_width = ov_max_width;
4930 final private void setOvXcorrectionFactor( final float f ) {
4931 _ov_x_correction_factor = f;
4934 final private void setOvXDistance( final float ov_x_distance ) {
4935 _ov_x_distance = ov_x_distance;
4938 final private void setOvXPosition( final int ov_x_position ) {
4939 _ov_x_position = ov_x_position;
4942 final private void setOvYDistance( final float ov_y_distance ) {
4943 _ov_y_distance = ov_y_distance;
4946 final private void setOvYPosition( final int ov_y_position ) {
4947 _ov_y_position = ov_y_position;
4950 final private void setOvYStart( final int ov_y_start ) {
4951 _ov_y_start = ov_y_start;
4954 final private void setScaleDistance( final double scale_distance ) {
4955 _scale_distance = scale_distance;
4958 final private void setScaleLabel( final String scale_label ) {
4959 _scale_label = scale_label;
4962 final private void setUpUrtFactor() {
4963 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
4964 : getVisibleRect().height;
4965 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4966 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
4969 final int max_depth = _circ_max_depth;
4970 if ( max_depth > 0 ) {
4971 setUrtFactor( d / ( 2 * max_depth ) );
4974 setUrtFactor( d / 2 );
4977 setUrtFactorOv( getUrtFactor() );
4980 final private void setUrtFactor( final float urt_factor ) {
4981 _urt_factor = urt_factor;
4984 final private void setUrtFactorOv( final float urt_factor_ov ) {
4985 _urt_factor_ov = urt_factor_ov;
4988 private void showExtDescNodeData( final PhylogenyNode node ) {
4989 final List<String> data = new ArrayList<String>();
4990 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
4991 switch ( getOptions().getExtDescNodeDataToReturn() ) {
4993 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
4994 data.add( n.getName() );
4998 if ( n.getNodeData().isHasSequence()
4999 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5000 data.add( n.getNodeData().getSequence().getName() );
5003 case SEQUENCE_SYMBOL:
5004 if ( n.getNodeData().isHasSequence()
5005 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5006 data.add( n.getNodeData().getSequence().getSymbol() );
5009 case SEQUENCE_MOL_SEQ:
5010 if ( n.getNodeData().isHasSequence()
5011 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5012 data.add( n.getNodeData().getSequence().getMolecularSequence() );
5016 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
5017 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
5018 data.add( n.getNodeData().getSequence().getAccession().toString() );
5021 case TAXONOMY_SCIENTIFIC_NAME:
5022 if ( n.getNodeData().isHasTaxonomy()
5023 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5024 data.add( n.getNodeData().getTaxonomy().getScientificName() );
5028 if ( n.getNodeData().isHasTaxonomy()
5029 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5030 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5034 AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
5037 throw new IllegalArgumentException( "unknown data element: "
5038 + getOptions().getExtDescNodeDataToReturn() );
5041 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
5042 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
5043 final StringBuilder sb = new StringBuilder();
5044 for( final String d : data ) {
5045 if ( !ForesterUtil.isEmpty( d ) ) {
5046 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
5047 System.out.println( d );
5050 sb.append( ForesterUtil.LINE_SEPARATOR );
5053 if ( sb.length() < 1 ) {
5054 clearCurrentExternalNodesDataBuffer();
5057 setCurrentExternalNodesDataBuffer( sb );
5060 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
5061 final StringBuilder sb = new StringBuilder();
5062 for( final String d : data ) {
5063 if ( !ForesterUtil.isEmpty( d ) ) {
5065 sb.append( ForesterUtil.LINE_SEPARATOR );
5068 if ( sb.length() < 1 ) {
5069 AptxUtil.showInformationMessage( this,
5070 "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
5071 "Descendants of selected node do not contain selected data" );
5072 clearCurrentExternalNodesDataBuffer();
5075 setCurrentExternalNodesDataBuffer( sb );
5076 final String title = "External Descendants "
5077 + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5078 : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
5079 + node.getNumberOfExternalNodes() + ") For Node " + node;
5080 final String s = sb.toString().trim();
5081 if ( getMainPanel().getMainFrame() == null ) {
5082 // Must be "E" applet version.
5083 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
5084 ae.showTextFrame( s, title );
5087 getMainPanel().getMainFrame().showTextFrame( s, title );
5093 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
5095 if ( ( node.getName().length() > 0 )
5096 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
5097 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
5098 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
5099 || node.getBranchData().isHasConfidences() ) {
5100 _popup_buffer.setLength( 0 );
5102 if ( node.getName().length() > 0 ) {
5104 _popup_buffer.append( node.getName() );
5106 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
5108 boolean enc_data = false;
5109 final Taxonomy tax = node.getNodeData().getTaxonomy();
5110 if ( _popup_buffer.length() > 0 ) {
5111 _popup_buffer.append( "\n" );
5113 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
5114 _popup_buffer.append( "[" );
5115 _popup_buffer.append( tax.getTaxonomyCode() );
5116 _popup_buffer.append( "]" );
5119 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
5121 _popup_buffer.append( " " );
5123 _popup_buffer.append( tax.getScientificName() );
5126 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
5128 _popup_buffer.append( " (" );
5131 _popup_buffer.append( "(" );
5133 _popup_buffer.append( tax.getCommonName() );
5134 _popup_buffer.append( ")" );
5137 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
5139 _popup_buffer.append( " (" );
5142 _popup_buffer.append( "(" );
5144 _popup_buffer.append( tax.getAuthority() );
5145 _popup_buffer.append( ")" );
5148 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
5150 _popup_buffer.append( " [" );
5153 _popup_buffer.append( "[" );
5155 _popup_buffer.append( tax.getRank() );
5156 _popup_buffer.append( "]" );
5159 if ( tax.getSynonyms().size() > 0 ) {
5161 _popup_buffer.append( " " );
5163 _popup_buffer.append( "[" );
5165 for( final String syn : tax.getSynonyms() ) {
5166 if ( !ForesterUtil.isEmpty( syn ) ) {
5168 _popup_buffer.append( syn );
5169 if ( counter < tax.getSynonyms().size() ) {
5170 _popup_buffer.append( ", " );
5175 _popup_buffer.append( "]" );
5178 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
5179 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
5180 _popup_buffer.append( "[" );
5181 _popup_buffer.append( tax.getIdentifier().getProvider() );
5182 _popup_buffer.append( "] " );
5184 _popup_buffer.append( tax.getIdentifier().getValue() );
5188 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
5190 boolean enc_data = false;
5191 if ( _popup_buffer.length() > 0 ) {
5192 _popup_buffer.append( "\n" );
5194 final Sequence seq = node.getNodeData().getSequence();
5195 if ( seq.getAccession() != null ) {
5196 _popup_buffer.append( "[" );
5197 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
5198 _popup_buffer.append( seq.getAccession().getSource() );
5199 _popup_buffer.append( ":" );
5201 _popup_buffer.append( seq.getAccession().getValue() );
5202 _popup_buffer.append( "]" );
5205 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
5207 _popup_buffer.append( " [" );
5210 _popup_buffer.append( "[" );
5212 _popup_buffer.append( seq.getSymbol() );
5213 _popup_buffer.append( "]" );
5216 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
5218 _popup_buffer.append( " " );
5220 _popup_buffer.append( seq.getName() );
5223 if ( node.getNodeData().isHasDate() ) {
5225 if ( _popup_buffer.length() > 0 ) {
5226 _popup_buffer.append( "\n" );
5228 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
5230 if ( node.getNodeData().isHasDistribution() ) {
5232 if ( _popup_buffer.length() > 0 ) {
5233 _popup_buffer.append( "\n" );
5235 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
5237 if ( node.getBranchData().isHasConfidences() ) {
5238 final List<Confidence> confs = node.getBranchData().getConfidences();
5239 for( final Confidence confidence : confs ) {
5241 if ( _popup_buffer.length() > 0 ) {
5242 _popup_buffer.append( "\n" );
5244 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
5245 _popup_buffer.append( "[" );
5246 _popup_buffer.append( confidence.getType() );
5247 _popup_buffer.append( "] " );
5250 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
5252 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5253 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5254 _popup_buffer.append( " (sd=" );
5255 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
5256 .getStandardDeviation(), getOptions()
5257 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5258 _popup_buffer.append( ")" );
5262 if ( node.getNodeData().isHasProperties() ) {
5263 final PropertiesMap properties = node.getNodeData().getProperties();
5264 for( final String ref : properties.getPropertyRefs() ) {
5265 _popup_buffer.append( "\n" );
5266 final Property p = properties.getProperty( ref );
5267 _popup_buffer.append( getPartAfterColon( p.getRef() ) );
5268 _popup_buffer.append( "=" );
5269 _popup_buffer.append( p.getValue() );
5270 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5271 _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
5275 if ( _popup_buffer.length() > 0 ) {
5276 if ( !getConfiguration().isUseNativeUI() ) {
5278 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
5279 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
5280 if ( isInFoundNodes( node ) ) {
5281 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
5283 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
5284 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
5287 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
5291 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
5293 _rollover_popup.setText( _popup_buffer.toString() );
5294 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
5296 e.getLocationOnScreen().x + 10,
5297 e.getLocationOnScreen().y
5299 _node_desc_popup.show();
5303 catch ( final Exception ex ) {
5308 final private void showNodeEditFrame( final PhylogenyNode n ) {
5309 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5310 // pop up edit box for single node
5311 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
5312 _node_frame_index++;
5315 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5319 final private void showNodeFrame( final PhylogenyNode n ) {
5320 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5321 // pop up edit box for single node
5322 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
5323 _node_frame_index++;
5326 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5330 final private void switchDisplaygetPhylogenyGraphicsType() {
5331 switch ( getPhylogenyGraphicsType() ) {
5333 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5334 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5337 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5338 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5341 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5342 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5345 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5346 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5349 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5350 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5353 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5354 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5357 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5358 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5361 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5362 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5365 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5367 if ( getControlPanel().getDynamicallyHideData() != null ) {
5368 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5369 getControlPanel().getDynamicallyHideData().setEnabled( false );
5372 getControlPanel().getDynamicallyHideData().setEnabled( true );
5375 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5376 getControlPanel().setDrawPhylogramEnabled( true );
5379 getControlPanel().setDrawPhylogramEnabled( false );
5381 if ( getMainPanel().getMainFrame() == null ) {
5382 // Must be "E" applet version.
5383 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5384 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5387 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5391 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
5392 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5395 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5396 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5399 final private static String getPartAfterColon( final String s ) {
5400 final int i = s.indexOf( ':' );
5401 if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
5404 return s.substring( i + 1, s.length() );
5407 final private static boolean isSequenceEmpty( final Sequence seq ) {
5408 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
5409 && ForesterUtil.isEmpty( seq.getSymbol() );
5412 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
5413 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
5414 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
5415 .getSynonyms().isEmpty() );
5418 final private static boolean plusPressed( final int key_code ) {
5419 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5420 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5423 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
5424 final Phylogeny new_phy = new Phylogeny();
5425 new_phy.setRooted( true );
5426 new_phy.setName( source_phy.getName() );
5427 new_phy.setDescription( source_phy.getDescription() );
5428 new_phy.setType( source_phy.getType() );
5429 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
5430 new_phy.setConfidence( source_phy.getConfidence() );
5431 new_phy.setIdentifier( source_phy.getIdentifier() );
5432 new_phy.setRoot( new_root.copyNodeDataShallow() );
5434 for( final PhylogenyNode n : new_root.getDescendants() ) {
5435 new_phy.getRoot().setChildNode( i++, n );
5440 final private class SubtreeColorizationActionListener implements ActionListener {
5442 JColorChooser _chooser;
5443 PhylogenyNode _node;
5445 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5451 public void actionPerformed( final ActionEvent e ) {
5452 final Color c = _chooser.getColor();
5454 colorizeSubtree( c, _node );