2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.archaeopteryx;
28 import java.awt.BasicStroke;
29 import java.awt.Color;
30 import java.awt.Cursor;
31 import java.awt.Dimension;
33 import java.awt.GradientPaint;
34 import java.awt.Graphics;
35 import java.awt.Graphics2D;
36 import java.awt.Point;
37 import java.awt.Polygon;
38 import java.awt.Rectangle;
39 import java.awt.RenderingHints;
40 import java.awt.event.ActionEvent;
41 import java.awt.event.ActionListener;
42 import java.awt.event.FocusAdapter;
43 import java.awt.event.FocusEvent;
44 import java.awt.event.InputEvent;
45 import java.awt.event.KeyAdapter;
46 import java.awt.event.KeyEvent;
47 import java.awt.event.MouseEvent;
48 import java.awt.event.MouseWheelEvent;
49 import java.awt.event.MouseWheelListener;
50 import java.awt.font.FontRenderContext;
51 import java.awt.font.TextLayout;
52 import java.awt.geom.AffineTransform;
53 import java.awt.geom.Arc2D;
54 import java.awt.geom.CubicCurve2D;
55 import java.awt.geom.Ellipse2D;
56 import java.awt.geom.Line2D;
57 import java.awt.geom.QuadCurve2D;
58 import java.awt.geom.Rectangle2D;
59 import java.awt.image.BufferedImage;
60 import java.awt.print.PageFormat;
61 import java.awt.print.Printable;
62 import java.awt.print.PrinterException;
64 import java.io.IOException;
65 import java.io.UnsupportedEncodingException;
67 import java.net.URISyntaxException;
68 import java.net.URLEncoder;
69 import java.text.DecimalFormat;
70 import java.text.DecimalFormatSymbols;
71 import java.text.NumberFormat;
72 import java.util.ArrayList;
73 import java.util.Collections;
74 import java.util.HashMap;
75 import java.util.HashSet;
76 import java.util.Hashtable;
77 import java.util.List;
79 import java.util.SortedSet;
81 import javax.swing.BorderFactory;
82 import javax.swing.JApplet;
83 import javax.swing.JColorChooser;
84 import javax.swing.JDialog;
85 import javax.swing.JMenuItem;
86 import javax.swing.JOptionPane;
87 import javax.swing.JPanel;
88 import javax.swing.JPopupMenu;
89 import javax.swing.JTextArea;
90 import javax.swing.Popup;
91 import javax.swing.PopupFactory;
93 import org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON;
94 import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
95 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
96 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
97 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
98 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
99 import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
100 import org.forester.archaeopteryx.tools.Blast;
101 import org.forester.archaeopteryx.tools.ImageLoader;
102 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
103 import org.forester.phylogeny.Phylogeny;
104 import org.forester.phylogeny.PhylogenyMethods;
105 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
106 import org.forester.phylogeny.PhylogenyNode;
107 import org.forester.phylogeny.data.Annotation;
108 import org.forester.phylogeny.data.BranchColor;
109 import org.forester.phylogeny.data.Confidence;
110 import org.forester.phylogeny.data.Event;
111 import org.forester.phylogeny.data.NodeData.NODE_DATA;
112 import org.forester.phylogeny.data.NodeVisualization;
113 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
114 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
115 import org.forester.phylogeny.data.PhylogenyDataUtil;
116 import org.forester.phylogeny.data.PropertiesMap;
117 import org.forester.phylogeny.data.Property;
118 import org.forester.phylogeny.data.Sequence;
119 import org.forester.phylogeny.data.SequenceRelation;
120 import org.forester.phylogeny.data.Taxonomy;
121 import org.forester.phylogeny.data.Uri;
122 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
123 import org.forester.phylogeny.iterators.PreorderTreeIterator;
124 import org.forester.util.BasicDescriptiveStatistics;
125 import org.forester.util.DescriptiveStatistics;
126 import org.forester.util.ForesterConstants;
127 import org.forester.util.ForesterUtil;
128 import org.forester.util.SequenceIdParser;
130 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
132 private static final float PI = ( float ) ( Math.PI );
133 private static final double TWO_PI = 2 * Math.PI;
134 private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
135 private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
136 private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
137 private static final short OV_BORDER = 10;
138 final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
139 final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
140 final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
141 final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
142 final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
143 private final static long serialVersionUID = -978349745916505029L;
144 private final static int EURO_D = 10;
145 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
146 private final static int MIN_ROOT_LENGTH = 3;
147 private final static int MAX_SUBTREES = 100;
148 private final static int MAX_NODE_FRAMES = 10;
149 private final static int MOVE = 20;
150 private final static NumberFormat FORMATTER_CONFIDENCE;
151 private final static NumberFormat FORMATTER_BRANCH_LENGTH;
152 private final static int WIGGLE = 2;
153 private final static int LIMIT_FOR_HQ_RENDERING = 1000;
154 private final static int CONFIDENCE_LEFT_MARGIN = 4;
155 private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
156 RenderingHints.VALUE_RENDER_DEFAULT );
157 private File _treefile = null;
158 private Configuration _configuration = null;
159 private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
160 private int _node_frame_index = 0;
161 private Phylogeny _phylogeny = null;
162 private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
163 private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
164 private int _subtree_index = 0;
165 private MainPanel _main_panel = null;
166 private Set<Integer> _found_nodes = null;
167 private PhylogenyNode _highlight_node = null;
168 private JPopupMenu _node_popup_menu = null;
169 private JMenuItem _node_popup_menu_items[] = null;
170 private int _longest_ext_node_info = 0;
171 private float _x_correction_factor = 0.0f;
172 private float _ov_x_correction_factor = 0.0f;
173 private float _x_distance = 0.0f;
174 private float _y_distance = 0.0f;
175 private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
176 private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
177 private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
178 private float _last_drag_point_x = 0;
179 private float _last_drag_point_y = 0;
180 private ControlPanel _control_panel = null;
181 private int _external_node_index = 0;
182 private final Polygon _polygon = new Polygon();
183 private final StringBuilder _sb = new StringBuilder();
184 private JColorChooser _color_chooser = null;
185 private double _scale_distance = 0.0;
186 private String _scale_label = null;
187 private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
188 private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
189 private final Line2D _line = new Line2D.Float();
190 private final Ellipse2D _ellipse = new Ellipse2D.Float();
191 private final Rectangle2D _rectangle = new Rectangle2D.Float();
192 private Options _options = null;
193 private float _ov_max_width = 0;
194 private float _ov_max_height = 0;
195 private int _ov_x_position = 0;
196 private int _ov_y_position = 0;
197 private int _ov_y_start = 0;
198 private float _ov_y_distance = 0;
199 private float _ov_x_distance = 0;
200 private boolean _ov_on = false;
201 private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
202 private float _urt_factor = 1;
203 private float _urt_factor_ov = 1;
204 private final boolean _phy_has_branch_lengths;
205 private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
206 private boolean _in_ov_rect = false;
207 private boolean _in_ov = false;
208 private final Rectangle _ov_virtual_rectangle = new Rectangle();
209 final private static double _180_OVER_PI = 180.0 / Math.PI;
210 private static final float ROUNDED_D = 8;
211 private int _circ_max_depth;
212 private PhylogenyNode _root;
213 final private Arc2D _arc = new Arc2D.Double();
214 final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
215 final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
216 final private Set<Integer> _collapsed_external_nodeid_set = new HashSet<Integer>();
217 HashMap<Integer, Short> _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
218 private AffineTransform _at;
219 private double _max_distance_to_root = -1;
220 private int _dynamic_hiding_factor = 0;
221 private boolean _edited = false;
222 private Popup _node_desc_popup;
223 private JTextArea _rollover_popup;
224 private final StringBuffer _popup_buffer = new StringBuffer();
225 final private static Font POPUP_FONT = new Font( Configuration
226 .getDefaultFontFamilyName(),
229 private Sequence _query_sequence = null;
230 private final FontRenderContext _frc = new FontRenderContext( null,
233 // expression values menu:
234 private DescriptiveStatistics _statistics_for_vector_data;
235 private PhylogenyNode[] _nodes_in_preorder = null;
236 private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
237 private int _current_external_nodes_data_buffer_change_counter = 0;
238 private Set<Integer> _current_external_nodes = null;
239 // private Image offscreenImage;
240 // private Graphics offscreenGraphics;
241 // private Dimension offscreenDimension;
243 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
244 dfs.setDecimalSeparator( '.' );
245 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
246 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
249 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
250 requestFocusInWindow();
251 addKeyListener( new KeyAdapter() {
254 public void keyPressed( final KeyEvent key_event ) {
255 keyPressedCalls( key_event );
256 requestFocusInWindow();
259 addFocusListener( new FocusAdapter() {
262 public void focusGained( final FocusEvent e ) {
263 requestFocusInWindow();
266 if ( ( t == null ) || t.isEmpty() ) {
267 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
269 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
271 _configuration = configuration;
273 _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
275 // if ( !_phylogeny.isEmpty() ) {
276 _phylogeny.recalculateNumberOfExternalDescendants( true );
277 checkForVectorProperties( _phylogeny );
279 setBackground( getTreeColorSet().getBackgroundColor() );
280 final MouseListener mouse_listener = new MouseListener( this );
281 addMouseListener( mouse_listener );
282 addMouseMotionListener( mouse_listener );
283 addMouseWheelListener( this );
284 calculateScaleDistance();
285 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
286 FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
287 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
291 final public void actionPerformed( final ActionEvent e ) {
292 boolean done = false;
293 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
294 for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
295 // NOTE: index corresponds to the indices of click-to options
296 // in the control panel.
297 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
298 // Set this as the new default click-to action
299 _main_panel.getControlPanel().setClickToAction( index );
300 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
301 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
302 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
307 requestFocusInWindow();
310 public void checkForVectorProperties( final Phylogeny phy ) {
311 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
312 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
313 final PhylogenyNode node = iter.next();
314 if ( node.getNodeData().getProperties() != null ) {
315 final PropertiesMap pm = node.getNodeData().getProperties();
316 final double[] vector = new double[ pm.getProperties().size() ];
318 for( final String ref : pm.getProperties().keySet() ) {
319 if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
320 final Property p = pm.getProperty( ref );
321 final String value_str = p.getValue();
322 final String index_str = ref
323 .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
326 d = Double.parseDouble( value_str );
328 catch ( final NumberFormatException e ) {
329 JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
330 + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
335 i = Integer.parseInt( index_str );
337 catch ( final NumberFormatException e ) {
338 JOptionPane.showMessageDialog( this,
339 "Could not parse \"" + index_str
340 + "\" into index for vector data",
341 "Problem with Vector Data",
342 JOptionPane.ERROR_MESSAGE );
346 JOptionPane.showMessageDialog( this,
347 "Attempt to use negative index for vector data",
348 "Problem with Vector Data",
349 JOptionPane.ERROR_MESSAGE );
357 final List<Double> vector_l = new ArrayList<Double>( counter );
358 for( int i = 0; i < counter; ++i ) {
359 vector_l.add( vector[ i ] );
361 node.getNodeData().setVector( vector_l );
364 if ( stats.getN() > 0 ) {
365 _statistics_for_vector_data = stats;
369 public synchronized Hashtable<String, BufferedImage> getImageMap() {
370 return getMainPanel().getImageMap();
373 final public MainPanel getMainPanel() {
378 * Get a pointer to the phylogeny
380 * @return a pointer to the phylogeny
382 public final Phylogeny getPhylogeny() {
387 final public void mouseWheelMoved( final MouseWheelEvent e ) {
388 final int notches = e.getWheelRotation();
389 if ( inOvVirtualRectangle( e ) ) {
390 if ( !isInOvRect() ) {
396 if ( isInOvRect() ) {
397 setInOvRect( false );
401 if ( e.isControlDown() ) {
403 getTreeFontSet().increaseFontSize();
404 getControlPanel().displayedPhylogenyMightHaveChanged( true );
407 getTreeFontSet().decreaseFontSize( 1 );
408 getControlPanel().displayedPhylogenyMightHaveChanged( true );
411 else if ( e.isShiftDown() ) {
412 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
413 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
415 for( int i = 0; i < ( -notches ); ++i ) {
416 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
417 getControlPanel().displayedPhylogenyMightHaveChanged( false );
421 for( int i = 0; i < notches; ++i ) {
422 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
423 if ( getStartingAngle() < 0 ) {
424 setStartingAngle( TWO_PI + getStartingAngle() );
426 getControlPanel().displayedPhylogenyMightHaveChanged( false );
432 for( int i = 0; i < ( -notches ); ++i ) {
433 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
434 getControlPanel().displayedPhylogenyMightHaveChanged( false );
438 for( int i = 0; i < notches; ++i ) {
439 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
440 getControlPanel().displayedPhylogenyMightHaveChanged( false );
447 for( int i = 0; i < ( -notches ); ++i ) {
448 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
449 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
450 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
451 getControlPanel().displayedPhylogenyMightHaveChanged( false );
455 for( int i = 0; i < notches; ++i ) {
456 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
457 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
458 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
459 getControlPanel().displayedPhylogenyMightHaveChanged( false );
464 requestFocusInWindow();
469 final public void paintComponent( final Graphics g ) {
470 // Dimension currentSize = getSize();
471 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
472 // call the 'java.awt.Component.createImage(...)' method to get an
474 // offscreenImage = createImage( currentSize.width, currentSize.height );
475 // offscreenGraphics = offscreenImage.getGraphics();
476 // offscreenDimension = currentSize;
478 // super.paintComponent( g ); //why?
479 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
480 final Graphics2D g2d = ( Graphics2D ) g;
481 g2d.setRenderingHints( _rendering_hints );
482 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
483 //g.drawImage( offscreenImage, 0, 0, this );
487 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
488 throws PrinterException {
489 if ( page_index > 0 ) {
490 return ( NO_SUCH_PAGE );
493 final Graphics2D g2d = ( Graphics2D ) g;
494 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
495 // Turn off double buffering !?
496 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
497 // Turn double buffering back on !?
498 return ( PAGE_EXISTS );
502 public final void setArrowCursor() {
503 setCursor( ARROW_CURSOR );
507 public final void setEdited( final boolean edited ) {
511 public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
512 getMainPanel().setImageMap( image_map );
516 * Set parameters for printing the displayed tree
521 public final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
522 // updateStyle(); not needed?
523 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
525 if ( recalc_longest_ext_node_info ) {
526 calculateLongestExtNodeInfo();
527 while ( ( getLongestExtNodeInfo() > ( x * 0.67 ) ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
528 getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize() );
529 calculateLongestExtNodeInfo();
532 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
533 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
534 if ( ext_nodes == 1 ) {
535 ext_nodes = max_depth;
536 if ( ext_nodes < 1 ) {
543 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
544 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
545 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
548 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
549 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
551 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
555 if ( ov_xdist < 0.0 ) {
561 setXdistance( xdist );
562 setYdistance( ydist );
563 setOvXDistance( ov_xdist );
564 final double height = _phylogeny.getHeight();
566 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
567 setXcorrectionFactor( corr > 0 ? corr : 0 );
568 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
569 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
572 setXcorrectionFactor( 0 );
573 setOvXcorrectionFactor( 0 );
575 _circ_max_depth = max_depth;
578 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
579 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
580 int dynamic_hiding_factor = calcDynamicHidingFactor();
581 if ( dynamic_hiding_factor > 1 ) {
582 while ( dynamic_hiding_factor > 1
583 && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
584 getTreeFontSet().decreaseFontSize( 1 );
585 dynamic_hiding_factor = calcDynamicHidingFactor();
589 while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
590 getTreeFontSet().increaseFontSize();
591 dynamic_hiding_factor = calcDynamicHidingFactor();
600 * Set a phylogeny tree.
603 * an instance of a Phylogeny
605 public final void setTree( final Phylogeny t ) {
606 setNodeInPreorderToNull();
610 public final void setWaitCursor() {
611 setCursor( WAIT_CURSOR );
616 public void update( final Graphics g ) {
620 final void calcMaxDepth() {
621 if ( _phylogeny != null ) {
622 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
626 final void calculateLongestExtNodeInfo() {
627 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
630 int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
631 * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
632 if ( max_length < 40 ) {
636 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
638 if ( node.isCollapse() ) {
641 if ( getControlPanel().isShowNodeNames() ) {
642 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
644 if ( node.getNodeData().isHasSequence() ) {
645 if ( getControlPanel().isShowSequenceAcc()
646 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
647 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
651 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
652 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
654 if ( getControlPanel().isShowGeneSymbols()
655 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
656 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
658 if ( getControlPanel().isShowAnnotation()
659 && ( node.getNodeData().getSequence().getAnnotations() != null )
660 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
661 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
665 if ( getControlPanel().isShowDomainArchitectures()
666 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
667 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
668 .getRenderingSize().getWidth();
671 if ( node.getNodeData().isHasTaxonomy() ) {
672 final Taxonomy tax = node.getNodeData().getTaxonomy();
673 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
674 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
676 if ( getControlPanel().isShowTaxonomyScientificNames()
677 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
678 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
680 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
681 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
684 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
685 sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
687 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
688 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
689 .getGainedCharactersAsStringBuffer().toString() );
691 if ( sum >= max_length ) {
692 setLongestExtNodeInfo( max_length );
695 if ( sum > longest ) {
699 if ( longest >= max_length ) {
700 setLongestExtNodeInfo( max_length );
703 setLongestExtNodeInfo( longest );
707 final void calculateScaleDistance() {
708 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
711 final double height = getMaxDistanceToRoot();
713 if ( ( height <= 0.5 ) ) {
714 setScaleDistance( 0.01 );
716 else if ( height <= 5.0 ) {
717 setScaleDistance( 0.1 );
719 else if ( height <= 50.0 ) {
720 setScaleDistance( 1 );
722 else if ( height <= 500.0 ) {
723 setScaleDistance( 10 );
726 setScaleDistance( 100 );
730 setScaleDistance( 0.0 );
732 String scale_label = String.valueOf( getScaleDistance() );
733 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
734 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
736 setScaleLabel( scale_label );
739 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
740 String species = tax.getTaxonomyCode();
741 if ( ForesterUtil.isEmpty( species ) ) {
742 species = tax.getScientificName();
743 if ( ForesterUtil.isEmpty( species ) ) {
744 species = tax.getCommonName();
747 if ( ForesterUtil.isEmpty( species ) ) {
748 return getTreeColorSet().getTaxonomyColor();
750 // Look in species hash
751 Color c = getControlPanel().getSpeciesColors().get( species );
753 c = AptxUtil.calculateColorFromString( species );
754 getControlPanel().getSpeciesColors().put( species, c );
759 void clearCurrentExternalNodesDataBuffer() {
760 setCurrentExternalNodesDataBuffer( new StringBuilder() );
764 * Collapse the tree from the given node
769 final void collapse( final PhylogenyNode node ) {
770 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
771 JOptionPane.showMessageDialog( this,
772 "Cannot collapse in unrooted display type",
773 "Attempt to collapse in unrooted display",
774 JOptionPane.WARNING_MESSAGE );
777 if ( !node.isExternal() && !node.isRoot() ) {
778 final boolean collapse = !node.isCollapse();
779 AptxUtil.collapseSubtree( node, collapse );
780 updateSetOfCollapsedExternalNodes();
781 _phylogeny.recalculateNumberOfExternalDescendants( true );
782 resetNodeIdToDistToLeafMap();
783 calculateLongestExtNodeInfo();
784 setNodeInPreorderToNull();
785 _control_panel.displayedPhylogenyMightHaveChanged( true );
786 resetPreferredSize();
788 _main_panel.adjustJScrollPane();
793 final void collapseSpeciesSpecificSubtrees() {
794 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
798 AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
799 updateSetOfCollapsedExternalNodes();
800 _phylogeny.recalculateNumberOfExternalDescendants( true );
801 resetNodeIdToDistToLeafMap();
802 calculateLongestExtNodeInfo();
803 setNodeInPreorderToNull();
804 resetPreferredSize();
805 _main_panel.adjustJScrollPane();
810 final void colorRank( final String rank ) {
811 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
815 AptxUtil.removeBranchColors( _phylogeny );
816 final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
817 if ( colorizations > 0 ) {
818 _control_panel.setColorBranches( true );
819 if ( _control_panel.getColorBranchesCb() != null ) {
820 _control_panel.getColorBranchesCb().setSelected( true );
822 if ( _control_panel.getColorAccSpeciesCb() != null ) {
823 _control_panel.getColorAccSpeciesCb().setSelected( false );
825 _options.setColorLabelsSameAsParentBranch( true );
826 _control_panel.repaint();
830 if ( colorizations > 0 ) {
831 String msg = "Taxonomy colorization via " + rank + " completed:\n";
832 if ( colorizations > 1 ) {
833 msg += "colorized " + colorizations + " subtrees";
836 msg += "colorized one subtree";
839 JOptionPane.showMessageDialog( this,
841 "Taxonomy Colorization Completed (" + rank + ")",
842 JOptionPane.INFORMATION_MESSAGE );
845 String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
846 msg += "Possible solutions (given that suitable taxonomic information is present):\n";
847 msg += "select a different rank (e.g. phylum, genus, ...)\n";
850 msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
851 msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
852 JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
856 final void confColor() {
857 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
861 AptxUtil.removeBranchColors( _phylogeny );
862 AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
863 _control_panel.setColorBranches( true );
864 if ( _control_panel.getColorBranchesCb() != null ) {
865 _control_panel.getColorBranchesCb().setSelected( true );
871 final void decreaseDomainStructureEvalueThreshold() {
872 if ( _domain_structure_e_value_thr_exp > -20 ) {
873 _domain_structure_e_value_thr_exp -= 1;
878 * Find the node, if any, at the given location
882 * @return pointer to the node at x,y, null if not found
884 final PhylogenyNode findNode( final int x, final int y ) {
885 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
888 final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
889 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
890 final PhylogenyNode node = iter.next();
891 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
892 && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
893 && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
894 && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
895 && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
902 final Configuration getConfiguration() {
903 return _configuration;
906 final ControlPanel getControlPanel() {
907 return _control_panel;
910 String getCurrentExternalNodesDataBufferAsString() {
911 return _current_external_nodes_data_buffer.toString();
914 int getCurrentExternalNodesDataBufferChangeCounter() {
915 return _current_external_nodes_data_buffer_change_counter;
918 final int getDomainStructureEvalueThreshold() {
919 return _domain_structure_e_value_thr_exp;
922 final Set<Integer> getFoundNodes() {
926 final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
927 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
928 return ( PhylogenyMethods.getBranchColorValue( node ) );
931 return ( getTreeColorSet().getBranchColor() );
935 final int getLongestExtNodeInfo() {
936 return _longest_ext_node_info;
939 final Options getOptions() {
940 if ( _options == null ) {
941 _options = getControlPanel().getOptions();
946 final Rectangle2D getOvRectangle() {
947 return _ov_rectangle;
950 final Rectangle getOvVirtualRectangle() {
951 return _ov_virtual_rectangle;
954 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
955 return _graphics_type;
958 final double getStartingAngle() {
959 return _urt_starting_angle;
962 DescriptiveStatistics getStatisticsForExpressionValues() {
963 return _statistics_for_vector_data;
967 * Find a color for this species name.
970 * @return the species color
972 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
973 if ( node.getNodeData().isHasTaxonomy() ) {
974 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
976 // return non-colorized color
977 return getTreeColorSet().getTaxonomyColor();
981 * @return pointer to colorset for tree drawing
983 final TreeColorSet getTreeColorSet() {
984 return getMainPanel().getTreeColorSet();
987 final File getTreeFile() {
991 final float getXcorrectionFactor() {
992 return _x_correction_factor;
995 final float getXdistance() {
999 final float getYdistance() {
1003 final void increaseDomainStructureEvalueThreshold() {
1004 if ( _domain_structure_e_value_thr_exp < 3 ) {
1005 _domain_structure_e_value_thr_exp += 1;
1009 final void initNodeData() {
1010 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1013 double max_original_domain_structure_width = 0.0;
1014 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1015 if ( node.getNodeData().isHasSequence()
1016 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1017 RenderableDomainArchitecture rds = null;
1018 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
1019 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1020 getConfiguration() );
1021 node.getNodeData().getSequence().setDomainArchitecture( rds );
1024 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1026 if ( getControlPanel().isShowDomainArchitectures() ) {
1027 final double dsw = rds.getOriginalSize().getWidth();
1028 if ( dsw > max_original_domain_structure_width ) {
1029 max_original_domain_structure_width = dsw;
1034 if ( getControlPanel().isShowDomainArchitectures() ) {
1035 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1036 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1037 if ( node.getNodeData().isHasSequence()
1038 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1039 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1040 .getSequence().getDomainArchitecture();
1041 rds.setRenderingFactorWidth( ds_factor_width );
1042 rds.setParameter( _domain_structure_e_value_thr_exp );
1048 final boolean inOv( final MouseEvent e ) {
1049 return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
1050 && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
1051 && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
1052 + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
1055 final boolean inOvRectangle( final MouseEvent e ) {
1056 return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
1057 && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
1058 && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
1059 + getOvRectangle().getHeight() + 1 ) ) );
1062 final boolean isApplet() {
1063 return getMainPanel() instanceof MainPanelApplets;
1066 final boolean isCanCollapse() {
1067 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1070 final boolean isCanColorSubtree() {
1071 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1074 final boolean isCanCopy() {
1075 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1078 final boolean isCanCut( final PhylogenyNode node ) {
1079 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1083 final boolean isCanDelete() {
1084 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1087 final boolean isCanPaste() {
1088 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1089 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1092 final boolean isCanReroot() {
1093 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1096 final boolean isCanSubtree( final PhylogenyNode node ) {
1097 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1098 .isRoot() || ( _subtree_index > 0 ) ) );
1101 final boolean isCurrentTreeIsSubtree() {
1102 return ( _subtree_index > 0 );
1105 final boolean isEdited() {
1109 final boolean isInOvRect() {
1113 final boolean isOvOn() {
1117 final boolean isPhyHasBranchLengths() {
1118 return _phy_has_branch_lengths;
1121 final void midpointRoot() {
1122 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1125 if ( !_phylogeny.isRerootable() ) {
1126 JOptionPane.showMessageDialog( this,
1127 "This is not rerootable",
1129 JOptionPane.WARNING_MESSAGE );
1132 setNodeInPreorderToNull();
1134 PhylogenyMethods.midpointRoot( _phylogeny );
1135 resetNodeIdToDistToLeafMap();
1141 final void mouseClicked( final MouseEvent e ) {
1142 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1143 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1144 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1145 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
1147 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
1155 final double max_x = getWidth() - getVisibleRect().width;
1156 final double max_y = getHeight() - getVisibleRect().height;
1163 getMainPanel().getCurrentScrollPane().getViewport()
1164 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1165 setInOvRect( true );
1169 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1170 if ( node != null ) {
1171 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1174 _highlight_node = node;
1175 // Check if shift key is down
1176 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1177 // Yes, so add to _found_nodes
1178 if ( getFoundNodes() == null ) {
1179 setFoundNodes( new HashSet<Integer>() );
1181 getFoundNodes().add( node.getId() );
1182 // Check if control key is down
1184 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1185 // Yes, so pop-up menu
1186 displayNodePopupMenu( node, e.getX(), e.getY() );
1187 // Handle unadorned click
1190 // Check for right mouse button
1191 if ( e.getModifiers() == 4 ) {
1192 displayNodePopupMenu( node, e.getX(), e.getY() );
1195 // if not in _found_nodes, clear _found_nodes
1196 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1201 // no node was clicked
1202 _highlight_node = null;
1208 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1209 setCursor( MOVE_CURSOR );
1210 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1211 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1212 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1213 if ( scroll_position.x < 0 ) {
1214 scroll_position.x = 0;
1217 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1218 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1219 if ( scroll_position.x > max_x ) {
1220 scroll_position.x = max_x;
1223 if ( scroll_position.y < 0 ) {
1224 scroll_position.y = 0;
1227 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1228 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1229 if ( scroll_position.y > max_y ) {
1230 scroll_position.y = max_y;
1233 if ( isOvOn() || getOptions().isShowScale() ) {
1236 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1239 final void mouseDragInOvRectangle( final MouseEvent e ) {
1240 setCursor( HAND_CURSOR );
1241 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1242 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1243 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1244 double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
1245 double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
1246 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1247 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1248 if ( scroll_position.x <= 0 ) {
1249 scroll_position.x = 0;
1253 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1254 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1255 if ( scroll_position.x >= max_x ) {
1257 scroll_position.x = max_x;
1260 if ( scroll_position.y <= 0 ) {
1262 scroll_position.y = 0;
1265 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1266 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1267 if ( scroll_position.y >= max_y ) {
1269 scroll_position.y = max_y;
1273 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1274 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1275 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1278 final void mouseMoved( final MouseEvent e ) {
1279 requestFocusInWindow();
1280 if ( _current_external_nodes != null ) {
1281 _current_external_nodes = null;
1284 if ( getControlPanel().isNodeDescPopup() ) {
1285 if ( _node_desc_popup != null ) {
1286 _node_desc_popup.hide();
1287 _node_desc_popup = null;
1290 if ( getOptions().isShowOverview() && isOvOn() ) {
1291 if ( inOvVirtualRectangle( e ) ) {
1292 if ( !isInOvRect() ) {
1293 setInOvRect( true );
1298 if ( isInOvRect() ) {
1299 setInOvRect( false );
1304 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
1313 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1314 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
1315 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
1316 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
1317 addToCurrentExternalNodes( n.getId() );
1319 setCursor( HAND_CURSOR );
1322 else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
1323 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
1324 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
1325 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
1326 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
1327 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
1328 setCursor( CUT_CURSOR );
1331 setCursor( HAND_CURSOR );
1332 if ( getControlPanel().isNodeDescPopup() ) {
1333 showNodeDataPopup( e, node );
1338 setCursor( ARROW_CURSOR );
1343 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
1344 setCursor( ARROW_CURSOR );
1347 final void multiplyUrtFactor( final float f ) {
1351 final JApplet obtainApplet() {
1352 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1355 final void paintBranchCircular( final PhylogenyNode p,
1356 final PhylogenyNode c,
1358 final boolean radial_labels,
1359 final boolean to_pdf,
1360 final boolean to_graphics_file ) {
1361 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1362 final double root_x = _root.getXcoord();
1363 final double root_y = _root.getYcoord();
1364 final double dx = root_x - p.getXcoord();
1365 final double dy = root_y - p.getYcoord();
1366 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1367 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1368 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
1369 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
1370 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
1371 final double r2 = 2.0 * parent_radius;
1372 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1374 drawLine( c.getXcoord(),
1376 root_x + ( Math.cos( angle ) * parent_radius ),
1377 root_y + ( Math.sin( angle ) * parent_radius ),
1379 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c )
1380 || isInCurrentExternalNodes( c ) );
1381 if ( c.isExternal() ) {
1382 final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c );
1383 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
1384 && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
1387 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
1391 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
1392 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1393 final double root_x = _root.getXSecondary();
1394 final double root_y = _root.getYSecondary();
1395 final double dx = root_x - p.getXSecondary();
1396 final double dy = root_y - p.getYSecondary();
1397 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1398 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1399 g.setColor( getTreeColorSet().getOvColor() );
1400 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
1401 final double r2 = 2.0 * parent_radius;
1402 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1404 drawLine( c.getXSecondary(),
1406 root_x + ( Math.cos( angle ) * parent_radius ),
1407 root_y + ( Math.sin( angle ) * parent_radius ),
1409 if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
1410 g.setColor( getTreeColorSet().getFoundColor() );
1411 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
1415 final void paintCircular( final Phylogeny phy,
1416 final double starting_angle,
1421 final boolean to_pdf,
1422 final boolean to_graphics_file ) {
1423 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
1424 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
1425 _root = phy.getRoot();
1426 _root.setXcoord( center_x );
1427 _root.setYcoord( center_y );
1428 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1429 double current_angle = starting_angle;
1431 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1432 final PhylogenyNode n = it.next();
1433 if ( !n.isCollapse() ) {
1434 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1435 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1436 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1437 _urt_nodeid_index_map.put( n.getId(), i++ );
1438 current_angle += ( TWO_PI / circ_num_ext_nodes );
1442 System.out.println( "is collapse" + n.getName() );
1445 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
1446 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
1449 final void paintCircularLite( final Phylogeny phy,
1450 final double starting_angle,
1454 final Graphics2D g ) {
1455 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
1456 _root = phy.getRoot();
1457 _root.setXSecondary( center_x );
1458 _root.setYSecondary( center_y );
1459 double current_angle = starting_angle;
1460 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1461 final PhylogenyNode n = it.next();
1462 n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1463 n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1464 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1465 current_angle += ( TWO_PI / circ_num_ext_nodes );
1467 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
1470 final void paintPhylogeny( final Graphics2D g,
1471 final boolean to_pdf,
1472 final boolean to_graphics_file,
1473 final int graphics_file_width,
1474 final int graphics_file_height,
1475 final int graphics_file_x,
1476 final int graphics_file_y ) {
1477 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1480 if ( _control_panel.isShowSequenceRelations() ) {
1481 _query_sequence = _control_panel.getSelectedQuerySequence();
1483 // Color the background
1485 final Rectangle r = getVisibleRect();
1486 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
1487 g.setColor( getTreeColorSet().getBackgroundColor() );
1488 if ( !to_graphics_file ) {
1492 if ( getOptions().isPrintBlackAndWhite() ) {
1493 g.setColor( Color.WHITE );
1495 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1499 if ( !to_graphics_file ) {
1500 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
1501 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
1505 g.setPaint( new GradientPaint( graphics_file_x,
1507 getTreeColorSet().getBackgroundColor(),
1509 graphics_file_y + graphics_file_height,
1510 getTreeColorSet().getBackgroundColorGradientBottom() ) );
1511 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1514 g.setStroke( new BasicStroke( 1 ) );
1517 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
1519 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1520 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1521 _external_node_index = 0;
1522 // Position starting X of tree
1523 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
1524 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
1526 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
1527 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
1528 .getDistanceToParent() * getXcorrectionFactor() ) ) );
1531 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
1533 // Position starting Y of tree
1534 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
1535 + ( TreePanel.MOVE / 2.0f ) );
1536 final int dynamic_hiding_factor = calcDynamicHidingFactor();
1537 if ( getControlPanel().isDynamicallyHideData() ) {
1538 if ( dynamic_hiding_factor > 1 ) {
1539 getControlPanel().setDynamicHidingIsOn( true );
1542 getControlPanel().setDynamicHidingIsOn( false );
1545 if ( _nodes_in_preorder == null ) {
1546 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
1548 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1549 _nodes_in_preorder[ i++ ] = it.next();
1552 //final PhylogenyNodeIterator it;
1553 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1554 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
1555 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1557 for( final PhylogenyNode element : _nodes_in_preorder ) {
1558 paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
1559 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1561 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
1562 if ( !( to_graphics_file || to_pdf ) ) {
1565 getVisibleRect().y + getVisibleRect().height,
1570 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1573 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1574 paintPhylogenyLite( g );
1577 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1578 if ( getControlPanel().getDynamicallyHideData() != null ) {
1579 getControlPanel().setDynamicHidingIsOn( false );
1581 final double angle = getStartingAngle();
1582 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1583 _dynamic_hiding_factor = 0;
1584 if ( getControlPanel().isDynamicallyHideData() ) {
1585 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1586 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
1588 if ( getControlPanel().getDynamicallyHideData() != null ) {
1589 if ( _dynamic_hiding_factor > 1 ) {
1590 getControlPanel().setDynamicHidingIsOn( true );
1593 getControlPanel().setDynamicHidingIsOn( false );
1596 paintUnrooted( _phylogeny.getRoot(),
1598 ( float ) ( angle + ( 2 * Math.PI ) ),
1603 if ( getOptions().isShowScale() ) {
1604 if ( !( to_graphics_file || to_pdf ) ) {
1607 getVisibleRect().y + getVisibleRect().height,
1612 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1615 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1616 g.setColor( getTreeColorSet().getOvColor() );
1617 paintUnrootedLite( _phylogeny.getRoot(),
1619 angle + ( 2 * Math.PI ),
1621 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
1622 paintOvRectangle( g );
1625 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1626 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
1627 final int d = radius + MOVE + getLongestExtNodeInfo();
1628 _dynamic_hiding_factor = 0;
1629 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
1630 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1631 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
1633 if ( getControlPanel().getDynamicallyHideData() != null ) {
1634 if ( _dynamic_hiding_factor > 1 ) {
1635 getControlPanel().setDynamicHidingIsOn( true );
1638 getControlPanel().setDynamicHidingIsOn( false );
1641 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
1642 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1643 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
1644 : getOvMaxWidth() / 2 );
1645 double x_scale = 1.0;
1646 double y_scale = 1.0;
1647 int x_pos = getVisibleRect().x + getOvXPosition();
1648 int y_pos = getVisibleRect().y + getOvYPosition();
1649 if ( getWidth() > getHeight() ) {
1650 x_scale = ( double ) getHeight() / getWidth();
1651 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
1654 y_scale = ( double ) getWidth() / getHeight();
1655 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
1657 _at = g.getTransform();
1658 g.scale( x_scale, y_scale );
1659 paintCircularLite( _phylogeny,
1663 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
1666 g.setTransform( _at );
1667 paintOvRectangle( g );
1672 private final int calcDynamicHidingFactor() {
1673 return ( int ) ( 0.5 + ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ) );
1676 final void recalculateMaxDistanceToRoot() {
1677 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
1681 * Remove all edit-node frames
1683 final void removeAllEditNodeJFrames() {
1684 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
1685 if ( _node_frames[ i ] != null ) {
1686 _node_frames[ i ].dispose();
1687 _node_frames[ i ] = null;
1690 _node_frame_index = 0;
1694 * Remove a node-edit frame.
1696 final void removeEditNodeFrame( final int i ) {
1697 _node_frame_index--;
1698 _node_frames[ i ] = null;
1699 if ( i < _node_frame_index ) {
1700 for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
1701 _node_frames[ j ] = _node_frames[ j + 1 ];
1703 _node_frames[ _node_frame_index ] = null;
1707 final void reRoot( final PhylogenyNode node ) {
1708 if ( !getPhylogeny().isRerootable() ) {
1709 JOptionPane.showMessageDialog( this,
1710 "This is not rerootable",
1712 JOptionPane.WARNING_MESSAGE );
1715 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1716 JOptionPane.showMessageDialog( this,
1717 "Cannot reroot in unrooted display type",
1718 "Attempt to reroot tree in unrooted display",
1719 JOptionPane.WARNING_MESSAGE );
1722 getPhylogeny().reRoot( node );
1723 getPhylogeny().recalculateNumberOfExternalDescendants( true );
1724 resetNodeIdToDistToLeafMap();
1725 setNodeInPreorderToNull();
1726 resetPreferredSize();
1727 getMainPanel().adjustJScrollPane();
1730 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1731 getControlPanel().showWhole();
1735 final void resetNodeIdToDistToLeafMap() {
1736 _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
1739 final void resetPreferredSize() {
1740 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
1746 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
1747 if ( getControlPanel().isDrawPhylogram() ) {
1749 + getLongestExtNodeInfo()
1751 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
1754 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
1756 + getLongestExtNodeInfo()
1757 + ForesterUtil.roundToInt( getXdistance()
1758 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
1762 + getLongestExtNodeInfo()
1763 + ForesterUtil.roundToInt( getXdistance()
1764 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
1767 setPreferredSize( new Dimension( x, y ) );
1770 final void selectNode( final PhylogenyNode node ) {
1771 if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
1772 getFoundNodes().remove( node.getId() );
1773 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1774 if ( getFoundNodes().size() < 1 ) {
1775 getControlPanel().searchReset();
1779 getControlPanel().getSearchFoundCountsLabel().setVisible( true );
1780 getControlPanel().getSearchResetButton().setEnabled( true );
1781 getControlPanel().getSearchResetButton().setVisible( true );
1782 if ( getFoundNodes() == null ) {
1783 setFoundNodes( new HashSet<Integer>() );
1785 getFoundNodes().add( node.getId() );
1786 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1790 final void setControlPanel( final ControlPanel atv_control ) {
1791 _control_panel = atv_control;
1794 void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
1795 increaseCurrentExternalNodesDataBufferChangeCounter();
1796 _current_external_nodes_data_buffer = sb;
1799 final void setFoundNodes( final Set<Integer> found_nodes ) {
1800 _found_nodes = found_nodes;
1803 final void setInOvRect( final boolean in_ov_rect ) {
1804 _in_ov_rect = in_ov_rect;
1807 final void setLargeFonts() {
1808 getTreeFontSet().largeFonts();
1811 final void setLastMouseDragPointX( final float x ) {
1812 _last_drag_point_x = x;
1815 final void setLastMouseDragPointY( final float y ) {
1816 _last_drag_point_y = y;
1819 final void setLongestExtNodeInfo( final int i ) {
1820 _longest_ext_node_info = i;
1823 final void setMediumFonts() {
1824 getTreeFontSet().mediumFonts();
1827 final void setNodeInPreorderToNull() {
1828 _nodes_in_preorder = null;
1831 final void setOvOn( final boolean ov_on ) {
1835 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
1836 _graphics_type = graphics_type;
1840 final void setSmallFonts() {
1841 getTreeFontSet().smallFonts();
1844 final void setStartingAngle( final double starting_angle ) {
1845 _urt_starting_angle = starting_angle;
1848 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
1849 _statistics_for_vector_data = statistics_for_expression_values;
1852 final void setSuperTinyFonts() {
1853 getTreeFontSet().superTinyFonts();
1856 final void setTextAntialias() {
1857 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
1858 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
1859 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
1862 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
1865 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
1866 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
1867 && !getMainPanel().getOptions().isShowDefaultNodeShapesInternal()
1868 && !getMainPanel().getOptions().isShowDefaultNodeShapesExternal()
1869 && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
1870 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1873 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
1876 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
1877 RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
1879 catch ( final Throwable e ) {
1880 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
1884 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
1885 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1889 final void setTinyFonts() {
1890 getTreeFontSet().tinyFonts();
1893 final void setTreeFile( final File treefile ) {
1894 _treefile = treefile;
1897 final void setXcorrectionFactor( final float f ) {
1898 _x_correction_factor = f;
1901 final void setXdistance( final float x ) {
1905 final void setYdistance( final float y ) {
1909 final void sortDescendants( final PhylogenyNode node ) {
1910 if ( !node.isExternal() ) {
1911 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
1912 if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
1913 .isShowTaxonomyCommonNames() ) ) {
1914 if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
1915 .isShowGeneSymbols() ) ) {
1916 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
1918 else if ( getControlPanel().isShowNodeNames() ) {
1919 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
1922 PhylogenyMethods.sortNodeDescendents( node, pri );
1923 setNodeInPreorderToNull();
1924 _phylogeny.externalNodesHaveChanged();
1925 _phylogeny.clearHashIdToNodeMap();
1926 _phylogeny.recalculateNumberOfExternalDescendants( true );
1927 resetNodeIdToDistToLeafMap();
1933 final void subTree( final PhylogenyNode node ) {
1934 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1935 JOptionPane.showMessageDialog( this,
1936 "Cannot get a sub/super tree in unrooted display",
1937 "Attempt to get sub/super tree in unrooted display",
1938 JOptionPane.WARNING_MESSAGE );
1941 if ( node.isExternal() ) {
1942 JOptionPane.showMessageDialog( this,
1943 "Cannot get a subtree of a external node",
1944 "Attempt to get subtree of external node",
1945 JOptionPane.WARNING_MESSAGE );
1948 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
1949 JOptionPane.showMessageDialog( this,
1950 "Cannot get a subtree of the root node",
1951 "Attempt to get subtree of root node",
1952 JOptionPane.WARNING_MESSAGE );
1955 setNodeInPreorderToNull();
1956 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
1957 _sub_phylogenies[ _subtree_index ] = _phylogeny;
1958 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
1960 _phylogeny = subTree( node, _phylogeny );
1961 updateSubSuperTreeButton();
1963 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
1966 _main_panel.getControlPanel().showWhole();
1970 final void superTree() {
1971 setNodeInPreorderToNull();
1972 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
1973 for( final PhylogenyNode n : temp_root.getDescendants() ) {
1974 n.setParent( temp_root );
1976 _sub_phylogenies[ _subtree_index ] = null;
1977 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
1978 _phylogeny = _sub_phylogenies[ --_subtree_index ];
1979 updateSubSuperTreeButton();
1982 final void swap( final PhylogenyNode node ) {
1983 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
1986 if ( node.getNumberOfDescendants() > 2 ) {
1987 JOptionPane.showMessageDialog( this,
1988 "Cannot swap descendants of nodes with more than 2 descendants",
1989 "Cannot swap descendants",
1990 JOptionPane.ERROR_MESSAGE );
1993 if ( !node.isExternal() ) {
1994 node.swapChildren();
1995 setNodeInPreorderToNull();
1996 _phylogeny.externalNodesHaveChanged();
1997 _phylogeny.clearHashIdToNodeMap();
1998 _phylogeny.recalculateNumberOfExternalDescendants( true );
1999 resetNodeIdToDistToLeafMap();
2005 final void taxColor() {
2006 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
2010 AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
2011 _control_panel.setColorBranches( true );
2012 if ( _control_panel.getColorBranchesCb() != null ) {
2013 _control_panel.getColorBranchesCb().setSelected( true );
2020 final void updateOvSettings() {
2021 switch ( getOptions().getOvPlacement() ) {
2023 setOvXPosition( OV_BORDER );
2024 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2025 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2028 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2029 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2030 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2033 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2034 setOvYPosition( OV_BORDER );
2035 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2038 setOvXPosition( OV_BORDER );
2039 setOvYPosition( OV_BORDER );
2040 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2045 final void updateOvSizes() {
2046 if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
2048 float l = getLongestExtNodeInfo();
2049 final float w_ratio = getOvMaxWidth() / getWidth();
2051 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
2052 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
2054 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
2055 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
2058 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
2060 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
2061 if ( ov_xdist < 0.0 ) {
2064 if ( ydist < 0.0 ) {
2067 setOvXDistance( ov_xdist );
2068 final double height = _phylogeny.getHeight();
2070 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
2071 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
2074 setOvXcorrectionFactor( 0 );
2082 void updateSetOfCollapsedExternalNodes() {
2083 final Phylogeny phy = getPhylogeny();
2084 _collapsed_external_nodeid_set.clear();
2085 if ( phy != null ) {
2086 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2087 final PhylogenyNode ext_node = it.next();
2088 PhylogenyNode n = ext_node;
2089 while ( !n.isRoot() ) {
2090 if ( n.isCollapse() ) {
2091 _collapsed_external_nodeid_set.add( ext_node.getId() );
2092 ext_node.setCollapse( true );
2101 final void updateSubSuperTreeButton() {
2102 if ( _subtree_index < 1 ) {
2103 getControlPanel().deactivateButtonToReturnToSuperTree();
2106 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
2110 final void zoomInDomainStructure() {
2111 if ( _domain_structure_width < 2000 ) {
2112 _domain_structure_width *= 1.2;
2116 final void zoomOutDomainStructure() {
2117 if ( _domain_structure_width > 20 ) {
2118 _domain_structure_width *= 0.8;
2122 private void abbreviateScientificName( final String sn ) {
2123 final String[] a = sn.split( "\\s+" );
2124 _sb.append( a[ 0 ].substring( 0, 1 ) );
2125 _sb.append( a[ 1 ].substring( 0, 2 ) );
2126 if ( a.length > 2 ) {
2127 for( int i = 2; i < a.length; i++ ) {
2129 _sb.append( a[ i ] );
2134 final private void addEmptyNode( final PhylogenyNode node ) {
2135 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2136 errorMessageNoCutCopyPasteInUnrootedDisplay();
2139 final String label = createASimpleTextRepresentationOfANode( node );
2141 if ( ForesterUtil.isEmpty( label ) ) {
2142 msg = "How to add the new, empty node?";
2145 msg = "How to add the new, empty node to node" + label + "?";
2147 final Object[] options = { "As sibling", "As descendant", "Cancel" };
2148 final int r = JOptionPane.showOptionDialog( this,
2150 "Addition of Empty New Node",
2151 JOptionPane.CLOSED_OPTION,
2152 JOptionPane.QUESTION_MESSAGE,
2156 boolean add_as_sibling = true;
2158 add_as_sibling = false;
2160 else if ( r != 0 ) {
2163 final Phylogeny phy = new Phylogeny();
2164 phy.setRoot( new PhylogenyNode() );
2165 phy.setRooted( true );
2166 if ( add_as_sibling ) {
2167 if ( node.isRoot() ) {
2168 JOptionPane.showMessageDialog( this,
2169 "Cannot add sibling to root",
2170 "Attempt to add sibling to root",
2171 JOptionPane.ERROR_MESSAGE );
2174 phy.addAsSibling( node );
2177 phy.addAsChild( node );
2179 setNodeInPreorderToNull();
2180 _phylogeny.externalNodesHaveChanged();
2181 _phylogeny.clearHashIdToNodeMap();
2182 _phylogeny.recalculateNumberOfExternalDescendants( true );
2183 resetNodeIdToDistToLeafMap();
2188 final private void addToCurrentExternalNodes( final int i ) {
2189 if ( _current_external_nodes == null ) {
2190 _current_external_nodes = new HashSet<Integer>();
2192 _current_external_nodes.add( i );
2195 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
2196 final boolean is_vertical,
2198 final boolean to_pdf,
2199 final boolean to_graphics_file ) {
2200 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
2201 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2202 g.setColor( Color.BLACK );
2204 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
2205 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
2206 && ( getCutOrCopiedTree() != null )
2207 && ( getCopiedAndPastedNodes() != null )
2209 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
2210 g.setColor( getTreeColorSet().getFoundColor() );
2212 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2213 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2215 else if ( to_pdf ) {
2216 g.setColor( getTreeColorSet().getBranchColorForPdf() );
2219 g.setColor( getTreeColorSet().getBranchColor() );
2223 final private void blast( final PhylogenyNode node ) {
2224 if ( !isCanBlast( node ) ) {
2225 JOptionPane.showMessageDialog( this,
2226 "Insufficient information present",
2228 JOptionPane.INFORMATION_MESSAGE );
2232 final String query = Blast.obtainQueryForBlast( node );
2233 System.out.println( "query for BLAST is: " + query );
2235 if ( !ForesterUtil.isEmpty( query ) ) {
2236 if ( node.getNodeData().isHasSequence() ) {
2237 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
2238 if ( node.getNodeData().getSequence().getType().toLowerCase()
2239 .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
2246 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2247 if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2255 if ( type == '?' ) {
2256 if ( SequenceIdParser.isProtein( query ) ) {
2263 JApplet applet = null;
2265 applet = obtainApplet();
2268 Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
2270 catch ( final Exception e ) {
2271 e.printStackTrace();
2273 if ( Constants.ALLOW_DDBJ_BLAST ) {
2275 System.out.println( "trying: " + query );
2276 final Blast s = new Blast();
2277 s.ddbjBlast( query );
2279 catch ( final Exception e ) {
2280 e.printStackTrace();
2288 * Calculate the length of the distance between the given node and its
2294 * @return the distance value
2296 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
2297 if ( getControlPanel().isDrawPhylogram() ) {
2298 if ( node.getDistanceToParent() < 0.0 ) {
2301 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
2304 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2305 return getXdistance();
2307 return getXdistance() * factor;
2311 final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
2312 Color c = getTreeColorSet().getAnnotationColor();
2313 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
2314 final StringBuilder sb = new StringBuilder();
2315 for( final Annotation a : ann ) {
2316 sb.append( !ForesterUtil.isEmpty( a.getRef() ) ? a.getRef() : a.getDesc() );
2318 final String ann_str = sb.toString();
2319 if ( !ForesterUtil.isEmpty( ann_str ) ) {
2320 c = getControlPanel().getAnnotationColors().get( ann_str );
2322 c = AptxUtil.calculateColorFromString( ann_str );
2323 getControlPanel().getAnnotationColors().put( ann_str, c );
2326 c = getTreeColorSet().getAnnotationColor();
2333 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
2334 if ( getControlPanel().isDrawPhylogram() ) {
2335 if ( node.getDistanceToParent() < 0.0 ) {
2338 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
2341 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2342 return getOvXDistance();
2344 return getOvXDistance() * factor;
2348 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
2349 JOptionPane.showMessageDialog( this,
2350 "Cannot launch web browser for " + type_type + " data of this node",
2351 "Cannot launch web browser",
2352 JOptionPane.WARNING_MESSAGE );
2355 final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
2356 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2357 JOptionPane.showMessageDialog( this,
2358 "Cannot colorize subtree in unrooted display type",
2359 "Attempt to colorize subtree in unrooted display",
2360 JOptionPane.WARNING_MESSAGE );
2363 _control_panel.setColorBranches( true );
2364 if ( _control_panel.getColorBranchesCb() != null ) {
2365 _control_panel.getColorBranchesCb().setSelected( true );
2367 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
2368 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
2373 final private void colorSubtree( final PhylogenyNode node ) {
2374 Color intitial_color = null;
2375 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
2376 && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
2377 intitial_color = PhylogenyMethods.getBranchColorValue( node );
2380 intitial_color = getTreeColorSet().getBranchColor();
2382 _color_chooser.setColor( intitial_color );
2383 _color_chooser.setPreviewPanel( new JPanel() );
2384 final JDialog dialog = JColorChooser
2385 .createDialog( this,
2386 "Subtree colorization",
2389 new SubtreeColorizationActionListener( _color_chooser, node ),
2391 dialog.setVisible( true );
2394 final private void copySubtree( final PhylogenyNode node ) {
2395 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2396 errorMessageNoCutCopyPasteInUnrootedDisplay();
2399 setNodeInPreorderToNull();
2400 setCutOrCopiedTree( _phylogeny.copy( node ) );
2401 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
2402 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
2403 for( final PhylogenyNode n : nodes ) {
2404 node_ids.add( n.getId() );
2406 node_ids.add( node.getId() );
2407 setCopiedAndPastedNodes( node_ids );
2411 private String createAnnotationString( final SortedSet<Annotation> ann ) {
2412 final StringBuilder sb = new StringBuilder();
2413 boolean first = true;
2414 for( final Annotation a : ann ) {
2421 sb.append( a.asSimpleText() );
2423 final String ann_str = sb.toString();
2427 final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
2428 final String tax = PhylogenyMethods.getSpecies( node );
2429 String label = node.getName();
2430 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
2431 label = label + " " + tax;
2433 else if ( !ForesterUtil.isEmpty( tax ) ) {
2439 if ( !ForesterUtil.isEmpty( label ) ) {
2440 label = " [" + label + "]";
2445 final private void cutSubtree( final PhylogenyNode node ) {
2446 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2447 errorMessageNoCutCopyPasteInUnrootedDisplay();
2450 if ( node.isRoot() ) {
2451 JOptionPane.showMessageDialog( this,
2452 "Cannot cut entire tree as subtree",
2453 "Attempt to cut entire tree",
2454 JOptionPane.ERROR_MESSAGE );
2457 final String label = createASimpleTextRepresentationOfANode( node );
2458 final int r = JOptionPane.showConfirmDialog( null,
2459 "Cut subtree" + label + "?",
2460 "Confirm Cutting of Subtree",
2461 JOptionPane.YES_NO_OPTION );
2462 if ( r != JOptionPane.OK_OPTION ) {
2465 setNodeInPreorderToNull();
2466 setCopiedAndPastedNodes( null );
2467 setCutOrCopiedTree( _phylogeny.copy( node ) );
2468 _phylogeny.deleteSubtree( node, true );
2469 _phylogeny.clearHashIdToNodeMap();
2470 _phylogeny.recalculateNumberOfExternalDescendants( true );
2471 resetNodeIdToDistToLeafMap();
2476 final private void cycleColors() {
2477 getMainPanel().getTreeColorSet().cycleColorScheme();
2478 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
2479 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
2483 final private void decreaseOvSize() {
2484 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
2485 setOvMaxWidth( getOvMaxWidth() - 5 );
2486 setOvMaxHeight( getOvMaxHeight() - 5 );
2488 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2492 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
2493 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2494 errorMessageNoCutCopyPasteInUnrootedDisplay();
2497 if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
2498 JOptionPane.showMessageDialog( this,
2499 "Cannot delete entire tree",
2500 "Attempt to delete entire tree",
2501 JOptionPane.ERROR_MESSAGE );
2504 final String label = createASimpleTextRepresentationOfANode( node );
2505 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
2506 final int r = JOptionPane.showOptionDialog( this,
2507 "Delete" + label + "?",
2508 "Delete Node/Subtree",
2509 JOptionPane.CLOSED_OPTION,
2510 JOptionPane.QUESTION_MESSAGE,
2514 setNodeInPreorderToNull();
2515 boolean node_only = true;
2519 else if ( r != 0 ) {
2523 PhylogenyMethods.removeNode( node, _phylogeny );
2526 _phylogeny.deleteSubtree( node, true );
2528 _phylogeny.externalNodesHaveChanged();
2529 _phylogeny.clearHashIdToNodeMap();
2530 _phylogeny.recalculateNumberOfExternalDescendants( true );
2531 resetNodeIdToDistToLeafMap();
2536 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
2537 makePopupMenus( node );
2538 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
2539 _node_popup_menu.show( this, x, y );
2542 final private void drawArc( final double x,
2545 final double heigth,
2546 final double start_angle,
2547 final double arc_angle,
2548 final Graphics2D g ) {
2549 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
2553 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
2554 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
2557 _line.setLine( x1, y1, x2, y2 );
2561 final private void drawOval( final double x,
2564 final double heigth,
2565 final Graphics2D g ) {
2566 _ellipse.setFrame( x, y, width, heigth );
2570 final private void drawOvalFilled( final double x,
2573 final double heigth,
2574 final Graphics2D g ) {
2575 _ellipse.setFrame( x, y, width, heigth );
2579 final private void drawOvalGradient( final double x,
2582 final double heigth,
2584 final Color color_1,
2585 final Color color_2,
2586 final Color color_border ) {
2587 _ellipse.setFrame( x, y, width, heigth );
2588 g.setPaint( new GradientPaint( ( float ) x,
2591 ( float ) ( x + width ),
2592 ( float ) ( y + heigth ),
2596 if ( color_border != null ) {
2597 g.setPaint( color_border );
2602 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
2603 _rectangle.setFrame( x, y, width, heigth );
2604 g.draw( _rectangle );
2607 final private void drawRectFilled( final double x,
2610 final double heigth,
2611 final Graphics2D g ) {
2612 _rectangle.setFrame( x, y, width, heigth );
2613 g.fill( _rectangle );
2616 final private void drawRectGradient( final double x,
2619 final double heigth,
2621 final Color color_1,
2622 final Color color_2,
2623 final Color color_border ) {
2624 _rectangle.setFrame( x, y, width, heigth );
2625 g.setPaint( new GradientPaint( ( float ) x,
2628 ( float ) ( x + width ),
2629 ( float ) ( y + heigth ),
2632 g.fill( _rectangle );
2633 if ( color_border != null ) {
2634 g.setPaint( color_border );
2635 g.draw( _rectangle );
2639 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2640 final List<Uri> us = new ArrayList<Uri>();
2641 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2642 for( final Uri uri : t.getUris() ) {
2647 for( final Uri uri : us ) {
2648 if ( uri != null ) {
2649 final String uri_str = uri.getValue().toString().toLowerCase();
2650 if ( getImageMap().containsKey( uri_str ) ) {
2651 final BufferedImage bi = getImageMap().get( uri_str );
2652 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2653 double scaling_factor = 1;
2654 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
2655 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
2656 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
2658 // y = y - ( 0.9 * getYdistance() );
2659 final double hs = bi.getHeight() * scaling_factor;
2660 double ws = ( bi.getWidth() * scaling_factor ) + offset;
2661 final double my_y = y - ( 0.5 * hs );
2662 final int x_w = ( int ) ( x + ws + 0.5 );
2663 final int y_h = ( int ) ( my_y + hs + 0.5 );
2664 if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
2666 ( int ) ( x + 0.5 + offset ),
2667 ( int ) ( my_y + 0.5 ),
2688 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
2689 JOptionPane.showMessageDialog( this,
2690 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
2691 "Attempt to cut/copy/paste/add/delete in unrooted display",
2692 JOptionPane.ERROR_MESSAGE );
2695 final private Set<Integer> getCopiedAndPastedNodes() {
2696 return getMainPanel().getCopiedAndPastedNodes();
2699 final private Set<Integer> getCurrentExternalNodes() {
2700 return _current_external_nodes;
2703 final private Phylogeny getCutOrCopiedTree() {
2704 return getMainPanel().getCutOrCopiedTree();
2707 final private float getLastDragPointX() {
2708 return _last_drag_point_x;
2711 final private float getLastDragPointY() {
2712 return _last_drag_point_y;
2715 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
2716 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
2717 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
2718 _nodeid_dist_to_leaf.put( node.getId(), m );
2722 return _nodeid_dist_to_leaf.get( node.getId() );
2726 final private double getMaxDistanceToRoot() {
2727 if ( _max_distance_to_root < 0 ) {
2728 recalculateMaxDistanceToRoot();
2730 return _max_distance_to_root;
2733 final private float getOvMaxHeight() {
2734 return _ov_max_height;
2737 final private float getOvMaxWidth() {
2738 return _ov_max_width;
2741 final private float getOvXcorrectionFactor() {
2742 return _ov_x_correction_factor;
2745 final private float getOvXDistance() {
2746 return _ov_x_distance;
2749 final private int getOvXPosition() {
2750 return _ov_x_position;
2753 final private float getOvYDistance() {
2754 return _ov_y_distance;
2757 final private int getOvYPosition() {
2758 return _ov_y_position;
2761 final private int getOvYStart() {
2765 final private double getScaleDistance() {
2766 return _scale_distance;
2769 final private String getScaleLabel() {
2770 return _scale_label;
2773 final private TreeFontSet getTreeFontSet() {
2774 return getMainPanel().getTreeFontSet();
2777 final private float getUrtFactor() {
2781 final private float getUrtFactorOv() {
2782 return _urt_factor_ov;
2785 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
2788 showNodeFrame( node );
2803 colorSubtree( node );
2818 copySubtree( node );
2821 pasteSubtree( node );
2823 case DELETE_NODE_OR_SUBTREE:
2824 deleteNodeOrSubtree( node );
2827 addEmptyNode( node );
2829 case EDIT_NODE_DATA:
2830 showNodeEditFrame( node );
2835 case SORT_DESCENDENTS:
2836 sortDescendants( node );
2838 case GET_EXT_DESC_DATA:
2839 showExtDescNodeData( node );
2842 throw new IllegalArgumentException( "unknown action: " + action );
2846 final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
2847 _current_external_nodes_data_buffer_change_counter++;
2850 final private void increaseOvSize() {
2851 if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
2852 && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
2853 .getHeight() / 2 ) ) ) {
2854 setOvMaxWidth( getOvMaxWidth() + 5 );
2855 setOvMaxHeight( getOvMaxHeight() + 5 );
2857 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2861 final private void init() {
2862 _color_chooser = new JColorChooser();
2863 _rollover_popup = new JTextArea();
2864 _rollover_popup.setFont( POPUP_FONT );
2865 resetNodeIdToDistToLeafMap();
2867 setTreeFile( null );
2869 initializeOvSettings();
2870 setStartingAngle( ( TWO_PI * 3 ) / 4 );
2871 final ImageLoader il = new ImageLoader( this );
2872 new Thread( il ).start();
2875 final private void initializeOvSettings() {
2876 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
2877 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
2880 final private boolean inOvVirtualRectangle( final int x, final int y ) {
2881 return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
2882 && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
2883 && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
2884 + getOvVirtualRectangle().height + 1 ) ) );
2887 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
2888 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
2891 final private boolean isCanBlast( final PhylogenyNode node ) {
2892 if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
2895 return Blast.isContainsQueryForBlast( node );
2898 final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
2899 if ( node.getNodeData().isHasSequence()
2900 && ( node.getNodeData().getSequence().getAccession() != null )
2901 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
2902 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
2903 && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
2904 .toLowerCase() ) ) {
2910 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
2911 if ( node.getNodeData().isHasTaxonomy()
2912 && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
2913 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
2914 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
2915 .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
2916 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
2917 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
2918 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
2919 .getNodeData().getTaxonomy().getIdentifier() != null )
2920 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
2921 .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
2929 final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
2930 return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
2933 final private boolean isInFoundNodes( final PhylogenyNode node ) {
2934 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
2937 final private boolean isInOv() {
2941 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
2943 if ( getControlPanel().isShowTaxonomyImages() ) {
2944 y_dist = 40 + ( int ) getYdistance();
2946 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
2947 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
2948 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
2951 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
2952 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
2953 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
2954 || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
2955 .getMaxX() + 20 ) ) );
2958 final private boolean isNonLinedUpCladogram() {
2959 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
2962 final private boolean isUniformBranchLengthsForCladogram() {
2963 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
2966 final private void keyPressedCalls( final KeyEvent e ) {
2967 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
2968 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
2969 if ( !isInOvRect() ) {
2970 setInOvRect( true );
2973 else if ( isInOvRect() ) {
2974 setInOvRect( false );
2977 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
2978 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2979 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2980 getMainPanel().getTreeFontSet().mediumFonts();
2981 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2983 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
2984 getMainPanel().getTreeFontSet().decreaseFontSize( 1 );
2985 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2987 else if ( plusPressed( e.getKeyCode() ) ) {
2988 getMainPanel().getTreeFontSet().increaseFontSize();
2989 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2993 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2994 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2995 getControlPanel().showWhole();
2997 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
2998 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
2999 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
3000 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
3001 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3002 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3004 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3005 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3006 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3008 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3009 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3010 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3011 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3013 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3014 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3015 Constants.WHEEL_ZOOM_IN_FACTOR );
3016 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3023 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3026 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3030 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3034 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
3035 scroll_position.x = scroll_position.x + dx;
3036 scroll_position.y = scroll_position.y + dy;
3037 if ( scroll_position.x <= 0 ) {
3038 scroll_position.x = 0;
3041 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
3042 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
3043 if ( scroll_position.x >= max_x ) {
3044 scroll_position.x = max_x;
3047 if ( scroll_position.y <= 0 ) {
3048 scroll_position.y = 0;
3051 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
3052 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
3053 if ( scroll_position.y >= max_y ) {
3054 scroll_position.y = max_y;
3058 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
3061 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3062 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3063 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3064 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3065 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3067 else if ( plusPressed( e.getKeyCode() ) ) {
3068 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3069 Constants.WHEEL_ZOOM_IN_FACTOR );
3070 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3071 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3073 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
3074 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3075 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3076 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
3077 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3080 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
3081 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3082 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3083 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
3084 if ( getStartingAngle() < 0 ) {
3085 setStartingAngle( TWO_PI + getStartingAngle() );
3087 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3090 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
3091 boolean selected = false;
3092 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
3093 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
3097 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
3099 if ( getMainPanel().getMainFrame() == null ) {
3100 // Must be "E" applet version.
3101 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
3102 if ( ae.getlabelDirectionCbmi() != null ) {
3103 ae.getlabelDirectionCbmi().setSelected( selected );
3107 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
3111 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
3112 switchDisplaygetPhylogenyGraphicsType();
3115 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
3119 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
3120 MainFrame.cycleOverview( getOptions(), this );
3123 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
3126 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
3133 final private void makePopupMenus( final PhylogenyNode node ) {
3134 _node_popup_menu = new JPopupMenu();
3135 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
3136 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
3137 for( int i = 0; i < clickto_names.size(); i++ ) {
3138 final String title = clickto_names.get( i );
3139 _node_popup_menu_items[ i ] = new JMenuItem( title );
3140 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
3141 _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
3143 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
3144 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
3146 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
3147 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
3149 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
3150 if ( !getOptions().isEditable() ) {
3153 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
3155 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
3156 if ( !getOptions().isEditable() ) {
3159 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
3161 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
3162 if ( !getOptions().isEditable() ) {
3165 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
3167 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
3168 if ( !getOptions().isEditable() ) {
3171 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
3173 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
3174 if ( !getOptions().isEditable() ) {
3178 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
3179 if ( !getOptions().isEditable() ) {
3183 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
3184 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
3186 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
3187 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
3189 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
3190 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
3192 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
3193 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
3195 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
3196 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
3198 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
3199 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
3201 _node_popup_menu_items[ i ].addActionListener( this );
3202 _node_popup_menu.add( _node_popup_menu_items[ i ] );
3206 private final String obtainTitleForExtDescNodeData() {
3207 switch ( getOptions().getExtDescNodeDataToReturn() ) {
3209 return "Node Names";
3211 return "Sequence Names";
3212 case SEQUENCE_SYMBOL:
3213 return "Sequence Symbols";
3214 case SEQUENCE_MOL_SEQ:
3215 return "Molecular Sequences";
3217 return "Sequence Accessors";
3218 case TAXONOMY_SCIENTIFIC_NAME:
3219 return "Scientific Names";
3221 return "Taxonomy Codes";
3223 return "User Selected Data";
3225 throw new IllegalArgumentException( "unknown data element: "
3226 + getOptions().getExtDescNodeDataToReturn() );
3230 final private void openSeqWeb( final PhylogenyNode node ) {
3231 if ( !isCanOpenSeqWeb( node ) ) {
3232 cannotOpenBrowserWarningMessage( "sequence" );
3235 String uri_str = null;
3236 final Sequence seq = node.getNodeData().getSequence();
3237 final String source = seq.getAccession().getSource().toLowerCase();
3239 if ( source.toLowerCase().equals( "ncbi" ) ) {
3240 url = Constants.NCBI_ALL_DATABASE_SEARCH;
3243 final WebLink weblink = getConfiguration().getWebLink( source );
3244 url = weblink.getUrl().toString();
3247 uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
3249 catch ( final UnsupportedEncodingException e ) {
3250 AptxUtil.showErrorMessage( this, e.toString() );
3251 e.printStackTrace();
3253 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3255 JApplet applet = null;
3257 applet = obtainApplet();
3259 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
3261 catch ( final IOException e ) {
3262 AptxUtil.showErrorMessage( this, e.toString() );
3263 e.printStackTrace();
3265 catch ( final URISyntaxException e ) {
3266 AptxUtil.showErrorMessage( this, e.toString() );
3267 e.printStackTrace();
3271 cannotOpenBrowserWarningMessage( "sequence" );
3275 final private void openTaxWeb( final PhylogenyNode node ) {
3276 if ( !isCanOpenTaxWeb( node ) ) {
3277 cannotOpenBrowserWarningMessage( "taxonomic" );
3280 String uri_str = null;
3281 final Taxonomy tax = node.getNodeData().getTaxonomy();
3282 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
3283 && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
3284 final String type = tax.getIdentifier().getProvider().toLowerCase();
3285 final WebLink weblink = getConfiguration().getWebLink( type );
3287 uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
3289 catch ( final UnsupportedEncodingException e ) {
3290 AptxUtil.showErrorMessage( this, e.toString() );
3291 e.printStackTrace();
3294 else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3295 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
3297 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
3299 catch ( final URISyntaxException e ) {
3300 AptxUtil.showErrorMessage( this, e.toString() );
3302 e.printStackTrace();
3305 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
3307 uri_str = "http://www.eol.org/search?q="
3308 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
3310 catch ( final UnsupportedEncodingException e ) {
3311 AptxUtil.showErrorMessage( this, e.toString() );
3312 e.printStackTrace();
3315 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
3317 uri_str = "http://www.uniprot.org/taxonomy/?query="
3318 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
3320 catch ( final UnsupportedEncodingException e ) {
3321 AptxUtil.showErrorMessage( this, e.toString() );
3322 e.printStackTrace();
3325 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
3327 uri_str = "http://www.eol.org/search?q="
3328 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
3330 catch ( final UnsupportedEncodingException e ) {
3331 AptxUtil.showErrorMessage( this, e.toString() );
3332 e.printStackTrace();
3335 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3337 JApplet applet = null;
3339 applet = obtainApplet();
3341 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
3343 catch ( final IOException e ) {
3344 AptxUtil.showErrorMessage( this, e.toString() );
3345 e.printStackTrace();
3347 catch ( final URISyntaxException e ) {
3348 AptxUtil.showErrorMessage( this, e.toString() );
3349 e.printStackTrace();
3353 cannotOpenBrowserWarningMessage( "taxonomic" );
3357 final private void paintBranchLength( final Graphics2D g,
3358 final PhylogenyNode node,
3359 final boolean to_pdf,
3360 final boolean to_graphics_file ) {
3361 g.setFont( getTreeFontSet().getSmallFont() );
3362 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3363 g.setColor( Color.BLACK );
3366 g.setColor( getTreeColorSet().getBranchLengthColor() );
3368 if ( !node.isRoot() ) {
3369 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3370 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3371 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3373 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3374 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3375 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3378 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3379 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3383 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
3384 - getTreeFontSet()._small_max_descent, g );
3388 final private void paintBranchLite( final Graphics2D g,
3393 final PhylogenyNode node ) {
3394 g.setColor( getTreeColorSet().getOvColor() );
3395 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3396 drawLine( x1, y1, x2, y2, g );
3398 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3399 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3400 ( g ).draw( _quad_curve );
3402 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3403 final float dx = x2 - x1;
3404 final float dy = y2 - y1;
3405 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3406 + ( dy * 0.8f ), x2, y2 );
3407 ( g ).draw( _cubic_curve );
3410 final float x2a = x2;
3411 final float x1a = x1;
3412 // draw the vertical line
3413 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
3414 drawLine( x1, y1, x1, y2, g );
3416 // draw the horizontal line
3417 drawLine( x1a, y2, x2a, y2, g );
3422 * Paint a branch which consists of a vertical and a horizontal bar
3423 * @param is_ind_found_nodes
3425 final private void paintBranchRectangular( final Graphics2D g,
3430 final PhylogenyNode node,
3431 final boolean to_pdf,
3432 final boolean to_graphics_file ) {
3433 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
3434 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3435 drawLine( x1, y1, x2, y2, g );
3437 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3438 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3439 g.draw( _quad_curve );
3441 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3442 final float dx = x2 - x1;
3443 final float dy = y2 - y1;
3444 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3445 + ( dy * 0.8f ), x2, y2 );
3446 g.draw( _cubic_curve );
3449 final float x2a = x2;
3450 final float x1a = x1;
3452 if ( node.isFirstChildNode() || node.isLastChildNode()
3453 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3454 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3455 if ( !to_graphics_file
3457 && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
3458 .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
3462 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3463 float x2c = x1 + EURO_D;
3467 drawLine( x1, y1, x2c, y2, g );
3469 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3471 y2_r = y2 - ROUNDED_D;
3475 drawLine( x1, y1, x1, y2_r, g );
3478 y2_r = y2 + ROUNDED_D;
3482 drawLine( x1, y1, x1, y2_r, g );
3486 drawLine( x1, y1, x1, y2, g );
3490 // draw the horizontal line
3491 if ( !to_graphics_file && !to_pdf
3492 && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
3496 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
3497 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3498 x1_r = x1a + ROUNDED_D;
3500 drawLine( x1_r, y2, x2a, y2, g );
3503 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3504 final float x1c = x1a + EURO_D;
3506 drawLine( x1c, y2, x2a, y2, g );
3510 drawLine( x1a, y2, x2a, y2, g );
3514 final double w = PhylogenyMethods.getBranchWidthValue( node );
3515 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3516 x1_r = x1a + ROUNDED_D;
3518 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
3521 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3522 final float x1c = x1a + EURO_D;
3524 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
3528 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
3531 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3536 final double diff = y2 - y2_r;
3537 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
3540 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
3545 if ( node.isExternal() ) {
3546 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
3547 || isInCurrentExternalNodes( node ) );
3551 final private double paintCirculars( final PhylogenyNode n,
3552 final Phylogeny phy,
3553 final float center_x,
3554 final float center_y,
3555 final double radius,
3556 final boolean radial_labels,
3558 final boolean to_pdf,
3559 final boolean to_graphics_file ) {
3560 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
3561 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
3562 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
3564 return _urt_nodeid_angle_map.get( n.getId() );
3567 final List<PhylogenyNode> descs = n.getDescendants();
3569 for( final PhylogenyNode desc : descs ) {
3570 sum += paintCirculars( desc,
3581 if ( !n.isRoot() ) {
3582 r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3584 final double theta = sum / descs.size();
3585 n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
3586 n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
3587 _urt_nodeid_angle_map.put( n.getId(), theta );
3588 for( final PhylogenyNode desc : descs ) {
3589 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
3595 final private void paintCircularsLite( final PhylogenyNode n,
3596 final Phylogeny phy,
3600 final Graphics2D g ) {
3601 if ( n.isExternal() ) {
3605 final List<PhylogenyNode> descs = n.getDescendants();
3606 for( final PhylogenyNode desc : descs ) {
3607 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
3610 if ( !n.isRoot() ) {
3611 r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3613 final double theta = _urt_nodeid_angle_map.get( n.getId() );
3614 n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
3615 n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
3616 for( final PhylogenyNode desc : descs ) {
3617 paintBranchCircularLite( n, desc, g );
3622 final private void paintCollapsedNode( final Graphics2D g,
3623 final PhylogenyNode node,
3624 final boolean to_graphics_file,
3625 final boolean to_pdf,
3626 final boolean is_in_found_nodes ) {
3628 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3631 else if ( is_in_found_nodes ) {
3632 c = getTreeColorSet().getFoundColor();
3634 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3635 c = getTaxonomyBasedColor( node );
3637 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3638 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3639 c = PhylogenyMethods.getBranchColorValue( node );
3642 c = getTreeColorSet().getCollapseFillColor();
3644 double d = node.getAllExternalDescendants().size();
3646 d = ( 3 * _y_distance ) / 3;
3649 d = ( Math.log10( d ) * _y_distance ) / 2.5;
3651 final int box_size = getOptions().getDefaultNodeShapeSize();
3652 if ( d < box_size ) {
3656 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
3657 ForesterUtil.roundToInt( node.getYcoord() ) );
3658 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
3659 ForesterUtil.roundToInt( node.getYcoord() - d ) );
3660 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
3661 ForesterUtil.roundToInt( node.getYcoord() + d ) );
3662 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3664 g.fillPolygon( _polygon );
3666 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3667 g.setColor( getBackground() );
3668 g.fillPolygon( _polygon );
3670 g.drawPolygon( _polygon );
3672 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3673 g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
3674 .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
3679 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3682 final private void paintConfidenceValues( final Graphics2D g,
3683 final PhylogenyNode node,
3684 final boolean to_pdf,
3685 final boolean to_graphics_file ) {
3686 final List<Confidence> confidences = node.getBranchData().getConfidences();
3687 // if ( confidences.size() == 1 ) {
3688 // final double value = node.getBranchData().getConfidence( 0 ).getValue();
3689 // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
3692 // conf_str = FORMATTER_CONFIDENCE.format( value );
3694 // else if ( confidences.size() > 1 ) {
3695 boolean one_ok = false;
3696 boolean not_first = false;
3697 Collections.sort( confidences );
3698 final StringBuilder sb = new StringBuilder();
3699 String conf_str = "";
3700 for( final Confidence confidence : confidences ) {
3701 final double value = confidence.getValue();
3702 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3703 if ( value >= getOptions().getMinConfidenceValue() ) {
3712 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
3713 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3714 if ( getOptions().isShowConfidenceStddev() ) {
3715 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3717 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
3719 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3726 conf_str = sb.toString();
3729 if ( conf_str.length() > 0 ) {
3730 final double parent_x = node.getParent().getXcoord();
3731 double x = node.getXcoord();
3732 g.setFont( getTreeFontSet().getSmallFont() );
3733 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3736 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3739 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3740 g.setColor( Color.BLACK );
3743 g.setColor( getTreeColorSet().getConfidenceColor() );
3746 .drawString( conf_str,
3748 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
3749 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
3754 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
3755 final int box_size = getOptions().getDefaultNodeShapeSize();
3756 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3757 g.setColor( getTreeColorSet().getFoundColor() );
3758 g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
3761 final private void paintGainedAndLostCharacters( final Graphics2D g,
3762 final PhylogenyNode node,
3763 final String gained,
3764 final String lost ) {
3765 if ( node.getParent() != null ) {
3766 final double parent_x = node.getParent().getXcoord();
3767 final double x = node.getXcoord();
3768 g.setFont( getTreeFontSet().getLargeFont() );
3769 g.setColor( getTreeColorSet().getGainedCharactersColor() );
3770 if ( Constants.SPECIAL_CUSTOM ) {
3771 g.setColor( Color.BLUE );
3774 .drawString( gained,
3775 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
3776 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
3778 g.setColor( getTreeColorSet().getLostCharactersColor() );
3779 TreePanel.drawString( lost,
3780 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
3781 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
3787 * Draw a box at the indicated node.
3794 final private void paintNodeBox( final double x,
3796 final PhylogenyNode node,
3798 final boolean to_pdf,
3799 final boolean to_graphics_file,
3800 final boolean is_in_found_nodes ) {
3801 if ( node.isCollapse() ) {
3804 // if this node should be highlighted, do so
3805 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
3806 g.setColor( getTreeColorSet().getFoundColor() );
3807 drawOval( x - 8, y - 8, 16, 16, g );
3808 drawOval( x - 9, y - 8, 17, 17, g );
3809 drawOval( x - 9, y - 9, 18, 18, g );
3811 if ( is_in_found_nodes ) {
3812 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
3815 Color outline_color = null;
3816 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3817 outline_color = Color.BLACK;
3819 else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
3820 final Event event = node.getNodeData().getEvent();
3821 if ( event.isDuplication() ) {
3822 outline_color = getTreeColorSet().getDuplicationBoxColor();
3824 else if ( event.isSpeciation() ) {
3825 outline_color = getTreeColorSet().getSpecBoxColor();
3827 else if ( event.isSpeciationOrDuplication() ) {
3828 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
3831 else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
3832 outline_color = getTaxonomyBasedColor( node );
3835 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
3836 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
3837 outline_color = getTreeColorSet().getBranchColorForPdf();
3840 final int box_size = getOptions().getDefaultNodeShapeSize();
3841 final int half_box_size = box_size / 2;
3842 if ( ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
3843 || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
3844 || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
3845 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
3846 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3847 drawOvalGradient( x - half_box_size,
3852 to_pdf ? Color.WHITE : outline_color,
3853 to_pdf ? outline_color : getBackground(),
3856 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
3857 Color background = getBackground();
3859 background = Color.WHITE;
3861 drawOvalGradient( x - half_box_size,
3870 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3871 g.setColor( outline_color );
3872 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3875 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
3876 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
3877 drawRectGradient( x - half_box_size,
3882 to_pdf ? Color.WHITE : outline_color,
3883 to_pdf ? outline_color : getBackground(),
3886 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3887 Color background = getBackground();
3889 background = Color.WHITE;
3891 drawRectGradient( x - half_box_size,
3900 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3901 g.setColor( outline_color );
3902 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3909 final private void paintNodeData( final Graphics2D g,
3910 final PhylogenyNode node,
3911 final boolean to_graphics_file,
3912 final boolean to_pdf,
3913 final boolean is_in_found_nodes ) {
3914 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
3917 if ( getOptions().isShowBranchLengthValues()
3918 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3919 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3920 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
3921 paintBranchLength( g, node, to_pdf, to_graphics_file );
3923 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
3927 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3928 if ( getControlPanel().isShowTaxonomyImages()
3929 && ( getImageMap() != null )
3930 && !getImageMap().isEmpty()
3931 && node.getNodeData().isHasTaxonomy()
3932 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
3933 .getUris().isEmpty() ) ) {
3934 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
3936 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3937 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
3938 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
3940 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3941 g.setColor( Color.BLACK );
3943 else if ( is_in_found_nodes ) {
3944 g.setColor( getTreeColorSet().getFoundColor() );
3946 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3947 g.setColor( getTaxonomyBasedColor( node ) );
3949 else if ( getControlPanel().isColorAccordingToAnnotation()
3950 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
3951 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
3952 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
3954 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3955 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3956 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3958 else if ( to_pdf ) {
3959 g.setColor( Color.BLACK );
3962 g.setColor( getTreeColorSet().getSequenceColor() );
3965 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3967 _sb.append( node.getAllExternalDescendants().size() );
3970 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3971 if ( _sb.length() > 0 ) {
3974 _sb.append( node.getName() );
3976 if ( node.getNodeData().isHasSequence() ) {
3977 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
3978 if ( _sb.length() > 0 ) {
3981 _sb.append( node.getNodeData().getSequence().getSymbol() );
3983 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3984 if ( _sb.length() > 0 ) {
3987 _sb.append( node.getNodeData().getSequence().getName() );
3989 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3990 if ( _sb.length() > 0 ) {
3993 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3994 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3997 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4000 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
4001 if ( _sb.length() > 0 ) {
4004 _sb.append( propertiesToString( node ) );
4006 g.setFont( getTreeFontSet().getLargeFont() );
4007 if ( is_in_found_nodes ) {
4008 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4010 double down_shift_factor = 3.0;
4011 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
4012 down_shift_factor = 1;
4014 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
4015 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
4016 final String sb_str = _sb.toString();
4017 // GUILHEM_BEG ______________
4018 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
4019 && ( _query_sequence != null ) ) {
4020 int nodeTextBoundsWidth = 0;
4021 if ( sb_str.length() > 0 ) {
4022 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
4023 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
4025 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
4026 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
4027 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
4028 g.setColor( getTreeColorSet().getBackgroundColor() );
4032 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
4033 for( final SequenceRelation seqRelation : seqRelations ) {
4034 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
4035 .getRef1().isEqual( _query_sequence ) )
4036 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
4037 .getSelectedItem() );
4038 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
4039 final double linePosX = node.getXcoord() + 2 + half_box_size;
4040 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
4041 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
4043 if ( sConfidence != null ) {
4044 double confidenceX = pos_x;
4045 if ( sb_str.length() > 0 ) {
4046 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
4047 + CONFIDENCE_LEFT_MARGIN;
4049 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
4050 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
4051 .getBounds().getWidth();
4052 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
4053 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
4056 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
4058 if ( nodeTextBoundsWidth == 0 ) {
4059 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
4062 nodeTextBoundsWidth += 2;
4064 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
4065 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
4072 if ( sb_str.length() > 0 ) {
4073 TreePanel.drawString( sb_str, pos_x, pos_y, g );
4075 // GUILHEM_END _____________
4076 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
4077 // TODO FIXME need to check this one!
4078 //if ( _sb.length() > 0 ) {
4079 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
4080 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4082 // COMMENTED_OUT_BY_GUILHEM_END ________________
4083 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
4084 && ( node.getNodeData().getSequence().getAnnotations() != null )
4085 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4086 if ( _sb.length() > 0 ) {
4087 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4089 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
4090 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4091 g.setColor( Color.BLACK );
4093 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
4094 g.setColor( calculateColorForAnnotation( ann ) );
4096 final String ann_str = createAnnotationString( ann );
4097 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
4098 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4100 _sb.append( ann_str );
4102 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4103 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
4104 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
4105 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
4106 && node.getNodeData().isHasBinaryCharacters() ) {
4107 if ( _sb.length() > 0 ) {
4108 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4110 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4111 g.setColor( Color.BLACK );
4114 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
4116 if ( getControlPanel().isShowBinaryCharacters() ) {
4117 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
4118 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
4119 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4120 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
4121 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
4122 .getLostCharactersAsStringBuffer().toString() );
4125 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
4126 node.getXcoord() + x + 4 + half_box_size,
4128 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
4130 paintGainedAndLostCharacters( g, node, "+"
4131 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
4132 + node.getNodeData().getBinaryCharacters().getLostCount() );
4138 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
4139 final PhylogenyNode node,
4140 final boolean to_pdf,
4141 final boolean to_graphics_file,
4142 final boolean radial_labels,
4143 final double ur_angle,
4144 final boolean is_in_found_nodes ) {
4145 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
4148 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4149 g.setColor( Color.BLACK );
4151 else if ( is_in_found_nodes ) {
4152 g.setColor( getTreeColorSet().getFoundColor() );
4154 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4155 g.setColor( getTaxonomyBasedColor( node ) );
4157 else if ( getControlPanel().isColorAccordingToAnnotation()
4158 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4159 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4160 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4163 g.setColor( getTreeColorSet().getSequenceColor() );
4167 if ( node.getNodeData().isHasTaxonomy()
4168 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4169 .isShowTaxonomyCommonNames() ) ) {
4170 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4171 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4172 _sb.append( taxonomy.getTaxonomyCode() );
4175 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4176 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4177 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4178 _sb.append( taxonomy.getScientificName() );
4180 _sb.append( taxonomy.getCommonName() );
4183 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4184 _sb.append( taxonomy.getScientificName() );
4187 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4188 _sb.append( taxonomy.getCommonName() );
4192 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4193 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4194 _sb.append( taxonomy.getScientificName() );
4198 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4199 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4200 _sb.append( taxonomy.getCommonName() );
4205 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4207 _sb.append( node.getAllExternalDescendants().size() );
4210 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4211 if ( _sb.length() > 0 ) {
4214 _sb.append( node.getName() );
4216 if ( node.getNodeData().isHasSequence() ) {
4217 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4218 if ( _sb.length() > 0 ) {
4221 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4222 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4225 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4227 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4228 if ( _sb.length() > 0 ) {
4231 _sb.append( node.getNodeData().getSequence().getName() );
4234 g.setFont( getTreeFontSet().getLargeFont() );
4235 if ( is_in_found_nodes ) {
4236 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4238 if ( _sb.length() > 1 ) {
4239 final String sb_str = _sb.toString();
4241 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4242 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
4245 m = ( float ) ( ur_angle % TWO_PI );
4247 _at = g.getTransform();
4248 boolean need_to_reset = false;
4249 final float x_coord = node.getXcoord();
4250 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
4251 if ( radial_labels ) {
4252 need_to_reset = true;
4253 boolean left = false;
4254 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4258 g.rotate( m, x_coord, node.getYcoord() );
4260 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
4264 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4265 need_to_reset = true;
4266 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
4269 TreePanel.drawString( sb_str, x_coord, y_coord, g );
4270 if ( need_to_reset ) {
4271 g.setTransform( _at );
4276 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
4277 if ( node.isCollapse() ) {
4278 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
4279 paintCollapsedNode( g, node, false, false, false );
4283 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4284 g.setColor( getTreeColorSet().getFoundColor() );
4285 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
4288 if ( !node.isExternal() && !node.isCollapse() ) {
4289 boolean first_child = true;
4291 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4292 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4293 final PhylogenyNode child_node = node.getChildNode( i );
4295 if ( !isUniformBranchLengthsForCladogram() ) {
4296 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4299 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4301 if ( first_child ) {
4302 first_child = false;
4303 y2 = node.getYSecondary()
4304 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
4305 .getNumberOfExternalNodes() ) );
4308 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4310 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
4311 new_x = x2 + node.getXSecondary();
4312 final float diff_y = node.getYSecondary() - y2;
4313 final float diff_x = node.getXSecondary() - new_x;
4314 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
4315 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
4317 child_node.setXSecondary( new_x );
4318 child_node.setYSecondary( y2 );
4319 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4324 final private void paintNodeRectangular( final Graphics2D g,
4325 final PhylogenyNode node,
4326 final boolean to_pdf,
4327 final boolean dynamically_hide,
4328 final int dynamic_hiding_factor,
4329 final boolean to_graphics_file ) {
4330 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
4331 if ( node.isCollapse() ) {
4332 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
4333 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4337 if ( node.isExternal() ) {
4338 ++_external_node_index;
4340 // Confidence values
4341 if ( getControlPanel().isShowConfidenceValues()
4342 && !node.isExternal()
4344 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
4345 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4346 && node.getBranchData().isHasConfidences() ) {
4347 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
4349 // Draw a line to root:
4350 if ( node.isRoot() && _phylogeny.isRooted() ) {
4351 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
4354 float new_x_min = Float.MAX_VALUE;
4355 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
4356 float min_dist = 1.5f;
4357 if ( !disallow_shortcutting ) {
4358 // System.out.println( dynamic_hiding_factor );
4359 if ( dynamic_hiding_factor > 4000 ) {
4362 else if ( dynamic_hiding_factor > 1000 ) {
4365 else if ( dynamic_hiding_factor > 100 ) {
4369 if ( !node.isExternal() && !node.isCollapse() ) {
4370 boolean first_child = true;
4372 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4373 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4374 final PhylogenyNode child_node = node.getChildNode( i );
4376 if ( !isUniformBranchLengthsForCladogram() ) {
4377 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4380 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4382 if ( first_child ) {
4383 first_child = false;
4384 y2 = node.getYcoord()
4385 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
4388 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4390 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
4391 new_x = x2 + node.getXcoord();
4392 if ( dynamically_hide && ( x2 < new_x_min ) ) {
4395 final float diff_y = node.getYcoord() - y2;
4396 final float diff_x = node.getXcoord() - new_x;
4397 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
4398 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
4399 paintBranchRectangular( g,
4408 child_node.setXcoord( new_x );
4409 child_node.setYcoord( y2 );
4410 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4412 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
4413 || isInCurrentExternalNodes( node ) );
4415 if ( dynamically_hide
4416 && !is_in_found_nodes
4417 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
4418 .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
4419 .getHeight() ) ) ) ) ) {
4422 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4423 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
4426 final private void paintNodeWithRenderableData( final Graphics2D g,
4427 final PhylogenyNode node,
4428 final boolean to_graphics_file,
4429 final boolean to_pdf ) {
4430 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
4433 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
4436 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4437 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4438 RenderableDomainArchitecture rds = null;
4439 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
4441 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
4443 catch ( final ClassCastException cce ) {
4444 cce.printStackTrace();
4446 if ( rds != null ) {
4447 rds.setRenderingHeight( 6 );
4449 if ( node.getNodeData().isHasTaxonomy() ) {
4450 if ( getControlPanel().isShowTaxonomyCode()
4451 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
4452 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4456 if ( getControlPanel().isShowTaxonomyScientificNames()
4457 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
4458 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4459 .getScientificName()
4462 if ( getControlPanel().isShowTaxonomyCommonNames()
4463 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
4464 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4469 if ( node.getNodeData().isHasSequence() ) {
4470 if ( getControlPanel().isShowGeneNames()
4471 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
4472 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
4475 if ( getControlPanel().isShowGeneSymbols()
4476 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
4477 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
4480 if ( getControlPanel().isShowSequenceAcc()
4481 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4482 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
4483 .getAccession().toString()
4487 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
4488 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
4490 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
4495 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4496 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
4497 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
4498 getStatisticsForExpressionValues(),
4499 getConfiguration() );
4502 PhylogenyNode my_node = node;
4503 if ( !getControlPanel().isDrawPhylogram() ) {
4504 my_node = getPhylogeny().getFirstExternalNode();
4506 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
4507 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
4509 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
4510 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
4512 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
4518 final private void paintOvRectangle( final Graphics2D g ) {
4519 final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
4520 final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
4521 final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
4522 final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
4523 final float width = getOvMaxWidth() / w_ratio;
4524 final float height = getOvMaxHeight() / h_ratio;
4525 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
4526 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
4527 g.setColor( getTreeColorSet().getFoundColor() );
4528 getOvRectangle().setRect( x, y, width, height );
4529 if ( ( width < 6 ) && ( height < 6 ) ) {
4530 drawRectFilled( x, y, 6, 6, g );
4531 getOvVirtualRectangle().setRect( x, y, 6, 6 );
4533 else if ( width < 6 ) {
4534 drawRectFilled( x, y, 6, height, g );
4535 getOvVirtualRectangle().setRect( x, y, 6, height );
4537 else if ( height < 6 ) {
4538 drawRectFilled( x, y, width, 6, g );
4539 getOvVirtualRectangle().setRect( x, y, width, 6 );
4542 drawRect( x, y, width, height, g );
4543 if ( isInOvRect() ) {
4544 drawRect( x + 1, y + 1, width - 2, height - 2, g );
4546 getOvVirtualRectangle().setRect( x, y, width, height );
4550 final private void paintPhylogenyLite( final Graphics2D g ) {
4553 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
4554 .getWidth() ) ) ) );
4555 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
4556 for( final PhylogenyNode element : _nodes_in_preorder ) {
4557 paintNodeLite( g, element );
4559 paintOvRectangle( g );
4563 * Paint the root branch. (Differs from others because it will always be a
4564 * single horizontal line).
4565 * @param to_graphics_file
4567 * @return new x1 value
4569 final private void paintRootBranch( final Graphics2D g,
4572 final PhylogenyNode root,
4573 final boolean to_pdf,
4574 final boolean to_graphics_file ) {
4575 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
4576 float d = getXdistance();
4577 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
4578 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
4580 if ( d < MIN_ROOT_LENGTH ) {
4581 d = MIN_ROOT_LENGTH;
4583 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
4584 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
4587 final double w = PhylogenyMethods.getBranchWidthValue( root );
4588 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
4590 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
4593 final private void paintScale( final Graphics2D g,
4596 final boolean to_pdf,
4597 final boolean to_graphics_file ) {
4599 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
4601 final int y2 = y1 - 8;
4602 final int y3 = y1 - 4;
4603 g.setFont( getTreeFontSet().getSmallFont() );
4604 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4605 g.setColor( Color.BLACK );
4608 g.setColor( getTreeColorSet().getBranchLengthColor() );
4610 drawLine( x1, y1, x1, y2, g );
4611 drawLine( x2, y1, x2, y2, g );
4612 drawLine( x1, y3, x2, y3, g );
4613 if ( getScaleLabel() != null ) {
4614 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
4618 final private int paintTaxonomy( final Graphics2D g,
4619 final PhylogenyNode node,
4620 final boolean is_in_found_nodes,
4621 final boolean to_pdf,
4622 final boolean to_graphics_file,
4623 final double x_shift ) {
4624 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4625 g.setFont( getTreeFontSet().getLargeItalicFont() );
4626 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4627 g.setColor( Color.BLACK );
4629 else if ( is_in_found_nodes ) {
4630 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
4631 g.setColor( getTreeColorSet().getFoundColor() );
4633 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4634 g.setColor( getTaxonomyBasedColor( node ) );
4636 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4637 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4638 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4640 else if ( to_pdf ) {
4641 g.setColor( Color.BLACK );
4644 g.setColor( getTreeColorSet().getTaxonomyColor() );
4646 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4647 final double start_y = node.getYcoord()
4648 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4650 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4651 _sb.append( taxonomy.getTaxonomyCode() );
4654 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4655 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4656 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4657 if ( getOptions().isAbbreviateScientificTaxonNames()
4658 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4659 abbreviateScientificName( taxonomy.getScientificName() );
4662 _sb.append( taxonomy.getScientificName() );
4665 _sb.append( taxonomy.getCommonName() );
4668 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4669 if ( getOptions().isAbbreviateScientificTaxonNames()
4670 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4671 abbreviateScientificName( taxonomy.getScientificName() );
4674 _sb.append( taxonomy.getScientificName() );
4678 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4679 _sb.append( taxonomy.getCommonName() );
4683 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4684 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4685 if ( getOptions().isAbbreviateScientificTaxonNames()
4686 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4687 abbreviateScientificName( taxonomy.getScientificName() );
4690 _sb.append( taxonomy.getScientificName() );
4695 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4696 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4697 _sb.append( taxonomy.getCommonName() );
4701 final String label = _sb.toString();
4703 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4704 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4705 // invert font color and background color to show that this is the query sequence
4706 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4710 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4711 g.setColor( getTreeColorSet().getBackgroundColor() );
4714 TreePanel.drawString( label, start_x, start_y, g );
4715 if ( is_in_found_nodes ) {
4716 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4719 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4723 final private void paintUnrooted( final PhylogenyNode n,
4724 final double low_angle,
4725 final double high_angle,
4726 final boolean radial_labels,
4728 final boolean to_pdf,
4729 final boolean to_graphics_file ) {
4731 n.setXcoord( getWidth() / 2 );
4732 n.setYcoord( getHeight() / 2 );
4734 if ( n.isExternal() ) {
4735 paintNodeDataUnrootedCirc( g,
4740 ( high_angle + low_angle ) / 2,
4741 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
4744 final float num_enclosed = n.getNumberOfExternalNodes();
4745 final float x = n.getXcoord();
4746 final float y = n.getYcoord();
4747 double current_angle = low_angle;
4748 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4749 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4750 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4751 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4752 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4753 final PhylogenyNode desc = n.getChildNode( i );
4754 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4755 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4756 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4757 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4760 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4763 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4766 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4767 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4769 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4770 if ( desc.getDistanceToParent() < 0 ) {
4774 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4778 length = getUrtFactor();
4780 final double mid_angle = current_angle + ( arc_size / 2 );
4781 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4782 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4783 desc.setXcoord( new_x );
4784 desc.setYcoord( new_y );
4785 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4786 current_angle += arc_size;
4787 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4788 drawLine( x, y, new_x, new_y, g );
4789 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc )
4790 || isInCurrentExternalNodes( desc ) );
4793 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
4797 final private void paintUnrootedLite( final PhylogenyNode n,
4798 final double low_angle,
4799 final double high_angle,
4801 final float urt_ov_factor ) {
4803 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
4804 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
4805 n.setXSecondary( x_pos );
4806 n.setYSecondary( y_pos );
4808 if ( n.isExternal() ) {
4811 final float num_enclosed = n.getNumberOfExternalNodes();
4812 final float x = n.getXSecondary();
4813 final float y = n.getYSecondary();
4814 double current_angle = low_angle;
4815 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4816 final PhylogenyNode desc = n.getChildNode( i );
4817 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4818 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4820 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4821 if ( desc.getDistanceToParent() < 0 ) {
4825 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
4829 length = urt_ov_factor;
4831 final double mid_angle = current_angle + ( arc_size / 2 );
4832 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4833 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4834 desc.setXSecondary( new_x );
4835 desc.setYSecondary( new_y );
4836 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
4837 g.setColor( getTreeColorSet().getFoundColor() );
4838 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
4839 g.setColor( getTreeColorSet().getOvColor() );
4841 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4842 current_angle += arc_size;
4843 drawLine( x, y, new_x, new_y, g );
4847 final private void pasteSubtree( final PhylogenyNode node ) {
4848 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4849 errorMessageNoCutCopyPasteInUnrootedDisplay();
4852 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
4853 JOptionPane.showMessageDialog( this,
4854 "No tree in buffer (need to copy or cut a subtree first)",
4855 "Attempt to paste with empty buffer",
4856 JOptionPane.ERROR_MESSAGE );
4859 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
4860 final Object[] options = { "As sibling", "As descendant", "Cancel" };
4861 final int r = JOptionPane.showOptionDialog( this,
4862 "How to paste subtree" + label + "?",
4864 JOptionPane.CLOSED_OPTION,
4865 JOptionPane.QUESTION_MESSAGE,
4869 boolean paste_as_sibling = true;
4871 paste_as_sibling = false;
4873 else if ( r != 0 ) {
4876 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
4877 buffer_phy.setAllNodesToNotCollapse();
4878 PhylogenyMethods.preOrderReId( buffer_phy );
4879 buffer_phy.setRooted( true );
4880 boolean need_to_show_whole = false;
4881 if ( paste_as_sibling ) {
4882 if ( node.isRoot() ) {
4883 JOptionPane.showMessageDialog( this,
4884 "Cannot paste sibling to root",
4885 "Attempt to paste sibling to root",
4886 JOptionPane.ERROR_MESSAGE );
4889 buffer_phy.addAsSibling( node );
4892 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
4893 need_to_show_whole = true;
4894 _phylogeny = buffer_phy;
4897 buffer_phy.addAsChild( node );
4900 if ( getCopiedAndPastedNodes() == null ) {
4901 setCopiedAndPastedNodes( new HashSet<Integer>() );
4903 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
4904 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
4905 for( final PhylogenyNode n : nodes ) {
4906 node_ids.add( n.getId() );
4908 node_ids.add( node.getId() );
4909 getCopiedAndPastedNodes().addAll( node_ids );
4910 setNodeInPreorderToNull();
4911 _phylogeny.externalNodesHaveChanged();
4912 _phylogeny.clearHashIdToNodeMap();
4913 _phylogeny.recalculateNumberOfExternalDescendants( true );
4914 resetNodeIdToDistToLeafMap();
4916 if ( need_to_show_whole ) {
4917 getControlPanel().showWhole();
4922 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
4923 final PropertiesMap properties = node.getNodeData().getProperties();
4924 final StringBuffer sb = new StringBuffer();
4925 boolean first = true;
4926 for( final String ref : properties.getPropertyRefs() ) {
4933 final Property p = properties.getProperty( ref );
4934 sb.append( getPartAfterColon( p.getRef() ) );
4936 sb.append( p.getValue() );
4937 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
4938 sb.append( getPartAfterColon( p.getUnit() ) );
4944 final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
4945 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4948 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4949 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4952 final private void setInOv( final boolean in_ov ) {
4956 final private void setOvMaxHeight( final float ov_max_height ) {
4957 _ov_max_height = ov_max_height;
4960 final private void setOvMaxWidth( final float ov_max_width ) {
4961 _ov_max_width = ov_max_width;
4964 final private void setOvXcorrectionFactor( final float f ) {
4965 _ov_x_correction_factor = f;
4968 final private void setOvXDistance( final float ov_x_distance ) {
4969 _ov_x_distance = ov_x_distance;
4972 final private void setOvXPosition( final int ov_x_position ) {
4973 _ov_x_position = ov_x_position;
4976 final private void setOvYDistance( final float ov_y_distance ) {
4977 _ov_y_distance = ov_y_distance;
4980 final private void setOvYPosition( final int ov_y_position ) {
4981 _ov_y_position = ov_y_position;
4984 final private void setOvYStart( final int ov_y_start ) {
4985 _ov_y_start = ov_y_start;
4988 final private void setScaleDistance( final double scale_distance ) {
4989 _scale_distance = scale_distance;
4992 final private void setScaleLabel( final String scale_label ) {
4993 _scale_label = scale_label;
4996 final private void setUpUrtFactor() {
4997 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
4998 : getVisibleRect().height;
4999 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
5000 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
5003 final int max_depth = _circ_max_depth;
5004 if ( max_depth > 0 ) {
5005 setUrtFactor( d / ( 2 * max_depth ) );
5008 setUrtFactor( d / 2 );
5011 setUrtFactorOv( getUrtFactor() );
5014 final private void setUrtFactor( final float urt_factor ) {
5015 _urt_factor = urt_factor;
5018 final private void setUrtFactorOv( final float urt_factor_ov ) {
5019 _urt_factor_ov = urt_factor_ov;
5022 private void showExtDescNodeData( final PhylogenyNode node ) {
5023 final List<String> data = new ArrayList<String>();
5024 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
5025 switch ( getOptions().getExtDescNodeDataToReturn() ) {
5027 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
5028 data.add( n.getName() );
5032 if ( n.getNodeData().isHasSequence()
5033 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5034 data.add( n.getNodeData().getSequence().getName() );
5037 case SEQUENCE_SYMBOL:
5038 if ( n.getNodeData().isHasSequence()
5039 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5040 data.add( n.getNodeData().getSequence().getSymbol() );
5043 case SEQUENCE_MOL_SEQ:
5044 if ( n.getNodeData().isHasSequence()
5045 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5046 data.add( n.getNodeData().getSequence().getMolecularSequence() );
5050 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
5051 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
5052 data.add( n.getNodeData().getSequence().getAccession().toString() );
5055 case TAXONOMY_SCIENTIFIC_NAME:
5056 if ( n.getNodeData().isHasTaxonomy()
5057 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5058 data.add( n.getNodeData().getTaxonomy().getScientificName() );
5062 if ( n.getNodeData().isHasTaxonomy()
5063 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5064 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5068 AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
5071 throw new IllegalArgumentException( "unknown data element: "
5072 + getOptions().getExtDescNodeDataToReturn() );
5075 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
5076 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
5077 final StringBuilder sb = new StringBuilder();
5078 for( final String d : data ) {
5079 if ( !ForesterUtil.isEmpty( d ) ) {
5080 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
5081 System.out.println( d );
5084 sb.append( ForesterUtil.LINE_SEPARATOR );
5087 if ( sb.length() < 1 ) {
5088 clearCurrentExternalNodesDataBuffer();
5091 setCurrentExternalNodesDataBuffer( sb );
5094 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
5095 final StringBuilder sb = new StringBuilder();
5096 for( final String d : data ) {
5097 if ( !ForesterUtil.isEmpty( d ) ) {
5099 sb.append( ForesterUtil.LINE_SEPARATOR );
5102 if ( sb.length() < 1 ) {
5103 AptxUtil.showInformationMessage( this,
5104 "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
5105 "Descendants of selected node do not contain selected data" );
5106 clearCurrentExternalNodesDataBuffer();
5109 setCurrentExternalNodesDataBuffer( sb );
5110 final String title = "External Descendants "
5111 + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5112 : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
5113 + node.getNumberOfExternalNodes() + ") For Node " + node;
5114 final String s = sb.toString().trim();
5115 if ( getMainPanel().getMainFrame() == null ) {
5116 // Must be "E" applet version.
5117 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
5118 ae.showTextFrame( s, title );
5121 getMainPanel().getMainFrame().showTextFrame( s, title );
5127 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
5129 if ( ( node.getName().length() > 0 )
5130 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
5131 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
5132 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
5133 || node.getBranchData().isHasConfidences() ) {
5134 _popup_buffer.setLength( 0 );
5136 if ( node.getName().length() > 0 ) {
5138 _popup_buffer.append( node.getName() );
5140 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
5142 boolean enc_data = false;
5143 final Taxonomy tax = node.getNodeData().getTaxonomy();
5144 if ( _popup_buffer.length() > 0 ) {
5145 _popup_buffer.append( "\n" );
5147 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
5148 _popup_buffer.append( "[" );
5149 _popup_buffer.append( tax.getTaxonomyCode() );
5150 _popup_buffer.append( "]" );
5153 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
5155 _popup_buffer.append( " " );
5157 _popup_buffer.append( tax.getScientificName() );
5160 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
5162 _popup_buffer.append( " (" );
5165 _popup_buffer.append( "(" );
5167 _popup_buffer.append( tax.getCommonName() );
5168 _popup_buffer.append( ")" );
5171 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
5173 _popup_buffer.append( " (" );
5176 _popup_buffer.append( "(" );
5178 _popup_buffer.append( tax.getAuthority() );
5179 _popup_buffer.append( ")" );
5182 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
5184 _popup_buffer.append( " [" );
5187 _popup_buffer.append( "[" );
5189 _popup_buffer.append( tax.getRank() );
5190 _popup_buffer.append( "]" );
5193 if ( tax.getSynonyms().size() > 0 ) {
5195 _popup_buffer.append( " " );
5197 _popup_buffer.append( "[" );
5199 for( final String syn : tax.getSynonyms() ) {
5200 if ( !ForesterUtil.isEmpty( syn ) ) {
5202 _popup_buffer.append( syn );
5203 if ( counter < tax.getSynonyms().size() ) {
5204 _popup_buffer.append( ", " );
5209 _popup_buffer.append( "]" );
5212 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
5213 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
5214 _popup_buffer.append( "[" );
5215 _popup_buffer.append( tax.getIdentifier().getProvider() );
5216 _popup_buffer.append( "] " );
5218 _popup_buffer.append( tax.getIdentifier().getValue() );
5222 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
5224 boolean enc_data = false;
5225 if ( _popup_buffer.length() > 0 ) {
5226 _popup_buffer.append( "\n" );
5228 final Sequence seq = node.getNodeData().getSequence();
5229 if ( seq.getAccession() != null ) {
5230 _popup_buffer.append( "[" );
5231 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
5232 _popup_buffer.append( seq.getAccession().getSource() );
5233 _popup_buffer.append( ":" );
5235 _popup_buffer.append( seq.getAccession().getValue() );
5236 _popup_buffer.append( "]" );
5239 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
5241 _popup_buffer.append( " [" );
5244 _popup_buffer.append( "[" );
5246 _popup_buffer.append( seq.getSymbol() );
5247 _popup_buffer.append( "]" );
5250 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
5252 _popup_buffer.append( " " );
5254 _popup_buffer.append( seq.getName() );
5257 if ( node.getNodeData().isHasDate() ) {
5259 if ( _popup_buffer.length() > 0 ) {
5260 _popup_buffer.append( "\n" );
5262 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
5264 if ( node.getNodeData().isHasDistribution() ) {
5266 if ( _popup_buffer.length() > 0 ) {
5267 _popup_buffer.append( "\n" );
5269 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
5271 if ( node.getBranchData().isHasConfidences() ) {
5272 final List<Confidence> confs = node.getBranchData().getConfidences();
5273 for( final Confidence confidence : confs ) {
5275 if ( _popup_buffer.length() > 0 ) {
5276 _popup_buffer.append( "\n" );
5278 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
5279 _popup_buffer.append( "[" );
5280 _popup_buffer.append( confidence.getType() );
5281 _popup_buffer.append( "] " );
5284 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
5286 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5287 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5288 _popup_buffer.append( " (sd=" );
5289 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
5290 .getStandardDeviation(), getOptions()
5291 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5292 _popup_buffer.append( ")" );
5296 if ( node.getNodeData().isHasProperties() ) {
5297 final PropertiesMap properties = node.getNodeData().getProperties();
5298 for( final String ref : properties.getPropertyRefs() ) {
5299 _popup_buffer.append( "\n" );
5300 final Property p = properties.getProperty( ref );
5301 _popup_buffer.append( getPartAfterColon( p.getRef() ) );
5302 _popup_buffer.append( "=" );
5303 _popup_buffer.append( p.getValue() );
5304 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5305 _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
5309 if ( _popup_buffer.length() > 0 ) {
5310 if ( !getConfiguration().isUseNativeUI() ) {
5312 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
5313 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
5314 if ( isInFoundNodes( node ) ) {
5315 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
5317 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
5318 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
5321 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
5325 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
5327 _rollover_popup.setText( _popup_buffer.toString() );
5328 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
5330 e.getLocationOnScreen().x + 10,
5331 e.getLocationOnScreen().y
5333 _node_desc_popup.show();
5337 catch ( final Exception ex ) {
5342 final private void showNodeEditFrame( final PhylogenyNode n ) {
5343 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5344 // pop up edit box for single node
5345 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
5346 _node_frame_index++;
5349 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5353 final private void showNodeFrame( final PhylogenyNode n ) {
5354 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5355 // pop up edit box for single node
5356 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
5357 _node_frame_index++;
5360 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5364 final private void switchDisplaygetPhylogenyGraphicsType() {
5365 switch ( getPhylogenyGraphicsType() ) {
5367 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5368 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5371 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5372 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5375 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5376 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5379 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5380 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5383 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5384 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5387 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5388 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5391 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5392 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5395 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5396 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5399 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5401 if ( getControlPanel().getDynamicallyHideData() != null ) {
5402 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5403 getControlPanel().getDynamicallyHideData().setEnabled( false );
5406 getControlPanel().getDynamicallyHideData().setEnabled( true );
5409 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5410 getControlPanel().setDrawPhylogramEnabled( true );
5413 getControlPanel().setDrawPhylogramEnabled( false );
5415 if ( getMainPanel().getMainFrame() == null ) {
5416 // Must be "E" applet version.
5417 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5418 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5421 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5425 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
5426 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5429 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5430 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5433 final private static String getPartAfterColon( final String s ) {
5434 final int i = s.indexOf( ':' );
5435 if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
5438 return s.substring( i + 1, s.length() );
5441 final private static boolean isSequenceEmpty( final Sequence seq ) {
5442 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
5443 && ForesterUtil.isEmpty( seq.getSymbol() );
5446 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
5447 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
5448 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
5449 .getSynonyms().isEmpty() );
5452 final private static boolean plusPressed( final int key_code ) {
5453 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5454 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5457 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
5458 final Phylogeny new_phy = new Phylogeny();
5459 new_phy.setRooted( true );
5460 new_phy.setName( source_phy.getName() );
5461 new_phy.setDescription( source_phy.getDescription() );
5462 new_phy.setType( source_phy.getType() );
5463 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
5464 new_phy.setConfidence( source_phy.getConfidence() );
5465 new_phy.setIdentifier( source_phy.getIdentifier() );
5466 new_phy.setRoot( new_root.copyNodeDataShallow() );
5468 for( final PhylogenyNode n : new_root.getDescendants() ) {
5469 new_phy.getRoot().setChildNode( i++, n );
5474 final private class SubtreeColorizationActionListener implements ActionListener {
5476 JColorChooser _chooser;
5477 PhylogenyNode _node;
5479 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5485 public void actionPerformed( final ActionEvent e ) {
5486 final Color c = _chooser.getColor();
5488 colorizeSubtree( c, _node );