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.Rectangle;
38 import java.awt.RenderingHints;
39 import java.awt.Stroke;
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.Path2D;
58 import java.awt.geom.QuadCurve2D;
59 import java.awt.geom.Rectangle2D;
60 import java.awt.image.BufferedImage;
61 import java.awt.print.PageFormat;
62 import java.awt.print.Printable;
63 import java.awt.print.PrinterException;
65 import java.io.IOException;
66 import java.io.UnsupportedEncodingException;
68 import java.net.URISyntaxException;
69 import java.net.URLEncoder;
70 import java.text.DecimalFormat;
71 import java.text.DecimalFormatSymbols;
72 import java.text.NumberFormat;
73 import java.util.ArrayList;
74 import java.util.Collections;
75 import java.util.HashMap;
76 import java.util.HashSet;
77 import java.util.Hashtable;
78 import java.util.List;
80 import java.util.SortedSet;
82 import javax.swing.BorderFactory;
83 import javax.swing.JApplet;
84 import javax.swing.JColorChooser;
85 import javax.swing.JDialog;
86 import javax.swing.JMenuItem;
87 import javax.swing.JOptionPane;
88 import javax.swing.JPanel;
89 import javax.swing.JPopupMenu;
90 import javax.swing.JTextArea;
91 import javax.swing.Popup;
92 import javax.swing.PopupFactory;
94 import org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON;
95 import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
96 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
97 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
98 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
99 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
100 import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
101 import org.forester.archaeopteryx.tools.Blast;
102 import org.forester.archaeopteryx.tools.ImageLoader;
103 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
104 import org.forester.io.writers.SequenceWriter;
105 import org.forester.phylogeny.Phylogeny;
106 import org.forester.phylogeny.PhylogenyMethods;
107 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
108 import org.forester.phylogeny.PhylogenyNode;
109 import org.forester.phylogeny.data.Accession;
110 import org.forester.phylogeny.data.Annotation;
111 import org.forester.phylogeny.data.BranchColor;
112 import org.forester.phylogeny.data.Confidence;
113 import org.forester.phylogeny.data.Event;
114 import org.forester.phylogeny.data.NodeData.NODE_DATA;
115 import org.forester.phylogeny.data.NodeVisualData;
116 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
117 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
118 import org.forester.phylogeny.data.PhylogenyDataUtil;
119 import org.forester.phylogeny.data.PropertiesMap;
120 import org.forester.phylogeny.data.Property;
121 import org.forester.phylogeny.data.Sequence;
122 import org.forester.phylogeny.data.SequenceRelation;
123 import org.forester.phylogeny.data.Taxonomy;
124 import org.forester.phylogeny.data.Uri;
125 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
126 import org.forester.phylogeny.iterators.PreorderTreeIterator;
127 import org.forester.util.BasicDescriptiveStatistics;
128 import org.forester.util.DescriptiveStatistics;
129 import org.forester.util.ForesterConstants;
130 import org.forester.util.ForesterUtil;
131 import org.forester.util.SequenceAccessionTools;
132 import org.forester.util.TaxonomyUtil;
134 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
136 final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
137 final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
138 final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
139 final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
140 final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
141 final private static double _180_OVER_PI = 180.0 / Math.PI;
142 private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
143 private final static int CONFIDENCE_LEFT_MARGIN = 4;
144 private final static int EURO_D = 10;
145 private final static NumberFormat FORMATTER_BRANCH_LENGTH;
146 private final static NumberFormat FORMATTER_CONFIDENCE;
147 private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
148 private final static int LIMIT_FOR_HQ_RENDERING = 2000;
149 private final static int MAX_NODE_FRAMES = 10;
150 private final static int MAX_SUBTREES = 100;
151 private final static int MIN_ROOT_LENGTH = 3;
152 private final static int MOVE = 20;
153 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
154 private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
155 private static final short OV_BORDER = 10;
156 private static final float PI = ( float ) ( Math.PI );
157 final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
160 private static final float ROUNDED_D = 8;
161 private final static long serialVersionUID = -978349745916505029L;
162 private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
163 private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
164 private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
165 private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
166 private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
167 private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
168 private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
169 private static final double TWO_PI = 2 * Math.PI;
170 private final static int WIGGLE = 2;
171 private final static double OVERVIEW_FOUND_NODE_BOX_SIZE = 2;
172 private final static double OVERVIEW_FOUND_NODE_BOX_SIZE_HALF = 1;
173 HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
174 final private Arc2D _arc = new Arc2D.Double();
175 private AffineTransform _at;
176 private int _circ_max_depth;
177 final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
178 private JColorChooser _color_chooser = null;
179 private Configuration _configuration = null;
180 private ControlPanel _control_panel = null;
181 private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
182 private Set<Long> _current_external_nodes = null;
183 private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
184 private int _current_external_nodes_data_buffer_change_counter = 0;
185 private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
186 private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
187 private int _dynamic_hiding_factor = 0;
188 private boolean _edited = false;
189 private final Ellipse2D _ellipse = new Ellipse2D.Float();
190 private int _external_node_index = 0;
191 private Set<Long> _found_nodes_0 = null;
192 private Set<Long> _found_nodes_1 = null;
193 private final FontRenderContext _frc = new FontRenderContext( null,
196 private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
197 private PhylogenyNode _highlight_node = null;
198 private boolean _in_ov = false;
199 private boolean _in_ov_rect = false;
200 private float _last_drag_point_x = 0;
201 private float _last_drag_point_y = 0;
202 private final Line2D _line = new Line2D.Float();
203 private int _longest_ext_node_info = 0;
204 private MainPanel _main_panel = null;
205 private double _max_distance_to_root = -1;
206 private Popup _node_desc_popup;
207 private int _node_frame_index = 0;
208 private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
209 private JPopupMenu _node_popup_menu = null;
210 private JMenuItem _node_popup_menu_items[] = null;
211 private PhylogenyNode[] _nodes_in_preorder = null;
212 private Options _options = null;
213 private float _ov_max_height = 0;
214 private float _ov_max_width = 0;
215 private boolean _ov_on = false;
216 private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
217 private final Rectangle _ov_virtual_rectangle = new Rectangle();
218 private float _ov_x_correction_factor = 0.0f;
219 private float _ov_x_distance = 0;
220 private int _ov_x_position = 0;
221 private float _ov_y_distance = 0;
222 private int _ov_y_position = 0;
223 private int _ov_y_start = 0;
224 private final boolean _phy_has_branch_lengths;
225 private Phylogeny _phylogeny = null;
226 private final Path2D.Float _polygon = new Path2D.Float();
227 private final StringBuffer _popup_buffer = new StringBuffer();
228 private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
229 private Sequence _query_sequence = null;
230 private final Rectangle2D _rectangle = new Rectangle2D.Float();
231 private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
232 RenderingHints.VALUE_RENDER_DEFAULT );
233 private JTextArea _rollover_popup;
234 private PhylogenyNode _root;
235 private final StringBuilder _sb = new StringBuilder();
236 private double _scale_distance = 0.0;
237 private String _scale_label = null;
238 // expression values menu:
239 private DescriptiveStatistics _statistics_for_vector_data;
240 private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
241 private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
242 private int _subtree_index = 0;
243 private File _treefile = null;
244 private float _urt_factor = 1;
245 private float _urt_factor_ov = 1;
246 final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
247 final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
248 private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
249 private float _x_correction_factor = 0.0f;
250 private float _x_distance = 0.0f;
251 private float _y_distance = 0.0f;
252 // private Image offscreenImage;
253 // private Graphics offscreenGraphics;
254 // private Dimension offscreenDimension;
256 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
257 dfs.setDecimalSeparator( '.' );
258 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
259 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
262 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
263 requestFocusInWindow();
264 addKeyListener( new KeyAdapter() {
267 public void keyPressed( final KeyEvent key_event ) {
268 keyPressedCalls( key_event );
269 requestFocusInWindow();
272 addFocusListener( new FocusAdapter() {
275 public void focusGained( final FocusEvent e ) {
276 requestFocusInWindow();
279 if ( ( t == null ) || t.isEmpty() ) {
280 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
282 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
284 _configuration = configuration;
286 _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
288 // if ( !_phylogeny.isEmpty() ) {
289 _phylogeny.recalculateNumberOfExternalDescendants( true );
290 checkForVectorProperties( _phylogeny );
292 setBackground( getTreeColorSet().getBackgroundColor() );
293 final MouseListener mouse_listener = new MouseListener( this );
294 addMouseListener( mouse_listener );
295 addMouseMotionListener( mouse_listener );
296 addMouseWheelListener( this );
297 calculateScaleDistance();
298 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
299 FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
300 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
304 final public void actionPerformed( final ActionEvent e ) {
305 boolean done = false;
306 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
307 for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
308 // NOTE: index corresponds to the indices of click-to options
309 // in the control panel.
310 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
311 // Set this as the new default click-to action
312 _main_panel.getControlPanel().setClickToAction( index );
313 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
314 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
315 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
320 requestFocusInWindow();
323 public synchronized Hashtable<String, BufferedImage> getImageMap() {
324 return getMainPanel().getImageMap();
327 final public MainPanel getMainPanel() {
332 * Get a pointer to the phylogeny
334 * @return a pointer to the phylogeny
336 public final Phylogeny getPhylogeny() {
341 final public void mouseWheelMoved( final MouseWheelEvent e ) {
342 final int notches = e.getWheelRotation();
343 if ( inOvVirtualRectangle( e ) ) {
344 if ( !isInOvRect() ) {
350 if ( isInOvRect() ) {
351 setInOvRect( false );
355 if ( e.isControlDown() ) {
357 getTreeFontSet().increaseFontSize();
358 getControlPanel().displayedPhylogenyMightHaveChanged( true );
361 getTreeFontSet().decreaseFontSize( 1, false );
362 getControlPanel().displayedPhylogenyMightHaveChanged( true );
365 else if ( e.isShiftDown() ) {
366 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
367 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
369 for( int i = 0; i < ( -notches ); ++i ) {
370 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
371 getControlPanel().displayedPhylogenyMightHaveChanged( false );
375 for( int i = 0; i < notches; ++i ) {
376 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
377 if ( getStartingAngle() < 0 ) {
378 setStartingAngle( TWO_PI + getStartingAngle() );
380 getControlPanel().displayedPhylogenyMightHaveChanged( false );
386 for( int i = 0; i < ( -notches ); ++i ) {
387 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
388 getControlPanel().displayedPhylogenyMightHaveChanged( false );
392 for( int i = 0; i < notches; ++i ) {
393 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
394 getControlPanel().displayedPhylogenyMightHaveChanged( false );
401 for( int i = 0; i < ( -notches ); ++i ) {
402 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
403 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
404 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
405 getControlPanel().displayedPhylogenyMightHaveChanged( false );
409 for( int i = 0; i < notches; ++i ) {
410 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
411 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
412 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
413 getControlPanel().displayedPhylogenyMightHaveChanged( false );
418 requestFocusInWindow();
423 final public void paintComponent( final Graphics g ) {
424 // Dimension currentSize = getSize();
425 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
426 // call the 'java.awt.Component.createImage(...)' method to get an
428 // offscreenImage = createImage( currentSize.width, currentSize.height );
429 // offscreenGraphics = offscreenImage.getGraphics();
430 // offscreenDimension = currentSize;
432 // super.paintComponent( g ); //why?
433 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
434 final Graphics2D g2d = ( Graphics2D ) g;
435 g2d.setRenderingHints( _rendering_hints );
436 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
437 //g.drawImage( offscreenImage, 0, 0, this );
441 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
442 throws PrinterException {
443 if ( page_index > 0 ) {
444 return ( NO_SUCH_PAGE );
447 final Graphics2D g2d = ( Graphics2D ) g;
448 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
449 // Turn off double buffering !?
450 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
451 // Turn double buffering back on !?
452 return ( PAGE_EXISTS );
456 public final void setEdited( final boolean edited ) {
460 public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
461 getMainPanel().setImageMap( image_map );
465 * Set a phylogeny tree.
468 * an instance of a Phylogeny
470 public final void setTree( final Phylogeny t ) {
471 setNodeInPreorderToNull();
475 public final void setWaitCursor() {
476 setCursor( WAIT_CURSOR );
481 public void update( final Graphics g ) {
485 final void calcMaxDepth() {
486 if ( _phylogeny != null ) {
487 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
492 * Set parameters for printing the displayed tree
495 final void calcParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
496 // updateStyle(); not needed?
497 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
499 if ( recalc_longest_ext_node_info ) {
500 calculateLongestExtNodeInfo();
501 if ( getOptions().isAllowFontSizeChange() ) {
502 if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
503 && ( getTreeFontSet().getLargeFont().getSize() > 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
504 while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
505 && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
506 getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(),
508 calculateLongestExtNodeInfo();
512 while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
513 && ( getTreeFontSet().getLargeFont().getSize() <= getTreeFontSet().getLargeFontMemory()
514 .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
515 getMainPanel().getTreeFontSet().increaseFontSize();
516 calculateLongestExtNodeInfo();
521 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
522 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
523 if ( ext_nodes == 1 ) {
524 ext_nodes = max_depth;
525 if ( ext_nodes < 1 ) {
532 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
533 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
534 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
537 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
538 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
540 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
544 if ( ov_xdist < 0.0 ) {
550 setXdistance( xdist );
551 setYdistance( ydist );
552 setOvXDistance( ov_xdist );
553 final double height = _phylogeny.getHeight();
555 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
556 setXcorrectionFactor( corr > 0 ? corr : 0 );
557 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
558 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
561 setXcorrectionFactor( 0 );
562 setOvXcorrectionFactor( 0 );
564 _circ_max_depth = max_depth;
567 if ( getOptions().isAllowFontSizeChange() ) {
568 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
569 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
570 // int dynamic_hiding_factor = calcDynamicHidingFactor();
571 // if ( dynamic_hiding_factor > 1 ) {
572 // while ( dynamic_hiding_factor > 1
573 // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
574 // getTreeFontSet().decreaseFontSize( 1, true );
575 // dynamic_hiding_factor = calcDynamicHidingFactor();
578 // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
579 // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
580 // getTreeFontSet().increaseFontSize();
581 // dynamic_hiding_factor = calcDynamicHidingFactor();
590 final void calculateLongestExtNodeInfo() {
591 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
594 int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
595 * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
596 if ( max_length < 40 ) {
600 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
602 if ( node.isCollapse() ) {
605 if ( getControlPanel().isShowNodeNames() ) {
606 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
608 if ( node.getNodeData().isHasSequence() ) {
609 if ( getControlPanel().isShowSequenceAcc()
610 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
611 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
615 if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
616 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
618 if ( getControlPanel().isShowSeqSymbols()
619 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
620 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
622 if ( getControlPanel().isShowGeneNames()
623 && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
624 sum += getTreeFontSet()._fm_large
625 .stringWidth( node.getNodeData().getSequence().getGeneName() + " " );
627 if ( getControlPanel().isShowAnnotation()
628 && ( node.getNodeData().getSequence().getAnnotations() != null )
629 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
630 sum += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
631 .getNodeData().getSequence().getAnnotations(), getOptions().isShowAnnotationRefSource() )
634 if ( getControlPanel().isShowDomainArchitectures()
635 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
636 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
637 .getRenderingSize().getWidth();
640 if ( node.getNodeData().isHasTaxonomy() ) {
641 final Taxonomy tax = node.getNodeData().getTaxonomy();
642 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
643 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
645 if ( getControlPanel().isShowTaxonomyScientificNames()
646 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
647 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
649 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
650 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
653 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
654 sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
656 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
657 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
658 .getGainedCharactersAsStringBuffer().toString() );
660 if ( sum >= max_length ) {
661 setLongestExtNodeInfo( max_length );
664 if ( sum > longest ) {
668 if ( longest >= max_length ) {
669 setLongestExtNodeInfo( max_length );
672 setLongestExtNodeInfo( longest );
676 final void calculateScaleDistance() {
677 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
680 final double height = getMaxDistanceToRoot();
682 if ( ( height <= 0.5 ) ) {
683 setScaleDistance( 0.01 );
685 else if ( height <= 5.0 ) {
686 setScaleDistance( 0.1 );
688 else if ( height <= 50.0 ) {
689 setScaleDistance( 1 );
691 else if ( height <= 500.0 ) {
692 setScaleDistance( 10 );
695 setScaleDistance( 100 );
699 setScaleDistance( 0.0 );
701 String scale_label = String.valueOf( getScaleDistance() );
702 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
703 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
705 setScaleLabel( scale_label );
708 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
709 if ( getOptions().isColorByTaxonomicGroup() ) {
710 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
714 group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
716 catch ( final Exception e ) {
719 if ( !ex && !ForesterUtil.isEmpty( group ) ) {
720 final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
726 return getTreeColorSet().getTaxonomyColor();
729 if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
730 return getTreeColorSet().getTaxonomyColor();
733 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
734 c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
736 if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
737 c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
740 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
741 c = TreePanelUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
742 getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
745 c = TreePanelUtil.calculateColorFromString( tax.getScientificName(), true );
746 getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
753 void checkForVectorProperties( final Phylogeny phy ) {
754 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
755 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
756 final PhylogenyNode node = iter.next();
757 if ( node.getNodeData().getProperties() != null ) {
758 final PropertiesMap pm = node.getNodeData().getProperties();
759 final double[] vector = new double[ pm.getProperties().size() ];
761 for( final String ref : pm.getProperties().keySet() ) {
762 if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
763 final Property p = pm.getProperty( ref );
764 final String value_str = p.getValue();
765 final String index_str = ref
766 .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
769 d = Double.parseDouble( value_str );
771 catch ( final NumberFormatException e ) {
772 JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
773 + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
778 i = Integer.parseInt( index_str );
780 catch ( final NumberFormatException e ) {
781 JOptionPane.showMessageDialog( this,
782 "Could not parse \"" + index_str
783 + "\" into index for vector data",
784 "Problem with Vector Data",
785 JOptionPane.ERROR_MESSAGE );
789 JOptionPane.showMessageDialog( this,
790 "Attempt to use negative index for vector data",
791 "Problem with Vector Data",
792 JOptionPane.ERROR_MESSAGE );
800 final List<Double> vector_l = new ArrayList<Double>( counter );
801 for( int i = 0; i < counter; ++i ) {
802 vector_l.add( vector[ i ] );
804 node.getNodeData().setVector( vector_l );
807 if ( stats.getN() > 0 ) {
808 _statistics_for_vector_data = stats;
812 void clearCurrentExternalNodesDataBuffer() {
813 setCurrentExternalNodesDataBuffer( new StringBuilder() );
817 * Collapse the tree from the given node
822 final void collapse( final PhylogenyNode node ) {
823 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
824 JOptionPane.showMessageDialog( this,
825 "Cannot collapse in unrooted display type",
826 "Attempt to collapse in unrooted display",
827 JOptionPane.WARNING_MESSAGE );
830 if ( !node.isExternal() && !node.isRoot() ) {
831 final boolean collapse = !node.isCollapse();
832 TreePanelUtil.collapseSubtree( node, collapse );
833 updateSetOfCollapsedExternalNodes();
834 _phylogeny.recalculateNumberOfExternalDescendants( true );
835 resetNodeIdToDistToLeafMap();
836 calculateLongestExtNodeInfo();
837 setNodeInPreorderToNull();
838 _control_panel.displayedPhylogenyMightHaveChanged( true );
839 resetPreferredSize();
841 _main_panel.adjustJScrollPane();
846 final void collapseSpeciesSpecificSubtrees() {
847 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
851 TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
852 updateSetOfCollapsedExternalNodes();
853 _phylogeny.recalculateNumberOfExternalDescendants( true );
854 resetNodeIdToDistToLeafMap();
855 calculateLongestExtNodeInfo();
856 setNodeInPreorderToNull();
857 resetPreferredSize();
858 _main_panel.adjustJScrollPane();
863 final void colorRank( final String rank ) {
864 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
868 AptxUtil.removeBranchColors( _phylogeny );
869 final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
870 if ( colorizations > 0 ) {
871 _control_panel.setColorBranches( true );
872 if ( _control_panel.getColorBranchesCb() != null ) {
873 _control_panel.getColorBranchesCb().setSelected( true );
875 if ( _control_panel.getColorAccSpeciesCb() != null ) {
876 _control_panel.getColorAccSpeciesCb().setSelected( false );
878 _options.setColorLabelsSameAsParentBranch( true );
879 _control_panel.repaint();
883 if ( colorizations > 0 ) {
884 String msg = "Taxonomy colorization via " + rank + " completed:\n";
885 if ( colorizations > 1 ) {
886 msg += "colorized " + colorizations + " subtrees";
889 msg += "colorized one subtree";
892 JOptionPane.showMessageDialog( this,
894 "Taxonomy Colorization Completed (" + rank + ")",
895 JOptionPane.INFORMATION_MESSAGE );
898 String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
899 msg += "Possible solutions (given that suitable taxonomic information is present):\n";
900 msg += "select a different rank (e.g. phylum, genus, ...)\n";
903 msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
904 msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
905 JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
909 final void confColor() {
910 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
914 AptxUtil.removeBranchColors( _phylogeny );
915 TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
916 _control_panel.setColorBranches( true );
917 if ( _control_panel.getColorBranchesCb() != null ) {
918 _control_panel.getColorBranchesCb().setSelected( true );
924 final void decreaseDomainStructureEvalueThreshold() {
925 if ( _domain_structure_e_value_thr_exp > -20 ) {
926 _domain_structure_e_value_thr_exp -= 1;
931 * Find the node, if any, at the given location
935 * @return pointer to the node at x,y, null if not found
937 final PhylogenyNode findNode( final int x, final int y ) {
938 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
941 final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
942 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
943 final PhylogenyNode node = iter.next();
944 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
945 && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
946 && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
947 && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
948 && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
955 final Configuration getConfiguration() {
956 return _configuration;
959 final ControlPanel getControlPanel() {
960 return _control_panel;
963 String getCurrentExternalNodesDataBufferAsString() {
964 return _current_external_nodes_data_buffer.toString();
967 int getCurrentExternalNodesDataBufferChangeCounter() {
968 return _current_external_nodes_data_buffer_change_counter;
971 final int getDomainStructureEvalueThreshold() {
972 return _domain_structure_e_value_thr_exp;
975 final Set<Long> getFoundNodes0() {
976 return _found_nodes_0;
979 final Set<Long> getFoundNodes1() {
980 return _found_nodes_1;
983 final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
984 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
985 return ( PhylogenyMethods.getBranchColorValue( node ) );
988 return ( getTreeColorSet().getBranchColor() );
992 final int getLongestExtNodeInfo() {
993 return _longest_ext_node_info;
996 final Options getOptions() {
997 if ( _options == null ) {
998 _options = getControlPanel().getOptions();
1003 final Rectangle2D getOvRectangle() {
1004 return _ov_rectangle;
1007 final Rectangle getOvVirtualRectangle() {
1008 return _ov_virtual_rectangle;
1011 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
1012 return _graphics_type;
1015 final double getStartingAngle() {
1016 return _urt_starting_angle;
1019 DescriptiveStatistics getStatisticsForExpressionValues() {
1020 return _statistics_for_vector_data;
1024 * Find a color for this species name.
1027 * @return the species color
1029 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
1030 if ( node.getNodeData().isHasTaxonomy() ) {
1031 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
1033 // return non-colorized color
1034 return getTreeColorSet().getTaxonomyColor();
1038 * @return pointer to colorset for tree drawing
1040 final TreeColorSet getTreeColorSet() {
1041 return getMainPanel().getTreeColorSet();
1044 final File getTreeFile() {
1048 final float getXcorrectionFactor() {
1049 return _x_correction_factor;
1052 final float getXdistance() {
1056 final float getYdistance() {
1060 final void increaseDomainStructureEvalueThreshold() {
1061 if ( _domain_structure_e_value_thr_exp < 3 ) {
1062 _domain_structure_e_value_thr_exp += 1;
1066 final void initNodeData() {
1067 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1070 double max_original_domain_structure_width = 0.0;
1071 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1072 if ( node.getNodeData().isHasSequence()
1073 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1074 RenderableDomainArchitecture rds = null;
1075 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
1076 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1077 getConfiguration() );
1078 node.getNodeData().getSequence().setDomainArchitecture( rds );
1081 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1083 if ( getControlPanel().isShowDomainArchitectures() ) {
1084 final double dsw = rds.getOriginalSize().getWidth();
1085 if ( dsw > max_original_domain_structure_width ) {
1086 max_original_domain_structure_width = dsw;
1091 if ( getControlPanel().isShowDomainArchitectures() ) {
1092 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1093 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1094 if ( node.getNodeData().isHasSequence()
1095 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1096 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1097 .getSequence().getDomainArchitecture();
1098 rds.setRenderingFactorWidth( ds_factor_width );
1099 rds.setParameter( _domain_structure_e_value_thr_exp );
1105 final boolean inOv( final MouseEvent e ) {
1106 return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
1107 && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
1108 && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
1109 + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
1112 final boolean inOvRectangle( final MouseEvent e ) {
1113 return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
1114 && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
1115 && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
1116 + getOvRectangle().getHeight() + 1 ) ) );
1119 final boolean isApplet() {
1120 return getMainPanel() instanceof MainPanelApplets;
1123 final boolean isCanCollapse() {
1124 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1127 final boolean isCanColorSubtree() {
1128 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1131 final boolean isCanCopy() {
1132 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1135 final boolean isCanCut( final PhylogenyNode node ) {
1136 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1140 final boolean isCanDelete() {
1141 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1144 final boolean isCanPaste() {
1145 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1146 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1149 final boolean isCanReroot() {
1150 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1153 final boolean isCanSubtree( final PhylogenyNode node ) {
1154 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1155 .isRoot() || ( _subtree_index > 0 ) ) );
1158 final boolean isCurrentTreeIsSubtree() {
1159 return ( _subtree_index > 0 );
1162 final boolean isEdited() {
1166 final boolean isInOvRect() {
1170 final boolean isOvOn() {
1174 final boolean isPhyHasBranchLengths() {
1175 return _phy_has_branch_lengths;
1178 final void midpointRoot() {
1179 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1182 if ( !_phylogeny.isRerootable() ) {
1183 JOptionPane.showMessageDialog( this,
1184 "This is not rerootable",
1186 JOptionPane.WARNING_MESSAGE );
1189 setNodeInPreorderToNull();
1191 PhylogenyMethods.midpointRoot( _phylogeny );
1192 resetNodeIdToDistToLeafMap();
1198 final void mouseClicked( final MouseEvent e ) {
1199 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1200 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1201 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1202 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
1204 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
1212 final double max_x = getWidth() - getVisibleRect().width;
1213 final double max_y = getHeight() - getVisibleRect().height;
1220 getMainPanel().getCurrentScrollPane().getViewport()
1221 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1222 setInOvRect( true );
1226 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1227 if ( node != null ) {
1228 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1231 _highlight_node = node;
1232 // Check if shift key is down
1233 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1234 // Yes, so add to _found_nodes
1235 if ( getFoundNodes0() == null ) {
1236 setFoundNodes0( new HashSet<Long>() );
1238 getFoundNodes0().add( node.getId() );
1239 // Check if control key is down
1241 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1242 // Yes, so pop-up menu
1243 displayNodePopupMenu( node, e.getX(), e.getY() );
1244 // Handle unadorned click
1247 // Check for right mouse button
1248 if ( e.getModifiers() == 4 ) {
1249 displayNodePopupMenu( node, e.getX(), e.getY() );
1252 // if not in _found_nodes, clear _found_nodes
1253 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1258 // no node was clicked
1259 _highlight_node = null;
1265 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1266 setCursor( MOVE_CURSOR );
1267 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1268 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1269 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1270 if ( scroll_position.x < 0 ) {
1271 scroll_position.x = 0;
1274 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1275 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1276 if ( scroll_position.x > max_x ) {
1277 scroll_position.x = max_x;
1280 if ( scroll_position.y < 0 ) {
1281 scroll_position.y = 0;
1284 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1285 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1286 if ( scroll_position.y > max_y ) {
1287 scroll_position.y = max_y;
1290 if ( isOvOn() || getOptions().isShowScale() ) {
1293 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1296 final void mouseDragInOvRectangle( final MouseEvent e ) {
1297 setCursor( HAND_CURSOR );
1298 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1299 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1300 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1301 double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
1302 double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
1303 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1304 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1305 if ( scroll_position.x <= 0 ) {
1306 scroll_position.x = 0;
1310 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1311 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1312 if ( scroll_position.x >= max_x ) {
1314 scroll_position.x = max_x;
1317 if ( scroll_position.y <= 0 ) {
1319 scroll_position.y = 0;
1322 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1323 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1324 if ( scroll_position.y >= max_y ) {
1326 scroll_position.y = max_y;
1330 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1331 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1332 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1335 final void mouseMoved( final MouseEvent e ) {
1336 requestFocusInWindow();
1337 if ( _current_external_nodes != null ) {
1338 _current_external_nodes = null;
1341 if ( getControlPanel().isNodeDescPopup() ) {
1342 if ( _node_desc_popup != null ) {
1343 _node_desc_popup.hide();
1344 _node_desc_popup = null;
1347 if ( getOptions().isShowOverview() && isOvOn() ) {
1348 if ( inOvVirtualRectangle( e ) ) {
1349 if ( !isInOvRect() ) {
1350 setInOvRect( true );
1355 if ( isInOvRect() ) {
1356 setInOvRect( false );
1361 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
1370 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1371 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
1372 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
1373 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
1374 addToCurrentExternalNodes( n.getId() );
1376 setCursor( HAND_CURSOR );
1379 else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
1380 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
1381 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
1382 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
1383 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
1384 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
1385 setCursor( CUT_CURSOR );
1388 setCursor( HAND_CURSOR );
1389 if ( getControlPanel().isNodeDescPopup() ) {
1390 showNodeDataPopup( e, node );
1395 setCursor( ARROW_CURSOR );
1400 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
1401 setCursor( ARROW_CURSOR );
1404 final void multiplyUrtFactor( final float f ) {
1408 final JApplet obtainApplet() {
1409 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1412 final void paintBranchCircular( final PhylogenyNode p,
1413 final PhylogenyNode c,
1415 final boolean radial_labels,
1416 final boolean to_pdf,
1417 final boolean to_graphics_file ) {
1418 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1419 final double root_x = _root.getXcoord();
1420 final double root_y = _root.getYcoord();
1421 final double dx = root_x - p.getXcoord();
1422 final double dy = root_y - p.getYcoord();
1423 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1424 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1425 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
1426 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
1427 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
1428 final double r2 = 2.0 * parent_radius;
1429 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1431 drawLine( c.getXcoord(),
1433 root_x + ( Math.cos( angle ) * parent_radius ),
1434 root_y + ( Math.sin( angle ) * parent_radius ),
1436 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file );
1437 if ( c.isExternal() ) {
1438 final boolean is_in_found_nodes = isInFoundNodes0( c ) || isInFoundNodes1( c )
1439 || isInCurrentExternalNodes( c );
1440 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
1441 && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
1444 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
1448 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
1449 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1450 final double root_x = _root.getXSecondary();
1451 final double root_y = _root.getYSecondary();
1452 final double dx = root_x - p.getXSecondary();
1453 final double dy = root_y - p.getYSecondary();
1454 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1455 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1456 g.setColor( getTreeColorSet().getOvColor() );
1457 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
1458 final double r2 = 2.0 * parent_radius;
1459 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1461 drawLine( c.getXSecondary(),
1463 root_x + ( Math.cos( angle ) * parent_radius ),
1464 root_y + ( Math.sin( angle ) * parent_radius ),
1466 if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
1467 g.setColor( getColorForFoundNode( c ) );
1468 drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, c.getYSecondary()
1469 - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
1473 final void paintCircular( final Phylogeny phy,
1474 final double starting_angle,
1479 final boolean to_pdf,
1480 final boolean to_graphics_file ) {
1481 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
1482 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
1483 _root = phy.getRoot();
1484 _root.setXcoord( center_x );
1485 _root.setYcoord( center_y );
1486 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1487 double current_angle = starting_angle;
1489 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1490 final PhylogenyNode n = it.next();
1491 if ( !n.isCollapse() ) {
1492 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1493 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1494 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1495 _urt_nodeid_index_map.put( n.getId(), i++ );
1496 current_angle += ( TWO_PI / circ_num_ext_nodes );
1500 System.out.println( "is collapse" + n.getName() );
1503 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
1504 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file );
1507 final void paintCircularLite( final Phylogeny phy,
1508 final double starting_angle,
1512 final Graphics2D g ) {
1513 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
1514 _root = phy.getRoot();
1515 _root.setXSecondary( center_x );
1516 _root.setYSecondary( center_y );
1517 double current_angle = starting_angle;
1518 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1519 final PhylogenyNode n = it.next();
1520 n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1521 n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1522 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1523 current_angle += ( TWO_PI / circ_num_ext_nodes );
1525 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
1528 final void paintPhylogeny( final Graphics2D g,
1529 final boolean to_pdf,
1530 final boolean to_graphics_file,
1531 final int graphics_file_width,
1532 final int graphics_file_height,
1533 final int graphics_file_x,
1534 final int graphics_file_y ) {
1535 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1538 if ( _control_panel.isShowSequenceRelations() ) {
1539 _query_sequence = _control_panel.getSelectedQuerySequence();
1541 // Color the background
1543 final Rectangle r = getVisibleRect();
1544 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
1545 g.setColor( getTreeColorSet().getBackgroundColor() );
1546 if ( !to_graphics_file ) {
1550 if ( getOptions().isPrintBlackAndWhite() ) {
1551 g.setColor( Color.WHITE );
1553 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1557 if ( !to_graphics_file ) {
1558 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
1559 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
1563 g.setPaint( new GradientPaint( graphics_file_x,
1565 getTreeColorSet().getBackgroundColor(),
1567 graphics_file_y + graphics_file_height,
1568 getTreeColorSet().getBackgroundColorGradientBottom() ) );
1569 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1575 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
1577 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1578 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1579 _external_node_index = 0;
1580 // Position starting X of tree
1581 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
1582 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
1584 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
1585 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
1586 .getDistanceToParent() * getXcorrectionFactor() ) ) );
1589 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
1591 // Position starting Y of tree
1592 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
1593 + ( TreePanel.MOVE / 2.0f ) );
1594 final int dynamic_hiding_factor = calcDynamicHidingFactor();
1595 if ( getControlPanel().isDynamicallyHideData() ) {
1596 if ( dynamic_hiding_factor > 1 ) {
1597 getControlPanel().setDynamicHidingIsOn( true );
1600 getControlPanel().setDynamicHidingIsOn( false );
1603 if ( _nodes_in_preorder == null ) {
1604 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
1606 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1607 _nodes_in_preorder[ i++ ] = it.next();
1610 //final PhylogenyNodeIterator it;
1611 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1612 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
1613 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1615 for( final PhylogenyNode element : _nodes_in_preorder ) {
1616 paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
1617 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1619 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
1620 if ( !( to_graphics_file || to_pdf ) ) {
1623 getVisibleRect().y + getVisibleRect().height,
1628 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1631 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1632 paintPhylogenyLite( g );
1635 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1636 if ( getControlPanel().getDynamicallyHideData() != null ) {
1637 getControlPanel().setDynamicHidingIsOn( false );
1639 final double angle = getStartingAngle();
1640 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1641 _dynamic_hiding_factor = 0;
1642 if ( getControlPanel().isDynamicallyHideData() ) {
1643 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1644 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
1646 if ( getControlPanel().getDynamicallyHideData() != null ) {
1647 if ( _dynamic_hiding_factor > 1 ) {
1648 getControlPanel().setDynamicHidingIsOn( true );
1651 getControlPanel().setDynamicHidingIsOn( false );
1654 paintUnrooted( _phylogeny.getRoot(),
1656 ( float ) ( angle + ( 2 * Math.PI ) ),
1661 if ( getOptions().isShowScale() ) {
1662 if ( !( to_graphics_file || to_pdf ) ) {
1665 getVisibleRect().y + getVisibleRect().height,
1670 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1673 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1674 g.setColor( getTreeColorSet().getOvColor() );
1675 paintUnrootedLite( _phylogeny.getRoot(),
1677 angle + ( 2 * Math.PI ),
1679 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
1680 paintOvRectangle( g );
1683 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1684 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
1685 final int d = radius + MOVE + getLongestExtNodeInfo();
1686 _dynamic_hiding_factor = 0;
1687 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
1688 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1689 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
1691 if ( getControlPanel().getDynamicallyHideData() != null ) {
1692 if ( _dynamic_hiding_factor > 1 ) {
1693 getControlPanel().setDynamicHidingIsOn( true );
1696 getControlPanel().setDynamicHidingIsOn( false );
1699 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
1700 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1701 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
1702 : getOvMaxWidth() / 2 );
1703 double x_scale = 1.0;
1704 double y_scale = 1.0;
1705 int x_pos = getVisibleRect().x + getOvXPosition();
1706 int y_pos = getVisibleRect().y + getOvYPosition();
1707 if ( getWidth() > getHeight() ) {
1708 x_scale = ( double ) getHeight() / getWidth();
1709 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
1712 y_scale = ( double ) getWidth() / getHeight();
1713 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
1715 _at = g.getTransform();
1716 g.scale( x_scale, y_scale );
1717 paintCircularLite( _phylogeny,
1721 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
1724 g.setTransform( _at );
1725 paintOvRectangle( g );
1730 final void recalculateMaxDistanceToRoot() {
1731 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
1735 * Remove all edit-node frames
1737 final void removeAllEditNodeJFrames() {
1738 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
1739 if ( _node_frames[ i ] != null ) {
1740 _node_frames[ i ].dispose();
1741 _node_frames[ i ] = null;
1744 _node_frame_index = 0;
1748 * Remove a node-edit frame.
1750 final void removeEditNodeFrame( final int i ) {
1751 _node_frame_index--;
1752 _node_frames[ i ] = null;
1753 if ( i < _node_frame_index ) {
1754 for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
1755 _node_frames[ j ] = _node_frames[ j + 1 ];
1757 _node_frames[ _node_frame_index ] = null;
1761 final void reRoot( final PhylogenyNode node ) {
1762 if ( !getPhylogeny().isRerootable() ) {
1763 JOptionPane.showMessageDialog( this,
1764 "This is not rerootable",
1766 JOptionPane.WARNING_MESSAGE );
1769 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1770 JOptionPane.showMessageDialog( this,
1771 "Cannot reroot in unrooted display type",
1772 "Attempt to reroot tree in unrooted display",
1773 JOptionPane.WARNING_MESSAGE );
1776 getPhylogeny().reRoot( node );
1777 getPhylogeny().recalculateNumberOfExternalDescendants( true );
1778 resetNodeIdToDistToLeafMap();
1779 setNodeInPreorderToNull();
1780 resetPreferredSize();
1781 getMainPanel().adjustJScrollPane();
1784 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1785 getControlPanel().showWhole();
1789 final void resetNodeIdToDistToLeafMap() {
1790 _nodeid_dist_to_leaf = new HashMap<Long, Short>();
1793 final void resetPreferredSize() {
1794 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
1800 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
1801 if ( getControlPanel().isDrawPhylogram() ) {
1803 + getLongestExtNodeInfo()
1805 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
1808 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
1810 + getLongestExtNodeInfo()
1811 + ForesterUtil.roundToInt( getXdistance()
1812 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
1816 + getLongestExtNodeInfo()
1817 + ForesterUtil.roundToInt( getXdistance()
1818 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
1821 setPreferredSize( new Dimension( x, y ) );
1824 final void selectNode( final PhylogenyNode node ) {
1825 if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) {
1826 getFoundNodes0().remove( node.getId() );
1827 getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
1828 if ( getFoundNodes0().size() < 1 ) {
1829 getControlPanel().searchReset0();
1833 getControlPanel().getSearchFoundCountsLabel0().setVisible( true );
1834 getControlPanel().getSearchResetButton0().setEnabled( true );
1835 getControlPanel().getSearchResetButton0().setVisible( true );
1836 if ( getFoundNodes0() == null ) {
1837 setFoundNodes0( new HashSet<Long>() );
1839 getFoundNodes0().add( node.getId() );
1840 getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
1844 final void setArrowCursor() {
1845 setCursor( ARROW_CURSOR );
1849 final void setControlPanel( final ControlPanel atv_control ) {
1850 _control_panel = atv_control;
1853 void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
1854 increaseCurrentExternalNodesDataBufferChangeCounter();
1855 _current_external_nodes_data_buffer = sb;
1858 final void setFoundNodes0( final Set<Long> found_nodes ) {
1859 _found_nodes_0 = found_nodes;
1862 final void setFoundNodes1( final Set<Long> found_nodes ) {
1863 _found_nodes_1 = found_nodes;
1866 final void setInOvRect( final boolean in_ov_rect ) {
1867 _in_ov_rect = in_ov_rect;
1870 final void setLargeFonts() {
1871 getTreeFontSet().largeFonts();
1874 final void setLastMouseDragPointX( final float x ) {
1875 _last_drag_point_x = x;
1878 final void setLastMouseDragPointY( final float y ) {
1879 _last_drag_point_y = y;
1882 final void setLongestExtNodeInfo( final int i ) {
1883 _longest_ext_node_info = i;
1886 final void setMediumFonts() {
1887 getTreeFontSet().mediumFonts();
1890 final void setNodeInPreorderToNull() {
1891 _nodes_in_preorder = null;
1894 final void setOvOn( final boolean ov_on ) {
1898 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
1899 _graphics_type = graphics_type;
1903 final void setSmallFonts() {
1904 getTreeFontSet().smallFonts();
1907 final void setStartingAngle( final double starting_angle ) {
1908 _urt_starting_angle = starting_angle;
1911 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
1912 _statistics_for_vector_data = statistics_for_expression_values;
1915 final void setSuperTinyFonts() {
1916 getTreeFontSet().superTinyFonts();
1919 final void setTextAntialias() {
1920 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
1921 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
1922 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
1925 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
1928 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
1929 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
1931 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
1933 // catch ( final Throwable e ) {
1934 // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
1938 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
1939 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1943 final void setTinyFonts() {
1944 getTreeFontSet().tinyFonts();
1947 final void setTreeFile( final File treefile ) {
1948 _treefile = treefile;
1951 final void setXcorrectionFactor( final float f ) {
1952 _x_correction_factor = f;
1955 final void setXdistance( final float x ) {
1959 final void setYdistance( final float y ) {
1963 final void sortDescendants( final PhylogenyNode node ) {
1964 if ( !node.isExternal() ) {
1965 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
1966 if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
1967 .isShowTaxonomyCommonNames() ) ) {
1968 if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowSeqNames() || getControlPanel()
1969 .isShowSeqSymbols() ) ) {
1970 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
1972 else if ( getControlPanel().isShowNodeNames() ) {
1973 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
1976 PhylogenyMethods.sortNodeDescendents( node, pri );
1977 setNodeInPreorderToNull();
1978 _phylogeny.externalNodesHaveChanged();
1979 _phylogeny.clearHashIdToNodeMap();
1980 _phylogeny.recalculateNumberOfExternalDescendants( true );
1981 resetNodeIdToDistToLeafMap();
1987 final void subTree( final PhylogenyNode node ) {
1988 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1989 JOptionPane.showMessageDialog( this,
1990 "Cannot get a sub/super tree in unrooted display",
1991 "Attempt to get sub/super tree in unrooted display",
1992 JOptionPane.WARNING_MESSAGE );
1995 if ( node.isExternal() ) {
1996 JOptionPane.showMessageDialog( this,
1997 "Cannot get a subtree of a external node",
1998 "Attempt to get subtree of external node",
1999 JOptionPane.WARNING_MESSAGE );
2002 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
2003 JOptionPane.showMessageDialog( this,
2004 "Cannot get a subtree of the root node",
2005 "Attempt to get subtree of root node",
2006 JOptionPane.WARNING_MESSAGE );
2009 setNodeInPreorderToNull();
2010 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
2011 _sub_phylogenies[ _subtree_index ] = _phylogeny;
2012 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
2014 _phylogeny = TreePanelUtil.subTree( node, _phylogeny );
2015 updateSubSuperTreeButton();
2017 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
2020 _main_panel.getControlPanel().showWhole();
2024 final void superTree() {
2025 setNodeInPreorderToNull();
2026 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
2027 for( final PhylogenyNode n : temp_root.getDescendants() ) {
2028 n.setParent( temp_root );
2030 _sub_phylogenies[ _subtree_index ] = null;
2031 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
2032 _phylogeny = _sub_phylogenies[ --_subtree_index ];
2033 updateSubSuperTreeButton();
2036 final void swap( final PhylogenyNode node ) {
2037 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
2040 if ( node.getNumberOfDescendants() > 2 ) {
2041 JOptionPane.showMessageDialog( this,
2042 "Cannot swap descendants of nodes with more than 2 descendants",
2043 "Cannot swap descendants",
2044 JOptionPane.ERROR_MESSAGE );
2047 if ( !node.isExternal() ) {
2048 node.swapChildren();
2049 setNodeInPreorderToNull();
2050 _phylogeny.externalNodesHaveChanged();
2051 _phylogeny.clearHashIdToNodeMap();
2052 _phylogeny.recalculateNumberOfExternalDescendants( true );
2053 resetNodeIdToDistToLeafMap();
2059 final void taxColor() {
2060 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
2064 TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
2065 _control_panel.setColorBranches( true );
2066 if ( _control_panel.getColorBranchesCb() != null ) {
2067 _control_panel.getColorBranchesCb().setSelected( true );
2074 final void updateOvSettings() {
2075 switch ( getOptions().getOvPlacement() ) {
2077 setOvXPosition( OV_BORDER );
2078 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2079 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2082 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2083 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2084 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2087 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2088 setOvYPosition( OV_BORDER );
2089 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2092 setOvXPosition( OV_BORDER );
2093 setOvYPosition( OV_BORDER );
2094 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2099 final void updateOvSizes() {
2100 if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
2102 float l = getLongestExtNodeInfo();
2103 final float w_ratio = getOvMaxWidth() / getWidth();
2105 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
2106 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
2108 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
2109 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
2112 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
2114 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
2115 if ( ov_xdist < 0.0 ) {
2118 if ( ydist < 0.0 ) {
2121 setOvXDistance( ov_xdist );
2122 final double height = _phylogeny.getHeight();
2124 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
2125 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
2128 setOvXcorrectionFactor( 0 );
2136 void updateSetOfCollapsedExternalNodes() {
2137 final Phylogeny phy = getPhylogeny();
2138 _collapsed_external_nodeid_set.clear();
2139 if ( phy != null ) {
2140 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2141 final PhylogenyNode ext_node = it.next();
2142 PhylogenyNode n = ext_node;
2143 while ( !n.isRoot() ) {
2144 if ( n.isCollapse() ) {
2145 _collapsed_external_nodeid_set.add( ext_node.getId() );
2146 ext_node.setCollapse( true );
2155 final void updateSubSuperTreeButton() {
2156 if ( _subtree_index < 1 ) {
2157 getControlPanel().deactivateButtonToReturnToSuperTree();
2160 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
2164 final void zoomInDomainStructure() {
2165 if ( _domain_structure_width < 2000 ) {
2166 _domain_structure_width *= 1.2;
2170 final void zoomOutDomainStructure() {
2171 if ( _domain_structure_width > 20 ) {
2172 _domain_structure_width *= 0.8;
2176 private void abbreviateScientificName( final String sn ) {
2177 final String[] a = sn.split( "\\s+" );
2178 _sb.append( a[ 0 ].substring( 0, 1 ) );
2179 _sb.append( a[ 1 ].substring( 0, 2 ) );
2180 if ( a.length > 2 ) {
2181 for( int i = 2; i < a.length; i++ ) {
2183 _sb.append( a[ i ] );
2188 final private void addEmptyNode( final PhylogenyNode node ) {
2189 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2190 errorMessageNoCutCopyPasteInUnrootedDisplay();
2193 final String label = createASimpleTextRepresentationOfANode( node );
2195 if ( ForesterUtil.isEmpty( label ) ) {
2196 msg = "How to add the new, empty node?";
2199 msg = "How to add the new, empty node to node" + label + "?";
2201 final Object[] options = { "As sibling", "As descendant", "Cancel" };
2202 final int r = JOptionPane.showOptionDialog( this,
2204 "Addition of Empty New Node",
2205 JOptionPane.CLOSED_OPTION,
2206 JOptionPane.QUESTION_MESSAGE,
2210 boolean add_as_sibling = true;
2212 add_as_sibling = false;
2214 else if ( r != 0 ) {
2217 final Phylogeny phy = new Phylogeny();
2218 phy.setRoot( new PhylogenyNode() );
2219 phy.setRooted( true );
2220 if ( add_as_sibling ) {
2221 if ( node.isRoot() ) {
2222 JOptionPane.showMessageDialog( this,
2223 "Cannot add sibling to root",
2224 "Attempt to add sibling to root",
2225 JOptionPane.ERROR_MESSAGE );
2228 phy.addAsSibling( node );
2231 phy.addAsChild( node );
2233 setNodeInPreorderToNull();
2234 _phylogeny.externalNodesHaveChanged();
2235 _phylogeny.clearHashIdToNodeMap();
2236 _phylogeny.recalculateNumberOfExternalDescendants( true );
2237 resetNodeIdToDistToLeafMap();
2242 final private void addToCurrentExternalNodes( final long i ) {
2243 if ( _current_external_nodes == null ) {
2244 _current_external_nodes = new HashSet<Long>();
2246 _current_external_nodes.add( i );
2249 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
2250 final boolean is_vertical,
2252 final boolean to_pdf,
2253 final boolean to_graphics_file ) {
2254 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
2255 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2256 g.setColor( Color.BLACK );
2258 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
2259 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
2260 && ( getCutOrCopiedTree() != null )
2261 && ( getCopiedAndPastedNodes() != null )
2263 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
2264 g.setColor( getTreeColorSet().getFoundColor0() );
2266 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2267 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2269 else if ( to_pdf ) {
2270 g.setColor( getTreeColorSet().getBranchColorForPdf() );
2273 g.setColor( getTreeColorSet().getBranchColor() );
2277 final private void blast( final PhylogenyNode node ) {
2278 if ( !isCanBlast( node ) ) {
2279 JOptionPane.showMessageDialog( this,
2280 "Insufficient information present",
2282 JOptionPane.INFORMATION_MESSAGE );
2286 final String query = Blast.obtainQueryForBlast( node );
2287 System.out.println( "query for BLAST is: " + query );
2289 if ( !ForesterUtil.isEmpty( query ) ) {
2290 if ( node.getNodeData().isHasSequence() ) {
2291 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
2292 if ( node.getNodeData().getSequence().getType().toLowerCase()
2293 .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
2300 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2301 if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2309 if ( type == '?' ) {
2310 if ( SequenceAccessionTools.isProteinDbQuery( query ) ) {
2317 JApplet applet = null;
2319 applet = obtainApplet();
2322 Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
2324 catch ( final Exception e ) {
2325 e.printStackTrace();
2327 if ( Constants.ALLOW_DDBJ_BLAST ) {
2329 System.out.println( "trying: " + query );
2330 final Blast s = new Blast();
2331 s.ddbjBlast( query );
2333 catch ( final Exception e ) {
2334 e.printStackTrace();
2341 private final int calcDynamicHidingFactor() {
2342 return ( int ) ( 0.5 + ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ) );
2346 * Calculate the length of the distance between the given node and its
2352 * @return the distance value
2354 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
2355 if ( getControlPanel().isDrawPhylogram() ) {
2356 if ( node.getDistanceToParent() < 0.0 ) {
2359 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
2362 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2363 return getXdistance();
2365 return getXdistance() * factor;
2369 final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
2370 Color c = getTreeColorSet().getAnnotationColor();
2371 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
2372 final StringBuilder sb = new StringBuilder();
2373 for( final Annotation a : ann ) {
2374 sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() );
2376 final String ann_str = sb.toString();
2377 if ( !ForesterUtil.isEmpty( ann_str ) ) {
2378 c = getControlPanel().getAnnotationColors().get( ann_str );
2380 c = TreePanelUtil.calculateColorFromString( ann_str, false );
2381 getControlPanel().getAnnotationColors().put( ann_str, c );
2384 c = getTreeColorSet().getAnnotationColor();
2391 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
2392 if ( getControlPanel().isDrawPhylogram() ) {
2393 if ( node.getDistanceToParent() < 0.0 ) {
2396 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
2399 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2400 return getOvXDistance();
2402 return getOvXDistance() * factor;
2406 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
2407 JOptionPane.showMessageDialog( this,
2408 "Cannot launch web browser for " + type_type + " data of this node",
2409 "Cannot launch web browser",
2410 JOptionPane.WARNING_MESSAGE );
2413 final private void colorizeSubtree( final Color c,
2414 final PhylogenyNode node,
2415 final List<PhylogenyNode> additional_nodes ) {
2416 _control_panel.setColorBranches( true );
2417 if ( _control_panel.getColorBranchesCb() != null ) {
2418 _control_panel.getColorBranchesCb().setSelected( true );
2420 if ( node != null ) {
2421 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
2422 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
2425 if ( additional_nodes != null ) {
2426 for( final PhylogenyNode n : additional_nodes ) {
2427 n.getBranchData().setBranchColor( new BranchColor( c ) );
2433 final private void colorizeNodes( final Color c,
2434 final PhylogenyNode node,
2435 final List<PhylogenyNode> additional_nodes ) {
2436 _control_panel.setColorBranches( true );
2437 if ( _control_panel.getColorBranchesCb() != null ) {
2438 _control_panel.getColorBranchesCb().setSelected( true );
2440 if ( node != null ) {
2441 colorizeNodesHelper( c, node );
2443 if ( additional_nodes != null ) {
2444 for( final PhylogenyNode n : additional_nodes ) {
2445 colorizeNodesHelper( c, n );
2451 private final static void colorizeNodesHelper( final Color c, final PhylogenyNode node ) {
2453 if ( node.getNodeData().getNodeVisualData() != null ) {
2454 v = node.getNodeData().getNodeVisualData();
2457 v = new NodeVisualData();
2459 v.setFontColor( new Color( c.getRed(), c.getGreen(), c.getBlue() ) );
2462 final private void colorSubtree( final PhylogenyNode node ) {
2463 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2464 JOptionPane.showMessageDialog( this,
2465 "Cannot colorize subtree in unrooted display type",
2466 "Attempt to colorize subtree in unrooted display",
2467 JOptionPane.WARNING_MESSAGE );
2470 _color_chooser.setPreviewPanel( new JPanel() );
2471 SubtreeColorizationActionListener al;
2472 if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
2473 final List<PhylogenyNode> additional_nodes = getFoundNodes0AsListOfPhylogenyNodes();
2474 al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
2477 al = new SubtreeColorizationActionListener( _color_chooser, node );
2479 final JDialog dialog = JColorChooser
2480 .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
2481 dialog.setVisible( true );
2484 private void colorNodeFont( PhylogenyNode node ) {
2485 _color_chooser.setPreviewPanel( new JPanel() );
2486 NodeColorizationActionListener al;
2487 if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
2488 final List<PhylogenyNode> additional_nodes = getFoundNodes0AsListOfPhylogenyNodes();
2489 al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
2492 al = new NodeColorizationActionListener( _color_chooser, node );
2494 final JDialog dialog = JColorChooser
2495 .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
2496 dialog.setVisible( true );
2499 private void changeNodeFont( PhylogenyNode node ) {
2500 // TODO Auto-generated method stub
2503 final private void copySubtree( final PhylogenyNode node ) {
2504 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2505 errorMessageNoCutCopyPasteInUnrootedDisplay();
2508 setNodeInPreorderToNull();
2509 setCutOrCopiedTree( _phylogeny.copy( node ) );
2510 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
2511 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
2512 for( final PhylogenyNode n : nodes ) {
2513 node_ids.add( n.getId() );
2515 node_ids.add( node.getId() );
2516 setCopiedAndPastedNodes( node_ids );
2520 final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
2521 final String tax = PhylogenyMethods.getSpecies( node );
2522 String label = node.getName();
2523 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
2524 label = label + " " + tax;
2526 else if ( !ForesterUtil.isEmpty( tax ) ) {
2532 if ( !ForesterUtil.isEmpty( label ) ) {
2533 label = " [" + label + "]";
2538 final private void cutSubtree( final PhylogenyNode node ) {
2539 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2540 errorMessageNoCutCopyPasteInUnrootedDisplay();
2543 if ( node.isRoot() ) {
2544 JOptionPane.showMessageDialog( this,
2545 "Cannot cut entire tree as subtree",
2546 "Attempt to cut entire tree",
2547 JOptionPane.ERROR_MESSAGE );
2550 final String label = createASimpleTextRepresentationOfANode( node );
2551 final int r = JOptionPane.showConfirmDialog( null,
2552 "Cut subtree" + label + "?",
2553 "Confirm Cutting of Subtree",
2554 JOptionPane.YES_NO_OPTION );
2555 if ( r != JOptionPane.OK_OPTION ) {
2558 setNodeInPreorderToNull();
2559 setCopiedAndPastedNodes( null );
2560 setCutOrCopiedTree( _phylogeny.copy( node ) );
2561 _phylogeny.deleteSubtree( node, true );
2562 _phylogeny.clearHashIdToNodeMap();
2563 _phylogeny.recalculateNumberOfExternalDescendants( true );
2564 resetNodeIdToDistToLeafMap();
2569 final private void cycleColors() {
2570 getMainPanel().getTreeColorSet().cycleColorScheme();
2571 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
2572 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
2576 final private void decreaseOvSize() {
2577 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
2578 setOvMaxWidth( getOvMaxWidth() - 5 );
2579 setOvMaxHeight( getOvMaxHeight() - 5 );
2581 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2585 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
2586 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2587 errorMessageNoCutCopyPasteInUnrootedDisplay();
2590 if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
2591 JOptionPane.showMessageDialog( this,
2592 "Cannot delete entire tree",
2593 "Attempt to delete entire tree",
2594 JOptionPane.ERROR_MESSAGE );
2597 final String label = createASimpleTextRepresentationOfANode( node );
2598 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
2599 final int r = JOptionPane.showOptionDialog( this,
2600 "Delete" + label + "?",
2601 "Delete Node/Subtree",
2602 JOptionPane.CLOSED_OPTION,
2603 JOptionPane.QUESTION_MESSAGE,
2607 setNodeInPreorderToNull();
2608 boolean node_only = true;
2612 else if ( r != 0 ) {
2616 PhylogenyMethods.removeNode( node, _phylogeny );
2619 _phylogeny.deleteSubtree( node, true );
2621 _phylogeny.externalNodesHaveChanged();
2622 _phylogeny.clearHashIdToNodeMap();
2623 _phylogeny.recalculateNumberOfExternalDescendants( true );
2624 resetNodeIdToDistToLeafMap();
2629 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
2630 makePopupMenus( node );
2631 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
2632 _node_popup_menu.show( this, x, y );
2635 final private void drawArc( final double x,
2638 final double heigth,
2639 final double start_angle,
2640 final double arc_angle,
2641 final Graphics2D g ) {
2642 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
2646 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
2647 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
2650 _line.setLine( x1, y1, x2, y2 );
2654 final private void drawOval( final double x,
2657 final double heigth,
2658 final Graphics2D g ) {
2659 _ellipse.setFrame( x, y, width, heigth );
2663 final private void drawOvalFilled( final double x,
2666 final double heigth,
2667 final Graphics2D g ) {
2668 _ellipse.setFrame( x, y, width, heigth );
2672 final private void drawOvalGradient( final double x,
2675 final double heigth,
2677 final Color color_1,
2678 final Color color_2,
2679 final Color color_border ) {
2680 _ellipse.setFrame( x, y, width, heigth );
2681 g.setPaint( new GradientPaint( ( float ) x,
2684 ( float ) ( x + width ),
2685 ( float ) ( y + heigth ),
2689 if ( color_border != null ) {
2690 g.setPaint( color_border );
2695 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
2696 _rectangle.setFrame( x, y, width, heigth );
2697 g.draw( _rectangle );
2700 final private void drawRectFilled( final double x,
2703 final double heigth,
2704 final Graphics2D g ) {
2705 _rectangle.setFrame( x, y, width, heigth );
2706 g.fill( _rectangle );
2709 final private void drawRectGradient( final double x,
2712 final double heigth,
2714 final Color color_1,
2715 final Color color_2,
2716 final Color color_border ) {
2717 _rectangle.setFrame( x, y, width, heigth );
2718 g.setPaint( new GradientPaint( ( float ) x,
2721 ( float ) ( x + width ),
2722 ( float ) ( y + heigth ),
2725 g.fill( _rectangle );
2726 if ( color_border != null ) {
2727 g.setPaint( color_border );
2728 g.draw( _rectangle );
2732 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2733 final List<Uri> us = new ArrayList<Uri>();
2734 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2735 for( final Uri uri : t.getUris() ) {
2740 for( final Uri uri : us ) {
2741 if ( uri != null ) {
2742 final String uri_str = uri.getValue().toString().toLowerCase();
2743 if ( getImageMap().containsKey( uri_str ) ) {
2744 final BufferedImage bi = getImageMap().get( uri_str );
2745 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2746 double scaling_factor = 1;
2747 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
2748 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
2749 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
2751 // y = y - ( 0.9 * getYdistance() );
2752 final double hs = bi.getHeight() * scaling_factor;
2753 double ws = ( bi.getWidth() * scaling_factor ) + offset;
2754 final double my_y = y - ( 0.5 * hs );
2755 final int x_w = ( int ) ( x + ws + 0.5 );
2756 final int y_h = ( int ) ( my_y + hs + 0.5 );
2757 if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
2759 ( int ) ( x + 0.5 + offset ),
2760 ( int ) ( my_y + 0.5 ),
2781 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
2782 JOptionPane.showMessageDialog( this,
2783 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
2784 "Attempt to cut/copy/paste/add/delete in unrooted display",
2785 JOptionPane.ERROR_MESSAGE );
2788 private final Color getColorForFoundNode( final PhylogenyNode n ) {
2789 if ( isInCurrentExternalNodes( n ) ) {
2790 return getTreeColorSet().getFoundColor0();
2792 else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
2793 return getTreeColorSet().getFoundColor0();
2795 else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
2796 return getTreeColorSet().getFoundColor1();
2799 return getTreeColorSet().getFoundColor0and1();
2803 final private Set<Long> getCopiedAndPastedNodes() {
2804 return getMainPanel().getCopiedAndPastedNodes();
2807 final private Set<Long> getCurrentExternalNodes() {
2808 return _current_external_nodes;
2811 final private Phylogeny getCutOrCopiedTree() {
2812 return getMainPanel().getCutOrCopiedTree();
2815 private List<PhylogenyNode> getFoundNodes0AsListOfPhylogenyNodes() {
2816 final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
2817 for( final Long id : getFoundNodes0() ) {
2818 additional_nodes.add( _phylogeny.getNode( id ) );
2820 return additional_nodes;
2823 private List<PhylogenyNode> getFoundNodes1AsListOfPhylogenyNodes() {
2824 final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
2825 for( final Long id : getFoundNodes1() ) {
2826 additional_nodes.add( _phylogeny.getNode( id ) );
2828 return additional_nodes;
2831 final private float getLastDragPointX() {
2832 return _last_drag_point_x;
2835 final private float getLastDragPointY() {
2836 return _last_drag_point_y;
2839 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
2840 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
2841 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
2842 _nodeid_dist_to_leaf.put( node.getId(), m );
2846 return _nodeid_dist_to_leaf.get( node.getId() );
2850 final private double getMaxDistanceToRoot() {
2851 if ( _max_distance_to_root < 0 ) {
2852 recalculateMaxDistanceToRoot();
2854 return _max_distance_to_root;
2857 final private float getOvMaxHeight() {
2858 return _ov_max_height;
2861 final private float getOvMaxWidth() {
2862 return _ov_max_width;
2865 final private float getOvXcorrectionFactor() {
2866 return _ov_x_correction_factor;
2869 final private float getOvXDistance() {
2870 return _ov_x_distance;
2873 final private int getOvXPosition() {
2874 return _ov_x_position;
2877 final private float getOvYDistance() {
2878 return _ov_y_distance;
2881 final private int getOvYPosition() {
2882 return _ov_y_position;
2885 final private int getOvYStart() {
2889 final private List<Accession> getPdbAccs( final PhylogenyNode node ) {
2890 final List<Accession> pdb_ids = new ArrayList<Accession>();
2891 if ( node.getNodeData().isHasSequence() ) {
2892 final Sequence seq = node.getNodeData().getSequence();
2893 if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
2894 final SortedSet<Accession> cross_refs = seq.getCrossReferences();
2895 for( final Accession acc : cross_refs ) {
2896 if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
2905 final private double getScaleDistance() {
2906 return _scale_distance;
2909 final private String getScaleLabel() {
2910 return _scale_label;
2913 final private TreeFontSet getTreeFontSet() {
2914 return getMainPanel().getTreeFontSet();
2917 final private float getUrtFactor() {
2921 final private float getUrtFactorOv() {
2922 return _urt_factor_ov;
2925 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
2928 showNodeFrame( node );
2943 colorSubtree( node );
2945 case COLOR_NODE_FONT:
2946 colorNodeFont( node );
2948 case CHANGE_NODE_FONT:
2949 changeNodeFont( node );
2967 copySubtree( node );
2970 pasteSubtree( node );
2972 case DELETE_NODE_OR_SUBTREE:
2973 deleteNodeOrSubtree( node );
2976 addEmptyNode( node );
2978 case EDIT_NODE_DATA:
2979 showNodeEditFrame( node );
2984 case SORT_DESCENDENTS:
2985 sortDescendants( node );
2987 case GET_EXT_DESC_DATA:
2988 showExtDescNodeData( node );
2991 throw new IllegalArgumentException( "unknown action: " + action );
2995 final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
2996 _current_external_nodes_data_buffer_change_counter++;
2999 final private void increaseOvSize() {
3000 if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
3001 && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
3002 .getHeight() / 2 ) ) ) {
3003 setOvMaxWidth( getOvMaxWidth() + 5 );
3004 setOvMaxHeight( getOvMaxHeight() + 5 );
3006 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3010 final private void init() {
3011 _color_chooser = new JColorChooser();
3012 _rollover_popup = new JTextArea();
3013 _rollover_popup.setFont( POPUP_FONT );
3014 resetNodeIdToDistToLeafMap();
3016 setTreeFile( null );
3018 initializeOvSettings();
3019 setStartingAngle( ( TWO_PI * 3 ) / 4 );
3020 final ImageLoader il = new ImageLoader( this );
3021 new Thread( il ).start();
3024 final private void initializeOvSettings() {
3025 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
3026 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
3029 final private boolean inOvVirtualRectangle( final int x, final int y ) {
3030 return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
3031 && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
3032 && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
3033 + getOvVirtualRectangle().height + 1 ) ) );
3036 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
3037 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
3040 final private boolean isCanBlast( final PhylogenyNode node ) {
3041 if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
3044 return Blast.isContainsQueryForBlast( node );
3047 final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
3048 final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node );
3050 return a.getValue();
3055 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
3056 if ( node.getNodeData().isHasTaxonomy()
3057 && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
3058 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
3059 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
3060 .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
3061 .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
3069 final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
3070 return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
3073 private boolean isInFoundNodes( final PhylogenyNode n ) {
3074 return isInFoundNodes0( n ) || isInFoundNodes1( n );
3077 final private boolean isInFoundNodes0( final PhylogenyNode node ) {
3078 return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) );
3081 final private boolean isInFoundNodes1( final PhylogenyNode node ) {
3082 return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) );
3085 final private boolean isInOv() {
3089 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
3091 if ( getControlPanel().isShowTaxonomyImages() ) {
3092 y_dist = 40 + ( int ) getYdistance();
3094 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
3095 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
3096 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
3099 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
3100 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
3101 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
3102 || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
3103 .getMaxX() + 20 ) ) );
3106 final private boolean isNonLinedUpCladogram() {
3107 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
3110 final private boolean isUniformBranchLengthsForCladogram() {
3111 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
3114 final private void keyPressedCalls( final KeyEvent e ) {
3115 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
3116 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
3117 if ( !isInOvRect() ) {
3118 setInOvRect( true );
3121 else if ( isInOvRect() ) {
3122 setInOvRect( false );
3125 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
3126 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
3127 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
3128 getMainPanel().getTreeFontSet().mediumFonts();
3129 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
3131 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3132 getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
3133 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
3135 else if ( plusPressed( e.getKeyCode() ) ) {
3136 getMainPanel().getTreeFontSet().increaseFontSize();
3137 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
3141 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
3142 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
3143 getControlPanel().showWhole();
3145 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
3146 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
3147 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
3148 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
3149 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3150 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3152 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3153 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3154 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3156 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3157 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3158 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3159 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3161 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3162 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3163 Constants.WHEEL_ZOOM_IN_FACTOR );
3164 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3171 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3174 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3178 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3182 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
3183 scroll_position.x = scroll_position.x + dx;
3184 scroll_position.y = scroll_position.y + dy;
3185 if ( scroll_position.x <= 0 ) {
3186 scroll_position.x = 0;
3189 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
3190 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
3191 if ( scroll_position.x >= max_x ) {
3192 scroll_position.x = max_x;
3195 if ( scroll_position.y <= 0 ) {
3196 scroll_position.y = 0;
3199 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
3200 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
3201 if ( scroll_position.y >= max_y ) {
3202 scroll_position.y = max_y;
3206 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
3209 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3210 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3211 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3212 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3213 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3215 else if ( plusPressed( e.getKeyCode() ) ) {
3216 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3217 Constants.WHEEL_ZOOM_IN_FACTOR );
3218 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3219 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3221 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
3222 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3223 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3224 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
3225 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3228 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
3229 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3230 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3231 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
3232 if ( getStartingAngle() < 0 ) {
3233 setStartingAngle( TWO_PI + getStartingAngle() );
3235 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3238 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
3239 boolean selected = false;
3240 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
3241 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
3245 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
3247 if ( getMainPanel().getMainFrame() == null ) {
3248 // Must be "E" applet version.
3249 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
3250 if ( ae.getlabelDirectionCbmi() != null ) {
3251 ae.getlabelDirectionCbmi().setSelected( selected );
3255 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
3259 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
3260 switchDisplaygetPhylogenyGraphicsType();
3263 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
3267 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
3268 MainFrame.cycleOverview( getOptions(), this );
3271 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
3274 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
3281 final private void makePopupMenus( final PhylogenyNode node ) {
3282 _node_popup_menu = new JPopupMenu();
3283 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
3284 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
3285 for( int i = 0; i < clickto_names.size(); i++ ) {
3286 final String title = clickto_names.get( i );
3287 _node_popup_menu_items[ i ] = new JMenuItem( title );
3288 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
3289 final String id = isCanOpenSeqWeb( node );
3290 if ( !ForesterUtil.isEmpty( id ) ) {
3291 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
3292 _node_popup_menu_items[ i ].setEnabled( true );
3295 _node_popup_menu_items[ i ].setEnabled( false );
3298 else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) {
3299 final List<Accession> accs = getPdbAccs( node );
3300 _node_popup_menu_items[ i ] = new JMenuItem( title );
3301 if ( !ForesterUtil.isEmpty( accs ) ) {
3302 if ( accs.size() == 1 ) {
3303 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
3304 + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" );
3305 _node_popup_menu_items[ i ].setEnabled( true );
3307 else if ( accs.size() == 2 ) {
3308 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
3309 + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
3310 + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" );
3311 _node_popup_menu_items[ i ].setEnabled( true );
3313 else if ( accs.size() == 3 ) {
3314 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
3315 + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
3316 + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
3317 + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" );
3318 _node_popup_menu_items[ i ].setEnabled( true );
3321 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
3322 + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
3323 + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
3324 + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" );
3325 _node_popup_menu_items[ i ].setEnabled( true );
3329 _node_popup_menu_items[ i ].setEnabled( false );
3333 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
3334 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
3336 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
3337 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
3339 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
3340 if ( !getOptions().isEditable() ) {
3343 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
3345 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
3346 if ( !getOptions().isEditable() ) {
3349 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
3351 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
3352 if ( !getOptions().isEditable() ) {
3355 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
3357 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
3358 if ( !getOptions().isEditable() ) {
3361 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
3363 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
3364 if ( !getOptions().isEditable() ) {
3368 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
3369 if ( !getOptions().isEditable() ) {
3373 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
3374 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
3376 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
3377 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
3379 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
3380 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
3382 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
3383 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
3385 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
3386 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
3388 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
3389 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
3391 _node_popup_menu_items[ i ].addActionListener( this );
3392 _node_popup_menu.add( _node_popup_menu_items[ i ] );
3396 private final String obtainTitleForExtDescNodeData() {
3397 switch ( getOptions().getExtDescNodeDataToReturn() ) {
3399 return "Node Names";
3401 return "Gene Names";
3403 return "Sequence Names";
3404 case SEQUENCE_SYMBOL:
3405 return "Sequence Symbols";
3406 case SEQUENCE_MOL_SEQ:
3407 return "Molecular Sequences";
3408 case SEQUENCE_MOL_SEQ_FASTA:
3409 return "Molecular Sequences (Fasta)";
3411 return "Sequence Accessors";
3412 case TAXONOMY_SCIENTIFIC_NAME:
3413 return "Scientific Names";
3415 return "Taxonomy Codes";
3416 case TAXONOMY_COMM0N_NAME:
3417 return "Taxonomy Common Names";
3419 return "User Selected Data";
3421 throw new IllegalArgumentException( "unknown data element: "
3422 + getOptions().getExtDescNodeDataToReturn() );
3426 final private void openPdbWeb( final PhylogenyNode node ) {
3427 final List<Accession> pdb_ids = getPdbAccs( node );
3428 if ( ForesterUtil.isEmpty( pdb_ids ) ) {
3429 cannotOpenBrowserWarningMessage( "PDB" );
3432 final List<String> uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this );
3433 if ( !ForesterUtil.isEmpty( uri_strs ) ) {
3434 for( final String uri_str : uri_strs ) {
3436 AptxUtil.launchWebBrowser( new URI( uri_str ),
3438 isApplet() ? obtainApplet() : null,
3441 catch ( final IOException e ) {
3442 AptxUtil.showErrorMessage( this, e.toString() );
3443 e.printStackTrace();
3445 catch ( final URISyntaxException e ) {
3446 AptxUtil.showErrorMessage( this, e.toString() );
3447 e.printStackTrace();
3452 cannotOpenBrowserWarningMessage( "PDB" );
3456 final private void openSeqWeb( final PhylogenyNode node ) {
3457 if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
3458 cannotOpenBrowserWarningMessage( "sequence" );
3461 final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
3462 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3464 AptxUtil.launchWebBrowser( new URI( uri_str ),
3466 isApplet() ? obtainApplet() : null,
3469 catch ( final IOException e ) {
3470 AptxUtil.showErrorMessage( this, e.toString() );
3471 e.printStackTrace();
3473 catch ( final URISyntaxException e ) {
3474 AptxUtil.showErrorMessage( this, e.toString() );
3475 e.printStackTrace();
3479 cannotOpenBrowserWarningMessage( "sequence" );
3483 final private void openTaxWeb( final PhylogenyNode node ) {
3484 if ( !isCanOpenTaxWeb( node ) ) {
3485 cannotOpenBrowserWarningMessage( "taxonomic" );
3488 String uri_str = null;
3489 final Taxonomy tax = node.getNodeData().getTaxonomy();
3490 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3491 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
3493 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
3495 catch ( final URISyntaxException e ) {
3496 AptxUtil.showErrorMessage( this, e.toString() );
3498 e.printStackTrace();
3501 else if ( ( tax.getIdentifier() != null )
3502 && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3503 && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
3504 && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
3505 .equalsIgnoreCase( "uniprot" ) ) ) {
3507 uri_str = "http://www.uniprot.org/taxonomy/"
3508 + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
3510 catch ( final UnsupportedEncodingException e ) {
3511 AptxUtil.showErrorMessage( this, e.toString() );
3512 e.printStackTrace();
3515 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
3517 uri_str = "http://www.uniprot.org/taxonomy/?query="
3518 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
3520 catch ( final UnsupportedEncodingException e ) {
3521 AptxUtil.showErrorMessage( this, e.toString() );
3522 e.printStackTrace();
3525 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
3527 uri_str = "http://www.uniprot.org/taxonomy/?query="
3528 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
3530 catch ( final UnsupportedEncodingException e ) {
3531 AptxUtil.showErrorMessage( this, e.toString() );
3532 e.printStackTrace();
3535 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
3537 uri_str = "http://www.uniprot.org/taxonomy/?query="
3538 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
3540 catch ( final UnsupportedEncodingException e ) {
3541 AptxUtil.showErrorMessage( this, e.toString() );
3542 e.printStackTrace();
3545 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3547 AptxUtil.launchWebBrowser( new URI( uri_str ),
3549 isApplet() ? obtainApplet() : null,
3552 catch ( final IOException e ) {
3553 AptxUtil.showErrorMessage( this, e.toString() );
3554 e.printStackTrace();
3556 catch ( final URISyntaxException e ) {
3557 AptxUtil.showErrorMessage( this, e.toString() );
3558 e.printStackTrace();
3562 cannotOpenBrowserWarningMessage( "taxonomic" );
3566 final private void paintBranchLength( final Graphics2D g,
3567 final PhylogenyNode node,
3568 final boolean to_pdf,
3569 final boolean to_graphics_file ) {
3570 g.setFont( getTreeFontSet().getSmallFont() );
3571 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3572 g.setColor( Color.BLACK );
3575 g.setColor( getTreeColorSet().getBranchLengthColor() );
3577 if ( !node.isRoot() ) {
3578 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3579 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3580 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3582 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3583 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3584 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3587 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3588 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3592 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
3593 - getTreeFontSet()._small_max_descent, g );
3597 final private void paintBranchLite( final Graphics2D g,
3602 final PhylogenyNode node ) {
3603 g.setColor( getTreeColorSet().getOvColor() );
3604 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3605 drawLine( x1, y1, x2, y2, g );
3607 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3608 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3609 ( g ).draw( _quad_curve );
3611 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3612 final float dx = x2 - x1;
3613 final float dy = y2 - y1;
3614 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3615 + ( dy * 0.8f ), x2, y2 );
3616 ( g ).draw( _cubic_curve );
3619 final float x2a = x2;
3620 final float x1a = x1;
3621 // draw the vertical line
3622 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
3623 drawLine( x1, y1, x1, y2, g );
3625 // draw the horizontal line
3626 drawLine( x1a, y2, x2a, y2, g );
3631 * Paint a branch which consists of a vertical and a horizontal bar
3632 * @param is_ind_found_nodes
3634 final private void paintBranchRectangular( final Graphics2D g,
3639 final PhylogenyNode node,
3640 final boolean to_pdf,
3641 final boolean to_graphics_file ) {
3642 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
3643 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3644 drawLine( x1, y1, x2, y2, g );
3646 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3647 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3648 g.draw( _quad_curve );
3650 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3651 final float dx = x2 - x1;
3652 final float dy = y2 - y1;
3653 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3654 + ( dy * 0.8f ), x2, y2 );
3655 g.draw( _cubic_curve );
3658 final float x2a = x2;
3659 final float x1a = x1;
3661 if ( node.isFirstChildNode() || node.isLastChildNode()
3662 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3663 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3664 if ( !to_graphics_file
3666 && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
3667 .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
3671 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3672 float x2c = x1 + EURO_D;
3676 drawLine( x1, y1, x2c, y2, g );
3678 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3680 y2_r = y2 - ROUNDED_D;
3684 drawLine( x1, y1, x1, y2_r, g );
3687 y2_r = y2 + ROUNDED_D;
3691 drawLine( x1, y1, x1, y2_r, g );
3695 drawLine( x1, y1, x1, y2, g );
3699 // draw the horizontal line
3700 if ( !to_graphics_file && !to_pdf
3701 && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
3705 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
3706 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3707 x1_r = x1a + ROUNDED_D;
3709 drawLine( x1_r, y2, x2a, y2, g );
3712 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3713 final float x1c = x1a + EURO_D;
3715 drawLine( x1c, y2, x2a, y2, g );
3719 drawLine( x1a, y2, x2a, y2, g );
3723 final double w = PhylogenyMethods.getBranchWidthValue( node );
3724 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3725 x1_r = x1a + ROUNDED_D;
3727 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
3730 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3731 final float x1c = x1a + EURO_D;
3733 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
3737 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
3740 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3745 final double diff = y2 - y2_r;
3746 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
3749 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
3754 if ( node.isExternal() ) {
3755 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file );
3759 final private double paintCirculars( final PhylogenyNode n,
3760 final Phylogeny phy,
3761 final float center_x,
3762 final float center_y,
3763 final double radius,
3764 final boolean radial_labels,
3766 final boolean to_pdf,
3767 final boolean to_graphics_file ) {
3768 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
3769 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
3770 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
3772 return _urt_nodeid_angle_map.get( n.getId() );
3775 final List<PhylogenyNode> descs = n.getDescendants();
3777 for( final PhylogenyNode desc : descs ) {
3778 sum += paintCirculars( desc,
3789 if ( !n.isRoot() ) {
3790 r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3792 final double theta = sum / descs.size();
3793 n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
3794 n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
3795 _urt_nodeid_angle_map.put( n.getId(), theta );
3796 for( final PhylogenyNode desc : descs ) {
3797 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
3803 final private void paintCircularsLite( final PhylogenyNode n,
3804 final Phylogeny phy,
3808 final Graphics2D g ) {
3809 if ( n.isExternal() ) {
3813 final List<PhylogenyNode> descs = n.getDescendants();
3814 for( final PhylogenyNode desc : descs ) {
3815 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
3818 if ( !n.isRoot() ) {
3819 r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3821 final double theta = _urt_nodeid_angle_map.get( n.getId() );
3822 n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
3823 n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
3824 for( final PhylogenyNode desc : descs ) {
3825 paintBranchCircularLite( n, desc, g );
3830 final private void paintCollapsedNode( final Graphics2D g,
3831 final PhylogenyNode node,
3832 final boolean to_graphics_file,
3833 final boolean to_pdf,
3834 final boolean is_in_found_nodes ) {
3836 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3839 else if ( is_in_found_nodes ) {
3840 c = getColorForFoundNode( node );
3842 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3843 c = getTaxonomyBasedColor( node );
3845 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3846 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3847 c = PhylogenyMethods.getBranchColorValue( node );
3850 c = getTreeColorSet().getCollapseFillColor();
3852 double d = node.getAllExternalDescendants().size();
3854 d = ( 3 * _y_distance ) / 3;
3857 d = ( Math.log10( d ) * _y_distance ) / 2.5;
3859 final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
3860 if ( d < box_size ) {
3863 final float xx = node.getXcoord() - ( 2 * box_size );
3864 final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
3866 _polygon.moveTo( xxx, node.getYcoord() );
3867 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
3868 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
3869 _polygon.closePath();
3870 if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
3874 else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
3875 g.setColor( getBackground() );
3880 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3881 g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
3882 .getYcoord() - d ), c, false ) );
3887 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3890 final private void paintConfidenceValues( final Graphics2D g,
3891 final PhylogenyNode node,
3892 final boolean to_pdf,
3893 final boolean to_graphics_file ) {
3894 final List<Confidence> confidences = node.getBranchData().getConfidences();
3895 boolean not_first = false;
3896 Collections.sort( confidences );
3897 final StringBuilder sb = new StringBuilder();
3898 for( final Confidence confidence : confidences ) {
3899 final double value = confidence.getValue();
3900 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3901 if ( value < getOptions().getMinConfidenceValue() ) {
3910 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
3911 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3912 if ( getOptions().isShowConfidenceStddev() ) {
3913 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3915 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
3917 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3923 if ( sb.length() > 0 ) {
3924 final double parent_x = node.getParent().getXcoord();
3925 double x = node.getXcoord();
3926 g.setFont( getTreeFontSet().getSmallFont() );
3927 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3930 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3933 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3934 g.setColor( Color.BLACK );
3937 g.setColor( getTreeColorSet().getConfidenceColor() );
3939 final String conf_str = sb.toString();
3941 .drawString( conf_str,
3943 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
3944 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
3949 final private void paintGainedAndLostCharacters( final Graphics2D g,
3950 final PhylogenyNode node,
3951 final String gained,
3952 final String lost ) {
3953 if ( node.getParent() != null ) {
3954 final double parent_x = node.getParent().getXcoord();
3955 final double x = node.getXcoord();
3956 g.setFont( getTreeFontSet().getLargeFont() );
3957 g.setColor( getTreeColorSet().getGainedCharactersColor() );
3958 if ( Constants.SPECIAL_CUSTOM ) {
3959 g.setColor( Color.BLUE );
3962 .drawString( gained,
3963 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
3964 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
3966 g.setColor( getTreeColorSet().getLostCharactersColor() );
3967 TreePanel.drawString( lost,
3968 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
3969 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
3975 * Draw a box at the indicated node.
3982 final private void paintNodeBox( final double x,
3984 final PhylogenyNode node,
3986 final boolean to_pdf,
3987 final boolean to_graphics_file ) {
3988 if ( node.isCollapse() ) {
3991 // if this node should be highlighted, do so
3992 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
3993 g.setColor( getTreeColorSet().getFoundColor0() );
3994 drawOval( x - 8, y - 8, 16, 16, g );
3995 drawOval( x - 9, y - 8, 17, 17, g );
3996 drawOval( x - 9, y - 9, 18, 18, g );
3998 if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
3999 || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
4000 || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
4001 || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
4003 || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
4004 .isSpeciationOrDuplication() ) ) ) {
4005 final double box_size = getOptions().getDefaultNodeShapeSize();
4006 final double half_box_size = box_size / 2.0;
4007 Color outline_color = null;
4008 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4009 outline_color = Color.BLACK;
4011 else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4012 outline_color = getColorForFoundNode( node );
4014 else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
4015 final Event event = node.getNodeData().getEvent();
4016 if ( event.isDuplication() ) {
4017 outline_color = getTreeColorSet().getDuplicationBoxColor();
4019 else if ( event.isSpeciation() ) {
4020 outline_color = getTreeColorSet().getSpecBoxColor();
4022 else if ( event.isSpeciationOrDuplication() ) {
4023 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
4027 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
4028 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
4029 outline_color = getTreeColorSet().getBranchColorForPdf();
4032 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
4033 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
4034 drawOvalGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
4035 : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
4037 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
4038 Color background = getBackground();
4040 background = Color.WHITE;
4042 drawOvalGradient( x - half_box_size,
4051 else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
4052 g.setColor( outline_color );
4053 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
4056 else if ( getOptions().getDefaultNodeShape() == NodeVisualData.NodeShape.RECTANGLE ) {
4057 if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.GRADIENT ) {
4058 drawRectGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
4059 : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
4061 else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
4062 Color background = getBackground();
4064 background = Color.WHITE;
4066 drawRectGradient( x - half_box_size,
4075 else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
4076 g.setColor( outline_color );
4077 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
4083 final private void paintNodeData( final Graphics2D g,
4084 final PhylogenyNode node,
4085 final boolean to_graphics_file,
4086 final boolean to_pdf,
4087 final boolean is_in_found_nodes ) {
4088 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
4091 if ( getOptions().isShowBranchLengthValues()
4092 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4093 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4094 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
4095 paintBranchLength( g, node, to_pdf, to_graphics_file );
4097 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
4102 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
4103 if ( getControlPanel().isShowTaxonomyImages()
4104 && ( getImageMap() != null )
4105 && !getImageMap().isEmpty()
4106 && node.getNodeData().isHasTaxonomy()
4107 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
4108 .getUris().isEmpty() ) ) {
4109 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
4111 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4112 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
4113 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
4115 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4116 g.setColor( Color.BLACK );
4118 else if ( is_in_found_nodes ) {
4119 g.setColor( getColorForFoundNode( node ) );
4121 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4122 g.setColor( getTaxonomyBasedColor( node ) );
4124 else if ( getControlPanel().isColorAccordingToAnnotation()
4125 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4126 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4127 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4129 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4130 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4131 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4133 else if ( to_pdf ) {
4134 g.setColor( Color.BLACK );
4137 g.setColor( getTreeColorSet().getSequenceColor() );
4139 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4140 if ( _sb.length() > 0 ) {
4143 _sb.append( node.getAllExternalDescendants().size() );
4150 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4151 if ( _sb.length() > 0 ) {
4154 _sb.append( node.getName() );
4156 if ( node.getNodeData().isHasSequence() ) {
4157 if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
4158 if ( _sb.length() > 0 ) {
4161 _sb.append( node.getNodeData().getSequence().getSymbol() );
4163 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
4164 if ( _sb.length() > 0 ) {
4167 _sb.append( node.getNodeData().getSequence().getGeneName() );
4169 if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4170 if ( _sb.length() > 0 ) {
4173 _sb.append( node.getNodeData().getSequence().getName() );
4175 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4176 if ( _sb.length() > 0 ) {
4179 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4180 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4183 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4186 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
4187 if ( _sb.length() > 0 ) {
4190 _sb.append( propertiesToString( node ) );
4192 g.setFont( getTreeFontSet().getLargeFont() );
4193 if ( is_in_found_nodes ) {
4194 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4196 double down_shift_factor = 3.0;
4197 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
4198 down_shift_factor = 1;
4200 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
4201 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
4202 final String sb_str = _sb.toString();
4203 // GUILHEM_BEG ______________
4204 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
4205 && ( _query_sequence != null ) ) {
4206 int nodeTextBoundsWidth = 0;
4207 if ( sb_str.length() > 0 ) {
4208 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
4209 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
4211 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
4212 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
4213 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
4214 g.setColor( getTreeColorSet().getBackgroundColor() );
4218 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
4219 for( final SequenceRelation seqRelation : seqRelations ) {
4220 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
4221 .getRef1().isEqual( _query_sequence ) )
4222 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
4223 .getSelectedItem() );
4224 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
4225 final double linePosX = node.getXcoord() + 2 + half_box_size;
4226 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
4227 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
4229 if ( sConfidence != null ) {
4230 double confidenceX = pos_x;
4231 if ( sb_str.length() > 0 ) {
4232 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
4233 + CONFIDENCE_LEFT_MARGIN;
4235 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
4236 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
4237 .getBounds().getWidth();
4238 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
4239 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
4242 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
4244 if ( nodeTextBoundsWidth == 0 ) {
4245 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
4248 nodeTextBoundsWidth += 2;
4250 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
4251 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
4258 if ( sb_str.length() > 0 ) {
4259 TreePanel.drawString( sb_str, pos_x, pos_y, g );
4261 // GUILHEM_END _____________
4262 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
4263 // TODO FIXME need to check this one!
4264 //if ( _sb.length() > 0 ) {
4265 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
4266 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4268 // COMMENTED_OUT_BY_GUILHEM_END ________________
4269 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
4270 && ( node.getNodeData().getSequence().getAnnotations() != null )
4271 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4272 if ( _sb.length() > 0 ) {
4273 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4275 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
4276 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4277 g.setColor( Color.BLACK );
4279 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
4280 g.setColor( calculateColorForAnnotation( ann ) );
4282 final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
4283 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
4284 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4286 _sb.append( ann_str );
4288 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4289 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
4290 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
4291 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
4292 && node.getNodeData().isHasBinaryCharacters() ) {
4293 if ( _sb.length() > 0 ) {
4294 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4296 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4297 g.setColor( Color.BLACK );
4300 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
4302 if ( getControlPanel().isShowBinaryCharacters() ) {
4303 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
4304 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
4305 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4306 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
4307 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
4308 .getLostCharactersAsStringBuffer().toString() );
4311 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
4312 node.getXcoord() + x + 4 + half_box_size,
4314 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
4316 paintGainedAndLostCharacters( g, node, "+"
4317 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
4318 + node.getNodeData().getBinaryCharacters().getLostCount() );
4324 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
4325 final PhylogenyNode node,
4326 final boolean to_pdf,
4327 final boolean to_graphics_file,
4328 final boolean radial_labels,
4329 final double ur_angle,
4330 final boolean is_in_found_nodes ) {
4331 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
4334 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4335 g.setColor( Color.BLACK );
4337 else if ( is_in_found_nodes ) {
4338 g.setColor( getColorForFoundNode( node ) );
4340 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4341 g.setColor( getTaxonomyBasedColor( node ) );
4343 else if ( getControlPanel().isColorAccordingToAnnotation()
4344 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4345 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4346 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4349 g.setColor( getTreeColorSet().getSequenceColor() );
4353 if ( node.getNodeData().isHasTaxonomy()
4354 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4355 .isShowTaxonomyCommonNames() ) ) {
4356 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4357 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4358 _sb.append( taxonomy.getTaxonomyCode() );
4361 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4362 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4363 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4364 _sb.append( taxonomy.getScientificName() );
4366 _sb.append( taxonomy.getCommonName() );
4369 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4370 _sb.append( taxonomy.getScientificName() );
4373 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4374 _sb.append( taxonomy.getCommonName() );
4378 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4379 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4380 _sb.append( taxonomy.getScientificName() );
4384 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4385 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4386 _sb.append( taxonomy.getCommonName() );
4391 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4393 _sb.append( node.getAllExternalDescendants().size() );
4396 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4397 if ( _sb.length() > 0 ) {
4400 _sb.append( node.getName() );
4402 if ( node.getNodeData().isHasSequence() ) {
4403 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4404 if ( _sb.length() > 0 ) {
4407 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4408 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4411 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4413 if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4414 if ( _sb.length() > 0 ) {
4417 _sb.append( node.getNodeData().getSequence().getName() );
4420 g.setFont( getTreeFontSet().getLargeFont() );
4421 if ( is_in_found_nodes ) {
4422 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4424 if ( _sb.length() > 1 ) {
4425 final String sb_str = _sb.toString();
4427 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4428 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
4431 m = ( float ) ( ur_angle % TWO_PI );
4433 _at = g.getTransform();
4434 boolean need_to_reset = false;
4435 final float x_coord = node.getXcoord();
4436 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
4437 if ( radial_labels ) {
4438 need_to_reset = true;
4439 boolean left = false;
4440 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4444 g.rotate( m, x_coord, node.getYcoord() );
4446 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
4450 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4451 need_to_reset = true;
4452 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
4455 TreePanel.drawString( sb_str, x_coord, y_coord, g );
4456 if ( need_to_reset ) {
4457 g.setTransform( _at );
4462 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
4463 if ( node.isCollapse() ) {
4464 if ( !node.isRoot() && !node.getParent().isCollapse() ) {
4465 paintCollapsedNode( g, node, false, false, false );
4469 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4470 g.setColor( getColorForFoundNode( node ) );
4471 drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, node.getYSecondary()
4472 - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
4475 if ( !node.isExternal() && !node.isCollapse() ) {
4476 boolean first_child = true;
4478 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4479 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4480 final PhylogenyNode child_node = node.getChildNode( i );
4482 if ( !isUniformBranchLengthsForCladogram() ) {
4483 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4486 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4488 if ( first_child ) {
4489 first_child = false;
4490 y2 = node.getYSecondary()
4491 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
4492 .getNumberOfExternalNodes() ) );
4495 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4497 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
4498 new_x = x2 + node.getXSecondary();
4499 final float diff_y = node.getYSecondary() - y2;
4500 final float diff_x = node.getXSecondary() - new_x;
4501 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
4502 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
4504 child_node.setXSecondary( new_x );
4505 child_node.setYSecondary( y2 );
4506 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4511 final private void paintNodeRectangular( final Graphics2D g,
4512 final PhylogenyNode node,
4513 final boolean to_pdf,
4514 final boolean dynamically_hide,
4515 final int dynamic_hiding_factor,
4516 final boolean to_graphics_file ) {
4517 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
4518 if ( node.isCollapse() ) {
4519 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
4520 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4524 if ( node.isExternal() ) {
4525 ++_external_node_index;
4527 // Confidence values
4528 if ( getControlPanel().isShowConfidenceValues()
4529 && !node.isExternal()
4531 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
4532 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4533 && node.getBranchData().isHasConfidences() ) {
4534 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
4536 // Draw a line to root:
4537 if ( node.isRoot() && _phylogeny.isRooted() ) {
4538 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
4541 float new_x_min = Float.MAX_VALUE;
4542 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
4543 float min_dist = 1.5f;
4544 if ( !disallow_shortcutting ) {
4545 // System.out.println( dynamic_hiding_factor );
4546 if ( dynamic_hiding_factor > 4000 ) {
4549 else if ( dynamic_hiding_factor > 1000 ) {
4552 else if ( dynamic_hiding_factor > 100 ) {
4556 if ( !node.isExternal() && !node.isCollapse() ) {
4557 boolean first_child = true;
4559 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4560 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4561 final PhylogenyNode child_node = node.getChildNode( i );
4563 if ( !isUniformBranchLengthsForCladogram() ) {
4564 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4567 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4569 if ( first_child ) {
4570 first_child = false;
4571 y2 = node.getYcoord()
4572 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
4575 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4577 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
4578 new_x = x2 + node.getXcoord();
4579 if ( dynamically_hide && ( x2 < new_x_min ) ) {
4582 final float diff_y = node.getYcoord() - y2;
4583 final float diff_x = node.getXcoord() - new_x;
4584 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
4585 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
4586 paintBranchRectangular( g,
4595 child_node.setXcoord( new_x );
4596 child_node.setYcoord( y2 );
4597 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4599 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
4601 if ( dynamically_hide
4602 && !is_in_found_nodes
4603 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
4604 .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
4605 .getHeight() ) ) ) ) ) {
4608 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4609 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
4612 final private void paintNodeWithRenderableData( final Graphics2D g,
4613 final PhylogenyNode node,
4614 final boolean to_graphics_file,
4615 final boolean to_pdf ) {
4616 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
4619 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
4622 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4623 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4624 RenderableDomainArchitecture rds = null;
4625 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
4627 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
4629 catch ( final ClassCastException cce ) {
4630 cce.printStackTrace();
4632 if ( rds != null ) {
4633 rds.setRenderingHeight( 6 );
4635 if ( node.getNodeData().isHasTaxonomy() ) {
4636 if ( getControlPanel().isShowTaxonomyCode()
4637 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
4638 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4642 if ( getControlPanel().isShowTaxonomyScientificNames()
4643 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
4644 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4645 .getScientificName()
4648 if ( getControlPanel().isShowTaxonomyCommonNames()
4649 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
4650 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4655 if ( node.getNodeData().isHasSequence() ) {
4656 if ( getControlPanel().isShowSeqNames()
4657 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
4658 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
4661 if ( getControlPanel().isShowSeqSymbols()
4662 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
4663 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
4666 if ( getControlPanel().isShowGeneNames()
4667 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) ) {
4668 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getGeneName()
4671 if ( getControlPanel().isShowSequenceAcc()
4672 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4673 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
4674 .getAccession().toString()
4677 if ( getControlPanel().isShowAnnotation()
4678 && ( node.getNodeData().getSequence().getAnnotations() != null )
4679 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4680 x += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
4681 .getNodeData().getSequence().getAnnotations(), getOptions()
4682 .isShowAnnotationRefSource() )
4686 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
4687 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
4689 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
4694 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4695 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
4696 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
4697 getStatisticsForExpressionValues(),
4698 getConfiguration() );
4701 PhylogenyNode my_node = node;
4702 if ( !getControlPanel().isDrawPhylogram() ) {
4703 my_node = getPhylogeny().getFirstExternalNode();
4705 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
4706 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
4708 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
4709 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
4711 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
4717 final private void paintOvRectangle( final Graphics2D g ) {
4718 final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
4719 final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
4720 final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
4721 final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
4722 final float width = getOvMaxWidth() / w_ratio;
4723 final float height = getOvMaxHeight() / h_ratio;
4724 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
4725 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
4726 g.setColor( getTreeColorSet().getFoundColor0() );
4727 getOvRectangle().setRect( x, y, width, height );
4728 final Stroke s = g.getStroke();
4729 g.setStroke( STROKE_1 );
4730 if ( ( width < 6 ) && ( height < 6 ) ) {
4731 drawRectFilled( x, y, 6, 6, g );
4732 getOvVirtualRectangle().setRect( x, y, 6, 6 );
4734 else if ( width < 6 ) {
4735 drawRectFilled( x, y, 6, height, g );
4736 getOvVirtualRectangle().setRect( x, y, 6, height );
4738 else if ( height < 6 ) {
4739 drawRectFilled( x, y, width, 6, g );
4740 getOvVirtualRectangle().setRect( x, y, width, 6 );
4743 drawRect( x, y, width, height, g );
4744 if ( isInOvRect() ) {
4745 drawRect( x + 1, y + 1, width - 2, height - 2, g );
4747 getOvVirtualRectangle().setRect( x, y, width, height );
4752 final private void paintPhylogenyLite( final Graphics2D g ) {
4755 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
4756 .getWidth() ) ) ) );
4757 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
4758 final Stroke s = g.getStroke();
4759 g.setStroke( STROKE_05 );
4760 for( final PhylogenyNode element : _nodes_in_preorder ) {
4761 paintNodeLite( g, element );
4764 paintOvRectangle( g );
4768 * Paint the root branch. (Differs from others because it will always be a
4769 * single horizontal line).
4770 * @param to_graphics_file
4772 * @return new x1 value
4774 final private void paintRootBranch( final Graphics2D g,
4777 final PhylogenyNode root,
4778 final boolean to_pdf,
4779 final boolean to_graphics_file ) {
4780 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
4781 float d = getXdistance();
4782 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
4783 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
4785 if ( d < MIN_ROOT_LENGTH ) {
4786 d = MIN_ROOT_LENGTH;
4788 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
4789 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
4792 final double w = PhylogenyMethods.getBranchWidthValue( root );
4793 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
4795 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file );
4798 final private void paintScale( final Graphics2D g,
4801 final boolean to_pdf,
4802 final boolean to_graphics_file ) {
4804 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
4806 final int y2 = y1 - 8;
4807 final int y3 = y1 - 4;
4808 g.setFont( getTreeFontSet().getSmallFont() );
4809 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4810 g.setColor( Color.BLACK );
4813 g.setColor( getTreeColorSet().getBranchLengthColor() );
4815 final Stroke s = g.getStroke();
4816 g.setStroke( STROKE_1 );
4817 drawLine( x1, y1, x1, y2, g );
4818 drawLine( x2, y1, x2, y2, g );
4819 drawLine( x1, y3, x2, y3, g );
4820 if ( getScaleLabel() != null ) {
4821 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
4826 final private int paintTaxonomy( final Graphics2D g,
4827 final PhylogenyNode node,
4828 final boolean is_in_found_nodes,
4829 final boolean to_pdf,
4830 final boolean to_graphics_file,
4831 final double x_shift ) {
4832 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4833 g.setFont( getTreeFontSet().getLargeItalicFont() );
4834 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4835 g.setColor( Color.BLACK );
4837 else if ( is_in_found_nodes ) {
4838 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
4839 g.setColor( getColorForFoundNode( node ) );
4841 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4842 g.setColor( getTaxonomyBasedColor( node ) );
4844 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4845 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4846 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4848 else if ( to_pdf ) {
4849 g.setColor( Color.BLACK );
4852 g.setColor( getTreeColorSet().getTaxonomyColor() );
4854 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4855 final double start_y = node.getYcoord()
4856 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4858 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4859 _sb.append( taxonomy.getTaxonomyCode() );
4862 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4863 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4864 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4865 if ( getOptions().isAbbreviateScientificTaxonNames()
4866 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4867 abbreviateScientificName( taxonomy.getScientificName() );
4870 _sb.append( taxonomy.getScientificName() );
4873 _sb.append( taxonomy.getCommonName() );
4876 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4877 if ( getOptions().isAbbreviateScientificTaxonNames()
4878 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4879 abbreviateScientificName( taxonomy.getScientificName() );
4882 _sb.append( taxonomy.getScientificName() );
4886 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4887 _sb.append( taxonomy.getCommonName() );
4891 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4892 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4893 if ( getOptions().isAbbreviateScientificTaxonNames()
4894 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4895 abbreviateScientificName( taxonomy.getScientificName() );
4898 _sb.append( taxonomy.getScientificName() );
4903 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4904 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4905 _sb.append( taxonomy.getCommonName() );
4909 final String label = _sb.toString();
4911 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4912 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4913 // invert font color and background color to show that this is the query sequence
4914 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4918 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4919 g.setColor( getTreeColorSet().getBackgroundColor() );
4922 TreePanel.drawString( label, start_x, start_y, g );
4923 if ( is_in_found_nodes ) {
4924 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4927 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4931 final private void paintUnrooted( final PhylogenyNode n,
4932 final double low_angle,
4933 final double high_angle,
4934 final boolean radial_labels,
4936 final boolean to_pdf,
4937 final boolean to_graphics_file ) {
4939 n.setXcoord( getWidth() / 2 );
4940 n.setYcoord( getHeight() / 2 );
4942 if ( n.isExternal() ) {
4943 paintNodeDataUnrootedCirc( g,
4948 ( high_angle + low_angle ) / 2,
4949 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
4952 final float num_enclosed = n.getNumberOfExternalNodes();
4953 final float x = n.getXcoord();
4954 final float y = n.getYcoord();
4955 double current_angle = low_angle;
4956 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4957 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4958 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4959 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4960 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4961 final PhylogenyNode desc = n.getChildNode( i );
4962 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4963 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4964 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4965 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4968 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4971 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4974 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4975 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4977 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4978 if ( desc.getDistanceToParent() < 0 ) {
4982 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4986 length = getUrtFactor();
4988 final double mid_angle = current_angle + ( arc_size / 2 );
4989 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4990 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4991 desc.setXcoord( new_x );
4992 desc.setYcoord( new_y );
4993 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4994 current_angle += arc_size;
4995 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4996 drawLine( x, y, new_x, new_y, g );
4997 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file );
5000 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file );
5004 final private void paintUnrootedLite( final PhylogenyNode n,
5005 final double low_angle,
5006 final double high_angle,
5008 final float urt_ov_factor ) {
5010 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
5011 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
5012 n.setXSecondary( x_pos );
5013 n.setYSecondary( y_pos );
5015 if ( n.isExternal() ) {
5018 final float num_enclosed = n.getNumberOfExternalNodes();
5019 final float x = n.getXSecondary();
5020 final float y = n.getYSecondary();
5021 double current_angle = low_angle;
5022 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
5023 final PhylogenyNode desc = n.getChildNode( i );
5024 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
5025 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
5027 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
5028 if ( desc.getDistanceToParent() < 0 ) {
5032 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
5036 length = urt_ov_factor;
5038 final double mid_angle = current_angle + ( arc_size / 2 );
5039 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
5040 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
5041 desc.setXSecondary( new_x );
5042 desc.setYSecondary( new_y );
5043 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
5044 g.setColor( getColorForFoundNode( desc ) );
5045 drawRectFilled( desc.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
5046 desc.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
5047 OVERVIEW_FOUND_NODE_BOX_SIZE,
5048 OVERVIEW_FOUND_NODE_BOX_SIZE,
5050 g.setColor( getTreeColorSet().getOvColor() );
5052 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
5053 current_angle += arc_size;
5054 drawLine( x, y, new_x, new_y, g );
5058 final private void pasteSubtree( final PhylogenyNode node ) {
5059 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5060 errorMessageNoCutCopyPasteInUnrootedDisplay();
5063 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
5064 JOptionPane.showMessageDialog( this,
5065 "No tree in buffer (need to copy or cut a subtree first)",
5066 "Attempt to paste with empty buffer",
5067 JOptionPane.ERROR_MESSAGE );
5070 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
5071 final Object[] options = { "As sibling", "As descendant", "Cancel" };
5072 final int r = JOptionPane.showOptionDialog( this,
5073 "How to paste subtree" + label + "?",
5075 JOptionPane.CLOSED_OPTION,
5076 JOptionPane.QUESTION_MESSAGE,
5080 boolean paste_as_sibling = true;
5082 paste_as_sibling = false;
5084 else if ( r != 0 ) {
5087 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
5088 buffer_phy.setAllNodesToNotCollapse();
5089 PhylogenyMethods.preOrderReId( buffer_phy );
5090 buffer_phy.setRooted( true );
5091 boolean need_to_show_whole = false;
5092 if ( paste_as_sibling ) {
5093 if ( node.isRoot() ) {
5094 JOptionPane.showMessageDialog( this,
5095 "Cannot paste sibling to root",
5096 "Attempt to paste sibling to root",
5097 JOptionPane.ERROR_MESSAGE );
5100 buffer_phy.addAsSibling( node );
5103 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
5104 need_to_show_whole = true;
5105 _phylogeny = buffer_phy;
5108 buffer_phy.addAsChild( node );
5111 if ( getCopiedAndPastedNodes() == null ) {
5112 setCopiedAndPastedNodes( new HashSet<Long>() );
5114 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
5115 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
5116 for( final PhylogenyNode n : nodes ) {
5117 node_ids.add( n.getId() );
5119 node_ids.add( node.getId() );
5120 getCopiedAndPastedNodes().addAll( node_ids );
5121 setNodeInPreorderToNull();
5122 _phylogeny.externalNodesHaveChanged();
5123 _phylogeny.clearHashIdToNodeMap();
5124 _phylogeny.recalculateNumberOfExternalDescendants( true );
5125 resetNodeIdToDistToLeafMap();
5127 if ( need_to_show_whole ) {
5128 getControlPanel().showWhole();
5133 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
5134 final PropertiesMap properties = node.getNodeData().getProperties();
5135 final StringBuffer sb = new StringBuffer();
5136 boolean first = true;
5137 for( final String ref : properties.getPropertyRefs() ) {
5144 final Property p = properties.getProperty( ref );
5145 sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
5147 sb.append( p.getValue() );
5148 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5149 sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
5155 final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
5156 getMainPanel().setCopiedAndPastedNodes( nodeIds );
5159 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
5160 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
5163 final private void setInOv( final boolean in_ov ) {
5167 final private void setOvMaxHeight( final float ov_max_height ) {
5168 _ov_max_height = ov_max_height;
5171 final private void setOvMaxWidth( final float ov_max_width ) {
5172 _ov_max_width = ov_max_width;
5175 final private void setOvXcorrectionFactor( final float f ) {
5176 _ov_x_correction_factor = f;
5179 final private void setOvXDistance( final float ov_x_distance ) {
5180 _ov_x_distance = ov_x_distance;
5183 final private void setOvXPosition( final int ov_x_position ) {
5184 _ov_x_position = ov_x_position;
5187 final private void setOvYDistance( final float ov_y_distance ) {
5188 _ov_y_distance = ov_y_distance;
5191 final private void setOvYPosition( final int ov_y_position ) {
5192 _ov_y_position = ov_y_position;
5195 final private void setOvYStart( final int ov_y_start ) {
5196 _ov_y_start = ov_y_start;
5199 final private void setScaleDistance( final double scale_distance ) {
5200 _scale_distance = scale_distance;
5203 final private void setScaleLabel( final String scale_label ) {
5204 _scale_label = scale_label;
5207 private final void setupStroke( final Graphics2D g ) {
5208 if ( getYdistance() < 0.001 ) {
5209 g.setStroke( STROKE_005 );
5211 else if ( getYdistance() < 0.01 ) {
5212 g.setStroke( STROKE_01 );
5214 else if ( getYdistance() < 0.5 ) {
5215 g.setStroke( STROKE_025 );
5217 else if ( getYdistance() < 1 ) {
5218 g.setStroke( STROKE_05 );
5220 else if ( getYdistance() < 2 ) {
5221 g.setStroke( STROKE_075 );
5223 else if ( getYdistance() < 20 ) {
5224 g.setStroke( STROKE_1 );
5227 g.setStroke( STROKE_2 );
5231 final private void setUpUrtFactor() {
5232 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
5233 : getVisibleRect().height;
5234 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
5235 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
5238 final int max_depth = _circ_max_depth;
5239 if ( max_depth > 0 ) {
5240 setUrtFactor( d / ( 2 * max_depth ) );
5243 setUrtFactor( d / 2 );
5246 setUrtFactorOv( getUrtFactor() );
5249 final private void setUrtFactor( final float urt_factor ) {
5250 _urt_factor = urt_factor;
5253 final private void setUrtFactorOv( final float urt_factor_ov ) {
5254 _urt_factor_ov = urt_factor_ov;
5257 private void showExtDescNodeData( final PhylogenyNode node ) {
5258 final List<String> data = new ArrayList<String>();
5259 final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
5260 if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
5261 for( final PhylogenyNode n : getFoundNodes0AsListOfPhylogenyNodes() ) {
5262 if ( !nodes.contains( n ) ) {
5267 if ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() ) {
5268 for( final PhylogenyNode n : getFoundNodes1AsListOfPhylogenyNodes() ) {
5269 if ( !nodes.contains( n ) ) {
5274 for( final PhylogenyNode n : nodes ) {
5275 switch ( getOptions().getExtDescNodeDataToReturn() ) {
5277 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
5278 data.add( n.getName() );
5282 if ( n.getNodeData().isHasSequence()
5283 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5284 data.add( n.getNodeData().getSequence().getName() );
5288 if ( n.getNodeData().isHasSequence()
5289 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
5290 data.add( n.getNodeData().getSequence().getGeneName() );
5293 case SEQUENCE_SYMBOL:
5294 if ( n.getNodeData().isHasSequence()
5295 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5296 data.add( n.getNodeData().getSequence().getSymbol() );
5299 case SEQUENCE_MOL_SEQ:
5300 if ( n.getNodeData().isHasSequence()
5301 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5302 data.add( n.getNodeData().getSequence().getMolecularSequence() );
5305 case SEQUENCE_MOL_SEQ_FASTA:
5306 final StringBuilder sb = new StringBuilder();
5307 if ( n.getNodeData().isHasSequence()
5308 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5309 final StringBuilder ann = new StringBuilder();
5310 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
5311 ann.append( n.getName() );
5314 if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5315 ann.append( "SYM=" );
5316 ann.append( n.getNodeData().getSequence().getSymbol() );
5319 if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5320 ann.append( "NAME=" );
5321 ann.append( n.getNodeData().getSequence().getName() );
5324 if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
5325 ann.append( "GN=" );
5326 ann.append( n.getNodeData().getSequence().getGeneName() );
5329 if ( n.getNodeData().getSequence().getAccession() != null ) {
5330 ann.append( "ACC=" );
5331 ann.append( n.getNodeData().getSequence().getAccession().asText() );
5334 if ( n.getNodeData().isHasTaxonomy() ) {
5335 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5336 ann.append( "TAXID=" );
5337 ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5340 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5341 ann.append( "SN=" );
5342 ann.append( n.getNodeData().getTaxonomy().getScientificName() );
5347 if ( ann.charAt( ann.length() - 1 ) == '|' ) {
5348 ann_str = ann.substring( 0, ann.length() - 1 );
5351 ann_str = ann.toString();
5353 sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
5354 .getMolecularSequence(), 60 ) );
5355 data.add( sb.toString() );
5359 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
5360 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
5361 data.add( n.getNodeData().getSequence().getAccession().toString() );
5364 case TAXONOMY_SCIENTIFIC_NAME:
5365 if ( n.getNodeData().isHasTaxonomy()
5366 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5367 data.add( n.getNodeData().getTaxonomy().getScientificName() );
5370 case TAXONOMY_COMM0N_NAME:
5371 if ( n.getNodeData().isHasTaxonomy()
5372 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
5373 data.add( n.getNodeData().getTaxonomy().getCommonName() );
5377 if ( n.getNodeData().isHasTaxonomy()
5378 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5379 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5383 TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
5386 throw new IllegalArgumentException( "unknown data element: "
5387 + getOptions().getExtDescNodeDataToReturn() );
5390 final StringBuilder sb = new StringBuilder();
5391 final int size = TreePanelUtil.makeSB( data, getOptions(), sb );
5392 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
5393 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
5394 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
5395 System.out.println( sb );
5397 if ( sb.length() < 1 ) {
5398 clearCurrentExternalNodesDataBuffer();
5401 setCurrentExternalNodesDataBuffer( sb );
5404 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
5405 if ( sb.length() < 1 ) {
5406 TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData()
5407 + ")", "Descendants of selected node do not contain selected data" );
5408 clearCurrentExternalNodesDataBuffer();
5411 setCurrentExternalNodesDataBuffer( sb );
5413 if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
5414 title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5415 : obtainTitleForExtDescNodeData() )
5418 + " nodes, unique entries: "
5422 title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5423 : obtainTitleForExtDescNodeData() )
5427 + node.getNumberOfExternalNodes()
5428 + " external descendats of node "
5430 + ", unique entries: " + size;
5432 final String s = sb.toString().trim();
5433 if ( getMainPanel().getMainFrame() == null ) {
5434 // Must be "E" applet version.
5435 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
5436 ae.showTextFrame( s, title );
5439 getMainPanel().getMainFrame().showTextFrame( s, title );
5445 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
5447 if ( ( node.getName().length() > 0 )
5448 || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData()
5450 || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData()
5451 .getSequence() ) ) || ( node.getNodeData().isHasDate() )
5452 || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) {
5453 _popup_buffer.setLength( 0 );
5455 if ( node.getName().length() > 0 ) {
5457 _popup_buffer.append( node.getName() );
5459 if ( node.getNodeData().isHasTaxonomy()
5460 && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
5462 boolean enc_data = false;
5463 final Taxonomy tax = node.getNodeData().getTaxonomy();
5464 if ( _popup_buffer.length() > 0 ) {
5465 _popup_buffer.append( "\n" );
5467 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
5468 _popup_buffer.append( "[" );
5469 _popup_buffer.append( tax.getTaxonomyCode() );
5470 _popup_buffer.append( "]" );
5473 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
5475 _popup_buffer.append( " " );
5477 _popup_buffer.append( tax.getScientificName() );
5480 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
5482 _popup_buffer.append( " (" );
5485 _popup_buffer.append( "(" );
5487 _popup_buffer.append( tax.getCommonName() );
5488 _popup_buffer.append( ")" );
5491 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
5493 _popup_buffer.append( " (" );
5496 _popup_buffer.append( "(" );
5498 _popup_buffer.append( tax.getAuthority() );
5499 _popup_buffer.append( ")" );
5502 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
5504 _popup_buffer.append( " [" );
5507 _popup_buffer.append( "[" );
5509 _popup_buffer.append( tax.getRank() );
5510 _popup_buffer.append( "]" );
5513 if ( tax.getSynonyms().size() > 0 ) {
5515 _popup_buffer.append( " " );
5517 _popup_buffer.append( "[" );
5519 for( final String syn : tax.getSynonyms() ) {
5520 if ( !ForesterUtil.isEmpty( syn ) ) {
5522 _popup_buffer.append( syn );
5523 if ( counter < tax.getSynonyms().size() ) {
5524 _popup_buffer.append( ", " );
5529 _popup_buffer.append( "]" );
5532 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
5533 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
5534 _popup_buffer.append( "[" );
5535 _popup_buffer.append( tax.getIdentifier().getProvider() );
5536 _popup_buffer.append( "] " );
5538 _popup_buffer.append( tax.getIdentifier().getValue() );
5542 if ( node.getNodeData().isHasSequence()
5543 && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
5545 boolean enc_data = false;
5546 if ( _popup_buffer.length() > 0 ) {
5547 _popup_buffer.append( "\n" );
5549 final Sequence seq = node.getNodeData().getSequence();
5550 if ( seq.getAccession() != null ) {
5551 _popup_buffer.append( "[" );
5552 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
5553 _popup_buffer.append( seq.getAccession().getSource() );
5554 _popup_buffer.append( ":" );
5556 _popup_buffer.append( seq.getAccession().getValue() );
5557 _popup_buffer.append( "]" );
5560 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
5562 _popup_buffer.append( " [" );
5565 _popup_buffer.append( "[" );
5567 _popup_buffer.append( seq.getSymbol() );
5568 _popup_buffer.append( "]" );
5571 if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
5573 _popup_buffer.append( " [" );
5576 _popup_buffer.append( "[" );
5578 _popup_buffer.append( seq.getGeneName() );
5579 _popup_buffer.append( "]" );
5582 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
5584 _popup_buffer.append( " " );
5586 _popup_buffer.append( seq.getName() );
5589 if ( node.getNodeData().isHasDate() ) {
5591 if ( _popup_buffer.length() > 0 ) {
5592 _popup_buffer.append( "\n" );
5594 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
5596 if ( node.getNodeData().isHasDistribution() ) {
5598 if ( _popup_buffer.length() > 0 ) {
5599 _popup_buffer.append( "\n" );
5601 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
5603 if ( node.getBranchData().isHasConfidences() ) {
5604 final List<Confidence> confs = node.getBranchData().getConfidences();
5605 for( final Confidence confidence : confs ) {
5607 if ( _popup_buffer.length() > 0 ) {
5608 _popup_buffer.append( "\n" );
5610 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
5611 _popup_buffer.append( "[" );
5612 _popup_buffer.append( confidence.getType() );
5613 _popup_buffer.append( "] " );
5616 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
5618 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5619 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5620 _popup_buffer.append( " (sd=" );
5621 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
5622 .getStandardDeviation(), getOptions()
5623 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5624 _popup_buffer.append( ")" );
5628 if ( node.getNodeData().isHasProperties() ) {
5629 final PropertiesMap properties = node.getNodeData().getProperties();
5630 for( final String ref : properties.getPropertyRefs() ) {
5631 _popup_buffer.append( "\n" );
5632 final Property p = properties.getProperty( ref );
5633 _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
5634 _popup_buffer.append( "=" );
5635 _popup_buffer.append( p.getValue() );
5636 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5637 _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
5641 if ( _popup_buffer.length() > 0 ) {
5642 if ( !getConfiguration().isUseNativeUI() ) {
5644 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
5645 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
5646 if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
5647 _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
5649 else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
5650 _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
5652 else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
5653 _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
5655 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
5656 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
5659 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
5663 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
5665 _rollover_popup.setText( _popup_buffer.toString() );
5666 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
5668 e.getLocationOnScreen().x + 10,
5669 e.getLocationOnScreen().y
5671 _node_desc_popup.show();
5675 catch ( final Exception ex ) {
5680 final private void showNodeEditFrame( final PhylogenyNode n ) {
5681 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5682 // pop up edit box for single node
5683 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
5684 _node_frame_index++;
5687 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5691 final private void showNodeFrame( final PhylogenyNode n ) {
5692 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5693 // pop up edit box for single node
5694 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
5695 _node_frame_index++;
5698 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5702 final private void switchDisplaygetPhylogenyGraphicsType() {
5703 switch ( getPhylogenyGraphicsType() ) {
5705 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5706 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5709 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5710 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5713 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5714 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5717 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5718 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5721 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5722 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5725 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5726 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5729 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5730 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5733 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5734 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5737 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5739 if ( getControlPanel().getDynamicallyHideData() != null ) {
5740 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5741 getControlPanel().getDynamicallyHideData().setEnabled( false );
5744 getControlPanel().getDynamicallyHideData().setEnabled( true );
5747 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5748 getControlPanel().setDrawPhylogramEnabled( true );
5751 getControlPanel().setDrawPhylogramEnabled( false );
5753 if ( getMainPanel().getMainFrame() == null ) {
5754 // Must be "E" applet version.
5755 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5756 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5759 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5763 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5764 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5767 final private static boolean plusPressed( final int key_code ) {
5768 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5769 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5772 final private class SubtreeColorizationActionListener implements ActionListener {
5774 List<PhylogenyNode> _additional_nodes = null;
5775 JColorChooser _chooser = null;
5776 PhylogenyNode _node = null;
5778 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5783 SubtreeColorizationActionListener( final JColorChooser chooser,
5784 final PhylogenyNode node,
5785 final List<PhylogenyNode> additional_nodes ) {
5788 _additional_nodes = additional_nodes;
5792 public void actionPerformed( final ActionEvent e ) {
5793 final Color c = _chooser.getColor();
5795 colorizeSubtree( c, _node, _additional_nodes );
5800 final private class NodeColorizationActionListener implements ActionListener {
5802 List<PhylogenyNode> _additional_nodes = null;
5803 JColorChooser _chooser = null;
5804 PhylogenyNode _node = null;
5806 NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5811 NodeColorizationActionListener( final JColorChooser chooser,
5812 final PhylogenyNode node,
5813 final List<PhylogenyNode> additional_nodes ) {
5816 _additional_nodes = additional_nodes;
5820 public void actionPerformed( final ActionEvent e ) {
5821 final Color c = _chooser.getColor();
5823 colorizeNodes( c, _node, _additional_nodes );