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.NodeVisualization;
116 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
117 import org.forester.phylogeny.data.NodeVisualization.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 colorSubtree( final PhylogenyNode node ) {
2434 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2435 JOptionPane.showMessageDialog( this,
2436 "Cannot colorize subtree in unrooted display type",
2437 "Attempt to colorize subtree in unrooted display",
2438 JOptionPane.WARNING_MESSAGE );
2441 _color_chooser.setPreviewPanel( new JPanel() );
2442 SubtreeColorizationActionListener al;
2443 if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
2444 final List<PhylogenyNode> additional_nodes = getFoundNodes0AsListOfPhylogenyNodes();
2445 al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
2448 al = new SubtreeColorizationActionListener( _color_chooser, node );
2450 final JDialog dialog = JColorChooser
2451 .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
2452 dialog.setVisible( true );
2455 final private void copySubtree( final PhylogenyNode node ) {
2456 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2457 errorMessageNoCutCopyPasteInUnrootedDisplay();
2460 setNodeInPreorderToNull();
2461 setCutOrCopiedTree( _phylogeny.copy( node ) );
2462 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
2463 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
2464 for( final PhylogenyNode n : nodes ) {
2465 node_ids.add( n.getId() );
2467 node_ids.add( node.getId() );
2468 setCopiedAndPastedNodes( node_ids );
2472 final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
2473 final String tax = PhylogenyMethods.getSpecies( node );
2474 String label = node.getName();
2475 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
2476 label = label + " " + tax;
2478 else if ( !ForesterUtil.isEmpty( tax ) ) {
2484 if ( !ForesterUtil.isEmpty( label ) ) {
2485 label = " [" + label + "]";
2490 final private void cutSubtree( final PhylogenyNode node ) {
2491 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2492 errorMessageNoCutCopyPasteInUnrootedDisplay();
2495 if ( node.isRoot() ) {
2496 JOptionPane.showMessageDialog( this,
2497 "Cannot cut entire tree as subtree",
2498 "Attempt to cut entire tree",
2499 JOptionPane.ERROR_MESSAGE );
2502 final String label = createASimpleTextRepresentationOfANode( node );
2503 final int r = JOptionPane.showConfirmDialog( null,
2504 "Cut subtree" + label + "?",
2505 "Confirm Cutting of Subtree",
2506 JOptionPane.YES_NO_OPTION );
2507 if ( r != JOptionPane.OK_OPTION ) {
2510 setNodeInPreorderToNull();
2511 setCopiedAndPastedNodes( null );
2512 setCutOrCopiedTree( _phylogeny.copy( node ) );
2513 _phylogeny.deleteSubtree( node, true );
2514 _phylogeny.clearHashIdToNodeMap();
2515 _phylogeny.recalculateNumberOfExternalDescendants( true );
2516 resetNodeIdToDistToLeafMap();
2521 final private void cycleColors() {
2522 getMainPanel().getTreeColorSet().cycleColorScheme();
2523 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
2524 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
2528 final private void decreaseOvSize() {
2529 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
2530 setOvMaxWidth( getOvMaxWidth() - 5 );
2531 setOvMaxHeight( getOvMaxHeight() - 5 );
2533 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2537 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
2538 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2539 errorMessageNoCutCopyPasteInUnrootedDisplay();
2542 if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
2543 JOptionPane.showMessageDialog( this,
2544 "Cannot delete entire tree",
2545 "Attempt to delete entire tree",
2546 JOptionPane.ERROR_MESSAGE );
2549 final String label = createASimpleTextRepresentationOfANode( node );
2550 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
2551 final int r = JOptionPane.showOptionDialog( this,
2552 "Delete" + label + "?",
2553 "Delete Node/Subtree",
2554 JOptionPane.CLOSED_OPTION,
2555 JOptionPane.QUESTION_MESSAGE,
2559 setNodeInPreorderToNull();
2560 boolean node_only = true;
2564 else if ( r != 0 ) {
2568 PhylogenyMethods.removeNode( node, _phylogeny );
2571 _phylogeny.deleteSubtree( node, true );
2573 _phylogeny.externalNodesHaveChanged();
2574 _phylogeny.clearHashIdToNodeMap();
2575 _phylogeny.recalculateNumberOfExternalDescendants( true );
2576 resetNodeIdToDistToLeafMap();
2581 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
2582 makePopupMenus( node );
2583 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
2584 _node_popup_menu.show( this, x, y );
2587 final private void drawArc( final double x,
2590 final double heigth,
2591 final double start_angle,
2592 final double arc_angle,
2593 final Graphics2D g ) {
2594 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
2598 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
2599 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
2602 _line.setLine( x1, y1, x2, y2 );
2606 final private void drawOval( final double x,
2609 final double heigth,
2610 final Graphics2D g ) {
2611 _ellipse.setFrame( x, y, width, heigth );
2615 final private void drawOvalFilled( final double x,
2618 final double heigth,
2619 final Graphics2D g ) {
2620 _ellipse.setFrame( x, y, width, heigth );
2624 final private void drawOvalGradient( final double x,
2627 final double heigth,
2629 final Color color_1,
2630 final Color color_2,
2631 final Color color_border ) {
2632 _ellipse.setFrame( x, y, width, heigth );
2633 g.setPaint( new GradientPaint( ( float ) x,
2636 ( float ) ( x + width ),
2637 ( float ) ( y + heigth ),
2641 if ( color_border != null ) {
2642 g.setPaint( color_border );
2647 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
2648 _rectangle.setFrame( x, y, width, heigth );
2649 g.draw( _rectangle );
2652 final private void drawRectFilled( final double x,
2655 final double heigth,
2656 final Graphics2D g ) {
2657 _rectangle.setFrame( x, y, width, heigth );
2658 g.fill( _rectangle );
2661 final private void drawRectGradient( final double x,
2664 final double heigth,
2666 final Color color_1,
2667 final Color color_2,
2668 final Color color_border ) {
2669 _rectangle.setFrame( x, y, width, heigth );
2670 g.setPaint( new GradientPaint( ( float ) x,
2673 ( float ) ( x + width ),
2674 ( float ) ( y + heigth ),
2677 g.fill( _rectangle );
2678 if ( color_border != null ) {
2679 g.setPaint( color_border );
2680 g.draw( _rectangle );
2684 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2685 final List<Uri> us = new ArrayList<Uri>();
2686 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2687 for( final Uri uri : t.getUris() ) {
2692 for( final Uri uri : us ) {
2693 if ( uri != null ) {
2694 final String uri_str = uri.getValue().toString().toLowerCase();
2695 if ( getImageMap().containsKey( uri_str ) ) {
2696 final BufferedImage bi = getImageMap().get( uri_str );
2697 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2698 double scaling_factor = 1;
2699 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
2700 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
2701 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
2703 // y = y - ( 0.9 * getYdistance() );
2704 final double hs = bi.getHeight() * scaling_factor;
2705 double ws = ( bi.getWidth() * scaling_factor ) + offset;
2706 final double my_y = y - ( 0.5 * hs );
2707 final int x_w = ( int ) ( x + ws + 0.5 );
2708 final int y_h = ( int ) ( my_y + hs + 0.5 );
2709 if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
2711 ( int ) ( x + 0.5 + offset ),
2712 ( int ) ( my_y + 0.5 ),
2733 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
2734 JOptionPane.showMessageDialog( this,
2735 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
2736 "Attempt to cut/copy/paste/add/delete in unrooted display",
2737 JOptionPane.ERROR_MESSAGE );
2740 private final Color getColorForFoundNode( final PhylogenyNode n ) {
2741 if ( isInCurrentExternalNodes( n ) ) {
2742 return getTreeColorSet().getFoundColor0();
2744 else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
2745 return getTreeColorSet().getFoundColor0();
2747 else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
2748 return getTreeColorSet().getFoundColor1();
2751 return getTreeColorSet().getFoundColor0and1();
2755 final private Set<Long> getCopiedAndPastedNodes() {
2756 return getMainPanel().getCopiedAndPastedNodes();
2759 final private Set<Long> getCurrentExternalNodes() {
2760 return _current_external_nodes;
2763 final private Phylogeny getCutOrCopiedTree() {
2764 return getMainPanel().getCutOrCopiedTree();
2767 private List<PhylogenyNode> getFoundNodes0AsListOfPhylogenyNodes() {
2768 final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
2769 for( final Long id : getFoundNodes0() ) {
2770 additional_nodes.add( _phylogeny.getNode( id ) );
2772 return additional_nodes;
2775 private List<PhylogenyNode> getFoundNodes1AsListOfPhylogenyNodes() {
2776 final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
2777 for( final Long id : getFoundNodes1() ) {
2778 additional_nodes.add( _phylogeny.getNode( id ) );
2780 return additional_nodes;
2783 final private float getLastDragPointX() {
2784 return _last_drag_point_x;
2787 final private float getLastDragPointY() {
2788 return _last_drag_point_y;
2791 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
2792 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
2793 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
2794 _nodeid_dist_to_leaf.put( node.getId(), m );
2798 return _nodeid_dist_to_leaf.get( node.getId() );
2802 final private double getMaxDistanceToRoot() {
2803 if ( _max_distance_to_root < 0 ) {
2804 recalculateMaxDistanceToRoot();
2806 return _max_distance_to_root;
2809 final private float getOvMaxHeight() {
2810 return _ov_max_height;
2813 final private float getOvMaxWidth() {
2814 return _ov_max_width;
2817 final private float getOvXcorrectionFactor() {
2818 return _ov_x_correction_factor;
2821 final private float getOvXDistance() {
2822 return _ov_x_distance;
2825 final private int getOvXPosition() {
2826 return _ov_x_position;
2829 final private float getOvYDistance() {
2830 return _ov_y_distance;
2833 final private int getOvYPosition() {
2834 return _ov_y_position;
2837 final private int getOvYStart() {
2841 final private List<Accession> getPdbAccs( final PhylogenyNode node ) {
2842 final List<Accession> pdb_ids = new ArrayList<Accession>();
2843 if ( node.getNodeData().isHasSequence() ) {
2844 final Sequence seq = node.getNodeData().getSequence();
2845 if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
2846 final SortedSet<Accession> cross_refs = seq.getCrossReferences();
2847 for( final Accession acc : cross_refs ) {
2848 if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
2857 final private double getScaleDistance() {
2858 return _scale_distance;
2861 final private String getScaleLabel() {
2862 return _scale_label;
2865 final private TreeFontSet getTreeFontSet() {
2866 return getMainPanel().getTreeFontSet();
2869 final private float getUrtFactor() {
2873 final private float getUrtFactorOv() {
2874 return _urt_factor_ov;
2877 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
2880 showNodeFrame( node );
2895 colorSubtree( node );
2913 copySubtree( node );
2916 pasteSubtree( node );
2918 case DELETE_NODE_OR_SUBTREE:
2919 deleteNodeOrSubtree( node );
2922 addEmptyNode( node );
2924 case EDIT_NODE_DATA:
2925 showNodeEditFrame( node );
2930 case SORT_DESCENDENTS:
2931 sortDescendants( node );
2933 case GET_EXT_DESC_DATA:
2934 showExtDescNodeData( node );
2937 throw new IllegalArgumentException( "unknown action: " + action );
2941 final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
2942 _current_external_nodes_data_buffer_change_counter++;
2945 final private void increaseOvSize() {
2946 if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
2947 && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
2948 .getHeight() / 2 ) ) ) {
2949 setOvMaxWidth( getOvMaxWidth() + 5 );
2950 setOvMaxHeight( getOvMaxHeight() + 5 );
2952 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2956 final private void init() {
2957 _color_chooser = new JColorChooser();
2958 _rollover_popup = new JTextArea();
2959 _rollover_popup.setFont( POPUP_FONT );
2960 resetNodeIdToDistToLeafMap();
2962 setTreeFile( null );
2964 initializeOvSettings();
2965 setStartingAngle( ( TWO_PI * 3 ) / 4 );
2966 final ImageLoader il = new ImageLoader( this );
2967 new Thread( il ).start();
2970 final private void initializeOvSettings() {
2971 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
2972 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
2975 final private boolean inOvVirtualRectangle( final int x, final int y ) {
2976 return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
2977 && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
2978 && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
2979 + getOvVirtualRectangle().height + 1 ) ) );
2982 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
2983 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
2986 final private boolean isCanBlast( final PhylogenyNode node ) {
2987 if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
2990 return Blast.isContainsQueryForBlast( node );
2993 final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
2994 final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node );
2996 return a.getValue();
3001 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
3002 if ( node.getNodeData().isHasTaxonomy()
3003 && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
3004 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
3005 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
3006 .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
3007 .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
3015 final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
3016 return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
3019 private boolean isInFoundNodes( final PhylogenyNode n ) {
3020 return isInFoundNodes0( n ) || isInFoundNodes1( n );
3023 final private boolean isInFoundNodes0( final PhylogenyNode node ) {
3024 return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) );
3027 final private boolean isInFoundNodes1( final PhylogenyNode node ) {
3028 return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) );
3031 final private boolean isInOv() {
3035 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
3037 if ( getControlPanel().isShowTaxonomyImages() ) {
3038 y_dist = 40 + ( int ) getYdistance();
3040 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
3041 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
3042 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
3045 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
3046 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
3047 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
3048 || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
3049 .getMaxX() + 20 ) ) );
3052 final private boolean isNonLinedUpCladogram() {
3053 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
3056 final private boolean isUniformBranchLengthsForCladogram() {
3057 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
3060 final private void keyPressedCalls( final KeyEvent e ) {
3061 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
3062 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
3063 if ( !isInOvRect() ) {
3064 setInOvRect( true );
3067 else if ( isInOvRect() ) {
3068 setInOvRect( false );
3071 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
3072 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
3073 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
3074 getMainPanel().getTreeFontSet().mediumFonts();
3075 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
3077 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3078 getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
3079 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
3081 else if ( plusPressed( e.getKeyCode() ) ) {
3082 getMainPanel().getTreeFontSet().increaseFontSize();
3083 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
3087 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
3088 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
3089 getControlPanel().showWhole();
3091 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
3092 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
3093 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
3094 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
3095 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3096 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3098 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3099 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3100 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3102 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3103 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3104 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3105 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3107 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3108 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3109 Constants.WHEEL_ZOOM_IN_FACTOR );
3110 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3117 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3120 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3124 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3128 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
3129 scroll_position.x = scroll_position.x + dx;
3130 scroll_position.y = scroll_position.y + dy;
3131 if ( scroll_position.x <= 0 ) {
3132 scroll_position.x = 0;
3135 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
3136 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
3137 if ( scroll_position.x >= max_x ) {
3138 scroll_position.x = max_x;
3141 if ( scroll_position.y <= 0 ) {
3142 scroll_position.y = 0;
3145 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
3146 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
3147 if ( scroll_position.y >= max_y ) {
3148 scroll_position.y = max_y;
3152 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
3155 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3156 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
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 ( plusPressed( e.getKeyCode() ) ) {
3162 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3163 Constants.WHEEL_ZOOM_IN_FACTOR );
3164 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3165 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3167 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
3168 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3169 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3170 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
3171 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3174 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
3175 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3176 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3177 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
3178 if ( getStartingAngle() < 0 ) {
3179 setStartingAngle( TWO_PI + getStartingAngle() );
3181 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3184 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
3185 boolean selected = false;
3186 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
3187 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
3191 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
3193 if ( getMainPanel().getMainFrame() == null ) {
3194 // Must be "E" applet version.
3195 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
3196 if ( ae.getlabelDirectionCbmi() != null ) {
3197 ae.getlabelDirectionCbmi().setSelected( selected );
3201 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
3205 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
3206 switchDisplaygetPhylogenyGraphicsType();
3209 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
3213 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
3214 MainFrame.cycleOverview( getOptions(), this );
3217 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
3220 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
3227 final private void makePopupMenus( final PhylogenyNode node ) {
3228 _node_popup_menu = new JPopupMenu();
3229 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
3230 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
3231 for( int i = 0; i < clickto_names.size(); i++ ) {
3232 final String title = clickto_names.get( i );
3233 _node_popup_menu_items[ i ] = new JMenuItem( title );
3234 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
3235 final String id = isCanOpenSeqWeb( node );
3236 if ( !ForesterUtil.isEmpty( id ) ) {
3237 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
3238 _node_popup_menu_items[ i ].setEnabled( true );
3241 _node_popup_menu_items[ i ].setEnabled( false );
3244 else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) {
3245 final List<Accession> accs = getPdbAccs( node );
3246 _node_popup_menu_items[ i ] = new JMenuItem( title );
3247 if ( !ForesterUtil.isEmpty( accs ) ) {
3248 if ( accs.size() == 1 ) {
3249 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
3250 + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" );
3251 _node_popup_menu_items[ i ].setEnabled( true );
3253 else if ( accs.size() == 2 ) {
3254 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
3255 + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
3256 + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" );
3257 _node_popup_menu_items[ i ].setEnabled( true );
3259 else if ( accs.size() == 3 ) {
3260 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
3261 + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
3262 + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
3263 + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" );
3264 _node_popup_menu_items[ i ].setEnabled( true );
3267 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
3268 + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
3269 + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
3270 + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" );
3271 _node_popup_menu_items[ i ].setEnabled( true );
3275 _node_popup_menu_items[ i ].setEnabled( false );
3279 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
3280 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
3282 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
3283 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
3285 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
3286 if ( !getOptions().isEditable() ) {
3289 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
3291 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
3292 if ( !getOptions().isEditable() ) {
3295 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
3297 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
3298 if ( !getOptions().isEditable() ) {
3301 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
3303 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
3304 if ( !getOptions().isEditable() ) {
3307 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
3309 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
3310 if ( !getOptions().isEditable() ) {
3314 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
3315 if ( !getOptions().isEditable() ) {
3319 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
3320 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
3322 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
3323 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
3325 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
3326 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
3328 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
3329 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
3331 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
3332 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
3334 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
3335 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
3337 _node_popup_menu_items[ i ].addActionListener( this );
3338 _node_popup_menu.add( _node_popup_menu_items[ i ] );
3342 private final String obtainTitleForExtDescNodeData() {
3343 switch ( getOptions().getExtDescNodeDataToReturn() ) {
3345 return "Node Names";
3347 return "Gene Names";
3349 return "Sequence Names";
3350 case SEQUENCE_SYMBOL:
3351 return "Sequence Symbols";
3352 case SEQUENCE_MOL_SEQ:
3353 return "Molecular Sequences";
3354 case SEQUENCE_MOL_SEQ_FASTA:
3355 return "Molecular Sequences (Fasta)";
3357 return "Sequence Accessors";
3358 case TAXONOMY_SCIENTIFIC_NAME:
3359 return "Scientific Names";
3361 return "Taxonomy Codes";
3362 case TAXONOMY_COMM0N_NAME:
3363 return "Taxonomy Common Names";
3365 return "User Selected Data";
3367 throw new IllegalArgumentException( "unknown data element: "
3368 + getOptions().getExtDescNodeDataToReturn() );
3372 final private void openPdbWeb( final PhylogenyNode node ) {
3373 final List<Accession> pdb_ids = getPdbAccs( node );
3374 if ( ForesterUtil.isEmpty( pdb_ids ) ) {
3375 cannotOpenBrowserWarningMessage( "PDB" );
3378 final List<String> uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this );
3379 if ( !ForesterUtil.isEmpty( uri_strs ) ) {
3380 for( final String uri_str : uri_strs ) {
3382 AptxUtil.launchWebBrowser( new URI( uri_str ),
3384 isApplet() ? obtainApplet() : null,
3387 catch ( final IOException e ) {
3388 AptxUtil.showErrorMessage( this, e.toString() );
3389 e.printStackTrace();
3391 catch ( final URISyntaxException e ) {
3392 AptxUtil.showErrorMessage( this, e.toString() );
3393 e.printStackTrace();
3398 cannotOpenBrowserWarningMessage( "PDB" );
3402 final private void openSeqWeb( final PhylogenyNode node ) {
3403 if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
3404 cannotOpenBrowserWarningMessage( "sequence" );
3407 final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
3408 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3410 AptxUtil.launchWebBrowser( new URI( uri_str ),
3412 isApplet() ? obtainApplet() : null,
3415 catch ( final IOException e ) {
3416 AptxUtil.showErrorMessage( this, e.toString() );
3417 e.printStackTrace();
3419 catch ( final URISyntaxException e ) {
3420 AptxUtil.showErrorMessage( this, e.toString() );
3421 e.printStackTrace();
3425 cannotOpenBrowserWarningMessage( "sequence" );
3429 final private void openTaxWeb( final PhylogenyNode node ) {
3430 if ( !isCanOpenTaxWeb( node ) ) {
3431 cannotOpenBrowserWarningMessage( "taxonomic" );
3434 String uri_str = null;
3435 final Taxonomy tax = node.getNodeData().getTaxonomy();
3436 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3437 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
3439 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
3441 catch ( final URISyntaxException e ) {
3442 AptxUtil.showErrorMessage( this, e.toString() );
3444 e.printStackTrace();
3447 else if ( ( tax.getIdentifier() != null )
3448 && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3449 && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
3450 && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
3451 .equalsIgnoreCase( "uniprot" ) ) ) {
3453 uri_str = "http://www.uniprot.org/taxonomy/"
3454 + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
3456 catch ( final UnsupportedEncodingException e ) {
3457 AptxUtil.showErrorMessage( this, e.toString() );
3458 e.printStackTrace();
3461 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
3463 uri_str = "http://www.uniprot.org/taxonomy/?query="
3464 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
3466 catch ( final UnsupportedEncodingException e ) {
3467 AptxUtil.showErrorMessage( this, e.toString() );
3468 e.printStackTrace();
3471 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
3473 uri_str = "http://www.uniprot.org/taxonomy/?query="
3474 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
3476 catch ( final UnsupportedEncodingException e ) {
3477 AptxUtil.showErrorMessage( this, e.toString() );
3478 e.printStackTrace();
3481 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
3483 uri_str = "http://www.uniprot.org/taxonomy/?query="
3484 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
3486 catch ( final UnsupportedEncodingException e ) {
3487 AptxUtil.showErrorMessage( this, e.toString() );
3488 e.printStackTrace();
3491 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3493 AptxUtil.launchWebBrowser( new URI( uri_str ),
3495 isApplet() ? obtainApplet() : null,
3498 catch ( final IOException e ) {
3499 AptxUtil.showErrorMessage( this, e.toString() );
3500 e.printStackTrace();
3502 catch ( final URISyntaxException e ) {
3503 AptxUtil.showErrorMessage( this, e.toString() );
3504 e.printStackTrace();
3508 cannotOpenBrowserWarningMessage( "taxonomic" );
3512 final private void paintBranchLength( final Graphics2D g,
3513 final PhylogenyNode node,
3514 final boolean to_pdf,
3515 final boolean to_graphics_file ) {
3516 g.setFont( getTreeFontSet().getSmallFont() );
3517 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3518 g.setColor( Color.BLACK );
3521 g.setColor( getTreeColorSet().getBranchLengthColor() );
3523 if ( !node.isRoot() ) {
3524 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3525 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3526 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3528 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3529 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3530 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3533 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3534 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3538 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
3539 - getTreeFontSet()._small_max_descent, g );
3543 final private void paintBranchLite( final Graphics2D g,
3548 final PhylogenyNode node ) {
3549 g.setColor( getTreeColorSet().getOvColor() );
3550 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3551 drawLine( x1, y1, x2, y2, g );
3553 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3554 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3555 ( g ).draw( _quad_curve );
3557 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3558 final float dx = x2 - x1;
3559 final float dy = y2 - y1;
3560 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3561 + ( dy * 0.8f ), x2, y2 );
3562 ( g ).draw( _cubic_curve );
3565 final float x2a = x2;
3566 final float x1a = x1;
3567 // draw the vertical line
3568 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
3569 drawLine( x1, y1, x1, y2, g );
3571 // draw the horizontal line
3572 drawLine( x1a, y2, x2a, y2, g );
3577 * Paint a branch which consists of a vertical and a horizontal bar
3578 * @param is_ind_found_nodes
3580 final private void paintBranchRectangular( final Graphics2D g,
3585 final PhylogenyNode node,
3586 final boolean to_pdf,
3587 final boolean to_graphics_file ) {
3588 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
3589 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3590 drawLine( x1, y1, x2, y2, g );
3592 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3593 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3594 g.draw( _quad_curve );
3596 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3597 final float dx = x2 - x1;
3598 final float dy = y2 - y1;
3599 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3600 + ( dy * 0.8f ), x2, y2 );
3601 g.draw( _cubic_curve );
3604 final float x2a = x2;
3605 final float x1a = x1;
3607 if ( node.isFirstChildNode() || node.isLastChildNode()
3608 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3609 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3610 if ( !to_graphics_file
3612 && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
3613 .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
3617 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3618 float x2c = x1 + EURO_D;
3622 drawLine( x1, y1, x2c, y2, g );
3624 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3626 y2_r = y2 - ROUNDED_D;
3630 drawLine( x1, y1, x1, y2_r, g );
3633 y2_r = y2 + ROUNDED_D;
3637 drawLine( x1, y1, x1, y2_r, g );
3641 drawLine( x1, y1, x1, y2, g );
3645 // draw the horizontal line
3646 if ( !to_graphics_file && !to_pdf
3647 && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
3651 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
3652 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3653 x1_r = x1a + ROUNDED_D;
3655 drawLine( x1_r, y2, x2a, y2, g );
3658 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3659 final float x1c = x1a + EURO_D;
3661 drawLine( x1c, y2, x2a, y2, g );
3665 drawLine( x1a, y2, x2a, y2, g );
3669 final double w = PhylogenyMethods.getBranchWidthValue( node );
3670 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3671 x1_r = x1a + ROUNDED_D;
3673 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
3676 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3677 final float x1c = x1a + EURO_D;
3679 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
3683 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
3686 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3691 final double diff = y2 - y2_r;
3692 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
3695 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
3700 if ( node.isExternal() ) {
3701 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file );
3705 final private double paintCirculars( final PhylogenyNode n,
3706 final Phylogeny phy,
3707 final float center_x,
3708 final float center_y,
3709 final double radius,
3710 final boolean radial_labels,
3712 final boolean to_pdf,
3713 final boolean to_graphics_file ) {
3714 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
3715 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
3716 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
3718 return _urt_nodeid_angle_map.get( n.getId() );
3721 final List<PhylogenyNode> descs = n.getDescendants();
3723 for( final PhylogenyNode desc : descs ) {
3724 sum += paintCirculars( desc,
3735 if ( !n.isRoot() ) {
3736 r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3738 final double theta = sum / descs.size();
3739 n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
3740 n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
3741 _urt_nodeid_angle_map.put( n.getId(), theta );
3742 for( final PhylogenyNode desc : descs ) {
3743 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
3749 final private void paintCircularsLite( final PhylogenyNode n,
3750 final Phylogeny phy,
3754 final Graphics2D g ) {
3755 if ( n.isExternal() ) {
3759 final List<PhylogenyNode> descs = n.getDescendants();
3760 for( final PhylogenyNode desc : descs ) {
3761 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
3764 if ( !n.isRoot() ) {
3765 r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3767 final double theta = _urt_nodeid_angle_map.get( n.getId() );
3768 n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
3769 n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
3770 for( final PhylogenyNode desc : descs ) {
3771 paintBranchCircularLite( n, desc, g );
3776 final private void paintCollapsedNode( final Graphics2D g,
3777 final PhylogenyNode node,
3778 final boolean to_graphics_file,
3779 final boolean to_pdf,
3780 final boolean is_in_found_nodes ) {
3782 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3785 else if ( is_in_found_nodes ) {
3786 c = getColorForFoundNode( node );
3788 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3789 c = getTaxonomyBasedColor( node );
3791 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3792 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3793 c = PhylogenyMethods.getBranchColorValue( node );
3796 c = getTreeColorSet().getCollapseFillColor();
3798 double d = node.getAllExternalDescendants().size();
3800 d = ( 3 * _y_distance ) / 3;
3803 d = ( Math.log10( d ) * _y_distance ) / 2.5;
3805 final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
3806 if ( d < box_size ) {
3809 final float xx = node.getXcoord() - ( 2 * box_size );
3810 final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
3812 _polygon.moveTo( xxx, node.getYcoord() );
3813 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
3814 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
3815 _polygon.closePath();
3816 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3820 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3821 g.setColor( getBackground() );
3826 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3827 g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
3828 .getYcoord() - d ), c, false ) );
3833 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3836 final private void paintConfidenceValues( final Graphics2D g,
3837 final PhylogenyNode node,
3838 final boolean to_pdf,
3839 final boolean to_graphics_file ) {
3840 final List<Confidence> confidences = node.getBranchData().getConfidences();
3841 boolean not_first = false;
3842 Collections.sort( confidences );
3843 final StringBuilder sb = new StringBuilder();
3844 for( final Confidence confidence : confidences ) {
3845 final double value = confidence.getValue();
3846 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3847 if ( value < getOptions().getMinConfidenceValue() ) {
3856 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
3857 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3858 if ( getOptions().isShowConfidenceStddev() ) {
3859 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3861 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
3863 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3869 if ( sb.length() > 0 ) {
3870 final double parent_x = node.getParent().getXcoord();
3871 double x = node.getXcoord();
3872 g.setFont( getTreeFontSet().getSmallFont() );
3873 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3876 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3879 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3880 g.setColor( Color.BLACK );
3883 g.setColor( getTreeColorSet().getConfidenceColor() );
3885 final String conf_str = sb.toString();
3887 .drawString( conf_str,
3889 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
3890 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
3895 final private void paintGainedAndLostCharacters( final Graphics2D g,
3896 final PhylogenyNode node,
3897 final String gained,
3898 final String lost ) {
3899 if ( node.getParent() != null ) {
3900 final double parent_x = node.getParent().getXcoord();
3901 final double x = node.getXcoord();
3902 g.setFont( getTreeFontSet().getLargeFont() );
3903 g.setColor( getTreeColorSet().getGainedCharactersColor() );
3904 if ( Constants.SPECIAL_CUSTOM ) {
3905 g.setColor( Color.BLUE );
3908 .drawString( gained,
3909 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
3910 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
3912 g.setColor( getTreeColorSet().getLostCharactersColor() );
3913 TreePanel.drawString( lost,
3914 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
3915 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
3921 * Draw a box at the indicated node.
3928 final private void paintNodeBox( final double x,
3930 final PhylogenyNode node,
3932 final boolean to_pdf,
3933 final boolean to_graphics_file ) {
3934 if ( node.isCollapse() ) {
3937 // if this node should be highlighted, do so
3938 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
3939 g.setColor( getTreeColorSet().getFoundColor0() );
3940 drawOval( x - 8, y - 8, 16, 16, g );
3941 drawOval( x - 9, y - 8, 17, 17, g );
3942 drawOval( x - 9, y - 9, 18, 18, g );
3944 if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
3945 || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
3946 || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
3947 || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
3949 || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
3950 .isSpeciationOrDuplication() ) ) ) {
3951 final double box_size = getOptions().getDefaultNodeShapeSize();
3952 final double half_box_size = box_size / 2.0;
3953 Color outline_color = null;
3954 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3955 outline_color = Color.BLACK;
3957 else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
3958 outline_color = getColorForFoundNode( node );
3960 else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
3961 final Event event = node.getNodeData().getEvent();
3962 if ( event.isDuplication() ) {
3963 outline_color = getTreeColorSet().getDuplicationBoxColor();
3965 else if ( event.isSpeciation() ) {
3966 outline_color = getTreeColorSet().getSpecBoxColor();
3968 else if ( event.isSpeciationOrDuplication() ) {
3969 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
3973 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
3974 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
3975 outline_color = getTreeColorSet().getBranchColorForPdf();
3978 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
3979 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3980 drawOvalGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
3981 : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
3983 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
3984 Color background = getBackground();
3986 background = Color.WHITE;
3988 drawOvalGradient( x - half_box_size,
3997 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3998 g.setColor( outline_color );
3999 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
4002 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
4003 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
4004 drawRectGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
4005 : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
4007 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
4008 Color background = getBackground();
4010 background = Color.WHITE;
4012 drawRectGradient( x - half_box_size,
4021 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
4022 g.setColor( outline_color );
4023 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
4029 final private void paintNodeData( final Graphics2D g,
4030 final PhylogenyNode node,
4031 final boolean to_graphics_file,
4032 final boolean to_pdf,
4033 final boolean is_in_found_nodes ) {
4034 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
4037 if ( getOptions().isShowBranchLengthValues()
4038 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4039 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4040 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
4041 paintBranchLength( g, node, to_pdf, to_graphics_file );
4043 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
4048 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
4049 if ( getControlPanel().isShowTaxonomyImages()
4050 && ( getImageMap() != null )
4051 && !getImageMap().isEmpty()
4052 && node.getNodeData().isHasTaxonomy()
4053 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
4054 .getUris().isEmpty() ) ) {
4055 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
4057 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4058 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
4059 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
4061 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4062 g.setColor( Color.BLACK );
4064 else if ( is_in_found_nodes ) {
4065 g.setColor( getColorForFoundNode( node ) );
4067 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4068 g.setColor( getTaxonomyBasedColor( node ) );
4070 else if ( getControlPanel().isColorAccordingToAnnotation()
4071 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4072 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4073 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4075 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4076 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4077 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4079 else if ( to_pdf ) {
4080 g.setColor( Color.BLACK );
4083 g.setColor( getTreeColorSet().getSequenceColor() );
4085 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4086 if ( _sb.length() > 0 ) {
4089 _sb.append( node.getAllExternalDescendants().size() );
4096 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4097 if ( _sb.length() > 0 ) {
4100 _sb.append( node.getName() );
4102 if ( node.getNodeData().isHasSequence() ) {
4103 if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
4104 if ( _sb.length() > 0 ) {
4107 _sb.append( node.getNodeData().getSequence().getSymbol() );
4109 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
4110 if ( _sb.length() > 0 ) {
4113 _sb.append( node.getNodeData().getSequence().getGeneName() );
4115 if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4116 if ( _sb.length() > 0 ) {
4119 _sb.append( node.getNodeData().getSequence().getName() );
4121 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4122 if ( _sb.length() > 0 ) {
4125 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4126 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4129 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4132 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
4133 if ( _sb.length() > 0 ) {
4136 _sb.append( propertiesToString( node ) );
4138 g.setFont( getTreeFontSet().getLargeFont() );
4139 if ( is_in_found_nodes ) {
4140 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4142 double down_shift_factor = 3.0;
4143 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
4144 down_shift_factor = 1;
4146 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
4147 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
4148 final String sb_str = _sb.toString();
4149 // GUILHEM_BEG ______________
4150 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
4151 && ( _query_sequence != null ) ) {
4152 int nodeTextBoundsWidth = 0;
4153 if ( sb_str.length() > 0 ) {
4154 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
4155 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
4157 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
4158 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
4159 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
4160 g.setColor( getTreeColorSet().getBackgroundColor() );
4164 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
4165 for( final SequenceRelation seqRelation : seqRelations ) {
4166 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
4167 .getRef1().isEqual( _query_sequence ) )
4168 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
4169 .getSelectedItem() );
4170 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
4171 final double linePosX = node.getXcoord() + 2 + half_box_size;
4172 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
4173 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
4175 if ( sConfidence != null ) {
4176 double confidenceX = pos_x;
4177 if ( sb_str.length() > 0 ) {
4178 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
4179 + CONFIDENCE_LEFT_MARGIN;
4181 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
4182 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
4183 .getBounds().getWidth();
4184 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
4185 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
4188 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
4190 if ( nodeTextBoundsWidth == 0 ) {
4191 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
4194 nodeTextBoundsWidth += 2;
4196 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
4197 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
4204 if ( sb_str.length() > 0 ) {
4205 TreePanel.drawString( sb_str, pos_x, pos_y, g );
4207 // GUILHEM_END _____________
4208 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
4209 // TODO FIXME need to check this one!
4210 //if ( _sb.length() > 0 ) {
4211 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
4212 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4214 // COMMENTED_OUT_BY_GUILHEM_END ________________
4215 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
4216 && ( node.getNodeData().getSequence().getAnnotations() != null )
4217 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4218 if ( _sb.length() > 0 ) {
4219 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4221 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
4222 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4223 g.setColor( Color.BLACK );
4225 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
4226 g.setColor( calculateColorForAnnotation( ann ) );
4228 final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
4229 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
4230 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4232 _sb.append( ann_str );
4234 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4235 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
4236 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
4237 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
4238 && node.getNodeData().isHasBinaryCharacters() ) {
4239 if ( _sb.length() > 0 ) {
4240 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4242 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4243 g.setColor( Color.BLACK );
4246 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
4248 if ( getControlPanel().isShowBinaryCharacters() ) {
4249 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
4250 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
4251 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4252 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
4253 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
4254 .getLostCharactersAsStringBuffer().toString() );
4257 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
4258 node.getXcoord() + x + 4 + half_box_size,
4260 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
4262 paintGainedAndLostCharacters( g, node, "+"
4263 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
4264 + node.getNodeData().getBinaryCharacters().getLostCount() );
4270 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
4271 final PhylogenyNode node,
4272 final boolean to_pdf,
4273 final boolean to_graphics_file,
4274 final boolean radial_labels,
4275 final double ur_angle,
4276 final boolean is_in_found_nodes ) {
4277 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
4280 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4281 g.setColor( Color.BLACK );
4283 else if ( is_in_found_nodes ) {
4284 g.setColor( getColorForFoundNode( node ) );
4286 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4287 g.setColor( getTaxonomyBasedColor( node ) );
4289 else if ( getControlPanel().isColorAccordingToAnnotation()
4290 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4291 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4292 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4295 g.setColor( getTreeColorSet().getSequenceColor() );
4299 if ( node.getNodeData().isHasTaxonomy()
4300 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4301 .isShowTaxonomyCommonNames() ) ) {
4302 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4303 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4304 _sb.append( taxonomy.getTaxonomyCode() );
4307 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4308 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4309 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4310 _sb.append( taxonomy.getScientificName() );
4312 _sb.append( taxonomy.getCommonName() );
4315 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4316 _sb.append( taxonomy.getScientificName() );
4319 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4320 _sb.append( taxonomy.getCommonName() );
4324 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4325 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4326 _sb.append( taxonomy.getScientificName() );
4330 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4331 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4332 _sb.append( taxonomy.getCommonName() );
4337 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4339 _sb.append( node.getAllExternalDescendants().size() );
4342 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4343 if ( _sb.length() > 0 ) {
4346 _sb.append( node.getName() );
4348 if ( node.getNodeData().isHasSequence() ) {
4349 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4350 if ( _sb.length() > 0 ) {
4353 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4354 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4357 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4359 if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4360 if ( _sb.length() > 0 ) {
4363 _sb.append( node.getNodeData().getSequence().getName() );
4366 g.setFont( getTreeFontSet().getLargeFont() );
4367 if ( is_in_found_nodes ) {
4368 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4370 if ( _sb.length() > 1 ) {
4371 final String sb_str = _sb.toString();
4373 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4374 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
4377 m = ( float ) ( ur_angle % TWO_PI );
4379 _at = g.getTransform();
4380 boolean need_to_reset = false;
4381 final float x_coord = node.getXcoord();
4382 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
4383 if ( radial_labels ) {
4384 need_to_reset = true;
4385 boolean left = false;
4386 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4390 g.rotate( m, x_coord, node.getYcoord() );
4392 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
4396 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4397 need_to_reset = true;
4398 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
4401 TreePanel.drawString( sb_str, x_coord, y_coord, g );
4402 if ( need_to_reset ) {
4403 g.setTransform( _at );
4408 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
4409 if ( node.isCollapse() ) {
4410 if ( !node.isRoot() && !node.getParent().isCollapse() ) {
4411 paintCollapsedNode( g, node, false, false, false );
4415 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4416 g.setColor( getColorForFoundNode( node ) );
4417 drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, node.getYSecondary()
4418 - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
4421 if ( !node.isExternal() && !node.isCollapse() ) {
4422 boolean first_child = true;
4424 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4425 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4426 final PhylogenyNode child_node = node.getChildNode( i );
4428 if ( !isUniformBranchLengthsForCladogram() ) {
4429 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4432 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4434 if ( first_child ) {
4435 first_child = false;
4436 y2 = node.getYSecondary()
4437 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
4438 .getNumberOfExternalNodes() ) );
4441 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4443 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
4444 new_x = x2 + node.getXSecondary();
4445 final float diff_y = node.getYSecondary() - y2;
4446 final float diff_x = node.getXSecondary() - new_x;
4447 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
4448 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
4450 child_node.setXSecondary( new_x );
4451 child_node.setYSecondary( y2 );
4452 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4457 final private void paintNodeRectangular( final Graphics2D g,
4458 final PhylogenyNode node,
4459 final boolean to_pdf,
4460 final boolean dynamically_hide,
4461 final int dynamic_hiding_factor,
4462 final boolean to_graphics_file ) {
4463 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
4464 if ( node.isCollapse() ) {
4465 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
4466 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4470 if ( node.isExternal() ) {
4471 ++_external_node_index;
4473 // Confidence values
4474 if ( getControlPanel().isShowConfidenceValues()
4475 && !node.isExternal()
4477 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
4478 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4479 && node.getBranchData().isHasConfidences() ) {
4480 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
4482 // Draw a line to root:
4483 if ( node.isRoot() && _phylogeny.isRooted() ) {
4484 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
4487 float new_x_min = Float.MAX_VALUE;
4488 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
4489 float min_dist = 1.5f;
4490 if ( !disallow_shortcutting ) {
4491 // System.out.println( dynamic_hiding_factor );
4492 if ( dynamic_hiding_factor > 4000 ) {
4495 else if ( dynamic_hiding_factor > 1000 ) {
4498 else if ( dynamic_hiding_factor > 100 ) {
4502 if ( !node.isExternal() && !node.isCollapse() ) {
4503 boolean first_child = true;
4505 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4506 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4507 final PhylogenyNode child_node = node.getChildNode( i );
4509 if ( !isUniformBranchLengthsForCladogram() ) {
4510 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4513 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4515 if ( first_child ) {
4516 first_child = false;
4517 y2 = node.getYcoord()
4518 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
4521 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4523 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
4524 new_x = x2 + node.getXcoord();
4525 if ( dynamically_hide && ( x2 < new_x_min ) ) {
4528 final float diff_y = node.getYcoord() - y2;
4529 final float diff_x = node.getXcoord() - new_x;
4530 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
4531 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
4532 paintBranchRectangular( g,
4541 child_node.setXcoord( new_x );
4542 child_node.setYcoord( y2 );
4543 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4545 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
4547 if ( dynamically_hide
4548 && !is_in_found_nodes
4549 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
4550 .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
4551 .getHeight() ) ) ) ) ) {
4554 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4555 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
4558 final private void paintNodeWithRenderableData( final Graphics2D g,
4559 final PhylogenyNode node,
4560 final boolean to_graphics_file,
4561 final boolean to_pdf ) {
4562 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
4565 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
4568 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4569 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4570 RenderableDomainArchitecture rds = null;
4571 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
4573 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
4575 catch ( final ClassCastException cce ) {
4576 cce.printStackTrace();
4578 if ( rds != null ) {
4579 rds.setRenderingHeight( 6 );
4581 if ( node.getNodeData().isHasTaxonomy() ) {
4582 if ( getControlPanel().isShowTaxonomyCode()
4583 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
4584 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4588 if ( getControlPanel().isShowTaxonomyScientificNames()
4589 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
4590 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4591 .getScientificName()
4594 if ( getControlPanel().isShowTaxonomyCommonNames()
4595 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
4596 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4601 if ( node.getNodeData().isHasSequence() ) {
4602 if ( getControlPanel().isShowSeqNames()
4603 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
4604 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
4607 if ( getControlPanel().isShowSeqSymbols()
4608 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
4609 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
4612 if ( getControlPanel().isShowGeneNames()
4613 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) ) {
4614 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getGeneName()
4617 if ( getControlPanel().isShowSequenceAcc()
4618 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4619 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
4620 .getAccession().toString()
4623 if ( getControlPanel().isShowAnnotation()
4624 && ( node.getNodeData().getSequence().getAnnotations() != null )
4625 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4626 x += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
4627 .getNodeData().getSequence().getAnnotations(), getOptions()
4628 .isShowAnnotationRefSource() )
4632 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
4633 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
4635 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
4640 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4641 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
4642 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
4643 getStatisticsForExpressionValues(),
4644 getConfiguration() );
4647 PhylogenyNode my_node = node;
4648 if ( !getControlPanel().isDrawPhylogram() ) {
4649 my_node = getPhylogeny().getFirstExternalNode();
4651 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
4652 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
4654 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
4655 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
4657 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
4663 final private void paintOvRectangle( final Graphics2D g ) {
4664 final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
4665 final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
4666 final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
4667 final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
4668 final float width = getOvMaxWidth() / w_ratio;
4669 final float height = getOvMaxHeight() / h_ratio;
4670 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
4671 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
4672 g.setColor( getTreeColorSet().getFoundColor0() );
4673 getOvRectangle().setRect( x, y, width, height );
4674 final Stroke s = g.getStroke();
4675 g.setStroke( STROKE_1 );
4676 if ( ( width < 6 ) && ( height < 6 ) ) {
4677 drawRectFilled( x, y, 6, 6, g );
4678 getOvVirtualRectangle().setRect( x, y, 6, 6 );
4680 else if ( width < 6 ) {
4681 drawRectFilled( x, y, 6, height, g );
4682 getOvVirtualRectangle().setRect( x, y, 6, height );
4684 else if ( height < 6 ) {
4685 drawRectFilled( x, y, width, 6, g );
4686 getOvVirtualRectangle().setRect( x, y, width, 6 );
4689 drawRect( x, y, width, height, g );
4690 if ( isInOvRect() ) {
4691 drawRect( x + 1, y + 1, width - 2, height - 2, g );
4693 getOvVirtualRectangle().setRect( x, y, width, height );
4698 final private void paintPhylogenyLite( final Graphics2D g ) {
4701 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
4702 .getWidth() ) ) ) );
4703 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
4704 final Stroke s = g.getStroke();
4705 g.setStroke( STROKE_05 );
4706 for( final PhylogenyNode element : _nodes_in_preorder ) {
4707 paintNodeLite( g, element );
4710 paintOvRectangle( g );
4714 * Paint the root branch. (Differs from others because it will always be a
4715 * single horizontal line).
4716 * @param to_graphics_file
4718 * @return new x1 value
4720 final private void paintRootBranch( final Graphics2D g,
4723 final PhylogenyNode root,
4724 final boolean to_pdf,
4725 final boolean to_graphics_file ) {
4726 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
4727 float d = getXdistance();
4728 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
4729 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
4731 if ( d < MIN_ROOT_LENGTH ) {
4732 d = MIN_ROOT_LENGTH;
4734 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
4735 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
4738 final double w = PhylogenyMethods.getBranchWidthValue( root );
4739 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
4741 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file );
4744 final private void paintScale( final Graphics2D g,
4747 final boolean to_pdf,
4748 final boolean to_graphics_file ) {
4750 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
4752 final int y2 = y1 - 8;
4753 final int y3 = y1 - 4;
4754 g.setFont( getTreeFontSet().getSmallFont() );
4755 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4756 g.setColor( Color.BLACK );
4759 g.setColor( getTreeColorSet().getBranchLengthColor() );
4761 final Stroke s = g.getStroke();
4762 g.setStroke( STROKE_1 );
4763 drawLine( x1, y1, x1, y2, g );
4764 drawLine( x2, y1, x2, y2, g );
4765 drawLine( x1, y3, x2, y3, g );
4766 if ( getScaleLabel() != null ) {
4767 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
4772 final private int paintTaxonomy( final Graphics2D g,
4773 final PhylogenyNode node,
4774 final boolean is_in_found_nodes,
4775 final boolean to_pdf,
4776 final boolean to_graphics_file,
4777 final double x_shift ) {
4778 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4779 g.setFont( getTreeFontSet().getLargeItalicFont() );
4780 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4781 g.setColor( Color.BLACK );
4783 else if ( is_in_found_nodes ) {
4784 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
4785 g.setColor( getColorForFoundNode( node ) );
4787 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4788 g.setColor( getTaxonomyBasedColor( node ) );
4790 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4791 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4792 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4794 else if ( to_pdf ) {
4795 g.setColor( Color.BLACK );
4798 g.setColor( getTreeColorSet().getTaxonomyColor() );
4800 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4801 final double start_y = node.getYcoord()
4802 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4804 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4805 _sb.append( taxonomy.getTaxonomyCode() );
4808 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4809 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4810 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4811 if ( getOptions().isAbbreviateScientificTaxonNames()
4812 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4813 abbreviateScientificName( taxonomy.getScientificName() );
4816 _sb.append( taxonomy.getScientificName() );
4819 _sb.append( taxonomy.getCommonName() );
4822 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4823 if ( getOptions().isAbbreviateScientificTaxonNames()
4824 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4825 abbreviateScientificName( taxonomy.getScientificName() );
4828 _sb.append( taxonomy.getScientificName() );
4832 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4833 _sb.append( taxonomy.getCommonName() );
4837 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4838 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4839 if ( getOptions().isAbbreviateScientificTaxonNames()
4840 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4841 abbreviateScientificName( taxonomy.getScientificName() );
4844 _sb.append( taxonomy.getScientificName() );
4849 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4850 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4851 _sb.append( taxonomy.getCommonName() );
4855 final String label = _sb.toString();
4857 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4858 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4859 // invert font color and background color to show that this is the query sequence
4860 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4864 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4865 g.setColor( getTreeColorSet().getBackgroundColor() );
4868 TreePanel.drawString( label, start_x, start_y, g );
4869 if ( is_in_found_nodes ) {
4870 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4873 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4877 final private void paintUnrooted( final PhylogenyNode n,
4878 final double low_angle,
4879 final double high_angle,
4880 final boolean radial_labels,
4882 final boolean to_pdf,
4883 final boolean to_graphics_file ) {
4885 n.setXcoord( getWidth() / 2 );
4886 n.setYcoord( getHeight() / 2 );
4888 if ( n.isExternal() ) {
4889 paintNodeDataUnrootedCirc( g,
4894 ( high_angle + low_angle ) / 2,
4895 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
4898 final float num_enclosed = n.getNumberOfExternalNodes();
4899 final float x = n.getXcoord();
4900 final float y = n.getYcoord();
4901 double current_angle = low_angle;
4902 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4903 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4904 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4905 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4906 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4907 final PhylogenyNode desc = n.getChildNode( i );
4908 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4909 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4910 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4911 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4914 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4917 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4920 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4921 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4923 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4924 if ( desc.getDistanceToParent() < 0 ) {
4928 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4932 length = getUrtFactor();
4934 final double mid_angle = current_angle + ( arc_size / 2 );
4935 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4936 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4937 desc.setXcoord( new_x );
4938 desc.setYcoord( new_y );
4939 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4940 current_angle += arc_size;
4941 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4942 drawLine( x, y, new_x, new_y, g );
4943 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file );
4946 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file );
4950 final private void paintUnrootedLite( final PhylogenyNode n,
4951 final double low_angle,
4952 final double high_angle,
4954 final float urt_ov_factor ) {
4956 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
4957 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
4958 n.setXSecondary( x_pos );
4959 n.setYSecondary( y_pos );
4961 if ( n.isExternal() ) {
4964 final float num_enclosed = n.getNumberOfExternalNodes();
4965 final float x = n.getXSecondary();
4966 final float y = n.getYSecondary();
4967 double current_angle = low_angle;
4968 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4969 final PhylogenyNode desc = n.getChildNode( i );
4970 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4971 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4973 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4974 if ( desc.getDistanceToParent() < 0 ) {
4978 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
4982 length = urt_ov_factor;
4984 final double mid_angle = current_angle + ( arc_size / 2 );
4985 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4986 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4987 desc.setXSecondary( new_x );
4988 desc.setYSecondary( new_y );
4989 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
4990 g.setColor( getColorForFoundNode( desc ) );
4991 drawRectFilled( desc.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
4992 desc.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
4993 OVERVIEW_FOUND_NODE_BOX_SIZE,
4994 OVERVIEW_FOUND_NODE_BOX_SIZE,
4996 g.setColor( getTreeColorSet().getOvColor() );
4998 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4999 current_angle += arc_size;
5000 drawLine( x, y, new_x, new_y, g );
5004 final private void pasteSubtree( final PhylogenyNode node ) {
5005 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5006 errorMessageNoCutCopyPasteInUnrootedDisplay();
5009 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
5010 JOptionPane.showMessageDialog( this,
5011 "No tree in buffer (need to copy or cut a subtree first)",
5012 "Attempt to paste with empty buffer",
5013 JOptionPane.ERROR_MESSAGE );
5016 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
5017 final Object[] options = { "As sibling", "As descendant", "Cancel" };
5018 final int r = JOptionPane.showOptionDialog( this,
5019 "How to paste subtree" + label + "?",
5021 JOptionPane.CLOSED_OPTION,
5022 JOptionPane.QUESTION_MESSAGE,
5026 boolean paste_as_sibling = true;
5028 paste_as_sibling = false;
5030 else if ( r != 0 ) {
5033 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
5034 buffer_phy.setAllNodesToNotCollapse();
5035 PhylogenyMethods.preOrderReId( buffer_phy );
5036 buffer_phy.setRooted( true );
5037 boolean need_to_show_whole = false;
5038 if ( paste_as_sibling ) {
5039 if ( node.isRoot() ) {
5040 JOptionPane.showMessageDialog( this,
5041 "Cannot paste sibling to root",
5042 "Attempt to paste sibling to root",
5043 JOptionPane.ERROR_MESSAGE );
5046 buffer_phy.addAsSibling( node );
5049 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
5050 need_to_show_whole = true;
5051 _phylogeny = buffer_phy;
5054 buffer_phy.addAsChild( node );
5057 if ( getCopiedAndPastedNodes() == null ) {
5058 setCopiedAndPastedNodes( new HashSet<Long>() );
5060 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
5061 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
5062 for( final PhylogenyNode n : nodes ) {
5063 node_ids.add( n.getId() );
5065 node_ids.add( node.getId() );
5066 getCopiedAndPastedNodes().addAll( node_ids );
5067 setNodeInPreorderToNull();
5068 _phylogeny.externalNodesHaveChanged();
5069 _phylogeny.clearHashIdToNodeMap();
5070 _phylogeny.recalculateNumberOfExternalDescendants( true );
5071 resetNodeIdToDistToLeafMap();
5073 if ( need_to_show_whole ) {
5074 getControlPanel().showWhole();
5079 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
5080 final PropertiesMap properties = node.getNodeData().getProperties();
5081 final StringBuffer sb = new StringBuffer();
5082 boolean first = true;
5083 for( final String ref : properties.getPropertyRefs() ) {
5090 final Property p = properties.getProperty( ref );
5091 sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
5093 sb.append( p.getValue() );
5094 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5095 sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
5101 final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
5102 getMainPanel().setCopiedAndPastedNodes( nodeIds );
5105 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
5106 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
5109 final private void setInOv( final boolean in_ov ) {
5113 final private void setOvMaxHeight( final float ov_max_height ) {
5114 _ov_max_height = ov_max_height;
5117 final private void setOvMaxWidth( final float ov_max_width ) {
5118 _ov_max_width = ov_max_width;
5121 final private void setOvXcorrectionFactor( final float f ) {
5122 _ov_x_correction_factor = f;
5125 final private void setOvXDistance( final float ov_x_distance ) {
5126 _ov_x_distance = ov_x_distance;
5129 final private void setOvXPosition( final int ov_x_position ) {
5130 _ov_x_position = ov_x_position;
5133 final private void setOvYDistance( final float ov_y_distance ) {
5134 _ov_y_distance = ov_y_distance;
5137 final private void setOvYPosition( final int ov_y_position ) {
5138 _ov_y_position = ov_y_position;
5141 final private void setOvYStart( final int ov_y_start ) {
5142 _ov_y_start = ov_y_start;
5145 final private void setScaleDistance( final double scale_distance ) {
5146 _scale_distance = scale_distance;
5149 final private void setScaleLabel( final String scale_label ) {
5150 _scale_label = scale_label;
5153 private final void setupStroke( final Graphics2D g ) {
5154 if ( getYdistance() < 0.001 ) {
5155 g.setStroke( STROKE_005 );
5157 else if ( getYdistance() < 0.01 ) {
5158 g.setStroke( STROKE_01 );
5160 else if ( getYdistance() < 0.5 ) {
5161 g.setStroke( STROKE_025 );
5163 else if ( getYdistance() < 1 ) {
5164 g.setStroke( STROKE_05 );
5166 else if ( getYdistance() < 2 ) {
5167 g.setStroke( STROKE_075 );
5169 else if ( getYdistance() < 20 ) {
5170 g.setStroke( STROKE_1 );
5173 g.setStroke( STROKE_2 );
5177 final private void setUpUrtFactor() {
5178 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
5179 : getVisibleRect().height;
5180 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
5181 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
5184 final int max_depth = _circ_max_depth;
5185 if ( max_depth > 0 ) {
5186 setUrtFactor( d / ( 2 * max_depth ) );
5189 setUrtFactor( d / 2 );
5192 setUrtFactorOv( getUrtFactor() );
5195 final private void setUrtFactor( final float urt_factor ) {
5196 _urt_factor = urt_factor;
5199 final private void setUrtFactorOv( final float urt_factor_ov ) {
5200 _urt_factor_ov = urt_factor_ov;
5203 private void showExtDescNodeData( final PhylogenyNode node ) {
5204 final List<String> data = new ArrayList<String>();
5205 final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
5206 if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
5207 for( final PhylogenyNode n : getFoundNodes0AsListOfPhylogenyNodes() ) {
5208 if ( !nodes.contains( n ) ) {
5213 if ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() ) {
5214 for( final PhylogenyNode n : getFoundNodes1AsListOfPhylogenyNodes() ) {
5215 if ( !nodes.contains( n ) ) {
5220 for( final PhylogenyNode n : nodes ) {
5221 switch ( getOptions().getExtDescNodeDataToReturn() ) {
5223 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
5224 data.add( n.getName() );
5228 if ( n.getNodeData().isHasSequence()
5229 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5230 data.add( n.getNodeData().getSequence().getName() );
5234 if ( n.getNodeData().isHasSequence()
5235 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
5236 data.add( n.getNodeData().getSequence().getGeneName() );
5239 case SEQUENCE_SYMBOL:
5240 if ( n.getNodeData().isHasSequence()
5241 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5242 data.add( n.getNodeData().getSequence().getSymbol() );
5245 case SEQUENCE_MOL_SEQ:
5246 if ( n.getNodeData().isHasSequence()
5247 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5248 data.add( n.getNodeData().getSequence().getMolecularSequence() );
5251 case SEQUENCE_MOL_SEQ_FASTA:
5252 final StringBuilder sb = new StringBuilder();
5253 if ( n.getNodeData().isHasSequence()
5254 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5255 final StringBuilder ann = new StringBuilder();
5256 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
5257 ann.append( n.getName() );
5260 if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5261 ann.append( "SYM=" );
5262 ann.append( n.getNodeData().getSequence().getSymbol() );
5265 if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5266 ann.append( "NAME=" );
5267 ann.append( n.getNodeData().getSequence().getName() );
5270 if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
5271 ann.append( "GN=" );
5272 ann.append( n.getNodeData().getSequence().getGeneName() );
5275 if ( n.getNodeData().getSequence().getAccession() != null ) {
5276 ann.append( "ACC=" );
5277 ann.append( n.getNodeData().getSequence().getAccession().asText() );
5280 if ( n.getNodeData().isHasTaxonomy() ) {
5281 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5282 ann.append( "TAXID=" );
5283 ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5286 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5287 ann.append( "SN=" );
5288 ann.append( n.getNodeData().getTaxonomy().getScientificName() );
5293 if ( ann.charAt( ann.length() - 1 ) == '|' ) {
5294 ann_str = ann.substring( 0, ann.length() - 1 );
5297 ann_str = ann.toString();
5299 sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
5300 .getMolecularSequence(), 60 ) );
5301 data.add( sb.toString() );
5305 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
5306 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
5307 data.add( n.getNodeData().getSequence().getAccession().toString() );
5310 case TAXONOMY_SCIENTIFIC_NAME:
5311 if ( n.getNodeData().isHasTaxonomy()
5312 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5313 data.add( n.getNodeData().getTaxonomy().getScientificName() );
5316 case TAXONOMY_COMM0N_NAME:
5317 if ( n.getNodeData().isHasTaxonomy()
5318 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
5319 data.add( n.getNodeData().getTaxonomy().getCommonName() );
5323 if ( n.getNodeData().isHasTaxonomy()
5324 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5325 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5329 TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
5332 throw new IllegalArgumentException( "unknown data element: "
5333 + getOptions().getExtDescNodeDataToReturn() );
5336 final StringBuilder sb = new StringBuilder();
5337 final int size = TreePanelUtil.makeSB( data, getOptions(), sb );
5338 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
5339 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
5340 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
5341 System.out.println( sb );
5343 if ( sb.length() < 1 ) {
5344 clearCurrentExternalNodesDataBuffer();
5347 setCurrentExternalNodesDataBuffer( sb );
5350 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
5351 if ( sb.length() < 1 ) {
5352 TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData()
5353 + ")", "Descendants of selected node do not contain selected data" );
5354 clearCurrentExternalNodesDataBuffer();
5357 setCurrentExternalNodesDataBuffer( sb );
5359 if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
5360 title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5361 : obtainTitleForExtDescNodeData() )
5364 + " nodes, unique entries: "
5368 title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5369 : obtainTitleForExtDescNodeData() )
5373 + node.getNumberOfExternalNodes()
5374 + " external descendats of node "
5376 + ", unique entries: " + size;
5378 final String s = sb.toString().trim();
5379 if ( getMainPanel().getMainFrame() == null ) {
5380 // Must be "E" applet version.
5381 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
5382 ae.showTextFrame( s, title );
5385 getMainPanel().getMainFrame().showTextFrame( s, title );
5391 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
5393 if ( ( node.getName().length() > 0 )
5394 || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData()
5396 || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData()
5397 .getSequence() ) ) || ( node.getNodeData().isHasDate() )
5398 || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) {
5399 _popup_buffer.setLength( 0 );
5401 if ( node.getName().length() > 0 ) {
5403 _popup_buffer.append( node.getName() );
5405 if ( node.getNodeData().isHasTaxonomy()
5406 && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
5408 boolean enc_data = false;
5409 final Taxonomy tax = node.getNodeData().getTaxonomy();
5410 if ( _popup_buffer.length() > 0 ) {
5411 _popup_buffer.append( "\n" );
5413 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
5414 _popup_buffer.append( "[" );
5415 _popup_buffer.append( tax.getTaxonomyCode() );
5416 _popup_buffer.append( "]" );
5419 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
5421 _popup_buffer.append( " " );
5423 _popup_buffer.append( tax.getScientificName() );
5426 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
5428 _popup_buffer.append( " (" );
5431 _popup_buffer.append( "(" );
5433 _popup_buffer.append( tax.getCommonName() );
5434 _popup_buffer.append( ")" );
5437 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
5439 _popup_buffer.append( " (" );
5442 _popup_buffer.append( "(" );
5444 _popup_buffer.append( tax.getAuthority() );
5445 _popup_buffer.append( ")" );
5448 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
5450 _popup_buffer.append( " [" );
5453 _popup_buffer.append( "[" );
5455 _popup_buffer.append( tax.getRank() );
5456 _popup_buffer.append( "]" );
5459 if ( tax.getSynonyms().size() > 0 ) {
5461 _popup_buffer.append( " " );
5463 _popup_buffer.append( "[" );
5465 for( final String syn : tax.getSynonyms() ) {
5466 if ( !ForesterUtil.isEmpty( syn ) ) {
5468 _popup_buffer.append( syn );
5469 if ( counter < tax.getSynonyms().size() ) {
5470 _popup_buffer.append( ", " );
5475 _popup_buffer.append( "]" );
5478 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
5479 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
5480 _popup_buffer.append( "[" );
5481 _popup_buffer.append( tax.getIdentifier().getProvider() );
5482 _popup_buffer.append( "] " );
5484 _popup_buffer.append( tax.getIdentifier().getValue() );
5488 if ( node.getNodeData().isHasSequence()
5489 && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
5491 boolean enc_data = false;
5492 if ( _popup_buffer.length() > 0 ) {
5493 _popup_buffer.append( "\n" );
5495 final Sequence seq = node.getNodeData().getSequence();
5496 if ( seq.getAccession() != null ) {
5497 _popup_buffer.append( "[" );
5498 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
5499 _popup_buffer.append( seq.getAccession().getSource() );
5500 _popup_buffer.append( ":" );
5502 _popup_buffer.append( seq.getAccession().getValue() );
5503 _popup_buffer.append( "]" );
5506 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
5508 _popup_buffer.append( " [" );
5511 _popup_buffer.append( "[" );
5513 _popup_buffer.append( seq.getSymbol() );
5514 _popup_buffer.append( "]" );
5517 if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
5519 _popup_buffer.append( " [" );
5522 _popup_buffer.append( "[" );
5524 _popup_buffer.append( seq.getGeneName() );
5525 _popup_buffer.append( "]" );
5528 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
5530 _popup_buffer.append( " " );
5532 _popup_buffer.append( seq.getName() );
5535 if ( node.getNodeData().isHasDate() ) {
5537 if ( _popup_buffer.length() > 0 ) {
5538 _popup_buffer.append( "\n" );
5540 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
5542 if ( node.getNodeData().isHasDistribution() ) {
5544 if ( _popup_buffer.length() > 0 ) {
5545 _popup_buffer.append( "\n" );
5547 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
5549 if ( node.getBranchData().isHasConfidences() ) {
5550 final List<Confidence> confs = node.getBranchData().getConfidences();
5551 for( final Confidence confidence : confs ) {
5553 if ( _popup_buffer.length() > 0 ) {
5554 _popup_buffer.append( "\n" );
5556 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
5557 _popup_buffer.append( "[" );
5558 _popup_buffer.append( confidence.getType() );
5559 _popup_buffer.append( "] " );
5562 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
5564 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5565 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5566 _popup_buffer.append( " (sd=" );
5567 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
5568 .getStandardDeviation(), getOptions()
5569 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5570 _popup_buffer.append( ")" );
5574 if ( node.getNodeData().isHasProperties() ) {
5575 final PropertiesMap properties = node.getNodeData().getProperties();
5576 for( final String ref : properties.getPropertyRefs() ) {
5577 _popup_buffer.append( "\n" );
5578 final Property p = properties.getProperty( ref );
5579 _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
5580 _popup_buffer.append( "=" );
5581 _popup_buffer.append( p.getValue() );
5582 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5583 _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
5587 if ( _popup_buffer.length() > 0 ) {
5588 if ( !getConfiguration().isUseNativeUI() ) {
5590 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
5591 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
5592 if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
5593 _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
5595 else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
5596 _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
5598 else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
5599 _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
5601 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
5602 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
5605 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
5609 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
5611 _rollover_popup.setText( _popup_buffer.toString() );
5612 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
5614 e.getLocationOnScreen().x + 10,
5615 e.getLocationOnScreen().y
5617 _node_desc_popup.show();
5621 catch ( final Exception ex ) {
5626 final private void showNodeEditFrame( final PhylogenyNode n ) {
5627 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5628 // pop up edit box for single node
5629 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
5630 _node_frame_index++;
5633 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5637 final private void showNodeFrame( final PhylogenyNode n ) {
5638 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5639 // pop up edit box for single node
5640 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
5641 _node_frame_index++;
5644 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5648 final private void switchDisplaygetPhylogenyGraphicsType() {
5649 switch ( getPhylogenyGraphicsType() ) {
5651 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5652 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5655 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5656 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5659 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5660 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5663 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5664 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5667 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5668 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5671 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5672 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5675 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5676 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5679 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5680 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5683 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5685 if ( getControlPanel().getDynamicallyHideData() != null ) {
5686 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5687 getControlPanel().getDynamicallyHideData().setEnabled( false );
5690 getControlPanel().getDynamicallyHideData().setEnabled( true );
5693 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5694 getControlPanel().setDrawPhylogramEnabled( true );
5697 getControlPanel().setDrawPhylogramEnabled( false );
5699 if ( getMainPanel().getMainFrame() == null ) {
5700 // Must be "E" applet version.
5701 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5702 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5705 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5709 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5710 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5713 final private static boolean plusPressed( final int key_code ) {
5714 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5715 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5718 final private class SubtreeColorizationActionListener implements ActionListener {
5720 List<PhylogenyNode> _additional_nodes = null;
5721 JColorChooser _chooser = null;
5722 PhylogenyNode _node = null;
5724 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5729 SubtreeColorizationActionListener( final JColorChooser chooser,
5730 final PhylogenyNode node,
5731 final List<PhylogenyNode> additional_nodes ) {
5734 _additional_nodes = additional_nodes;
5738 public void actionPerformed( final ActionEvent e ) {
5739 final Color c = _chooser.getColor();
5741 colorizeSubtree( c, _node, _additional_nodes );