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.Annotation;
110 import org.forester.phylogeny.data.BranchColor;
111 import org.forester.phylogeny.data.Confidence;
112 import org.forester.phylogeny.data.Event;
113 import org.forester.phylogeny.data.NodeData.NODE_DATA;
114 import org.forester.phylogeny.data.NodeVisualization;
115 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
116 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
117 import org.forester.phylogeny.data.PhylogenyDataUtil;
118 import org.forester.phylogeny.data.PropertiesMap;
119 import org.forester.phylogeny.data.Property;
120 import org.forester.phylogeny.data.Sequence;
121 import org.forester.phylogeny.data.SequenceRelation;
122 import org.forester.phylogeny.data.Taxonomy;
123 import org.forester.phylogeny.data.Uri;
124 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
125 import org.forester.phylogeny.iterators.PreorderTreeIterator;
126 import org.forester.util.BasicDescriptiveStatistics;
127 import org.forester.util.DescriptiveStatistics;
128 import org.forester.util.ForesterConstants;
129 import org.forester.util.ForesterUtil;
130 import org.forester.util.SequenceIdParser;
132 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
134 private static final float PI = ( float ) ( Math.PI );
135 private static final double TWO_PI = 2 * Math.PI;
136 private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
137 private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
138 private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
139 private static final short OV_BORDER = 10;
140 final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
141 final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
142 final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
143 final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
144 final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
145 private final static long serialVersionUID = -978349745916505029L;
146 private final static int EURO_D = 10;
147 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
148 private final static int MIN_ROOT_LENGTH = 3;
149 private final static int MAX_SUBTREES = 100;
150 private final static int MAX_NODE_FRAMES = 10;
151 private final static int MOVE = 20;
152 private final static NumberFormat FORMATTER_CONFIDENCE;
153 private final static NumberFormat FORMATTER_BRANCH_LENGTH;
154 private final static int WIGGLE = 2;
155 private final static int LIMIT_FOR_HQ_RENDERING = 2000;
156 private final static int CONFIDENCE_LEFT_MARGIN = 4;
157 private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
158 RenderingHints.VALUE_RENDER_DEFAULT );
159 private File _treefile = null;
160 private Configuration _configuration = null;
161 private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
162 private int _node_frame_index = 0;
163 private Phylogeny _phylogeny = null;
164 private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
165 private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
166 private int _subtree_index = 0;
167 private MainPanel _main_panel = null;
168 private Set<Long> _found_nodes = null;
169 private PhylogenyNode _highlight_node = null;
170 private JPopupMenu _node_popup_menu = null;
171 private JMenuItem _node_popup_menu_items[] = null;
172 private int _longest_ext_node_info = 0;
173 private float _x_correction_factor = 0.0f;
174 private float _ov_x_correction_factor = 0.0f;
175 private float _x_distance = 0.0f;
176 private float _y_distance = 0.0f;
177 private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
178 private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
179 private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
180 private float _last_drag_point_x = 0;
181 private float _last_drag_point_y = 0;
182 private ControlPanel _control_panel = null;
183 private int _external_node_index = 0;
184 private final Path2D.Float _polygon = new Path2D.Float();
185 private final StringBuilder _sb = new StringBuilder();
186 private JColorChooser _color_chooser = null;
187 private double _scale_distance = 0.0;
188 private String _scale_label = null;
189 private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
190 private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
191 private final Line2D _line = new Line2D.Float();
192 private final Ellipse2D _ellipse = new Ellipse2D.Float();
193 private final Rectangle2D _rectangle = new Rectangle2D.Float();
194 private Options _options = null;
195 private float _ov_max_width = 0;
196 private float _ov_max_height = 0;
197 private int _ov_x_position = 0;
198 private int _ov_y_position = 0;
199 private int _ov_y_start = 0;
200 private float _ov_y_distance = 0;
201 private float _ov_x_distance = 0;
202 private boolean _ov_on = false;
203 private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
204 private float _urt_factor = 1;
205 private float _urt_factor_ov = 1;
206 private final boolean _phy_has_branch_lengths;
207 private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
208 private boolean _in_ov_rect = false;
209 private boolean _in_ov = false;
210 private final Rectangle _ov_virtual_rectangle = new Rectangle();
211 final private static double _180_OVER_PI = 180.0 / Math.PI;
212 private static final float ROUNDED_D = 8;
213 private int _circ_max_depth;
214 private PhylogenyNode _root;
215 final private Arc2D _arc = new Arc2D.Double();
216 final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
217 final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
218 final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
219 HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
220 private AffineTransform _at;
221 private double _max_distance_to_root = -1;
222 private int _dynamic_hiding_factor = 0;
223 private boolean _edited = false;
224 private Popup _node_desc_popup;
225 private JTextArea _rollover_popup;
226 private final StringBuffer _popup_buffer = new StringBuffer();
227 final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
230 private Sequence _query_sequence = null;
231 private final FontRenderContext _frc = new FontRenderContext( null,
234 // expression values menu:
235 private DescriptiveStatistics _statistics_for_vector_data;
236 private PhylogenyNode[] _nodes_in_preorder = null;
237 private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
238 private int _current_external_nodes_data_buffer_change_counter = 0;
239 private Set<Long> _current_external_nodes = null;
240 // private Image offscreenImage;
241 // private Graphics offscreenGraphics;
242 // private Dimension offscreenDimension;
244 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
245 dfs.setDecimalSeparator( '.' );
246 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
247 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
250 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
251 requestFocusInWindow();
252 addKeyListener( new KeyAdapter() {
255 public void keyPressed( final KeyEvent key_event ) {
256 keyPressedCalls( key_event );
257 requestFocusInWindow();
260 addFocusListener( new FocusAdapter() {
263 public void focusGained( final FocusEvent e ) {
264 requestFocusInWindow();
267 if ( ( t == null ) || t.isEmpty() ) {
268 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
270 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
272 _configuration = configuration;
274 _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
276 // if ( !_phylogeny.isEmpty() ) {
277 _phylogeny.recalculateNumberOfExternalDescendants( true );
278 checkForVectorProperties( _phylogeny );
280 setBackground( getTreeColorSet().getBackgroundColor() );
281 final MouseListener mouse_listener = new MouseListener( this );
282 addMouseListener( mouse_listener );
283 addMouseMotionListener( mouse_listener );
284 addMouseWheelListener( this );
285 calculateScaleDistance();
286 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
287 FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
288 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
292 final public void actionPerformed( final ActionEvent e ) {
293 boolean done = false;
294 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
295 for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
296 // NOTE: index corresponds to the indices of click-to options
297 // in the control panel.
298 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
299 // Set this as the new default click-to action
300 _main_panel.getControlPanel().setClickToAction( index );
301 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
302 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
303 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
308 requestFocusInWindow();
311 public synchronized Hashtable<String, BufferedImage> getImageMap() {
312 return getMainPanel().getImageMap();
315 final public MainPanel getMainPanel() {
320 * Get a pointer to the phylogeny
322 * @return a pointer to the phylogeny
324 public final Phylogeny getPhylogeny() {
329 final public void mouseWheelMoved( final MouseWheelEvent e ) {
330 final int notches = e.getWheelRotation();
331 if ( inOvVirtualRectangle( e ) ) {
332 if ( !isInOvRect() ) {
338 if ( isInOvRect() ) {
339 setInOvRect( false );
343 if ( e.isControlDown() ) {
345 getTreeFontSet().increaseFontSize();
346 getControlPanel().displayedPhylogenyMightHaveChanged( true );
349 getTreeFontSet().decreaseFontSize( 1, false );
350 getControlPanel().displayedPhylogenyMightHaveChanged( true );
353 else if ( e.isShiftDown() ) {
354 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
355 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
357 for( int i = 0; i < ( -notches ); ++i ) {
358 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
359 getControlPanel().displayedPhylogenyMightHaveChanged( false );
363 for( int i = 0; i < notches; ++i ) {
364 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
365 if ( getStartingAngle() < 0 ) {
366 setStartingAngle( TWO_PI + getStartingAngle() );
368 getControlPanel().displayedPhylogenyMightHaveChanged( false );
374 for( int i = 0; i < ( -notches ); ++i ) {
375 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
376 getControlPanel().displayedPhylogenyMightHaveChanged( false );
380 for( int i = 0; i < notches; ++i ) {
381 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
382 getControlPanel().displayedPhylogenyMightHaveChanged( false );
389 for( int i = 0; i < ( -notches ); ++i ) {
390 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
391 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
392 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
393 getControlPanel().displayedPhylogenyMightHaveChanged( false );
397 for( int i = 0; i < notches; ++i ) {
398 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
399 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
400 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
401 getControlPanel().displayedPhylogenyMightHaveChanged( false );
406 requestFocusInWindow();
411 final public void paintComponent( final Graphics g ) {
412 // Dimension currentSize = getSize();
413 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
414 // call the 'java.awt.Component.createImage(...)' method to get an
416 // offscreenImage = createImage( currentSize.width, currentSize.height );
417 // offscreenGraphics = offscreenImage.getGraphics();
418 // offscreenDimension = currentSize;
420 // super.paintComponent( g ); //why?
421 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
422 final Graphics2D g2d = ( Graphics2D ) g;
423 g2d.setRenderingHints( _rendering_hints );
424 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
425 //g.drawImage( offscreenImage, 0, 0, this );
429 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
430 throws PrinterException {
431 if ( page_index > 0 ) {
432 return ( NO_SUCH_PAGE );
435 final Graphics2D g2d = ( Graphics2D ) g;
436 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
437 // Turn off double buffering !?
438 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
439 // Turn double buffering back on !?
440 return ( PAGE_EXISTS );
444 public final void setEdited( final boolean edited ) {
448 public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
449 getMainPanel().setImageMap( image_map );
453 * Set a phylogeny tree.
456 * an instance of a Phylogeny
458 public final void setTree( final Phylogeny t ) {
459 setNodeInPreorderToNull();
463 public final void setWaitCursor() {
464 setCursor( WAIT_CURSOR );
469 public void update( final Graphics g ) {
473 final void calcMaxDepth() {
474 if ( _phylogeny != null ) {
475 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
480 * Set parameters for printing the displayed tree
483 final void calcParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
484 // updateStyle(); not needed?
485 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
487 if ( recalc_longest_ext_node_info ) {
488 calculateLongestExtNodeInfo();
489 if ( getOptions().isAllowFontSizeChange() ) {
490 if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
491 && ( getTreeFontSet().getLargeFont().getSize() > 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
492 while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
493 && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
494 getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(),
496 calculateLongestExtNodeInfo();
500 while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
501 && ( getTreeFontSet().getLargeFont().getSize() <= getTreeFontSet().getLargeFontMemory()
502 .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
503 getMainPanel().getTreeFontSet().increaseFontSize();
504 calculateLongestExtNodeInfo();
509 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
510 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
511 if ( ext_nodes == 1 ) {
512 ext_nodes = max_depth;
513 if ( ext_nodes < 1 ) {
520 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
521 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
522 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
525 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
526 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
528 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
532 if ( ov_xdist < 0.0 ) {
538 setXdistance( xdist );
539 setYdistance( ydist );
540 setOvXDistance( ov_xdist );
541 final double height = _phylogeny.getHeight();
543 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
544 setXcorrectionFactor( corr > 0 ? corr : 0 );
545 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
546 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
549 setXcorrectionFactor( 0 );
550 setOvXcorrectionFactor( 0 );
552 _circ_max_depth = max_depth;
555 if ( getOptions().isAllowFontSizeChange() ) {
556 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
557 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
558 // int dynamic_hiding_factor = calcDynamicHidingFactor();
559 // if ( dynamic_hiding_factor > 1 ) {
560 // while ( dynamic_hiding_factor > 1
561 // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
562 // getTreeFontSet().decreaseFontSize( 1, true );
563 // dynamic_hiding_factor = calcDynamicHidingFactor();
566 // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
567 // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
568 // getTreeFontSet().increaseFontSize();
569 // dynamic_hiding_factor = calcDynamicHidingFactor();
578 final void calculateLongestExtNodeInfo() {
579 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
582 int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
583 * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
584 if ( max_length < 40 ) {
588 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
590 if ( node.isCollapse() ) {
593 if ( getControlPanel().isShowNodeNames() ) {
594 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
596 if ( node.getNodeData().isHasSequence() ) {
597 if ( getControlPanel().isShowSequenceAcc()
598 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
599 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
603 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
604 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
606 if ( getControlPanel().isShowGeneSymbols()
607 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
608 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
610 if ( getControlPanel().isShowAnnotation()
611 && ( node.getNodeData().getSequence().getAnnotations() != null )
612 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
613 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
617 if ( getControlPanel().isShowDomainArchitectures()
618 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
619 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
620 .getRenderingSize().getWidth();
623 if ( node.getNodeData().isHasTaxonomy() ) {
624 final Taxonomy tax = node.getNodeData().getTaxonomy();
625 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
626 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
628 if ( getControlPanel().isShowTaxonomyScientificNames()
629 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
630 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
632 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
633 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
636 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
637 sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
639 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
640 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
641 .getGainedCharactersAsStringBuffer().toString() );
643 if ( sum >= max_length ) {
644 setLongestExtNodeInfo( max_length );
647 if ( sum > longest ) {
651 if ( longest >= max_length ) {
652 setLongestExtNodeInfo( max_length );
655 setLongestExtNodeInfo( longest );
659 final void calculateScaleDistance() {
660 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
663 final double height = getMaxDistanceToRoot();
665 if ( ( height <= 0.5 ) ) {
666 setScaleDistance( 0.01 );
668 else if ( height <= 5.0 ) {
669 setScaleDistance( 0.1 );
671 else if ( height <= 50.0 ) {
672 setScaleDistance( 1 );
674 else if ( height <= 500.0 ) {
675 setScaleDistance( 10 );
678 setScaleDistance( 100 );
682 setScaleDistance( 0.0 );
684 String scale_label = String.valueOf( getScaleDistance() );
685 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
686 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
688 setScaleLabel( scale_label );
691 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
692 String species = tax.getTaxonomyCode();
693 if ( ForesterUtil.isEmpty( species ) ) {
694 species = tax.getScientificName();
695 if ( ForesterUtil.isEmpty( species ) ) {
696 species = tax.getCommonName();
699 if ( ForesterUtil.isEmpty( species ) ) {
700 return getTreeColorSet().getTaxonomyColor();
702 // Look in species hash
703 Color c = getControlPanel().getSpeciesColors().get( species );
705 c = AptxUtil.calculateColorFromString( species );
706 getControlPanel().getSpeciesColors().put( species, c );
711 void checkForVectorProperties( final Phylogeny phy ) {
712 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
713 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
714 final PhylogenyNode node = iter.next();
715 if ( node.getNodeData().getProperties() != null ) {
716 final PropertiesMap pm = node.getNodeData().getProperties();
717 final double[] vector = new double[ pm.getProperties().size() ];
719 for( final String ref : pm.getProperties().keySet() ) {
720 if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
721 final Property p = pm.getProperty( ref );
722 final String value_str = p.getValue();
723 final String index_str = ref
724 .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
727 d = Double.parseDouble( value_str );
729 catch ( final NumberFormatException e ) {
730 JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
731 + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
736 i = Integer.parseInt( index_str );
738 catch ( final NumberFormatException e ) {
739 JOptionPane.showMessageDialog( this,
740 "Could not parse \"" + index_str
741 + "\" into index for vector data",
742 "Problem with Vector Data",
743 JOptionPane.ERROR_MESSAGE );
747 JOptionPane.showMessageDialog( this,
748 "Attempt to use negative index for vector data",
749 "Problem with Vector Data",
750 JOptionPane.ERROR_MESSAGE );
758 final List<Double> vector_l = new ArrayList<Double>( counter );
759 for( int i = 0; i < counter; ++i ) {
760 vector_l.add( vector[ i ] );
762 node.getNodeData().setVector( vector_l );
765 if ( stats.getN() > 0 ) {
766 _statistics_for_vector_data = stats;
770 void clearCurrentExternalNodesDataBuffer() {
771 setCurrentExternalNodesDataBuffer( new StringBuilder() );
775 * Collapse the tree from the given node
780 final void collapse( final PhylogenyNode node ) {
781 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
782 JOptionPane.showMessageDialog( this,
783 "Cannot collapse in unrooted display type",
784 "Attempt to collapse in unrooted display",
785 JOptionPane.WARNING_MESSAGE );
788 if ( !node.isExternal() && !node.isRoot() ) {
789 final boolean collapse = !node.isCollapse();
790 AptxUtil.collapseSubtree( node, collapse );
791 updateSetOfCollapsedExternalNodes();
792 _phylogeny.recalculateNumberOfExternalDescendants( true );
793 resetNodeIdToDistToLeafMap();
794 calculateLongestExtNodeInfo();
795 setNodeInPreorderToNull();
796 _control_panel.displayedPhylogenyMightHaveChanged( true );
797 resetPreferredSize();
799 _main_panel.adjustJScrollPane();
804 final void collapseSpeciesSpecificSubtrees() {
805 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
809 AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
810 updateSetOfCollapsedExternalNodes();
811 _phylogeny.recalculateNumberOfExternalDescendants( true );
812 resetNodeIdToDistToLeafMap();
813 calculateLongestExtNodeInfo();
814 setNodeInPreorderToNull();
815 resetPreferredSize();
816 _main_panel.adjustJScrollPane();
821 final void colorRank( final String rank ) {
822 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
826 AptxUtil.removeBranchColors( _phylogeny );
827 final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
828 if ( colorizations > 0 ) {
829 _control_panel.setColorBranches( true );
830 if ( _control_panel.getColorBranchesCb() != null ) {
831 _control_panel.getColorBranchesCb().setSelected( true );
833 if ( _control_panel.getColorAccSpeciesCb() != null ) {
834 _control_panel.getColorAccSpeciesCb().setSelected( false );
836 _options.setColorLabelsSameAsParentBranch( true );
837 _control_panel.repaint();
841 if ( colorizations > 0 ) {
842 String msg = "Taxonomy colorization via " + rank + " completed:\n";
843 if ( colorizations > 1 ) {
844 msg += "colorized " + colorizations + " subtrees";
847 msg += "colorized one subtree";
850 JOptionPane.showMessageDialog( this,
852 "Taxonomy Colorization Completed (" + rank + ")",
853 JOptionPane.INFORMATION_MESSAGE );
856 String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
857 msg += "Possible solutions (given that suitable taxonomic information is present):\n";
858 msg += "select a different rank (e.g. phylum, genus, ...)\n";
861 msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
862 msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
863 JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
867 final void confColor() {
868 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
872 AptxUtil.removeBranchColors( _phylogeny );
873 AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
874 _control_panel.setColorBranches( true );
875 if ( _control_panel.getColorBranchesCb() != null ) {
876 _control_panel.getColorBranchesCb().setSelected( true );
882 final void decreaseDomainStructureEvalueThreshold() {
883 if ( _domain_structure_e_value_thr_exp > -20 ) {
884 _domain_structure_e_value_thr_exp -= 1;
889 * Find the node, if any, at the given location
893 * @return pointer to the node at x,y, null if not found
895 final PhylogenyNode findNode( final int x, final int y ) {
896 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
899 final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
900 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
901 final PhylogenyNode node = iter.next();
902 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
903 && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
904 && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
905 && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
906 && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
913 final Configuration getConfiguration() {
914 return _configuration;
917 final ControlPanel getControlPanel() {
918 return _control_panel;
921 String getCurrentExternalNodesDataBufferAsString() {
922 return _current_external_nodes_data_buffer.toString();
925 int getCurrentExternalNodesDataBufferChangeCounter() {
926 return _current_external_nodes_data_buffer_change_counter;
929 final int getDomainStructureEvalueThreshold() {
930 return _domain_structure_e_value_thr_exp;
933 final Set<Long> getFoundNodes() {
937 final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
938 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
939 return ( PhylogenyMethods.getBranchColorValue( node ) );
942 return ( getTreeColorSet().getBranchColor() );
946 final int getLongestExtNodeInfo() {
947 return _longest_ext_node_info;
950 final Options getOptions() {
951 if ( _options == null ) {
952 _options = getControlPanel().getOptions();
957 final Rectangle2D getOvRectangle() {
958 return _ov_rectangle;
961 final Rectangle getOvVirtualRectangle() {
962 return _ov_virtual_rectangle;
965 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
966 return _graphics_type;
969 final double getStartingAngle() {
970 return _urt_starting_angle;
973 DescriptiveStatistics getStatisticsForExpressionValues() {
974 return _statistics_for_vector_data;
978 * Find a color for this species name.
981 * @return the species color
983 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
984 if ( node.getNodeData().isHasTaxonomy() ) {
985 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
987 // return non-colorized color
988 return getTreeColorSet().getTaxonomyColor();
992 * @return pointer to colorset for tree drawing
994 final TreeColorSet getTreeColorSet() {
995 return getMainPanel().getTreeColorSet();
998 final File getTreeFile() {
1002 final float getXcorrectionFactor() {
1003 return _x_correction_factor;
1006 final float getXdistance() {
1010 final float getYdistance() {
1014 final void increaseDomainStructureEvalueThreshold() {
1015 if ( _domain_structure_e_value_thr_exp < 3 ) {
1016 _domain_structure_e_value_thr_exp += 1;
1020 final void initNodeData() {
1021 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1024 double max_original_domain_structure_width = 0.0;
1025 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1026 if ( node.getNodeData().isHasSequence()
1027 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1028 RenderableDomainArchitecture rds = null;
1029 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
1030 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1031 getConfiguration() );
1032 node.getNodeData().getSequence().setDomainArchitecture( rds );
1035 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1037 if ( getControlPanel().isShowDomainArchitectures() ) {
1038 final double dsw = rds.getOriginalSize().getWidth();
1039 if ( dsw > max_original_domain_structure_width ) {
1040 max_original_domain_structure_width = dsw;
1045 if ( getControlPanel().isShowDomainArchitectures() ) {
1046 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1047 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1048 if ( node.getNodeData().isHasSequence()
1049 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1050 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1051 .getSequence().getDomainArchitecture();
1052 rds.setRenderingFactorWidth( ds_factor_width );
1053 rds.setParameter( _domain_structure_e_value_thr_exp );
1059 final boolean inOv( final MouseEvent e ) {
1060 return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
1061 && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
1062 && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
1063 + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
1066 final boolean inOvRectangle( final MouseEvent e ) {
1067 return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
1068 && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
1069 && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
1070 + getOvRectangle().getHeight() + 1 ) ) );
1073 final boolean isApplet() {
1074 return getMainPanel() instanceof MainPanelApplets;
1077 final boolean isCanCollapse() {
1078 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1081 final boolean isCanColorSubtree() {
1082 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1085 final boolean isCanCopy() {
1086 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1089 final boolean isCanCut( final PhylogenyNode node ) {
1090 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1094 final boolean isCanDelete() {
1095 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1098 final boolean isCanPaste() {
1099 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1100 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1103 final boolean isCanReroot() {
1104 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1107 final boolean isCanSubtree( final PhylogenyNode node ) {
1108 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1109 .isRoot() || ( _subtree_index > 0 ) ) );
1112 final boolean isCurrentTreeIsSubtree() {
1113 return ( _subtree_index > 0 );
1116 final boolean isEdited() {
1120 final boolean isInOvRect() {
1124 final boolean isOvOn() {
1128 final boolean isPhyHasBranchLengths() {
1129 return _phy_has_branch_lengths;
1132 final void midpointRoot() {
1133 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1136 if ( !_phylogeny.isRerootable() ) {
1137 JOptionPane.showMessageDialog( this,
1138 "This is not rerootable",
1140 JOptionPane.WARNING_MESSAGE );
1143 setNodeInPreorderToNull();
1145 PhylogenyMethods.midpointRoot( _phylogeny );
1146 resetNodeIdToDistToLeafMap();
1152 final void mouseClicked( final MouseEvent e ) {
1153 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1154 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1155 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1156 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
1158 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
1166 final double max_x = getWidth() - getVisibleRect().width;
1167 final double max_y = getHeight() - getVisibleRect().height;
1174 getMainPanel().getCurrentScrollPane().getViewport()
1175 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1176 setInOvRect( true );
1180 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1181 if ( node != null ) {
1182 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1185 _highlight_node = node;
1186 // Check if shift key is down
1187 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1188 // Yes, so add to _found_nodes
1189 if ( getFoundNodes() == null ) {
1190 setFoundNodes( new HashSet<Long>() );
1192 getFoundNodes().add( node.getId() );
1193 // Check if control key is down
1195 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1196 // Yes, so pop-up menu
1197 displayNodePopupMenu( node, e.getX(), e.getY() );
1198 // Handle unadorned click
1201 // Check for right mouse button
1202 if ( e.getModifiers() == 4 ) {
1203 displayNodePopupMenu( node, e.getX(), e.getY() );
1206 // if not in _found_nodes, clear _found_nodes
1207 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1212 // no node was clicked
1213 _highlight_node = null;
1219 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1220 setCursor( MOVE_CURSOR );
1221 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1222 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1223 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1224 if ( scroll_position.x < 0 ) {
1225 scroll_position.x = 0;
1228 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1229 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1230 if ( scroll_position.x > max_x ) {
1231 scroll_position.x = max_x;
1234 if ( scroll_position.y < 0 ) {
1235 scroll_position.y = 0;
1238 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1239 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1240 if ( scroll_position.y > max_y ) {
1241 scroll_position.y = max_y;
1244 if ( isOvOn() || getOptions().isShowScale() ) {
1247 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1250 final void mouseDragInOvRectangle( final MouseEvent e ) {
1251 setCursor( HAND_CURSOR );
1252 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1253 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1254 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1255 double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
1256 double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
1257 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1258 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1259 if ( scroll_position.x <= 0 ) {
1260 scroll_position.x = 0;
1264 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1265 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1266 if ( scroll_position.x >= max_x ) {
1268 scroll_position.x = max_x;
1271 if ( scroll_position.y <= 0 ) {
1273 scroll_position.y = 0;
1276 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1277 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1278 if ( scroll_position.y >= max_y ) {
1280 scroll_position.y = max_y;
1284 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1285 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1286 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1289 final void mouseMoved( final MouseEvent e ) {
1290 requestFocusInWindow();
1291 if ( _current_external_nodes != null ) {
1292 _current_external_nodes = null;
1295 if ( getControlPanel().isNodeDescPopup() ) {
1296 if ( _node_desc_popup != null ) {
1297 _node_desc_popup.hide();
1298 _node_desc_popup = null;
1301 if ( getOptions().isShowOverview() && isOvOn() ) {
1302 if ( inOvVirtualRectangle( e ) ) {
1303 if ( !isInOvRect() ) {
1304 setInOvRect( true );
1309 if ( isInOvRect() ) {
1310 setInOvRect( false );
1315 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
1324 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1325 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
1326 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
1327 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
1328 addToCurrentExternalNodes( n.getId() );
1330 setCursor( HAND_CURSOR );
1333 else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
1334 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
1335 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
1336 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
1337 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
1338 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
1339 setCursor( CUT_CURSOR );
1342 setCursor( HAND_CURSOR );
1343 if ( getControlPanel().isNodeDescPopup() ) {
1344 showNodeDataPopup( e, node );
1349 setCursor( ARROW_CURSOR );
1354 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
1355 setCursor( ARROW_CURSOR );
1358 final void multiplyUrtFactor( final float f ) {
1362 final JApplet obtainApplet() {
1363 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1366 final void paintBranchCircular( final PhylogenyNode p,
1367 final PhylogenyNode c,
1369 final boolean radial_labels,
1370 final boolean to_pdf,
1371 final boolean to_graphics_file ) {
1372 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1373 final double root_x = _root.getXcoord();
1374 final double root_y = _root.getYcoord();
1375 final double dx = root_x - p.getXcoord();
1376 final double dy = root_y - p.getYcoord();
1377 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1378 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1379 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
1380 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
1381 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
1382 final double r2 = 2.0 * parent_radius;
1383 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1385 drawLine( c.getXcoord(),
1387 root_x + ( Math.cos( angle ) * parent_radius ),
1388 root_y + ( Math.sin( angle ) * parent_radius ),
1390 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c )
1391 || isInCurrentExternalNodes( c ) );
1392 if ( c.isExternal() ) {
1393 final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c );
1394 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
1395 && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
1398 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
1402 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
1403 final double angle = _urt_nodeid_angle_map.get( c.getId() );
1404 final double root_x = _root.getXSecondary();
1405 final double root_y = _root.getYSecondary();
1406 final double dx = root_x - p.getXSecondary();
1407 final double dy = root_y - p.getYSecondary();
1408 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
1409 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
1410 g.setColor( getTreeColorSet().getOvColor() );
1411 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
1412 final double r2 = 2.0 * parent_radius;
1413 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
1415 drawLine( c.getXSecondary(),
1417 root_x + ( Math.cos( angle ) * parent_radius ),
1418 root_y + ( Math.sin( angle ) * parent_radius ),
1420 if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
1421 g.setColor( getTreeColorSet().getFoundColor() );
1422 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
1426 final void paintCircular( final Phylogeny phy,
1427 final double starting_angle,
1432 final boolean to_pdf,
1433 final boolean to_graphics_file ) {
1434 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
1435 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
1436 _root = phy.getRoot();
1437 _root.setXcoord( center_x );
1438 _root.setYcoord( center_y );
1439 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1440 double current_angle = starting_angle;
1442 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1443 final PhylogenyNode n = it.next();
1444 if ( !n.isCollapse() ) {
1445 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1446 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1447 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1448 _urt_nodeid_index_map.put( n.getId(), i++ );
1449 current_angle += ( TWO_PI / circ_num_ext_nodes );
1453 System.out.println( "is collapse" + n.getName() );
1456 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
1457 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
1460 final void paintCircularLite( final Phylogeny phy,
1461 final double starting_angle,
1465 final Graphics2D g ) {
1466 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
1467 _root = phy.getRoot();
1468 _root.setXSecondary( center_x );
1469 _root.setYSecondary( center_y );
1470 double current_angle = starting_angle;
1471 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
1472 final PhylogenyNode n = it.next();
1473 n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
1474 n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
1475 _urt_nodeid_angle_map.put( n.getId(), current_angle );
1476 current_angle += ( TWO_PI / circ_num_ext_nodes );
1478 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
1481 final void paintPhylogeny( final Graphics2D g,
1482 final boolean to_pdf,
1483 final boolean to_graphics_file,
1484 final int graphics_file_width,
1485 final int graphics_file_height,
1486 final int graphics_file_x,
1487 final int graphics_file_y ) {
1488 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1491 if ( _control_panel.isShowSequenceRelations() ) {
1492 _query_sequence = _control_panel.getSelectedQuerySequence();
1494 // Color the background
1496 final Rectangle r = getVisibleRect();
1497 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
1498 g.setColor( getTreeColorSet().getBackgroundColor() );
1499 if ( !to_graphics_file ) {
1503 if ( getOptions().isPrintBlackAndWhite() ) {
1504 g.setColor( Color.WHITE );
1506 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1510 if ( !to_graphics_file ) {
1511 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
1512 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
1516 g.setPaint( new GradientPaint( graphics_file_x,
1518 getTreeColorSet().getBackgroundColor(),
1520 graphics_file_y + graphics_file_height,
1521 getTreeColorSet().getBackgroundColorGradientBottom() ) );
1522 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
1525 g.setStroke( new BasicStroke( 1 ) );
1528 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
1530 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1531 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1532 _external_node_index = 0;
1533 // Position starting X of tree
1534 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
1535 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
1537 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
1538 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
1539 .getDistanceToParent() * getXcorrectionFactor() ) ) );
1542 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
1544 // Position starting Y of tree
1545 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
1546 + ( TreePanel.MOVE / 2.0f ) );
1547 final int dynamic_hiding_factor = calcDynamicHidingFactor();
1548 if ( getControlPanel().isDynamicallyHideData() ) {
1549 if ( dynamic_hiding_factor > 1 ) {
1550 getControlPanel().setDynamicHidingIsOn( true );
1553 getControlPanel().setDynamicHidingIsOn( false );
1556 if ( _nodes_in_preorder == null ) {
1557 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
1559 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1560 _nodes_in_preorder[ i++ ] = it.next();
1563 //final PhylogenyNodeIterator it;
1564 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
1565 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
1566 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1568 for( final PhylogenyNode element : _nodes_in_preorder ) {
1569 paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
1570 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
1572 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
1573 if ( !( to_graphics_file || to_pdf ) ) {
1576 getVisibleRect().y + getVisibleRect().height,
1581 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1584 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1585 paintPhylogenyLite( g );
1588 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1589 if ( getControlPanel().getDynamicallyHideData() != null ) {
1590 getControlPanel().setDynamicHidingIsOn( false );
1592 final double angle = getStartingAngle();
1593 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
1594 _dynamic_hiding_factor = 0;
1595 if ( getControlPanel().isDynamicallyHideData() ) {
1596 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1597 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
1599 if ( getControlPanel().getDynamicallyHideData() != null ) {
1600 if ( _dynamic_hiding_factor > 1 ) {
1601 getControlPanel().setDynamicHidingIsOn( true );
1604 getControlPanel().setDynamicHidingIsOn( false );
1607 paintUnrooted( _phylogeny.getRoot(),
1609 ( float ) ( angle + ( 2 * Math.PI ) ),
1614 if ( getOptions().isShowScale() ) {
1615 if ( !( to_graphics_file || to_pdf ) ) {
1618 getVisibleRect().y + getVisibleRect().height,
1623 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
1626 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1627 g.setColor( getTreeColorSet().getOvColor() );
1628 paintUnrootedLite( _phylogeny.getRoot(),
1630 angle + ( 2 * Math.PI ),
1632 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
1633 paintOvRectangle( g );
1636 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1637 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
1638 final int d = radius + MOVE + getLongestExtNodeInfo();
1639 _dynamic_hiding_factor = 0;
1640 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
1641 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
1642 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
1644 if ( getControlPanel().getDynamicallyHideData() != null ) {
1645 if ( _dynamic_hiding_factor > 1 ) {
1646 getControlPanel().setDynamicHidingIsOn( true );
1649 getControlPanel().setDynamicHidingIsOn( false );
1652 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
1653 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
1654 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
1655 : getOvMaxWidth() / 2 );
1656 double x_scale = 1.0;
1657 double y_scale = 1.0;
1658 int x_pos = getVisibleRect().x + getOvXPosition();
1659 int y_pos = getVisibleRect().y + getOvYPosition();
1660 if ( getWidth() > getHeight() ) {
1661 x_scale = ( double ) getHeight() / getWidth();
1662 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
1665 y_scale = ( double ) getWidth() / getHeight();
1666 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
1668 _at = g.getTransform();
1669 g.scale( x_scale, y_scale );
1670 paintCircularLite( _phylogeny,
1674 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
1677 g.setTransform( _at );
1678 paintOvRectangle( g );
1683 final void recalculateMaxDistanceToRoot() {
1684 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
1688 * Remove all edit-node frames
1690 final void removeAllEditNodeJFrames() {
1691 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
1692 if ( _node_frames[ i ] != null ) {
1693 _node_frames[ i ].dispose();
1694 _node_frames[ i ] = null;
1697 _node_frame_index = 0;
1701 * Remove a node-edit frame.
1703 final void removeEditNodeFrame( final int i ) {
1704 _node_frame_index--;
1705 _node_frames[ i ] = null;
1706 if ( i < _node_frame_index ) {
1707 for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
1708 _node_frames[ j ] = _node_frames[ j + 1 ];
1710 _node_frames[ _node_frame_index ] = null;
1714 final void reRoot( final PhylogenyNode node ) {
1715 if ( !getPhylogeny().isRerootable() ) {
1716 JOptionPane.showMessageDialog( this,
1717 "This is not rerootable",
1719 JOptionPane.WARNING_MESSAGE );
1722 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1723 JOptionPane.showMessageDialog( this,
1724 "Cannot reroot in unrooted display type",
1725 "Attempt to reroot tree in unrooted display",
1726 JOptionPane.WARNING_MESSAGE );
1729 getPhylogeny().reRoot( node );
1730 getPhylogeny().recalculateNumberOfExternalDescendants( true );
1731 resetNodeIdToDistToLeafMap();
1732 setNodeInPreorderToNull();
1733 resetPreferredSize();
1734 getMainPanel().adjustJScrollPane();
1737 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1738 getControlPanel().showWhole();
1742 final void resetNodeIdToDistToLeafMap() {
1743 _nodeid_dist_to_leaf = new HashMap<Long, Short>();
1746 final void resetPreferredSize() {
1747 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
1753 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
1754 if ( getControlPanel().isDrawPhylogram() ) {
1756 + getLongestExtNodeInfo()
1758 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
1761 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
1763 + getLongestExtNodeInfo()
1764 + ForesterUtil.roundToInt( getXdistance()
1765 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
1769 + getLongestExtNodeInfo()
1770 + ForesterUtil.roundToInt( getXdistance()
1771 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
1774 setPreferredSize( new Dimension( x, y ) );
1777 final void selectNode( final PhylogenyNode node ) {
1778 if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
1779 getFoundNodes().remove( node.getId() );
1780 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1781 if ( getFoundNodes().size() < 1 ) {
1782 getControlPanel().searchReset();
1786 getControlPanel().getSearchFoundCountsLabel().setVisible( true );
1787 getControlPanel().getSearchResetButton().setEnabled( true );
1788 getControlPanel().getSearchResetButton().setVisible( true );
1789 if ( getFoundNodes() == null ) {
1790 setFoundNodes( new HashSet<Long>() );
1792 getFoundNodes().add( node.getId() );
1793 getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
1797 final void setArrowCursor() {
1798 setCursor( ARROW_CURSOR );
1802 final void setControlPanel( final ControlPanel atv_control ) {
1803 _control_panel = atv_control;
1806 void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
1807 increaseCurrentExternalNodesDataBufferChangeCounter();
1808 _current_external_nodes_data_buffer = sb;
1811 final void setFoundNodes( final Set<Long> found_nodes ) {
1812 _found_nodes = found_nodes;
1815 final void setInOvRect( final boolean in_ov_rect ) {
1816 _in_ov_rect = in_ov_rect;
1819 final void setLargeFonts() {
1820 getTreeFontSet().largeFonts();
1823 final void setLastMouseDragPointX( final float x ) {
1824 _last_drag_point_x = x;
1827 final void setLastMouseDragPointY( final float y ) {
1828 _last_drag_point_y = y;
1831 final void setLongestExtNodeInfo( final int i ) {
1832 _longest_ext_node_info = i;
1835 final void setMediumFonts() {
1836 getTreeFontSet().mediumFonts();
1839 final void setNodeInPreorderToNull() {
1840 _nodes_in_preorder = null;
1843 final void setOvOn( final boolean ov_on ) {
1847 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
1848 _graphics_type = graphics_type;
1852 final void setSmallFonts() {
1853 getTreeFontSet().smallFonts();
1856 final void setStartingAngle( final double starting_angle ) {
1857 _urt_starting_angle = starting_angle;
1860 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
1861 _statistics_for_vector_data = statistics_for_expression_values;
1864 final void setSuperTinyFonts() {
1865 getTreeFontSet().superTinyFonts();
1868 final void setTextAntialias() {
1869 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
1870 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
1871 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
1874 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
1877 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
1878 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
1880 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
1882 // catch ( final Throwable e ) {
1883 // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
1887 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
1888 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1892 final void setTinyFonts() {
1893 getTreeFontSet().tinyFonts();
1896 final void setTreeFile( final File treefile ) {
1897 _treefile = treefile;
1900 final void setXcorrectionFactor( final float f ) {
1901 _x_correction_factor = f;
1904 final void setXdistance( final float x ) {
1908 final void setYdistance( final float y ) {
1912 final void sortDescendants( final PhylogenyNode node ) {
1913 if ( !node.isExternal() ) {
1914 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
1915 if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
1916 .isShowTaxonomyCommonNames() ) ) {
1917 if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
1918 .isShowGeneSymbols() ) ) {
1919 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
1921 else if ( getControlPanel().isShowNodeNames() ) {
1922 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
1925 PhylogenyMethods.sortNodeDescendents( node, pri );
1926 setNodeInPreorderToNull();
1927 _phylogeny.externalNodesHaveChanged();
1928 _phylogeny.clearHashIdToNodeMap();
1929 _phylogeny.recalculateNumberOfExternalDescendants( true );
1930 resetNodeIdToDistToLeafMap();
1936 final void subTree( final PhylogenyNode node ) {
1937 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1938 JOptionPane.showMessageDialog( this,
1939 "Cannot get a sub/super tree in unrooted display",
1940 "Attempt to get sub/super tree in unrooted display",
1941 JOptionPane.WARNING_MESSAGE );
1944 if ( node.isExternal() ) {
1945 JOptionPane.showMessageDialog( this,
1946 "Cannot get a subtree of a external node",
1947 "Attempt to get subtree of external node",
1948 JOptionPane.WARNING_MESSAGE );
1951 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
1952 JOptionPane.showMessageDialog( this,
1953 "Cannot get a subtree of the root node",
1954 "Attempt to get subtree of root node",
1955 JOptionPane.WARNING_MESSAGE );
1958 setNodeInPreorderToNull();
1959 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
1960 _sub_phylogenies[ _subtree_index ] = _phylogeny;
1961 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
1963 _phylogeny = subTree( node, _phylogeny );
1964 updateSubSuperTreeButton();
1966 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
1969 _main_panel.getControlPanel().showWhole();
1973 final void superTree() {
1974 setNodeInPreorderToNull();
1975 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
1976 for( final PhylogenyNode n : temp_root.getDescendants() ) {
1977 n.setParent( temp_root );
1979 _sub_phylogenies[ _subtree_index ] = null;
1980 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
1981 _phylogeny = _sub_phylogenies[ --_subtree_index ];
1982 updateSubSuperTreeButton();
1985 final void swap( final PhylogenyNode node ) {
1986 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
1989 if ( node.getNumberOfDescendants() > 2 ) {
1990 JOptionPane.showMessageDialog( this,
1991 "Cannot swap descendants of nodes with more than 2 descendants",
1992 "Cannot swap descendants",
1993 JOptionPane.ERROR_MESSAGE );
1996 if ( !node.isExternal() ) {
1997 node.swapChildren();
1998 setNodeInPreorderToNull();
1999 _phylogeny.externalNodesHaveChanged();
2000 _phylogeny.clearHashIdToNodeMap();
2001 _phylogeny.recalculateNumberOfExternalDescendants( true );
2002 resetNodeIdToDistToLeafMap();
2008 final void taxColor() {
2009 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
2013 AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
2014 _control_panel.setColorBranches( true );
2015 if ( _control_panel.getColorBranchesCb() != null ) {
2016 _control_panel.getColorBranchesCb().setSelected( true );
2023 final void updateOvSettings() {
2024 switch ( getOptions().getOvPlacement() ) {
2026 setOvXPosition( OV_BORDER );
2027 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2028 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2031 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2032 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
2033 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
2036 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
2037 setOvYPosition( OV_BORDER );
2038 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2041 setOvXPosition( OV_BORDER );
2042 setOvYPosition( OV_BORDER );
2043 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
2048 final void updateOvSizes() {
2049 if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
2051 float l = getLongestExtNodeInfo();
2052 final float w_ratio = getOvMaxWidth() / getWidth();
2054 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
2055 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
2057 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
2058 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
2061 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
2063 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
2064 if ( ov_xdist < 0.0 ) {
2067 if ( ydist < 0.0 ) {
2070 setOvXDistance( ov_xdist );
2071 final double height = _phylogeny.getHeight();
2073 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
2074 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
2077 setOvXcorrectionFactor( 0 );
2085 void updateSetOfCollapsedExternalNodes() {
2086 final Phylogeny phy = getPhylogeny();
2087 _collapsed_external_nodeid_set.clear();
2088 if ( phy != null ) {
2089 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2090 final PhylogenyNode ext_node = it.next();
2091 PhylogenyNode n = ext_node;
2092 while ( !n.isRoot() ) {
2093 if ( n.isCollapse() ) {
2094 _collapsed_external_nodeid_set.add( ext_node.getId() );
2095 ext_node.setCollapse( true );
2104 final void updateSubSuperTreeButton() {
2105 if ( _subtree_index < 1 ) {
2106 getControlPanel().deactivateButtonToReturnToSuperTree();
2109 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
2113 final void zoomInDomainStructure() {
2114 if ( _domain_structure_width < 2000 ) {
2115 _domain_structure_width *= 1.2;
2119 final void zoomOutDomainStructure() {
2120 if ( _domain_structure_width > 20 ) {
2121 _domain_structure_width *= 0.8;
2125 private void abbreviateScientificName( final String sn ) {
2126 final String[] a = sn.split( "\\s+" );
2127 _sb.append( a[ 0 ].substring( 0, 1 ) );
2128 _sb.append( a[ 1 ].substring( 0, 2 ) );
2129 if ( a.length > 2 ) {
2130 for( int i = 2; i < a.length; i++ ) {
2132 _sb.append( a[ i ] );
2137 final private void addEmptyNode( final PhylogenyNode node ) {
2138 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2139 errorMessageNoCutCopyPasteInUnrootedDisplay();
2142 final String label = createASimpleTextRepresentationOfANode( node );
2144 if ( ForesterUtil.isEmpty( label ) ) {
2145 msg = "How to add the new, empty node?";
2148 msg = "How to add the new, empty node to node" + label + "?";
2150 final Object[] options = { "As sibling", "As descendant", "Cancel" };
2151 final int r = JOptionPane.showOptionDialog( this,
2153 "Addition of Empty New Node",
2154 JOptionPane.CLOSED_OPTION,
2155 JOptionPane.QUESTION_MESSAGE,
2159 boolean add_as_sibling = true;
2161 add_as_sibling = false;
2163 else if ( r != 0 ) {
2166 final Phylogeny phy = new Phylogeny();
2167 phy.setRoot( new PhylogenyNode() );
2168 phy.setRooted( true );
2169 if ( add_as_sibling ) {
2170 if ( node.isRoot() ) {
2171 JOptionPane.showMessageDialog( this,
2172 "Cannot add sibling to root",
2173 "Attempt to add sibling to root",
2174 JOptionPane.ERROR_MESSAGE );
2177 phy.addAsSibling( node );
2180 phy.addAsChild( node );
2182 setNodeInPreorderToNull();
2183 _phylogeny.externalNodesHaveChanged();
2184 _phylogeny.clearHashIdToNodeMap();
2185 _phylogeny.recalculateNumberOfExternalDescendants( true );
2186 resetNodeIdToDistToLeafMap();
2191 final private void addToCurrentExternalNodes( final long i ) {
2192 if ( _current_external_nodes == null ) {
2193 _current_external_nodes = new HashSet<Long>();
2195 _current_external_nodes.add( i );
2198 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
2199 final boolean is_vertical,
2201 final boolean to_pdf,
2202 final boolean to_graphics_file ) {
2203 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
2204 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2205 g.setColor( Color.BLACK );
2207 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
2208 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
2209 && ( getCutOrCopiedTree() != null )
2210 && ( getCopiedAndPastedNodes() != null )
2212 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
2213 g.setColor( getTreeColorSet().getFoundColor() );
2215 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2216 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2218 else if ( to_pdf ) {
2219 g.setColor( getTreeColorSet().getBranchColorForPdf() );
2222 g.setColor( getTreeColorSet().getBranchColor() );
2226 final private void blast( final PhylogenyNode node ) {
2227 if ( !isCanBlast( node ) ) {
2228 JOptionPane.showMessageDialog( this,
2229 "Insufficient information present",
2231 JOptionPane.INFORMATION_MESSAGE );
2235 final String query = Blast.obtainQueryForBlast( node );
2236 System.out.println( "query for BLAST is: " + query );
2238 if ( !ForesterUtil.isEmpty( query ) ) {
2239 if ( node.getNodeData().isHasSequence() ) {
2240 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
2241 if ( node.getNodeData().getSequence().getType().toLowerCase()
2242 .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
2249 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2250 if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
2258 if ( type == '?' ) {
2259 if ( SequenceIdParser.isProtein( query ) ) {
2266 JApplet applet = null;
2268 applet = obtainApplet();
2271 Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
2273 catch ( final Exception e ) {
2274 e.printStackTrace();
2276 if ( Constants.ALLOW_DDBJ_BLAST ) {
2278 System.out.println( "trying: " + query );
2279 final Blast s = new Blast();
2280 s.ddbjBlast( query );
2282 catch ( final Exception e ) {
2283 e.printStackTrace();
2290 private final int calcDynamicHidingFactor() {
2291 return ( int ) ( 0.5 + ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ) );
2295 * Calculate the length of the distance between the given node and its
2301 * @return the distance value
2303 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
2304 if ( getControlPanel().isDrawPhylogram() ) {
2305 if ( node.getDistanceToParent() < 0.0 ) {
2308 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
2311 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2312 return getXdistance();
2314 return getXdistance() * factor;
2318 final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
2319 Color c = getTreeColorSet().getAnnotationColor();
2320 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
2321 final StringBuilder sb = new StringBuilder();
2322 for( final Annotation a : ann ) {
2323 sb.append( !ForesterUtil.isEmpty( a.getRef() ) ? a.getRef() : a.getDesc() );
2325 final String ann_str = sb.toString();
2326 if ( !ForesterUtil.isEmpty( ann_str ) ) {
2327 c = getControlPanel().getAnnotationColors().get( ann_str );
2329 c = AptxUtil.calculateColorFromString( ann_str );
2330 getControlPanel().getAnnotationColors().put( ann_str, c );
2333 c = getTreeColorSet().getAnnotationColor();
2340 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
2341 if ( getControlPanel().isDrawPhylogram() ) {
2342 if ( node.getDistanceToParent() < 0.0 ) {
2345 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
2348 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
2349 return getOvXDistance();
2351 return getOvXDistance() * factor;
2355 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
2356 JOptionPane.showMessageDialog( this,
2357 "Cannot launch web browser for " + type_type + " data of this node",
2358 "Cannot launch web browser",
2359 JOptionPane.WARNING_MESSAGE );
2362 final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
2363 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2364 JOptionPane.showMessageDialog( this,
2365 "Cannot colorize subtree in unrooted display type",
2366 "Attempt to colorize subtree in unrooted display",
2367 JOptionPane.WARNING_MESSAGE );
2370 _control_panel.setColorBranches( true );
2371 if ( _control_panel.getColorBranchesCb() != null ) {
2372 _control_panel.getColorBranchesCb().setSelected( true );
2374 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
2375 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
2380 final private void colorSubtree( final PhylogenyNode node ) {
2381 Color intitial_color = null;
2382 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
2383 && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
2384 intitial_color = PhylogenyMethods.getBranchColorValue( node );
2387 intitial_color = getTreeColorSet().getBranchColor();
2389 _color_chooser.setColor( intitial_color );
2390 _color_chooser.setPreviewPanel( new JPanel() );
2391 final JDialog dialog = JColorChooser
2392 .createDialog( this,
2393 "Subtree colorization",
2396 new SubtreeColorizationActionListener( _color_chooser, node ),
2398 dialog.setVisible( true );
2401 final private void copySubtree( final PhylogenyNode node ) {
2402 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2403 errorMessageNoCutCopyPasteInUnrootedDisplay();
2406 setNodeInPreorderToNull();
2407 setCutOrCopiedTree( _phylogeny.copy( node ) );
2408 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
2409 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
2410 for( final PhylogenyNode n : nodes ) {
2411 node_ids.add( n.getId() );
2413 node_ids.add( node.getId() );
2414 setCopiedAndPastedNodes( node_ids );
2418 private String createAnnotationString( final SortedSet<Annotation> ann ) {
2419 final StringBuilder sb = new StringBuilder();
2420 boolean first = true;
2421 for( final Annotation a : ann ) {
2428 sb.append( a.asSimpleText() );
2430 final String ann_str = sb.toString();
2434 final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
2435 final String tax = PhylogenyMethods.getSpecies( node );
2436 String label = node.getName();
2437 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
2438 label = label + " " + tax;
2440 else if ( !ForesterUtil.isEmpty( tax ) ) {
2446 if ( !ForesterUtil.isEmpty( label ) ) {
2447 label = " [" + label + "]";
2452 final private void cutSubtree( final PhylogenyNode node ) {
2453 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2454 errorMessageNoCutCopyPasteInUnrootedDisplay();
2457 if ( node.isRoot() ) {
2458 JOptionPane.showMessageDialog( this,
2459 "Cannot cut entire tree as subtree",
2460 "Attempt to cut entire tree",
2461 JOptionPane.ERROR_MESSAGE );
2464 final String label = createASimpleTextRepresentationOfANode( node );
2465 final int r = JOptionPane.showConfirmDialog( null,
2466 "Cut subtree" + label + "?",
2467 "Confirm Cutting of Subtree",
2468 JOptionPane.YES_NO_OPTION );
2469 if ( r != JOptionPane.OK_OPTION ) {
2472 setNodeInPreorderToNull();
2473 setCopiedAndPastedNodes( null );
2474 setCutOrCopiedTree( _phylogeny.copy( node ) );
2475 _phylogeny.deleteSubtree( node, true );
2476 _phylogeny.clearHashIdToNodeMap();
2477 _phylogeny.recalculateNumberOfExternalDescendants( true );
2478 resetNodeIdToDistToLeafMap();
2483 final private void cycleColors() {
2484 getMainPanel().getTreeColorSet().cycleColorScheme();
2485 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
2486 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
2490 final private void decreaseOvSize() {
2491 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
2492 setOvMaxWidth( getOvMaxWidth() - 5 );
2493 setOvMaxHeight( getOvMaxHeight() - 5 );
2495 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2499 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
2500 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
2501 errorMessageNoCutCopyPasteInUnrootedDisplay();
2504 if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
2505 JOptionPane.showMessageDialog( this,
2506 "Cannot delete entire tree",
2507 "Attempt to delete entire tree",
2508 JOptionPane.ERROR_MESSAGE );
2511 final String label = createASimpleTextRepresentationOfANode( node );
2512 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
2513 final int r = JOptionPane.showOptionDialog( this,
2514 "Delete" + label + "?",
2515 "Delete Node/Subtree",
2516 JOptionPane.CLOSED_OPTION,
2517 JOptionPane.QUESTION_MESSAGE,
2521 setNodeInPreorderToNull();
2522 boolean node_only = true;
2526 else if ( r != 0 ) {
2530 PhylogenyMethods.removeNode( node, _phylogeny );
2533 _phylogeny.deleteSubtree( node, true );
2535 _phylogeny.externalNodesHaveChanged();
2536 _phylogeny.clearHashIdToNodeMap();
2537 _phylogeny.recalculateNumberOfExternalDescendants( true );
2538 resetNodeIdToDistToLeafMap();
2543 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
2544 makePopupMenus( node );
2545 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
2546 _node_popup_menu.show( this, x, y );
2549 final private void drawArc( final double x,
2552 final double heigth,
2553 final double start_angle,
2554 final double arc_angle,
2555 final Graphics2D g ) {
2556 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
2560 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
2561 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
2564 _line.setLine( x1, y1, x2, y2 );
2568 final private void drawOval( final double x,
2571 final double heigth,
2572 final Graphics2D g ) {
2573 _ellipse.setFrame( x, y, width, heigth );
2577 final private void drawOvalFilled( final double x,
2580 final double heigth,
2581 final Graphics2D g ) {
2582 _ellipse.setFrame( x, y, width, heigth );
2586 final private void drawOvalGradient( final double x,
2589 final double heigth,
2591 final Color color_1,
2592 final Color color_2,
2593 final Color color_border ) {
2594 _ellipse.setFrame( x, y, width, heigth );
2595 g.setPaint( new GradientPaint( ( float ) x,
2598 ( float ) ( x + width ),
2599 ( float ) ( y + heigth ),
2603 if ( color_border != null ) {
2604 g.setPaint( color_border );
2609 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
2610 _rectangle.setFrame( x, y, width, heigth );
2611 g.draw( _rectangle );
2614 final private void drawRectFilled( final double x,
2617 final double heigth,
2618 final Graphics2D g ) {
2619 _rectangle.setFrame( x, y, width, heigth );
2620 g.fill( _rectangle );
2623 final private void drawRectGradient( final double x,
2626 final double heigth,
2628 final Color color_1,
2629 final Color color_2,
2630 final Color color_border ) {
2631 _rectangle.setFrame( x, y, width, heigth );
2632 g.setPaint( new GradientPaint( ( float ) x,
2635 ( float ) ( x + width ),
2636 ( float ) ( y + heigth ),
2639 g.fill( _rectangle );
2640 if ( color_border != null ) {
2641 g.setPaint( color_border );
2642 g.draw( _rectangle );
2646 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2647 final List<Uri> us = new ArrayList<Uri>();
2648 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2649 for( final Uri uri : t.getUris() ) {
2654 for( final Uri uri : us ) {
2655 if ( uri != null ) {
2656 final String uri_str = uri.getValue().toString().toLowerCase();
2657 if ( getImageMap().containsKey( uri_str ) ) {
2658 final BufferedImage bi = getImageMap().get( uri_str );
2659 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2660 double scaling_factor = 1;
2661 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
2662 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
2663 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
2665 // y = y - ( 0.9 * getYdistance() );
2666 final double hs = bi.getHeight() * scaling_factor;
2667 double ws = ( bi.getWidth() * scaling_factor ) + offset;
2668 final double my_y = y - ( 0.5 * hs );
2669 final int x_w = ( int ) ( x + ws + 0.5 );
2670 final int y_h = ( int ) ( my_y + hs + 0.5 );
2671 if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
2673 ( int ) ( x + 0.5 + offset ),
2674 ( int ) ( my_y + 0.5 ),
2695 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
2696 JOptionPane.showMessageDialog( this,
2697 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
2698 "Attempt to cut/copy/paste/add/delete in unrooted display",
2699 JOptionPane.ERROR_MESSAGE );
2702 final private Set<Long> getCopiedAndPastedNodes() {
2703 return getMainPanel().getCopiedAndPastedNodes();
2706 final private Set<Long> getCurrentExternalNodes() {
2707 return _current_external_nodes;
2710 final private Phylogeny getCutOrCopiedTree() {
2711 return getMainPanel().getCutOrCopiedTree();
2714 final private float getLastDragPointX() {
2715 return _last_drag_point_x;
2718 final private float getLastDragPointY() {
2719 return _last_drag_point_y;
2722 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
2723 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
2724 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
2725 _nodeid_dist_to_leaf.put( node.getId(), m );
2729 return _nodeid_dist_to_leaf.get( node.getId() );
2733 final private double getMaxDistanceToRoot() {
2734 if ( _max_distance_to_root < 0 ) {
2735 recalculateMaxDistanceToRoot();
2737 return _max_distance_to_root;
2740 final private float getOvMaxHeight() {
2741 return _ov_max_height;
2744 final private float getOvMaxWidth() {
2745 return _ov_max_width;
2748 final private float getOvXcorrectionFactor() {
2749 return _ov_x_correction_factor;
2752 final private float getOvXDistance() {
2753 return _ov_x_distance;
2756 final private int getOvXPosition() {
2757 return _ov_x_position;
2760 final private float getOvYDistance() {
2761 return _ov_y_distance;
2764 final private int getOvYPosition() {
2765 return _ov_y_position;
2768 final private int getOvYStart() {
2772 final private double getScaleDistance() {
2773 return _scale_distance;
2776 final private String getScaleLabel() {
2777 return _scale_label;
2780 final private TreeFontSet getTreeFontSet() {
2781 return getMainPanel().getTreeFontSet();
2784 final private float getUrtFactor() {
2788 final private float getUrtFactorOv() {
2789 return _urt_factor_ov;
2792 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
2795 showNodeFrame( node );
2810 colorSubtree( node );
2825 copySubtree( node );
2828 pasteSubtree( node );
2830 case DELETE_NODE_OR_SUBTREE:
2831 deleteNodeOrSubtree( node );
2834 addEmptyNode( node );
2836 case EDIT_NODE_DATA:
2837 showNodeEditFrame( node );
2842 case SORT_DESCENDENTS:
2843 sortDescendants( node );
2845 case GET_EXT_DESC_DATA:
2846 showExtDescNodeData( node );
2849 throw new IllegalArgumentException( "unknown action: " + action );
2853 final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
2854 _current_external_nodes_data_buffer_change_counter++;
2857 final private void increaseOvSize() {
2858 if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
2859 && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
2860 .getHeight() / 2 ) ) ) {
2861 setOvMaxWidth( getOvMaxWidth() + 5 );
2862 setOvMaxHeight( getOvMaxHeight() + 5 );
2864 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2868 final private void init() {
2869 _color_chooser = new JColorChooser();
2870 _rollover_popup = new JTextArea();
2871 _rollover_popup.setFont( POPUP_FONT );
2872 resetNodeIdToDistToLeafMap();
2874 setTreeFile( null );
2876 initializeOvSettings();
2877 setStartingAngle( ( TWO_PI * 3 ) / 4 );
2878 final ImageLoader il = new ImageLoader( this );
2879 new Thread( il ).start();
2882 final private void initializeOvSettings() {
2883 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
2884 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
2887 final private boolean inOvVirtualRectangle( final int x, final int y ) {
2888 return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
2889 && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
2890 && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
2891 + getOvVirtualRectangle().height + 1 ) ) );
2894 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
2895 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
2898 final private boolean isCanBlast( final PhylogenyNode node ) {
2899 if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
2902 return Blast.isContainsQueryForBlast( node );
2905 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
2906 if ( node.getNodeData().isHasTaxonomy()
2907 && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
2908 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
2909 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
2910 .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
2911 .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
2919 final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
2920 return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
2923 final private boolean isInFoundNodes( final PhylogenyNode node ) {
2924 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
2927 final private boolean isInOv() {
2931 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
2933 if ( getControlPanel().isShowTaxonomyImages() ) {
2934 y_dist = 40 + ( int ) getYdistance();
2936 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
2937 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
2938 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
2941 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
2942 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
2943 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
2944 || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
2945 .getMaxX() + 20 ) ) );
2948 final private boolean isNonLinedUpCladogram() {
2949 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
2952 final private boolean isUniformBranchLengthsForCladogram() {
2953 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
2956 final private void keyPressedCalls( final KeyEvent e ) {
2957 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
2958 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
2959 if ( !isInOvRect() ) {
2960 setInOvRect( true );
2963 else if ( isInOvRect() ) {
2964 setInOvRect( false );
2967 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
2968 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2969 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2970 getMainPanel().getTreeFontSet().mediumFonts();
2971 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2973 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
2974 getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
2975 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2977 else if ( plusPressed( e.getKeyCode() ) ) {
2978 getMainPanel().getTreeFontSet().increaseFontSize();
2979 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
2983 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
2984 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
2985 getControlPanel().showWhole();
2987 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
2988 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
2989 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
2990 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
2991 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
2992 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2994 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
2995 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
2996 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
2998 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
2999 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3000 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3001 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3003 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3004 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3005 Constants.WHEEL_ZOOM_IN_FACTOR );
3006 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3013 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
3016 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
3020 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
3024 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
3025 scroll_position.x = scroll_position.x + dx;
3026 scroll_position.y = scroll_position.y + dy;
3027 if ( scroll_position.x <= 0 ) {
3028 scroll_position.x = 0;
3031 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
3032 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
3033 if ( scroll_position.x >= max_x ) {
3034 scroll_position.x = max_x;
3037 if ( scroll_position.y <= 0 ) {
3038 scroll_position.y = 0;
3041 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
3042 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
3043 if ( scroll_position.y >= max_y ) {
3044 scroll_position.y = max_y;
3048 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
3051 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
3052 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
3053 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
3054 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
3055 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3057 else if ( plusPressed( e.getKeyCode() ) ) {
3058 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
3059 Constants.WHEEL_ZOOM_IN_FACTOR );
3060 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
3061 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
3063 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
3064 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3065 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3066 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
3067 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3070 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
3071 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3072 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3073 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
3074 if ( getStartingAngle() < 0 ) {
3075 setStartingAngle( TWO_PI + getStartingAngle() );
3077 getControlPanel().displayedPhylogenyMightHaveChanged( false );
3080 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
3081 boolean selected = false;
3082 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
3083 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
3087 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
3089 if ( getMainPanel().getMainFrame() == null ) {
3090 // Must be "E" applet version.
3091 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
3092 if ( ae.getlabelDirectionCbmi() != null ) {
3093 ae.getlabelDirectionCbmi().setSelected( selected );
3097 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
3101 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
3102 switchDisplaygetPhylogenyGraphicsType();
3105 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
3109 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
3110 MainFrame.cycleOverview( getOptions(), this );
3113 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
3116 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
3123 final private void makePopupMenus( final PhylogenyNode node ) {
3124 _node_popup_menu = new JPopupMenu();
3125 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
3126 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
3127 for( int i = 0; i < clickto_names.size(); i++ ) {
3128 final String title = clickto_names.get( i );
3129 _node_popup_menu_items[ i ] = new JMenuItem( title );
3130 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
3131 final String id = isCanOpenSeqWeb( node );
3132 if ( !ForesterUtil.isEmpty( id ) ) {
3133 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
3134 _node_popup_menu_items[ i ].setEnabled( true );
3137 _node_popup_menu_items[ i ].setEnabled( false );
3140 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
3141 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
3143 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
3144 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
3146 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
3147 if ( !getOptions().isEditable() ) {
3150 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
3152 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
3153 if ( !getOptions().isEditable() ) {
3156 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
3158 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
3159 if ( !getOptions().isEditable() ) {
3162 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
3164 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
3165 if ( !getOptions().isEditable() ) {
3168 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
3170 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
3171 if ( !getOptions().isEditable() ) {
3175 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
3176 if ( !getOptions().isEditable() ) {
3180 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
3181 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
3183 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
3184 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
3186 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
3187 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
3189 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
3190 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
3192 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
3193 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
3195 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
3196 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
3198 _node_popup_menu_items[ i ].addActionListener( this );
3199 _node_popup_menu.add( _node_popup_menu_items[ i ] );
3203 private final String obtainTitleForExtDescNodeData() {
3204 switch ( getOptions().getExtDescNodeDataToReturn() ) {
3206 return "Node Names";
3208 return "Sequence Names";
3209 case SEQUENCE_SYMBOL:
3210 return "Sequence Symbols";
3211 case SEQUENCE_MOL_SEQ:
3212 return "Molecular Sequences";
3213 case SEQUENCE_MOL_SEQ_FASTA:
3214 return "Molecular Sequences (Fasta)";
3216 return "Sequence Accessors";
3217 case TAXONOMY_SCIENTIFIC_NAME:
3218 return "Scientific Names";
3220 return "Taxonomy Codes";
3222 return "User Selected Data";
3224 throw new IllegalArgumentException( "unknown data element: "
3225 + getOptions().getExtDescNodeDataToReturn() );
3229 final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
3230 String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
3231 if ( ForesterUtil.isEmpty( v ) ) {
3232 v = ForesterUtil.extractGenbankAccessor( node );
3234 if ( ForesterUtil.isEmpty( v ) ) {
3235 v = ForesterUtil.extractRefSeqAccessorAccessor( node );
3237 if ( ForesterUtil.isEmpty( v ) ) {
3238 v = ForesterUtil.extractGInumber( node );
3243 final private void openSeqWeb( final PhylogenyNode node ) {
3244 if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
3245 cannotOpenBrowserWarningMessage( "sequence" );
3248 final String uri_str = AptxUtil.createUriForSeqWeb( node, getConfiguration(), this );
3249 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3251 AptxUtil.launchWebBrowser( new URI( uri_str ),
3253 isApplet() ? obtainApplet() : null,
3256 catch ( final IOException e ) {
3257 AptxUtil.showErrorMessage( this, e.toString() );
3258 e.printStackTrace();
3260 catch ( final URISyntaxException e ) {
3261 AptxUtil.showErrorMessage( this, e.toString() );
3262 e.printStackTrace();
3266 cannotOpenBrowserWarningMessage( "sequence" );
3270 final private void openTaxWeb( final PhylogenyNode node ) {
3271 if ( !isCanOpenTaxWeb( node ) ) {
3272 cannotOpenBrowserWarningMessage( "taxonomic" );
3275 String uri_str = null;
3276 final Taxonomy tax = node.getNodeData().getTaxonomy();
3277 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3278 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
3280 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
3282 catch ( final URISyntaxException e ) {
3283 AptxUtil.showErrorMessage( this, e.toString() );
3285 e.printStackTrace();
3288 else if ( ( tax.getIdentifier() != null )
3289 && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
3290 && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
3291 && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
3292 .equalsIgnoreCase( "uniprot" ) ) ) {
3294 uri_str = "http://www.uniprot.org/taxonomy/"
3295 + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
3297 catch ( final UnsupportedEncodingException e ) {
3298 AptxUtil.showErrorMessage( this, e.toString() );
3299 e.printStackTrace();
3302 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
3304 uri_str = "http://www.uniprot.org/taxonomy/?query="
3305 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
3307 catch ( final UnsupportedEncodingException e ) {
3308 AptxUtil.showErrorMessage( this, e.toString() );
3309 e.printStackTrace();
3312 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
3314 uri_str = "http://www.uniprot.org/taxonomy/?query="
3315 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
3317 catch ( final UnsupportedEncodingException e ) {
3318 AptxUtil.showErrorMessage( this, e.toString() );
3319 e.printStackTrace();
3322 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
3324 uri_str = "http://www.uniprot.org/taxonomy/?query="
3325 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
3327 catch ( final UnsupportedEncodingException e ) {
3328 AptxUtil.showErrorMessage( this, e.toString() );
3329 e.printStackTrace();
3332 if ( !ForesterUtil.isEmpty( uri_str ) ) {
3334 AptxUtil.launchWebBrowser( new URI( uri_str ),
3336 isApplet() ? obtainApplet() : null,
3339 catch ( final IOException e ) {
3340 AptxUtil.showErrorMessage( this, e.toString() );
3341 e.printStackTrace();
3343 catch ( final URISyntaxException e ) {
3344 AptxUtil.showErrorMessage( this, e.toString() );
3345 e.printStackTrace();
3349 cannotOpenBrowserWarningMessage( "taxonomic" );
3353 final private void paintBranchLength( final Graphics2D g,
3354 final PhylogenyNode node,
3355 final boolean to_pdf,
3356 final boolean to_graphics_file ) {
3357 g.setFont( getTreeFontSet().getSmallFont() );
3358 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3359 g.setColor( Color.BLACK );
3362 g.setColor( getTreeColorSet().getBranchLengthColor() );
3364 if ( !node.isRoot() ) {
3365 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3366 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3367 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3369 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3370 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3371 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3374 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
3375 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
3379 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
3380 - getTreeFontSet()._small_max_descent, g );
3384 final private void paintBranchLite( final Graphics2D g,
3389 final PhylogenyNode node ) {
3390 g.setColor( getTreeColorSet().getOvColor() );
3391 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3392 drawLine( x1, y1, x2, y2, g );
3394 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3395 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3396 ( g ).draw( _quad_curve );
3398 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3399 final float dx = x2 - x1;
3400 final float dy = y2 - y1;
3401 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3402 + ( dy * 0.8f ), x2, y2 );
3403 ( g ).draw( _cubic_curve );
3406 final float x2a = x2;
3407 final float x1a = x1;
3408 // draw the vertical line
3409 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
3410 drawLine( x1, y1, x1, y2, g );
3412 // draw the horizontal line
3413 drawLine( x1a, y2, x2a, y2, g );
3418 * Paint a branch which consists of a vertical and a horizontal bar
3419 * @param is_ind_found_nodes
3421 final private void paintBranchRectangular( final Graphics2D g,
3426 final PhylogenyNode node,
3427 final boolean to_pdf,
3428 final boolean to_graphics_file ) {
3429 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
3430 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
3431 drawLine( x1, y1, x2, y2, g );
3433 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
3434 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
3435 g.draw( _quad_curve );
3437 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
3438 final float dx = x2 - x1;
3439 final float dy = y2 - y1;
3440 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
3441 + ( dy * 0.8f ), x2, y2 );
3442 g.draw( _cubic_curve );
3445 final float x2a = x2;
3446 final float x1a = x1;
3448 if ( node.isFirstChildNode() || node.isLastChildNode()
3449 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3450 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3451 if ( !to_graphics_file
3453 && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
3454 .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
3458 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3459 float x2c = x1 + EURO_D;
3463 drawLine( x1, y1, x2c, y2, g );
3465 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3467 y2_r = y2 - ROUNDED_D;
3471 drawLine( x1, y1, x1, y2_r, g );
3474 y2_r = y2 + ROUNDED_D;
3478 drawLine( x1, y1, x1, y2_r, g );
3482 drawLine( x1, y1, x1, y2, g );
3486 // draw the horizontal line
3487 if ( !to_graphics_file && !to_pdf
3488 && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
3492 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
3493 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3494 x1_r = x1a + ROUNDED_D;
3496 drawLine( x1_r, y2, x2a, y2, g );
3499 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3500 final float x1c = x1a + EURO_D;
3502 drawLine( x1c, y2, x2a, y2, g );
3506 drawLine( x1a, y2, x2a, y2, g );
3510 final double w = PhylogenyMethods.getBranchWidthValue( node );
3511 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3512 x1_r = x1a + ROUNDED_D;
3514 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
3517 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3518 final float x1c = x1a + EURO_D;
3520 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
3524 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
3527 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3532 final double diff = y2 - y2_r;
3533 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
3536 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
3541 if ( node.isExternal() ) {
3542 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
3543 || isInCurrentExternalNodes( node ) );
3547 final private double paintCirculars( final PhylogenyNode n,
3548 final Phylogeny phy,
3549 final float center_x,
3550 final float center_y,
3551 final double radius,
3552 final boolean radial_labels,
3554 final boolean to_pdf,
3555 final boolean to_graphics_file ) {
3556 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
3557 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
3558 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
3560 return _urt_nodeid_angle_map.get( n.getId() );
3563 final List<PhylogenyNode> descs = n.getDescendants();
3565 for( final PhylogenyNode desc : descs ) {
3566 sum += paintCirculars( desc,
3577 if ( !n.isRoot() ) {
3578 r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3580 final double theta = sum / descs.size();
3581 n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
3582 n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
3583 _urt_nodeid_angle_map.put( n.getId(), theta );
3584 for( final PhylogenyNode desc : descs ) {
3585 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
3591 final private void paintCircularsLite( final PhylogenyNode n,
3592 final Phylogeny phy,
3596 final Graphics2D g ) {
3597 if ( n.isExternal() ) {
3601 final List<PhylogenyNode> descs = n.getDescendants();
3602 for( final PhylogenyNode desc : descs ) {
3603 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
3606 if ( !n.isRoot() ) {
3607 r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
3609 final double theta = _urt_nodeid_angle_map.get( n.getId() );
3610 n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
3611 n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
3612 for( final PhylogenyNode desc : descs ) {
3613 paintBranchCircularLite( n, desc, g );
3618 final private void paintCollapsedNode( final Graphics2D g,
3619 final PhylogenyNode node,
3620 final boolean to_graphics_file,
3621 final boolean to_pdf,
3622 final boolean is_in_found_nodes ) {
3624 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3627 else if ( is_in_found_nodes ) {
3628 c = getTreeColorSet().getFoundColor();
3630 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3631 c = getTaxonomyBasedColor( node );
3633 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3634 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3635 c = PhylogenyMethods.getBranchColorValue( node );
3638 c = getTreeColorSet().getCollapseFillColor();
3640 double d = node.getAllExternalDescendants().size();
3642 d = ( 3 * _y_distance ) / 3;
3645 d = ( Math.log10( d ) * _y_distance ) / 2.5;
3647 final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
3648 if ( d < box_size ) {
3651 final float xx = node.getXcoord() - ( 2 * box_size );
3652 final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
3654 _polygon.moveTo( xxx, node.getYcoord() );
3655 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
3656 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
3657 _polygon.closePath();
3658 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3662 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3663 g.setColor( getBackground() );
3668 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3669 g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
3670 .getYcoord() - d ), c, false ) );
3675 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3678 final private void paintConfidenceValues( final Graphics2D g,
3679 final PhylogenyNode node,
3680 final boolean to_pdf,
3681 final boolean to_graphics_file ) {
3682 final List<Confidence> confidences = node.getBranchData().getConfidences();
3683 // if ( confidences.size() == 1 ) {
3684 // final double value = node.getBranchData().getConfidence( 0 ).getValue();
3685 // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
3688 // conf_str = FORMATTER_CONFIDENCE.format( value );
3690 // else if ( confidences.size() > 1 ) {
3691 boolean one_ok = false;
3692 boolean not_first = false;
3693 Collections.sort( confidences );
3694 final StringBuilder sb = new StringBuilder();
3695 String conf_str = "";
3696 for( final Confidence confidence : confidences ) {
3697 final double value = confidence.getValue();
3698 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3699 if ( value >= getOptions().getMinConfidenceValue() ) {
3708 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
3709 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3710 if ( getOptions().isShowConfidenceStddev() ) {
3711 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
3713 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
3715 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
3722 conf_str = sb.toString();
3725 if ( conf_str.length() > 0 ) {
3726 final double parent_x = node.getParent().getXcoord();
3727 double x = node.getXcoord();
3728 g.setFont( getTreeFontSet().getSmallFont() );
3729 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
3732 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
3735 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3736 g.setColor( Color.BLACK );
3739 g.setColor( getTreeColorSet().getConfidenceColor() );
3742 .drawString( conf_str,
3744 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
3745 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
3750 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
3751 final int box_size = getOptions().getDefaultNodeShapeSize();
3752 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3753 g.setColor( getTreeColorSet().getFoundColor() );
3754 g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
3757 final private void paintGainedAndLostCharacters( final Graphics2D g,
3758 final PhylogenyNode node,
3759 final String gained,
3760 final String lost ) {
3761 if ( node.getParent() != null ) {
3762 final double parent_x = node.getParent().getXcoord();
3763 final double x = node.getXcoord();
3764 g.setFont( getTreeFontSet().getLargeFont() );
3765 g.setColor( getTreeColorSet().getGainedCharactersColor() );
3766 if ( Constants.SPECIAL_CUSTOM ) {
3767 g.setColor( Color.BLUE );
3770 .drawString( gained,
3771 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
3772 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
3774 g.setColor( getTreeColorSet().getLostCharactersColor() );
3775 TreePanel.drawString( lost,
3776 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
3777 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
3783 * Draw a box at the indicated node.
3790 final private void paintNodeBox( final double x,
3792 final PhylogenyNode node,
3794 final boolean to_pdf,
3795 final boolean to_graphics_file,
3796 final boolean is_in_found_nodes ) {
3797 if ( node.isCollapse() ) {
3800 // if this node should be highlighted, do so
3801 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
3802 g.setColor( getTreeColorSet().getFoundColor() );
3803 drawOval( x - 8, y - 8, 16, 16, g );
3804 drawOval( x - 9, y - 8, 17, 17, g );
3805 drawOval( x - 9, y - 9, 18, 18, g );
3807 if ( is_in_found_nodes ) {
3808 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
3811 Color outline_color = null;
3812 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3813 outline_color = Color.BLACK;
3815 else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
3816 final Event event = node.getNodeData().getEvent();
3817 if ( event.isDuplication() ) {
3818 outline_color = getTreeColorSet().getDuplicationBoxColor();
3820 else if ( event.isSpeciation() ) {
3821 outline_color = getTreeColorSet().getSpecBoxColor();
3823 else if ( event.isSpeciationOrDuplication() ) {
3824 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
3827 else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
3828 outline_color = getTaxonomyBasedColor( node );
3831 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
3832 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
3833 outline_color = getTreeColorSet().getBranchColorForPdf();
3836 final int box_size = getOptions().getDefaultNodeShapeSize();
3837 final int half_box_size = box_size / 2;
3838 if ( ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
3839 || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
3840 || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
3841 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
3842 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
3843 drawOvalGradient( x - half_box_size,
3848 to_pdf ? Color.WHITE : outline_color,
3849 to_pdf ? outline_color : getBackground(),
3852 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
3853 Color background = getBackground();
3855 background = Color.WHITE;
3857 drawOvalGradient( x - half_box_size,
3866 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3867 g.setColor( outline_color );
3868 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3871 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
3872 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
3873 drawRectGradient( x - half_box_size,
3878 to_pdf ? Color.WHITE : outline_color,
3879 to_pdf ? outline_color : getBackground(),
3882 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
3883 Color background = getBackground();
3885 background = Color.WHITE;
3887 drawRectGradient( x - half_box_size,
3896 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
3897 g.setColor( outline_color );
3898 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
3905 final private void paintNodeData( final Graphics2D g,
3906 final PhylogenyNode node,
3907 final boolean to_graphics_file,
3908 final boolean to_pdf,
3909 final boolean is_in_found_nodes ) {
3910 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
3913 if ( getOptions().isShowBranchLengthValues()
3914 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3915 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3916 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
3917 paintBranchLength( g, node, to_pdf, to_graphics_file );
3919 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
3924 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3925 if ( getControlPanel().isShowTaxonomyImages()
3926 && ( getImageMap() != null )
3927 && !getImageMap().isEmpty()
3928 && node.getNodeData().isHasTaxonomy()
3929 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
3930 .getUris().isEmpty() ) ) {
3931 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
3933 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3934 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
3935 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
3937 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3938 g.setColor( Color.BLACK );
3940 else if ( is_in_found_nodes ) {
3941 g.setColor( getTreeColorSet().getFoundColor() );
3943 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3944 g.setColor( getTaxonomyBasedColor( node ) );
3946 else if ( getControlPanel().isColorAccordingToAnnotation()
3947 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
3948 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
3949 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
3951 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3952 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3953 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3955 else if ( to_pdf ) {
3956 g.setColor( Color.BLACK );
3959 g.setColor( getTreeColorSet().getSequenceColor() );
3961 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3962 if ( _sb.length() > 0 ) {
3965 _sb.append( node.getAllExternalDescendants().size() );
3972 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3973 if ( _sb.length() > 0 ) {
3976 _sb.append( node.getName() );
3978 if ( node.getNodeData().isHasSequence() ) {
3979 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
3980 if ( _sb.length() > 0 ) {
3983 _sb.append( node.getNodeData().getSequence().getSymbol() );
3985 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3986 if ( _sb.length() > 0 ) {
3989 _sb.append( node.getNodeData().getSequence().getName() );
3991 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3992 if ( _sb.length() > 0 ) {
3995 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3996 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3999 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4002 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
4003 if ( _sb.length() > 0 ) {
4006 _sb.append( propertiesToString( node ) );
4008 g.setFont( getTreeFontSet().getLargeFont() );
4009 if ( is_in_found_nodes ) {
4010 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4012 double down_shift_factor = 3.0;
4013 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
4014 down_shift_factor = 1;
4016 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
4017 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
4018 final String sb_str = _sb.toString();
4019 // GUILHEM_BEG ______________
4020 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
4021 && ( _query_sequence != null ) ) {
4022 int nodeTextBoundsWidth = 0;
4023 if ( sb_str.length() > 0 ) {
4024 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
4025 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
4027 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
4028 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
4029 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
4030 g.setColor( getTreeColorSet().getBackgroundColor() );
4034 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
4035 for( final SequenceRelation seqRelation : seqRelations ) {
4036 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
4037 .getRef1().isEqual( _query_sequence ) )
4038 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
4039 .getSelectedItem() );
4040 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
4041 final double linePosX = node.getXcoord() + 2 + half_box_size;
4042 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
4043 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
4045 if ( sConfidence != null ) {
4046 double confidenceX = pos_x;
4047 if ( sb_str.length() > 0 ) {
4048 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
4049 + CONFIDENCE_LEFT_MARGIN;
4051 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
4052 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
4053 .getBounds().getWidth();
4054 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
4055 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
4058 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
4060 if ( nodeTextBoundsWidth == 0 ) {
4061 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
4064 nodeTextBoundsWidth += 2;
4066 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
4067 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
4074 if ( sb_str.length() > 0 ) {
4075 TreePanel.drawString( sb_str, pos_x, pos_y, g );
4077 // GUILHEM_END _____________
4078 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
4079 // TODO FIXME need to check this one!
4080 //if ( _sb.length() > 0 ) {
4081 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
4082 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4084 // COMMENTED_OUT_BY_GUILHEM_END ________________
4085 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
4086 && ( node.getNodeData().getSequence().getAnnotations() != null )
4087 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
4088 if ( _sb.length() > 0 ) {
4089 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4091 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
4092 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4093 g.setColor( Color.BLACK );
4095 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
4096 g.setColor( calculateColorForAnnotation( ann ) );
4098 final String ann_str = createAnnotationString( ann );
4099 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
4100 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4102 _sb.append( ann_str );
4104 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4105 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
4106 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
4107 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
4108 && node.getNodeData().isHasBinaryCharacters() ) {
4109 if ( _sb.length() > 0 ) {
4110 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
4112 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4113 g.setColor( Color.BLACK );
4116 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
4118 if ( getControlPanel().isShowBinaryCharacters() ) {
4119 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
4120 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
4121 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
4122 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
4123 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
4124 .getLostCharactersAsStringBuffer().toString() );
4127 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
4128 node.getXcoord() + x + 4 + half_box_size,
4130 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
4132 paintGainedAndLostCharacters( g, node, "+"
4133 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
4134 + node.getNodeData().getBinaryCharacters().getLostCount() );
4140 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
4141 final PhylogenyNode node,
4142 final boolean to_pdf,
4143 final boolean to_graphics_file,
4144 final boolean radial_labels,
4145 final double ur_angle,
4146 final boolean is_in_found_nodes ) {
4147 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
4150 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4151 g.setColor( Color.BLACK );
4153 else if ( is_in_found_nodes ) {
4154 g.setColor( getTreeColorSet().getFoundColor() );
4156 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4157 g.setColor( getTaxonomyBasedColor( node ) );
4159 else if ( getControlPanel().isColorAccordingToAnnotation()
4160 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
4161 .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
4162 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
4165 g.setColor( getTreeColorSet().getSequenceColor() );
4169 if ( node.getNodeData().isHasTaxonomy()
4170 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
4171 .isShowTaxonomyCommonNames() ) ) {
4172 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4173 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4174 _sb.append( taxonomy.getTaxonomyCode() );
4177 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4178 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4179 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4180 _sb.append( taxonomy.getScientificName() );
4182 _sb.append( taxonomy.getCommonName() );
4185 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4186 _sb.append( taxonomy.getScientificName() );
4189 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4190 _sb.append( taxonomy.getCommonName() );
4194 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4195 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4196 _sb.append( taxonomy.getScientificName() );
4200 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4201 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4202 _sb.append( taxonomy.getCommonName() );
4207 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
4209 _sb.append( node.getAllExternalDescendants().size() );
4212 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
4213 if ( _sb.length() > 0 ) {
4216 _sb.append( node.getName() );
4218 if ( node.getNodeData().isHasSequence() ) {
4219 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4220 if ( _sb.length() > 0 ) {
4223 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
4224 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
4227 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
4229 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
4230 if ( _sb.length() > 0 ) {
4233 _sb.append( node.getNodeData().getSequence().getName() );
4236 g.setFont( getTreeFontSet().getLargeFont() );
4237 if ( is_in_found_nodes ) {
4238 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
4240 if ( _sb.length() > 1 ) {
4241 final String sb_str = _sb.toString();
4243 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4244 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
4247 m = ( float ) ( ur_angle % TWO_PI );
4249 _at = g.getTransform();
4250 boolean need_to_reset = false;
4251 final float x_coord = node.getXcoord();
4252 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
4253 if ( radial_labels ) {
4254 need_to_reset = true;
4255 boolean left = false;
4256 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4260 g.rotate( m, x_coord, node.getYcoord() );
4262 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
4266 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
4267 need_to_reset = true;
4268 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
4271 TreePanel.drawString( sb_str, x_coord, y_coord, g );
4272 if ( need_to_reset ) {
4273 g.setTransform( _at );
4278 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
4279 if ( node.isCollapse() ) {
4280 if ( !node.isRoot() && !node.getParent().isCollapse() ) {
4281 paintCollapsedNode( g, node, false, false, false );
4285 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
4286 g.setColor( getTreeColorSet().getFoundColor() );
4287 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
4290 if ( !node.isExternal() && !node.isCollapse() ) {
4291 boolean first_child = true;
4293 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4294 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4295 final PhylogenyNode child_node = node.getChildNode( i );
4297 if ( !isUniformBranchLengthsForCladogram() ) {
4298 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4301 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4303 if ( first_child ) {
4304 first_child = false;
4305 y2 = node.getYSecondary()
4306 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
4307 .getNumberOfExternalNodes() ) );
4310 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4312 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
4313 new_x = x2 + node.getXSecondary();
4314 final float diff_y = node.getYSecondary() - y2;
4315 final float diff_x = node.getXSecondary() - new_x;
4316 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
4317 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
4319 child_node.setXSecondary( new_x );
4320 child_node.setYSecondary( y2 );
4321 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
4326 final private void paintNodeRectangular( final Graphics2D g,
4327 final PhylogenyNode node,
4328 final boolean to_pdf,
4329 final boolean dynamically_hide,
4330 final int dynamic_hiding_factor,
4331 final boolean to_graphics_file ) {
4332 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
4333 if ( node.isCollapse() ) {
4334 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
4335 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4339 if ( node.isExternal() ) {
4340 ++_external_node_index;
4342 // Confidence values
4343 if ( getControlPanel().isShowConfidenceValues()
4344 && !node.isExternal()
4346 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
4347 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
4348 && node.getBranchData().isHasConfidences() ) {
4349 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
4351 // Draw a line to root:
4352 if ( node.isRoot() && _phylogeny.isRooted() ) {
4353 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
4356 float new_x_min = Float.MAX_VALUE;
4357 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
4358 float min_dist = 1.5f;
4359 if ( !disallow_shortcutting ) {
4360 // System.out.println( dynamic_hiding_factor );
4361 if ( dynamic_hiding_factor > 4000 ) {
4364 else if ( dynamic_hiding_factor > 1000 ) {
4367 else if ( dynamic_hiding_factor > 100 ) {
4371 if ( !node.isExternal() && !node.isCollapse() ) {
4372 boolean first_child = true;
4374 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
4375 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
4376 final PhylogenyNode child_node = node.getChildNode( i );
4378 if ( !isUniformBranchLengthsForCladogram() ) {
4379 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
4382 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
4384 if ( first_child ) {
4385 first_child = false;
4386 y2 = node.getYcoord()
4387 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
4390 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4392 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
4393 new_x = x2 + node.getXcoord();
4394 if ( dynamically_hide && ( x2 < new_x_min ) ) {
4397 final float diff_y = node.getYcoord() - y2;
4398 final float diff_x = node.getXcoord() - new_x;
4399 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
4400 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
4401 paintBranchRectangular( g,
4410 child_node.setXcoord( new_x );
4411 child_node.setYcoord( y2 );
4412 y2 += _y_distance * child_node.getNumberOfExternalNodes();
4414 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
4415 || isInCurrentExternalNodes( node ) );
4417 if ( dynamically_hide
4418 && !is_in_found_nodes
4419 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
4420 .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
4421 .getHeight() ) ) ) ) ) {
4424 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
4425 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
4428 final private void paintNodeWithRenderableData( final Graphics2D g,
4429 final PhylogenyNode node,
4430 final boolean to_graphics_file,
4431 final boolean to_pdf ) {
4432 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
4435 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
4438 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4439 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4440 RenderableDomainArchitecture rds = null;
4441 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
4443 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
4445 catch ( final ClassCastException cce ) {
4446 cce.printStackTrace();
4448 if ( rds != null ) {
4449 rds.setRenderingHeight( 6 );
4451 if ( node.getNodeData().isHasTaxonomy() ) {
4452 if ( getControlPanel().isShowTaxonomyCode()
4453 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
4454 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4458 if ( getControlPanel().isShowTaxonomyScientificNames()
4459 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
4460 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4461 .getScientificName()
4464 if ( getControlPanel().isShowTaxonomyCommonNames()
4465 && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
4466 x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
4471 if ( node.getNodeData().isHasSequence() ) {
4472 if ( getControlPanel().isShowGeneNames()
4473 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
4474 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
4477 if ( getControlPanel().isShowGeneSymbols()
4478 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
4479 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
4482 if ( getControlPanel().isShowSequenceAcc()
4483 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
4484 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
4485 .getAccession().toString()
4489 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
4490 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
4492 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
4497 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4498 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
4499 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
4500 getStatisticsForExpressionValues(),
4501 getConfiguration() );
4504 PhylogenyNode my_node = node;
4505 if ( !getControlPanel().isDrawPhylogram() ) {
4506 my_node = getPhylogeny().getFirstExternalNode();
4508 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
4509 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
4511 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
4512 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
4514 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
4520 final private void paintOvRectangle( final Graphics2D g ) {
4521 final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
4522 final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
4523 final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
4524 final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
4525 final float width = getOvMaxWidth() / w_ratio;
4526 final float height = getOvMaxHeight() / h_ratio;
4527 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
4528 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
4529 g.setColor( getTreeColorSet().getFoundColor() );
4530 getOvRectangle().setRect( x, y, width, height );
4531 if ( ( width < 6 ) && ( height < 6 ) ) {
4532 drawRectFilled( x, y, 6, 6, g );
4533 getOvVirtualRectangle().setRect( x, y, 6, 6 );
4535 else if ( width < 6 ) {
4536 drawRectFilled( x, y, 6, height, g );
4537 getOvVirtualRectangle().setRect( x, y, 6, height );
4539 else if ( height < 6 ) {
4540 drawRectFilled( x, y, width, 6, g );
4541 getOvVirtualRectangle().setRect( x, y, width, 6 );
4544 drawRect( x, y, width, height, g );
4545 if ( isInOvRect() ) {
4546 drawRect( x + 1, y + 1, width - 2, height - 2, g );
4548 getOvVirtualRectangle().setRect( x, y, width, height );
4552 final private void paintPhylogenyLite( final Graphics2D g ) {
4555 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
4556 .getWidth() ) ) ) );
4557 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
4558 final Stroke s = g.getStroke();
4559 g.setStroke( new BasicStroke( 0.5f ) ); //TODO
4560 for( final PhylogenyNode element : _nodes_in_preorder ) {
4561 paintNodeLite( g, element );
4564 paintOvRectangle( g );
4568 * Paint the root branch. (Differs from others because it will always be a
4569 * single horizontal line).
4570 * @param to_graphics_file
4572 * @return new x1 value
4574 final private void paintRootBranch( final Graphics2D g,
4577 final PhylogenyNode root,
4578 final boolean to_pdf,
4579 final boolean to_graphics_file ) {
4580 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
4581 float d = getXdistance();
4582 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
4583 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
4585 if ( d < MIN_ROOT_LENGTH ) {
4586 d = MIN_ROOT_LENGTH;
4588 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
4589 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
4592 final double w = PhylogenyMethods.getBranchWidthValue( root );
4593 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
4595 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
4598 final private void paintScale( final Graphics2D g,
4601 final boolean to_pdf,
4602 final boolean to_graphics_file ) {
4604 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
4606 final int y2 = y1 - 8;
4607 final int y3 = y1 - 4;
4608 g.setFont( getTreeFontSet().getSmallFont() );
4609 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4610 g.setColor( Color.BLACK );
4613 g.setColor( getTreeColorSet().getBranchLengthColor() );
4615 drawLine( x1, y1, x1, y2, g );
4616 drawLine( x2, y1, x2, y2, g );
4617 drawLine( x1, y3, x2, y3, g );
4618 if ( getScaleLabel() != null ) {
4619 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
4623 final private int paintTaxonomy( final Graphics2D g,
4624 final PhylogenyNode node,
4625 final boolean is_in_found_nodes,
4626 final boolean to_pdf,
4627 final boolean to_graphics_file,
4628 final double x_shift ) {
4629 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
4630 g.setFont( getTreeFontSet().getLargeItalicFont() );
4631 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
4632 g.setColor( Color.BLACK );
4634 else if ( is_in_found_nodes ) {
4635 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
4636 g.setColor( getTreeColorSet().getFoundColor() );
4638 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4639 g.setColor( getTaxonomyBasedColor( node ) );
4641 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
4642 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4643 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4645 else if ( to_pdf ) {
4646 g.setColor( Color.BLACK );
4649 g.setColor( getTreeColorSet().getTaxonomyColor() );
4651 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4652 final double start_y = node.getYcoord()
4653 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4655 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4656 _sb.append( taxonomy.getTaxonomyCode() );
4659 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4660 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4661 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4662 if ( getOptions().isAbbreviateScientificTaxonNames()
4663 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4664 abbreviateScientificName( taxonomy.getScientificName() );
4667 _sb.append( taxonomy.getScientificName() );
4670 _sb.append( taxonomy.getCommonName() );
4673 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4674 if ( getOptions().isAbbreviateScientificTaxonNames()
4675 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4676 abbreviateScientificName( taxonomy.getScientificName() );
4679 _sb.append( taxonomy.getScientificName() );
4683 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4684 _sb.append( taxonomy.getCommonName() );
4688 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4689 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4690 if ( getOptions().isAbbreviateScientificTaxonNames()
4691 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4692 abbreviateScientificName( taxonomy.getScientificName() );
4695 _sb.append( taxonomy.getScientificName() );
4700 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4701 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4702 _sb.append( taxonomy.getCommonName() );
4706 final String label = _sb.toString();
4708 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4709 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4710 // invert font color and background color to show that this is the query sequence
4711 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4715 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4716 g.setColor( getTreeColorSet().getBackgroundColor() );
4719 TreePanel.drawString( label, start_x, start_y, g );
4720 if ( is_in_found_nodes ) {
4721 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4724 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4728 final private void paintUnrooted( final PhylogenyNode n,
4729 final double low_angle,
4730 final double high_angle,
4731 final boolean radial_labels,
4733 final boolean to_pdf,
4734 final boolean to_graphics_file ) {
4736 n.setXcoord( getWidth() / 2 );
4737 n.setYcoord( getHeight() / 2 );
4739 if ( n.isExternal() ) {
4740 paintNodeDataUnrootedCirc( g,
4745 ( high_angle + low_angle ) / 2,
4746 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
4749 final float num_enclosed = n.getNumberOfExternalNodes();
4750 final float x = n.getXcoord();
4751 final float y = n.getYcoord();
4752 double current_angle = low_angle;
4753 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4754 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4755 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4756 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4757 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4758 final PhylogenyNode desc = n.getChildNode( i );
4759 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4760 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4761 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4762 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4765 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4768 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4771 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4772 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4774 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4775 if ( desc.getDistanceToParent() < 0 ) {
4779 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4783 length = getUrtFactor();
4785 final double mid_angle = current_angle + ( arc_size / 2 );
4786 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4787 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4788 desc.setXcoord( new_x );
4789 desc.setYcoord( new_y );
4790 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4791 current_angle += arc_size;
4792 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4793 drawLine( x, y, new_x, new_y, g );
4794 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc )
4795 || isInCurrentExternalNodes( desc ) );
4798 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
4802 final private void paintUnrootedLite( final PhylogenyNode n,
4803 final double low_angle,
4804 final double high_angle,
4806 final float urt_ov_factor ) {
4808 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
4809 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
4810 n.setXSecondary( x_pos );
4811 n.setYSecondary( y_pos );
4813 if ( n.isExternal() ) {
4816 final float num_enclosed = n.getNumberOfExternalNodes();
4817 final float x = n.getXSecondary();
4818 final float y = n.getYSecondary();
4819 double current_angle = low_angle;
4820 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4821 final PhylogenyNode desc = n.getChildNode( i );
4822 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4823 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4825 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4826 if ( desc.getDistanceToParent() < 0 ) {
4830 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
4834 length = urt_ov_factor;
4836 final double mid_angle = current_angle + ( arc_size / 2 );
4837 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
4838 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
4839 desc.setXSecondary( new_x );
4840 desc.setYSecondary( new_y );
4841 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
4842 g.setColor( getTreeColorSet().getFoundColor() );
4843 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
4844 g.setColor( getTreeColorSet().getOvColor() );
4846 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4847 current_angle += arc_size;
4848 drawLine( x, y, new_x, new_y, g );
4852 final private void pasteSubtree( final PhylogenyNode node ) {
4853 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4854 errorMessageNoCutCopyPasteInUnrootedDisplay();
4857 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
4858 JOptionPane.showMessageDialog( this,
4859 "No tree in buffer (need to copy or cut a subtree first)",
4860 "Attempt to paste with empty buffer",
4861 JOptionPane.ERROR_MESSAGE );
4864 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
4865 final Object[] options = { "As sibling", "As descendant", "Cancel" };
4866 final int r = JOptionPane.showOptionDialog( this,
4867 "How to paste subtree" + label + "?",
4869 JOptionPane.CLOSED_OPTION,
4870 JOptionPane.QUESTION_MESSAGE,
4874 boolean paste_as_sibling = true;
4876 paste_as_sibling = false;
4878 else if ( r != 0 ) {
4881 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
4882 buffer_phy.setAllNodesToNotCollapse();
4883 PhylogenyMethods.preOrderReId( buffer_phy );
4884 buffer_phy.setRooted( true );
4885 boolean need_to_show_whole = false;
4886 if ( paste_as_sibling ) {
4887 if ( node.isRoot() ) {
4888 JOptionPane.showMessageDialog( this,
4889 "Cannot paste sibling to root",
4890 "Attempt to paste sibling to root",
4891 JOptionPane.ERROR_MESSAGE );
4894 buffer_phy.addAsSibling( node );
4897 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
4898 need_to_show_whole = true;
4899 _phylogeny = buffer_phy;
4902 buffer_phy.addAsChild( node );
4905 if ( getCopiedAndPastedNodes() == null ) {
4906 setCopiedAndPastedNodes( new HashSet<Long>() );
4908 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
4909 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
4910 for( final PhylogenyNode n : nodes ) {
4911 node_ids.add( n.getId() );
4913 node_ids.add( node.getId() );
4914 getCopiedAndPastedNodes().addAll( node_ids );
4915 setNodeInPreorderToNull();
4916 _phylogeny.externalNodesHaveChanged();
4917 _phylogeny.clearHashIdToNodeMap();
4918 _phylogeny.recalculateNumberOfExternalDescendants( true );
4919 resetNodeIdToDistToLeafMap();
4921 if ( need_to_show_whole ) {
4922 getControlPanel().showWhole();
4927 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
4928 final PropertiesMap properties = node.getNodeData().getProperties();
4929 final StringBuffer sb = new StringBuffer();
4930 boolean first = true;
4931 for( final String ref : properties.getPropertyRefs() ) {
4938 final Property p = properties.getProperty( ref );
4939 sb.append( getPartAfterColon( p.getRef() ) );
4941 sb.append( p.getValue() );
4942 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
4943 sb.append( getPartAfterColon( p.getUnit() ) );
4949 final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
4950 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4953 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4954 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4957 final private void setInOv( final boolean in_ov ) {
4961 final private void setOvMaxHeight( final float ov_max_height ) {
4962 _ov_max_height = ov_max_height;
4965 final private void setOvMaxWidth( final float ov_max_width ) {
4966 _ov_max_width = ov_max_width;
4969 final private void setOvXcorrectionFactor( final float f ) {
4970 _ov_x_correction_factor = f;
4973 final private void setOvXDistance( final float ov_x_distance ) {
4974 _ov_x_distance = ov_x_distance;
4977 final private void setOvXPosition( final int ov_x_position ) {
4978 _ov_x_position = ov_x_position;
4981 final private void setOvYDistance( final float ov_y_distance ) {
4982 _ov_y_distance = ov_y_distance;
4985 final private void setOvYPosition( final int ov_y_position ) {
4986 _ov_y_position = ov_y_position;
4989 final private void setOvYStart( final int ov_y_start ) {
4990 _ov_y_start = ov_y_start;
4993 final private void setScaleDistance( final double scale_distance ) {
4994 _scale_distance = scale_distance;
4997 final private void setScaleLabel( final String scale_label ) {
4998 _scale_label = scale_label;
5001 final private void setUpUrtFactor() {
5002 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
5003 : getVisibleRect().height;
5004 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
5005 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
5008 final int max_depth = _circ_max_depth;
5009 if ( max_depth > 0 ) {
5010 setUrtFactor( d / ( 2 * max_depth ) );
5013 setUrtFactor( d / 2 );
5016 setUrtFactorOv( getUrtFactor() );
5019 final private void setUrtFactor( final float urt_factor ) {
5020 _urt_factor = urt_factor;
5023 final private void setUrtFactorOv( final float urt_factor_ov ) {
5024 _urt_factor_ov = urt_factor_ov;
5027 private void showExtDescNodeData( final PhylogenyNode node ) {
5028 final List<String> data = new ArrayList<String>();
5029 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
5030 switch ( getOptions().getExtDescNodeDataToReturn() ) {
5032 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
5033 data.add( n.getName() );
5037 if ( n.getNodeData().isHasSequence()
5038 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5039 data.add( n.getNodeData().getSequence().getName() );
5042 case SEQUENCE_SYMBOL:
5043 if ( n.getNodeData().isHasSequence()
5044 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
5045 data.add( n.getNodeData().getSequence().getSymbol() );
5048 case SEQUENCE_MOL_SEQ:
5049 if ( n.getNodeData().isHasSequence()
5050 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5051 data.add( n.getNodeData().getSequence().getMolecularSequence() );
5054 case SEQUENCE_MOL_SEQ_FASTA:
5055 final StringBuilder sb = new StringBuilder();
5056 if ( n.getNodeData().isHasSequence()
5057 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
5058 if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
5059 sb.append( SequenceWriter.toFasta( n.getNodeData().getSequence().getName(), n.getNodeData()
5060 .getSequence().getMolecularSequence(), 60 ) );
5063 sb.append( SequenceWriter.toFasta( n.getName(), n.getNodeData().getSequence()
5064 .getMolecularSequence(), 60 ) );
5066 data.add( sb.toString() );
5070 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
5071 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
5072 data.add( n.getNodeData().getSequence().getAccession().toString() );
5075 case TAXONOMY_SCIENTIFIC_NAME:
5076 if ( n.getNodeData().isHasTaxonomy()
5077 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
5078 data.add( n.getNodeData().getTaxonomy().getScientificName() );
5082 if ( n.getNodeData().isHasTaxonomy()
5083 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
5084 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
5088 AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
5091 throw new IllegalArgumentException( "unknown data element: "
5092 + getOptions().getExtDescNodeDataToReturn() );
5095 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
5096 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
5097 final StringBuilder sb = new StringBuilder();
5098 for( final String d : data ) {
5099 if ( !ForesterUtil.isEmpty( d ) ) {
5100 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
5101 System.out.println( d );
5104 sb.append( ForesterUtil.LINE_SEPARATOR );
5107 if ( sb.length() < 1 ) {
5108 clearCurrentExternalNodesDataBuffer();
5111 setCurrentExternalNodesDataBuffer( sb );
5114 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
5115 final StringBuilder sb = new StringBuilder();
5116 for( final String d : data ) {
5117 if ( !ForesterUtil.isEmpty( d ) ) {
5119 sb.append( ForesterUtil.LINE_SEPARATOR );
5122 if ( sb.length() < 1 ) {
5123 AptxUtil.showInformationMessage( this,
5124 "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
5125 "Descendants of selected node do not contain selected data" );
5126 clearCurrentExternalNodesDataBuffer();
5129 setCurrentExternalNodesDataBuffer( sb );
5130 final String title = "External Descendants "
5131 + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
5132 : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
5133 + node.getNumberOfExternalNodes() + ") For Node " + node;
5134 final String s = sb.toString().trim();
5135 if ( getMainPanel().getMainFrame() == null ) {
5136 // Must be "E" applet version.
5137 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
5138 ae.showTextFrame( s, title );
5141 getMainPanel().getMainFrame().showTextFrame( s, title );
5147 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
5149 if ( ( node.getName().length() > 0 )
5150 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
5151 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
5152 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
5153 || node.getBranchData().isHasConfidences() ) {
5154 _popup_buffer.setLength( 0 );
5156 if ( node.getName().length() > 0 ) {
5158 _popup_buffer.append( node.getName() );
5160 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
5162 boolean enc_data = false;
5163 final Taxonomy tax = node.getNodeData().getTaxonomy();
5164 if ( _popup_buffer.length() > 0 ) {
5165 _popup_buffer.append( "\n" );
5167 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
5168 _popup_buffer.append( "[" );
5169 _popup_buffer.append( tax.getTaxonomyCode() );
5170 _popup_buffer.append( "]" );
5173 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
5175 _popup_buffer.append( " " );
5177 _popup_buffer.append( tax.getScientificName() );
5180 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
5182 _popup_buffer.append( " (" );
5185 _popup_buffer.append( "(" );
5187 _popup_buffer.append( tax.getCommonName() );
5188 _popup_buffer.append( ")" );
5191 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
5193 _popup_buffer.append( " (" );
5196 _popup_buffer.append( "(" );
5198 _popup_buffer.append( tax.getAuthority() );
5199 _popup_buffer.append( ")" );
5202 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
5204 _popup_buffer.append( " [" );
5207 _popup_buffer.append( "[" );
5209 _popup_buffer.append( tax.getRank() );
5210 _popup_buffer.append( "]" );
5213 if ( tax.getSynonyms().size() > 0 ) {
5215 _popup_buffer.append( " " );
5217 _popup_buffer.append( "[" );
5219 for( final String syn : tax.getSynonyms() ) {
5220 if ( !ForesterUtil.isEmpty( syn ) ) {
5222 _popup_buffer.append( syn );
5223 if ( counter < tax.getSynonyms().size() ) {
5224 _popup_buffer.append( ", " );
5229 _popup_buffer.append( "]" );
5232 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
5233 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
5234 _popup_buffer.append( "[" );
5235 _popup_buffer.append( tax.getIdentifier().getProvider() );
5236 _popup_buffer.append( "] " );
5238 _popup_buffer.append( tax.getIdentifier().getValue() );
5242 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
5244 boolean enc_data = false;
5245 if ( _popup_buffer.length() > 0 ) {
5246 _popup_buffer.append( "\n" );
5248 final Sequence seq = node.getNodeData().getSequence();
5249 if ( seq.getAccession() != null ) {
5250 _popup_buffer.append( "[" );
5251 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
5252 _popup_buffer.append( seq.getAccession().getSource() );
5253 _popup_buffer.append( ":" );
5255 _popup_buffer.append( seq.getAccession().getValue() );
5256 _popup_buffer.append( "]" );
5259 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
5261 _popup_buffer.append( " [" );
5264 _popup_buffer.append( "[" );
5266 _popup_buffer.append( seq.getSymbol() );
5267 _popup_buffer.append( "]" );
5270 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
5272 _popup_buffer.append( " " );
5274 _popup_buffer.append( seq.getName() );
5277 if ( node.getNodeData().isHasDate() ) {
5279 if ( _popup_buffer.length() > 0 ) {
5280 _popup_buffer.append( "\n" );
5282 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
5284 if ( node.getNodeData().isHasDistribution() ) {
5286 if ( _popup_buffer.length() > 0 ) {
5287 _popup_buffer.append( "\n" );
5289 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
5291 if ( node.getBranchData().isHasConfidences() ) {
5292 final List<Confidence> confs = node.getBranchData().getConfidences();
5293 for( final Confidence confidence : confs ) {
5295 if ( _popup_buffer.length() > 0 ) {
5296 _popup_buffer.append( "\n" );
5298 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
5299 _popup_buffer.append( "[" );
5300 _popup_buffer.append( confidence.getType() );
5301 _popup_buffer.append( "] " );
5304 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
5306 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5307 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
5308 _popup_buffer.append( " (sd=" );
5309 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
5310 .getStandardDeviation(), getOptions()
5311 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
5312 _popup_buffer.append( ")" );
5316 if ( node.getNodeData().isHasProperties() ) {
5317 final PropertiesMap properties = node.getNodeData().getProperties();
5318 for( final String ref : properties.getPropertyRefs() ) {
5319 _popup_buffer.append( "\n" );
5320 final Property p = properties.getProperty( ref );
5321 _popup_buffer.append( getPartAfterColon( p.getRef() ) );
5322 _popup_buffer.append( "=" );
5323 _popup_buffer.append( p.getValue() );
5324 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
5325 _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
5329 if ( _popup_buffer.length() > 0 ) {
5330 if ( !getConfiguration().isUseNativeUI() ) {
5332 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
5333 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
5334 if ( isInFoundNodes( node ) ) {
5335 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
5337 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
5338 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
5341 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
5345 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
5347 _rollover_popup.setText( _popup_buffer.toString() );
5348 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
5350 e.getLocationOnScreen().x + 10,
5351 e.getLocationOnScreen().y
5353 _node_desc_popup.show();
5357 catch ( final Exception ex ) {
5362 final private void showNodeEditFrame( final PhylogenyNode n ) {
5363 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5364 // pop up edit box for single node
5365 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
5366 _node_frame_index++;
5369 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5373 final private void showNodeFrame( final PhylogenyNode n ) {
5374 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
5375 // pop up edit box for single node
5376 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
5377 _node_frame_index++;
5380 JOptionPane.showMessageDialog( this, "too many node windows are open" );
5384 final private void switchDisplaygetPhylogenyGraphicsType() {
5385 switch ( getPhylogenyGraphicsType() ) {
5387 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5388 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5391 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5392 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5395 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5396 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5399 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5400 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5403 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5404 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5407 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5408 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5411 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5412 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5415 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5416 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5419 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5421 if ( getControlPanel().getDynamicallyHideData() != null ) {
5422 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5423 getControlPanel().getDynamicallyHideData().setEnabled( false );
5426 getControlPanel().getDynamicallyHideData().setEnabled( true );
5429 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5430 getControlPanel().setDrawPhylogramEnabled( true );
5433 getControlPanel().setDrawPhylogramEnabled( false );
5435 if ( getMainPanel().getMainFrame() == null ) {
5436 // Must be "E" applet version.
5437 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5438 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5441 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5445 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
5446 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5449 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5450 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5453 final private static String getPartAfterColon( final String s ) {
5454 final int i = s.indexOf( ':' );
5455 if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
5458 return s.substring( i + 1, s.length() );
5461 final private static boolean isSequenceEmpty( final Sequence seq ) {
5462 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
5463 && ForesterUtil.isEmpty( seq.getSymbol() );
5466 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
5467 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
5468 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
5469 .getSynonyms().isEmpty() );
5472 final private static boolean plusPressed( final int key_code ) {
5473 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5474 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5477 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
5478 final Phylogeny new_phy = new Phylogeny();
5479 new_phy.setRooted( true );
5480 new_phy.setName( source_phy.getName() );
5481 new_phy.setDescription( source_phy.getDescription() );
5482 new_phy.setType( source_phy.getType() );
5483 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
5484 new_phy.setConfidence( source_phy.getConfidence() );
5485 new_phy.setIdentifier( source_phy.getIdentifier() );
5486 new_phy.setRoot( new_root.copyNodeDataShallow() );
5488 for( final PhylogenyNode n : new_root.getDescendants() ) {
5489 new_phy.getRoot().setChildNode( i++, n );
5494 final private class SubtreeColorizationActionListener implements ActionListener {
5496 JColorChooser _chooser;
5497 PhylogenyNode _node;
5499 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5505 public void actionPerformed( final ActionEvent e ) {
5506 final Color c = _chooser.getColor();
5508 colorizeSubtree( c, _node );