2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.archaeopteryx;
28 import java.awt.BasicStroke;
29 import java.awt.Color;
30 import java.awt.Cursor;
31 import java.awt.Dimension;
33 import java.awt.GradientPaint;
34 import java.awt.Graphics;
35 import java.awt.Graphics2D;
36 import java.awt.Point;
37 import java.awt.Polygon;
38 import java.awt.Rectangle;
39 import java.awt.RenderingHints;
40 import java.awt.event.ActionEvent;
41 import java.awt.event.ActionListener;
42 import java.awt.event.FocusAdapter;
43 import java.awt.event.FocusEvent;
44 import java.awt.event.InputEvent;
45 import java.awt.event.KeyAdapter;
46 import java.awt.event.KeyEvent;
47 import java.awt.event.MouseEvent;
48 import java.awt.event.MouseWheelEvent;
49 import java.awt.event.MouseWheelListener;
50 import java.awt.font.FontRenderContext;
51 import java.awt.font.TextLayout;
52 import java.awt.geom.AffineTransform;
53 import java.awt.geom.Arc2D;
54 import java.awt.geom.CubicCurve2D;
55 import java.awt.geom.Ellipse2D;
56 import java.awt.geom.Line2D;
57 import java.awt.geom.QuadCurve2D;
58 import java.awt.geom.Rectangle2D;
59 import java.awt.image.BufferedImage;
60 import java.awt.print.PageFormat;
61 import java.awt.print.Printable;
62 import java.awt.print.PrinterException;
64 import java.io.IOException;
65 import java.io.UnsupportedEncodingException;
67 import java.net.URISyntaxException;
68 import java.net.URLEncoder;
69 import java.text.DecimalFormat;
70 import java.text.DecimalFormatSymbols;
71 import java.text.NumberFormat;
72 import java.util.ArrayList;
73 import java.util.Collections;
74 import java.util.HashMap;
75 import java.util.HashSet;
76 import java.util.Hashtable;
77 import java.util.List;
80 import javax.swing.BorderFactory;
81 import javax.swing.JApplet;
82 import javax.swing.JColorChooser;
83 import javax.swing.JDialog;
84 import javax.swing.JMenuItem;
85 import javax.swing.JOptionPane;
86 import javax.swing.JPanel;
87 import javax.swing.JPopupMenu;
88 import javax.swing.JTextArea;
89 import javax.swing.Popup;
90 import javax.swing.PopupFactory;
92 import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
93 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
94 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
95 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
96 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
97 import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
98 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
99 import org.forester.phylogeny.Phylogeny;
100 import org.forester.phylogeny.PhylogenyMethods;
101 import org.forester.phylogeny.PhylogenyNode;
102 import org.forester.phylogeny.data.Annotation;
103 import org.forester.phylogeny.data.BranchColor;
104 import org.forester.phylogeny.data.Confidence;
105 import org.forester.phylogeny.data.Event;
106 import org.forester.phylogeny.data.PhylogenyData;
107 import org.forester.phylogeny.data.PropertiesMap;
108 import org.forester.phylogeny.data.Property;
109 import org.forester.phylogeny.data.Sequence;
110 import org.forester.phylogeny.data.SequenceRelation;
111 import org.forester.phylogeny.data.Taxonomy;
112 import org.forester.phylogeny.data.Uri;
113 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
114 import org.forester.phylogeny.iterators.PreorderTreeIterator;
115 import org.forester.util.BasicDescriptiveStatistics;
116 import org.forester.util.DescriptiveStatistics;
117 import org.forester.util.ForesterConstants;
118 import org.forester.util.ForesterUtil;
120 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
122 private static final float PI = ( float ) ( Math.PI );
123 private static final double TWO_PI = 2 * Math.PI;
124 private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
125 private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
126 private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
127 private static final short OV_BORDER = 10;
128 final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
129 final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
130 final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
131 final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
132 final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
133 private final static long serialVersionUID = -978349745916505029L;
134 private final static int EURO_D = 10;
135 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
136 private final static int MIN_ROOT_LENGTH = 3;
137 private final static int BOX_SIZE = 4;
138 private final static int HALF_BOX_SIZE = TreePanel.BOX_SIZE / 2;
139 private final static int MAX_SUBTREES = 100;
140 private final static int MAX_NODE_FRAMES = 10;
141 private final static int MOVE = 20;
142 private final static NumberFormat FORMATTER_CONFIDENCE;
143 private final static NumberFormat FORMATTER_BRANCH_LENGTH;
144 private final static int WIGGLE = 2;
145 private final static int HALF_BOX_SIZE_PLUS_WIGGLE = HALF_BOX_SIZE + WIGGLE;
146 private final static int LIMIT_FOR_HQ_RENDERING = 1000;
147 private final static int CONFIDENCE_LEFT_MARGIN = 4;
148 // TODO "rendering_hints" was static before. Need to make sure everything is OK with it not
149 // being static anymore (02/20/2009).
150 private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
151 RenderingHints.VALUE_RENDER_DEFAULT );
152 private File _treefile = null;
153 private Configuration _configuration = null;
154 private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
155 private int _node_frame_index = 0;
156 private Phylogeny _phylogeny = null;
157 private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
158 private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
159 private int _subtree_index = 0;
160 private MainPanel _main_panel = null;
161 private Set<Integer> _found_nodes = null;
162 private PhylogenyNode _highlight_node = null;
163 private JPopupMenu _node_popup_menu = null;
164 private JMenuItem _node_popup_menu_items[] = null;
165 private int _longest_ext_node_info = 0;
166 private float _x_correction_factor = 0.0f;
167 private float _ov_x_correction_factor = 0.0f;
168 private float _x_distance = 0.0f;
169 private float _y_distance = 0.0f;
170 private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
171 private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
172 private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
173 private float _last_drag_point_x = 0;
174 private float _last_drag_point_y = 0;
175 private ControlPanel _control_panel = null;
176 private int _external_node_index = 0;
177 private final Polygon _polygon = new Polygon();
178 private final StringBuilder _sb = new StringBuilder();
179 private JColorChooser _color_chooser = null;
180 private double _scale_distance = 0.0;
181 private String _scale_label = null;
182 private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
183 private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
184 private final Line2D _line = new Line2D.Float();
185 private final Ellipse2D _ellipse = new Ellipse2D.Float();
186 private final Rectangle2D _rectangle = new Rectangle2D.Float();
187 private Options _options = null;
188 private float _ov_max_width = 0;
189 private float _ov_max_height = 0;
190 private int _ov_x_position = 0;
191 private int _ov_y_position = 0;
192 private int _ov_y_start = 0;
193 private float _ov_y_distance = 0;
194 private float _ov_x_distance = 0;
195 private boolean _ov_on = false;
196 private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
197 private float _urt_factor = 1;
198 private float _urt_factor_ov = 1;
199 private final boolean _phy_has_branch_lengths;
200 private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
201 private boolean _in_ov_rect = false;
202 private boolean _in_ov = false;
203 private final Rectangle _ov_virtual_rectangle = new Rectangle();
204 final private static double _180_OVER_PI = 180.0 / Math.PI;
205 private static final float ROUNDED_D = 8;
206 private int _circ_max_depth;
207 private int _circ_num_ext_nodes;
208 private PhylogenyNode _root;
209 final private Arc2D _arc = new Arc2D.Double();
210 final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
211 final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
212 HashMap<Integer, Short> _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
213 private AffineTransform _at;
214 private double _max_distance_to_root = -1;
215 private int _dynamic_hiding_factor = 0;
216 private boolean _edited = false;
217 private Popup _node_desc_popup;
218 private JTextArea _rollover_popup;
219 //private final short _skip_counter = 0;
220 private final StringBuffer _popup_buffer = new StringBuffer();
221 final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
224 private static final boolean DRAW_MEAN_COUNTS = true; //TODO remove me later
225 private Sequence _query_sequence = null;
226 private final FontRenderContext _frc = new FontRenderContext( null,
229 // expression values menu:
230 private DescriptiveStatistics _statistics_for_vector_data;
231 private PhylogenyNode[] _nodes_in_preorder = null;
232 // private Image offscreenImage;
233 // private Graphics offscreenGraphics;
234 // private Dimension offscreenDimension;
236 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
237 dfs.setDecimalSeparator( '.' );
238 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
239 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
242 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
243 requestFocusInWindow();
244 addKeyListener( new KeyAdapter() {
247 public void keyPressed( final KeyEvent key_event ) {
248 keyPressedCalls( key_event );
249 requestFocusInWindow();
252 addFocusListener( new FocusAdapter() {
255 public void focusGained( final FocusEvent e ) {
256 requestFocusInWindow();
259 if ( ( t == null ) || t.isEmpty() ) {
260 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
262 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
264 _configuration = configuration;
266 _phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
268 // if ( !_phylogeny.isEmpty() ) {
269 _phylogeny.recalculateNumberOfExternalDescendants( true );
270 checkForVectorProperties( _phylogeny );
272 setBackground( getTreeColorSet().getBackgroundColor() );
273 final MouseListener mouse_listener = new MouseListener( this );
274 addMouseListener( mouse_listener );
275 addMouseMotionListener( mouse_listener );
276 addMouseWheelListener( this );
277 calculateScaleDistance();
278 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
279 FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
280 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
283 public void checkForVectorProperties( final Phylogeny phy ) {
284 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
285 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
286 final PhylogenyNode node = iter.next();
287 if ( node.getNodeData().getProperties() != null ) {
288 final PropertiesMap pm = node.getNodeData().getProperties();
289 final double[] vector = new double[ pm.getProperties().size() ];
291 for( final String ref : pm.getProperties().keySet() ) {
292 if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
293 final Property p = pm.getProperty( ref );
294 final String value_str = p.getValue();
295 final String index_str = ref
296 .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
299 d = Double.parseDouble( value_str );
301 catch ( final NumberFormatException e ) {
302 JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
303 + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
308 i = Integer.parseInt( index_str );
310 catch ( final NumberFormatException e ) {
311 JOptionPane.showMessageDialog( this,
312 "Could not parse \"" + index_str
313 + "\" into index for vector data",
314 "Problem with Vector Data",
315 JOptionPane.ERROR_MESSAGE );
319 JOptionPane.showMessageDialog( this,
320 "Attempt to use negative index for vector data",
321 "Problem with Vector Data",
322 JOptionPane.ERROR_MESSAGE );
330 final List<Double> vector_l = new ArrayList<Double>( counter );
331 for( int i = 0; i < counter; ++i ) {
332 vector_l.add( vector[ i ] );
334 node.getNodeData().setVector( vector_l );
337 if ( stats.getN() > 0 ) {
338 _statistics_for_vector_data = stats;
342 final public void actionPerformed( final ActionEvent e ) {
344 boolean done = false;
345 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
346 for( index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
347 // NOTE: index corresponds to the indices of click-to options
348 // in the control panel.
349 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
350 // Set this as the new default click-to action
351 _main_panel.getControlPanel().setClickToAction( index );
352 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
353 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
354 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
359 requestFocusInWindow();
362 final private void addEmptyNode( final PhylogenyNode node ) {
363 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
364 errorMessageNoCutCopyPasteInUnrootedDisplay();
367 final String label = getASimpleTextRepresentationOfANode( node );
369 if ( ForesterUtil.isEmpty( label ) ) {
370 msg = "How to add the new, empty node?";
373 msg = "How to add the new, empty node to node" + label + "?";
375 final Object[] options = { "As sibling", "As descendant", "Cancel" };
376 final int r = JOptionPane.showOptionDialog( this,
378 "Addition of Empty New Node",
379 JOptionPane.CLOSED_OPTION,
380 JOptionPane.QUESTION_MESSAGE,
384 boolean add_as_sibling = true;
386 add_as_sibling = false;
391 final Phylogeny phy = new Phylogeny();
392 phy.setRoot( new PhylogenyNode() );
393 phy.setRooted( true );
394 if ( add_as_sibling ) {
395 if ( node.isRoot() ) {
396 JOptionPane.showMessageDialog( this,
397 "Cannot add sibling to root",
398 "Attempt to add sibling to root",
399 JOptionPane.ERROR_MESSAGE );
402 phy.addAsSibling( node );
405 phy.addAsChild( node );
407 _phylogeny.externalNodesHaveChanged();
408 _phylogeny.hashIDs();
409 _phylogeny.recalculateNumberOfExternalDescendants( true );
410 resetNodeIdToDistToLeafMap();
415 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
416 final boolean is_vertical,
418 final boolean to_pdf,
419 final boolean to_graphics_file ) {
420 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
421 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
422 g.setColor( Color.BLACK );
424 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
425 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
426 && ( getCutOrCopiedTree() != null )
427 && ( getCopiedAndPastedNodes() != null )
429 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
430 g.setColor( getTreeColorSet().getFoundColor() );
432 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
433 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
436 g.setColor( getTreeColorSet().getBranchColorForPdf() );
439 g.setColor( getTreeColorSet().getBranchColor() );
443 final void assignGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node, final Graphics g ) {
444 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
445 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
448 g.setColor( getTreeColorSet().getBranchColor() );
452 final private void blast( final PhylogenyNode node ) {
453 if ( !isCanBlast( node ) ) {
454 JOptionPane.showMessageDialog( this,
455 "No sequence information present",
457 JOptionPane.WARNING_MESSAGE );
460 if ( node.getNodeData().isHasSequence() ) {
462 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
463 name = node.getNodeData().getSequence().getName();
465 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
466 name = node.getNodeData().getSequence().getSymbol();
468 else if ( node.getNodeData().getSequence().getAccession() != null ) {
469 name = node.getNodeData().getSequence().getAccession().getValue();
471 if ( !ForesterUtil.isEmpty( name ) ) {
473 System.out.println( "trying: " + name );
474 final Blast s = new Blast();
477 catch ( final Exception e ) {
484 final void calcMaxDepth() {
485 if ( _phylogeny != null ) {
486 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
491 * Calculate the length of the distance between the given node and its
497 * @return the distance value
499 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
500 if ( getControlPanel().isDrawPhylogram() ) {
501 if ( node.getDistanceToParent() < 0.0 ) {
504 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
507 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
508 return getXdistance();
510 return getXdistance() * factor;
514 final private Color calculateColorForAnnotation( final PhylogenyData ann ) {
515 Color c = getTreeColorSet().getAnnotationColor();
516 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
517 c = getControlPanel().getAnnotationColors().get( ann.asSimpleText().toString() );
519 c = getTreeColorSet().getAnnotationColor();
525 final void calculateLongestExtNodeInfo() {
526 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
530 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
532 if ( node.isCollapse() ) {
535 if ( getControlPanel().isShowNodeNames() ) {
536 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
538 if ( node.getNodeData().isHasSequence() ) {
539 if ( getControlPanel().isShowSequenceAcc()
540 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
541 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
545 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
546 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
548 if ( getControlPanel().isShowGeneSymbols()
549 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
550 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
552 if ( getControlPanel().isShowAnnotation()
553 && ( node.getNodeData().getSequence().getAnnotations() != null )
554 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
555 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
560 if ( node.getNodeData().isHasTaxonomy() ) {
561 final Taxonomy tax = node.getNodeData().getTaxonomy();
562 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
563 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
565 if ( getControlPanel().isShowTaxonomyScientificNames()
566 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
567 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
569 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
570 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
573 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
574 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
575 .getGainedCharactersAsStringBuffer().toString() );
577 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
578 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
579 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
580 .getRenderingSize().getWidth();
582 if ( sum >= Constants.EXT_NODE_INFO_LENGTH_MAX ) {
583 setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX );
586 if ( sum > longest ) {
590 if ( longest >= Constants.EXT_NODE_INFO_LENGTH_MAX ) {
591 setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX );
594 setLongestExtNodeInfo( longest );
598 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
599 if ( getControlPanel().isDrawPhylogram() ) {
600 if ( node.getDistanceToParent() < 0.0 ) {
603 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
606 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
607 return getOvXDistance();
609 return getOvXDistance() * factor;
613 final void calculateScaleDistance() {
614 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
617 final double height = getMaxDistanceToRoot();
619 if ( ( height <= 0.5 ) ) {
620 setScaleDistance( 0.01 );
622 else if ( height <= 5.0 ) {
623 setScaleDistance( 0.1 );
625 else if ( height <= 50.0 ) {
626 setScaleDistance( 1 );
628 else if ( height <= 500.0 ) {
629 setScaleDistance( 10 );
632 setScaleDistance( 100 );
636 setScaleDistance( 0.0 );
638 String scale_label = String.valueOf( getScaleDistance() );
639 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
640 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
642 setScaleLabel( scale_label );
645 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
646 String species = tax.getTaxonomyCode();
647 if ( ForesterUtil.isEmpty( species ) ) {
648 species = tax.getScientificName();
649 if ( ForesterUtil.isEmpty( species ) ) {
650 species = tax.getCommonName();
653 if ( ForesterUtil.isEmpty( species ) ) {
654 return getTreeColorSet().getTaxonomyColor();
656 // Look in species hash
657 Color c = getControlPanel().getSpeciesColors().get( species );
659 c = Util.calculateColorFromString( species );
660 getControlPanel().getSpeciesColors().put( species, c );
665 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
666 JOptionPane.showMessageDialog( this,
667 "Cannot launch web browser for " + type_type + " data of this node",
668 "Cannot launch web browser",
669 JOptionPane.WARNING_MESSAGE );
673 * Collapse the tree from the given node
678 final void collapse( final PhylogenyNode node ) {
679 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
680 JOptionPane.showMessageDialog( this,
681 "Cannot collapse in unrooted display type",
682 "Attempt to collapse in unrooted display",
683 JOptionPane.WARNING_MESSAGE );
686 if ( !node.isExternal() && !node.isRoot() ) {
687 final boolean collapse = !node.isCollapse();
688 Util.collapseSubtree( node, collapse );
689 _phylogeny.recalculateNumberOfExternalDescendants( true );
690 resetNodeIdToDistToLeafMap();
691 calculateLongestExtNodeInfo();
692 resetPreferredSize();
694 _main_panel.adjustJScrollPane();
699 final void collapseSpeciesSpecificSubtrees() {
700 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
704 Util.collapseSpeciesSpecificSubtrees( _phylogeny );
705 _phylogeny.recalculateNumberOfExternalDescendants( true );
706 resetNodeIdToDistToLeafMap();
707 calculateLongestExtNodeInfo();
708 resetPreferredSize();
709 _main_panel.adjustJScrollPane();
714 final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
715 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
716 JOptionPane.showMessageDialog( this,
717 "Cannot colorize subtree in unrooted display type",
718 "Attempt to colorize subtree in unrooted display",
719 JOptionPane.WARNING_MESSAGE );
722 _control_panel.setColorBranches( true );
723 if ( _control_panel.getColorBranchesCb() != null ) {
724 _control_panel.getColorBranchesCb().setSelected( true );
726 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
727 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
732 final private void colorSubtree( final PhylogenyNode node ) {
733 Color intitial_color = null;
734 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
735 && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
736 intitial_color = PhylogenyMethods.getBranchColorValue( node );
739 intitial_color = getTreeColorSet().getBranchColor();
741 _color_chooser.setColor( intitial_color );
742 _color_chooser.setPreviewPanel( new JPanel() );
743 final JDialog dialog = JColorChooser
745 "Subtree colorization",
748 new SubtreeColorizationActionListener( _color_chooser, node ),
750 dialog.setVisible( true );
753 final void confColor() {
754 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
758 Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
759 _control_panel.setColorBranches( true );
760 if ( _control_panel.getColorBranchesCb() != null ) {
761 _control_panel.getColorBranchesCb().setSelected( true );
767 final private void copySubtree( final PhylogenyNode node ) {
768 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
769 errorMessageNoCutCopyPasteInUnrootedDisplay();
772 setCutOrCopiedTree( _phylogeny.copy( node ) );
773 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
774 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
775 for( final PhylogenyNode n : nodes ) {
776 node_ids.add( n.getId() );
778 node_ids.add( node.getId() );
779 setCopiedAndPastedNodes( node_ids );
783 final private void cutSubtree( final PhylogenyNode node ) {
784 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
785 errorMessageNoCutCopyPasteInUnrootedDisplay();
788 if ( node.isRoot() ) {
789 JOptionPane.showMessageDialog( this,
790 "Cannot cut entire tree as subtree",
791 "Attempt to cut entire tree",
792 JOptionPane.ERROR_MESSAGE );
795 final String label = getASimpleTextRepresentationOfANode( node );
796 final int r = JOptionPane.showConfirmDialog( null,
797 "Cut subtree" + label + "?",
798 "Confirm Cutting of Subtree",
799 JOptionPane.YES_NO_OPTION );
800 if ( r != JOptionPane.OK_OPTION ) {
803 setCopiedAndPastedNodes( null );
804 setCutOrCopiedTree( _phylogeny.copy( node ) );
805 _phylogeny.deleteSubtree( node, true );
806 _phylogeny.hashIDs();
807 _phylogeny.recalculateNumberOfExternalDescendants( true );
808 resetNodeIdToDistToLeafMap();
813 final private void cycleColors() {
814 getMainPanel().getTreeColorSet().cycleColorScheme();
815 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
816 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
820 final void decreaseDomainStructureEvalueThreshold() {
821 if ( _domain_structure_e_value_thr_exp > -20 ) {
822 _domain_structure_e_value_thr_exp -= 1;
826 final private void decreaseOvSize() {
827 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
828 setOvMaxWidth( getOvMaxWidth() - 5 );
829 setOvMaxHeight( getOvMaxHeight() - 5 );
831 getControlPanel().displayedPhylogenyMightHaveChanged( false );
835 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
836 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
837 errorMessageNoCutCopyPasteInUnrootedDisplay();
840 if ( node.isRoot() ) {
841 JOptionPane.showMessageDialog( this,
842 "Cannot delete entire tree",
843 "Attempt to delete entire tree",
844 JOptionPane.ERROR_MESSAGE );
847 final String label = getASimpleTextRepresentationOfANode( node );
848 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
849 final int r = JOptionPane.showOptionDialog( this,
850 "Delete" + label + "?",
851 "Delete Node/Subtree",
852 JOptionPane.CLOSED_OPTION,
853 JOptionPane.QUESTION_MESSAGE,
857 boolean node_only = true;
865 PhylogenyMethods.removeNode( node, _phylogeny );
868 _phylogeny.deleteSubtree( node, true );
870 _phylogeny.externalNodesHaveChanged();
871 _phylogeny.hashIDs();
872 _phylogeny.recalculateNumberOfExternalDescendants( true );
873 resetNodeIdToDistToLeafMap();
878 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
879 makePopupMenus( node );
880 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
881 _node_popup_menu.show( this, x, y );
884 final private void drawArc( final double x,
888 final double start_angle,
889 final double arc_angle,
890 final Graphics2D g ) {
891 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
895 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
896 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
899 _line.setLine( x1, y1, x2, y2 );
903 final private void drawOval( final double x,
907 final Graphics2D g ) {
908 _ellipse.setFrame( x, y, width, heigth );
912 final private void drawOvalFilled( final double x,
916 final Graphics2D g ) {
917 _ellipse.setFrame( x, y, width, heigth );
921 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
922 _rectangle.setFrame( x, y, width, heigth );
923 g.draw( _rectangle );
926 final private void drawRectFilled( final double x,
930 final Graphics2D g ) {
931 _rectangle.setFrame( x, y, width, heigth );
932 g.fill( _rectangle );
935 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
936 JOptionPane.showMessageDialog( this,
937 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
938 "Attempt to cut/copy/paste/add/delete in unrooted display",
939 JOptionPane.ERROR_MESSAGE );
943 * Find the node, if any, at the given location
947 * @return pointer to the node at x,y, null if not found
949 final PhylogenyNode findNode( final int x, final int y ) {
950 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
953 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
954 final PhylogenyNode node = iter.next();
955 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
956 && ( ( node.getXcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= x )
957 && ( ( node.getXcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= x )
958 && ( ( node.getYcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= y )
959 && ( ( node.getYcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= y ) ) {
966 final private String getASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
967 final String tax = PhylogenyMethods.getSpecies( node );
968 String label = node.getName();
969 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
970 label = label + " " + tax;
972 else if ( !ForesterUtil.isEmpty( tax ) ) {
978 if ( !ForesterUtil.isEmpty( label ) ) {
979 label = " [" + label + "]";
984 final Configuration getConfiguration() {
985 return _configuration;
988 final ControlPanel getControlPanel() {
989 return _control_panel;
992 final private Set<Integer> getCopiedAndPastedNodes() {
993 return getMainPanel().getCopiedAndPastedNodes();
996 final private Phylogeny getCutOrCopiedTree() {
997 return getMainPanel().getCutOrCopiedTree();
1000 final int getDomainStructureEvalueThreshold() {
1001 return _domain_structure_e_value_thr_exp;
1004 final Set<Integer> getFoundNodes() {
1005 return _found_nodes;
1008 final private float getLastDragPointX() {
1009 return _last_drag_point_x;
1012 final private float getLastDragPointY() {
1013 return _last_drag_point_y;
1016 final int getLongestExtNodeInfo() {
1017 return _longest_ext_node_info;
1020 final public MainPanel getMainPanel() {
1024 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
1025 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
1026 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
1027 _nodeid_dist_to_leaf.put( node.getId(), m );
1031 return _nodeid_dist_to_leaf.get( node.getId() );
1035 final private double getMaxDistanceToRoot() {
1036 if ( _max_distance_to_root < 0 ) {
1037 recalculateMaxDistanceToRoot();
1039 return _max_distance_to_root;
1042 final Options getOptions() {
1043 if ( _options == null ) {
1044 _options = getControlPanel().getOptions();
1049 final private float getOvMaxHeight() {
1050 return _ov_max_height;
1053 final private float getOvMaxWidth() {
1054 return _ov_max_width;
1057 final Rectangle2D getOvRectangle() {
1058 return _ov_rectangle;
1061 final Rectangle getOvVirtualRectangle() {
1062 return _ov_virtual_rectangle;
1065 final private float getOvXcorrectionFactor() {
1066 return _ov_x_correction_factor;
1069 final private float getOvXDistance() {
1070 return _ov_x_distance;
1073 final private int getOvXPosition() {
1074 return _ov_x_position;
1077 final private float getOvYDistance() {
1078 return _ov_y_distance;
1081 final private int getOvYPosition() {
1082 return _ov_y_position;
1085 final private int getOvYStart() {
1090 * Get a pointer to the phylogeny
1092 * @return a pointer to the phylogeny
1094 final Phylogeny getPhylogeny() {
1098 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
1099 return _graphics_type;
1102 final private double getScaleDistance() {
1103 return _scale_distance;
1106 final private String getScaleLabel() {
1107 return _scale_label;
1110 final double getStartingAngle() {
1111 return _urt_starting_angle;
1115 * Find a color for this species name.
1118 * @return the species color
1120 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
1121 if ( node.getNodeData().isHasTaxonomy() ) {
1122 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
1124 // return non-colorized color
1125 return getTreeColorSet().getTaxonomyColor();
1129 * @return pointer to colorset for tree drawing
1131 final TreeColorSet getTreeColorSet() {
1132 return getMainPanel().getTreeColorSet();
1135 final File getTreeFile() {
1139 final private TreeFontSet getTreeFontSet() {
1140 return getMainPanel().getTreeFontSet();
1143 final private float getUrtFactor() {
1147 final private float getUrtFactorOv() {
1148 return _urt_factor_ov;
1151 final float getXcorrectionFactor() {
1152 return _x_correction_factor;
1155 final float getXdistance() {
1159 final float getYdistance() {
1163 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
1166 showNodeFrame( node );
1181 colorSubtree( node );
1196 copySubtree( node );
1199 pasteSubtree( node );
1201 case DELETE_NODE_OR_SUBTREE:
1202 deleteNodeOrSubtree( node );
1205 addEmptyNode( node );
1207 case EDIT_NODE_DATA:
1208 showNodeEditFrame( node );
1211 throw new IllegalArgumentException( "unknown action: " + action );
1215 final void increaseDomainStructureEvalueThreshold() {
1216 if ( _domain_structure_e_value_thr_exp < 3 ) {
1217 _domain_structure_e_value_thr_exp += 1;
1221 final private void increaseOvSize() {
1222 if ( ( getOvMaxWidth() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 )
1223 && ( getOvMaxHeight() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
1224 .getHeight() / 2 ) ) {
1225 setOvMaxWidth( getOvMaxWidth() + 5 );
1226 setOvMaxHeight( getOvMaxHeight() + 5 );
1228 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1232 final void inferCommonPartOfScientificNames() {
1233 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1237 Util.inferCommonPartOfScientificNames( _phylogeny );
1242 final private void init() {
1243 _color_chooser = new JColorChooser();
1244 _rollover_popup = new JTextArea();
1245 _rollover_popup.setFont( POPUP_FONT );
1246 resetNodeIdToDistToLeafMap();
1248 setTreeFile( null );
1250 initializeOvSettings();
1251 setStartingAngle( TWO_PI * 3 / 4 );
1252 final ImageLoader il = new ImageLoader( this );
1253 new Thread( il ).start();
1256 final private void initializeOvSettings() {
1257 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
1258 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
1261 final void initNodeData() {
1262 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1265 double max_original_domain_structure_width = 0.0;
1266 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1267 if ( node.getNodeData().isHasSequence()
1268 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1269 RenderableDomainArchitecture rds = null;
1270 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
1271 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1272 getConfiguration() );
1273 node.getNodeData().getSequence().setDomainArchitecture( rds );
1276 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1278 if ( getControlPanel().isShowDomainArchitectures() ) {
1279 final double dsw = rds.getOriginalSize().getWidth();
1280 if ( dsw > max_original_domain_structure_width ) {
1281 max_original_domain_structure_width = dsw;
1286 if ( getControlPanel().isShowDomainArchitectures() ) {
1287 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1288 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1289 if ( node.getNodeData().isHasSequence()
1290 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1291 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1292 .getSequence().getDomainArchitecture();
1293 rds.setRenderingFactorWidth( ds_factor_width );
1294 rds.setParameter( _domain_structure_e_value_thr_exp );
1300 final boolean inOv( final MouseEvent e ) {
1301 return ( ( e.getX() > getVisibleRect().x + getOvXPosition() + 1 )
1302 && ( e.getX() < getVisibleRect().x + getOvXPosition() + getOvMaxWidth() - 1 )
1303 && ( e.getY() > getVisibleRect().y + getOvYPosition() + 1 ) && ( e.getY() < getVisibleRect().y
1304 + getOvYPosition() + getOvMaxHeight() - 1 ) );
1307 final boolean inOvRectangle( final MouseEvent e ) {
1308 return ( ( e.getX() >= getOvRectangle().getX() - 1 )
1309 && ( e.getX() <= getOvRectangle().getX() + getOvRectangle().getWidth() + 1 )
1310 && ( e.getY() >= getOvRectangle().getY() - 1 ) && ( e.getY() <= getOvRectangle().getY()
1311 + getOvRectangle().getHeight() + 1 ) );
1314 final private boolean inOvVirtualRectangle( final int x, final int y ) {
1315 return ( ( x >= getOvVirtualRectangle().x - 1 )
1316 && ( x <= getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 )
1317 && ( y >= getOvVirtualRectangle().y - 1 ) && ( y <= getOvVirtualRectangle().y
1318 + getOvVirtualRectangle().height + 1 ) );
1321 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
1322 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
1325 final boolean isApplet() {
1326 return getMainPanel() instanceof MainPanelApplets;
1329 final private boolean isCanBlast( final PhylogenyNode node ) {
1330 return ( node.getNodeData().isHasSequence() && ( ( ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil
1331 .isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) )
1332 || !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) || !ForesterUtil.isEmpty( node
1333 .getNodeData().getSequence().getSymbol() ) ) );
1336 final boolean isCanCollapse() {
1337 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1340 final boolean isCanColorSubtree() {
1341 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1344 final boolean isCanCopy() {
1345 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1348 final boolean isCanCut( final PhylogenyNode node ) {
1349 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1353 final boolean isCanDelete() {
1354 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1357 final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
1358 if ( node.getNodeData().isHasSequence()
1359 && ( node.getNodeData().getSequence().getAccession() != null )
1360 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
1361 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
1362 && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
1363 .toLowerCase() ) ) {
1369 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
1370 if ( node.getNodeData().isHasTaxonomy()
1371 && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
1372 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
1373 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
1374 .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
1375 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
1376 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
1377 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
1378 .getNodeData().getTaxonomy().getIdentifier() != null )
1379 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
1380 .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
1388 final boolean isCanPaste() {
1389 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1390 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1393 final boolean isCanReroot() {
1394 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1397 final boolean isCanSubtree( final PhylogenyNode node ) {
1398 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1399 .isRoot() || ( _subtree_index > 0 ) ) );
1402 final boolean isEdited() {
1406 final private boolean isInFoundNodes( final PhylogenyNode node ) {
1407 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
1410 final private boolean isInOv() {
1414 final boolean isInOvRect() {
1418 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
1420 if ( getControlPanel().isShowTaxonomyImages() ) {
1421 y_dist = 40 + ( int ) getYdistance();
1423 return ( ( node.getYcoord() < getVisibleRect().getMinY() - y_dist )
1424 || ( node.getYcoord() > getVisibleRect().getMaxY() + y_dist ) || ( ( node.getParent() != null ) && ( node
1425 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
1428 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
1429 return ( ( node.getYcoord() < getVisibleRect().getMinY() - 20 )
1430 || ( node.getYcoord() > getVisibleRect().getMaxY() + 20 )
1431 || ( node.getXcoord() < getVisibleRect().getMinX() - 20 ) || ( node.getXcoord() > getVisibleRect()
1432 .getMaxX() + 20 ) );
1435 final private boolean isNonLinedUpCladogram() {
1436 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
1439 final boolean isOvOn() {
1443 final boolean isPhyHasBranchLengths() {
1444 return _phy_has_branch_lengths;
1447 final private boolean isUniformBranchLengthsForCladogram() {
1448 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
1451 final private void keyPressedCalls( final KeyEvent e ) {
1452 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
1453 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
1454 if ( !isInOvRect() ) {
1455 setInOvRect( true );
1458 else if ( isInOvRect() ) {
1459 setInOvRect( false );
1462 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
1463 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
1464 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
1465 getMainPanel().getTreeFontSet().mediumFonts();
1466 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1468 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
1469 getMainPanel().getTreeFontSet().decreaseFontSize();
1470 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1472 else if ( plusPressed( e.getKeyCode() ) ) {
1473 getMainPanel().getTreeFontSet().increaseFontSize();
1474 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1478 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
1479 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
1480 getControlPanel().showWhole();
1482 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
1483 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
1484 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
1485 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
1486 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1487 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1489 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
1490 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1491 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1493 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
1494 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
1495 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1496 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1498 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
1499 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
1500 Constants.WHEEL_ZOOM_IN_FACTOR );
1501 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1508 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
1511 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
1515 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
1519 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1520 scroll_position.x = scroll_position.x + dx;
1521 scroll_position.y = scroll_position.y + dy;
1522 if ( scroll_position.x <= 0 ) {
1523 scroll_position.x = 0;
1526 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1527 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1528 if ( scroll_position.x >= max_x ) {
1529 scroll_position.x = max_x;
1532 if ( scroll_position.y <= 0 ) {
1533 scroll_position.y = 0;
1536 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1537 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1538 if ( scroll_position.y >= max_y ) {
1539 scroll_position.y = max_y;
1543 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1546 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
1547 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1548 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
1549 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1550 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1552 else if ( plusPressed( e.getKeyCode() ) ) {
1553 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
1554 Constants.WHEEL_ZOOM_IN_FACTOR );
1555 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1556 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1558 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
1559 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1560 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1561 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
1562 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1565 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
1566 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1567 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1568 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
1569 if ( getStartingAngle() < 0 ) {
1570 setStartingAngle( TWO_PI + getStartingAngle() );
1572 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1575 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
1576 boolean selected = false;
1577 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
1578 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1582 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1584 if ( getMainPanel().getMainFrame() == null ) {
1585 // Must be "E" applet version.
1586 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1587 if ( ae.getlabelDirectionCbmi() != null ) {
1588 ae.getlabelDirectionCbmi().setSelected( selected );
1592 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
1596 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
1597 switchDisplaygetPhylogenyGraphicsType();
1600 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
1604 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
1605 MainFrame.cycleOverview( getOptions(), this );
1608 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
1611 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
1618 final private void makePopupMenus( final PhylogenyNode node ) {
1619 _node_popup_menu = new JPopupMenu();
1620 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
1621 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
1622 for( int i = 0; i < clickto_names.size(); i++ ) {
1623 final String title = clickto_names.get( i );
1624 _node_popup_menu_items[ i ] = new JMenuItem( title );
1625 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
1626 _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
1628 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
1629 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
1631 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
1632 if ( Constants.__RELEASE || Constants.__SNAPSHOT_RELEASE ) {
1635 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
1637 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
1638 if ( !getOptions().isEditable() ) {
1641 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
1643 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
1644 if ( !getOptions().isEditable() ) {
1647 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
1649 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
1650 if ( !getOptions().isEditable() ) {
1653 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
1655 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
1656 if ( !getOptions().isEditable() ) {
1659 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
1661 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
1662 if ( !getOptions().isEditable() ) {
1666 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
1667 if ( !getOptions().isEditable() ) {
1671 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
1672 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
1674 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
1675 _node_popup_menu_items[ i ].setEnabled( isCanCollapse() );
1677 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
1678 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
1680 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
1681 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
1683 _node_popup_menu_items[ i ].addActionListener( this );
1684 _node_popup_menu.add( _node_popup_menu_items[ i ] );
1688 final void midpointRoot() {
1689 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1692 if ( !_phylogeny.isRerootable() ) {
1693 JOptionPane.showMessageDialog( this,
1694 "This is not rerootable",
1696 JOptionPane.WARNING_MESSAGE );
1700 PhylogenyMethods.midpointRoot( _phylogeny );
1701 resetNodeIdToDistToLeafMap();
1706 final void mouseClicked( final MouseEvent e ) {
1707 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1708 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1709 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1710 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - getOvRectangle().getWidth() / 2.0 )
1712 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - getOvRectangle().getHeight() / 2.0 )
1720 final double max_x = getWidth() - getVisibleRect().width;
1721 final double max_y = getHeight() - getVisibleRect().height;
1728 getMainPanel().getCurrentScrollPane().getViewport()
1729 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1730 setInOvRect( true );
1734 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1735 if ( node != null ) {
1736 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1739 _highlight_node = node;
1740 // Check if shift key is down
1741 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1742 // Yes, so add to _found_nodes
1743 if ( getFoundNodes() == null ) {
1744 setFoundNodes( new HashSet<Integer>() );
1746 getFoundNodes().add( node.getId() );
1747 // Check if control key is down
1749 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1750 // Yes, so pop-up menu
1751 displayNodePopupMenu( node, e.getX(), e.getY() );
1752 // Handle unadorned click
1755 // Check for right mouse button
1756 if ( e.getModifiers() == 4 ) {
1757 displayNodePopupMenu( node, e.getX(), e.getY() );
1760 // if not in _found_nodes, clear _found_nodes
1761 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1766 // no node was clicked
1767 _highlight_node = null;
1773 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1774 setCursor( MOVE_CURSOR );
1775 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1776 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1777 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1778 if ( scroll_position.x < 0 ) {
1779 scroll_position.x = 0;
1782 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1783 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1784 if ( scroll_position.x > max_x ) {
1785 scroll_position.x = max_x;
1788 if ( scroll_position.y < 0 ) {
1789 scroll_position.y = 0;
1792 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1793 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1794 if ( scroll_position.y > max_y ) {
1795 scroll_position.y = max_y;
1798 if ( isOvOn() || getOptions().isShowScale() ) {
1801 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1804 final void mouseDragInOvRectangle( final MouseEvent e ) {
1805 setCursor( HAND_CURSOR );
1806 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1807 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1808 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1809 double dx = ( w_ratio * e.getX() - w_ratio * getLastDragPointX() );
1810 double dy = ( h_ratio * e.getY() - h_ratio * getLastDragPointY() );
1811 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1812 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1813 if ( scroll_position.x <= 0 ) {
1814 scroll_position.x = 0;
1818 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1819 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1820 if ( scroll_position.x >= max_x ) {
1822 scroll_position.x = max_x;
1825 if ( scroll_position.y <= 0 ) {
1827 scroll_position.y = 0;
1830 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1831 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1832 if ( scroll_position.y >= max_y ) {
1834 scroll_position.y = max_y;
1838 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1839 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1840 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1843 final void mouseMoved( final MouseEvent e ) {
1844 requestFocusInWindow();
1845 if ( getControlPanel().isNodeDescPopup() ) {
1846 if ( _node_desc_popup != null ) {
1847 _node_desc_popup.hide();
1848 _node_desc_popup = null;
1851 if ( getOptions().isShowOverview() && isOvOn() ) {
1852 if ( inOvVirtualRectangle( e ) ) {
1853 if ( !isInOvRect() ) {
1854 setInOvRect( true );
1859 if ( isInOvRect() ) {
1860 setInOvRect( false );
1865 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
1874 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1875 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
1876 // cursor is over a tree node
1877 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
1878 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
1879 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
1880 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
1881 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
1882 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
1883 setCursor( CUT_CURSOR );
1886 setCursor( HAND_CURSOR );
1887 if ( getControlPanel().isNodeDescPopup() ) {
1888 showNodeDataPopup( e, node );
1893 setCursor( ARROW_CURSOR );
1898 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
1899 setCursor( ARROW_CURSOR );
1902 final public void mouseWheelMoved( final MouseWheelEvent e ) {
1903 final int notches = e.getWheelRotation();
1904 if ( inOvVirtualRectangle( e ) ) {
1905 if ( !isInOvRect() ) {
1906 setInOvRect( true );
1911 if ( isInOvRect() ) {
1912 setInOvRect( false );
1916 if ( e.isControlDown() ) {
1917 if ( notches < 0 ) {
1918 getTreeFontSet().increaseFontSize();
1919 getControlPanel().displayedPhylogenyMightHaveChanged( true );
1922 getTreeFontSet().decreaseFontSize();
1923 getControlPanel().displayedPhylogenyMightHaveChanged( true );
1926 else if ( e.isShiftDown() ) {
1927 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1928 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1929 if ( notches < 0 ) {
1930 for( int i = 0; i < ( -notches ); ++i ) {
1931 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
1932 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1936 for( int i = 0; i < notches; ++i ) {
1937 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
1938 if ( getStartingAngle() < 0 ) {
1939 setStartingAngle( TWO_PI + getStartingAngle() );
1941 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1946 if ( notches < 0 ) {
1947 for( int i = 0; i < ( -notches ); ++i ) {
1948 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1949 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1953 for( int i = 0; i < notches; ++i ) {
1954 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1955 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1961 if ( notches < 0 ) {
1962 for( int i = 0; i < ( -notches ); ++i ) {
1963 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
1964 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
1965 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1966 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1970 for( int i = 0; i < notches; ++i ) {
1971 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1972 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
1973 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1974 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1979 requestFocusInWindow();
1983 final void multiplyUrtFactor( final float f ) {
1987 final JApplet obtainApplet() {
1988 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1991 final private void openSeqWeb( final PhylogenyNode node ) {
1992 if ( !isCanOpenSeqWeb( node ) ) {
1993 cannotOpenBrowserWarningMessage( "sequence" );
1996 String uri_str = null;
1997 final Sequence seq = node.getNodeData().getSequence();
1998 final String source = seq.getAccession().getSource().toLowerCase();
2000 if ( source.toLowerCase().equals( "ncbi" ) ) {
2001 url = Constants.NCBI_ALL_DATABASE_SEARCH;
2004 final WebLink weblink = getConfiguration().getWebLink( source );
2005 url = weblink.getUrl().toString();
2008 uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
2010 catch ( final UnsupportedEncodingException e ) {
2011 Util.showErrorMessage( this, e.toString() );
2012 e.printStackTrace();
2014 if ( !ForesterUtil.isEmpty( uri_str ) ) {
2016 JApplet applet = null;
2018 applet = obtainApplet();
2020 Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
2022 catch ( final IOException e ) {
2023 Util.showErrorMessage( this, e.toString() );
2024 e.printStackTrace();
2026 catch ( final URISyntaxException e ) {
2027 Util.showErrorMessage( this, e.toString() );
2028 e.printStackTrace();
2032 cannotOpenBrowserWarningMessage( "sequence" );
2036 final private void openTaxWeb( final PhylogenyNode node ) {
2037 if ( !isCanOpenTaxWeb( node ) ) {
2038 cannotOpenBrowserWarningMessage( "taxonomic" );
2041 String uri_str = null;
2042 final Taxonomy tax = node.getNodeData().getTaxonomy();
2043 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
2044 && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
2045 final String type = tax.getIdentifier().getProvider().toLowerCase();
2046 final WebLink weblink = getConfiguration().getWebLink( type );
2048 uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
2050 catch ( final UnsupportedEncodingException e ) {
2051 Util.showErrorMessage( this, e.toString() );
2052 e.printStackTrace();
2055 else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
2056 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
2058 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
2060 catch ( final URISyntaxException e ) {
2061 Util.showErrorMessage( this, e.toString() );
2063 e.printStackTrace();
2066 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
2068 uri_str = "http://www.eol.org/search?q="
2069 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
2071 catch ( final UnsupportedEncodingException e ) {
2072 Util.showErrorMessage( this, e.toString() );
2073 e.printStackTrace();
2076 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
2078 uri_str = "http://www.uniprot.org/taxonomy/?query="
2079 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
2081 catch ( final UnsupportedEncodingException e ) {
2082 Util.showErrorMessage( this, e.toString() );
2083 e.printStackTrace();
2086 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
2088 uri_str = "http://www.eol.org/search?q="
2089 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
2091 catch ( final UnsupportedEncodingException e ) {
2092 Util.showErrorMessage( this, e.toString() );
2093 e.printStackTrace();
2096 if ( !ForesterUtil.isEmpty( uri_str ) ) {
2098 JApplet applet = null;
2100 applet = obtainApplet();
2102 Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
2104 catch ( final IOException e ) {
2105 Util.showErrorMessage( this, e.toString() );
2106 e.printStackTrace();
2108 catch ( final URISyntaxException e ) {
2109 Util.showErrorMessage( this, e.toString() );
2110 e.printStackTrace();
2114 cannotOpenBrowserWarningMessage( "taxonomic" );
2118 final void paintBranchCircular( final PhylogenyNode p,
2119 final PhylogenyNode c,
2121 final boolean radial_labels,
2122 final boolean to_pdf,
2123 final boolean to_graphics_file ) {
2124 final double angle = _urt_nodeid_angle_map.get( c.getId() );
2125 final double root_x = _root.getXcoord();
2126 final double root_y = _root.getYcoord();
2127 final double dx = root_x - p.getXcoord();
2128 final double dy = root_y - p.getYcoord();
2129 final double parent_radius = Math.sqrt( dx * dx + dy * dy );
2130 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
2131 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
2132 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
2133 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
2134 final double r2 = 2.0 * parent_radius;
2135 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
2137 drawLine( c.getXcoord(),
2139 root_x + ( Math.cos( angle ) * parent_radius ),
2140 root_y + ( Math.sin( angle ) * parent_radius ),
2142 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c ) );
2143 if ( c.isExternal() ) {
2144 final boolean is_in_found_nodes = isInFoundNodes( c );
2145 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
2146 && ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor != 1 ) ) {
2149 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
2153 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
2154 final double angle = _urt_nodeid_angle_map.get( c.getId() );
2155 final double root_x = _root.getXSecondary();
2156 final double root_y = _root.getYSecondary();
2157 final double dx = root_x - p.getXSecondary();
2158 final double dy = root_y - p.getYSecondary();
2159 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
2160 final double parent_radius = Math.sqrt( dx * dx + dy * dy );
2161 g.setColor( getTreeColorSet().getOvColor() );
2162 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
2163 final double r2 = 2.0 * parent_radius;
2164 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
2166 drawLine( c.getXSecondary(),
2168 root_x + ( Math.cos( angle ) * parent_radius ),
2169 root_y + ( Math.sin( angle ) * parent_radius ),
2171 if ( isInFoundNodes( c ) ) {
2172 g.setColor( getTreeColorSet().getFoundColor() );
2173 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
2177 final private void paintBranchLength( final Graphics2D g,
2178 final PhylogenyNode node,
2179 final boolean to_pdf,
2180 final boolean to_graphics_file ) {
2181 g.setFont( getTreeFontSet().getSmallFont() );
2182 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2183 g.setColor( Color.BLACK );
2186 g.setColor( getTreeColorSet().getBranchLengthColor() );
2188 if ( !node.isRoot() ) {
2189 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2190 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2191 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
2193 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2194 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2195 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
2198 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2199 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
2203 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
2204 - getTreeFontSet()._small_max_descent, g );
2208 final private void paintBranchLite( final Graphics2D g,
2213 final PhylogenyNode node ) {
2214 g.setColor( getTreeColorSet().getOvColor() );
2215 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
2216 drawLine( x1, y1, x2, y2, g );
2218 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
2219 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
2220 ( g ).draw( _quad_curve );
2222 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
2223 final float dx = x2 - x1;
2224 final float dy = y2 - y1;
2225 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
2226 + ( dy * 0.8f ), x2, y2 );
2227 ( g ).draw( _cubic_curve );
2230 final float x2a = x2;
2231 final float x1a = x1;
2232 // draw the vertical line
2233 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
2234 drawLine( x1, y1, x1, y2, g );
2236 // draw the horizontal line
2237 drawLine( x1a, y2, x2a, y2, g );
2242 * Paint a branch which consists of a vertical and a horizontal bar
2243 * @param is_ind_found_nodes
2245 final private void paintBranchRectangular( final Graphics2D g,
2250 final PhylogenyNode node,
2251 final boolean to_pdf,
2252 final boolean to_graphics_file ) {
2253 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
2254 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
2255 drawLine( x1, y1, x2, y2, g );
2257 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
2258 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
2259 g.draw( _quad_curve );
2261 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
2262 final float dx = x2 - x1;
2263 final float dy = y2 - y1;
2264 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
2265 + ( dy * 0.8f ), x2, y2 );
2266 g.draw( _cubic_curve );
2271 // draw the vertical line
2272 boolean draw_horizontal = true;
2274 if ( node.isFirstChildNode() || node.isLastChildNode()
2275 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
2276 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2277 boolean draw_vertical = true;
2278 final PhylogenyNode parent = node.getParent();
2279 if ( ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file ) || ( ( getControlPanel()
2280 .isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) )
2281 && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) )
2282 && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent
2283 .isDuplication() ) ) {
2284 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
2285 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2286 if ( Math.abs( y2 - y1 ) <= TreePanel.HALF_BOX_SIZE ) {
2287 draw_vertical = false;
2291 y1 += TreePanel.HALF_BOX_SIZE;
2295 y1 -= TreePanel.HALF_BOX_SIZE + 1;
2298 y1 -= TreePanel.HALF_BOX_SIZE;
2303 if ( ( x2 - x1 ) <= TreePanel.HALF_BOX_SIZE ) {
2304 draw_horizontal = false;
2306 else if ( !draw_vertical ) {
2307 x1a += TreePanel.HALF_BOX_SIZE;
2309 if ( ( ( x2 - x1a ) > TreePanel.HALF_BOX_SIZE )
2310 && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node
2311 .isDuplication() ) ) {
2312 x2a -= TreePanel.HALF_BOX_SIZE;
2315 if ( draw_vertical ) {
2316 if ( !to_graphics_file
2318 && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
2319 .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
2323 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2324 float x2c = x1 + EURO_D;
2328 drawLine( x1, y1, x2c, y2, g );
2330 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2332 y2_r = y2 - ROUNDED_D;
2336 drawLine( x1, y1, x1, y2_r, g );
2339 y2_r = y2 + ROUNDED_D;
2343 drawLine( x1, y1, x1, y2_r, g );
2347 drawLine( x1, y1, x1, y2, g );
2352 // draw the horizontal line
2353 if ( !to_graphics_file && !to_pdf
2354 && ( ( y2 < getVisibleRect().getMinY() - 20 ) || ( y2 > getVisibleRect().getMaxY() + 20 ) ) ) {
2358 if ( draw_horizontal ) {
2359 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
2360 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2361 x1_r = x1a + ROUNDED_D;
2363 drawLine( x1_r, y2, x2a, y2, g );
2366 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2367 final float x1c = x1a + EURO_D;
2369 drawLine( x1c, y2, x2a, y2, g );
2373 drawLine( x1a, y2, x2a, y2, g );
2377 final double w = PhylogenyMethods.getBranchWidthValue( node );
2378 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2379 x1_r = x1a + ROUNDED_D;
2381 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
2384 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2385 final float x1c = x1a + EURO_D;
2387 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
2391 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
2395 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2400 final double diff = y2 - y2_r;
2401 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
2404 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
2409 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
2412 final void paintCircular( final Phylogeny phy,
2413 final double starting_angle,
2418 final boolean to_pdf,
2419 final boolean to_graphics_file ) {
2420 _circ_num_ext_nodes = phy.getNumberOfExternalNodes();
2421 _root = phy.getRoot();
2422 _root.setXcoord( center_x );
2423 _root.setYcoord( center_y );
2424 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
2425 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
2426 double current_angle = starting_angle;
2428 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2429 final PhylogenyNode n = it.next();
2430 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
2431 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
2432 _urt_nodeid_angle_map.put( n.getId(), current_angle );
2433 _urt_nodeid_index_map.put( n.getId(), i++ );
2434 current_angle += ( TWO_PI / _circ_num_ext_nodes );
2436 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
2439 final void paintCircularLite( final Phylogeny phy,
2440 final double starting_angle,
2444 final Graphics2D g ) {
2445 _circ_num_ext_nodes = phy.getNumberOfExternalNodes();
2446 _root = phy.getRoot();
2447 _root.setXSecondary( center_x );
2448 _root.setYSecondary( center_y );
2449 double current_angle = starting_angle;
2450 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2451 final PhylogenyNode n = it.next();
2452 n.setXSecondary( ( float ) ( center_x + radius * Math.cos( current_angle ) ) );
2453 n.setYSecondary( ( float ) ( center_y + radius * Math.sin( current_angle ) ) );
2454 _urt_nodeid_angle_map.put( n.getId(), current_angle );
2455 current_angle += ( TWO_PI / _circ_num_ext_nodes );
2457 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
2460 final private double paintCirculars( final PhylogenyNode n,
2461 final Phylogeny phy,
2462 final float center_x,
2463 final float center_y,
2464 final double radius,
2465 final boolean radial_labels,
2467 final boolean to_pdf,
2468 final boolean to_graphics_file ) {
2469 if ( n.isExternal() ) {
2470 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
2471 System.out.println( "no " + n + ", fucker!" );//TODO
2473 return _urt_nodeid_angle_map.get( n.getId() );
2476 final List<PhylogenyNode> descs = n.getDescendants();
2478 for( final PhylogenyNode desc : descs ) {
2479 sum += paintCirculars( desc,
2490 if ( !n.isRoot() ) {
2491 r = 1 - ( ( ( double ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
2493 final double theta = sum / descs.size();
2494 n.setXcoord( ( float ) ( center_x + r * radius * Math.cos( theta ) ) );
2495 n.setYcoord( ( float ) ( center_y + r * radius * Math.sin( theta ) ) );
2496 _urt_nodeid_angle_map.put( n.getId(), theta );
2497 for( final PhylogenyNode desc : descs ) {
2498 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
2504 final private void paintCircularsLite( final PhylogenyNode n,
2505 final Phylogeny phy,
2509 final Graphics2D g ) {
2510 if ( n.isExternal() ) {
2514 final List<PhylogenyNode> descs = n.getDescendants();
2515 for( final PhylogenyNode desc : descs ) {
2516 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
2519 if ( !n.isRoot() ) {
2520 r = 1 - ( ( ( float ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
2522 final double theta = _urt_nodeid_angle_map.get( n.getId() );
2523 n.setXSecondary( ( float ) ( center_x + radius * r * Math.cos( theta ) ) );
2524 n.setYSecondary( ( float ) ( center_y + radius * r * Math.sin( theta ) ) );
2525 for( final PhylogenyNode desc : descs ) {
2526 paintBranchCircularLite( n, desc, g );
2531 final private void paintCollapsedNode( final Graphics2D g,
2532 final PhylogenyNode node,
2533 final boolean to_graphics_file,
2534 final boolean to_pdf,
2535 final boolean is_in_found_nodes ) {
2536 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2537 g.setColor( Color.BLACK );
2539 else if ( is_in_found_nodes ) {
2540 g.setColor( getTreeColorSet().getFoundColor() );
2542 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
2543 g.setColor( getTaxonomyBasedColor( node ) );
2545 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
2546 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2547 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2550 g.setColor( getTreeColorSet().getCollapseFillColor() );
2552 double d = node.getAllExternalDescendants().size();
2554 d = ( 3 * _y_distance ) / 3;
2557 d = ( Math.log10( d ) * _y_distance ) / 2.5;
2559 if ( d < BOX_SIZE ) {
2563 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - TreePanel.BOX_SIZE ),
2564 ForesterUtil.roundToInt( node.getYcoord() ) );
2565 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ),
2566 ForesterUtil.roundToInt( node.getYcoord() - d ) );
2567 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ),
2568 ForesterUtil.roundToInt( node.getYcoord() + d ) );
2569 g.fillPolygon( _polygon );
2570 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
2574 final public void paintComponent( final Graphics g ) {
2575 // Dimension currentSize = getSize();
2576 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
2577 // call the 'java.awt.Component.createImage(...)' method to get an
2579 // offscreenImage = createImage( currentSize.width, currentSize.height );
2580 // offscreenGraphics = offscreenImage.getGraphics();
2581 // offscreenDimension = currentSize;
2583 // super.paintComponent( g ); //why?
2584 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
2585 final Graphics2D g2d = ( Graphics2D ) g;
2586 g2d.setRenderingHints( _rendering_hints );
2587 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
2588 //g.drawImage( offscreenImage, 0, 0, this );
2592 public void update( final Graphics g ) {
2596 final private void paintConfidenceValues( final Graphics2D g,
2597 final PhylogenyNode node,
2598 final boolean to_pdf,
2599 final boolean to_graphics_file ) {
2600 String conf_str = "";
2601 final List<Confidence> confidences = node.getBranchData().getConfidences();
2602 if ( confidences.size() == 1 ) {
2603 final double value = node.getBranchData().getConfidence( 0 ).getValue();
2604 if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
2607 conf_str = FORMATTER_CONFIDENCE.format( value );
2609 else if ( confidences.size() > 1 ) {
2610 boolean one_ok = false;
2611 boolean not_first = false;
2612 Collections.sort( confidences );
2613 final StringBuilder sb = new StringBuilder();
2614 for( final Confidence confidence : confidences ) {
2615 final double value = confidence.getValue();
2616 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
2617 if ( value >= getOptions().getMinConfidenceValue() ) {
2626 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
2627 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
2631 conf_str = sb.toString();
2634 if ( conf_str.length() > 0 ) {
2635 final double parent_x = node.getParent().getXcoord();
2636 double x = node.getXcoord();
2637 g.setFont( getTreeFontSet().getSmallFont() );
2638 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2641 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2644 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2645 g.setColor( Color.BLACK );
2648 g.setColor( getTreeColorSet().getConfidenceColor() );
2651 .drawString( conf_str,
2653 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
2654 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
2659 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
2660 g.setColor( getTreeColorSet().getFoundColor() );
2661 g.fillRect( x - TreePanel.HALF_BOX_SIZE, y - TreePanel.HALF_BOX_SIZE, TreePanel.BOX_SIZE, TreePanel.BOX_SIZE );
2664 final private void paintGainedAndLostCharacters( final Graphics2D g,
2665 final PhylogenyNode node,
2666 final String gained,
2667 final String lost ) {
2668 if ( node.getParent() != null ) {
2669 final double parent_x = node.getParent().getXcoord();
2670 final double x = node.getXcoord();
2671 g.setFont( getTreeFontSet().getLargeFont() );
2672 g.setColor( getTreeColorSet().getGainedCharactersColor() );
2673 if ( Constants.SPECIAL_CUSTOM ) {
2674 g.setColor( Color.BLUE );
2677 .drawString( gained,
2678 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
2679 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
2681 g.setColor( getTreeColorSet().getLostCharactersColor() );
2682 TreePanel.drawString( lost,
2683 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
2684 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
2690 * Draw a box at the indicated node.
2697 final private void paintNodeBox( final double x,
2699 final PhylogenyNode node,
2701 final boolean to_pdf,
2702 final boolean to_graphics_file,
2703 final boolean is_in_found_nodes ) {
2704 if ( node.isCollapse() ) {
2707 // if this node should be highlighted, do so
2708 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
2709 g.setColor( getTreeColorSet().getFoundColor() );
2710 drawOval( x - 8, y - 8, 16, 16, g );
2711 drawOval( x - 9, y - 8, 17, 17, g );
2712 drawOval( x - 9, y - 9, 18, 18, g );
2714 if ( is_in_found_nodes ) {
2715 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
2718 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2719 g.setColor( Color.BLACK );
2721 else if ( getControlPanel().isEvents() && Util.isHasAssignedEvent( node ) ) {
2722 final Event event = node.getNodeData().getEvent();
2723 if ( event.isDuplication() ) {
2724 g.setColor( getTreeColorSet().getDuplicationBoxColor() );
2726 else if ( event.isSpeciation() ) {
2727 g.setColor( getTreeColorSet().getSpecBoxColor() );
2729 else if ( event.isSpeciationOrDuplication() ) {
2730 g.setColor( getTreeColorSet().getDuplicationOrSpeciationColor() );
2734 assignGraphicsForNodeBoxWithColorForParentBranch( node, g );
2736 if ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file )
2737 || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
2738 if ( to_pdf || to_graphics_file ) {
2739 if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) {
2740 drawOvalFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
2744 drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
2750 final private void paintNodeData( final Graphics2D g,
2751 final PhylogenyNode node,
2752 final boolean to_graphics_file,
2753 final boolean to_pdf,
2754 final boolean is_in_found_nodes ) {
2755 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
2758 if ( getOptions().isShowBranchLengthValues()
2759 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
2760 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
2761 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) ) {
2762 paintBranchLength( g, node, to_pdf, to_graphics_file );
2764 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
2768 if ( getControlPanel().isShowTaxonomyImages()
2769 && ( getImageMap() != null )
2770 && !getImageMap().isEmpty()
2771 && node.getNodeData().isHasTaxonomy()
2772 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
2773 .getUris().isEmpty() ) ) {
2774 x += drawTaxonomyImage( node.getXcoord() + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord(), node, g );
2776 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
2777 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
2778 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
2780 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2781 g.setColor( Color.BLACK );
2783 else if ( is_in_found_nodes ) {
2784 g.setColor( getTreeColorSet().getFoundColor() );
2786 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
2787 g.setColor( getTaxonomyBasedColor( node ) );
2789 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
2790 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2791 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2793 else if ( to_pdf ) {
2794 g.setColor( Color.BLACK );
2797 g.setColor( getTreeColorSet().getSequenceColor() );
2800 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
2802 _sb.append( node.getAllExternalDescendants().size() );
2805 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
2806 if ( _sb.length() > 0 ) {
2809 _sb.append( node.getName() );
2811 if ( node.getNodeData().isHasSequence() ) {
2812 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
2813 if ( _sb.length() > 0 ) {
2816 _sb.append( node.getNodeData().getSequence().getSymbol() );
2818 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
2819 if ( _sb.length() > 0 ) {
2822 _sb.append( node.getNodeData().getSequence().getName() );
2824 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
2825 if ( _sb.length() > 0 ) {
2828 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
2829 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
2832 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
2835 g.setFont( getTreeFontSet().getLargeFont() );
2836 if ( is_in_found_nodes ) {
2837 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
2839 double down_shift_factor = 3.0;
2840 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
2841 down_shift_factor = 1;
2843 final double pos_x = node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE;
2844 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
2845 final String sb_str = _sb.toString();
2846 // GUILHEM_BEG ______________
2847 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
2848 && ( _query_sequence != null ) ) {
2849 int nodeTextBoundsWidth = 0;
2850 if ( sb_str.length() > 0 ) {
2851 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
2852 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
2854 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
2855 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
2856 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
2857 g.setColor( getTreeColorSet().getBackgroundColor() );
2861 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
2862 for( final SequenceRelation seqRelation : seqRelations ) {
2863 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
2864 .getRef1().isEqual( _query_sequence ) )
2865 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
2866 .getSelectedItem() );
2867 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
2868 final double linePosX = node.getXcoord() + 2 + TreePanel.HALF_BOX_SIZE;
2869 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
2870 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
2872 if ( sConfidence != null ) {
2873 double confidenceX = pos_x;
2874 if ( sb_str.length() > 0 ) {
2875 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
2876 + CONFIDENCE_LEFT_MARGIN;
2878 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
2879 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
2880 .getBounds().getWidth();
2881 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
2882 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
2885 if ( x + nodeTextBoundsWidth > 0 ) /* we only underline if there is something displayed */
2887 if ( nodeTextBoundsWidth == 0 ) {
2888 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
2891 nodeTextBoundsWidth += 2;
2893 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
2894 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
2901 if ( sb_str.length() > 0 ) {
2902 TreePanel.drawString( sb_str, pos_x, pos_y, g );
2904 // GUILHEM_END _____________
2905 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
2906 // TODO FIXME need to check this one!
2907 //if ( _sb.length() > 0 ) {
2908 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
2909 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
2911 // COMMENTED_OUT_BY_GUILHEM_END ________________
2912 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
2913 && ( node.getNodeData().getSequence().getAnnotations() != null )
2914 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
2915 if ( _sb.length() > 0 ) {
2916 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
2918 final Annotation ann = node.getNodeData().getSequence().getAnnotation( 0 );
2919 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2920 g.setColor( Color.BLACK );
2923 g.setColor( calculateColorForAnnotation( ann ) );
2925 final String ann_str = ann.asSimpleText().toString();
2926 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
2927 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
2929 _sb.append( ann_str );
2931 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
2932 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
2933 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2934 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
2935 && node.getNodeData().isHasBinaryCharacters() ) {
2936 if ( _sb.length() > 0 ) {
2937 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
2939 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2940 g.setColor( Color.BLACK );
2943 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
2945 if ( getControlPanel().isShowBinaryCharacters() ) {
2946 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
2947 .toString(), node.getXcoord() + x + 1 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
2948 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
2949 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
2950 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
2951 .getLostCharactersAsStringBuffer().toString() );
2954 if ( DRAW_MEAN_COUNTS && node.isInternal() ) {
2955 final List<PhylogenyNode> ec = node.getAllExternalDescendants();
2958 for( final PhylogenyNode phylogenyNode : ec ) {
2960 if ( phylogenyNode.getNodeData().getBinaryCharacters() != null ) {
2961 sum += phylogenyNode.getNodeData().getBinaryCharacters().getPresentCount();
2964 final double mean = ForesterUtil.round( sum / count, 1 );
2965 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " ["
2966 + mean + "]", node.getXcoord() + x + 4 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
2967 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
2970 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
2971 node.getXcoord() + x + 4 + TreePanel.HALF_BOX_SIZE,
2973 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
2976 paintGainedAndLostCharacters( g, node, "+"
2977 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
2978 + node.getNodeData().getBinaryCharacters().getLostCount() );
2984 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2985 final List<Uri> us = new ArrayList<Uri>();
2986 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2987 for( final Uri uri : t.getUris() ) {
2992 for( final Uri uri : us ) {
2993 if ( uri != null ) {
2994 final String uri_str = uri.getValue().toString().toLowerCase();
2995 if ( getImageMap().containsKey( uri_str ) ) {
2996 final BufferedImage bi = getImageMap().get( uri_str );
2997 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2998 double scaling_factor = 1;
2999 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
3000 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
3001 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
3003 // y = y - ( 0.9 * getYdistance() );
3004 final double hs = bi.getHeight() * scaling_factor;
3005 double ws = bi.getWidth() * scaling_factor + offset;
3006 final double my_y = y - ( 0.5 * hs );
3007 final int x_w = ( int ) ( x + ws + 0.5 );
3008 final int y_h = ( int ) ( my_y + hs + 0.5 );
3009 if ( ( x_w - x > 7 ) && ( y_h - my_y > 7 ) ) {
3011 ( int ) ( x + 0.5 + offset ),
3012 ( int ) ( my_y + 0.5 ),
3033 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
3034 final PhylogenyNode node,
3035 final boolean to_pdf,
3036 final boolean to_graphics_file,
3037 final boolean radial_labels,
3038 final double ur_angle,
3039 final boolean is_in_found_nodes ) {
3040 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
3043 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3044 g.setColor( Color.BLACK );
3046 else if ( is_in_found_nodes ) {
3047 g.setColor( getTreeColorSet().getFoundColor() );
3049 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3050 g.setColor( getTaxonomyBasedColor( node ) );
3053 g.setColor( getTreeColorSet().getSequenceColor() );
3057 if ( node.getNodeData().isHasTaxonomy()
3058 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3059 .isShowTaxonomyCommonNames() ) ) {
3060 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
3061 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
3062 _sb.append( taxonomy.getTaxonomyCode() );
3065 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
3066 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
3067 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3068 _sb.append( taxonomy.getScientificName() );
3070 _sb.append( taxonomy.getCommonName() );
3073 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3074 _sb.append( taxonomy.getScientificName() );
3077 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3078 _sb.append( taxonomy.getCommonName() );
3082 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
3083 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3084 _sb.append( taxonomy.getScientificName() );
3088 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
3089 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3090 _sb.append( taxonomy.getCommonName() );
3095 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3097 _sb.append( node.getAllExternalDescendants().size() );
3100 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3101 if ( _sb.length() > 0 ) {
3104 _sb.append( node.getName() );
3106 if ( node.getNodeData().isHasSequence() ) {
3107 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3108 if ( _sb.length() > 0 ) {
3111 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3112 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3115 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3117 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3118 if ( _sb.length() > 0 ) {
3121 _sb.append( node.getNodeData().getSequence().getName() );
3124 g.setFont( getTreeFontSet().getLargeFont() );
3125 if ( is_in_found_nodes ) {
3126 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3128 if ( _sb.length() > 1 ) {
3129 final String sb_str = _sb.toString();
3131 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
3132 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
3135 m = ( float ) ( ur_angle % TWO_PI );
3137 _at = g.getTransform();
3138 boolean need_to_reset = false;
3139 final float x_coord = node.getXcoord();
3140 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
3141 if ( radial_labels ) {
3142 need_to_reset = true;
3143 boolean left = false;
3144 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
3148 g.rotate( m, x_coord, node.getYcoord() );
3150 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
3154 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
3155 need_to_reset = true;
3156 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
3159 TreePanel.drawString( sb_str, x_coord, y_coord, g );
3160 if ( need_to_reset ) {
3161 g.setTransform( _at );
3166 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
3167 if ( node.isCollapse() ) {
3168 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
3169 paintCollapsedNode( g, node, false, false, false );
3173 if ( isInFoundNodes( node ) ) {
3174 g.setColor( getTreeColorSet().getFoundColor() );
3175 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
3178 if ( !node.isExternal() && !node.isCollapse() ) {
3179 boolean first_child = true;
3181 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
3182 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
3183 final PhylogenyNode child_node = node.getChildNode( i );
3185 if ( !isUniformBranchLengthsForCladogram() ) {
3186 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
3189 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
3191 if ( first_child ) {
3192 first_child = false;
3193 y2 = node.getYSecondary()
3194 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
3195 .getNumberOfExternalNodes() ) );
3198 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
3200 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
3201 new_x = x2 + node.getXSecondary();
3202 final float diff_y = node.getYSecondary() - y2;
3203 final float diff_x = node.getXSecondary() - new_x;
3204 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
3205 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
3207 child_node.setXSecondary( new_x );
3208 child_node.setYSecondary( y2 );
3209 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
3214 final private void paintNodeRectangular( final Graphics2D g,
3215 final PhylogenyNode node,
3216 final boolean to_pdf,
3217 final boolean dynamically_hide,
3218 final int dynamic_hiding_factor,
3219 final boolean to_graphics_file ) {
3220 final boolean is_in_found_nodes = isInFoundNodes( node );
3221 if ( node.isCollapse() ) {
3222 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
3223 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3227 if ( node.isExternal() ) {
3228 ++_external_node_index;
3230 // Confidence values
3231 if ( getControlPanel().isShowBootstrapValues()
3232 && !node.isExternal()
3234 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
3235 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3236 && node.getBranchData().isHasConfidences() ) {
3237 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
3239 // Draw a line to root:
3240 if ( node.isRoot() && _phylogeny.isRooted() ) {
3241 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
3244 float new_x_min = Float.MAX_VALUE;
3245 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
3246 float min_dist = 1.5f;
3247 if ( !disallow_shortcutting ) {
3248 // System.out.println( dynamic_hiding_factor );
3249 if ( dynamic_hiding_factor > 4000 ) {
3252 else if ( dynamic_hiding_factor > 1000 ) {
3255 else if ( dynamic_hiding_factor > 100 ) {
3259 if ( !node.isExternal() && !node.isCollapse() ) {
3260 boolean first_child = true;
3262 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
3263 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
3264 final PhylogenyNode child_node = node.getChildNode( i );
3266 if ( !isUniformBranchLengthsForCladogram() ) {
3267 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
3270 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
3272 if ( first_child ) {
3273 first_child = false;
3274 y2 = node.getYcoord()
3275 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
3278 y2 += _y_distance * child_node.getNumberOfExternalNodes();
3280 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
3281 new_x = x2 + node.getXcoord();
3282 if ( dynamically_hide && ( x2 < new_x_min ) ) {
3285 final float diff_y = node.getYcoord() - y2;
3286 final float diff_x = node.getXcoord() - new_x;
3287 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
3288 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
3289 paintBranchRectangular( g,
3298 child_node.setXcoord( new_x );
3299 child_node.setYcoord( y2 );
3300 y2 += _y_distance * child_node.getNumberOfExternalNodes();
3303 if ( dynamically_hide
3304 && !is_in_found_nodes
3305 && ( ( node.isExternal() && ( _external_node_index % dynamic_hiding_factor != 1 ) ) || ( !node
3306 .isExternal() && ( ( new_x_min < 20 ) || ( _y_distance * node.getNumberOfExternalNodes() < getTreeFontSet()._fm_large
3307 .getHeight() ) ) ) ) ) {
3310 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3311 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
3314 final private void paintNodeWithRenderableData( final Graphics2D g,
3315 final PhylogenyNode node,
3316 final boolean to_graphics_file,
3317 final boolean to_pdf ) {
3318 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
3321 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
3324 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
3325 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
3326 RenderableDomainArchitecture rds = null;
3327 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
3329 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
3331 catch ( final ClassCastException cce ) {
3332 cce.printStackTrace();
3335 rds.setRenderingHeight( 6 );
3337 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( node ).length() > 0 ) ) {
3338 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " );
3340 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3341 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
3343 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
3347 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
3348 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
3349 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
3350 getStatisticsForExpressionValues(),
3351 getConfiguration() );
3353 PhylogenyNode my_node = node;
3354 if ( !getControlPanel().isDrawPhylogram() ) {
3355 my_node = getPhylogeny().getFirstExternalNode();
3357 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
3358 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
3360 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
3361 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
3363 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
3368 final private void paintOvRectangle( final Graphics2D g ) {
3369 final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
3370 final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
3371 final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
3372 final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
3373 final float width = getOvMaxWidth() / w_ratio;
3374 final float height = getOvMaxHeight() / h_ratio;
3375 final float x = getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / x_ratio;
3376 final float y = getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / y_ratio;
3377 g.setColor( getTreeColorSet().getFoundColor() );
3378 getOvRectangle().setRect( x, y, width, height );
3379 if ( ( width < 6 ) && ( height < 6 ) ) {
3380 drawRectFilled( x, y, 6, 6, g );
3381 getOvVirtualRectangle().setRect( x, y, 6, 6 );
3383 else if ( width < 6 ) {
3384 drawRectFilled( x, y, 6, height, g );
3385 getOvVirtualRectangle().setRect( x, y, 6, height );
3387 else if ( height < 6 ) {
3388 drawRectFilled( x, y, width, 6, g );
3389 getOvVirtualRectangle().setRect( x, y, width, 6 );
3392 drawRect( x, y, width, height, g );
3393 if ( isInOvRect() ) {
3394 drawRect( x + 1, y + 1, width - 2, height - 2, g );
3396 getOvVirtualRectangle().setRect( x, y, width, height );
3400 final void paintPhylogeny( final Graphics2D g,
3401 final boolean to_pdf,
3402 final boolean to_graphics_file,
3403 final int graphics_file_width,
3404 final int graphics_file_height,
3405 final int graphics_file_x,
3406 final int graphics_file_y ) {
3407 if ( _control_panel.isShowSequenceRelations() ) {
3408 _query_sequence = _control_panel.getSelectedQuerySequence();
3410 // Color the background
3412 final Rectangle r = getVisibleRect();
3413 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
3414 g.setColor( getTreeColorSet().getBackgroundColor() );
3415 if ( !to_graphics_file ) {
3419 if ( getOptions().isPrintBlackAndWhite() ) {
3420 g.setColor( Color.WHITE );
3422 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
3426 if ( !to_graphics_file ) {
3427 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
3428 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
3432 g.setPaint( new GradientPaint( graphics_file_x,
3434 getTreeColorSet().getBackgroundColor(),
3436 graphics_file_y + graphics_file_height,
3437 getTreeColorSet().getBackgroundColorGradientBottom() ) );
3438 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
3441 g.setStroke( new BasicStroke( 1 ) );
3444 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
3446 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3447 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3448 _external_node_index = 0;
3449 // Position starting X of tree
3450 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
3451 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
3453 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
3454 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
3455 .getDistanceToParent() * getXcorrectionFactor() ) ) );
3458 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
3460 // Position starting Y of tree
3461 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
3462 + ( TreePanel.MOVE / 2.0f ) );
3463 final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) );
3464 if ( getControlPanel().isDynamicallyHideData() ) {
3465 if ( dynamic_hiding_factor > 1 ) {
3466 getControlPanel().setDynamicHidingIsOn( true );
3469 getControlPanel().setDynamicHidingIsOn( false );
3472 if ( _nodes_in_preorder == null ) {
3473 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
3474 System.out.println( "total nodes: " + _nodes_in_preorder.length );
3476 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3477 _nodes_in_preorder[ i++ ] = it.next();
3480 //final PhylogenyNodeIterator it;
3481 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3482 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
3483 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
3485 for( int i = 0; i < _nodes_in_preorder.length; ++i ) {
3486 paintNodeRectangular( g, _nodes_in_preorder[ i ], to_pdf, getControlPanel().isDynamicallyHideData()
3487 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
3489 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
3490 if ( !( to_graphics_file || to_pdf ) ) {
3493 getVisibleRect().y + getVisibleRect().height,
3498 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
3501 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3502 paintPhylogenyLite( g );
3505 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
3506 if ( getControlPanel().getDynamicallyHideData() != null ) {
3507 getControlPanel().setDynamicHidingIsOn( false );
3509 final double angle = getStartingAngle();
3510 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
3511 _dynamic_hiding_factor = 0;
3512 if ( getControlPanel().isDynamicallyHideData() ) {
3513 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
3514 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
3516 if ( getControlPanel().getDynamicallyHideData() != null ) {
3517 if ( _dynamic_hiding_factor > 1 ) {
3518 getControlPanel().setDynamicHidingIsOn( true );
3521 getControlPanel().setDynamicHidingIsOn( false );
3524 paintUnrooted( _phylogeny.getRoot(),
3526 ( float ) ( angle + 2 * Math.PI ),
3531 if ( getOptions().isShowScale() ) {
3532 if ( !( to_graphics_file || to_pdf ) ) {
3535 getVisibleRect().y + getVisibleRect().height,
3540 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
3543 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3544 g.setColor( getTreeColorSet().getOvColor() );
3545 paintUnrootedLite( _phylogeny.getRoot(),
3547 angle + 2 * Math.PI,
3549 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
3550 paintOvRectangle( g );
3553 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
3554 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
3555 final int d = radius + MOVE + getLongestExtNodeInfo();
3556 _dynamic_hiding_factor = 0;
3557 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
3558 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
3559 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
3561 if ( getControlPanel().getDynamicallyHideData() != null ) {
3562 if ( _dynamic_hiding_factor > 1 ) {
3563 getControlPanel().setDynamicHidingIsOn( true );
3566 getControlPanel().setDynamicHidingIsOn( false );
3569 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
3570 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3571 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
3572 : getOvMaxWidth() / 2 );
3573 double x_scale = 1.0;
3574 double y_scale = 1.0;
3575 int x_pos = getVisibleRect().x + getOvXPosition();
3576 int y_pos = getVisibleRect().y + getOvYPosition();
3577 if ( getWidth() > getHeight() ) {
3578 x_scale = ( double ) getHeight() / getWidth();
3579 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
3582 y_scale = ( double ) getWidth() / getHeight();
3583 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
3585 _at = g.getTransform();
3586 g.scale( x_scale, y_scale );
3587 paintCircularLite( _phylogeny,
3591 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
3594 g.setTransform( _at );
3595 paintOvRectangle( g );
3600 final private void paintPhylogenyLite( final Graphics2D g ) {
3601 //System.out.println( getVisibleRect().x + " " + getVisibleRect().y );
3604 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
3605 .getWidth() ) ) ) );
3606 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
3607 //final PhylogenyNodeIterator it;
3608 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3609 // paintNodeLite( g, it.next() );
3611 for( int i = 0; i < _nodes_in_preorder.length; ++i ) {
3612 paintNodeLite( g, _nodes_in_preorder[ i ] );
3614 paintOvRectangle( g );
3618 * Paint the root branch. (Differs from others because it will always be a
3619 * single horizontal line).
3620 * @param to_graphics_file
3622 * @return new x1 value
3624 final private void paintRootBranch( final Graphics2D g,
3627 final PhylogenyNode root,
3628 final boolean to_pdf,
3629 final boolean to_graphics_file ) {
3630 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
3631 float d = getXdistance();
3632 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
3633 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
3635 if ( d < MIN_ROOT_LENGTH ) {
3636 d = MIN_ROOT_LENGTH;
3638 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
3639 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
3642 final double w = PhylogenyMethods.getBranchWidthValue( root );
3643 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
3645 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
3648 final private void paintScale( final Graphics2D g,
3651 final boolean to_pdf,
3652 final boolean to_graphics_file ) {
3654 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
3656 final int y2 = y1 - 8;
3657 final int y3 = y1 - 4;
3658 g.setFont( getTreeFontSet().getSmallFont() );
3659 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3660 g.setColor( Color.BLACK );
3663 g.setColor( getTreeColorSet().getBranchLengthColor() );
3665 drawLine( x1, y1, x1, y2, g );
3666 drawLine( x2, y1, x2, y2, g );
3667 drawLine( x1, y3, x2, y3, g );
3668 if ( getScaleLabel() != null ) {
3669 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
3673 final private int paintTaxonomy( final Graphics2D g,
3674 final PhylogenyNode node,
3675 final boolean is_in_found_nodes,
3676 final boolean to_pdf,
3677 final boolean to_graphics_file,
3678 final double x_shift ) {
3679 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
3680 g.setFont( getTreeFontSet().getLargeItalicFont() );
3681 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3682 g.setColor( Color.BLACK );
3684 else if ( is_in_found_nodes ) {
3685 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
3686 g.setColor( getTreeColorSet().getFoundColor() );
3688 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3689 g.setColor( getTaxonomyBasedColor( node ) );
3691 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3692 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3693 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3695 else if ( to_pdf ) {
3696 g.setColor( Color.BLACK );
3699 g.setColor( getTreeColorSet().getTaxonomyColor() );
3701 final double start_x = node.getXcoord() + 3 + TreePanel.HALF_BOX_SIZE + x_shift;
3702 final double start_y = node.getYcoord()
3703 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
3705 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
3706 _sb.append( taxonomy.getTaxonomyCode() );
3709 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
3710 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
3711 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3712 if ( getOptions().isAbbreviateScientificTaxonNames()
3713 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
3714 abbreviateScientificName( taxonomy.getScientificName() );
3717 _sb.append( taxonomy.getScientificName() );
3720 _sb.append( taxonomy.getCommonName() );
3723 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3724 if ( getOptions().isAbbreviateScientificTaxonNames()
3725 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
3726 abbreviateScientificName( taxonomy.getScientificName() );
3729 _sb.append( taxonomy.getScientificName() );
3733 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3734 _sb.append( taxonomy.getCommonName() );
3738 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
3739 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3740 if ( getOptions().isAbbreviateScientificTaxonNames()
3741 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
3742 abbreviateScientificName( taxonomy.getScientificName() );
3745 _sb.append( taxonomy.getScientificName() );
3750 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
3751 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3752 _sb.append( taxonomy.getCommonName() );
3756 final String label = _sb.toString();
3758 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
3759 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
3760 // invert font color and background color to show that this is the query sequence
3761 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
3765 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
3766 g.setColor( getTreeColorSet().getBackgroundColor() );
3769 TreePanel.drawString( label, start_x, start_y, g );
3770 if ( is_in_found_nodes ) {
3771 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
3774 return getTreeFontSet()._fm_large_italic.stringWidth( label );
3778 private void abbreviateScientificName( final String sn ) {
3779 final String[] a = sn.split( "\\s+" );
3780 _sb.append( a[ 0 ].substring( 0, 1 ) );
3781 _sb.append( a[ 1 ].substring( 0, 2 ) );
3782 if ( a.length > 2 ) {
3783 for( int i = 2; i < a.length; i++ ) {
3785 _sb.append( a[ i ] );
3790 final private void paintUnrooted( final PhylogenyNode n,
3791 final double low_angle,
3792 final double high_angle,
3793 final boolean radial_labels,
3795 final boolean to_pdf,
3796 final boolean to_graphics_file ) {
3798 n.setXcoord( getWidth() / 2 );
3799 n.setYcoord( getHeight() / 2 );
3800 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
3802 if ( n.isExternal() ) {
3803 paintNodeDataUnrootedCirc( g,
3808 ( high_angle + low_angle ) / 2,
3809 isInFoundNodes( n ) );
3812 final float num_enclosed = n.getNumberOfExternalNodes();
3813 final float x = n.getXcoord();
3814 final float y = n.getYcoord();
3815 double current_angle = low_angle;
3816 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
3817 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
3818 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
3819 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
3820 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
3821 final PhylogenyNode desc = n.getChildNode( i );
3822 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
3823 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
3824 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
3825 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
3828 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
3831 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
3834 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
3835 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
3837 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
3838 if ( desc.getDistanceToParent() < 0 ) {
3842 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
3846 length = getUrtFactor();
3848 final double mid_angle = current_angle + arc_size / 2;
3849 final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
3850 final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
3851 desc.setXcoord( new_x );
3852 desc.setYcoord( new_y );
3853 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
3854 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
3855 current_angle += arc_size;
3856 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
3857 drawLine( x, y, new_x, new_y, g );
3861 final private void paintUnrootedLite( final PhylogenyNode n,
3862 final double low_angle,
3863 final double high_angle,
3865 final float urt_ov_factor ) {
3867 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / 2 );
3868 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / 2 );
3869 n.setXSecondary( x_pos );
3870 n.setYSecondary( y_pos );
3872 if ( n.isExternal() ) {
3875 final float num_enclosed = n.getNumberOfExternalNodes();
3876 final float x = n.getXSecondary();
3877 final float y = n.getYSecondary();
3878 double current_angle = low_angle;
3879 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
3880 final PhylogenyNode desc = n.getChildNode( i );
3881 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
3882 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
3884 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
3885 if ( desc.getDistanceToParent() < 0 ) {
3889 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
3893 length = urt_ov_factor;
3895 final double mid_angle = current_angle + arc_size / 2;
3896 final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
3897 final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
3898 desc.setXSecondary( new_x );
3899 desc.setYSecondary( new_y );
3900 if ( isInFoundNodes( desc ) ) {
3901 g.setColor( getTreeColorSet().getFoundColor() );
3902 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
3903 g.setColor( getTreeColorSet().getOvColor() );
3905 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
3906 current_angle += arc_size;
3907 drawLine( x, y, new_x, new_y, g );
3911 final private void pasteSubtree( final PhylogenyNode node ) {
3912 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
3913 errorMessageNoCutCopyPasteInUnrootedDisplay();
3916 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
3917 JOptionPane.showMessageDialog( this,
3918 "No tree in buffer (need to copy or cut a subtree first)",
3919 "Attempt to paste with empty buffer",
3920 JOptionPane.ERROR_MESSAGE );
3923 final String label = getASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
3924 final Object[] options = { "As sibling", "As descendant", "Cancel" };
3925 final int r = JOptionPane.showOptionDialog( this,
3926 "How to paste subtree" + label + "?",
3928 JOptionPane.CLOSED_OPTION,
3929 JOptionPane.QUESTION_MESSAGE,
3933 boolean paste_as_sibling = true;
3935 paste_as_sibling = false;
3937 else if ( r != 0 ) {
3940 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
3941 buffer_phy.setAllNodesToNotCollapse();
3942 buffer_phy.preOrderReId();
3943 buffer_phy.setRooted( true );
3944 boolean need_to_show_whole = false;
3945 if ( paste_as_sibling ) {
3946 if ( node.isRoot() ) {
3947 JOptionPane.showMessageDialog( this,
3948 "Cannot paste sibling to root",
3949 "Attempt to paste sibling to root",
3950 JOptionPane.ERROR_MESSAGE );
3953 buffer_phy.addAsSibling( node );
3956 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
3957 need_to_show_whole = true;
3958 _phylogeny = buffer_phy;
3961 buffer_phy.addAsChild( node );
3964 if ( getCopiedAndPastedNodes() == null ) {
3965 setCopiedAndPastedNodes( new HashSet<Integer>() );
3967 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
3968 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
3969 for( final PhylogenyNode n : nodes ) {
3970 node_ids.add( n.getId() );
3972 node_ids.add( node.getId() );
3973 getCopiedAndPastedNodes().addAll( node_ids );
3974 _phylogeny.externalNodesHaveChanged();
3975 _phylogeny.hashIDs();
3976 _phylogeny.recalculateNumberOfExternalDescendants( true );
3977 resetNodeIdToDistToLeafMap();
3979 if ( need_to_show_whole ) {
3980 getControlPanel().showWhole();
3985 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
3986 throws PrinterException {
3987 if ( page_index > 0 ) {
3988 return ( NO_SUCH_PAGE );
3991 final Graphics2D g2d = ( Graphics2D ) g;
3992 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
3993 // Turn off double buffering !?
3994 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
3995 // Turn double buffering back on !?
3996 return ( PAGE_EXISTS );
4000 final void recalculateMaxDistanceToRoot() {
4001 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
4005 * Remove all edit-node frames
4007 final void removeAllEditNodeJFrames() {
4008 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
4009 if ( _node_frames[ i ] != null ) {
4010 _node_frames[ i ].dispose();
4011 _node_frames[ i ] = null;
4014 _node_frame_index = 0;
4018 * Remove a node-edit frame.
4020 final void removeEditNodeFrame( final int i ) {
4021 _node_frame_index--;
4022 _node_frames[ i ] = null;
4023 if ( i < _node_frame_index ) {
4024 for( int j = 0; j < _node_frame_index - 1; j++ ) {
4025 _node_frames[ j ] = _node_frames[ j + 1 ];
4027 _node_frames[ _node_frame_index ] = null;
4031 final void reRoot( final PhylogenyNode node ) {
4032 if ( !getPhylogeny().isRerootable() ) {
4033 JOptionPane.showMessageDialog( this,
4034 "This is not rerootable",
4036 JOptionPane.WARNING_MESSAGE );
4039 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4040 JOptionPane.showMessageDialog( this,
4041 "Cannot reroot in unrooted display type",
4042 "Attempt to reroot tree in unrooted display",
4043 JOptionPane.WARNING_MESSAGE );
4046 getPhylogeny().reRoot( node );
4047 getPhylogeny().recalculateNumberOfExternalDescendants( true );
4048 resetNodeIdToDistToLeafMap();
4049 _nodes_in_preorder = null;
4050 resetPreferredSize();
4051 getMainPanel().adjustJScrollPane();
4053 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4054 getControlPanel().showWhole();
4058 final void resetNodeIdToDistToLeafMap() {
4059 _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
4062 final void resetPreferredSize() {
4063 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
4069 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
4070 if ( getControlPanel().isDrawPhylogram() ) {
4072 + getLongestExtNodeInfo()
4074 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
4077 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
4079 + getLongestExtNodeInfo()
4080 + ForesterUtil.roundToInt( getXdistance()
4081 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
4085 + getLongestExtNodeInfo()
4086 + ForesterUtil.roundToInt( getXdistance()
4087 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
4090 setPreferredSize( new Dimension( x, y ) );
4093 final void setArrowCursor() {
4094 setCursor( ARROW_CURSOR );
4098 final void setControlPanel( final ControlPanel atv_control ) {
4099 _control_panel = atv_control;
4102 final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
4103 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4106 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4107 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4110 final void setEdited( final boolean edited ) {
4114 final void setFoundNodes( final Set<Integer> found_nodes ) {
4115 _found_nodes = found_nodes;
4118 final private void setInOv( final boolean in_ov ) {
4122 final void setInOvRect( final boolean in_ov_rect ) {
4123 _in_ov_rect = in_ov_rect;
4126 final void setLargeFonts() {
4127 getTreeFontSet().largeFonts();
4130 final void setLastMouseDragPointX( final float x ) {
4131 _last_drag_point_x = x;
4134 final void setLastMouseDragPointY( final float y ) {
4135 _last_drag_point_y = y;
4138 final void setLongestExtNodeInfo( final int i ) {
4139 _longest_ext_node_info = i;
4142 final void setMediumFonts() {
4143 getTreeFontSet().mediumFonts();
4146 final private void setOvMaxHeight( final float ov_max_height ) {
4147 _ov_max_height = ov_max_height;
4150 final private void setOvMaxWidth( final float ov_max_width ) {
4151 _ov_max_width = ov_max_width;
4154 final void setOvOn( final boolean ov_on ) {
4158 final private void setOvXcorrectionFactor( final float f ) {
4159 _ov_x_correction_factor = f;
4162 final private void setOvXDistance( final float ov_x_distance ) {
4163 _ov_x_distance = ov_x_distance;
4166 final private void setOvXPosition( final int ov_x_position ) {
4167 _ov_x_position = ov_x_position;
4170 final private void setOvYDistance( final float ov_y_distance ) {
4171 _ov_y_distance = ov_y_distance;
4174 final private void setOvYPosition( final int ov_y_position ) {
4175 _ov_y_position = ov_y_position;
4178 final private void setOvYStart( final int ov_y_start ) {
4179 _ov_y_start = ov_y_start;
4183 * Set parameters for printing the displayed tree
4188 final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
4189 // updateStyle(); not needed?
4190 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
4192 if ( recalc_longest_ext_node_info ) {
4193 calculateLongestExtNodeInfo();
4195 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
4196 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
4197 if ( ext_nodes == 1 ) {
4198 ext_nodes = max_depth;
4199 if ( ext_nodes < 1 ) {
4206 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
4207 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
4208 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
4211 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
4212 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
4214 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
4215 if ( xdist < 0.0 ) {
4218 if ( ov_xdist < 0.0 ) {
4221 if ( ydist < 0.0 ) {
4224 setXdistance( xdist );
4225 setYdistance( ydist );
4226 setOvXDistance( ov_xdist );
4227 final double height = _phylogeny.getHeight();
4229 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
4230 setXcorrectionFactor( corr > 0 ? corr : 0 );
4231 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
4232 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
4235 setXcorrectionFactor( 0 );
4236 setOvXcorrectionFactor( 0 );
4238 _circ_max_depth = max_depth;
4243 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
4244 _graphics_type = graphics_type;
4248 final private void setScaleDistance( final double scale_distance ) {
4249 _scale_distance = scale_distance;
4252 final private void setScaleLabel( final String scale_label ) {
4253 _scale_label = scale_label;
4256 final void setSmallFonts() {
4257 getTreeFontSet().smallFonts();
4260 final void setStartingAngle( final double starting_angle ) {
4261 _urt_starting_angle = starting_angle;
4264 final void setSuperTinyFonts() {
4265 getTreeFontSet().superTinyFonts();
4268 final void setTextAntialias() {
4269 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
4270 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
4271 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
4274 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
4277 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
4278 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) {
4279 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
4282 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
4285 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
4286 RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
4288 catch ( final Throwable e ) {
4289 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
4293 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
4294 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
4298 final void setTinyFonts() {
4299 getTreeFontSet().tinyFonts();
4303 * Set a phylogeny tree.
4306 * an instance of a Phylogeny
4308 final void setTree( final Phylogeny t ) {
4312 final void setTreeFile( final File treefile ) {
4313 _treefile = treefile;
4316 final private void setUpUrtFactor() {
4317 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
4318 : getVisibleRect().height;
4319 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4320 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
4323 final int max_depth = _circ_max_depth;
4324 if ( max_depth > 0 ) {
4325 setUrtFactor( d / ( 2 * max_depth ) );
4328 setUrtFactor( d / 2 );
4331 setUrtFactorOv( getUrtFactor() );
4334 final private void setUrtFactor( final float urt_factor ) {
4335 _urt_factor = urt_factor;
4338 final private void setUrtFactorOv( final float urt_factor_ov ) {
4339 _urt_factor_ov = urt_factor_ov;
4342 final void setWaitCursor() {
4343 setCursor( WAIT_CURSOR );
4347 final void setXcorrectionFactor( final float f ) {
4348 _x_correction_factor = f;
4351 final void setXdistance( final float x ) {
4355 final void setYdistance( final float y ) {
4359 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
4361 if ( ( node.getName().length() > 0 )
4362 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
4363 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
4364 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
4365 || node.getBranchData().isHasConfidences() ) {
4366 _popup_buffer.setLength( 0 );
4368 if ( node.getName().length() > 0 ) {
4370 _popup_buffer.append( node.getName() );
4372 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
4374 boolean enc_data = false;
4375 final Taxonomy tax = node.getNodeData().getTaxonomy();
4376 if ( _popup_buffer.length() > 0 ) {
4377 _popup_buffer.append( "\n" );
4379 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
4380 _popup_buffer.append( "[" );
4381 _popup_buffer.append( tax.getTaxonomyCode() );
4382 _popup_buffer.append( "]" );
4385 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
4387 _popup_buffer.append( " " );
4389 _popup_buffer.append( tax.getScientificName() );
4392 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
4394 _popup_buffer.append( " (" );
4397 _popup_buffer.append( "(" );
4399 _popup_buffer.append( tax.getCommonName() );
4400 _popup_buffer.append( ")" );
4403 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
4405 _popup_buffer.append( " (" );
4408 _popup_buffer.append( "(" );
4410 _popup_buffer.append( tax.getAuthority() );
4411 _popup_buffer.append( ")" );
4414 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
4416 _popup_buffer.append( " [" );
4419 _popup_buffer.append( "[" );
4421 _popup_buffer.append( tax.getRank() );
4422 _popup_buffer.append( "]" );
4425 if ( tax.getSynonyms().size() > 0 ) {
4427 _popup_buffer.append( " " );
4429 _popup_buffer.append( "[" );
4431 for( final String syn : tax.getSynonyms() ) {
4432 if ( !ForesterUtil.isEmpty( syn ) ) {
4434 _popup_buffer.append( syn );
4435 if ( counter < tax.getSynonyms().size() ) {
4436 _popup_buffer.append( ", " );
4441 _popup_buffer.append( "]" );
4444 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
4445 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
4446 _popup_buffer.append( "[" );
4447 _popup_buffer.append( tax.getIdentifier().getProvider() );
4448 _popup_buffer.append( "] " );
4450 _popup_buffer.append( tax.getIdentifier().getValue() );
4454 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
4456 boolean enc_data = false;
4457 if ( _popup_buffer.length() > 0 ) {
4458 _popup_buffer.append( "\n" );
4460 final Sequence seq = node.getNodeData().getSequence();
4461 if ( seq.getAccession() != null ) {
4462 _popup_buffer.append( "[" );
4463 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
4464 _popup_buffer.append( seq.getAccession().getSource() );
4465 _popup_buffer.append( ":" );
4467 _popup_buffer.append( seq.getAccession().getValue() );
4468 _popup_buffer.append( "]" );
4471 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
4473 _popup_buffer.append( " [" );
4476 _popup_buffer.append( "[" );
4478 _popup_buffer.append( seq.getSymbol() );
4479 _popup_buffer.append( "]" );
4482 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
4484 _popup_buffer.append( " " );
4486 _popup_buffer.append( seq.getName() );
4489 if ( node.getNodeData().isHasDate() ) {
4491 if ( _popup_buffer.length() > 0 ) {
4492 _popup_buffer.append( "\n" );
4494 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
4496 if ( node.getNodeData().isHasDistribution() ) {
4498 if ( _popup_buffer.length() > 0 ) {
4499 _popup_buffer.append( "\n" );
4501 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
4503 if ( node.getBranchData().isHasConfidences() ) {
4504 final List<Confidence> confs = node.getBranchData().getConfidences();
4505 for( final Confidence confidence : confs ) {
4507 if ( _popup_buffer.length() > 0 ) {
4508 _popup_buffer.append( "\n" );
4510 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
4511 _popup_buffer.append( "[" );
4512 _popup_buffer.append( confidence.getType() );
4513 _popup_buffer.append( "] " );
4516 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
4518 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
4521 if ( _popup_buffer.length() > 0 ) {
4522 if ( !getConfiguration().isUseNativeUI() ) {
4524 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
4525 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
4526 if ( isInFoundNodes( node ) ) {
4527 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
4529 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4530 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
4533 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
4537 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
4539 _rollover_popup.setText( _popup_buffer.toString() );
4540 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
4542 e.getLocationOnScreen().x + 10,
4543 e.getLocationOnScreen().y
4545 _node_desc_popup.show();
4549 catch ( final Exception ex ) {
4554 final private void showNodeEditFrame( final PhylogenyNode n ) {
4555 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
4556 // pop up edit box for single node
4557 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
4558 _node_frame_index++;
4561 JOptionPane.showMessageDialog( this, "too many node windows are open" );
4565 final private void showNodeFrame( final PhylogenyNode n ) {
4566 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
4567 // pop up edit box for single node
4568 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
4569 _node_frame_index++;
4572 JOptionPane.showMessageDialog( this, "too many node windows are open" );
4576 final void subTree( final PhylogenyNode node ) {
4577 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4578 JOptionPane.showMessageDialog( this,
4579 "Cannot get a sub/super tree in unrooted display",
4580 "Attempt to get sub/super tree in unrooted display",
4581 JOptionPane.WARNING_MESSAGE );
4584 if ( node.isExternal() ) {
4585 JOptionPane.showMessageDialog( this,
4586 "Cannot get a subtree of a external node",
4587 "Attempt to get subtree of external node",
4588 JOptionPane.WARNING_MESSAGE );
4591 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
4592 JOptionPane.showMessageDialog( this,
4593 "Cannot get a subtree of the root node",
4594 "Attempt to get subtree of root node",
4595 JOptionPane.WARNING_MESSAGE );
4598 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
4599 _sub_phylogenies[ _subtree_index ] = _phylogeny;
4600 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
4602 _phylogeny = subTree( node, _phylogeny );
4603 updateSubSuperTreeButton();
4605 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
4608 _main_panel.getControlPanel().showWhole();
4612 final boolean isCurrentTreeIsSubtree() {
4613 return ( _subtree_index > 0 );
4616 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
4617 final Phylogeny new_phy = new Phylogeny();
4618 new_phy.setRooted( true );
4619 new_phy.setName( source_phy.getName() );
4620 new_phy.setDescription( source_phy.getDescription() );
4621 new_phy.setType( source_phy.getType() );
4622 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
4623 new_phy.setConfidence( source_phy.getConfidence() );
4624 new_phy.setIdentifier( source_phy.getIdentifier() );
4625 new_phy.setRoot( new_root.copyNodeDataShallow() );
4627 for( final PhylogenyNode n : new_root.getDescendants() ) {
4628 new_phy.getRoot().setChildNode( i++, n );
4633 final void superTree() {
4634 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
4635 for( final PhylogenyNode n : temp_root.getDescendants() ) {
4636 n.setParent( temp_root );
4638 _sub_phylogenies[ _subtree_index ] = null;
4639 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
4640 _phylogeny = _sub_phylogenies[ --_subtree_index ];
4641 updateSubSuperTreeButton();
4644 final void swap( final PhylogenyNode node ) {
4645 if ( !node.isExternal() ) {
4646 _phylogeny.swapChildren( node );
4651 final private void switchDisplaygetPhylogenyGraphicsType() {
4652 switch ( getPhylogenyGraphicsType() ) {
4654 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
4655 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
4658 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
4659 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
4662 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
4663 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
4666 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
4667 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
4670 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
4671 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
4674 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
4675 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
4678 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
4679 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
4682 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
4683 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
4686 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
4688 if ( getControlPanel().getDynamicallyHideData() != null ) {
4689 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4690 getControlPanel().getDynamicallyHideData().setEnabled( false );
4693 getControlPanel().getDynamicallyHideData().setEnabled( true );
4696 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
4697 getControlPanel().setDrawPhylogramEnabled( true );
4700 getControlPanel().setDrawPhylogramEnabled( false );
4702 if ( getMainPanel().getMainFrame() == null ) {
4703 // Must be "E" applet version.
4704 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
4705 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
4708 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
4712 final void taxColor() {
4713 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
4717 Util.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
4718 _control_panel.setColorBranches( true );
4719 if ( _control_panel.getColorBranchesCb() != null ) {
4720 _control_panel.getColorBranchesCb().setSelected( true );
4726 final void updateOvSettings() {
4727 switch ( getOptions().getOvPlacement() ) {
4729 setOvXPosition( OV_BORDER );
4730 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
4731 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
4734 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
4735 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
4736 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
4739 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
4740 setOvYPosition( OV_BORDER );
4741 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
4744 setOvXPosition( OV_BORDER );
4745 setOvYPosition( OV_BORDER );
4746 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
4751 final void updateOvSizes() {
4752 if ( ( getWidth() > 1.05 * getVisibleRect().width ) || ( getHeight() > 1.05 * getVisibleRect().height ) ) {
4754 float l = getLongestExtNodeInfo();
4755 final float w_ratio = getOvMaxWidth() / getWidth();
4757 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
4758 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
4760 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
4761 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
4764 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
4766 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
4767 if ( ov_xdist < 0.0 ) {
4770 if ( ydist < 0.0 ) {
4773 setOvXDistance( ov_xdist );
4774 final double height = _phylogeny.getHeight();
4776 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
4777 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
4780 setOvXcorrectionFactor( 0 );
4788 final void updateSubSuperTreeButton() {
4789 if ( _subtree_index < 1 ) {
4790 getControlPanel().deactivateButtonToReturnToSuperTree();
4793 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
4797 final void zoomInDomainStructure() {
4798 if ( _domain_structure_width < 2000 ) {
4799 _domain_structure_width *= 1.2;
4803 final void zoomOutDomainStructure() {
4804 if ( _domain_structure_width > 20 ) {
4805 _domain_structure_width *= 0.8;
4809 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
4810 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
4813 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
4814 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
4817 final private static boolean isSequenceEmpty( final Sequence seq ) {
4818 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
4819 && ForesterUtil.isEmpty( seq.getSymbol() );
4822 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
4823 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
4824 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
4825 .getSynonyms().isEmpty() );
4828 final private static boolean plusPressed( final int key_code ) {
4829 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
4830 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
4833 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
4834 _statistics_for_vector_data = statistics_for_expression_values;
4837 DescriptiveStatistics getStatisticsForExpressionValues() {
4838 return _statistics_for_vector_data;
4841 final private class SubtreeColorizationActionListener implements ActionListener {
4843 JColorChooser _chooser;
4844 PhylogenyNode _node;
4846 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
4852 public void actionPerformed( final ActionEvent e ) {
4853 final Color c = _chooser.getColor();
4855 colorizeSubtree( c, _node );
4860 synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
4861 getMainPanel().setImageMap( image_map );
4864 synchronized Hashtable<String, BufferedImage> getImageMap() {
4865 return getMainPanel().getImageMap();